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Investigating protein- protein interactions in order to develop novel therapeutics for the treatment of Alzheimer’s disease

2013-05-20T10:29:28Z

Abstract: Alzheimer’s disease (AD) accounts for around two thirds of all dementia cases and an increase in life expectancy of the population has resulted in a substantial increase in dementia cases and with that a rise in AD. AD is a debilitating and ultimately fatal neurodegenerative disorder of the elderly, and despite being identified over a century ago, the current treatments do not treat the underlying causes behind the disease, instead they help to mask the symptoms of the disease and prolong the brain’s remaining function. It is therefore vital that an effective, disease modifying treatment for this disease is established as soon as possible. Soluble intracellular forms of amyloid β (peptide Aβ), a hallmark of AD have been identified and intracellular targets of Aβ are being investigated as potential drug targets for the disease. Two key intracellular, mitochondrial proteins investigated as potential drug targets: amyloid binding alcohol dehydrogenase (ABAD) and cyclophilin D (CypD) are the focus of the work reported in this thesis. To begin identifying potential inhibitors of the ABAD-Aβ interaction, a two-pronged approach was taken. Firstly, a series of analogues based on a known inhibitor of the interaction were tested using a variety of biophysical assays, for their therapeutic affect on the interaction, and secondly a fragment based screening approach was used to identify new small molecule binding partners of ABAD which could potentially be modified to produced inhibitors of the ABAD-Aβ interaction. Three different CypD constructs have been successfully expressed and purified, and taken into crystal trials. It is hoped that these constructs can be used to significantly aid the progress of identifying any potential inhibitors and binding partners of CypD that may produce therapeutic effects, and in the future could lead to the identification of an effective disease modifying drug in the treatment of AD. The work reported in this thesis has built upon previously reported findings and the groundwork has also been established for several in vitro biophysical assays, these include for example: measuring ABAD enzyme activity, and the novel morphology specific Aβ aggregation assay, which can be used as screening tools to help identify potential inhibitors of these interactions. Both the ABAD-Aβ interaction, and the blockade of CypD are known to be drug targets in the treatment of AD, and by elucidating the molecular mechanisms behind these interactions, through implementing biophysical assays, this will help in the identification and design of potential new therapeutic agents for the treatment of AD.

Structural insights into the mechanism and inhibition of the beta-Hydroxydecanoyl-Acyl carrier protein dehydratase from pseudomonas aeruginosa

2013-05-03T13:01:03Z

Abstract: Fatty acid biosynthesis is an essential component of metabolism in both eukaryotes and prokaryotes. The fatty acid biosynthetic pathway of Gram-negative bacteria is an established therapeutic target. Two homologous enzymes FabA and FabZ catalyze a key step in fatty acid biosynthesis; both dehydrate hydroxyacyl fatty acids that are coupled via a phosphopantetheine to an acyl carrier protein (ACP). The resulting trans-2-enoyl-ACP is further polymerized in a processive manner. FabA, however, carries out a second reaction involving isomerization of trans-2-enoyl fatty acid to cis-3-enoyl fatty acid. We have solved the structure of Pseudomonas aeruginosa FabA with a substrate allowing detailed molecular insight into the interactions of the active site. This has allowed a detailed examination of the factors governing the second catalytic step. We have also determined the structure of FabA in complex with small molecules (so-called fragments). These small molecules occupy distinct regions of the active site and form the basis for a rational inhibitor design program. (C) 2012 Elsevier Ltd. All rights reserved.

Models incorporating chromatin modification data identify functionally important p53 binding sites

2013-05-01T15:01:03Z

Abstract: Genome-wide prediction of transcription factor binding sites is notoriously difficult. We have developed and applied a logistic regression approach for prediction of binding sites for the p53 transcription factor that incorporates sequence information and chromatin modification data. We tested this by comparison of predicted sites with known binding sites defined by chromatin immunoprecipitation (ChIP), by the location of predictions relative to genes, by the function of nearby genes and by analysis of gene expression data after p53 activation. We compared the predictions made by our novel model with predictions based only on matches to a sequence position weight matrix (PWM). In whole genome assays, the fraction of known sites identified by the two models was similar, suggesting that there was little to be gained from including chromatin modification data. In contrast, there were highly significant and biologically relevant differences between the two models in the location of the predicted binding sites relative to genes, in the function of nearby genes and in the responsiveness of nearby genes to p53 activation. We propose that these contradictory results can be explained by PWM and ChIP data reflecting primarily biophysical properties of protein–DNA interactions, whereas chromatin modification data capture biologically important functional information.

Stressed but stable : Canopy loss decreased species synchrony and metabolic variability in an intertidal hard-bottom community

2013-04-28T13:31:02Z

Abstract: The temporal stability of aggregate community properties depends on the dynamics of the component species. Since species growth can compensate for the decline of other species, synchronous species dynamics can maintain stability (i.e. invariability) in aggregate properties such as community abundance and metabolism. In field experiments we tested the separate and interactive effects of two stressors associated with storminess–loss of a canopy-forming species and mechanical disturbances–on species synchrony and community respiration of intertidal hard-bottom communities on Helgoland Island, NE Atlantic. Treatments consisted of regular removal of the canopy-forming seaweed Fucus serratus and a mechanical disturbance applied once at the onset of the experiment in March 2006. The level of synchrony in species abundances was assessed from estimates of species percentage cover every three months until September 2007. Experiments at two sites consistently showed that canopy loss significantly reduced species synchrony. Mechanical disturbance had neither separate nor interactive effects on species synchrony. Accordingly, in situ measurements of CO2-fluxes showed that canopy loss, but not mechanical disturbances, significantly reduced net primary productivity and temporal variation in community respiration during emersion periods. Our results support the idea that compensatory dynamics may stabilise aggregate properties. They further suggest that the ecological consequences of the loss of a single structurally important species may be stronger than those derived from smaller-scale mechanical disturbances in natural ecosystems.

Estimating animal population density using passive acoustics

2013-04-26T08:31:02Z

Abstract: Reliable estimation of the size or density of wild animal populations is very important for effective wildlife management, conservation and ecology. Currently, the most widely used methods for obtaining such estimates involve either sighting animals from transect lines or some form of capture-recapture on marked or uniquely identifiable individuals. However, many species are difficult to sight, and cannot be easily marked or recaptured. Some of these species produce readily identifiable sounds, providing an opportunity to use passive acoustic data to estimate animal density. In addition, even for species for which other visually based methods are feasible, passive acoustic methods offer the potential for greater detection ranges in some environments (e.g. underwater or in dense forest), and hence potentially better precision. Automated data collection means that surveys can take place at times and in places where it would be too expensive or dangerous to send human observers. Here, we present an overview of animal density estimation using passive acoustic data, a relatively new and fast-developing field. We review the types of data and methodological approaches currently available to researchers and we provide a framework for acoustics-based density estimation, illustrated with examples from real-world case studies. We mention moving sensor platforms (e.g. towed acoustics), but then focus on methods involving sensors at fixed locations, particularly hydrophones to survey marine mammals, as acoustic-based density estimation research to date has been concentrated in this area. Primary among these are methods based on distance sampling and spatially explicit capture-recapture. The methods are also applicable to other aquatic and terrestrial sound-producing taxa. We conclude that, despite being in its infancy, density estimation based on passive acoustic data likely will become an important method for surveying a number of diverse taxa, such as sea mammals, fish, birds, amphibians, and insects, especially in situations where inferences are required over long periods of time. There is considerable work ahead, with several potentially fruitful research areas, including the development of (i) hardware and software for data acquisition, (ii) efficient, calibrated, automated detection and classification systems, and (iii) statistical approaches optimized for this application. Further, survey design will need to be developed, and research is needed on the acoustic behaviour of target species. Fundamental research on vocalization rates and group sizes, and the relation between these and other factors such as season or behaviour state, is critical. Evaluation of the methods under known density scenarios will be important for empirically validating the approaches presented here

Variation in sexual dimorphism and assortative mating do not predict genetic divergence in the sexually dimorphic Goodeid fish Girardinichthys multiradiatus

2013-04-17T10:01:02Z

Abstract: Sexual dimorphism is often used as a proxy for the intensity of sexual selection in comparative studies of sexual selection and diversification. The Mexican Goodeinae are a group of livebearing freshwater fishes with large variation between species in sexual dimorphism in body shape. Previously we found an association between variation in morphological sexual dimorphism between species and the amount of gene flow within populations in the Goodeinae. Here we have examined if morphological differentiation within a single dimorphic species is related to assortative mating or gene flow between populations. In the Amarillo fish Girardinichthys multiradiatus studies have shown that exaggerated male fins are targets of female preferences. We find that populations of the species differ in the level of sexual dimorphism displayed due to faster evolution of differences in male than female morphology. However, this does not predict variation in assortative mating tests in the laboratory; in fact differences in male morphology are negatively correlated with assortative mating. Microsatellite markers reveal significant genetic differences between populations. However, gene flow is not predicted by either morphological differences or assortative mating. Rather, it demonstrates a pattern of isolation by distance with greater differentiation between watersheds. We discuss the caveats of predicting behavioural and genetic divergence from so-called proxies of sexual selection [Current Zoology 58 (3): 440-452, 2012].

Willin, an upstream component of the Hippo signaling pathway, orchestrates mammalian peripheral nerve fibroblasts

2013-04-10T13:31:04Z

Abstract: Willin/FRMD6 was first identified in the rat sciatic nerve, which is composed of neurons, Schwann cells, and fibroblasts. Willin is an upstream component of the Hippo signaling pathway, which results in the inactivation of the transcriptional coactivator YAP through Ser127 phosphorylation. This in turn suppresses the expression of genes involved in cell growth, proliferation and cancer development ensuring the control of organ size, cell contact inhibition and apoptosis. Here we show that in the mammalian sciatic nerve, Willin is predominantly expressed in fibroblasts and that Willin expression activates the Hippo signaling cascade and induces YAP translocation from the nucleus to the cytoplasm. In addition within these cells, although it inhibits cellular proliferation, Willin expression induces a quicker directional migration towards scratch closure and an increased expression of factors linked to nerve regeneration. These results show that Willin modulates sciatic nerve fibroblast activity indicating that Willin may have a potential role in the regeneration of the peripheral nervous system.

Development of a contact call in black-capped chickadees (Poecile atricapillus) hand-reared in different acoustic environments

2013-04-06T20:31:02Z

Abstract: The tseet contact call, common to black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli), is the most frequently produced vocalization of each species. Previous work has characterized the tseet call of black-capped and mountain chickadees from different geographic locations in terms of nine acoustic features. In the current study, using similar methods, the tseet call of black-capped chickadees that were hand reared with either conspecifics, heterospecifics (mountain chickadees), or in isolation from adult chickadees are described. Analysis of call features examined which acoustic features were most affected by rearing environment, and revealed that starting frequency and the slope of the descending portion of the tseet call differed between black-capped chickadees reared with either conspecific or heterospecific adults. Birds reared in isolation from adults differed from the other hand-reared groups on almost every acoustic feature. Chickadee tseet calls are more individualized when they are reared with adult conspecifics or heterospecifics compared to chickadees that are reared in isolation from adults. The current results suggest a role of learning in this commonly used contact call.

Estimating whale abundance using sparse hydrophone arrays

2013-04-03T14:34:48Z

Abstract: Passive acoustic monitoring has been used to investigate many aspects of marine mammal ecology, although methods to estimate absolute abundance and density using acoustic data have only been developed in recent years. The instrument configuration in an acoustic survey determines which abundance estimation methods can be used. Sparsely distributed arrays of instruments are useful because wide geographic areas can be covered. However, instrument spacing in sparse arrays is such that the same vocalisation will not be detected on multiple instruments, excluding the use of some abundance estimation methods. The aim of this thesis was to explore cetacean abundance and density estimation using novel sparse array datasets, applying existing methods where possible, or developing new approaches. The wealth of data collected by sparse arrays was demonstrated by analysing a 10-year dataset collected by the U.S. Navy’s Sound Surveillance System in the north-east Atlantic. Spatial and temporal patterns of blue (Balaenoptera musculus) and fin whale (Balaenoptera physalus) vocal activity were investigated using generalised additive models. Distance sampling-based methods were applied to fin whale calls recorded by an array of Ocean Bottom Seismometers in the north-east Atlantic. Estimated call density was 993 calls/1000 km².hr⁻¹ (CV: 0.39). Animal density could not be estimated because the call rate was unknown. Further development of the call localisation method is required so the current density estimate may be biased. Furthermore, analysing a single day of data resulted in a high variance estimate. Finally, a new simulation-based method developed to estimate density from single hydrophones was applied to blue whale calls recorded in the northern Indian Ocean. Estimated call density was 3 calls/1000 km².hr⁻¹ (CV: 0.17). Again, density of whales could not be estimated as the vocalisation rate was unknown. Lack of biological knowledge poses the greatest limitation to abundance and density estimation using acoustic data.

Competing conservation objectives for predators and prey : estimating killer whale prey requirements for Chinook salmon

2013-05-12T04:08:58Z

Abstract: Ecosystem-based management (EBM) of marine resources attempts to conserve interacting species. In contrast to single-species fisheries management, EBM aims to identify and resolve conflicting objectives for different species. Such a conflict may be emerging in the northeastern Pacific for southern resident killer whales (Orcinus orca) and their primary prey, Chinook salmon (Oncorhynchus tshawytscha). Both species have at-risk conservation status and transboundary (Canada–US) ranges. We modeled individual killer whale prey requirements from feeding and growth records of captive killer whales and morphometric data from historic live-capture fishery and whaling records worldwide. The models, combined with caloric value of salmon, and demographic and diet data for wild killer whales, allow us to predict salmon quantities needed to maintain and recover this killer whale population, which numbered 87 individuals in 2009. Our analyses provide new information on cost of lactation and new parameter estimates for other killer whale populations globally. Prey requirements of southern resident killer whales are difficult to reconcile with fisheries and conservation objectives for Chinook salmon, because the number of fish required is large relative to annual returns and fishery catches. For instance, a U.S. recovery goal (2.3% annual population growth of killer whales over 28 years) implies a 75% increase in energetic requirements. Reducing salmon fisheries may serve as a temporary mitigation measure to allow time for management actions to improve salmon productivity to take effect. As ecosystem-based fishery management becomes more prevalent, trade-offs between conservation objectives for predators and prey will become increasingly necessary. Our approach offers scenarios to compare relative influence of various sources of uncertainty on the resulting consumption estimates to prioritise future research efforts, and a general approach for assessing the extent of conflict between conservation objectives for threatened or protected wildlife where the interaction between affected species can be quantified.

Estimating seasonal abundance of a central place forager using counts and telemetry data

2013-05-12T01:32:43Z

Abstract: Obtaining population estimates of species that are not easily observed directly can be problematic. However, central place foragers can often be observed some of the time, e.g. when seals are hauled out. In these instances, population estimates can be derived from counts, combined with information on the proportion of time that animals can be observed. We present a modelling framework to estimate seasonal absolute abundance using counts and information from satellite telemetry data. The method was tested on a harbour seal population in an area of southeast Scotland. Counts were made monthly, between November 2001 and June 2003, when seals were hauled out on land and were corrected for the proportion of time the seals were at sea using satellite telemetry. Harbour seals (n=25) were tagged with satellite relay data loggers between November 2001 and March 2003. To estimate the proportion of time spent hauled out, time at sea on foraging trips was modelled separately from haul-out behaviour close to haul-out sites because of the different factors affecting these processes. A generalised linear mixed model framework was developed to capture the longitudinal nature of the data and the repeated measures across individuals. Despite seasonal variability in the number of seals counted at haul-out sites, the model generated estimates of abundance, with an overall mean of 846 (95% CI: 767 to 979). The methodology shows the value of using count and telemetry data collected concurrently for estimating absolute abundance, information that is essential to assess interactions between predators, fish stocks and fisheries. Description: R.J.S. was supported by a Natural Environment Research Council studentship.

Male mating tactics in the rose bitterling (Rhodeus ocellatus) and European bitterling (Rhodeus amarus)

2013-03-28T14:59:06Z

Abstract: The aim of this study was to investigate the basis to male mating decisions in two related species of bitterling: Rhodeus ocellatus and R. amarus. Bitterling have a resource-based mating system; females lay eggs in the gills of live freshwater mussels and males fertilize the eggs by releasing sperm into the inhalant syphon of the mussel. Male bitterling perform courtship behaviour and aggressively defend mussels in a territory from which they exclude other males. Using laboratory and field experiments it was shown that male aggressive behaviour is inherited through additive maternal genes. Male aggression is also influenced by the number of conspecific males encountered in competition for a mussel, and by the degree of clustering of mussels. Limited availability of mussels results in stronger selection on traits males use in mating context: hence they are more aggressive, larger and more colourful. The differences in mating behaviours in different environments may indicate a conflict between male dominance and female choice, but have not led to reproductive isolation. Resource availability during ontogenesis and male density during embryogenesis, however, do not exert an effect on male aggressive behaviour. Red carotenoid-based nuptial coloration functions as an inter- and intra-sexual signal and undergoes rapid variation in response to changes in mating context. Male bitterling do not modulate their courtship and aggressive behaviour in response to variation in female size, and their choice of mussel species is influenced by, and consistent with, female oviposition choice.

Photo-grammetric measurements of swimming speed and body length of basking sharks observed around the Hebrides, Scotland

2013-05-12T04:33:52Z

Abstract: Photo-grammetric techniques developed for measuring body length and small scale movement patterns of cetaceans were applied to surface swimming basking sharks off the west coast of Scotland. These methods removed the need for close approaches, reducing the likelihood of disturbing the focal animal. Average swimming speed was calculated from the total path length between shark locations measured at approximately one minute intervals. These average speeds varied from 0.49 to 0.73 ms−1 for tracks of between 30 and 170 minutes' duration. Body length measurements ranged between 2.35 and 6.43 m. For ten sharks where body length and swimming speed were measured there was a significant correlation between body length (L) and swimming speed (V) expressed as V = 0.36L033.

Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends

2013-03-27T16:01:02Z

Abstract: Archaeal chromatin proteins share molecular and functional similarities with both bacterial and eukaryotic chromatin proteins. These proteins play an important role in functionally organizing the genomic DNA into a compact nucleoid. Cren7 and Sul7 are two crenarchaeal nucleoid-associated proteins, which are structurally homologous, but not conserved at the sequence level. Co-crystal structures have shown that these two proteins induce a sharp bend on binding to DNA. In this study, we have investigated the architectural properties of these proteins using atomic force microscopy, molecular dynamics simulations and magnetic tweezers. We demonstrate that Cren7 and Sul7 both compact DNA molecules to a similar extent. Using a theoretical model, we quantify the number of individual proteins bound to the DNA as a function of protein concentration and show that forces up to 3.5 pN do not affect this binding. Moreover, we investigate the flexibility of the bending angle induced by Cren7 and Sul7 and show that the protein-DNA complexes differ in flexibility from analogous bacterial and eukaryotic DNA-bending proteins.

hSSB1 interacts directly with the MRN complex stimulating its recruitment to DNA double-strand breaks and its endo-nuclease activity

2013-05-12T04:05:28Z

Abstract: hSSB1 is a recently discovered single-stranded DNA binding protein that is essential for efficient repair of DNA double-strand breaks (DSBs) by the homologous recombination pathway. hSSB1 is required for the efficient recruitment of the MRN complex to sites of DSBs and for the efficient initiation of ATM dependent signalling. Here we explore the interplay between hSSB1 and MRN. We demonstrate that hSSB1 binds directly to NBS1, a component of the MRN complex, in a DNA damage independent manner. Consistent with the direct interaction, we observe that hSSB1 greatly stimulates the endo-nuclease activity of the MRN complex, a process that requires the C-terminal tail of hSSB1. Interestingly, analysis of two point mutations in NBS1, associated with Nijmegen breakage syndrome, revealed weaker binding to hSSB1, suggesting a possible disease mechanism.

hSSB1 rapidly binds at the sites of DNA double-strand breaks and is required for the efficient recruitment of the MRN complex

2013-05-12T04:04:25Z

Abstract: hSSB1 is a newly discovered single-stranded DNA (ssDNA)-binding protein that is essential for efficient DNA double-strand break signalling through ATM. However, the mechanism by which hSSB1 functions to allow efficient signalling is unknown. Here, we show that hSSB1 is recruited rapidly to sites of double-strand DNA breaks (DSBs) in all interphase cells (G1, S and G2) independently of, CtIP, MDC1 and the MRN complex (Rad50, Mre11, NBS1). However expansion of hSSB1 from the DSB site requires the function of MRN. Strikingly, silencing of hSSB1 prevents foci formation as well as recruitment of MRN to sites of DSBs and leads to a subsequent defect in resection of DSBs as evident by defective RPA and ssDNA generation. Our data suggests that hSSB1 functions upstream of MRN to promote its recruitment at DSBs and is required for efficient resection of DSBs. These findings, together with previous work establish essential roles of hSSB1 in controlling ATM activation and activity, and subsequent DSB resection and homologous recombination (HR).

Crystallization of Ranasmurfin, a blue coloured protein from Polypedates leucomystax

2013-05-12T02:01:33Z

Abstract: Ranasmurfin, a previously uncharacterized similar to 13 kDa blue protein found in the nests of the frog Polypedates leucomystax, has been purified and crystallized. The crystals are an intense blue colour and diffract to 1.51 angstrom with P2(1) symmetry and unit-cell parameters a = 40.9, b = 59.9, c = 45.0 angstrom, beta = 93.3 degrees. Self-rotation function analysis indicates the presence of a dimer in the asymmetric unit. Biochemical data suggest that the blue colour of the protein is related to dimer formation. Sequence data for the protein are incomplete, but thus far have identified no model for molecular replacement. A fluorescence scan shows a peak at 9.676 keV, indicating that the protein binds zinc and suggesting a route for structure solution.

Runaway sexual selection without genetic correlations : social environments and flexible mate choice initiate and enhance the Fisher process

2013-05-12T04:13:35Z

Abstract: Female mating preferences are often flexible, reflecting the social environment in which they are expressed. Associated indirect genetic effects (IGEs) can affect the rate and direction of evolutionary change, but sexual selection models do not capture these dynamics. We incorporate IGEs into quantitative genetic models to explore how variation in social environments and mate choice flexibility influence Fisherian sexual selection. The importance of IGEs is that runaway sexual selection can occur in the absence of a genetic correlation between male traits and female preferences. Social influences can facilitate the initiation of the runaway process and increase the rate of trait elaboration. Incorporating costs to choice do not alter the main findings. Our model provides testable predictions: (1) genetic covariances between male traits and female preferences may not exist, (2) social flexibility in female choice will be common in populations experiencing strong sexual selection, (3) variation in social environments should be associated with rapid sexual trait divergence, and (4) secondary sexual traits will be more elaborate than previously predicted. Allowing feedback from the social environment resolves discrepancies between theoretical predictions and empirical data, such as why indirect selection on female preferences, theoretically weak, might be sufficient for preferences to become elaborated.

Iso-seco-tanapartholides : isolation, synthesis and biological evaluation

2013-05-12T04:10:20Z

Abstract: The isolation, identification and total synthesis of two plant-derived inhibitors of the NF-kappa B signaling pathway from the iso-seco-tanapartholide family of natural products is described. A key step in the efficient reaction sequence is a late-stage oxidative cleavage reaction that was carried out in the absence of protecting groups to give the natural products directly. A detailed comparison of the synthetic material with samples of the natural products proved informative. Biological studies on synthetic material confirmed that these compounds act late in the NF-kappa B signaling pathway. ((C) Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)

The effect of interferon on the transcription pattern of parainfluenza virus 5

2013-03-20T14:15:13Z

Abstract: Interferon (IFN) is activated in response to virus infections and upregulates interferon-stimulated genes (ISGs) resulting in the expression of hundreds of proteins, many of which have direct or indirect antiviral activity. Parainfluenza virus 5 (PIV5) of the Paramyxoviridae family is a non-segmented negative sense single-stranded RNA virus with seven genes encoding eight proteins. Here we present that IFN induces alterations in the pattern of both virus transcription and translation and that ISG56 is primarily responsible for these effects. We report that when cells were treated with IFN post-infection, virus protein synthesis was inhibited while virus transcription levels were increased. These results suggest that ISG56 selectively inhibits the translation of viral mRNAs. In addition, the relationship of various PIV5 isolates was analysed by next generation sequencing. Four areas with a high degree of single nucleotide polymorphisms (SNPs) were identified and mapped to the intergenic regions of NP-V/P, M-F and HN-L, as well as the entire SH gene. Three of the isolates, the porcine strain SER and the canine strains CPI+ and CPI-, did not express an SH protein due to the lack of a start codon. A low degree of variation was found in the amino acid sequence of the HN glycoprotein suggesting that PIV5 may be less pressured to evolve in order to evade immune responses, such as neutralising antibodies.

To ping or not to ping : the use of active acoustic devices in mitigating interactions between small cetaceans and gillnet fisheries

2013-03-15T12:01:02Z

Abstract: Active sound emitters (‘pingers’) are used in several gillnet fisheries to reduce bycatch of small cetaceans, and/or to reduce depredation by dolphins. Here, we review studies conducted to determine how effective these devices may be as management tools. Significant reductions in bycatch of harbour porpoise Phocoena phocoena, franciscana Pontoporia blainvillei, common Delphinus delphis and striped dolphin Stenella coeruleoalba, and beaked whales as a group have been demonstrated. For harbour porpoise this result has been replicated in 14 controlled experiments in North America and Europe, and appears to be due to porpoises avoiding the area ensonified by pingers. Two gillnet fisheries (California-Oregon driftnet fishery for swordfish; New England groundfish fishery) with mandatory pinger use have been studied for over a decade. Bycatch rates of dolphins/porpoises have fallen by 50 to 60%, and there is no evidence of bycatch increasing over time due to habituation. In both fisheries, bycatch rates were significantly higher in nets sparsely equipped with pingers or in which pingers had failed, than in nets without any pingers at all. Studies of pinger use to reduce depredation by bottlenose dolphins Tursiops truncatus generally show small and inconsistent improvements in fish catches and somewhat reduced net damage. Dolphin bycatch in these fisheries is rare, but still occurs in nets with pingers. Taken together, these studies suggest that the most promising candidates for bycatch reduction via pinger use will be gillnet fisheries in developed countries in which the bycaught cetaceans are generally neophobic species with large home ranges. We offer a set of lessons learned from the last decade of bycatch management.

Tissue-specific transcriptomics in the field cricket Teleogryllus oceanicus

2013-03-14T12:33:17Z

Abstract: Field crickets (family Gryllidae) frequently are used in studies of behavioral genetics, sexual selection, and sexual conflict, but there have been no studies of transcriptomic differences among different tissue types. We evaluated transcriptome variation among testis, accessory gland, and the remaining whole-body preparations from males of the field cricket, Teleogryllus oceanicus. Non-normalized cDNA libraries from each tissue were sequenced on the Roche 454 platform, and a master assembly was constructed using testis, accessory gland, and whole-body preparations. A total of 940,200 reads were assembled into 41,962 contigs, to which 36,856 singletons (reads not assembled into a contig) were added to provide a total of 78,818 sequences used in annotation analysis. A total of 59,072 sequences (75%) were unique to one of the three tissues. Testis tissue had the greatest proportion of tissue-specific sequences (62.6%), followed by general body (56.43%) and accessory gland tissue (44.16%). We tested the hypothesis that tissues expressing gene products expected to evolve rapidly as a result of sexual selection—testis and accessory gland—would yield a smaller proportion of BLASTx matches to homologous genes in the model organism Drosophila melanogaster compared with whole-body tissue. Uniquely expressed sequences in both testis and accessory gland showed a significantly lower rate of matching to annotated D. melanogaster genes compared with those from general body tissue. These results correspond with empirical evidence that genes expressed in testis and accessory gland tissue are rapidly evolving targets of selection. Description: This work was supported by a Natural Environment Research Council Junior Postdoctoral Fellowship (NE/G014906/1) and Pacific Rim Foundation funding (08-T-PRRP-05-0029) to N.W.B.

A computational approach to discovering p53 binding sites in the human genome

2013-03-13T15:33:06Z

Abstract: The tumour suppressor p53 protein plays a central role in the DNA damage response/checkpoint pathways leading to DNA repair, cell cycle arrest, apoptosis and senescence. The activation of p53-mediated pathways is primarily facilitated by the binding of tetrameric p53 to two 'half-sites', each consisting of a decameric p53 response element (RE). Functional REs are directly adjacent or separated by a small number of 1-13 'spacer' base pairs (bp). The p53 RE is detected by exact or inexact matches to the palindromic sequence represented by the regular expression [AG][AG][AG]C[AT][TA]G[TC][TC][TC] or a position weight matrix (PWM). The use of matrix-based and regular expression pattern-matching techniques, however, leads to an overwhelming number of false positives. A more specific model, which combines multiple factors known to influence p53-dependent transcription, is required for accurate detection of the binding sites. In this thesis, we present a logistic regression based model which integrates sequence information and epigenetic information to predict human p53 binding sites. Sequence information includes the PWM score and the spacer length between the two half-sites of the observed binding site. To integrate epigenetic information, we analyzed the surrounding region of the binding site for the presence of mono- and trimethylation patterns of histone H3 lysine 4 (H3K4). Our model showed a high level of performance on both a high-resolution data set of functional p53 binding sites from the experimental literature (ChIP data) and the whole human genome. Comparing our model with a simpler sequence-only model, we demonstrated that the prediction accuracy of the sequence-only model could be improved by incorporating epigenetic information, such as the two histone modification marks H3K4me1 and H3K4me3.

Dimer-dimer stacking interactions are important for nucleic acid binding by the archaeal chromatin protein Alba

2013-05-12T03:03:55Z

Abstract: Archaea use a variety of small basic proteins to package their DNA. One of the most widespread and highly conserved is the Alba (Sso10b) protein. Alba interacts with both DNA and RNA in vitro, and we show in the present study that it binds more tightly to dsDNA (double-stranded DNA) than to either ssDNA (single-stranded DNA) or RNA. The Alba protein is dimeric in solution, and forms distinct ordered complexes with DNA that have been visualized by electron microscopy studies; these studies suggest that, on binding dsDNA, the protein forms extended helical protein fibres. An end-to-end association of consecutive Alba dimers is suggested by the presence of a dimer-dimer interface in crystal structures of Alba from several species, and by the strong conservation of the interface residues, centred on Are and Phe(60). In the present study we map perturbation of the polypeptide backbone of Alba upon binding to DNA and RNA by NMR, and demonstrate the central role of Phe(60) in forming the dimer dimer interface. Site-directed spin labelling and pulsed ESR are used to confirm that an end-to-end, dimer dimer interaction forms in the presence of dsDNA.

Seasonal inflow of warm water onto the southern Weddell Sea continental shelf, Antarctica

2013-05-12T04:14:28Z

Abstract: To capture the austral summer to winter transition in water mass properties over the southern Weddell Sea continental shelf and slope region Weddell seals were tagged with miniaturized conductivity–temperature–depth sensors in February 2011. During the following 8 months the instruments yielded about 9000 temperature–salinity profiles from a previously undersampled area. This allows, for the first time, a description of the seasonality of warm water intrusions onto the shelf. A temperature section across the Filchner Depression and eastern shelf shows a pronounced decrease in warm water inflow from summer to winter, further supported by an almost 3–year long time series from a shelf–break mooring. The seasonal variability is related to the surface wind stress and an associated deepening of the off–shore core of Warm Deep Water.

Genetic analysis of life-history constraint and evolution in a wild ungulate population

2013-05-12T04:13:38Z

Abstract: Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.

Vocal copying of individually distinctive signature whistles in bottlenose dolphins

2013-03-17T19:01:00Z

Abstract: Vocal learning is relatively common in birds but less so in mammals. Sexual selection and individual or group recognition have been identified as major forces in its evolution. While important in the development of vocal displays, vocal learning also allows signal copying in social interactions. Such copying can function in addressing or labelling selected conspecifics. Most examples of addressing in non-humans come from bird song, where matching occurs in an aggressive context. However, in other animals, addressing with learned signals is very much an affiliative signal. We studied the function of vocal copying in a mammal that shows vocal learning as well as complex cognitive and social behaviour, the bottlenose dolphin (Tursiops truncatus). Copying occurred almost exclusively between close associates such as mother–calf pairs and male alliances during separation and was not followed by aggression. All copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it. We found no evidence for the use of copying in aggression or deception. This use of vocal copying is similar to its use in human language, where the maintenance of social bonds appears to be more important than the immediate defence of resources.

A class of 5-nitro-2-furancarboxylamides with potent trypanocidal activity against Trypanosoma brucei in vitro

2013-05-12T04:36:57Z

Abstract: Recently, the World Health Organization approved the nifurtimox–eflornithine combination therapy for the treatment of human African trypanosomiasis, renewing interest in nitroheterocycle therapies for this and associated diseases. In this study, we have synthesized a series of novel 5-nitro-2-furancarboxylamides that show potent trypanocidal activity, 1000-fold more potent than nifurtimox against in vitro Trypanosoma brucei with very low cytotoxicity against human HeLa cells. More importantly, the most potent analogue showed very limited cross-resistance to nifurtimox-resistant cells and vice versa. This implies that our novel, relatively easy to synthesize and therefore cheap, 5-nitro-2-furancarboxylamides are targeting a different, but still essential, biochemical process to those targeted by nifurtimox or its metabolites in the parasites. The significant increase in potency (smaller dose probably required) has the potential for greatly reducing unwanted side effects and also reducing the likelihood of drug resistance. Collectively, these findings have important implications for the future therapeutic treatment of African sleeping sickness.

Fast silencing reveals a lost role for reciprocal inhibition in locomotion

2013-02-18T10:01:02Z

Abstract: Summary Alternating contractions of antagonistic muscle groups during locomotion are generated by spinal “half-center” networks coupled in antiphase by reciprocal inhibition. It is widely thought that reciprocal inhibition only coordinates the activity of these muscles. We have devised two methods to rapidly and selectively silence neurons on just one side of Xenopus tadpole spinal cord and hindbrain, which generate swimming rhythms. Silencing activity on one side led to rapid cessation of activity on the other side. Analyses reveal that this resulted from the depression of reciprocal inhibition connecting the two sides. Although critical neurons in intact tadpoles are capable of pacemaker firing individually, an effect that could support motor rhythms without inhibition, the swimming network itself requires ∼23 min to regain rhythmic activity after blocking inhibition pharmacologically, implying some homeostatic changes. We conclude therefore that reciprocal inhibition is critical for the generation of normal locomotor rhythm.

The role of endosymbionts in the evolution of haploid-male genetic systems in scale insects (Coccoidea)

2013-02-13T10:31:02Z

Abstract: There is an extraordinary diversity in genetic systems across species, but this variation remains poorly understood. In part, this is because the mechanisms responsible for transitions between systems are often unknown. A recent hypothesis has suggested that conflict between hosts and endosymbiotic microorganisms over transmission could drive the transition from diplodiploidy to systems with male haploidy (haplodiploidy, including arrhenotoky and paternal genome elimination [PGE]). Here, we present the first formal test of this idea with a comparative analysis across scale insects (Hemiptera: Coccoidea). Scale insects are renowned for their large variation in genetic systems, and multiple transitions between diplodiploidy and haplodiploidy have taken place within this group. Additionally, most species rely on endosymbiotic microorganisms to provide them with essential nutrients lacking in their diet. We show that species harboring endosymbionts are indeed more likely to have a genetic system with male haploidy, which supports the hypothesis that endosymbionts might have played a role in the transition to haplodiploidy. We also extend our analysis to consider the relationship between endosymbiont presence and transitions to parthenogenesis. Although in scale insects there is no such overall association, species harboring eukaryote endosymbionts were more likely to be parthenogenetic than those with bacterial symbionts. These results support the idea that intergenomic conflict can drive the evolution of novel genetic systems and affect host reproduction.

Functional analysis of Leishmania cyclopropane fatty acid synthetase

2013-02-11T16:31:06Z

Abstract: The single gene encoding cyclopropane fatty acid synthetase (CFAS) is present in Leishmania infantum, L. mexicana and L. braziliensis but absent from L. major, a causative agent of cutaneous leishmaniasis. In L. infantum, usually causative agent of visceral leishmaniasis, the CFAS gene is transcribed in both insect (extracellular) and host (intracellular) stages of the parasite life cycle. Tagged CFAS protein is stably detected in intracellular L. infantum but only during the early log phase of extracellular growth, when it shows partial localisation to the endoplasmic reticulum. Lipid analyses of L. infantum wild type, CFAS null and complemented parasites detect a low abundance CFAS-dependent C19 Delta fatty acid, characteristic of a cyclopropanated species, in wild type and add-back cells. Sub-cellular fractionation studies locate the C19 Delta fatty acid to both ER and plasma membrane-enriched fractions. This fatty acid is not detectable in wild type L. major, although expression of the L. infantum CFAS gene in L. major generates cyclopropanated fatty acids, indicating that the substrate for this modification is present in L. major, despite the absence of the modifying enzyme. Loss of the L. infantum CFAS gene does not affect extracellular parasite growth, phagocytosis or early survival in macrophages. However, while endocytosis is also unaffected in the extracellular CFAS nulls, membrane transporter activity is defective and the null parasites are more resistant to oxidative stress. Following infection in vivo, L. infantum CFAS nulls exhibit lower parasite burdens in both the liver and spleen of susceptible hosts but it has not been possible to complement this phenotype, suggesting that loss of C19 Delta fatty acid may lead to irreversible changes in cell physiology that cannot be rescued by re-expression. Aberrant cyclopropanation in L. major decreases parasite virulence but does not influence parasite tissue tropism.

The AEROPATH project targeting Pseudomonas aeruginosa : crystallographic studies for assessment of potential targets in early-stage drug discovery

2013-05-07T14:38:46Z

Abstract: Bacterial infections are increasingly difficult to treat owing to the spread of antibiotic resistance. A major concern is Gram-negative bacteria, for which the discovery of new antimicrobial drugs has been particularly scarce. In an effort to accelerate early steps in drug discovery, the EU-funded AEROPATH project aims to identify novel targets in the opportunistic pathogen Pseudomonas aeruginosa by applying a multidisciplinary approach encompassing target validation, structural characterization, assay development and hit identification from small-molecule libraries. Here, the strategies used for target selection are described and progress in protein production and structure analysis is reported. Of the 102 selected targets, 84 could be produced in soluble form and the de novo structures of 39 proteins have been determined. The crystal structures of eight of these targets, ranging from hypothetical unknown proteins to metabolic enzymes from different functional classes (PA1645, PA1648, PA2169, PA3770, PA4098, PA4485, PA4992 and PA5259), are reported here. The structural information is expected to provide a firm basis for the improvement of hit compounds identified from fragment-based and high-throughput screening campaigns.

The development of free-swimming in Xenopus laevis larvae

2013-02-11T12:19:38Z

Abstract: In Xenopus laevis frog tadpoles, highly self-motive, free-swimming behaviour emerges at the onset of feeding. This is in contrast to the earlier post-hatched larval form, which is capable of escape swimming when stimulated, but normally lies dormant. This developmental transition in behaviour has been documented here and studied in a semi-intact preparation developed to examine the motor output from larvae at the onset of filter feeding. There is a progressive increase in spontaneous motor activity during this period, where spontaneous fictive swimming occurs in episodes of variable duration but with significantly larger burst durations. This spontaneous activity persists after removal of both the fore- and midbrain, but is absent in spinalised preparations. The spontaneous activity is similar to NMDA (100µM) induced rhythm but shows greater periodic variability in the frequency and occurrence of swimming activity. The activity is not dependent on inhibitory synaptic transmission, but is under the control of central GABAergic restraint, as blocking this inhibition with bicuculine (10µM) increased spontaneous locomotor activity. This is distinct to the role of glycinergic inhibition which influences the character of the ventral root bursts, as strychnine (5µM) caused an initial increase in frequency before bursts were synchronised on both the left and right sides, but not the presence of spontaneous activity. However, activity is abolished by the persistent sodium current blocker riluzole (5µM) and enhanced by veratridine (90nM) which potentiates the current, which may suggest that it originates in neurons with pacemaker-like properties - possibly within the hindbrain. Evidence is also provided which shows that the neuromodulatory gas nitric oxide becomes an excitatory modulator of the Xenopus swimming network at the onset of a free-swimming existence, switching from having a global inhibitory role on locomotion in early larval life. The nitric oxide donor DEA/NO (200µM) increased spontaneous fictive swimming in the semi-intact preparation. In contrast, the nitric oxide synthase inhibitor L-NAME combined with PTIO, which sequesters nitric oxide, decreased spontaneous fictive swimming. It is proposed that the emergence of this rhythmic, spontaneous motor activity parallels the increase in swimming at the onset of feeding, suggesting a direct behavioural role for spontaneous network activity in the developing animal.

Estimating demographic parameters for capture-recapture data in the presence of multiple mark types

2013-05-19T00:32:10Z

Abstract: In mark-recapture studies, various techniques can be used to uniquely identify individual animals, such as ringing, tagging or photo-identification using natural markings. In some long-term studies more than one type of marking procedure may be implemented during the study period. In these circumstances, ignoring the different mark types can produce biased survival estimates since the assumption that the different mark types are equally catchable (homogeneous capture probability across mark types) may be incorrect.We implement an integrated approach where we simultaneously analyse data obtained using three different marking techniques, assuming that animals can be cross-classified across the different mark types. We discriminate between competing models using the AIC statistic. This technique also allows us to estimate both relative mark-loss probabilities and relative recapture efficiency rates for the different marking methods.We initially perform a simulation study to explore the different biases that can be introduced if we assume a homogeneous recapture probability over mark type, before applying the method to a real dataset. We make use of data obtained from an intensive long-term observational study of UK female grey seals (Halichoerus grypus) at a single breeding colony, where three different methods are used to identify individuals within a single study: branding, tagging and photo-identification based on seal coat pattern or pelage.

Evolution of ancient functions in the vertebrate insulin-like growth factor system uncovered by study of duplicated salmonid fish genomes

2013-02-07T15:01:03Z

Abstract: Whole genome duplication (WGD) was experienced twice by the vertebrate ancestor (2 rounds; 2R), again by the teleost fish ancestor (3R) and most recently in certain teleost lineages (4R). Consequently, vertebrate gene families are often expanded in 3R and 4R genomes. Arguably, many types of ‘functional divergence’ present across 2R gene families will exceed that between 3R/4R paralogues of genes comprising 2R families. Accordingly, 4R offers a form of replication of 2R. Examining if this concept has implications for molecular evolutionary research, we studied insulin-like growth factor (IGF) binding proteins (IGFBPs), whose six 2R family members carry IGF hormones and regulate interactions between IGFs and IGF1-receptors (IGF1Rs). Using phylogenomic approaches, we resolved the complete IGFBP repertoire of 4R-derived salmonid fishes (nineteen genes; thirteen more than human) and established evolutionary relationships/nomenclature with respect to WGDs. Traits central to IGFBP action were determined for all genes, including atomic interactions in IGFBP-IGF1/IGF2 complexes regulating IGF-IGF1R binding. Using statistical methods, we demonstrate that attributes of these protein interfaces are overwhelming a product of 2R IGFBP family membership, explain 49-68% of variation in IGFBP mRNA concentration in several different tissues and strongly predict the strength and direction of IGFBP transcriptional regulation under differing nutritional-states. The results support a model where vertebrate IGFBP family members evolved divergent structural attributes to provide distinct competition for IGFs with IGF1Rs, pre-disposing different functions in the regulation of IGF-signaling. Evolution of gene expression acted to ensure the appropriate physiological production of IGFBPs according to their structural specializations, leading to optimal IGF-signaling according to nutritional-status and the endocrine/local mode of action. This study demonstrates that relatively recent gene family expansion can facilitate inference of functional evolution within ancient genetic systems. Description: This work was supported by the Marine Alliance for Science and Technology for Scotland pooling initiative, funded by the Scottish Funding Council (grant number HR09011) and contributing institutions.

Development temperature has persistent effects on muscle growth responses in gilthead sea bream

2013-01-25T14:31:02Z

Abstract: Initially we characterised growth responses to altered nutritional input at the transcriptional and tissue levels in the fast skeletal muscle of juvenile gilthead sea bream. Fish reared at 21–22°C (range) were fed a commercial diet at 3% body mass d−1 (non-satiation feeding, NSF) for 4 weeks, fasted for 4d (F) and then fed to satiation (SF) for 21d. 13 out of 34 genes investigated showed consistent patterns of regulation between nutritional states. Fasting was associated with a 20-fold increase in MAFbx, and a 5-fold increase in Six1 and WASp expression, which returned to NSF levels within 16h of SF. Refeeding to satiation was associated with a rapid (<24 h) 12 to 17-fold increase in UNC45, Hsp70 and Hsp90α transcripts coding for molecular chaperones associated with unfolded protein response pathways. The growth factors FGF6 and IGF1 increased 6.0 and 4.5-fold within 16 h and 24 h of refeeding respectively. The average growth in diameter of fast muscle fibres was checked with fasting and significant fibre hypertrophy was only observed after 13d and 21d SF. To investigate developmental plasticity in growth responses we used the same experimental protocol with fish reared at either 17.5–18.5°C (range) (LT) or 21–22°C (range) (HT) to metamorphosis and then transferred to 21–22°C. There were persistent effects of development temperature on muscle growth patterns with 20% more fibres of lower average diameter in LT than HT group of similar body size. Altering the nutritional input to the muscle to stimulate growth revealed cryptic changes in the expression of UNC45 and Hsp90α with higher transcript abundance in the LT than HT groups, whereas there were no differences in the expression of MAFbx and Six1. It was concluded that myogenesis and gene expression patterns during growth are not fixed, but can be modified by temperature during the early stages of the life cycle.

Unusual features of pomoviral RNA movement

2013-01-21T16:31:02Z

Abstract: Potato mop-top pomovirus (PMTV) is one of a few viruses that can move systemically in plants in the absence of the capsid protein (CP). Pomoviruses encode the triple gene block genetic module of movement proteins (TGB 1, 2, and 3) and recent research suggests that PMTV RNA is transported either as ribonucleoprotein (RNP) complexes containing TGB1 or encapsidated in virions containing TGB1. Furthermore, there are different requirements for local or systemic (long-distance) movement. Research suggests that nucleolar passage of TGB1 may be important for the long-distance movement of both RNP and virions. Moreover, and uniquely, the long-distance movement of the CP-encoding RNA requires expression of both major and minor CP subunits and is inhibited when only the major CP sub unit is expressed. This paper reviews pomovirus research and presents a current model for RNA movement.

Phasing of muscle gene expression with fasting-induced recovery growth in Atlantic salmon

2013-05-12T03:31:39Z

Abstract: Background: Many fish species experience long periods of fasting in nature often associated with seasonal reductions in water temperature and prey availability or spawning migrations. During periods of nutrient restriction, changes in metabolism occur to provide cellular energy via catabolic processes. Muscle is particularly affected by prolonged fasting as myofibrillar proteins act as a major energy source. To investigate the mechanisms of metabolic reorganisation with fasting and refeeding in a saltwater stage of Atlantic salmon (Salmo salar L.) we analysed the expression of genes involved in myogenesis, growth signalling, lipid biosynthesis and myofibrillar protein degradation and synthesis pathways using qPCR. Results: Hierarchical clustering of gene expression data revealed three clusters. The first cluster comprised genes involved in lipid metabolism and triacylglycerol synthesis (ALDOB, DGAT1 and LPL) which had peak expression 3-14d after refeeding. The second cluster comprised ADIPOQ, MLC2, IGF-I and TALDO1, with peak expression 14-32d after refeeding. Cluster III contained genes strongly down regulated as an initial response to feeding and included the ubiquitin ligases MuRF1 and MAFbx, myogenic regulatory factors and some metabolic genes. Conclusion: Early responses to refeeding in fasted salmon included the synthesis of triacylglycerols and activation of the adipogenic differentiation program. Inhibition of MuRF1 and MAFbx respectively may result in decreased degradation and concomitant increased production of myofibrillar proteins. Both of these processes preceded any increase in expression of myogenic regulatory factors and IGF-I. These responses could be a necessary strategy for an animal adapted to long periods of food deprivation whereby energy reserves are replenished prior to the resumption of myogenesis.

Mechanisms of gene duplication and translocation and progress towards understanding their relative contributions to animal genome evolution

2013-01-07T16:36:18Z

Abstract: Duplication of genetic material is clearly a major route to genetic change, with consequences for both evolution and disease. A variety of forms and mechanisms of duplication are recognised, operating across the scales of a few base pairs upto entire genomes. With the ever-increasing amounts of gene and genome sequence data that are becoming available, our understanding of the extent of duplication is greatly improving, both in terms of the scales of duplication events as well as their rates of occurrence. An accurate understanding of these processes is vital if we are to properly understand important events in evolution as well as mechanisms operating at the level of genome organisation. Here we will focus on duplication in animal genomes and how the duplicated sequences are distributed, with the aim of maintaining a focus on principles of evolution and organisation that are most directly applicable to the shaping of our own genome.

How many seals were there? The global shelf loss during the Last Glacial Maximum and its effect on the size and distribution of grey seal populations

2013-03-14T16:31:13Z

Abstract: Predicting how marine mammal populations act to habitat changes will be essential for developing conservation management strategies by marine mammal ecologists in the 21st century. Responses to previous environmental change may be informative in the development of predictive models. Here we describe the likely effects of the last ice age on grey seal population size and distribution. We use satellite telemetry data to define grey seal foraging habitat in terms of the temperature and depth ranges exploited by the contemporary populations. We estimate the available extent of such habitat in the North Atlantic at present and at the last glacial maximum (LGM); taking account of glacial and seasonal sea-ice coverage, estimated reductions of sea-level (123m) and seawater temperature hind-casts from GLAMAP-2000. Most of the extensive continental shelf waters (North Sea, Baltic Sea and Scotian Shelf), currently supporting >95% of grey seals, were unavailable at the LGM. A combination of lower sea-level and extensive ice-sheets, massively increased seasonal sea-ice coverage and southerly extent of cold water would have pushed grey seals into areas with no significant shelf waters. The habitat during the LGM might have been as small as 4%, when compared to today’s extent and grey seal populations may have fallen to similarly. An alternative scenario involving a major change to a pelagic/bathy-pelagic foraging niche cannot be discounted. However, hooded seals that appear to out-compete and effectively exclude grey seals from such habitat currently dominate that niche. If as seems likely, the grey seal population fell to very low levels it would have remained low for several thousand years before expanding into current habitats over the last 12000 years or so.

Variation in female grey seal (Halichoerus grypus) reproductive performance correlates to proactive-reactive behavioural types

2013-03-14T16:31:12Z

Abstract: Consistent individual differences (CIDs) in behaviour, indicative of behavioural types or personalities, have been shown in taxa ranging from Cnidaria to Mammalia. However, despite numerous theoretical explanations there remains limited empirical evidence for selective mechanisms that maintain such variation within natural populations. We examined behavioural types and fitness proxies in wild female grey seals at the North Rona breeding colony. Experiments in 2009 and 2010 employed a remotely-controlled vehicle to deliver a novel auditory stimulus to females to elicit changes in pup-checking behaviour. Mothers tested twice during lactation exhibited highly repeatable individual pup-checking rates within and across breeding seasons. Observations of undisturbed mothers (i.e. experiencing no disturbance from conspecifics or experimental test) also revealed CIDs in pup-checking behaviour. However, there was no correlation between an individuals’ pup-checking rate during undisturbed observations with the rate in response to the auditory test, indicating plasticity across situations. The extent to which individuals changed rates of pup-checking from undisturbed to disturbed conditions revealed a continuum of behavioural types from proactive females, who maintained a similar rate throughout, to reactive females, who increased pup-checking markedly in response to the test. Variation in maternal expenditure (daily mass loss rate) was greater among more reactive mothers than proactive mothers. Consequently pups of more reactive mothers had more varied growth rates centred around the long-term population mean. These patterns could not be accounted for by other measured covariates as behavioural type was unrelated to a mother’s prior experience, degree of inter-annual site fidelity, physical characteristics of their pupping habitat, pup sex or pup activity. These findings are consistent with the hypothesis that variation in behavioural types is maintained by spatial and temporal environmental variation combined with limits to phenotype-environment matching.

What is biodiversity?

2013-05-12T04:04:03Z

The geometric mean of relative abundance indices : a biodiversity measure with a difference

2012-12-19T11:01:02Z

Abstract: The 2010 Biodiversity Target of the Convention on Biological Diversity (CBD), set in 2002, which stated that there should be ‘a significant reduction of the current rate of biodiversity loss' by 2010, highlighted the need for informative and tractable metrics that can be used to evaluate change in biological diversity. While the subsequent Aichi 2020 targets are more wide-ranging, they also seek to reduce the rate of biodiversity loss. The geometric mean of relative abundance indices, G, is increasingly being used to examine trends in biological diversity and to assess whether biodiversity targets are being met. Here, we explore the mathematical and statistical properties of G that make it useful for judging temporal change in biological diversity, and we discuss its advantages and limitations relative to other measures. We demonstrate that the index reflects trends in both abundance and evenness, and that it is not prone to bias when detectability of individuals varies by species. We note that it allows data from different surveys to be combined to generate a composite index. However, the index exhibits high variance and unstable behaviour when rarely-recorded species are included in the analyses. Read More: http://www.esajournals.org/doi/abs/10.1890/ES11-00186.1

Local and regional rarity in a diverse tropical fish assemblage

2013-05-12T04:14:38Z

Abstract: Because most species in an ecological assemblage are rare, much of the species richness we value is due to taxa with few individuals or a restricted distribution. It has been apparent since the time of ecological pioneers such as Bates and Darwin that tropical systems have disproportionately large numbers of rare species, yet the distribution and abundance patterns of these species remain largely unknown. Here, we examine the diversity of freshwater fish in a series of lakes in the Amazonian várzea, and relate relative abundance, both as numbers of individuals and as biomass, to the occurrence of species in space and time. We find a bimodal relationship of occurrence that distinguishes temporally and spatially persistent species from those that are infrequent in both space and time. Logistic regression reveals that information on occurrence helps distinguish those species that are rare in this locality but abundant elsewhere, from those that are rare throughout the region. These results form a link between different approaches used to evaluate commonness and rarity. In doing so, they provide a tool for identifying species of high conservation priority in poorly documented but species rich localities.

A model for 3-methyladenine recognition by 3-methyladenine DNA glycosylase I (TAG) from Staphylococcus aureus

2013-05-12T04:36:35Z

Abstract: The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 angstrom resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that chargecharge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection.

Estimated tissue and blood N2 levels and risk of in vivo bubble formation in deep-, intermediate- and shallow diving toothed whales during exposure to naval sonar.

2013-05-12T04:36:37Z

Abstract: Naval sonar has been accused of causing whale stranding by a mechanism which increases formation of tissue N2 gas bubbles. Increased tissue and blood N2 levels, and thereby increased risk of decompression sickness (DCS), is thought to result from changes in behavior or physiological responses during diving. Previous theoretical studies have used hypothetical sonar-induced changes in both behavior and physiology to model blood and tissue N2 tension PN2, but this is the first attempt to estimate the changes during actual behavioral responses to sonar. We used an existing mathematical model to estimate blood and tissue N2 tension PN2 from dive data recorded from sperm, killer, long-finned pilot, Blainville’s beaked, and Cuvier’s beaked whales before and during exposure to Low- (1–2 kHz) and Mid- (2–7 kHz) frequency active sonar. Our objectives were: (1) to determine if differences in dive behavior affects risk of bubble formation, and if (2) behavioral- or (3) physiological responses to sonar are plausible risk factors. Our results suggest that all species have natural high N2 levels, with deep diving generally resulting in higher end-dive PN2 as compared with shallow diving. Sonar exposure caused some changes in dive behavior in both killer whales, pilot whales and beaked whales, but this did not lead to any increased risk of DCS. However, in three of eight exposure session with sperm whales, the animal changed to shallower diving, and in all these cases this seem to result in an increased risk of DCS, although risk was still within the normal risk range of this species. When a hypothetical removal of the normal dive response (bradycardia and peripheral vasoconstriction), was added to the behavioral response during model simulations, this led to an increased variance in the estimated end-dive N2 levels, but no consistent change of risk. In conclusion, we cannot rule out the possibility that a combination of behavioral and physiological responses to sonar have the potential to alter the blood and tissue end-dive N2 tension to levels which could cause DCS and formation of in vivo bubbles, but the actually observed behavioral responses of cetaceans to sonar in our study, do not imply any significantly increased risk of DCS.

Conventional and unconventional antimicrobials from fish, marine invertebrates and micro-algae

2013-05-12T03:33:41Z

Abstract: All eukaryotic organisms, single-celled or multi-cellular, produce a diverse array of natural anti-infective agents that, in addition to conventional antimicrobial peptides, also include proteins and other molecules often not regarded as part of the innate defences. Examples range from histones, fatty acids, and other structural components of cells to pigments and regulatory proteins. These probably represent very ancient defence factors that have been re-used in new ways during evolution. This review discusses the nature, biological role in host protection and potential biotechnological uses of some of these compounds, focusing on those from fish, marine invertebrates and marine micro-algae.

Discovery and validation of SIRT2 inhibitors based on tenovin-6 : use of a H-1-NMR method to assess deacetylase activity

2012-12-14T11:31:01Z

Abstract: The search for potent and selective sirtuin inhibitors continues as chemical tools of this type are of use in helping to assign the function of this interesting class of deacetylases. Here we describe SAR studies starting from the unselective sirtuin inhibitor tenovin-6. These studies identify a sub-micromolar inhibitor that has increased selectivity for SIRT2 over SIRT1 compared to tenovin-6. In addition, a H-1-NMR-based method is developed and used to validate further this class of sirtuin inhibitors. A thermal shift analysis of SIRT2 in the presence of tenovin-6, -43, a control tenovin and the known SIRT2 inhibitor AGK2 is also presented.

Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin-labeling and PELDOR

2013-02-28T09:01:01Z

Abstract: Site-directed spin labeling and pulsed electron–electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.

Quantifying temporal change in biodiversity : challenges and opportunities

2013-05-07T14:39:11Z

Abstract: Growing concern about biodiversity loss underscores the need to quantify and understand temporal change. Here, we review the opportunities presented by biodiversity time series, and address three related issues: (i) recognizing the characteristics of temporal data; (ii) selecting appropriate statistical procedures for analysing temporal data; and (iii) inferring and forecasting biodiversity change. With regard to the first issue, we draw attention to defining characteristics of biodiversity time series—lack of physical boundaries, uni-dimensionality, autocorrelation and directionality—that inform the choice of analytic methods. Second, we explore methods of quantifying change in biodiversity at different timescales, noting that autocorrelation can be viewed as a feature that sheds light on the underlying structure of temporal change. Finally, we address the transition from inferring to forecasting biodiversity change, highlighting potential pitfalls associated with phase-shifts and novel conditions.

Reasons for the invasive success of a guppy (Poecilia reticulata) population in Trinidad

2012-12-12T16:14:06Z

Abstract: The introduction of non-native species into new habitats poses a major threat to native populations. Of particular interest, though often overlooked, are introductions of populations that are not fully reproductively isolated from native individuals and can hybridize with them. To address this important topic we used different approaches in a multi-pronged study, combining the effects of mate choice, shoaling behaviour and genetics. Here we present evidence that behavioural traits such as shoaling and mate choice can promote population mixing if individuals do not distinguish between native and foreign conspecifics. We examined this in the context of two guppy (Poecilia reticulata) populations that have been subject to an introduction and subsequent population mixing event in Trinidad. The introduction of Guanapo River guppies into the Turure River more than 50 years ago led to a marked reduction of the original genotype. In our experiments, female guppies did not distinguish between shoaling partners when given the choice between native and foreign individuals. Introduced fish are therefore likely to benefit from the protection of a shoal and will improve their survival chances as a result. The additional finding that male guppies do not discriminate between females on the basis of origin will further increase the process of population mixing, especially if males encounter mixed shoals. In a mesocosm experiment, in which the native and foreign populations were allowed to mate freely, we found, as expected on the basis of these behavioural interactions, that the distribution of offspring genotypes could be predicted from the proportions of the two types of founding fish. This result suggests that stochastic and environmental processes have reinforced the biological ones to bring about the genetic dominance of the invading population in the Turure River. Re-sampling the Turure for genetic analysis using SNP markers confirmed the population mixing process and showed that it is an on-going process in this river and has led to the nearly complete disappearance of the original genotype.

Role of Bunyamwera orthobunyavirus NSs protein in infection of mosquito cells

2012-12-12T16:14:03Z

Abstract: Background: Bunyamwera orthobunyavirus is both the prototype and study model of the Bunyaviridae family. The viral NSs protein seems to contribute to the different outcomes of infection in mammalian and mosquito cell lines. However, only limited information is available on the growth of Bunyamwera virus in cultured mosquito cells other than the Aedes albopictus C6/36 line. Methodology and Principal Findings: To determine potential functions of the NSs protein in mosquito cells, replication of wild-type virus and a recombinant NSs deletion mutant was compared in Ae. albopictus C6/36, C7-10 and U4.4 cells, and in Ae. aegypti Ae cells by monitoring N protein production and virus yields at various times post infection. Both viruses established persistent infections, with the exception of NSs deletion mutant in U4.4 cells. The NSs protein was nonessential for growth in C6/36 and C7-10 cells, but was important for productive replication in U4.4 and Ae cells. Fluorescence microscopy studies using recombinant viruses expressing green fluorescent protein allowed observation of three stages of infection, early, acute and late, during which infected cells underwent morphological changes. In the absence of NSs, these changes were less pronounced. An RNAi response efficiently reduced virus replication in U4.4 cells transfected with virus specific dsRNA, but not in C6/36 or C7/10 cells. Lastly, Ae. aegypti mosquitoes were exposed to blood-meal containing either wild-type or NSs deletion virus, and at various times post-feeding, infection and disseminated infection rates were measured. Compared to wild-type virus, infection rates by the mutant virus were lower and more variable. If the NSs deletion virus was able to establish infection, it was detected in salivary glands at 6 days post-infection, 3 days later than wild-type virus. Conclusions/Significance: Bunyamwera virus NSs is required for efficient replication in certain mosquito cell lines and in Ae. aegypti mosquitoes.

Photoacclimation, growth and distribution of massive coral species in clear and turbid waters

2013-05-19T00:32:08Z

Abstract: ABSTRACT: Massive coral species play a key role in coral reef ecosystems, adding significantly to physical integrity, long term stability and reef biodiversity. This study coupled the assessment of the distribution and abundance of 4 dominant massive coral species, Diploastrea heliopora, Favia speciosa, F. matthaii and Porites lutea, with investigations into species-specific photoacclimatory responses within the Wakatobi Marine National Park of southeast Sulawesi, Indonesia, to determine the potential of photoacclimation to be a driver of biological success. For this, rapid light curves using pulse amplitude modulated (PAM) chlorophyll a fluorescence techniques were employed with additional manipulations to circumvent differences of light quality and absorption between species and across environmental gradients. P. lutea was examined over a range of depths and sites to determine patterns of photoacclimation, and all 4 species were assessed at a single depth between sites for which long-term data for coral community structure and growth existed. Light availability was more highly constrained with depth than between sites; consequently, photoacclimation patterns for P. lutea appeared greater with depth than across environmental gradients. All 4 species were found to differentially modify the extent of non-photochemical quenching to maintain a constant photochemical operating efficiency (qP). Therefore, our results suggest that these massive corals photoacclimate to ensure a constant light-dependent rate of reduction of the plastoquinone pool across growth environments.

Evolution of the multifaceted eukaryotic akirin gene family

2013-05-12T04:05:31Z

Abstract: Background: Akirins are nuclear proteins that form part of an innate immune response pathway conserved in Drosophila and mice. This studies aim was to characterise the evolution of akirin gene structure and protein function in the eukaryotes. Results: akirin genes are present throughout the metazoa and arose before the separation of animal, plant and fungi lineages. Using comprehensive phylogenetic analysis, coupled with comparisons of conserved synteny and genomic organisation, we show that the intron-exon structure of metazoan akirin genes was established prior to the bilateria and that a single proto-orthologue duplicated in the vertebrates, before the gnathostome-agnathan separation, producing akirin1 and akirin2. Phylogenetic analyses of seven vertebrate gene families with members in chromosomal proximity to both akirin1 and akirin2 were compatible with a common duplication event affecting the genomic neighbourhood of the akirin proto-orthologue. A further duplication of akirins occurred in the teleost lineage and was followed by lineage-specific patterns of paralogue loss. Remarkably, akirins have been independently characterised by five research groups under different aliases and a comparison of the available literature revealed diverse functions, generally in regulating gene expression. For example, akirin was characterised in arthropods as subolesin, an important growth factor and in Drosophila as bhringi, which has an essential myogenic role. In vertebrates, akirin1 was named mighty in mice and was shown to regulate myogenesis, whereas akirin2 was characterised as FB11 in rats and promoted carcinogenesis, acting as a transcriptional repressor when bound to a 14-3-3 protein. Both vertebrate Akirins have evolved under comparably strict constraints of purifying selection, although a likelihood ratio test predicted that functional divergence has occurred between paralogues. Bayesian and maximum likelihood tests identified amino-acid positions where the rate of evolution had shifted significantly between paralogues. Interestingly, the highest scoring position was within a conserved, validated binding-site for 14-3-3 proteins. Conclusion: This work offers an evolutionary framework to facilitate future studies of eukaryotic akirins and provides insight into their multifaceted and conserved biochemical functions.

Evolution of a complex locus : exon gain, loss and divergence at the Gr39a locus in Drosophila

2013-05-12T03:31:21Z

Abstract: Background. Gene families typically evolve by gene duplication followed by the adoption of new or altered gene functions. A different way to evolve new but related functions is alternative splicing of existing exons of a complex gene. The chemosensory gene families of animals are characterised by numerous loci of related function. Alternative splicing has only rarely been reported in chemosensory loci, for example in 5 out of around 120 loci in Drosophila melanogaster. The gustatory receptor gene Gr39a has four large exons that are alternatively spliced with three small conserved exons. Recently the genome sequences of eleven additional species of Drosophila have become available allowing us to examine variation in the structure of the Gr39a locus across a wide phylogenetic range of fly species. Methodology/Principal Findings. We describe a fifth exon and show that the locus has a complex evolutionary history with several duplications, pseudogenisations and losses of exons. PAML analyses suggested that the whole gene has a history of purifying selection, although this was less strong in exons which underwent duplication. Conclusions/Significance. Estimates of functional divergence between exons were similar in magnitude to functional divergence between duplicated genes, suggesting that exon divergence is broadly equivalent to gene duplication.

An update on MyoD evolution in teleosts and a proposed consensus nomenclature to accommodate the tetraploidization of different vertebrate genomes

2013-05-12T03:04:05Z

Abstract: Background: MyoD is a muscle specific transcription factor that is essential for vertebrate myogenesis. In several teleost species, including representatives of the Salmonidae and Acanthopterygii, but not zebrafish, two or more MyoD paralogues are conserved that are thought to have arisen from distinct, possibly lineage-specific duplication events. Additionally, two MyoD paralogues have been characterised in the allotetraploid frog, Xenopus laevis. This has lead to a confusing nomenclature since MyoD paralogues have been named outside of an appropriate phylogenetic framework. Methods and Principal Findings: Here we initially show that directly depicting the evolutionary relationships of teleost MyoD orthologues and paralogues is hindered by the asymmetric evolutionary rate of Acanthopterygian MyoD2 relative to other MyoD proteins. Thus our aim was to confidently position the event from which teleost paralogues arose in different lineages by a comparative investigation of genes neighbouring myod across the vertebrates. To this end, we show that genes on the single myod-containing chromosome of mammals and birds are retained in both zebrafish and Acanthopterygian teleosts in a striking pattern of double conserved synteny. Further, phylogenetic reconstruction of these neighbouring genes using Bayesian and maximum likelihood methods supported a common origin for teleost paralogues following the split of the Actinopterygii and Sarcopterygii. Conclusion: Our results strongly suggest that myod was duplicated during the basal teleost whole genome duplication event, but was subsequently lost in the Ostariophysi ( zebrafish) and Protacanthopterygii lineages. We propose a sensible consensus nomenclature for vertebrate myod genes that accommodates polyploidization events in teleost and tetrapod lineages and is justified from a phylogenetic perspective. Description: DJM was supported by a Natural Environment Research Council studentship (NERC/S/A/2004/12435).

The CRISPR associated protein Cas4 Is a 5' to 3' DNA exonuclease with an iron-sulfur cluster

2012-12-12T16:13:48Z

Abstract: The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the prokaryotic CRISPR system for antiviral defence. Cas4 is thought to play a role in the capture of new viral DNA sequences for incorporation into the host genome. No biochemical activity has been reported for Cas4, but it is predicted to include a RecB nuclease domain. We show here that Cas4 family proteins from the archaeon Sulfolobus solfataricus utilise four conserved cysteine residues to bind an iron-sulfur cluster in an arrangement reminiscent of the AddB nuclease of Bacillus subtilis. The Cas4 family protein Sso0001 is a 5' to 3' single stranded DNA exonuclease in vitro that is stalled by extrahelical DNA adducts. A role for Cas4 in DNA duplex strand resectioning to generate recombinogenic 3' single stranded DNA overhangs is proposed. Comparison of the AddB structure with that of a related bacterial nuclease from Eubacterium rectales reveals that the iron-sulfur cluster can be replaced by a zinc ion without disrupting the protein structure, with implications for the evolution of iron-sulfur binding proteins.

The functional response of a generalist predator

2012-12-12T12:34:35Z

Abstract: Background: Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species. Methodology and principal findings: Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a “predator pit” for one prey species only occurs when the availability of other prey species is low. Conclusions and significance: The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.

Repeated elicitation of the acoustic startle reflex leads to sensitisation in subsequent avoidance behaviour and induces fear conditioning

2013-05-12T04:04:36Z

Abstract: Background: Autonomous reflexes enable animals to respond quickly to potential threats, prevent injury and mediate fight or flight responses. Intense acoustic stimuli with sudden onsets elicit a startle reflex while stimuli of similar intensity but with longer rise times only cause a cardiac defence response. In laboratory settings, habituation appears to affect all of these reflexes so that the response amplitude generally decreases with repeated exposure to the stimulus. The startle reflex has become a model system for the study of the neural basis of simple learning processes and emotional processing and is often used as a diagnostic tool in medical applications. However, previous studies did not allow animals to avoid the stimulus and the evolutionary function and long-term behavioural consequences of repeated startling remain speculative. In this study we investigate the follow-up behaviour associated with the startle reflex in wild-captured animals using an experimental setup that allows individuals to exhibit avoidance behaviour. Results: We present evidence that repeated elicitation of the acoustic startle reflex leads to rapid and pronounced sensitisation of sustained spatial avoidance behaviour in grey seals (Halichoerus grypus). Animals developed rapid flight responses, left the exposure pool and showed clear signs of fear conditioning. Once sensitised, seals even avoided a known food source that was close to the sound source. In contrast, animals exposed to non-startling (long rise time) stimuli of the same maximum sound pressure habituated and flight responses waned or were absent from the beginning. The startle threshold of grey seals expressed in units of sensation levels was comparable to thresholds reported for other mammals (93 dB). Conclusions: Our results demonstrate that the acoustic startle reflex plays a crucial role in mediating flight responses and strongly influences the motivational state of an animal beyond a short-term muscular response by mediating long-term avoidance. The reflex is therefore not only a measure of emotional state but also influences emotional processing. The biological function of the startle reflex is most likely associated with mediating rapid flight responses. The data indicate that repeated startling by anthropogenic noise sources might have severe effects on long-term behaviour. Future, studies are needed to investigate whether such effects can be associated with reduced individual fitness or even longevity of individuals.

Models of cultural niche construction with selection and assortative mating

2012-12-12T16:13:49Z

Abstract: Niche construction is a process through which organisms modify their environment and, as a result, alter the selection pressures on themselves and other species. In cultural niche construction, one or more cultural traits can influence the evolution of other cultural or biological traits by affecting the social environment in which the latter traits may evolve. Cultural niche construction may include either gene-culture or culture-culture interactions. Here we develop a model of this process and suggest some applications of this model. We examine the interactions between cultural transmission, selection, and assorting, paying particular attention to the complexities that arise when selection and assorting are both present, in which case stable polymorphisms of all cultural phenotypes are possible. We compare our model to a recent model for the joint evolution of religion and fertility and discuss other potential applications of cultural niche construction theory, including the evolution and maintenance of large-scale human conflict and the relationship between sex ratio bias and marriage customs. The evolutionary framework we introduce begins to address complexities that arise in the quantitative analysis of multiple interacting cultural traits.

Motion dazzle and camouflage as distinct anti-predator defenses

2013-05-12T04:36:31Z

Abstract: Background: Camouflage patterns that hinder detection and/or recognition by antagonists are widely studied in both human and animal contexts. Patterns of contrasting stripes that purportedly degrade an observer's ability to judge the speed and direction of moving prey ('motion dazzle') are, however, rarely investigated. This is despite motion dazzle having been fundamental to the appearance of warships in both world wars and often postulated as the selective agent leading to repeated patterns on many animals (such as zebra and many fish, snake, and invertebrate species). Such patterns often appear conspicuous, suggesting that protection while moving by motion dazzle might impair camouflage when stationary. However, the relationship between motion dazzle and camouflage is unclear because disruptive camouflage relies on high-contrast markings. In this study, we used a computer game with human subjects detecting and capturing either moving or stationary targets with different patterns, in order to provide the first empirical exploration of the interaction of these two protective coloration mechanisms. Results: Moving targets with stripes were caught significantly less often and missed more often than targets with camouflage patterns. However, when stationary, targets with camouflage markings were captured less often and caused more false detections than those with striped patterns, which were readily detected. Conclusions: Our study provides the clearest evidence to date that some patterns inhibit the capture of moving targets, but that camouflage and motion dazzle are not complementary strategies. Therefore, the specific coloration that evolves in animals will depend on how the life history and ontogeny of each species influence the trade-off between the costs and benefits of motion dazzle and camouflage.

Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes

2013-05-12T02:31:41Z

Abstract: Background The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the more recently discovered ParaHox cluster. ParaHox gene clustering, and its relationship to expression, has only been described in deuterostomes. Conventional protostome models (Drosophila melanogaster and Caenorhabditis elegans) are secondarily derived with respect to ParaHox genes, suffering gene loss and cluster break-up. Results We provide the first evidence for ParaHox gene clustering from a less-derived protostome animal, the annelid Platynereis dumerilii. Clustering of these genes is thus not a sole preserve of the deuterostome lineage within Bilateria. This protostome ParaHox cluster is not entirely intact however, with Pdu-Cdx being on the opposite end of the same chromosome arm from Pdu-Gsx and Pdu-Xlox. From the genomic sequence around the P. dumerilii ParaHox genes the neighbouring genes are identified, compared with other taxa, and the ancestral arrangement deduced. Conclusion We relate the organisation of the ParaHox genes to their expression, and from comparisons with other taxa hypothesise that a relatively complex pattern of ParaHox gene expression existed in the protostome-deuterostome ancestor, which was secondarily simplified along several invertebrate lineages. Detailed comparisons of the gene content around the ParaHox genes enables the reconstruction of the genome surrounding the ParaHox cluster of the protostome-deuterostome ancestor, which existed over 550 million years ago.

Tunicates push the limits of animal evo-devo

2013-05-12T04:02:38Z

Abstract: The phylum to which humans belong, Chordata, takes its name from one of the major shared derived features of the group, the notochord. All chordates have a notochord, at least during embryogenesis, and there is little doubt about notochord homology at the morphological level. A study in BMC Evolutionary Biology now shows that there is greater variability in the molecular genetics underlying notochord development than previously appreciated.

Sexual and postmating reproductive isolation between allopatric Drosophila montana populations suggest speciation potential

2013-05-12T04:06:30Z

Abstract: Background: Widely distributed species with populations adapted to different environmental conditions can provide valuable opportunities for tracing the onset of reproductive incompatibilities and their role in the speciation process. Drosophila montana, a D. virilis group species found in high latitude boreal forests in Nearctic and Palearctic regions around the globe, could be an excellent model system for studying the early stages of speciation, as a wealth of information concerning this species' ecology, mating system, life history, genetics and phylogeography is available. However, reproductive barriers between populations have hereto not been investigated. Results: We report both pre- and postmating barriers to reproduction between flies from European (Finnish) and North American (Canadian) populations of Drosophila montana. Using a series of mate-choice designs, we show that flies from these two populations mate assortatively (i.e., exhibit significant sexual isolation) while emphasizing the importance of experimental design in these kinds of studies. We also assessed potential postmating isolation by quantifying egg and progeny production in intra-and interpopulation crosses and show a significant one-way reduction in progeny production, affecting both male and female offspring equally. Conclusion: We provide evidence that allopatric D. montana populations exhibit reproductive isolation and we discuss the potential mechanisms involved. Our data emphasize the importance of experimental design in studies on premating isolation between recently diverged taxa and suggest that postmating barriers may be due to postcopulatory-prezygotic mechanisms. D. montana populations seem to be evolving multiple barriers to gene flow in allopatry and our study lays the groundwork for future investigations of the genetic and phenotypic mechanisms underlying these barriers.

Fitness consequences of female multiple mating : A direct test of indirect benefits

2012-12-12T16:13:44Z

Abstract: Background The observation that females mate multiply when males provide nothing but sperm - which sexual selection theory suggests is unlikely to be limiting - continues to puzzle evolutionary biologists. Here we test the hypothesis that multiple mating is prevalent under such circumstances because it enhances female fitness. We do this by allowing female Trinidadian guppies to mate with either a single male or with multiple males, and then tracking the consequences of these matings across two generations. Results Overall, multiply mated females produced 67% more F2 grand-offspring than singly mated females. These offspring, however, did not grow or mature faster, nor were they larger at birth, than F2 grand-offspring of singly mated females. Our results, however, show that multiple mating yields benefits to females in the form of an increase in the production of F1. The higher fecundity among multiply mated mothers was driven by greater production of sons but not daughters. However, contrary to expectation, individually, the offspring of multiply mated females do not grow at different rates than offspring of singly mated females, nor do any indirect fitness benefits or costs accrue to second-generation offspring. Conclusions The study provides strong evidence that multiple mating is advantageous to females, even when males contribute only sperm. This benefit is achieved through an increase in fecundity in the first generation, rather than through other fitness correlates such as size at birth, growth rate, time to sexual maturation and survival. Considered alongside previous work that female guppies can choose to mate with multiple partners, our results provide compelling evidence that direct fitness benefits underpin these mating decisions.

Why do adaptive immune responses cross-react?

2013-05-12T02:05:47Z

Abstract: Antigen specificity of adaptive immune responses is often in the host's best interests, but with important and as yet unpredictable exceptions. For example, antibodies that bind to multiple flaviviral or malarial species can provide hosts with simultaneous protection against many parasite genotypes. Vaccinology often aims to harness such imprecision, because cross-reactive antibodies might provide broad-spectrum protection in the face of antigenic variation by parasites. However, the causes of cross-reactivity among immune responses are not always known, and here, we explore potential proximate and evolutionary explanations for cross-reactivity. We particularly consider whether cross-reactivity is the result of constraints on the ability of the immune system to process information about the world of antigens, or whether an intermediate level of cross-reactivity may instead represent an evolutionary optimum. We conclude with a series of open questions for future interdisciplinary research, including the suggestion that the evolutionary ecology of information processing might benefit from close examination of immunological data.

Attenuation of bunyavirus replication by modification of genomic untranslated regions

2012-10-25T15:27:47Z

Abstract: Bunyamwera orthobunyavirus (BUNV) is the prototype for the family Bunyaviridae. BUNV has a tripartite RNA genome of negative polarity composed of the large(L),medium (M)and small(S)segments. Each segment contains an open reading frame (ORF) flanked by untranslated regions (UTRs). The eleven terminal nucleotides are conserved between the three segments while the internal regions are unique. The UTRs play an important role in the virus life cycle by promoting transcription, replication and encapsidation of the viral genome.The work presented in this thesis explores UTRs plasticity and examines ways to engineere attenuated viruses by modifying only their UTRs. Using reverse genetics, mainly two ways of attenuation were explored: rescue of viruses either carrying deletions within their 3’ and/or 5’ UTRs in all three segments, or of viruses carrying one segment bearing heterologous UTRs. Both approaches resulted in virus attenuation in tissue culture, with viruses producing smaller plaques or even no plaques, and growing to lower titres than wild-type BUNV. Through serial passage, viruses were shown to regain some level of fitness while the mutations introduced in the UTRs proved to be stable. Thus, to investigate the mechanism behind fitness recovery, the nucleotide sequence of the entire genome of viruses with deletions in their UTRs was determined. Amino acid changes were observed in the viral polymerase (L protein) of most mutant viruses and the vast majority of the amino acid changes occured in the C-terminal region. The function of this domain is unclear to date, however data obtained using a mini-replicon assay suggest that the C-terminal domain of the L protein might be involved in UTR recognition. Full genome sequencing also allowed the identification of an amino acid mutation within the polymerase that resulted in a temperature sensitive phenotype when introduced in an otherwise wild-type BUNV. Thus, it was shown that mutations introduced within the UTR regions of the genome were stable through serial passage and resulted in attenuation. Such a strategy could be used in combination with mutations of the ORF to design live-attenuated vaccines against serious pathogens within the family Bunyaviridae.

The influence of mid-ocean ridges on euphausiid and pelagic ecology

2012-10-25T15:02:41Z

Abstract: 1 & 2. Euphausiids comprise a major component of ecosystems in the pelagic realm, the world’s largest habitat, but basin scale drivers of euphausiids diversity and abundance are poorly understood. Mid-Ocean Ridges are the largest topographical feature in the pelagic realm and their benthic and pelagic fauna have only just recently become the focus of research. This thesis present new analyses on the drivers of euphausiids species richness in the Atlantic and the Pacific, giving specific attention to the influence of Mid- Ocean Ridges. New information is given on the biogeography of euphausiids and pelagic food-web trophology of the Mid-Atlantic Ridge, and on the biogeography of pelagic decapods on the South-West Indian Ocean ridge. 3. A Generalized Additive Model framework was used to explore spatial patterns of variability in euphausiid species richness (from recognized areas of occurrence) and in numerical abundance (from the Continuous Plankton Recorder survey) in conjunction with variability in a suite of biological, physical and environmental parameters on, and at either side of, the Mid-Atlantic Ridge. Euphausiid species richness peaked in midlatitudes and was significantly higher on the ridge than in adjacent waters, but the ridge did not influence numerical abundance in the top 10 m significantly. Sea surface temperature (SST) was the most important single factor influencing both euphausiid numerical abundance (-76.7%) and species richness (34.44%). Dissolved silicate concentration, a proxy for diatom abundance, significantly increased species richness (29.46%). Increases in sea surface height variance, a proxy for mixing, increased the numerical abundance of euphausiids. GAM predictions of variability in species richness as a function of SST and depth of the mixed layer were consistent with present theories, which suggest that pelagic niche-availability is related to the thermal structure of the near surface water. 4. Using a Generalized Additive Model in the Pacific, the main drivers of species richness, in order of decreasing importance, were found to be sea surface temperature (explaining 29.53% in species variability), salinity (20.29%), longitude (-15.01%, species richness decreased from West to East), distance to coast (10.99%), and dissolved silicate concentration (9.03%). An additional linear model poorly predicted numerical abundance. The practical differences in drivers of species richness in the Atlantic and Pacific Ocean were compared. Predictions of future species richness changes in the Pacific and Atlantic were made using projected environmental change from the IPCC A1B climate scenario, suggesting an increase in species richness in temperature latitudes (30° to 60° N and S) and little to no change in low latitudes (20° N to 20° S). 5. New baseline information is presented on biogeography, abundance and vertical distribution of euphausiids along the Mid-Atlantic Ridge (40° to 62° N). 18 species were recorded, with Euphausia krohni and Thysanoessa longicaudata being most abundant. Eight species had not been recorded in the area previously. The Subpolar Front is a northern boundary to some southern species, but not a southern boundary to northern ubiquitous species that show submergence. Four major species assemblages were identified and characterised in terms of spatial distribution and species composition. Numerical abundance was highly variable but decreased by orders of magnitude with depth. The Mid-Atlantic Ridge showed only a marginal effect on euphausiid distribution and abundance patterns. 6. Zooplankton and micronektic invertebrate epi- and mesopelagic (0-200 and 200- 800m) vertical distribution (e.g. Euphausiacea, Decapoda, Amphipoda, Thecosomata, Lophogastrida) on either side of the Subpolar Front of the Mid-Atlantic Ridge is described. Dietary relationships are explored, using stable isotope ratios and fatty acid trophic marker (FATM) composition. An increase in trophic level with size was observed. Individuals from southern stations were higher in dinoflagellate Fatty Acid Trophic Markers (FATM) (22:6(n-3)) and individuals from northern stations were higher in Calanus spp and storage FATMs (20:1(n-9) and 22:1(n-9)) reflecting primary production patterns in the two survey sectors. Observations on the geographical and vertical variability in trophodynamics are discussed. 7. New baseline information is presented on the biogeography, abundance, and vertical distribution of mesopelagic (200-1000 m), crustacean micronekton on- and offseamounts of the South-West Indian Ocean Ridge (26° to 42° S). Species richness and numerical abundance were typically higher near seamounts and lower over the abyssal plains, with several species being caught uniquely on seamounts. Observations suggest that the ‘oasis effect’ of seamounts conventionally associated with higher trophic levels is also applicable to pelagic micronektic crustaceans at lower trophic levels. Biophysical coupling of micronekton to seamounts may be an important factor controlling benthopelagic coupling in seamount food-webs. 8. Euphausiid and pelagic diversity is driven primarily by geographical variability in temperature, by longitudinal patterns in upwellings, and by variability in nutrient concentration. Mid-Ocean Ridges modify pelagic ecology, by raising the seafloor and by bringing in proximity true pelagic and bathypelagic predators associated with the seabed. The increase in specialized fauna and biomass associated with ridges and seamounts serves to deplete zooplankton in the near bottom layer (0-200 m) and affect systems in and above the benthic boundary layer (<200 m from the seafloor), and the benthopelagic faunal layer. Mid-Ocean Ridges may serve to structure pelagic faunal distribution, and increase the overall diversity of the world ocean. The influence of ridges in the ocean basin may be comparable to that of hedges in a farmland; whilst delimiting the extent of crops (or zooplankton assemblages), hedges serve as local hotspots of mammal and avian diversity.

Evolutionary genetics and genomics of the female side of sexual interactions in Drosophila

2012-10-25T09:20:57Z

Abstract: Sexual interactions play an important role in generating sexual selection and antagonistic co-evolution. These forces can shape differences between the sexes, but also have the potential to generate population divergence and contribute to speciation. The aim in this thesis was to provide new insights into the genes involved in different stages of female sexual interactions, using Drosophila as a model system. In chapter 2 I tested whether a candidate gene (period) that influences species-specific rhythmic characteristics in male courtship song in D. melanogaster also has a pleiotropic effect on female song preference. Using mutant and transgenic strains I found support for this. In chapter 3 I examined further how females respond to the song at the level of gene expression, using microarrays. Expression profiles revealed modest changes in transcripts abundance overall, which were dominated by antennal olfactory genes, neuropeptide encoding genes and immunity genes. Many of these have previously been found to respond to mating. In chapter 4 I therefore studied further two of these genes, TurandotM and TurandotC and their role in female post-mating fitness. Using RNA interference I found that knocking down these genes influenced immediate fecundity. In chapter 5 I focused on analysing post-mating gene expression patterns in relation to sexual selection in D. pseudoobscura using microarrays. I explored the consequences of experimental variation in female promiscuity on gene expression divergence as a whole, and in response to mating. I found large-scale expression divergence between monandrous and polyandrous females after 100 generations of experimental evolution. Experimental polyandry increased the expression of genes that show female-biased expression in wild-type individuals and decreased male- biased gene expression. Females experiencing no sexual selection showed the opposite pattern. Out of the genes affected by mating, the majority showed increased expression in polyandrous compared to monandrous females, with enrichment e.g. in oogenesis-related genes.

Examining the response of top marine predators to ecological change using stable isotope proxies

2012-10-24T14:55:15Z

Abstract: Monitoring the response of upper trophic level animals to ecological change is important to understanding the state and stability of ecosystems. Marine predators integrate information over large geographical scales and are relatively long-lived; furthermore, many of these organisms are restricted to terrestrial or freshwater habitats at certain times during their life history and are accessible to researchers. This thesis investigated the response of marine predators to ecological change at a variety of spatial and temporal scales using stable isotope ratio methods with the aims of developing meaningful proxies, or indices, of variability in marine ecosystems. The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental) factors important to modulating variation in the stable isotope ratios of C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the Southern Ocean. In the second study, long-term records of variation in δ15N δ13C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus) tooth dentin provided evidence for large-scale climate forcing across the eastern North Atlantic. In the following study, a more detailed examination of intra- and inter-individual stable isotope variation in Atlantic salmon within a single year was undertaken in an attempt to better understand recent declines in somatic condition of these fish. The last two studies were concerned with the development of high resolution sampling of fish otoliths using secondary mass spectrometry (SIMS) and the application of this technique to reconstructing the thermal and metabolic histories of individual Atlantic salmon from intra-otolith δ13C and δ18O values. Stable isotope proxies can be used to document shifts in trophic dynamics and animal movement that may be associated with ecological change. Using multiple tissues, elements and species, such studies provide unique monitoring tools at a range of spatial and temporal scales.

Putting pollination quality into analyses of floral ecology: testing syndromes through pollinator performance

2012-10-24T13:25:07Z

Abstract: Over recent years, the extent of specialised and generalised plant-pollinator relationships, and the predictive powers of floral traits (often grouped into “pollination syndromes”) as indicators of the most effective pollinators of plant species, have been questioned. Such studies, however, have used proxies such as visitation frequency rather than direct measurements of pollinator effectiveness (PE). The main objective of this thesis was to test the predictive powers of various pollination syndromes using a specific measure of PE: single-visit stigmatic pollen deposition (SVSPD). Six different classical pollination syndromes were tested, using 13 different plant species from tropical and temperate habitats, and in the case of flowers typical of the hummingbird, hoverfly, bee, oil flower and long-tongued insect syndromes, the expected pollinators were the most effective at a single-visit scale. For generalist pollination syndrome flowers, not all observed visitors were significant pollinators, and the species studied were not as broadly generalised as their visitor assemblages would suggest. In all 13 plant species, pollinator performance could appear consistent within functional visitor groups but was variable between visitor species, and in almost all cases not all of the observed visitors were effective pollinators. The pollinator performance proxies of visit duration and feeding behaviour were neither significantly, nor consistently, related to PE. Visit duration was not an accurate indicator of pollinator performance on its own, though it was useful when combined with SVSPD to define pollinator performance at a given time scale, for example per hour, per day or per season. My findings suggest that the results of recent “pollination” networks and webs, based on visitors but not necessarily pollinators, should be treated with caution. SVSPD therefore proved to be an effective and relatively simple direct measure of PE, confirming the predictive powers of pollination syndromes, and giving further insight into the extent of specialisation and generalisation.

The activity of amyloid beta binding alcohol dehydrogenase in Alzheimer's disease

2012-10-24T13:04:35Z

Abstract: The mitochondria are a vibrant hub for many problems that occur in Alzheimer’s disease. The enzyme amyloid-ß binding alcohol dehydrogenase (ABAD) and Cyclophilin D (CypD) are two key mitochondrial proteins that have essential functions in Alzheimer’s disease. ABAD is crucial in the generation of energy via the ß-oxidation of fatty acids, and CypD has been linked to Alzheimer’s disease through the initiation of necrosis. Changes in glucose metabolism have been observed in the brains of Alzheimer’s disease sufferers. This suggests that neurons require an alternative energy source that can bypass glycolysis in order to produce energy. The oxidation of fatty acids is crucial at this point as the products of this catabolism can feed into the second stage of the respiratory cycle. In Alzheimer’s disease, Amyloid-ß (Aß) has been found to bind to ABAD distorting the catalytic site changing its activity. The first objective of this thesis was to investigate a potential previously reported interaction between ABAD and CypD. To explore this further, FRET analysis and immunoprecipitation studies were conducted. Though no strong interactions were observed from the immunoprecipitation studies, live cell FRET analysis did reveal a small/weak interaction between CypD and ABAD. Additional studies also showed a decrease in ABAD activity in the presence of CypD, suggesting that there could be functional consequences from this interaction between CypD and ABAD.I also explored the effect of changing cellular energy sources on the activity of ABAD. ABAD activity was found to increase under conditions of reduced glucose in both HEK 293 and SK-N-SH cells expressing ABAD. In addition, Alois Alzheimer initially reported changes in lipids. These reported changes in lipids were explored under conditions where there was increased expression of ABAD and in the presence of Aß. On the whole, the changes suggested that there was a shift in the metabolism of fatty acids when ABAD was expressed further implying a change in energy sources in the Alzheimer’s disease brain.

Resolving ant-plant conflicts: mechanisms and functions of floral ant-repellence

2013-05-01T08:16:57Z

Abstract: Although ants have numerous, often beneficial interactions with plants, as pollinators they are poor. Potential reasons for this include restrictions resulting from their morphology and specific foraging behaviours, and detrimental effects of their surface secretions on pollen. This, coupled with other possible negative effects of ants on floral structures, puts pressure on plants to exclude ants from flowers. One common strategy to achieve this is via behaviour- modifying repellent floral volatiles; however, few studies have identified the volatiles concerned. Here I considered two aspects of this interaction. Firstly, I assessed seven temperate angiosperm species for floral repellence to Formica aquilonia ants using a simple two-way olfactometer. In agreement with previous studies showing that floral ant-repellence is common, significant repellent effects were found in 3/7 species. I also analysed the floral bouquet of Petasites fragrans, a plant previously shown to possess ant-repellent floral volatiles. The most prominent volatile was identified as 4- methoxybenzaldehyde and olfactometer testing of a pure sample of this confirmed it as the likely source of floral repellence in P. fragrans. Although the natural interactions between P. fragrans and ants are unknown, intriguingly 4-methoxybenzaldehyde has been detected from floral volatiles of two further species with frequent ant interactions. A second study compared effects of ants and bees on pollen function to explore the supposed significance of ant-induced reductions in pollen viability. Lily pollen was exposed to either F. aquilonia, Apis mellifera, or Bombus pascuorum, germinated in vitro and assessed for viability. Small, marginally significant reductions in viability were identified for all three insects compared to a control, but with no differences in the reduction between each insect. Although this indicates that the pollen inviability hypothesis for the scarcity of ant pollination may be incorrect, a comparative study with several pollinator and plant species is needed to substantiate this conclusion.

An investigation into the effects of a simulated human gastro-intestinal tract has on Bacillus cereus and Bacillus weihenstephanensis viability and pathogenicity

2012-10-30T14:58:08Z

Abstract: Bacillus cereus is one of the known causes of diarrhoeal food poisoning. In their natural environment of soil surviving as spores facilitates their colonisation of raw food ingredients enabling their access to the food chain. Recently psychrotrophic strains of B. cereus have been reclassified based on divergent cold shock gene (cspA) sequences and renamed B. weihenstephanensis. It is the modified cspA gene that is thought to confer the psychrotolerant phenotype witnessed by these strains. Aside from cspA, B. cereus and B. weihenstephanensis are closely related, leading to questions about its pathogenicity and ability to mediate diarrhoeal food poisoning outbreaks. Food producers use a variety of processes to limit microbial contamination within food products. Although effective against vegetative cells, spores are often resistant and as such can persist within this environment. Chilled temperatures (4°C) are often used to limit the growth of any contaminating microbes. Under such conditions B. cereus spores would remain dormant however B. weihenstephanensis spores have been shown to germinate and outgrow under refrigerated conditions. This could result in the consumption of both B. cereus and B. weihenstephanensis spores and vegetative cells. The effect that the human gastro-intestinal tract (GI) has on B. cereus and B. weihenstephanensis vegetative cells and spores is unclear. This study showed no difference in the viability of B. cereus or B. weihenstephanensis strains to survive and grow within a simulated human GI tract. Vegetative cells were revealed to die quickly in the stomach. Spore viability was shown to reduce in the stomach environment by approximately 10⁴-fold. With a larger initial inoculum, 10⁷ spore/ml, viable spores were still recorded after 4 hours. These spores subsequently germinated within the small intestinal simulation and the resulting vegetative cells rapidly proliferated. Mass spectrometry illustrated the ability of vegetative cells from both B. cereus and B. weihenstephanensis to produce an array of secreted proteins whose function were predominately related to virulence and pathogenesis. B.weihenstephanensis strain 10202 was shown to produce the potent cytotoxin, CytK-1, while other B. weihenstephanensis and B. cereus tested strains possessed either or both Nhe and Hbl toxins. The primary diarrhoeal virulence factor/haemolysin BL was shown to be present in the supernatant of each strain through western blotting. Significantly smaller concentrations of each protein were detected, however, under simulated human GI tract conditions when compared to optimal conditions. The effects of the simulated human GI tract on virulence gene expression were monitored through real time PCR. No pattern between B. cereus and B. weihenstephanensis strains was found confirming that virulence gene expression is strain specific. Some genes were shown to be significantly upregulated such as fur, (the ferric iron uptake regulator and groEL, encoding a molecular chaperone. The expression of others however was reduced such as haemolysin BL components, hblA and hblC. Overall there were no significant differences detected between B. cereus and B. weihenstephanensis strains in their ability to survive the human GI tract and express virulence factors associated with diarrhoeal food poisoning.

The effects of sound propagation and avoidance behaviour on naval sonar levels received by cetaceans

2012-10-26T21:29:31Z

Abstract: The use of active sonar is deemed to be essential for naval operations, but its potential impact on marine life has raised concerns worldwide. In a risk-assessment framework, characterisation of risk of harm is accomplished by combining exposure assessment and dose−response relationships. The overall topic of this thesis is an evaluation of factors that influence exposure assessment, including analysis of how sound levels received by cetaceans are affected by in-situ sound propagation and the influence of diving, movement and possible avoidance behaviour of the whales themselves. Data from an international research programme based on controlled exposure experiments (CEEs) were available for this study. During these experiments, low-frequency active sonar (LFAS: 1-2 kHz band) and mid-frequency active sonar (MFAS: 6-7 kHz band) signals were recorded by suction-cup tags attached to killer whales, long-finned pilot whales and sperm whales, and by a hydrophone array towed near the whales. Chapter two describes how the sonar signals recorded by these systems were quantified, and investigates the influences of range, depth and propagation conditions on the received sound levels. Chapter three focuses upon the effect of simulated vertical and horizontal exposure-avoidance strategies of whales in response to an approaching source on the received sound levels. A total of 7,091 sonar signals were analysed from the towed-array (2,794) and tag (4,297) recordings. Transmission loss (TL) and excess attenuation (EA) from a simple 20log(range) model were compared among species, signal types and acoustic receivers. TLs followed expected geometric spreading versus range and TL coefficients were 15.5−20.1 for LFAS and 18.8−23.6 for MFAS. One experiment where levels on the animal-attached tag were attenuated due to ‘body shielding’ (when the animal’s body is interposed between the sound recording tag and the sound source) was documented, and other sources of variation in received level dataset were discussed. Variations in EA with depth were consistent with TL patterns predicted using the acoustic propagation model Bellhop with the highest EAs occurring near the sea surface. The effect of depth on EA was clearest in killer and pilot whale experiments which occurred at locations with stronger gradients in the sound-speed profile, while sperm whale experiments in deeper homogenous offshore waters showed little influence of depth on EA. The results indicate that a simple TL model like 20log(range)+absorption does not accurately predict attenuation levels over the distances (0.1−11.1 km) from a sonar source to a freely-diving animal, but that the overall patterns of TL can be fairly well explained using sound propagation models that take into account local environmental conditions. A consistent different in TL between LFAS and MFAS signals was not explained by the Bellhop model, however, indicating that unidentified sources of variation do influence the sonar signals recorded on freely-diving whales. To evaluate the potential effect of avoidance strategies of whales on received sound levels, whale positions were simulated with a Monte Carlo method in which a simulated source vessel directly approached the whale. The cumulative sound exposure level (SELcum) received by the whales was estimated using the Bellhop model. Horizontally-stationary animals received the highest levels. The optimal course in terms of reducing SELcum for animals moving in a straight line was 100° from the heading of the source vessel, while 120−130° was optimal for animals dynamically moving relative to the position of the source. Moving horizontally in the optimal direction away from the vessel path yielded 9−17 dB reduction of SELcum and vertical avoidance led to reductions of up to 10 dB in certain circumstances. Actual observations of the whales during the sonar experiments indicated that animals often move sideways out of the path of the approaching vessel, close to the optimal angle predicted. The simulation approach is therefore potentially useful to predict how whales react to an approaching sound source. This type of analysis may also be useful to understand the patterns of cetacean strandings relative to the movement of sonar-transmitting military vessels.

The vocal imitation of bottlenose dolphin (Tursiops truncatus) signature whistles: their use in vocal matching interactions and their role as vocal labels

2012-10-16T15:39:26Z

Abstract: The bottlenose dolphin uses vocal learning to develop its own unique acoustic signal. This signal encodes the identity of the signaller, and is known as the animal’s signature whistle. The dolphin’s ability for vocal learning means that the signature whistle of one animal may be found in the vocal repertoire of other animals. This copying of signature whistle types may allow conspecifics to label or address one another. This thesis investigated the use of signature whistle copying in both captive and wild animals. Dolphins have been known to rapidly imitate each other’s signature whistle in vocal matching exchanges. This matching of sounds has an aggressive connotation in songbirds, yet the function in bottlenose dolphins remains unclear. I have shown, through playback experiments with captive animals, that signature whistle matching in dolphins is not aggressive but appears to be affiliative, and may be used as a tool to initiate contact with the signature whistle owner. In addition, the rapid matching of whistle types in wild dolphins appears to play a specific role in their foraging behaviour, indicating the function of vocal matching may indeed be multi-faceted. This thesis also uses a unique dataset to extensively describe the occurrence of signature whistle copying in wild animals. The imitation of individual signature whistles occurred almost exclusively between close associates during separations. All copies were accurate representations of the original signature whistle, but were clearly recognisable due to fine-scale differences in selected acoustic parameters, and are therefore unlikely to be used deceptively. Finally, I provide evidence that wild bottlenose dolphins respond to hearing a copy of their own signature whistle by calling back. This offers support to the notion that signature whistles function as distinctive labels that are used to address individuals, and perhaps even label them referentially.

The role of intertidal seagrass Zostera spp. in sediment deposition and coastal stability in the Tay Estuary, Scotland

2012-10-16T13:40:45Z

Abstract: The Tay estuary is situated on the east coast of Scotland. The estuary is dominated by sediment biotopes, including mudflats which support sparse beds of two nationally scarce seagrass species, Zostera marina var. angustfolia (Hornem.) and Z. noltii (Hornem.). Seagrasses have been described as ecosystem engineers, shaping their sediment environment, and this may increase sediment deposition and stability. In this thesis the ecosystem engineering characteristics of seagrass habitats are explored. In 2008, the distribution of Zostera spp. in the Tay estuary was surveyed and mapped for the first time. Sediments within beds of Z. marina and Z. noltii were compared to investigate the influence of seagrasses on sediment characteristics. To explore the role of seagrass in sediment deposition and erosion, and coastal stability, sediment depth measurements were made in patches of Z. noltii, Z. marina and bare sediment over one year. The role of the root/rhizome system on sediment retention over winter was also considered. Sediment deposition in Z. noltii beds, and the influence of the plants on near-bed flow dynamics was further explored in the laboratory, using an 8 m seawater flume. In the field the retention of particles over 2 and 14 tides was measured, and the results of this experiment led to a study of the influence of leaf and sediment biofilms on particle retention, using the novel method of magnetic particle induction (MagPI). The efficacy of artificial seagrass beds and Z. noltii transplantation as habitat restoration techniques were compared over one year. During the trial, sediment deposition and changes in sediment characteristics were determined, and the protection given to saltmarsh cliffs fringing the study plots was assessed. Mechanisms underlying the results are suggested and the findings discussed. This study provides an insight into the ecology of seagrass in the Tay estuary and its role as an ecosystem manager. It may offer valuable data which could be utilised for future conservation policies, habitat restoration schemes and management planning of the area.

Impact of interferon β and interferon stimulated gene induction on Bunyamwera virus replication

2012-10-25T15:12:10Z

Abstract: The first line of defence against viral infection is the interferon (IFN) response, which must be overcome by a virus for successful replication. Pattern recognition receptors detect virus which triggers induction of IFNβ. Secreted IFNβ stimulates the JAK/STAT signal transduction pathway and the upregulation of IFN stimulated genes (ISGs) culminating with expression of hundreds of antiviral proteins. Bunyamwera virus (BUNV) is the prototype virus for the genus Orthobunyavirus and the family Bunyaviridae. BUNV is a trisegmented single stranded negative sense RNA virus whose genome comprises the Large (L), Medium (M) and Small (S) RNA segments. The L segment encodes the RNA polymerase, the M segment the two glycoproteins Gn and Gc and a non-structural protein NSm, and the S segment the nucleoprotein and a non-structural protein NSs in overlapping reading frames. The NSs protein interferes with RNA polymerase II mediated transcription thereby inhibiting cellular mRNA production, including IFN mRNA, and hence it is the primary IFN antagonist. A recombinant virus, rBUNdelNSs, that is unable to express the NSs protein, does not inhibit cellular transcription and is thus a strong IFN inducer. The aim of this thesis was to understand how IFN inhibits BUNV replication. Cells stimulated into the antiviral state by IFN treatment were protected against BUNV infection but addition of IFN 6 hours (or later) post infection had little effect on the replication cycle. However, addition of IFN immediately following infection conferred restriction on BUNV replication by initially increasing viral protein synthesis and then by blocking translation of positive sense viral RNA. To identify ISGs with anti-BUNV activity, I screened a panel of 26 cell lines that inducibly express individual ISGs. To aid screening, recombinant BUNV that expressed green fluorescent protein (GFP) were employed, including an NSs deletion virus with GFP fused to the Gc, rBUNGceGFPdelNSs, that I created and characterised. By a combination of virus yield assays, Western blotting and fluorescence techniques, three cell lines that inducibly express PKR, viperin or MTAP44 were shown to restrict BUNV replication. More detailed studies revealed PKR to restrict BUNV RNA and protein synthesis, but when PKR was knocked-down in IFN competent A549 cells viral replication was not blocked in cells pre-treated with IFN. Viperin inhibited viral protein synthesis and virally-induced host cell protein synthesis shut-off. Additionally, viral RNA synthesis was restricted by viperin and this was dependent on the CX₃CX₂C motif 1 of viperin. Taken together, these data show that the restriction of BUNV replication mediated by IFN is an accumulated effect of several different ISGs acting on different stages of the viral life cycle.

Statistical developments for understanding anthropogenic impacts on marine ecosystems

2012-10-05T10:12:47Z

Abstract: Over the past decades technological developments have both changed and increased human in influence on the marine environment. We now have greater potential than ever before to introduce disturbance and deplete marine resources. Two of the issues currently under public scrutiny are the exploitation of fish stocks worldwide and levels of anthropogenic noise in the marine environment. The aim of this thesis is to investigate and develop novel analyses and simulations to provide additional insight into some of the challenges facing the marine ecosystem today. These methodologies will improve the management of these risks to marine ecosystems. This thesis first addresses the issue of competition between humans and grey seals (Halichoerus grypus) for marine resources, providing compelling evidence that a substantial proportion of the sandeels consumed by grey seals in the North Sea are in fact H. lanceolatus, which is not commercially exploited, rather than the commercially important A. marinus. In addition, we present quantitative results regarding sources of bias when estimating the total biomass of sandeels consumed by grey seals. Secondly, we investigate spatially adaptive 2-dimensional smoothing to improve the prediction of both the presence and density of marine species, information that is often key in the management of marine ecosystems. Particularly, we demonstrate the benefits of such methods in the prediction of sandeel occurrence. Lastly this thesis provides a quantitative assessment of the protocols for real-time monitoring of marine mammal presence, which require that acoustic operations cease when an animal is detected within a certain distance (i.e. the "monitoring zone") of the sound source. We assess monitoring zones of different sizes with regards to their effectiveness in reducing the risks of temporary and permanent damage to the animals' hearing, and demonstrate that a monitoring zone of 2 km is generally recommendable.

MtsslWizard : in silico spin-labelling and generation of distance distributions in PyMOL

2013-05-12T04:06:51Z

Abstract: MtsslWizard is a computer program, which operates as a plugin for the PyMOL molecular graphics system. MtsslWizard estimates distances between spin labels on proteins quickly with user configurable options through a simple graphical interface. The program searches for ensembles of possible MTSSL conformations that do not clash with a static model of the protein. Options include restricting the search procedure to published rotamer libraries of MTSSL or scoring for contacts with protein. Once conformations are assigned, distance distributions between two or more sites are calculated, displayed and can be exported to other software. The program's use is evaluated in a number of challenging test cases and its performance discussed. The strength of the program is its accuracy and simplicity.

Biological diversity of freshwater fishes in small streams in peninsular Malaysia

2013-04-30T15:04:15Z

Abstract: Peninsular Malaysia has a diverse flora and fauna, much of which is yet to be documented. The freshwater fishes are one important group that have received little attention. Accordingly, the overarching goal of my study is to investigate the pattern of species richness and analyse the community composition and assemblage structure of fishes in the small streams in Peninsular Malaysia. Small stream habitats appeared to be particularly important repositories of fish biodiversity in this region thus obtaining a reliable census of species occurring in such habitats is critical for conservation and management of biodiversity. Although samplings were far from completed, these habitats support a great variety of species with more than 100 species were recorded from fifty streams sampled in this study. A few are extremely rare with restricted distribution and can thus be considered important in biodiversity conservation of the Peninsular Malaysian ichthyofauna. Human-influenced modification of lowland, headwater stream habitats in Peninsular Malaysia is common and often exemplified by the creation of pools in stretches of rapids and riffles. However, it was not possible to separate pristine and disturbed sites which contained almost identical for species diversity. These findings suggest that local habitat modification does not necessarily cause a decrease in freshwater fish diversity, with only minor negative consequences for other community variables recorded in this study, and therefore raise interesting issues regarding conservation. That said it remains premature to conclude that small stream fishes are insensitive to disturbance and thus their potential utility as bioindicators of disturbance-influenced community changes remain to be confirmed. The maintenance practises being applied to small streams modified for recreational usage were not imposing detectable negative consequences, at least across the sites sampled in this study. The rich diversity of tropical stream environments is the result of both within-habitat (alpha) diversity and between-habitat (beta) diversity. The results showed that there was substantial beta diversity particularly amongst sites that are geographically separated from one another. On the contrary, the lowest beta diversity values were portrayed by contiguous sites. Many fishes exhibited discontinuous patterns of distribution and were considered to be rare while only a handful were widely distributed and abundant. Ordination based on the relative resemblance of fish communities to one another support the existence of two distinct ichthyogeographic divisions in Peninsular Malaysia. It was possible to assign the species recorded to all seven of Rabinowitz’s categories of rarity, with at least 10 restricted to a single stream and locally scarce, although not all of these could be described as hyper-endemic. It is recommended that a sizeable augmentation of the existing protected areas is needed to safeguard Malaysia’s exceptionally diverse stream-dwelling fauna of which fishes are simply the most well-known inhabitants. Conservation managers should therefore place particular emphasis on small streams since localities in close proximity to one another can exhibit surprisingly high beta diversity, meaning that partial or small-scale habitat protection may prove insufficient.

The function of roll in foraging behaviour of sperm whales

2013-04-30T15:46:16Z

Abstract: Though direct experiments to test echolocation in sperm whales (Physeter macrocephalus) remain impossible, the indirect evidence is overwhelming that one function of their clicks is echolocation used during foraging, as has been shown for other toothed whales. In this thesis, the aim was to test: 1) the hypothesis by Fristrup and Harbison (2002) that the sperm whale might be using downwelling light during the day to spot prey or prey patches as silhouettes against the lighter sea surface. 2) A second hypothesis by Fristrup and Harbison (2002) suggested that the sperm whales use vision to look for bioluminescence in prey at depth, or during the night when no light is available. 3) Indications that the sperm whales changed their roll-behaviour, rolling more extensively when they were producing regular clicks during the descent as well as for the ascent. Data from 51 sperm whales tagged in the Gulf of Mexico, the Atlantic, the Mediterranean and northern Norway, were tested to explore how large a proportion of the bottom-interval the whales spent at angles where they were able to see towards the lighter sea surface at three different pitch-modes while either searching or buzzing, for each dive. The majority of whales were found to be swimming predominantly upside down or on the side during both the day and night time. The whales were not found to change the way they use roll at night compared to the day time, when looking at the bottom-interval when the whales were both searching for prey and buzzing. Looking at another function for roll and a possible association with the echolocation of the sperm whales, it was found that during the descent, the whales had a tendency to have a higher variance of roll when they were producing regular clicks. A very similar trend showed for the ascent-phase as well, that they seemed to roll more when clicking compared to when they were not, before they reached the sea surface. These analyses of the roll-behaviour of sperm whales used to test the hypotheses put forward by Fristrup and Harbison do not seem to support the use of vision to detect prey during foraging at depth, but might indicate that the sperm whale was intentionally changing its roll-behaviour, when they were producing regular clicks during the ascent and descent-phase in the Gulf of Mexico, the Atlantic, the Mediterranean and Norway.

Sexual selection and sex allocation in the gregarious parasitoid wasp Nasonia vitripennis

2013-05-01T09:23:19Z

Abstract: Sex allocation and sexual selection have been heavily studied, but rarely linked. In this thesis I investigated the interface between them in the gregarious parasitoid wasp Nasonia vitripennis, both directly and through their interactions with the mating system and sexual conflict. Chapter 2 investigated sexual selection and mating at the natal site: earlier eclosing males mated more females independently of body size. Nasonia follows Local Mate Competition, which describes how a female laying eggs alone on a patch of resources (a so-called single-foundress) should lay an extremely female-biased brood to minimise competition between her sons, yet ensure all her daughters are fertilised. Based on this I predicted that males with with fewer brothers would be better inseminators. Despite finding significant among-strain variation in (1) single-foundress sex ratio, (2) mate competitiveness when alone and (3) when in competition, (4) sperm resources, but not (5) sperm-depletion (Chapters 3 & 4), I did not find the predicted relationship. Conversely males from strains with more brothers had a higher mating success under competition (Chapter 3) leading to the question: does mating success select on sex ratio or vice versa? Either way it is a result of an interaction between sexual selection and sex allocation. Chapter 5 investigated the role of male post-copulatory courtship on female re-mating, and found that among- strain variation in female re-mating was not associated with variation in the duration of the post-copulatory courtship. Chapter 6 reviewed sexual conflict in the Hymenoptera: their haplodiploid genetics, newly sequenced genomes and varied life- histories provides a base for future research to build on. Finally I highlight the novel links between sexual selection, sex allocation, sexual conflict and the mating system found during my studies that will hopefully prompt future research on this topic.

An investigation of human protein interactions using the comparative method

2012-10-24T14:00:28Z

Abstract: There is currently a large increase in the speed of production of DNA sequence data as next generation sequencing technologies become more widespread. As such there is a need for rapid computational techniques to functionally annotate data as it is generated. One computational method for the functional annotation of protein-coding genes is via detection of interaction partners. If the putative partner has a functional annotation then this annotation can be extended to the initial protein via the established principle of “guilt by association”. This work presents a method for rapid detection of functional interaction partners for proteins through the use of the comparative method. Functional links are sought between proteins through analysis of their patterns of presence and absence amongst a set of 54 eukaryotic organisms. These links can be either direct or indirect protein interactions. These patterns are analysed in the context of a phylogenetic tree. The method used is a heuristic combination of an established accurate methodology involving comparison of models of evolution the parameters of which are estimated using maximum likelihood, with a novel technique involving the reconstruction of ancestral states using Dollo parsimony and analysis of these reconstructions through the use of logistic regression. The methodology achieves comparable specificity to the use of gene coexpression as a means to predict functional linkage between proteins. The application of this method permitted a genome-wide analysis of the human genome, which would have otherwise demanded a potentially prohibitive amount of computational resource. Proteins within the human genome were clustered into orthologous groups. 10 of these proteins, which were ubiquitous across all 54 eukaryotes, were used to reconstruct a phylogeny. An application of the heuristic predicted a set of functional protein interactions in human cells. 1,142 functional interactions were predicted. Of these predictions 1,131 were not present in current protein-protein interaction databases.

The genetic basis of flesh quality traits in farmed Atlantic salmon

2012-10-25T08:51:51Z

Abstract: The aim was to develop new methods for measuring texture of Atlantic salmon (Salmo salar L.) fillets and investigate the genetic basis of flesh quality traits. Firstly, a new tensile strength method was developed to quantify the force required to tear a standardized block of salmon muscle with the aim of identifying those samples more prone to factory downgrading as a result of gaping. The repeatability, sensitivity and predictability of the new technique was evaluated against other common instrumental texture measurement methods. Data from the new method were shown to have the strongest correlations with gaping severity r=-0.514, P<0.001) and the highest level of repeatability of data when analysing cold-smoked samples. The Warner Bratzler shear method gave the most repeatable data from fresh samples and had the highest correlations between fresh and smoked product from the same fish (r=0.811, P<0.001). It is therefore recommended that the new method be adopted for measuring gaping potential and the Warner Bratzler method become the standard for firmness assessment. Genes associated with post mortem softening in mammals were characterised in Atlantic salmon. A previously unknown ancient paralogue of calpastatin (here named CAST2) was identified. Evidence was provided for the existence of highly homologous recent paralogues of CAST2 and CTSD1. Evidence for the ancestral history of these paralogues was provided by phylogenetic analysis. Recent gene duplicates of 6 further genes were identified. In all cases, homology between recent paralogues was greater than 94%. Analysis of synonymous vs non-synonymous nucleotide substitution between the observed paralogue pairs shows a significant purifying selection in most cases. The CTSD1 gene shows significant purifying selection in a pairwise analysis between 12 teleost species (all cases P<0.0001) but a similar analysis of CTSD2 revealed no significant occurrence of purifying selection. The present study provides further support for the idea of asymmetrical selective pressure on paralogues. Genetic markers were developed that can distinguish individuals with above average fillet yield and texture. A database of firmness, tensile strength and fillet yield was made from 254 individuals from 5 batches of farmed salmon and these fish were genotyped at 7 novel SNP loci. Individuals with the combined favourable genotype at CAPN1a and MYOD1b were associated with an average increase in fillet yield of 2.7% above batch average. A combined genotype of CAPN1a, MYOD1b and MYF5 was significantly associated with an average increase in tensile strength of 9.8% above batch average (P=0.015). In both cases individuals with the combined favourable genotype occurred with a frequency of c. 6% across all batches. The favourable genotypes had no unfavourable effects on other traits. Highly polymorphic microsatellite loci were used to perform tests of assignment, which revealed an overall correct assignment rate of 92.7% to batch of origin and a minimum reference sample number of 25 was empirically determined. A phylogenetic analysis supported the results of the assignment tests. Given that 7 microsatellites is a relatively small number for a study of this nature, these results suggest that reliable assignment of unknown fish to the true batch of origin is potentially rapid and cost effective. Overall, the thesis presents molecular markers for broodstock selection, new genes of relevance to flesh quality, a new method of texture analysis and a proposal for an escapee traceability project.

Nitrate transport and assimilation in Aspergillus nidulans

2012-10-24T14:53:42Z

Abstract: In this study, several aspects of nitrate assimilation and transport have been studied using the filamentous fungus Aspergillus nidulans, which has been shown to be safe laboratory organism as judged by it’s pathogenicity towards insect larvae. In silico analysis of the A. nidulans genome sequence, identified two putative genes designated cnxL and cnxK that might be involved in molybdenum cofactor (a component of nitrate reductase) biosynthesis as well as two putative nitrate reductases encoding genes niaB and niaC. All four genes are hitherto unknown. Although many features of these proteins provided clues of functionality, biochemical and genetical approaches employed in this present study failed to elicit expression of any of these four genes. A NrtA protein structure model was developed based on residue homology with the E. coli GlpT a protein, the structure of which has been solved. The results of thiol cross-linking of three double cysteine mutants in four NrtA essential residues, R87, R368, N168 and N459, indicated that the molecular distance between R87 and R368 is ~ 0.4 Å, R368 and N168 ~ 6.2 Å, R87 and N459 is ~ 2.2 Å. Another important observation was the change in the confirmation of Tm 2 and Tm 8 in the presence of nitrate. This shift resulted in an increase of ~ 2 Å gap between the residues R87 and R368. Distances between amino acid residue pairs estimated using such molecular rulers contradicted the NrtA existing model. Cysteine-scanning mutagenesis studies were extended to the generation of a library of single cysteine mutants of NrtA residues spanning Tm 2 and Tm 8. The majority of single cysteine mutants possessed wild type NrtA protein expression levels but unfortunately most were found to be loss-of-function. Consequently, thiol chemistry of this crop of mutants was not perused. Attempts were also made to overexpress and crystallise the bacterial nitrate transporters but none of the transporter tested proved to be a successful candidate for crystallisation. In this regard, bacterial nitrate transporters, NarU (E. coli), Nar (Bacillus cereus), NarK1 and NarK2 (Pseudomonas aeruginosa) and NarK2 (Thermus thermophilus) fused with GFP were expressed in E. coli and used in crystallisation trials. Although this approach has proved successful for a number of membrane proteins, unfortunately was not helpful with regard to the purification of any of the above bacterial nitrate transporters to yield protein expression levels required for successful protein crystallography. Finally, the effects of potential nitrate transport inhibitors were studied on net nitrate transport by NrtA and NrtB proteins of A. nidulans. The results indicated that chlorate had more of an inhibitory effect on NrtA net nitrate transport than that by NrtB. Chlorite and sulphite equally affected net nitrate transport by either NrtA or NrtB proteins while caesium strongly inhibited the net nitrate transport by NrtB transporter.

New intracellular mechanisms involved in Alzheimer's disease and frontotemporal dementia

2012-10-24T14:47:52Z

Abstract: Dementia causes an increasing social and economic burden worldwide, demanding action regarding its diagnosis, treatment and everyday management. Recent years have seen many advances in neurodegeneration research, but the search for new truly disease modifying therapies for Alzheimer's disease (AD) and frontotemporal dementia (FTD) has so far not been successful. This is mainly due to a lack of understanding of the precise intracellular events that lead up to neuronal dysfunction in early and in late stages of the disease. This thesis describes the approaches taken to extend the current knowledge about the intracellular effects of neuronal amyloid-beta and the signalling pathways causing neuronal death or disturbed synaptic function in dementia. Endophilin-1(Ep-1), amyloid-binding alcohol dehydrogenase (ABAD), peroxiredoxin-2 (Prx-2) and the EF-hand domain family, member D2 (EFHD2) have been found to be elevated in the human brain with dementia and in mouse models for frontotemporal lobar degeneration (FTLD) or AD. The expression of these proteins as well as the expression of c-Jun N-terminal kinase (JNK), c-Jun and APP were analysed by western blotting and real-time PCR in human brains affected by AD or FTLD as well as in mouse models for AD. This provided a new insight into the regulation of these proteins in relation to each other in the ageing brain and uncovered a new potential link between elevated levels of EFHD2, Prx-2 and APP in FTLD. By studying the effects of the overexpression of Ep-1 in neurons, this research has led to a better understanding of its role in JNK-activation. It furthermore verified a protective role for Prx-2 against neurotoxicity and pointed towards a new function for Prx-2 in the regulation of JNK-signalling. The analysis of the effect of increased levels of EFHD2 uncovered for the first time its involvement in the PI3K-signalling cascade in neuronal cells. The current work has therefore contributed to the knowledge about the cellular processes that are affected by Ep-1, Prx-2 and EFHD2 in different types of dementia and will greatly benefit future research into their actions in the neuronal network.

Characterisation of proteins involved in CRISPR-mediated antiviral defence in Sulfolobus solfataricus

2012-10-24T14:27:07Z

Abstract: One of the most surprising realisations to emerge from metagenomics studies in the early ‘00s was that the population of viruses and phages in nature is about 10 times larger than the population of prokaryotic organisms. Thus, bacteria and archaea are under constant pressure to develop resistance methods against a population of viruses with extremely high turnover and evolution rates, in what has been described as an evolutionary “arms race”. A novel, adaptive and heritable immune system encoded by prokaryotic genomes is the CRISPR/Cas system. Arrays of clustered regularly interspersed short palindromic repeats (CRISPR) are able to incorporate viral or plasmid sequences which are then used to inactivate the corresponding invader element via an RNA interference mechanism. A number of CRISPR-associated (Cas) protein families are responsible for the maintenance, expansion and function of the CRISPR loci. This system can be classified in a number of types and subtypes that differ widely in their gene composition and mode of action. This thesis describes the biochemical characteristics of CRISPR-mediated defense in the crenarchaeon Sulfolobus solfataricus. The process of CRISPR loci transcription and their subsequent maturation into small guide crRNA units by the processing endonuclease of the system (Cas6) is investigated. After this step, different pathways and effector proteins are involved in the recognition and silencing of DNA or RNA exogenous nucleic acids. This thesis reports the identification and purification of a native multiprotein complex from S. solfataricus P2, the Cmr complex, a homologue of which has been found to recognise and cleave RNA targets in P. furiosus. The recognition and silencing of DNA targets in E. coli has been shown to involve a multiprotein complex termed CASCADE as well as Cas3, a putative helicase-HD nuclease. S. solfataricus encodes orthologues for the core proteins of this complex, and the formation and function of an archaeal CASCADE is investigated in this thesis.

A modulatory role for the NMDA receptor glycine binding site during fictive locomotion in Xenopus laevis larvae

2012-10-24T14:05:13Z

Identification of learning mechanisms in a wild meerkat population

2013-05-12T04:36:35Z

Abstract: Vigorous debates as to the evolutionary origins of culture remain unresolved due to an absence of methods for identifying learning mechanisms in natural populations. While laboratory experiments on captive animals have revealed evidence for a number of mechanisms, these may not necessarily reflect the processes typically operating in nature. We developed a novel method that allows social and asocial learning mechanisms to be determined in animal groups from the patterns of interaction with, and solving of, a task. We deployed it to analyse learning in groups of wild meerkats (Suricata suricatta) presented with a novel foraging apparatus. We identify nine separate learning processes underlying the meerkats' foraging behaviour, in each case precisely quantifying their strength and duration, including local enhancement, emulation, and a hitherto unrecognized form of social learning, which we term `observational perseverance'. Our analysis suggests a key factor underlying the stability of behavioural traditions is a high ratio of specific to generalized social learning effects. The approach has widespread potential as an ecologically valid tool to investigate learning mechanisms in natural groups of animals, including humans.

Vessel noise affects beaked whale behavior : Results of a dedicated acoustic response study

2013-05-12T04:35:54Z

Abstract: Some beaked whale species are susceptible to the detrimental effects of anthropogenic noise. Most studies have concentrated on the effects of military sonar, but other forms of acoustic disturbance (e.g. shipping noise) may disrupt behavior. An experiment involving the exposure of target whale groups to intense vessel-generated noise tested how these exposures influenced the foraging behavior of Blainville’s beaked whales (Mesoplodon densirostris) in the Tongue of the Ocean (Bahamas). A military array of bottom-mounted hydrophones was used to measure the response based upon changes in the spatial and temporal pattern of vocalizations. The archived acoustic data were used to compute metrics the echolocation-based foraging behavior for 16 targeted groups, 10 groups further away on the range, and 26 nonexposed groups. The duration of foraging bouts was not significantly affected by the exposure. Changes in the hydrophone over which the group was most frequently detected occurred as the animals moved around within a foraging bout, and their number was significantly less the closer the whales were to the sound source. Non-exposed groups also had significantly more changes in the primary hydrophone than exposed groups irrespective of distance. Our results suggested that broadband ship noise caused a significant change in beaked whale behavior up to at least 5.2 kilometers away from the vessel. The observed change could potentially correspond to a restriction in the movement of groups, a period of more directional travel, a reduction in the number of individuals clicking within the group, or a response to changes in prey movement.

Spatial variation in foraging behaviour of a marine top predator (Phoca vitulina) determined by a large-scale satellite tagging program

2013-05-12T04:09:55Z

Abstract: The harbour seal (Phoca vitulina) is a widespread marine predator in Northern Hemisphere waters. British populations have been subject to rapid declines in recent years. Food supply or inter-specific competition may be implicated but basic ecological data are lacking and there are few studies of harbour seal foraging distribution and habits. In this study, satellite tagging conducted at the major seal haul outs around the British Isles showed both that seal movements were highly variable among individuals and that foraging strategy appears to be specialized within particular regions. We investigated whether these apparent differences could be explained by individual level factors: by modelling measures of trip duration and distance travelled as a function of size, sex and body condition. However, these were not found to be good predictors of foraging trip duration or distance, which instead was best predicted by tagging region, time of year and inter-trip duration. Therefore, we propose that local habitat conditions and the constraints they impose are the major determinants of foraging movements. Specifically the distance to profitable feeding grounds from suitable haul-out locations may dictate foraging strategy and behaviour. Accounting for proximity to productive foraging resources is likely to be an important component of understanding population processes. Despite more extensive offshore movements than expected, there was also marked fidelity to the local haul-out region with limited connectivity between study regions. These empirical observations of regional exchange at short time scales demonstrates the value of large scale electronic tagging programs for robust characterization of at-sea foraging behaviour at a wide spatial scale.

Global coverage of cetacean line-transect surveys : status quo, data gaps and future challenges

2013-05-12T04:35:49Z

Abstract: Knowledge of abundance, trends and distribution of cetacean populations is needed to inform marine conservation efforts, ecosystem models and spatial planning. We compiled a geo-spatial database of published data on cetacean abundance from dedicated visual line-transect surveys and encoded >1100 abundance estimates for 47 species from 430 surveys conducted worldwide from 1975-2005. Our subsequent analyses revealed large spatial, temporal and taxonomic variability and gaps in survey coverage. With the exception of Antarctic waters, survey coverage was biased toward the northern hemisphere, especially US and northern European waters. Overall, <25% of the world’s ocean surface was surveyed and only 6% had been covered frequently enough (≥ 5 times) to allow trend estimation. Almost half the global survey effort, defined as total area (km2) covered by all survey study areas across time, was concentrated in the Eastern Tropical Pacific (ETP). Neither the number of surveys conducted nor the survey effort had increased in recent years. Across species, an average of 10% of a species’ predicted range had been covered by at least one survey, but there was considerable variation among species. With the exception of three delphinid species, <1% of all species’ ranges had been covered frequently enough for trend analysis. We use a data-rich species, sperm whale, as an example to illustrate the challenges of using available data from line-transect surveys for the detection of trends or for spatial planning. Finally, we propose and contrast several field and analytical methods to fill in data gaps to improve future cetacean conservation management efforts.

ATG5 Is Essential for ATG8-Dependent Autophagy and Mitochondrial Homeostasis in Leishmania major

2013-05-19T00:34:38Z

Abstract: Macroautophagy has been shown to be important for the cellular remodelling required for Leishmania differentiation. We now demonstrate that L. major contains a functional ATG12-ATG5 conjugation system, which is required for ATG8-dependent autophagosome formation. Nascent autophagosomes were found commonly associated with the mitochondrion. L. major mutants lacking ATG5 (Δatg5) were viable as promastigotes but were unable to form autophagosomes, had morphological abnormalities including a much reduced flagellum, were less able to differentiate and had greatly reduced virulence to macrophages and mice. Analyses of the lipid metabolome of Δatg5 revealed marked elevation of phosphatidylethanolamines (PE) in comparison to wild type parasites. The Δatg5 mutants also had increased mitochondrial mass but reduced mitochondrial membrane potential and higher levels of reactive oxygen species. These findings indicate that the lack of ATG5 and autophagy leads to perturbation of the phospholipid balance in the mitochondrion, possibly through ablation of membrane use and conjugation of mitochondrial PE to ATG8 for autophagosome biogenesis, resulting in a dysfunctional mitochondrion with impaired oxidative ability and energy generation. The overall result of this is reduced virulence.

Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing

2013-05-12T04:36:07Z

Abstract: Background: The gilthead sea bream (Sparus aurata L.) occurs around the Mediterranean and along Eastern Atlantic coasts from Great Britain to Senegal. It is tolerant of a wide range of temperatures and salinities and is often found in brackish coastal lagoons and estuarine areas, particularly early in its life cycle. Gilthead sea bream are extensively cultivated in the Mediterranean with an annual production of 125,000 metric tonnes. Here we present a de novo assembly of the fast skeletal muscle transcriptome of gilthead sea bream using 454 reads and identify gene paralogues, splice variants and microsatellite repeats. An annotated transcriptome of the skeletal muscle will facilitate understanding of the genetic and molecular basis of traits linked to production in this economically important species. Results: Around 2.7 million reads of mRNA sequence data were generated from the fast myotomal of adult fish (~2 kg) and juvenile fish (~0.09 kg) that had been either fed to satiation, fasted for 3-5d or transferred to low (11°C) or high (33°C) temperatures for 3-5d. Newbler v2.5 assembly resulted in 43,461 isotigs >100 bp. The number of sequences annotated by searching protein and gene ontology databases was 10,465. The average coverage of the annotated isotigs was x40 containing 5655 unique gene IDs and 785 full-length cDNAs coding for proteins containing 58–1536 amino acids. The v2.5 assembly was found to be of good quality based on validation using 200 full-length cDNAs from GenBank. Annotated isotigs from the reference transcriptome were attributable to 344 KEGG pathway maps. We identified 26 gene paralogues (20 of them teleost-specific) and 43 splice variants, of which 12 had functional domains missing that were likely to affect their biological function. Many key transcription factors, signaling molecules and structural proteins necessary for myogenesis and muscle growth have been identified. Physiological status affected the number of reads that mapped to isotigs, reflecting changes in gene expression between treatments. Conclusions: We have produced a comprehensive fast skeletal muscle transcriptome for the gilthead sea bream, which will provide a resource for SNP discovery in genes with a large effect on production traits of commercial interest and for expression studies of growth and adaptation.

ALDH2 mediates 5-nitrofuran activity in multiple species

2013-05-12T04:33:59Z

Abstract: Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of pro-drugs widely used to treat bacterial and trypanosome infections, but despite relative specificity 5-nitrofurans often cause serious toxic side-effects in people. Here, we use yeast, zebrafish and human in vitro systems to assess the biological activity of 5-nitrofurans, and identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome pro-drug, is dependent on zebrafish Aldh2 and that nifurtimox is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5nitrofuran treatment.

In and out of Madagascar : dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae)

2013-05-12T04:34:50Z

Abstract: Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.

Conservation ecology and phylogenetics of the Indus River dolphin (Platanista gangetica minor)

2012-08-07T14:00:29Z

Abstract: The historical range of the Indus River dolphin has declined by 80% since the 19th century and has been fragmented into 17 river sections by construction of irrigation barrages. Dolphin sighting and interview surveys showed that river dolphins persist in six river sections, have been extirpated from ten, and are of unknown status in the remaining section. Logistic regression and survival modelling showed that low dry season river discharge was the primary factor responsible for the Indus dolphins range decline. Abundance of the three largest Indus dolphin subpopulations was estimated using tandem vessel-based direct counts, corrected for missed animals using conditional likelihood capture-recapture models. The entire subspecies was estimated to number between 1550-1750 in 2006. Dolphin encounter rates within the Guddu-Sukkur subpopulation (10.35/km) were the highest reported for any river dolphin and direct counts suggest that this subpopulation may have been increasing in abundance since the 1970s when hunting was banned. The dry season habitat selection of Indus dolphins was explored using Generalised Linear Models of dolphin distribution and abundance in relation to river geomorphology, and channel geometry in cross-section. Channel cross-sectional area was shown to be the most important factor determining dolphin presence. Indus dolphins avoided channels with small cross-sectional area <700m2, presumably due to the risk of entrapment and reduced foraging opportunities. The phylogenetics of Indus and Ganges River dolphins was explored using Mitochondrial control region sequences. Genetic diversity was low, and all 20 Indus River dolphin samples were identical. There were no haplotypes shared by Indus and Ganges River dolphins, phylogenetic trees demonstrated reciprocal monophyletic separation and Bayesian modelling suggested that the two dolphin populations diverged approximately 0.66 million years ago. Declining river flows threaten Indus dolphins especially at the upstream end of their range, and it is important to determine how much water is required to sustain a dolphin population through the dry season. Fisheries interactions are an increasing problem that will be best addressed through localised, community-based conservation activities.

How selection structures species abundance distributions

2013-05-12T04:14:38Z

Abstract: How do species divide resources to produce the characteristic species abundance distributions seen in nature? One way to resolve this problem is to examine how the biomass (or capacity) of the spatial guilds that combine to produce an abundance distribution is allocated among species. Here we argue that selection on body size varies across guilds occupying spatially distinct habitats. Using an exceptionally well-characterized estuarine fish community, we show that biomass is concentrated in large bodied species in guilds where habitat structure provides protection from predators, but not in those guilds associated with open habitats and where safety in numbers is a mechanism for reducing predation risk. We further demonstrate that while there is temporal turnover in the abundances and identities of species that comprise these guilds, guild rank order is conserved across our 30-year time series. These results demonstrate that ecological communities are not randomly assembled but can be decomposed into guilds where capacity is predictably allocated among species.

Modulation of mammalian spinal motor networks by group I metabotropic glutamate receptors : implications for locomotor control and the motor neuron disease amyotrophic lateral sclerosis

2012-11-23T11:33:12Z

Abstract: The present study examined the role of group I metabotropic glutamate receptors (mGluRs) in mammalian spinal motor networks and investigated the potential role of mGluRs in the fatal neurodegenerative disease amyotrophic lateral sclerosis (ALS). Group I mGluR activation was found to modulate locomotor-related activity recorded from ventral roots of in vitro mouse spinal cord preparations. Activation of group I mGluRs led to an increase in the frequency of locomotor-related bursts and a decrease in their amplitude. The cellular mechanisms underlying group I mGluR-mediated modulation were investigated using whole-cell patch-clamp recordings from spinal neurons. Recordings from motoneurons revealed a wide range of effects, some of which were expected to increase motoneuron excitability, such as membrane depolarisation and hyperpolarisation of action potential thresholds. However, the net modulatory effect of group I mGluR activation was a reduction in motoneuron excitability, likely reflecting a reduction in the density of fast inactivating Na+ currents. The activation of group I mGluRs also reduced excitatory synaptic input to motoneurons, suggesting that modulation of motoneuron properties and synaptic transmission both contribute to group I mGluR-mediated reductions in locomotor motoneuron output. Recordings from spinal interneurons revealed a smaller range of modulatory effects for group I mGluRs. The clearest effect on interneurons, membrane depolarisation, may underlie group I mGluR-mediated increases in the frequency of locomotor activity. Finally, the potential role of group I mGluRs in the pathogenesis of ALS was investigated using a mouse model of the disease. Although no major perturbations in group I mGluR-mediated modulation were demonstrated in ALS affected spinal cords, there appeared to be a difference in the intrinsic excitability of spinal interneurons between wild type and ALS affected animals. Together these data highlight group I mGluRs as important sources of neuromodulation within the spinal cord and potential targets for the treatment of ALS.

Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates

2012-12-12T13:29:36Z

Abstract: 14-3-3 proteins regulate cellular responses to stimuli by docking onto pairs of phosphorylated residues on target proteins. The present study shows that the human 14-3-3-binding phosphoproteome is highly enriched in 2R-ohnologues, which are proteins in families of two to four members that were generated by two rounds of whole genome duplication at the origin of the vertebrates. We identify 2R-ohnologue families whose members share a ‘lynchpin’, defined as a 14-3-3-binding phosphosite that is conserved across members of a given family, and aligns with a Ser/Thr residue in pro-orthologues from the invertebrate chordates. For example, the human receptor expression enhancing protein (REEP) 1–4 family has the commonest type of lynchpin motif in current datasets, with a phosphorylatable serine in the –2 position relative to the 14-3-3-binding phosphosite. In contrast, the second 14-3-3-binding sites of REEPs 1–4 differ and are phosphorylated by different kinases, and hence the REEPs display different affinities for 14-3-3 dimers. We suggest a conceptual model for intracellular regulation involving protein families whose evolution into signal multiplexing systems was facilitated by 14-3-3 dimer binding to lynchpins, which gave freedom for other regulatory sites to evolve. While increased signalling complexity was needed for vertebrate life, these systems also generate vulnerability to genetic disorders.

Incipient speciation in Drosophila melanogaster involves chemical signals

2013-05-12T04:12:29Z

Abstract: The sensory and genetic bases of incipient speciation between strains of Drosophila melanogaster from Zimbabwe and those from elsewhere are unknown. We studied mating behaviour between eight strains - six from Zimbabwe, together with two cosmopolitan strains. The Zimbabwe strains showed significant sexual isolation when paired with cosmopolitan males, due to Zimbabwe females discriminating against these males. Our results show that flies' cuticular hydrocarbons (CHs) were involved in this sexual isolation, but that visual and acoustic signals were not. The mating frequency of Zimbabwe females was highly significantly negatively correlated with the male's relative amount of 7-tricosene (%7-T), while the mating of cosmopolitan females was positively correlated with %7-T. Variation in transcription levels of two hydrocarbon-determining genes, desat1 and desat2, did not correlate with the observed mating patterns. Our study represents a step forward in our understanding of the sensory processes involved in this classic case of incipient speciation.

Temperature, age of mating and starvation determine the role of maternal effects on sex allocation in the mealybug Planococcus citri

2013-05-12T04:08:56Z

Abstract: Environmental effects on sex allocation are common, yet the evolutionary significance of these effects remains poorly understood. Environmental effects might influence parents, such that their condition directly influences sex allocation by altering the relative benefits of producing sons versus daughters. Alternatively, the environment might influence the offspring themselves, such that the conditions they find themselves in influence their contribution to parental fitness. In both cases, parents might be selected to bias their sex ratio according to the prevailing environmental conditions. Here, we consider sex allocation in the citrus mealybug Planococcus citri, a species with an unusual genetic system in which paternal genes are lost from the germline in males. We test environmental factors that may influence either female condition directly (rearing temperature and food restriction) or that may be used as cues of the future environment (age at mating). Using cytological techniques to obtain primary sex ratios, we show that high temperature, older age at mating and starvation all affect sex allocation, resulting in female-biased sex ratios. However, the effect of temperature is rather weak, and food restriction appears to be strongly associated with reduced longevity and a truncation of the usual schedule of male and offspring production across a female's reproductive lifetime. Instead, facultative sex allocation seems most convincingly affected by age at mating, supporting previous work that suggests that social interactions experienced by adult P. citri females are used when allocating sex. Our results highlight that, even within one species, different aspects of the environment may have conflicting effects on sex allocation.

How reproductive ecology contributes to the spread of a globally invasive fish

2013-05-12T04:08:07Z

Abstract: Invasive freshwater fish represent a major threat to biodiversity. Here, we first demonstrate the dramatic, human-mediated range expansion of the Trinidadian guppy (Poecilia reticulata), an invasive fish with a reputation for negatively impacting native freshwater communities. Next, we explore possible mechanisms that might explain successful global establishment of this species. Guppies, along with some other notable invasive fish species such as mosquitofish (Gambusia spp.), have reproductive adaptations to ephemeral habitats that may enable introductions of very small numbers of founders to succeed. The remarkable ability of single pregnant guppies to routinely establish viable populations is demonstrated using a replicated mesocosm set up. In 86% of cases, these populations persisted for two years (the duration of the experiment). Establishment success was independent of founder origin (high and low predation habitats), and there was no loss of behavioural performance amongst mesocosm juveniles. Behavioural "signatures" of the founding locality were, however, evident in mesocosm fish. Our results demonstrate that introductions consisting of a single individual can lead to thriving populations of this invasive fish and suggest that particular caution should be exercised when introducing this species, or other livebearers, to natural water bodies. Description: The work was funded by Natural Environment Research Council (NERC) (UK) and the European Research Council.

The quantitative genetic basis of sex ratio variation in Nasonia vitripennis : a QTL study

2013-05-12T04:03:46Z

Abstract: Our understanding of how natural selection should shape sex allocation is perhaps more developed than for any other trait. However, this understanding is not matched by our knowledge of the genetic basis of sex allocation. Here, we examine the genetic basis of sex ratio variation in the parasitoid wasp Nasonia vitripennis, a species well known for its response to local mate competition (LMC). We identified a quantitative trait locus (QTL) for sex ratio on chromosome 2 and three weaker QTL on chromosomes 3 and 5. We tested predictions that genes associated with sex ratio should be pleiotropic for other traits by seeing if sex ratio QTL co-occurred with clutch size QTL. We found one clutch size QTL on chromosome 1, and six weaker QTL across chromosomes 2, 3 and 5, with some overlap to regions associated with sex ratio. The results suggest rather limited scope for pleiotropy between these traits.

Phocid seal leptin : tertiary structure and hydrophobic receptor binding site preservation during distinct leptin gene evolution

2013-03-14T16:31:13Z

Abstract: The cytokine hormone leptin is a key signalling molecule in many pathways that control physiological functions. Although leptin demonstrates structural conservation in mammals, there is evidence of positive selection in primates, lagomorphs and chiropterans. We previously reported that the leptin genes of the grey and harbour seals (phocids) have significantly diverged from other mammals. Therefore we further investigated the diversification of leptin in phocids, other marine mammals and terrestrial taxa by sequencing the leptin genes of representative species. Phylogenetic reconstruction revealed that leptin diversification was pronounced within the phocid seals with a high dN/dS ratio of 2.8, indicating positive selection. We found significant evidence of positive selection along the branch leading to the phocids, within the phocid clade, but not over the dataset as a whole. Structural predictions indicate that the individual residues under selection are away from the leptin receptor (LEPR) binding site. Predictions of the surface electrostatic potential indicate that phocid seal leptin is notably different to other mammalian leptins, including the otariids. Cloning the grey seal leptin binding domain of LEPR confirmed that this was structurally conserved. These data, viewed in toto, support a hypothesis that phocid leptin divergence is unlikely to have arisen by random mutation. Based upon these phylogenetic and structural assessments, and considering the comparative physiology and varying life histories among species, we postulate that the unique phocid diving behaviour has produced this selection pressure. The Phocidae includes some of the deepest diving species, yet have the least modified lung structure to cope with pressure and volume changes experienced at depth. Therefore, greater surfactant production is required to facilitate rapid lung re-inflation upon surfacing, while maintaining patent airways. We suggest that this additional surfactant requirement is met by the leptin pulmonary surfactant production pathway which normally appears only to function in the mammalian foetus.

The multifunctional NS1 protein of influenza virus

2013-05-19T00:32:12Z

Abstract: The non-structural (NS1) protein of influenza A viruses is a non-essential virulence factor that has multiple accessory functions during viral infection. In recent years, the major role ascribed to NS1 has been its inhibition of host immune responses, especially the limitation of both interferon (IFN) production and the antiviral effects of IFN-induced proteins, such as dsRNA-dependent protein kinase R (PKR) and 2'5'-oligoadenylate synthetase (OAS)/RNase L. However, it is clear that NS1 also acts directly to modulate other important aspects of the virus replication cycle, including viral RNA replication, viral protein synthesis, and general host-cell physiology. Here, we review the current literature on this remarkably multifunctional viral protein. In the first part of this article, we summarize the basic biochemistry of NS1, in particular its synthesis, structure, and intracellular localization. We then discuss the various roles NS1 has in regulating viral replication mechanisms, host innate/adaptive immune responses, and cellular signalling pathways. We focus on the NS1-RNA and NS1-protein interactions that are fundamental to these processes, and highlight apparent strain-specific ways in which different NS1 proteins may act. In this regard, the contributions of certain NS1 functions to the pathogenicity of human and animal influenza A viruses are also discussed. Finally, we outline practical applications that future studies on NS1 may lead to, including the rational design and manufacture of influenza vaccines, the development of novel antiviral drugs, and the use of oncolytic influenza A viruses as potential anti-cancer agents.

Clasp-mediated microtubule bundling regulates persistent motility and contact repulsion in Drosophila macrophages in vivo

2013-05-12T03:32:56Z

Abstract: Drosophila melanogaster macrophages are highly migratory cells that lend themselves beautifully to high resolution in vivo imaging experiments. By expressing fluorescent probes to reveal actin and microtubules, we can observe the dynamic interplay of these two cytoskeletal networks as macrophages migrate and interact with one another within a living organism. We show that before an episode of persistent motility, whether responding to developmental guidance or wound cues, macrophages assemble a polarized array of microtubules that bundle into a compass-like arm that appears to anticipate the direction of migration. Whenever cells collide with one another, their microtubule arms transiently align just before cell–cell repulsion, and we show that forcing depolymerization of microtubules by expression of Spastin leads to their defective polarity and failure to contact inhibit from one another. The same is true in orbit/clasp mutants, indicating a pivotal role for this microtubule-binding protein in the assembly and/or functioning of the microtubule arm during polarized migration and contact repulsion. Description: P. Martin and W. Wood contributed equally to this paper

Novel sialic acid derivatives lock open the 150-loop of an influenza A virus group-1 sialidase

2013-05-12T03:36:38Z

Abstract: Influenza virus sialidase has an essential role in the virus’ life cycle. Two distinct groups of influenza A virus sialidases have been established, that differ in the flexibility of the ‘150-loop’, providing a more open active site in the apo form of the group-1 compared to group-2 enzymes. In this study we show, through a multidisciplinary approach, that novel sialic acid-based derivatives can exploit this structural difference and selectively inhibit the activity of group-1 sialidases. We also demonstrate that group-1 sialidases from drug-resistant mutant influenza viruses are sensitive to these designed compounds. Moreover, we have determined, by protein X-ray crystallography, that these inhibitors lock open the group-1 sialidase flexible 150-loop, in agreement with our molecular modelling prediction. This is the first direct proof that compounds may be developed to selectively target the pandemic A/H1N1, avian A/H5N1 and other group-1 sialidase-containing viruses, based on an open 150-loop conformation of the enzyme. Description: This work was supported by the Medical Research Council and the Scottish Funding Council.

Conservation of a crystallographic interface suggests a role for beta-sheet augmentation in influenza virus NS1 multifunctionality

2013-05-12T04:05:16Z

Abstract: The effector domain (ED) of the influenza virus virulence factor NS1 is capable of interaction with a variety of cellular and viral targets, although regulation of these events is poorly understood. Introduction of a W187A mutation into the ED abolishes dimer formation; however, strand-strand interactions between mutant NS1 ED monomers have been observed in two previous crystal forms. A new condition for crystallization of this protein [0.1 M Bis-Tris pH 6.0, 0.2 M NaCl, 22%(w/v) PEG 3350, 20 mM xylitol] was discovered using the hanging-drop vapour-diffusion method. Diffraction data extending to 1.8 Å resolution were collected from a crystal grown in the presence of 40 mM thieno[2,3-b]pyridin-2-ylmethanol. It was observed that there is conservation of the strand-strand interface in crystals of this monomeric NS1 ED in three different space groups. This observation, coupled with conformational changes in the interface region, suggests a potential role for [beta]-sheet augmentation in NS1 function. Description: This research was supported by grants from the Medical Research Council (MRC) and the Scottish Funding Council (SFC).

The passage of electric currents through tissues : (with particular reference to the percutaneous stimulation of human nerve and muscle)

2012-07-13T09:24:41Z

Abstract: The physiologist enjoys a great advantage over the clinical neurologist in the electrical stimulation of muscle, in that he is generally able to kill or anaesthetise his experimental animal and to excise or expose the tissues to be stimulated. The electrical impedance of the preparation is predominantly resistive, and the question of the comfort and safety of the animal scarcely arises. The stimulation of human muscle, on the other hand, normally has to be carried out on ac cious subject, whose comfort and safety must be considered, by means of electric currents applied through electrodes placed in contact with the skin, which exhibits very complex electrical properties. Conflict arises between the requirements of technical accuracy and ease of interpretation of results on the one hand, and comfort and convenience on the other. This thesis represents an attempt to assemble as much as possible of the information required for intelligent solution of the problems encountered in the percutaneous stimulation of muscle. Part I of the thesis reviews published information on nerve, muscle and denervated muscle, the electrical impedance of tissues, and diagnostic and therapeutic stimulation of muscle. Part II describes the author's personal research into the electrical impedance of the body, the interplay between body impedance, stimulator impedance and the electrical excitability characteristics of nerve and muscle, and the influence of these various factors on stimulator performance. In view of the variety of topics involved, the material has been arranged in separate more or less self-contained sections, including discussion of the implications of the results in each section. Technical details of the main electronic devices used are given in the Appendix, (Part III, together with details of the various mathematical analyses and calculations. Part of the work on which this thesis is based was carried out during the tenure of a temporary lectureship in Biophysics donated by the late Sir David Russell, to whom the author is deeply indebted. The author is also greatly indebted to Professor A. E. Ritchie for creating the circumstances which made this work possible, for permitting the author access to unpublished material, and for his patient encouragement and support of this protracted project; to Dr J. Crossland for assistance in the translation of German texts, and to Mr E. Carstairs for advice and assistance in devising the photographic techniques used in recording and reproducing the experimental results.

The development of a system to facilitate the stable expression of mammalian proteins in the filamentous fungus 'Aspergillus oryzae'

2012-07-23T10:39:25Z

Abstract: Human interleukin 6 (hIL6) is a multifunctional cytokine effecting the function and proliferation of many cell types. The further understanding of hIL6 and its possible medical applications rely on the availability of this protein. The filamentous fungus Aspergillus oryzae is an important industrial organism and is used for the large scale production of many enzymes. As this fungus has an impressive secretory output it was decided to attempt to produce hIL6 in this organism. The initial work was based on the development of a gene transfer system for A. oryzae in order that the hIL6 gene could be introduced to the organism. A transformation system based on the homologous nitrate reductase gene is described. This system yielded up to 800 transformants per µg plasmid DNA. Additionally, the adaptation of the transformation system based on the A. nidulans anuiS gene and the use of other transformation systems is reported. In order to ensure that the hIL6 gene was efficiently transcribed it was considered important that homologous control regions from highly produced and regulated A. oryzae genes were linked to the hIL6 gene. Therefore the genes encoding glucoamylase and a-amylase were isolated from A. oryzae. A method for the purification of A. oryzae Si nuclease is described and the amino acid sequence of the N terminus is reported. A. oryzae produces large amounts of extracellular proteases, a feature unlikely to be attractive in a heterologous host. Therefore the production of protease production in A. oryzae was studied. A method is described for the selection of protease deficient mutants. Using this method two protease mutants were isolated and these have been characterized. One mutation designated prtA2 protects against the degradation of hJL6 in vitro. The A. oryzae alkaline protease gene was isolated and mutagenised and the attempts made to produce specific protease mutant by reverse genetics are described. A system is described where by A. oryzae can be engineered to produce relatively high levels of hIL6. Using gene fusion constructs transformants producing in the range of 1 mg per Litre have been isolated. This system is heterologous, recommendations for increasing hIL6 production are included.

Studies on the pollination biology and breeding systems of some genera with sympatric species in the Brazilian cerrados

2012-07-04T14:40:57Z

Abstract: Flowering phenology, floral strategies pollinator activity and breeding system were investigated in 14 species of the cerrado vegetation in Braeflia (DF), from April 1985 to April 1986 in Tabebuia caraiba (Mart.) Bur., T. ochracea (Cham.) Standl.; Erythroxylum campestre St. Hil., E. suberosum St. Hil., E. tortuosum Mart.; Diplueodon crulsianue Pohl., D. oblongus Pohl., D. ramosissimus Pohl., D. roomarinifolius St. Hil., D. villosus Pohl.; Kielneyera abdita Saddi, K. coriacea Mart., K. speciosa St. Hil. and K. variabilis Mart. The species occur sympatrically, often only a few meters apart, and conspecifics frequently occur in clumps. The majority of the species flowered during the dry season (May to August) except D. oblongue, D. villosue and K. speciosa which flowered during the wet season (December to March). Most of them flowered for several months except Tabebuia (one month). The most frequent flowering pattern was the "Cornucopian"' type, except for D. crulsianue and D. Villosus which were "Steady-State" types. Most congeners flowered synchronously, except K. speciosa which showed displacement. Flowers of all species are pollen donors (Tabebuia and Erythroxylum also have nectar rewards), but each genus presents specific floral strategies; Tabebuia, Massflowering, Erythroxylum, distyly and cauliflory, Diplueodon, enantiostyly and Kielmeyera, andromonoecy. Flowers were visited by a large spectrum of bees (38spp. ) and Erythroxylum were also visited by wasps (16 app. ). However, each genus had particular pollen vectors. Tabebuia; Centris and Bombus; Erythroxylum: wasps; Diplueodon; Apia and Trigona; and Kielmeyera; Xylocopa, despite the fact that other bees occur all year round. Controlled pollination experiments (self-, intraspecific-, interspecific crosses, tests for apomixis and from untreated bagged flowers), revealed that all species have a high outcrossing level and are selfincompatible. Only E. campeatre (shrub), D. crulsianus and D. villosus (hemixyles), showed some self-compatibility. Fluorescence microscopy indicated that pollen tubes from selfing and from interspecific cross pollinations were blocked in the ovary, suggesting that the selfincompatibility barrier operates late. Only in Erythroxylum the blockage occurred in the stigma (Thrum flowers) or in the style (Pin flowers). Fruit-set number from hand-pollinations and from natural pollination were low, but the former frequently yielded a higher number of fruits than the latter. Low fruit-set was associated with lack of resources allocated by the maternal parent for fruit maturation. In addition, it seemed that, in all species, many flowers were programmed to be pollen donors only, since they dropped without any sign of ovary enlargement even if they were hand-pollinated or were frequently visited by pollinators.

Isolation and characterisation of chlorate resistant mutants of barley

2012-07-04T10:31:13Z

Abstract: The object of this study has been to characterise barley mutants which lack the functional nitrate reductase (NR) enzyme system. In the long term it is hoped that such studies will lead to improved nitrate utilisation and ultimately to improved quality barley protein. The progeny of nine chlorate resistant selections, in the barley cultivars Mavis Mink and Golden Promise, were studied. Four (R9201, R11301, R12202 and R12801) lacked NADH-NR and FMNH2-NR activities, the rest had the NR+ phenotype. None of the four were nitrate uptake mutants since they all possesed wild type or greater levels of nitrate. R9201, R11301 and the previously characterised R9401 (Bright et al, 1983) were not molybdenum uptake or Mo-accumulation mutants. R9201, R11301 and R12202 lacked xanthine dehydrogenase (XDH) (an enzyme which contains the same molybdenum-containing cofactor, MoCo) activity suggesting that these lines have defective MoCo's, whilst R12801 possessed XDH activity indicating that it might have defective apoprotein subunits. These four lines are similar to R9401 since they lack "NR activity and are unlike other previously selected ' barley NR mutants (Kleinhofs ' et al, 1980) which are leaky and possess up to 5% of the wild type (cv. Steptoe) in vitro NR activity. R9201 and R11301, like R9401, were all caused by single recessive nuclear gene mutations. The MoCo mutants, R9201, R9401, R11301 and R12202, could be divided into two groups on the basis of i) allelism, ii) presence or absence of wild type levels of dimeric NR and iii) the ability of their extracted MoCo's to reconstitute NADPH-NR in an extract of N. crassa nitl mutant (which supplies NR monomers) in the presence of excess molybdate. R11301 is not allelic to R9201, whilst R9201 and R9401 are allelic. R9401 is also thought to be allelic to Az 34, a barley MoCo mutant isolated and characterised by Kleinhofs et al (1980). Az 34 has been designated nar2a and it is proposed that the allelic R9401 and R9201 should be classified as nar2b and nar2c respectively. It is possible that R11301 is either allelic with one of the other barley MoCo lines, nar3, nar4 or it is defective in a different MoCo gene. The same is also true for R12202. R11301 was shown to possess inactive NR dimer at wild type concentrations, whilst R9201, R9401 and R12202 had little or no NR (inactive dimer) present under these conditions. R12801 possessed no dimer. The MoCo extracted from R11301 was able to reconstitute the same level of NADPH-NR in the Hill extract as MoCo extracted from-the wild types. R9201, R9401 and R12202 lacked this ability.

Endocrine control of reproduction of the powan of Loch Lomond, 'Coregonus lavaretus (L.)' (Teleostei): with special reference to the pituitary gonadotrophin-gonadal steroid axis

2012-07-03T08:44:40Z

Abstract: In order to provide an accurate basis for the correlation of endocrine changes and phases of the reproductive (and associated) cycles in the powan of Loch Lomond, 'Coregonus- lavaretus (L.), the following experiments were carried out, Cell types in the pituitary were identified using light microscopy and transmission electron microscopy. To locate gonadotropic cells an immunofluorescence technique was employed using antibody prepared in rabbit and an immunodiffusion method to detect the presence of antibody in the rabbit serum. In order to purify pituitary gonadotropin, two purification techniques 'were used. One was alcoholic extraction followed by gel filtration on sephadex; the other was buffer extraction followed by affinity chromatography on Concanavalin A-sepharose. To characterise the fractions from columns, two in vitro bioassays were employed; (i) ovulation of the oocytes of medaka (Oryzias latipes); (ii) Cyclic AMP production in immature trout gonads. The concentration of pituitary gonadotropins was measured using a heterologous radioimmunoassay technique. Using a radioimmunoassay technique, the serum testosterone and oestradiol-17β concentrations were determined. Serum proteins were characterised using SDS gel electrophoresis.

The small genome segment of Bunyamwera orthobunyavirus harbours a single transcription-termination signal

2013-05-12T04:34:39Z

Abstract: Transcription termination of the mRNA produced from the small (S) genome segment of Bunyamwera orthobunyavirus (BUNV) has previously been mapped to two cis-acting sequences located within the 5′ UTR using a virus-free replication assay. The ability of these sequences to terminate transcription was attributed to the shared pentanucleotide motif 3′-UGUCG-5′. Taking advantage of our plasmid-based rescue system to generate recombinant viruses, we re-evaluated the importance of both pentanucleotide motifs as well as that of two other conserved sequences in transcription termination in vivo. Analysis of the 3′ ends of positive-stranded viral RNAs derived from the S segment revealed that only the region around the upstream pentanucleotide motif mediated transcription termination in cells infected with wild-type BUNV, leading to mRNAs that were about 100 nt shorter than antigenome RNA. Furthermore, the downstream motif was not recognized in recombinant viruses in which the upstream signal has been disrupted. Our results suggest that in the context of virus infection transcription termination of the BUNV S genome segment mRNA is exclusively directed by the upstream-termination signal. Interestingly, within this region we identified a motif similar to a transcription-termination sequence used by Rift Valley fever phlebovirus.

Bunyaviruses and the type I interferon system

2012-12-12T12:54:43Z

Abstract: The family Bunyaviridae contains more than 350 viruses that are distributed throughout the world. Most members of the family are transmitted by arthopods, and several cause disease in man, domesticated animals and crop plants. Despite being recognized as an emerging threat, details of the virulence mechanisms employed by bunyaviruses are scant. In this article we summarise the information currently available on how these viruses are able to establish infection when confronted with a powerful antiviral interferon system.

Modeling distribution and abundance of Antarctic baleen whales using ships of opportunity

2013-05-12T03:01:46Z

Abstract: Information on animal abundance and distribution is at the cornerstone of many wildlife and conservation strategies. However, these data can be difficult and costly to obtain for cetacean species. The expense of sufficient ship time to conduct design-unbiased line transect surveys may be simply out of reach for researchers in many countries, which nonetheless grapple with problems of conservation of endangered species, by-catch of small cetaceans in commercial fisheries, and progression toward ecosystem-based fisheries management. Recently developed spatial modeling techniques show promise for estimating wildlife abundance using non-randomized surveys, but have yet to receive much field-testing in areas where designed surveys have also been conducted. Effort and sightings data were collected along 9 650 km of transects aboard ships of opportunity in the Southern Ocean during the austral summers of 2000 - 2001 and 2001 - 2002. Generalized additive models with generalized cross-validation were used to express heterogeneity of cetacean sightings as functions of spatial covariates. Models were used to map predicted densities and to estimate abundance of humpback, minke, and fin whales in the Drake Passage and along the Antarctic Peninsula. All species' distribution maps showed strong density gradients, which were robust to jackknife resampling when each of 14 trips was removed sequentially with replacement. Looped animations of model predictions of whale density illustrate uncertainty in distribution estimates in a way that is informative to non-scientists. The best abundance estimate for humpback whales was 1 829 (95% CI: 978- 3 422). Abundance of fin whales was 4 487 ( 95% CI: 1 326 - 15 179) and minke whales was 1,544 ( 95% CI: 1,221 - 1,953). These estimates agreed roughly with those reported from a designed survey conducted in the region during the previous austral summer. These estimates assumed that all animals on the trackline were detected, but preliminary results suggest that any negative bias due to violation of this assumption was likely small. Similarly, current methodological limitations prohibit inclusion of all known sources of uncertainty in the favored variance estimator. Meanwhile, our approach can be seen generally as an inexpensive pilot study to identify areas of predicted high density that could be targeted to: inform stratified designs for future line transect surveys, making them less expensive and more precise; increase efficiency of future photo-identification or biopsy studies; identify candidate time-area fisheries closures to minimize by-catch; or direct ecotourism activities. The techniques are likely to apply to areas where funding is limiting, where cetacean studies or wilderness-based tourism are just beginning, or in regions where even a very rough estimate of animal abundance is needed for conservation or management purposes.

Methods for investigating measurement error in cetacean line-transect surveys

2013-05-12T01:34:47Z

Abstract: Line-transect estimates of abundance generally assume that distances and angles to animals are measured without error. Biased distance measurements will lead to corresponding bias in abundance estimates. Efforts to address this have been made, but measuring distance to cetaceans at sea remains problematic. Four distance-estimation experiments were conducted to explore relationships between estimated and measured distance, Heteroscedasticity was found in all four cases. Preliminary evidence suggested that an observer differed in the ability to judge distance to fixed, continuously-visible cues and ephemeral, cetacean cues, which calls into the question the common practice of using marker buoys as cetacean proxies in distance-estimation experiments. Two studies found visual estimates to be positively biased, and two studies found reticule measurements to be negatively biased. Suitable correction factors were developed to address systematic bias from visual estimates, but these varied widely among observers and were sometimes non-linear. Errors in three studies showed positive skew, suggesting that ranges were overestimated to a larger degree than they were underestimated. if reticule and photogrammetric measurements yield log-normally distributed errors generally, then a least-squares regression will always overstimate the correction factor, underestimate range, and overestimate abundance. Photogrammetric methods to measure range to cetaceans performed well, and their use is encouraged. When measurements cannot be made to all sightings, however, it is recommended that experiements be conducted that generate sufficient sample size (of the target species, across typical survey conditions, and beyond the maximum range that most estimates will be made during the survey) to assess error distributions, examine evidence for non-linearity, and to consider inter-observer differences. Distance experiments, and training on survey protocols, and be conducted using ships of opportunity prior to the beginning of a dedicated survey, which would improve observer efficiency while reducing the costs of dedicated vessel time.

Measurement of changes in marine benthic ecosystem function following physical disturbance by dredging

2012-08-07T14:07:53Z

Abstract: Measuring the impact of physical disturbance on macrofaunal communities and sediment composition is important given the increased demand for the exploitation and disturbance of marine ecosystems. The aim of the present investigation was to provide a comprehensive study about the extent to which the disturbance (especially aggregate dredging) may affect benthic ecosystem function. The first part of the thesis concerns a field investigation of the impacts of dredging on the benthic community and related ecosystem function which was measured by different approaches including traditional methods based on benthic community structure and a more novel approach based on the functional traits of benthic organisms. The assessment was done by comparing dredged sites (Area 222, southeast England) with nearby undisturbed reference sites from the years 2001 to 2004 and in 2007. In general, low dredging intensity did not appear to impose great impacts on the benthic community and related ecosystem function compared to the higher intensity activity. Most of the analyses suggested that the community at the high dredging intensity site had yet to recover at the end of this study period. Among many factors related to the recovery of the benthic community was sediment composition where gravel deposits appeared to support a faster biological recovery. Meanwhile, the recovery of species with specific traits, such as tube-building and filter feeding also indicate a faster recovery for the whole community. The experimental work to determine different impacts of Hediste diversicolor on its surrounding depending on its relative size is discussed in Appendix 1.

Cetacean studies using platforms of opportunity

2012-06-27T15:38:50Z

Abstract: As human impact on marine ecosystems continues to grow, so too does the need for sound conservation and management strategies that are informed by science. Cetaceans, the whales, dolphins and porpoises, epitomise this challenge, because they are hard to study, they have been heavily exploited in the past, and because some of their habitats, behaviours and life-history strategies make them acutely vulnerable to human activities. Unfortunately, research on free-ranging cetaceans in remote areas is costly, and financial resources are limited. The approach used in this thesis to acquire inexpensive quantitative information on cetacean populations and behaviour was to seek out platforms of opportunity. Tourism and environmental education projects provided access to remote areas of importance to cetaceans. The topic was explored in two main areas. First, studies were conducted to investigate the use of ships of opportunity in estimating distribution and abundance, namely of Antarctic baleen whales. The second area of interest was the effect of boats on killer whales in the northeast Pacific. Platforms of opportunity proved valuable for collecting data to model the role of measurement error on abundance estimation. Measurement error was found to be a potential source of bias in four distance estimation experiments. Platforms of opportunity could be used to train observers on protocols, and to learn to use range- finding photogrammetric equipment well before conducting dedicated surveys, which would eliminate this source of bias, as well as estimating abundance in some cases. Abundance and distribution of three whale species were modelled using data collected aboard Antarctic tourist ships. Spatial modelling techniques were used to model distribution of minke, fin and humpback whales using line-transect data collected from a survey that could not be randomised. Strong gradients in animal density were predicted, which could be used to inform future surveys. In the meantime, rough estimates of abundance were obtained, and this approach shows promise for other areas where lack of resources makes systematic surveys prohibitively expensive. A government-funded environmental education project provided logistical support for two studies that dealt with effects of boats on killer whale behaviour. One quantified the extent to which a particular style of whalewatching was disruptive to whale behaviour, and commercial whalewatchers agreed to halt this activity. The other found that a protected area conferred benefit to killer whales, even though it protects only a fraction of the whales' habitat for a fraction of the year. The thesis contains four case studies that illustrate how inexpensive methods may be used to obtain practical quantitative information to aid decision-making about conservation and management of wild cetaceans that interact with (i.e., whalewatching), compete with (i.e., fishing) or are exploited by (i.e., whaling) humans. Description: Chapters 1-5 of this thesis have been updated and subsequently published in multi-authored articles in peer-reviewed journals. If required, citations should be made to these updated articles listed in the full item record below

Biodiversity of freshwater fishes of Trinidad and Tobago, West Indies

2012-08-09T11:43:54Z

Abstract: The proximity of the speciose South American continent to Trinidad and Tobago ensures that these islands have a rich and dynamic fauna. According to the equilibrium theory of island biogeography (MacArthur & Wilson 1967), these islands should be subjected to frequent immigrations from the nearby continent, and these additions will, in response, fuel local extinctions to maintain a balance of species richness. The aquatic habitat is further impacted by man's activities, (Government of Trinidad and Tobago 1962; Government of Trinidad and Tobago 1976b) which have the potential to amplify the natural rates of immigration and extinction. Despite the possible consequences, the effects of this disturbance on the fish fauna have not been studied. A survey of the islands' freshwater fishes was therefore carried out to investigate the natural spatial and temporal dynamics of local fish communities, and the effects of anthropogenic perturbations, on these. These baseline data can be used as a benchmark to address some of the problems that are threatening the fish diversity of Trinidad and Tobago. The fish fauna of Trinidad and Tobago is diverse. Total species richness was estimated at between 37 and 40. Four zoogeographic zones were recognised. A zone of Antillean fishes included Tobago and the north coast of Trinidad. A zone of recent colonising South American fauna existed along the south coast of Trinidad. The rest of Trinidad contained a relict South American fauna dating back to the time when Trinidad was still part of the mainland. Included here was a centrally located zone of unstable fauna at risk of local extinction. The fish fauna was temporally dynamic due to frequent colonisation and extinction events. Examination of the historic record showed that observed species richness varied from 38 to 43 between the mid 1950s and the present. During this time there were 15 introductions and 12 local extinctions. A conservative estimate was that a new species was recorded for Trinidad almost every three years. The geographic distribution of species also showed temporal changes which indicated a natural tendency of the fauna to vary over time. Human interference, particularly the introduction of exotic fish species and long-term habitat alteration, has affected species diversity. Forty seven percent of the new introductions and 43% of the extinctions were human-introduced exotics. About four fifths of sites in Trinidad, and almost one fifth of the sites in Tobago, were either perturbed or polluted. Polluted rivers coincided with areas of high urbanisation and industrial development in the west and southwest of Trinidad. Several effects of human interference on the fauna were recorded. Almost 8% of the sites examined contained one of the three exotic species still extant on the island. At each of these sites, the exotic species accounted for between 1.3% and 80.4%, by number, of the fish caught. Some of the effects of habitat disturbance on individual sites were increased frequency of diseases, extirpation of species, changes in species richness and other diversity measures, and the eventual regression of the fish community to opportunistic species (r-strategists). The potential of two fishes, Poecilia reticulata and Astyanax bimaculatus, as indicator species was examined. Astyanax showed better potential as an indicator of habitat quality as it was not found in depauperate communities, typical of severely disturbed habitats, and its proportional abundance and biomass were negatively affected by pollution. Poecilia populations, on the other hand, were found to be insensitive to habitat quality when the above-mentioned criteria were used. They did, however, have a high frequency of diseased individuals at polluted sites. One of the aims of conservation is to protect that portion of biodiversity most at risk of extinction, the rare species (Rabinowitz 1986). Over 70% of freshwater fish species found in Trinidad and Tobago were classified as rare in these islands. This fact, in addition to the loss of diversity recorded for some sites indicates that the implementation of a management strategy for the conservation of the freshwater fish fauna of Trinidad and Tobago is imperative. The management strategy should focus on the amelioration and protection of aquatic habitats since at least 80% of the rare species had either a restricted geographic distribution or narrow habitat specificity. Additionally, protection from overexploitation should be offered to commercially important species with only small populations. Finally, a minimum sample size of 35 sites, spread over different zoogeographic areas, is recommended for estimating species richness for monitoring, an intrinsic part of any management strategy.

Molecular systematics of 'Rhododendron ponticum' L. and its close allies

2012-06-20T15:31:47Z

Abstract: Rhododendron ponticum, introduced to the British Isles in 1763, has become a noxious invasive pest species, particularly in the west. Material of R. ponticum and its close allies in subsection Pontica were subjected to chloroplast DNA RFLP analysis. A preliminary phylogeny based on all cpDNA variation detected is presented. Suggestions regarding the interrelationships of these species are made, and a cpDNA-type of unknown taxonomic identity is tentatively identified. Chloroplast DNA differences were detected between native material of R. ponticum from Turkey, Spain and Portugal. Based on these differences, it was determined that approximately 90% of material naturalised in the British Isles originates from Spain and 10% from Portugal. These two types of material occur in roughly the same proportion throughout the British Isles. About 10% of naturalised accessions were found to contain an rDNA marker indicating nuclear introgression from R. catawbiense. Introgressed individuals are shown to be most common in the coldest region of the British Isles surveyed, i.e. E. Scotland, and it is suggested that introgression from R. catawbiense may confer increased frost tolerance to R. ponticum. The occurrence of the rDNA marker was not correlated with that of morphological markers indicating introgression. Correlations were found between morphological characteristics, which may result from introgression from cultivated species, such as R. maximum. Molecular evidence for the involvement of R. maximum in the ancestry of British R. ponticum was found in two accessions which resembled R. maximum. in certain morphological characteristics. It was established that another unidentified species was involved in the parentage of naturalised material. Five natural hybrid combinations amongst Turkish Rhododendron species were detected using morphological, cpDNA and nuclear rDNA markers. These were R. ponticum x R. ungernii, with introgression in both directions; R. ponticum x R. smirnovii; R. smirnovii x R. ungernii with introgression at least towards R. ungernii; R. smirnovii x R. caucasicum; and R. ponticum x R. caucasicum. The unusual characteristics of the last combination are discussed in some detail.

The gaseous messenger molecule, nitric oxide : a modulator of locomotor movements during early amphibian development

2012-10-04T09:01:29Z

Abstract: 1. The free radical gas nitric oxide (NO) is now recognised as a ubiquitous and versatile signalling molecule and the investigation of its biological roles has involved a wide range of scientific disciplines in many different species. Yet despite this, its potential roles in the development of rhythmic motor activities in vertebrates have been largely ignored. 2. Physiological experiments recording extracellular ventral root output suggest that NO is playing an inhibitory role in the swimming system of Xenopus laevis larvae, shortening the duration of swim episodes and slowing swim frequency. Nicotinamide adenine dinucleotide phosphate (NADPH)-diaphorase histochemistry labelled three populations of neurons in the brainstem, which putatively co-localise NO with the aminergic neuromodulators serotonin (5-HT) and noradranaline (NA), and the fast descending inhibitory neurotransmitter, y-aminobutyric acid (GABA). This suggests that the inhibitory role is supraspinal in origin. 3. Intracellular recordings from neurons presumed to be spinal motor neurons provide further evidence for the inhibitory influence of NO. My experiments suggest that NO potentiates both glycinergic and y-aminobutyric acid (GABA)-ergic inhibition onto spinal motor neurons. The facilitation of the release of these inhibitory transmitters is consistent with the observed effects on swim frequency and swim episode duration, respectively. Additionally, NO appears to affect membrane properties, causing a pronounced membrane potential depolarisation and a decrease in membrane conductance. This suggests that NO shuts off a resting membrane conductance. 4. NADPH-diaphorase histochemistry was subsequently applied to determine the four dimensional expression of putative nitrergic neurons in the central nervous system and related structures. The developmental sequence of staining identifies groups and subgroups of interconnected intemeurons, and provides further clues to their identity. NADPH-diaphorase labelling was also located in the eyes, skin and blood vessels, further confirming the validity of this staining technique for identirying nitric oxide synthase. 5. In the related anuran species, Rana temporaria nitric oxide donor drugs appear to have no affect on swimming, but instead reliably initiates a non-rhythmic "lashing" motor pattern similar to that elicited by dimming of the illumination. Interestingly the NADPH-diaphorase technique labelled three clusters of apparently homologous interneurons in the brainstem and additionally the inner layer of the skin was intensely stained, implicating a species-specific role for NO released from brainstem neurons.

Aspects of olfaction, social behaviour and ecology of an island population of the European rabbit (Oryctolagus cuniculus)

2012-06-20T11:50:24Z

Abstract: Olfactory behaviour in the European rabbit (Oryctolagus cuniculus) has been studied extensively under laboratory and semi-natural conditions. Results of observations on aspects of the olfactory behaviour of a free-living population of rabbits are presented. To facilitate interpretation of these results, considerable preliminary information about the population was collected. The study was conducted over a three year period on the Isle of May off the east coast of Scotland. A total of 326 rabbits were trapped and marked to permit identification in the field, and data on sex, age and social status of these individuals was collated. Data on the overall structure and fluctuations in the population are presented. The social organisation and home ranges of rabbits at four study sites throughout the three years are described. Observations indicate that the social organisation of free-living populations is more complex and variable than previous descriptions of semi-natural populations would have led us to expect. The reproductive performance of the population was investigated and intra and interwarren variations are analysed with respect to warren and group size. Results indicate an inverse relationship between warren size and reproductive success. The most frequently observed group composition (2 males, 2 females) was also the most reproductively successful. Daily and seasonal activity patterns of different age, sex and social status classes of rabbits are described. Olfactory communication was investigated by analysis of the frequency, daily and seasonal variation, and behavioural context of odour related activities performed by members of different age, sex and social status classes. The importance of using appropriate methods for the sampling of behaviour in field studies of olfaction is stressed. The present study concentrates on behaviour related to latrines; chin marking of the substrate and of conspecifics; enurination and urine squirting; and pawscraping. The results suggest that different scent products may carry similar information but analysis of variations in the frequency and context of odour deposition suggests that the deposition of scent fulfills a variety of functions.

Natural history and conservation of pirarucu, Àrapaima gigas', at the Amazonian Várzea : red giants in muddy waters

2012-06-20T10:03:43Z

Abstract: The pirarucu, Arapaima gigas (Osteoglossidae, Teleostei), an important natural resource in the Amazonian flooded forest, has been exploited for centuries and is now threatened by overfishing. The aim of this thesis, therefore, is to investigate the biology and ecology of this species so that sustainable management programmes can be put in place and the conservation of this fish ensured. Most of the research was carried out at Mamiraua Reserve, a protected area of Varzea forest in the Central Brazilian Amazon. Additional data were also recorded at the aquarium of the Amazonian Museum of Natural History, at Manaus, Brazil. A study of the main environmental aspects varzea aquatic systems, showed that the lakes at Mamiraua Reserve could be grouped into two main categories based on their limnological morphological features. The investigation of the fisheries management by local fishermen revealed that the use of traditional fishing technology was responsible for the maintenance of local stocks. However, recent technological changes had increased CPUE to alarming level. The analysis of pirarucu feeding habits demonstrated that pirarucus are specialised carnivores, living mainly on fishes. Other invertebrate species are also important in their diet. High degrees of food selectivity and strong seasonal changes in diet proved to be the most important factor affecting the seasonal growth of pirarucus. Pirarucu growth was examined by analysing the growth marks deposited on scales twice a year, at times of high ingestion of food. L was circa 2.5.m and k was about 0.18. No significant differences in growth patterns between the sexes were found. Ten cohorts or annual age classes were identified. These ranged from 0.80m to 2.25m in total length. Very high annual growth rates during the first years are replaced by moderate rates after the age of first sexual maturation. Maturity is reached when pirarucus are around 5 years of age, or about 1.65m in total length. Fecundity increases with age of females, and so does oocyte diameter. However, fecundity is divided between 4 to 6 clutches of gametes that can be used throughout the breeding season. Each clutch is spawned separately, in small batches with less than 500 eggs in average. This strategy probably protects pirarucu against the unpredictability of the environment and avoids reproductive failures - total loss of fertilised eggs - due to catastrophic events. By spawning eggs in separate batches pairs may breed again if the first attempt was not successful. Males perform parental care, protecting the nest and guarding the offspring for about 6 months. The typical red coloration of pirarucus is particularly evident in males after sexual maturation. Almost 70% of male body surface may be covered in bright red pigmentation, brighter than among females. It is proposed that red coloration signals the size and/or age of pirarucus, and is used in the context of sexual selection. Male-male competition and female choice of males are likely to be operating in this species. The information in this thesis leads to several recommendations for the conservation of pirarucus. Criteria for selection of lakes in a rotational system of fisheries management, and age-specific impact of fishing and natural mortality rates on the stock are major topics discussed. The aim is the maximisation of breeding stock and local natural recruitment. Pirarucu farming and large scale conservation actions are also considered. Suggestions for future research on the biology of conservation of pirarucus are made.

The physiology of the reproductive cycle of the powan of Loch Lomond, Coregonus lavaretus (L) (Euteleostei, Salmonidae) in relation to the deposition and mobilization of storage products

2012-06-14T13:40:43Z

Abstract: There have been numerous studies in which the reproductive cycles of teleosts have been correlated with either environmental cycles or associated physiological cycles, or both. Such correlation is seldom accurately achieved; usually because the reproductive cycle of the species concerned is lax, sometimes because only one or two factors of an integrated whole were examined. The powan of Loch Lomond, Coregonus lavaretus (L. ) (Teleostei, Salmoniformes) is the subject of a long-term study investigating its growth, in particular reproduction. This race is a freshwater glacial relict form of a boreal group, and thus has an exceptionally strictly times reproductive cycle. It thus represents an ideal subject for cyclical studies. This thesis investigates the relationship between lipid storage and the reproductive cycle and the role of thyroid gland.

The food and feeding of powan Coregonus lavaretus (L.) (Salmonidae: Coregoninae) in two Scottish lochs

2012-06-14T13:14:38Z

Abstract: The present study is mainly a descriptive account of the food and feeding of the two Scottish powan populations from Loch Lomond and Loch Eck. Quantitative and qualitative comparisons of powan diet are made. Seasonal variations of diet are determined for the two populations and some aspects of the planktivorous feeding of adult pawan in Loch Lomond are examined. The partitioning of the ingested energy into somatic and non-somatic growth is considered. Factors affecting the feeding of the two populations are discussed.

Growth processes in the two Scottish populations of powan, Coregonus lavaretus (L.) (Eateleosteia, Salmonidae)

2012-06-14T08:35:03Z

Abstract: The powan, Coregonus lavaretus (L.) is endemic to only two British waters, Loch Lomond and Loch Eck, Scotland. This thesis describes the seasonal and longer term growth processes of the two populations, concentrating on growth in length back-calculated from scales, factors affecting recruitment and mortality, reproductive cycles, and seasonal deposition and mobilisation of storage products, particularly lipid. The interrelationships of these cycles is discussed. The populations differ in their diet and duration of feeding, and it is shown that most of the inter-population differences in seasonal cycles of growth relate to these feeding differences. The Loch Eck population is the more variable. In addition to adult and immature powan, a third category is identified, termed adolescents. These are fish which are entering their first reproductive cycle. Immature and adolescent fish are analysed separately and compared with the adults. There are some differences in seasonal cycles between the juveniles and adults, mainly in relation to the presence or absence of the reproductive cycle. A preliminary histological study of the ovaries of adolescent females is carried out. Comparison of historical data with the results of the present study shows that there has been little change in the Loch Lomond powan in the past 200 years. Both lochs are coming under increasing human pressure, and conservational measures urgently need to be taken if the powan populations are to survive.

Foraging strategies, diet and competition in olive baboons

2012-06-27T12:54:58Z

Abstract: Savannah baboons are amongst the most intensively studied taxa of primates, but our understanding of their foraging strategies and diet selection, and the relationship of these to social processes is still rudimentary. These issues were addressed in a 12-month field study of olive baboons (Papio anubis) on the Laikipia plateau in Kenya. Seasonal fluctuations in food availability were closely related to rainfall patterns, with the end of the dry season representing a significant energy bottleneck. The distribution of water and of sleeping sites were the predominant influences on home range use, but certain vegetation zones were occupied preferentially in seasons when food availability within them was high. The influence of rainfall on monthly variation in dietary composition generally mirrored inter-population variation. Phytochemical analysis revealed that simplistic dietary taxonomies can be misleading in the evaluation of diet quality. Food preferences were correlated with nutrient and secondary compound content. The differences between males and females in daily nutrient intakes were smaller than expected on the basis of the great difference in body size; this was partly attributable to the energetic costs of reproduction, and possibly also to greater energetic costs of thermoregulation and lower digestive efficiency in females. A strongly linear dominance hierarchy was found amongst the adult females. Dominance rank was positively correlated with food ingestion rates and daily intakes, but not with time spent feeding or with dietary quality or diversity. In a provisioned group, high-ranking females occupied central positions, while low-ranking females were more peripheral and were supplanted more frequently. In the naturally-foraging group, the intensity of competition was related to the pattern of food distribution, but not to food quality, and was greater in the dry season than in the wet season. The number of neighbours and rates of supplanting were correlated with rank, and evidence was presented that high-rankers monopolised arboreal feeding sites.

Global analysis of cetacean line-transect surveys : detecting trends in cetacean density

2013-05-12T04:14:22Z

Abstract: Measuring the effect of anthropogenic change on cetacean populations is hampered by our lack of understanding about population status and a lack of power in the available data to detect trends in abundance. Often long-term data from repeated surveys are lacking, and alternative approaches to trend detection must be considered. We utilised an existing database of line transect survey records to determine whether temporal trends could be detected when survey effort from around the world was combined. We extracted density estimates for 25 species and fitted generalised additive models (GAMs) to investigate whether taxonomic, spatial or methodological differences among systematic line-transect surveys affect estimates of density and whether we can identify temporal trends in the data once these factors are accounted for. The selected GAM consisted of 2 parts: an intercept term that was a complex interaction of taxonomic, spatial and methodological factors and a smooth temporal term with trends varying by family and ocean basin. We discuss the trends found and assess the suitability of published density estimates for detecting temporal trends using retrospective power analysis. In conclusion, increasing sample size through combining survey effort across a global scale does not necessarily result in sufficient power to detect trends because of the extent of variability across surveys, species and oceans. Instead, results from repeated dedicated surveys designed specifically for the species and geographical region of interest should be used to inform conservation and management.

The control of mitochondrial morphology and dynamics in Arabidopis thaliana

2012-06-12T14:02:02Z

Abstract: Mitochondria are ubiquitous eukaryotic organelles which carry out a range of essential functions, most notably the production of ATP through the process of oxidative phosphorylation. While the main biochemical function of mitochondria was established over 50 years ago, the processes which control mitochondrial morphology are, at present, poorly understood. The thesis aims to add to our knowledge of the factors that control mitochondrial morphology and dynamics in the model plant species, Arabidopsis thaliana. The phenotypic characteristics of two novel mitochondrial morphology mutants, motley mitochondria I (mmtl) and network mitochondria (nmt), were examined and quantified. mmtl has an increased heterogeneity of mitochondrial plan area relative to wild-type, which is matched by a similar chloroplast phenotype. nmt exhibits a reticular mitochondrial morphology, similar to the mitochondria found in yeast and animals. Genetic mapping of the two mutant loci has established that mmtl resides on a short region of chromosome 11w, hile nmt was mapped to a small area of chromosome V. This thesis describes the identification and functional analysis of two novel orthologs of yeast and animal mitochondrial division genes. Using TDNA reverse genetics, it is shown that disruption of the dynamin-like DRP3A or BIGYIN (an Arabidopsis orthologue of yeast FISI) led to an increase in mitochondrial plan area, which is coupled with a decrease in the number of physically discrete mitochondria per cell. Finally, the morphology and behaviour of Arabiclopsis mitochondria is investigated upon the induction of cell death. Abiotic stress treatments that induce cell death led to fast and irreversible changes in mitochondrial morphology. The role of these changes, as possible early indicators of cell death, are discussed.

Changes in intra-nuclear mobility of mature snRNPs provide a mechanism for splicing defects in Spinal Muscular Atrophy

2013-05-12T04:14:24Z

Abstract: It is becoming increasingly clear that defects in RNA metabolism can lead to disease. Spinal Muscular Atrophy (SMA), a leading genetic cause of infant mortality, results from insufficient amounts of survival motor neuron (SMN) protein. SMN is required for the biogenesis of snRNPs: essential components of the spliceosome. Splicing abnormalities have been detected in models of SMA but it is unclear how lowered SMN affects the fidelity of pre-mRNA splicing. We have examined the dynamics of mature snRNPs in cells depleted of SMN and demonstrated that SMN depletion increases the mobility of mature snRNPs within the nucleus. To dissect the molecular mechanism by which SMN deficiency affects intra-nuclear snRNP mobility, we employed a panel of inhibitors of different stages of pre-mRNA processing. This in vivo modeling demonstrates that snRNP mobility is altered directly as a result of impaired snRNP maturation. Current models of nuclear dynamics predict that sub-nuclear structures, including the spliceosome, form by self-organization mediated by stochastic interactions between their molecular components. Thus, alteration of the intra-nuclear mobility of snRNPs provides a molecular mechanism for splicing defects in SMA. Description: This work was funded by the Wellcome Trust (grant ID WT078810MA)

Transcriptional regulation mediated through the conjugation and deconjugation of the small ubiquitin-like modifiers SUMO-1, SUMO-2, and SUMO-3

2012-06-11T14:25:36Z

Abstract: SUMO-1/2/3 are members of the ubiquitin-like family of protein modifiers. These proteins are covalently attached to numerous proteins in a directed and controlled manner. SUMO conjugation primarily occurs to proteins containing an exposed SUMO conjugation motif, (I, V, L, F)KxE, where x represents any amino acid. SUMO conjugation is controlled by key enzymes, a SUMO activating enzyme, SAE1/2 and a SUMO conjugating enzyme, Ubc9, which is responsible for substrate recognition, and the efficiency of this pathway can be increased by one of many SUMO ligase enzymes. This modification alters the substrate's characteristics and results in a change of state, such as stability, localisation, or activity. p300, a transcriptional co-activator, contains an evolutionary conserved tandem SUMO modification motif, located in a transcriptional repression domain. p300 was efficiently conjugated, both in vitro and in vivo, by SUMO-1/2/3, within this repression domain to both SUMO conjugation motifs. The SUMO conjugation to p300 correlated with p300 ability to repress transcription, requiring both SUMO conjugation motifs for full transcription repression activity. This repression activity was mediated through SUMO recruitment of histone deacetylase 6. Repression could be alleviated through co-expression of a SUMO-specific protease thereby suggesting a potential regulatory mechanism for transcription control of SUMO modified substrates. Despite utilising the same conjugation machinery, there remained the potential for distinct roles for the SUMO isoforms. SUMO -2/3, which form a distinct group from SUMO-1, were shown to preferentially mediate the transcription repression abilities of a number of known SUMO modifiable substrates: p300, Elk-1, and SP3. Further differences were observed in the ability of SUMO-1 and SUMO-2/3 to influence the nuclear organisation of p80 coilin.

Role of SUMO-1 modification in transcriptional activation

2012-06-11T11:34:41Z

Abstract: In unstimulated cells, the transcription factor NF-κB is held in the cytoplasm in an inactive state by IκB inhibitor proteins. Activation of NF--KB is mediated by signal induced degradation of IκBα via the ubiquitin proteasome-dependent pathway. Targeting the proteins for ubiquitin-mediated proteolysis is an irrevocable decision, and as such, the process needs to be highly specific and tightly regulated. This task is achieved by conjugation and deconjugation enzymes that act in a dynamic and coordinated mechanism. In a yeast two hybrid screen designed to identify proteins involved in IκBα signalling Ubch9 was found to interact with the N-terminal regulatory region of IκBα. Although Ubch9 is an enzyme homologous to E2 ubiquitin conjugating enzymes we have shown that is unable to form a thioester with ubiquitin but it is capable to form a thioester with the small ubiquitin-like protein SUMO- 1. To fully characterise the SUMO-1 modification reaction we have purified the proteins and cloned the genes encoding the SUMO-1 activating enzyme (SAEl/SAE2) and shown that it is homologous to enzymes involved in the activation of ubiquitin, Smt3p, the yeast SUMO-1 homologue, and Rublp/Nedd8, another ubiquitin-like protein. SUMO-1 is conjugated to target proteins by a pathway that is distinct from, but analogous to, ubiquitin conjugation. SUMO-1 was efficiently conjugated, both in vivo and in vitro, to IκBα on lysine 21, which is also utilised for ubiquitin modification. Thus, by blocking ubiquitination SUMO-1 modification acts antagonistically to generate a pool of IκBα resistant to proteasome-mediated degradation which consequently inhibits NF-κB dependent transcription activation. In view of several lines of similarity between NF-kB and p53, the involvement of SUMO-1 modification in the metabolism of the tumour supressor p53 was investigated. We have shown that p53 is modified by SUMO-1 at a single site, lysine 386 in the C-terminus of p53. Although p53 is regulated by ubiquitination, SUMO-1 and ubiquitin modification do not compete for the same lysine in p53. However, overexpression of SUMO-1 activates the transcriptional activity of wild type p53, but not K386R p53 where the SUMO-1 acceptor site has been mutated. A consensus sequence was obtained by comparison of the sequences surrounding the SUMO-1 acceptor lysine in proteins that have been shown to be modified by SUMO-1 and revealed a possible recognition site for SUMO-1 conjugation machinery. Tagging of proteins with SUMO-1 regulates transcriptional activation, either by interfering with subcellular location or with the ubiquitination pathway. The pathway may represent a novel target for drug development.

The physiological ecology and life history strategies of the nudibranch molluscs 'Adalaria proxima' (Alder & Hancock) and 'Onchidoris muricata' (Müller) (Gastropoda: Opisthobranchia)

2012-10-24T14:24:15Z

Abstract: This study investigated the physiological ecology, larval biology and population genetics of the nudibranch molluscs Adalaria proxima (A & H) and Onchidoris muricata (Müller). These two species are annual, simultaneous hermaphrodites and are ecologically very similar with the exception that A. proxima reproduces by means of pelagic lecithotrophic larvae whereas Omuricata has long-term planktotrophic larvae. The aim of the study was therefore to determine the selective pressures which resulted in the evolution of different larval types in these two species, and to ascertain the ecological and population genetic consequences thereof. Simple energy budgets comprising the major components (consumption, growth, respiration and reproduction) were constructed for laboratory populations of each species. In both A. proxima and O. muricata, feeding rate displayed an asymptotic increase with body size. Mean feeding rates of A. proxima were greater than those of comparable O. muricata individuals, and overall assimilation efficiency was higher in A. proxima than in O. muricata. This difference was reflected in the somatic growth rates which were correspondingly greater in A. proxima than in O. muricata. Net growth efficiencies were broadly comparable between the two species, however, growth of A. proxima was approximately linear over' time whilst that of O. muricata displayed a curvilinear, almost exponential, pattern. This is interpreted as demonstrating that some form of constraint (possibly feeding rate) operated on the growth rates of A. proxima but not on those of O. muricata. Respiration rates were found to be relatively constant within given animals, but significant differences were found between individuals. The allometry of respiration rate was not constant; Omuricata demonstrated a more rapid increase in respiration rate with increasing body size than did A. proxima. Individual variations in respiration rate did not reflect variations in the energy partitioned to either growth or reproduction. Reproductive patterns in the two species were dissimilar. A. proxima laid fewer spawn masses containing fewer, larger ova than those laid by O. muricata individuals. In addition, the spawning period of A. proxima was shorter than that of O. muricata (60 days and 105 days respectively). Both species exhibited a similar (proportional) degree of somatic catabolism over these periods. The consequently more rapid "degrowth" of A. proxima is interpreted as the necessary utilization of an energy resource (i. e. the soma) caused by an inability to meet the energy demands of reproduction through feeding alone. This was not the case in Oanuricata individuals which exhibited a much smaller maximum body size and were able to feed at a sufficiently rapid rate to maintain reproduction. In the latter case, the longer reproductive period served to maximise the total reproductive output. Several different measures of "Reproductive Effort" (RE) were calculated. These generally indicated that the RE of Omuricata was considerably greater than that of A. proxima. Although such differences have been used in the literature to classify the respective costs of different larval types or "reproductive strategies", the variability of the RE's obtained from the different measures used here has led to the suggestion that the general lack of association between RE and reproductive strategy which has been reported elsewhere may (partially) be attributable to the different measures of RE employed in different studies. Studies of the embryonic and larval period showed that the egg-to-juvenile period of O. muricata was approximately 50% longer than that of A. proxima. This difference was primarily attributable to the extended pelagic development of O. muricata larvae. Estimates of the degree of dispersal, and hence gene-flow, between populations of these species were tested by investigating the biochemical genetics of such populations. No data were available for O. muricata, but A. proxima populations proved to be more genetically heterogeneous than had been expected. It is therefore concluded that actual pelagic dispersal may be considerably abbreviated over that expected on the basis of larval culture data alone. A model is developed to explain the possible consequences of different egg-to-juvenile periods (which accrue from different larval types) on both the ecology of the benthic adult, and on overall energy partitioning to reproduction. However, although (probable) proximate causes and effects of the different reproductive traits exhibited by A. proxima and Oanuricata are shown, it has not been possible to determine the exact selective pressures which caused A. proxima to diverge from the ancestral "O. muricata" stock through the evolution of a pelagic lecithotrophic larva.

Characteristics of breeding passerine communities at Earlshallmuir and Tentsmuir, North-East Fife

2012-06-08T13:46:11Z

Abstract: The literature pertaining to a variety of methods for estimating the abundances of songbirds is reviewed, and the use of two of the main methods - mapping and transects - is described and discussed. The mapping method is found to be the most efficient and reliable in the context of the present study, and work elsewhere in the British Isles suggests that the method has wide applicability in the region. Various methods for describing the habitats in which birds occur are discussed. In the present study the method chosen involved measuring various parameters of the vegetation within a limited area at each of several sampling points in five study plots in North-east Fife. It proved a useful method in the habitats studied - dune grassland, commercial and semi-natural coniferous woodlands, and deciduous scrub and mature woodland - and results of the vegetation sampling are discussed in terms of habitat structure and succession, and in the relationship of this structure to the breeding bird communities. The composition of these communities in the study plots is described, as are the changes over the three breeding seasons 1979-1981, which followed on from a meteorologically "hard" winter. Over the study period there was an overall increase in the populations of all five study plots, and this increase was greatest in the poorest habitat - the dune grassland - and least in the richest habitat - the mature deciduous woodland. Using indices to compare the study plots a major difference was found between the grassland plot and all four woodland plots, amongst which the two coniferous ones were most similar. Of the more abundant bird species, Robin, Song Thrush and Coal Tit were more prevalent in coniferous habitats; Willow Warbler and Blue Tit were more prevalent in the deciduous habitats. In relation to habitat structure, the more diverse bird communities were found in the more complex habitats, and there was evidence of succession in the bird communities concomitant with habitat succession. The present study is one of very few in Europe involving woodland habitats especially of a commercial nature near sea-level, and it was found that the four woodland study plots were rich in terms of the diversities and densities of their passerine breeding populations when compared with other European studies.

Studies on the preservation of flowers

2012-06-08T11:47:05Z

Abstract: A known method for the preservation of green foliage was adapted in order to preserve floral tissues, retaining the colour and texture, thereby providing a method suitable for the preservation of whole flowers. Initially, the effects of the existing foliage preservation process on floral tissues were studied and the resulting problems of limp sticky petals and colour loss were identified. Subsequently, with a knowledge of basic plant anatomy and of the properties of the main floral pigments, the anthocyanins, a series of experiments on petals and whole flowers were carried out in an attempt to rectify these problems and to incorporate the remedies into a method for preserving whole flowers. The problem of improving the texture and firmness of flower heads was tackled by investigating the effects of adding bulking or setting ingredients to the process fluid and establishing their optimum concentrations. In the case of flower colour, the addition of acid was required in order to maintain the bright anthocyanin colours and a range of acids was investigated. Furthermore, since it is known that in nature the anthocyanin pigments are stabilised by metal ions and copigments, the use of these agents in the preservation process was also considered. This empirical work was then validated by confirming the identity of the main pigments involved and by studying various aspects of the new preservation process. Factors examined included acid concentration, temperature, solvent composition and the addition of metal ions and copigments to solutions of petal extracts containing anthocyanin pigments. Physical changes resulting from processing, including process fluid content and the moisture absorption properties of processed petals were also measured. Finally, the application of a selection of coating materials was assessed in an attempt to increase the life span of the processed flowers by providing extra protection against environmental stresses.

Systematics and biogeography of Myricaceae

2012-06-08T10:56:53Z

Abstract: Two molecular phylogenetic studies were undertaken to examine relationships within Myricaceae. Analyses of DNA sequences of the plastid rbcL gene, trnL-Fregion and nuclear ITS region showed the family to be monophyletic. In all analyses Canacomyrica, a monotypic genus endemic to New Caledonian that bears several distinctive features such as staminodes in the female flowers, fell into a well- supported clade sister to the rest of Myricaceae. Phylogenetic analyses of ITS and trnL-F sequence data, representing all genera and subgeneric groups, were undertaken using maximum parsimony and Bayesian methods. The following relationships were strongly supported: (Canacomyrica (Comptonia (Myrica, Morella))). The clade containing all species formerly considered to comprise Myrica s.l. was split into two strongly supported clades corresponding to Myrica s.s. and Morella; this finding strengthens the argument for recognition of these as separate genera. Within Morella, two clades corresponded to previously recognized subgenera. Molecular dating analyses were performed using Penalized Likelihood. Close correlations between lineage-specific diversification and major orogenic or climatic events were inferred. This study suggests that much of the diversity in Morella arose during the Neogene and seed-dispersal by birds has been a significant factor in determining the modem distribution. A study of the conservation status of Canacomyrica was conducted using field observations and data from herbarium specimens. This species was found to occur in just eleven fragmented localities: six outside protected areas and three threatened by mining or bush fires. IUCN Red List status of Endangered was recommended. The morphology and ecology of Canacomyrica was studied to enhance knowledge of this poorly known species and provide comparative data for use in a study of the morphology of the entire family. A new classification scheme with keys was presented including, for the first time, Canacomyrica. New combinations in Morella were recommended.

The structure and function of microphytobenthic biofilms

2012-08-07T14:08:15Z

Abstract: Microphytobenthos are the dominant primary producers on estuarine mudflats playing a key role in the functioning of the ecosystem. Studies into microphytobenthic ecology have previously been limited by scale but the advent of fine scale analysis techniques (gm) as well as non-destructive sampling has enabled the system to be examined at a level not previously possible. This study examined the formation, structure and function of microphytobenthic biofilms using non-destructive (remote sensing by PAM fluorescence; fibreoptic light microprofiling) and destructive (cryo-freezing and Low temperature scanning electron microscopy) sampling. Many microphytobenthic organisms are motile and have evolved complex migratory strategies. Microphytobenthic migratory patterns are widely described but much remains to be elucidated about the controlling factors. The fluorescence parameter F015 (minimum fluorescence yield after 15 minutes dark adaptation) was used to monitor short-term changes in biomass at the sediment surface. Light, tidal state, endogeny and combinations thereof were all shown to control migration, demonstrating that predictable migratory rhythms cannot be assumed. Microscale sectioning showed that chlorophyll a was always concentrated in the top 400 gm (the photosynthetically active biomass). Clear migratory patterns were not detected using microscale sectioning therefore indicating that migration occurs over a scale < 400gm. Despite no changes in the chlorophyll a content in the surface layers, LTSEM analysis demonstrated diurnal taxonomic shifts providing circumstantial evidence that microphytobenthic cells sub-cycle at the sediment surface to optimise fitness. The light extinction co-efficient (k) of microphytobenthic biofilms significantly vaned with site, assemblage and also over time. 90% of the surface PPFD had always been attenuated by 400, and in many cases before 200. Traditional microphytobenthic primary productivity models do not account for changes in the spatial and temporal distribution of biomass or light attenuation and therefore their applicability to the real situation may be limited.

Environmental timing and control of reproduction in the powan of Loch Lomond 'Coregonus lavaretus (L) (Teleostei)' in relation to its pineal organ

2012-06-06T09:13:21Z

Abstract: The reproductive cycle of Coregonus lavaretus (L. ) in Loch Lomond was investigated by monthly sampling. The stages of the cycle occurred at the same time each year and were precisely timed. The environment followed a regular pattern which varied seasonally and was repeated annually. Spawning synchrony within the population during the short breeding period may be in response to lunar phases. A qualitative echosounding survey was made. The spatial distribution of the fish is probably related to their feeding behaviour and was mainly pelagic in summer and benthic in winter. Diel vertical migrations were recorded at dawn and dusk and appeared to be related to negative solar altitudes. The fish occurred at the surface during the night and persisted with their diel vertical migrations when feeding behaviour was benthic. The regulation of the reproductive cycle in the common sole Solea solea was investigated. The timing of spawning is ultimately determined by sea temperature, and spawning synchrony within the population is probably achieved in the initiation of exogenous vitellogenesis by a unified response within the breeding population to a stimulatory photoperiod. In both Solea solea and Coregonus lavaretus, initiation of exogenous vitellogenesis occurred during a rapid rise in the condition of the fish. The photosensitivity of the reproductive system may possibly be linked to a threshold condition. The pineal organ of Coregonus lavaretus is typically salmonid and the convoluted epithelium contained photoreceptors, interstitial cells, and neurones. The interstitial cells gave rise to processes which extended into the perivascular space. Photoreceptor cells synapsed with neurones, photoreceptor cells (lateral processes) and possibly other cell types. The results suggest that the pineal organ functions as a photoreceptor.

Some aspects of the anatomy of the alimentary canal of the lesser octopus, Eledone cirrhosa (Lamarck 1817), with special reference to the nervous system

2012-06-14T08:37:25Z

Abstract: The modern cephalopod molluscs, particularly the octopods, are highly developed macrophageous predators which have a pronounced ability to learn. Striking resemblances are found between these animals and the vertebrates, particularly the fish. The study of cephalopods therefore provides an opportunity to examine systems which are composed of structural units common to molluscs but which may be similar in function and performance to those of vertebrates. This investigation concerns the alimentary canal and its innervation in the lesser octopus Eledone cirrhosa. Detailed anatomical investigation shows the alimentary canal of E. cirrhosa to be very similar to that of the better known Octopus vulgaris. Current concepts of the functions of the alimentary organs are discussed utilizing data from both E. cirrhosa and O. vulgaris. Silver staining reveals a basic pattern of innervation in the alimentary organs. Large nerve trunks running in the external collagenous layer give rise to a nerve plexus within the circular muscle. The longitudinal muscle plexus arises from branches of the circular muscle plexus or direct from the nerves of the external layer, Nerves of both plexuses contact muscle fibres in an 'en passant' manner. Fibres run out from the longitudinal muscle to the subepithelium, where they are observed associated with muscle fibres and beneath the epithelial basal lamina. Good evidence for fibres crossing into the epithelium was observed only in the cuticularized regions of the digestive tract. The digestive gland ducts differ from this pattern in the very large numbers of major nerves seen in their external and muscular regions. Outwith the alimentary ganglia nerve cells are only regularly observed within the major intestinal nerves. Receptor like cells were also repeatedly observed only in the posterior intestine. These results axe compared with data from O. vulgaris and the physiological evidence for the presence of receptors. The blood vessels of the alimentary canal are innervated at all levels. The distribution of other densely staining cells is reported. Evidence for the presence of particular neurotransmitters within the alimentary canal and alimentary nerve centres is reviewed. Fluorescence histochemistry shows that at least two types of nerves are present in the alimentary wall. The majority axe aminergic (including those associated with blood vessels and some sphincters), as the pattern of fluorescent nerves is predominantly that shown by silver studies. However, fluorescent nerves decrease and then disappear anteriorly from the crop/oesophageal sphincter and posteriorly from the mid-intestine. The stomach has fluorescent nerves, other than those associated with blood vessels. Fluorescent fibres enter the gut via the sympathetic and possibly the digestive gland duct nerves. Non-fluorescent fibres enter via the atrio-rectal nerves and from the gastric ganglion. The fluorescence is ascribed to catecholamines as no evidence of 5HT was obtained, Specific fluorescence was also observed in some cells of the subepithelium and the external region. These results are discussed with reference to available physiological data. The anterior intestine was the representative region chosen for fine structural studies. These show the alimentary muscles to be the same basic type (cross or pseudo-striated) as that found in cephalopod somatic or heart muscle. Three types of myomuscular and neuromuscular junctions axe described. The presence of mineralized concretions (spherites) in the external layer of the intestine, together with the complex relations of its epithelial cells and heavy vascularization suggest a secondary function of mineral and/or water balance for this organ. These results are discussed. Finally, a pathological condition affecting the octopuses during this study is described.

Parasitological studies : on the structure, biology and taxonomy of Nucellicola kilrymontis gen. et. sp., nov., (Crustacea : Copepoda) parasitic in Nucella lapillus (L.), (Gastropoda : Prosobranchia)

2012-06-04T13:16:04Z

Transcriptional regulation in skeletal muscle of zebrafish in response to nutritional status, photoperiod and experimental selection for body size

2012-05-23T15:38:11Z

Abstract: In the present study, the ease of rearing, short generation time and molecular research tools available for the zebrafish model (Danio rerio, Hamilton) were exploited to investigate transcriptional regulation in relation to feeding, photoperiod and experimental selection. Chapter 2 describes transcriptional regulation in fast skeletal muscle following fasting and a single satiating meal of bloodworms. Changes in transcript abundance were investigated in relation to the food content in the gut. Using qPCR, the transcription patterns of 16 genes comprising the insulin-like growth factor (IGF) system were characterized, and differential regulation between some of the paralogues was recorded. For example, feeding was associated with upregulation of igf1a and igf2b at 3 and 6h after the single-meal was offered, respectively, whereas igf1b was not detected in skeletal muscle. On the other hand, fasting triggered the upregulation of the igf1 receptors and igfbp1a/b, the only binding proteins whose transcription was responsive to a single-satiating meal. In addition to the investigation of the IGF-axis, an agnostic approach was used to discover other genes involved in transcriptional response to nutritional status, by employing a whole-genome microarray containing 44K probes. This resulted in the discovery of 147 genes in skeletal muscle that were differentially expressed between fasting and satiation. Ubiquitin-ligases involved in proteasome-mediated protein degradation, and antiproliferative and pro-apoptotic genes were among the genes upregulated during fasting, whereas satiation resulted in an upregulation of genes involved in protein synthesis and folding, and a gene highly correlated with growth in mice and fish, the enzyme ornithine decarboxylase 1. Zebrafish exhibit circadian rhythms of breeding, locomotor activity and feeding that are controlled by molecular clock mechanisms in central and peripheral organs. In chapter 3 the transcription of 17 known clock genes was investigated in skeletal muscle in relation to the photoperiod and food content in the gut. The hypothesis that myogenic regulatory factors and components of the IGF-pathway were clock-controlled was also tested. Positive (clock1 and bmal1 paralogues) and negative oscillators (cry1a and per genes) showed a strong circadian pattern in skeletal muscle in anti-phase with each other. MyoD was not clock-controlled in zebrafish in contrast to findings in mice, whereas myf6 showed a circadian pattern of expression in phase with clock and bmal. Similarly, the expression of two IGF binding proteins (igfbp3 and 5b) was circadian and in phase with the positive oscillators clock and bmal. It was also found that some paralogues responded differently to photoperiod. For example, clock1a was 3-fold more responsive than clock1b. Cry1b did not show a circadian pattern of expression. These patterns of expression provide evidence that the molecular clock mechanisms in skeletal muscle are synchronized with the molecular clock in central pacemaker organs such as eyes and the pineal gland. Using the short generation time of zebrafish the effects of selective breeding for body size at age were investigated and are described in chapter 4. Three rounds of artificial selection for small (S-lineage) and large body size (L-lineage) resulted in zebrafish populations whose average standard length were, respectively, 2% lower and 10% higher than an unselected control lineage (U-lineage). Fish from the L-lineage showed an increased egg production and bigger egg size with more yolk, possibly contributing to the larger body size observed in the early larval stage (6dpf) of fish from this lineage. Fish from S- and L-lineage exposed to fasting and refeeding showed very similar feed intake, providing evidence that experimental selection did not cause significant changes in appetite control. Investigation of the expression of the IGF-axis and nutritionally-response in skeletal muscle after fasting and refeeding revealed that the pattern of expression was not different between the selected lineages, but that a differential responsiveness was observed in a limited number of genes, providing evidence that experimental selection might have changed the way fish allocate the energy acquired through feeding. For example, a constitutive higher expression of igf1a was recorded in skeletal muscle of fish from the L-lineage whereas igfbp1a/b transcripts were higher in muscle of fish from the S-lineage. These findings demonstrate the rapid changes in growth and transcriptional response in skeletal muscle of zebrafish after only three rounds of selection. Furthermore, it provides evidences that differences in growth during embryonic and larval stages might be related to higher levels of energy deposited during oogenesis, whereas differences in adult fish were better explained by changes in energy allocation instead of energy acquisition. In chapter 5 the main findings made during this study and their impact on the literature are discussed.

Inbreeding and selection on sex ratio in the bark beetle Xylosandrus germanus

2013-05-12T04:14:16Z

Abstract: Background: Local Mate Competition (LMC) theory predicts a female should produce a more female-biased sex ratio if her sons compete with each other for mates. Because it provides quantitative predictions that can be experimentally tested, LMC is a textbook example of the predictive power of evolutionary theory. A limitation of many earlier studies in the field is that the population structure and mating system of the studied species are often estimated only indirectly. Here we use microsatellites to characterize the levels of inbreeding of the bark beetle Xylosandrus germanus, a species where the level of LMC is expected to be high. Results: For three populations studied, genetic variation for our genetic markers was very low, indicative of an extremely high level of inbreeding (F-IS = 0.88). There was also strong linkage disequilibrium between microsatellite loci and a very strong genetic differentiation between populations. The data suggest that matings among non-siblings are very rare (3%), although sex ratios from X. germanus in both the field and the laboratory have suggested more matings between non-sibs, and so less intense LMC. Conclusions: Our results confirm that caution is needed when inferring mating systems from sex ratio data, especially when a lack of biological detail means the use of overly simple forms of the model of interest.

A general discrete-time modeling framework for animal movement using multi-state random walks

2013-05-12T03:36:19Z

Abstract: Recent developments in animal tracking technology have permitted the collection of detailed data on the movement paths of individuals from many species. However, analysis methods for these data have not developed at a similar pace, largely due to a lack of suitable candidate models, coupled with the technical difficulties of fitting such models to data. To facilitate a general modeling framework, we propose that complex movement paths can be conceived as a series of movement strategies among which animals transition as they are affected by changes in their internal and external environment. We synthesize previously existing and novel methodologies to develop a general suite of mechanistic models based on biased and correlated random walks that allow different behavioral states for directed (e.g., migration), exploratory (e.g., dispersal), area-restricted (e.g., foraging), and other types of movement. Using this “tool-box” of nested model components, multi-state movement models may be custom-built for a wide variety of species and applications. As a unified state-space modeling framework, it allows the simultaneous investigation of numerous hypotheses about animal movement from imperfectly observed data, including time allocations to different movement behavior states, transitions between states, the use of memory or navigation, and strengths of attraction (or repulsion) to specific locations. The inclusion of covariate information permits further investigation of specific hypotheses related to factors driving different types of movement behavior. Using reversible jump Markov chain Monte Carlo methods to facilitate Bayesian model selection and multi-model inference, we apply the proposed methodology to real data by adapting it to the natural history of the grey seal (Halichoerus grypus) in the North Sea. Although previous grey seal studies tended to focus on correlated movements, we found overwhelming evidence that bias towards haul-out or foraging locations better explained seal movement than simple or correlated random walks. Posterior model probabilities also provided evidence that seals transition among directed, area-restricted, and exploratory movements associated with haul-out, foraging, and other behaviors. With this intuitive framework for modeling and interpreting animal movement, we believe the development and application of bespoke movement models will become more accessible to ecologists and non-statisticians.

The influence of the freshwater environment and the biological characteristics of Atlantic salmon smolts on their subsequent marine survival

2013-05-12T04:13:48Z

Abstract: Atlantic salmon have declined markedly in the past 20-30 years throughout their range. Much of the focus for this decline has been on increased mortality during the marine phase of the life cycle. However, marine mortality does not operate independently of factors acting in freshwater and the biological characteristics of smolts migrating to sea. Over recent decades, juvenile salmon in many rivers have grown faster and migrated to sea at a younger age, and thus typically smaller. This has shortened the generation time for many individuals, and may dampen the impact of increased marine mortality, assuming expected higher in-river survival prior to smolting is not outweighed by increased mortality of smaller smolts at sea. Over the same period, smolt run-timing across the geographic range has been occurring earlier, at a rate of almost three days per decade, on average. This has given rise to growing concerns about smolts potentially missing the optimum environmental migration “window”, the timing of which may also be changing. Contaminants and other factors operating in freshwater also impact on smolt quality with adverse consequences for their physiological readiness for life at sea. Given that managers have very limited ability to influence the broad scale factors limiting salmon survival at sea, it is vital that freshwater habitats are managed to both maximise smolt output and to minimise the impact of factors acting in freshwater which may compromise salmon once they migrate to sea.

Biosonar performance of foraging beaked whales (Mesoplodon densirostris)

2013-05-12T04:13:29Z

Abstract: Toothed whales (Cetacea, odontoceti) emit sound pulses to probe their surroundings by active echolocation. Noninvasive, acoustic Dtags were placed on deep-diving Blainville's beaked whales (Mesoplodon densirostris) to record their ultrasonic clicks and the returning echoes from prey items, providing a unique view on how a whale operates its biosonar during foraging in the wild. The process of echolocation during prey capture in this species can be divided into search, approach and terminal phases, as in echolocating bats. The approach phase, defined by the onset of detectable echoes recorded on the tag for click sequences terminated by a buzz, has interclick intervals (ICI) of 300-400 ms. These ICIs are more than a magnitude longer than the decreasing two-way travel time to the targets, showing that ICIs are not given by the two-way-travel times plus a fixed, short lag time. During the approach phase, the received echo energy increases by 10.4((+/-)2) dB when the target range is halved, demonstrating that the whales do not employ range compensating gain control of the transmitter, as has been implicated for some bats and dolphins. The terminal/buzz phase with ICIs of around 10 ms is initiated when one or more targets are within approximately a body length of the whale (2-5 m), so that strong echo returns in the approach phase are traded for rapid updates in the terminal phase. It is suggested that stable ICIs in the search and approach phases facilitate auditory scene analysis in a complex multi-target environment, and that a concomitant low click rate allows the whales to maintain high sound pressure outputs for prey detection and discrimination with a pneumatically driven, bi-modal sound generator. demonstrating that the whales do not employ range-compensating gain control of the transmitter, as has been implicated for some bats and dolphins. The terminal/buzz phase with ICIs of around 10 ms is initiated when one or more targets are within approximately a body length of the whale (2-5 m), so that strong echo returns in the approach phase are traded for rapid updates in the terminal phase. It is suggested that stable ICIs in the search and approach phases facilitate auditory scene analysis in a complex multi-target environment, and that a concomitant low click rate allows the whales to maintain high sound pressure outputs for prey detection and discrimination with a pneumatically driven, bi-modal sound generator.

A digital acoustic recording tag for measuring the response of wild marine mammals to sound

2013-05-12T04:11:40Z

Abstract: Definitive studies on the response of marine mammals to anthropogenic sound are hampered by the short surface time and deep-diving lifestyle of many species. A novel archival tag, called the DTAG, has been developed to monitor the behavior of marine mammals, and their response to sound, continuously throughout the dive cycle. The tag contains a large array of solid-state memory and records continuously from a built-in hydrophone and suite of sensors. The sensors sample the orientation of the animal in three dimensions with sufficient speed and resolution to capture individual fluke strokes. Audio and sensor recording is synchronous so the relative timing of sounds and motion can be determined precisely. The DTAG has been attached to more than 30 northern right whales (Eubalaena glacialis) and 20 sperm whales (Physeter macrocephalus) with recording duration of up to 12 h per deployment. Several deployments have included sound playbacks to the tagged whale and a transient response to at least one playback is evident in the tag data.

The maintenance of genetic variation due to asymmetric gene flow in dendritic metapopulations

2013-05-12T04:13:37Z

Abstract: Dendritic landscapes can have ecological properties that differ importantly from simpler spatial arrangements of habitats. Most dendritic landscapes are structured by elevation, and therefore, migration is likely to be directionally biased. While the population‐genetic consequences of both dendritic landscape arrangements and asymmetric migration have begun to be studied, these processes have not been considered together. Simple conceptual models predict that if migration into branch (headwater) populations is limited, such populations can act as reservoirs for potentially unique alleles. As a consequence of the fact that dendritic landscapes have, by definition, more branches than internal habitat patches, this process may lead to the maintenance of higher overall genetic diversities in metapopulations inhabiting dendritic networks where migration is directionally biased. Here we begin to address the generality of these simple predictions using genetic models and a review of empirical literature. We show, for a range of demographic parameters, that dendritic systems with asymmetric migration can maintain levels of genetic variation that are very different, sometimes very elevated, compared with more classical models of geographical population structure. Furthermore, predicted patterns of genetic variation within metapopulations—that is, stepwise increases in genetic diversity at nodes—do occur in some empirical data.

What does it mean to experience paediatric depression?: the ethics of mental health diagnosis and treatment in children and adolescents

2012-05-28T14:19:42Z

Abstract: This thesis explores the ethics of mental health diagnosis and treatment in children and adolescents through a collection of different perspectives based on literature analysis and interviews with practising clinicians. Compared to other medical fields, paediatric psychiatry is considerably novel; it has only recently become a medical specialty and differs from other medicine by involving both biological and psychological aspects of care. Recently, human brain development has become better understood, but the effect of mental illness on the trajectory of development is only just beginning to be studied. Despite this limited understanding, children who may not have been diagnosed for psychiatric disorders in the past are increasingly receiving off-label prescription treatments. This trend may be due to improved sensitivity of diagnostic practices as well as the medicalisation of normal, classifying previously healthy borderline behaviours as pathological. What are the implications of increasing medicalisation? How are child-specific diagnoses and treatment plans determined? I focus on identity development in young people with mental disorders, specifically depression, and try to explain the effects of labelling and medication on that development. Also the physiological impact of psychopathology and psychotropic treatment on neurodevelopment is examined, as well as the lack of long-term clinical data for drug treatment in children. Though the key source material has been from literature in the US and UK, the thesis broadens to an international perspective with a global look at the relationship between culture and paediatric psychiatry practices. Finally, mental health care professionals were interviewed to provide a clinical perspective to supplement the literature analysis. By drawing historical, philosophical, psychological, biological, cultural, and professional perspectives together in this novel way, ethical considerations necessary in the psychiatric care of paediatric patients are given a more thorough understanding, and a framework for assessing these considerations is presented through a focused interdisciplinary lens.

Structural studies of Vibrio cholerae quorum sensing proteins

2012-04-19T11:49:50Z

Abstract: The spread of cholera is always associated with contaminated food or water and this is the reason this disease has been endemic in developing countries for centuries due to their lack of proper sanitation facilities and poor or no infrastructure for sewage systems. Cholera can spread quickly and sporadically after any natural disaster that destroys the sewage system or safe drinking water supply of both developed and undeveloped countries. In Southeast Asia in December 2004 and in Pakistan and Haiti 2010, cholera outbreaks followed the natural disasters; with most of the cholera victims being children. Although it is known that the best way to prevent cholera outbreak is the development of the infrastructure, provision of a safe drinking water supply and proper sanitation, this is a very long-term process, and most of the developing countries cannot afford such improvements. These situations can be made worse by natural disasters. Therefore there is a pressing need for the development of a cholera vaccine and there have been numerous research projects working towards this end for several decades. A few of them have been successful to date but because of the severe side effects and narrow range of protection, more effective and wider range vaccine development is still ongoing. In this study, crystallographic and enzymatic studies have been carried out on several novel proteins involved in the control of the production of the factors required for quorum sensing. Quorum sensing is a process in which bacterial cells communicate among themselves by the synthesis, release and detection of small chemical compounds called autoinducers. In this work, structural analysis was carried out on proteins involved in the synthesis and detection of the major autoinducer of Vibrio cholerae, named CAI-1. The crystal structure of CqsA involved in CAI-1 synthesis has been successfully solved and its enzymatic properties have been characterized. The structure of one domain of the cytoplasmic region of the CAI-1 receptor CqsS was also elucidated, and other domains were expressed. The crystal structure of another enzyme (VCA0859, an aldo-keto reductase) thought to have been involved in the synthesis of CAI-1 was also determined. Another protein named VCA0939 was also studied, due to its importance in biofilm development, and its ability to control quorum-sensing in an alternative pathway in the mutated version of pathogenic strains of V. cholerae that were responsible for the seventh cholera pandemic. The aim of this project was to understand the three dimensional structure of some proteins that are involved in quorum sensing and control of the expression of virulence genes for the pathogenesis of V. cholerae. Understanding the three dimensional structure of the proteins and the mode of autoinducer binding to its specific receptor could be highly valuable in the development of a chemical compound that could lead to the discovery of a novel drug with the ability to target cross species specification.

Functional design and use of acoustic signals produced by killer whales (Orcinus orca)

2012-04-18T16:07:57Z

Abstract: This study aimed to investigate possible functions of the sounds produced by herring-eating killer whales in the Northeast Atlantic. In this study, I investigated the whistle repertoire of killer whales, which had previously only been studied in British Columbia, where it appeared to be restricted to the audible range. However, I show that high frequency whistles (> 17 kHz) were detected in Northeast Atlantic populations but not in Northeast Pacific populations. These results indicated substantial intraspecific variation in whistle production in killer whales. Little variation was observed in high frequency whistles recorded from three different sites in the Northeast Atlantic, suggesting this signal has a similar function across locations. The estimated active space of high frequency whistles and burst-pulse calls suggested that these are short-range signals used for within-group communication. Source levels of burst-pulse calls were lower than what was previously described in British Columbia, which possibly reflected the fact that these sounds do not need to propagate far because distances between group members are generally short. Calls, high frequency whistles and herding calls produced at different depths did not appear to suffer effects due to increased pressure, such as changing frequency or duration characteristics. Feeding appeared to take place below 10 m of depth, as suggested by the localisation of depth of production of feeding-related sounds. These depths were consistent with those at which tailslaps were produced in Dtags attached to individual whales. Feeding periods were characterised by deep diving, increased sound production and highly non-directional movement. These findings suggested that killer whales in a herring spawning ground use a feeding strategy different from carousel feeding used in herring overwintering grounds. These findings showed that Northeast Atlantic killer whales have a different sound repertoire to other populations, and suggested that they may employ different feeding strategies depending on prey behaviour.

Ants as flower visitors : floral ant-repellence and the impact of ant scent-marks on pollinator behaviour

2012-04-04T11:33:24Z

Abstract: As flower visitors, ants rarely benefit a plant, commonly disrupting pollination by deterring other flower visitors, or stealing nectar. This thesis examines three aspects of ant-flower interactions, focusing on the occurrence of floral traits that prevent disruption of pollination and a novel means by which ants may influence pollinator behaviour. To assess which types of plant species possess ant-repelling floral traits I carried out a survey of 49 Neotropical plant species. Around a third of these species were repellent to the common generalist ant Camponotus novograndensis (Formicinae). This repellence was positively correlated with large nectar volumes within individual flowers. It appears that there has been selection for floral ant-repellence as a defence against ant thieves in plant species that invest in large volumes of nectar. In some cases these repellent traits were effective against a wide range of ant species. However, in no plant species were predacious ants particularly repelled, indicating that there may be little selective pressure on non-ant-plants to defend potential pollinators from aggressive ants. To investigate the importance of coevolution in determining the effectiveness of ant-repellents, a small but diverse range of Mediterranean plant species were tested with the invasive nectar thieving ant Linepithema humile (Dolichoderinae) and the native but non-nectar thieving ant Messor bouvieri (Myrmecinae). Responses of both ant species to floral traits were very similar. The ability of some plants to restrict access to ant species with which they have no evolutionary history may help to reduce the impact invasive species, as nectar thieves, have on plant-pollinator interactions. It is reported that flowers recently visited by bees and hoverflies may be rejected for a period of time by subsequent bee visitors through the detection of scent-marks. Nectar-thieving ants could potentially influence the foraging decisions of bees in a similar way if they come to associate ant trail pheromones or footprint hydrocarbons with poor reward levels. However, my empirical work found no differences were found in bee visitation behaviour between flowers of Digitalis pupurea (Plantaginaceae), Bupleurum fruticosum (Apiaceae) or Brassica juncea (Brassicaceae) that had been in contact with ants and control flowers. Ant-attendance at flowers of these species may not reduce reward levels sufficiently to make it worthwhile for bees to incorporate ant scent-marks into foraging decisions. Investigations like these into the interactions between ants, flowers and other flower visitors are essential if we hope to understand the part ants play in pollination ecology, and determine how ants have helped shape floral evolution.

Willin as a novel 4.1 ezrin radixin moesin (FERM) domain protein in the mammalian hippo signalling pathway

2012-04-09T13:58:15Z

Abstract: The Salvador/Warts/Hippo (Hippo) pathway deﬁnes a novel signalling cascade regulating cell contact inhibition, organ size control, cell growth, proliferation, apoptosis and cancer development in mammals. The Hippo pathway was initially utilised in D. melanogaster, where the Expanded protein acts in the Hippo signalling cascade to control organ size. Willin is the proposed human orthologue of Expanded and the aim of this thesis is to investigate whether willin can activate the mammalian Hippo signalling pathway. Ectopic willin expression causes an increase in phosphorylation of the core Hippo signalling pathway components MST1/2, LATS1 and YAP, an effect which can be antagonised by ezrin. In MCF10A cells, willin over-expression antagonises a YAP-induced epithelial-to-mesenchymal transition via the N- terminal FERM (Four-point-one Ezrin Radixin Moesin) domain of willin. Preliminary results show that willin is expressed within the sciatic nerve of rat and mice, and within the neuromast cells in the zebraﬁsh; suggesting that willin and the Hippo pathway may play a vital role in the developmental regulation within the peripheral nervous system. To conclude, willin inﬂuences Hippo signalling activity by activating the core Hippo pathway kinase cassette in mammalian cells. Description: Electronic version excludes material for which permission has not been granted by the rights holder

The desaturase gene family : an evolutionary study of putative speciation genes in 12 species of Drosophila

2012-04-06T08:55:32Z

Abstract: The formation and persistence of species are the subject of much debate among biologists. Many species of Drosophila are behaviourally isolated, meaning that heterospecific individuals are not attracted to one another and do not interbreed. Often, this behavioural isolation is at least in part due to differences in pheromonal preference. Drosophila pheromones are long-chain cuticular hydrocarbons (CHCs). Desaturases are enzymes that are important for the production of CHCs. This thesis investigates the evolution of the gene family across 12 species of Drosophila. Desaturase genes were located in all species. Some genes, those that have previously been shown to have important roles in pheromonal communication, have experienced duplication and loss in several species. Two previously undiscovered duplicates were identified. Generally the desaturase gene family is governed by purifying selection, although following duplication these constraints are relaxed and in some cases duplicated genes show compelling evidence of positive selection. One of the loci under positive selection, the novel duplicate desat1b of the obscura group, was found to have a sex-biased expression pattern and alternative splicing in its 5′ UTR. In RNAi knock-down experiments of desaturase gene function in D. melanogaster, several desaturases were shown to affect CHC profiles of males and females, including some that were previously unlinked to CHC production.

Deadly diving? Physiological and behavioural management of decompression stress in diving mammals

2013-05-12T04:12:08Z

Abstract: Decompression sickness (DCS; 'the bends') is a disease associated with gas uptake at pressure. The basic pathology and cause are relatively well known to human divers. Breath-hold diving marine mammals were thought to be relatively immune to DCS owing to multiple anatomical, physiological and behavioural adaptations that reduce nitrogen gas (N-2) loading during dives. However, recent observations have shown that gas bubbles may form and tissue injury may occur in marine mammals under certain circumstances. Gas kinetic models based on measured time-depth profiles further suggest the potential occurrence of high blood and tissue N-2 tensions. We review evidence for gas-bubble incidence in marine mammal tissues and discuss the theory behind gas loading and bubble formation. We suggest that diving mammals vary their physiological responses according to multiple stressors, and that the perspective on marine mammal diving physiology should change from simply minimizing N-2 loading to management of the N-2 load. This suggests several avenues for further study, ranging from the effects of gas bubbles at molecular, cellular and organ function levels, to comparative studies relating the presence/absence of gas bubbles to diving behaviour. Technological advances in imaging and remote instrumentation are likely to advance this field in coming years.

Temporal turnover and the maintenance of diversity in ecological assemblages

2013-05-12T04:04:04Z

Abstract: Temporal variation in species abundances occurs in all ecological communities. Here, we explore the role that this temporal turnover plays in maintaining assemblage diversity. We investigate a three-decade time series of estuarine fishes and show that the abundances of the individual species fluctuate asynchronously around their mean levels. We then use a time-series modelling approach to examine the consequences of different patterns of turnover, by asking how the correlation between the abundance of a species in a given year and its abundance in the previous year influences the structure of the overall assemblage. Classical diversity measures that ignore species identities reveal that the observed assemblage structure will persist under all but the most extreme conditions. However, metrics that track species identities indicate a narrower set of turnover scenarios under which the predicted assemblage resembles the natural one. Our study suggests that species diversity metrics are insensitive to change and that measures that track species ranks may provide better early warning that an assemblage is being perturbed. It also highlights the need to incorporate temporal turnover in investigations of assemblage structure and function.

Ancient homeobox gene loss and the evolution of chordate brain and pharynx development : deductions from amphioxus gene expression

2013-05-12T03:34:18Z

Abstract: Homeobox genes encode a large superclass of transcription factors with widespread roles in animal development. Within chordates there are over 100 homeobox genes in the invertebrate cephalochordate amphioxus and over 200 in humans. Set against this general trend of increasing gene number in vertebrate evolution, some ancient homeobox genes that were present in the last common ancestor of chordates have been lost from vertebrates. Here, we describe the embryonic expression of four amphioxus descendants of these genes—AmphiNedxa, AmphiNedxb, AmphiMsxlx and AmphiNKx7. All four genes are expressed with a striking asymmetry about the left–right axis in the pharyngeal region of neurula embryos, mirroring the pronounced asymmetry of amphioxus embryogenesis. AmphiMsxlx and AmphiNKx7 are also transiently expressed in an anterior neural tube region destined to become the cerebral vesicle. These findings suggest significant rewiring of developmental gene regulatory networks occurred during chordate evolution, coincident with homeobox gene loss. We propose that loss of otherwise widely conserved genes is possible when these genes function in a confined role in development that is subsequently lost or significantly modified during evolution. In the case of these homeobox genes, we propose that this has occurred in relation to the evolution of the chordate pharynx and brain.

Sexual selection on song and cuticular hydrocarbons in two distinct populations of Drosophila montana

2012-12-12T13:18:32Z

Abstract: Sexual selection has the potential to contribute to population divergence and speciation. Most studies of sexual selection in Drosophila have concentrated on a single signaling modality, usually either courtship song or cuticular hydrocarbons (CHCs), which can act as contact pheromones. We have examined the relationship between both signal types and reproductive success using F1–3 offspring of wild- collected flies, raised in the lab. We used two populations of the Holarctic species Drosophila montana that represent different phylogeographic clades that have been separate for ca. 0.5 million years (MY), and differ to some extent in both traits. Here, we characterize the nature and identify the targets of sexual selection on song, CHCs, and both traits combined within the populations. Three measures of courtship outcome were used as fitness proxies. They were the probability of mating, mating latency, and the production of rejection song by females, and showed patterns of association with different traits that included both linear and quadratic selection. Courtship song predicted courtship outcome better than CHCs and the signal modalities acted in an additive rather than synergistic manner. Selection was generally consistent in direction and strength between the two populations and favored males that sang more vigorously. Sexual selection differed in the extent, strength, and nature on some of the traits between populations. However, the differences in the directionality of selection detected were not a good predictor of population differences. In addition, a character previously shown to be important for species recognition, interpulse interval, was found to be under sexual selection. Our results highlight the complexity of understanding the relationship between within-population sexual selection and population differences. Sexual selection alone cannot predict differences between populations.

Beaked whales respond to simulated and actual navy sonar

2013-05-12T04:31:29Z

Abstract: Beaked whales have mass stranded during some naval sonar exercises, but the cause is unknown. They are difficult to sight but can reliably be detected by listening for echolocation clicks produced during deep foraging dives. Listening for these clicks, we documented Blainville's beaked whales, Mesoplodon densirostris, in a naval underwater range where sonars are in regular use near Andros Island, Bahamas. An array of bottom-mounted hydrophones can detect beaked whales when they click anywhere within the range. We used two complementary methods to investigate behavioral responses of beaked whales to sonar: an opportunistic approach that monitored whale responses to multi-day naval exercises involving tactical mid-frequency sonars, and an experimental approach using playbacks of simulated sonar and control sounds to whales tagged with a device that records sound, movement, and orientation. Here we show that in both exposure conditions beaked whales stopped echolocating during deep foraging dives and moved away. During actual sonar exercises, beaked whales were primarily detected near the periphery of the range, on average 16 km away from the sonar transmissions. Once the exercise stopped, beaked whales gradually filled in the center of the range over 2-3 days. A satellite tagged whale moved outside the range during an exercise, returning over 2-3 days post-exercise. The experimental approach used tags to measure acoustic exposure and behavioral reactions of beaked whales to one controlled exposure each of simulated military sonar, killer whale calls, and band-limited noise. The beaked whales reacted to these three sound playbacks at sound pressure levels below 142 dB re 1 mu Pa by stopping echolocation followed by unusually long and slow ascents from their foraging dives. The combined results indicate similar disruption of foraging behavior and avoidance by beaked whales in the two different contexts, at exposures well below those used by regulators to define disturbance.

Activation of the beta interferon promoter by paramyxoviruses in the absence of virus protein synthesis

2013-05-19T00:34:25Z

Abstract: Conflicting reports exist regarding the requirement for virus replication in interferon (IFN) induction by paramyxoviruses. Our previous work has demonstrated that pathogen-associated molecular patterns capable of activating the IFN-induction cascade are not normally generated during virus replication, but are associated instead with the presence of defective interfering (DI) viruses. We demonstrate here that DIs of paramyxoviruses, including parainfluenza virus 5, mumps virus and Sendai virus, can activate the IFN-induction cascade and the IFN-beta promoter in the absence of virus protein synthesis. As virus protein synthesis is an absolute requirement for paramyxovirus genome replication, our results indicate that these DI viruses do not require replication to activate the IFN-induction cascade.

Identification of essential and non-essential single-stranded DNA-binding proteins in a model archaeal organism

2013-05-12T04:07:53Z

Abstract: Single-stranded DNA-binding proteins (SSBs) play vital roles in all aspects of DNA metabolism in all three domains of life and are characterized by the presence of one or more OB fold ssDNA-binding domains. Here, using the genetically tractable euryarchaeon Haloferax volcanii as a model, we present the first genetic analysis of SSB function in the archaea. We show that genes encoding the OB fold and zinc finger-containing RpaA1 and RpaB1 proteins are individually non-essential for cell viability but share an essential function, whereas the gene encoding the triple OB fold RpaC protein is essential. Loss of RpaC function can however be rescued by elevated expression of RpaB, indicative of functional overlap between the two classes of haloarchaeal SSB. Deletion analysis is used to demonstrate important roles for individual OB folds in RpaC and to show that conserved N- and C-terminal domains are required for efficient repair of DNA damage. Consistent with a role for RpaC in DNA repair, elevated expression of this protein leads to enhanced resistance to DNA damage. Taken together, our results offer important insights into archaeal SSB function and establish the haloarchaea as a valuable model for further studies.

Sphingolipid and ceramide homeostasis : potential therapeutic targets

2013-05-12T04:06:43Z

Abstract: Sphingolipids are ubiquitous in eukaryotic cells where they have been attributed a plethora of functions from the formation of structural domains to polarized cellular trafficking and signal transduction. Recent research has identified and characterised many of the key enzymes involved in sphingolipid metabolism and this has lead to a heightened interest in the possibility of targeting these processes for therapies against cancers, Alzheimer’s disease and numerous important human pathogens. In this review we outline the major pathways in eukaryotic sphingolipid metabolism and discuss these in relation to disease and therapy for both chronic and infectious conditions.

Mitochondrial β-amyloid in Alzheimer's disease

2013-05-12T04:04:45Z

Abstract: It is well established that the intracellular accumulation of beta-amyloid is associated with Alzheimer’s disease and that this accumulation is toxic to neurons. The precise mechanism by which this toxicity occurs is not well understood, however, identifying the causes of this toxicity is an essential step in developing treatments for Alzheimer’s disease. One intracellular location where the accumulation of beta-amyloid can have a major effect is within mitochondria has identified mitochondrial proteins that act as binding sites for beta-amyloid and when binding occurs a toxic response results. For one of these identified sites, an enzyme known as ‘ABAD’, we have identified the changes in gene expression in the brain cortex following beta-amyloid accumulation within mitochondria. Specifically, we have identified two proteins that are upregulated in the brains of transgenic animal models for Alzheimer’s disease but also human sufferers. The increased expression of these proteins demonstrates the complex and counter-acting pathways that are activated in Alzheimer’s disease. Previous studies have identified the approximate contact sites between ABAD and beta-amyloid, and based on these observations we have shown that using a modified peptide approach, it is possible to reverse the expression of these two proteins in living transgenic animals and also recover both mitochondrial and behavioural deficits. This indicates that the ABAD-beta-amyloid interaction is potentially an interesting target for therapeutic intervention. To explore this further we used a fluorescing substrate mimic to measure the activity of ABAD within living cells, and in addition we have identified chemical fragments that bind to ABAD, by using a thermal shift assay. Description: This research is supported by Alzheimer's Research UK, the Wellcome Trust and the Biotechnology and Biological Sciences Research Council.

A critical review of the literature on population modelling

2012-12-12T10:19:28Z

Abstract: The 2005 report of the National Research Council’s ‘Committee on Characterizing Biologically Significant Marine Mammal Behavior’ proposed a framework, which they called PCAD - Population Consequences of Acoustic Disturbance, that uses a series of transfer functions to link behavioural responses to sound with life functions, vital rates, and population change. The Committee suggested that the best understood transfer functions are those linking vital rates to population change. One of the main aims of this report is to document that understanding. However, we also show how the existing frameworks for modelling the dynamics of marine mammal populations can be extended to include the effects of behavioural responses on vital rates. In Chapter 1 we introduce the central concept of the rate of increase (lambda) of a population, which we believe is the most useful measure of the effects of behavioural responses on the dynamics of a population. If the value of lambda exceeds one, then thepopulation will increase over time; if it is less than one it will decrease. We show how changes in lambda provide a measure of the impact of human activities (such as exploitation, conservation, or disturbance) on a population. We also introduce structured population models, which take account of the fact that all individuals in a population are not identical, and show how the dynamics of different parts of a population can be modelled using a population projection matrix. The mathematical properties of this projection matrix can be used to determine the sensitivity of lambda to small changes in vital rates. Finally, we provide a very brief introduction to the concept of stochasticity, and the use of lambda to predict when (and if) a population might be driven to extinction. Chapter 2 describes how lambda also provides a measure of the Darwinian fitness of the individual members of a population. An individual’s fitness, the contribution it will make to future generations, depends to a large extent on its body condition and on the risks of mortality to which it is exposed. Both of these could be affected by behaviour responses to sound. We also explain current theories about the relationship between an individual’s feeding behaviour and the abundance and distribution of prey, and how this can affect body condition. Chapter 3 provides a more detailed description of how elasticity analysis can be used to investigate the impact of changes in vital rates on lambda . Elasticity analysis is a useful tool for detecting which vital rates are most important in determining the dynamics of a population. However, its value is limited because it does not take account of random variations (stochasticity) and, in theory, it can only predict the effect of small changes in vital rates. Chapter 4 describes the fundamental concept of density dependence: the way in which vital rates change with population size or the availability of resources, such as prey. Not only is density dependence an essential prerequisite for population stability and sustainable use, but the form it takes will also determine how a population responds to behavioural changes. This is because behaviour, and particularly the effect of behavioural change on body condition, plays a central role in many of the mechanistic models of density dependence. Chapters 5 and 6 explore the way in which additional complexities, such as social structure and the way in which populations are distributed in space, can affect the dynamics of populations. Models that account for these complexities behave in a much less predictable way than the relatively simple structured models that form the core of Chapters 1-4. So far, the models of population dynamics that we have reviewed have been deterministic. That is, they have assumed that the only way in which vital rates can vary is in response to a change in abundance, via density dependent mechanisms. In Chapters 7 and 8 we investigate the effect of random variation (stochasticity) on population dynamics. We distinguish the effects of demographic stochasticity, chance variations in the number of animals that die or give birth in a time interval that occur even if vital rates do not vary over time, and environmental stochasticity, which is the result of variations in vital rates across years. Variation in abundance may also occur as a result of environmental change and changes in the ecological community of which a population is a part. The effect of all these sources of variation is to reduce the realised growth rate of a population, and therefore its risk of extinction. In Chapter 9 we consider how the basic population modelling framework described in Chapters 1-8 might be extended to take account of the life functions identified by the NRC Committee. We suggest that these life functions are useful for defining the context in which behavioural responses might affect vital rates, but that they do not need to be modelled explicitly. Removing vital functions from the PCAD framework results in a much simpler structure, which is compatible with existing population modelling frameworks. However, these will have to be extended to allow population states, like body condition, that vary continuously to be modelled. Chapter 10 describes how changes in lambda can be detected. The simple analytical frameworks that are available for this are all vulnerable to the effects of variability that we introduced in Chapter 7. However, there is a framework (state-space and hidden Markov process modelling) that can account for the effects of this variability, and we recommend its use for detecting trends. The additional benefit of this approach is that its use results in a detailed model of the dynamics of the population that is under investigation. Chapter 11 reviews the different model structures that can be used to describe the dynamics of a population, and explains when different forms of population models (e.g. discrete vs. continuous time, deterministic vs. stochastic) are most appropriate. We also discuss how these different frameworks can be extended to account for continuous population states, as recommended in Chapter 8. The final focus is on how state-space models can be fitted to time series of abundance estimates and information on vital rates. Chapter 12 looks at the relevance of the different modelling approaches described in the previous chapters for analysing the potential effects of behavioural responses to sound on population dynamics, particularly the kinds of sounds that may be generated by the oil and gas industry. We conclude that lambda , the population rate of increase, and its variation provides a useful measure of these effects. We also believe that the models used for this purpose will certainly have to account for the effects of variability and density dependence. They will probably also have to account for the effects of social structure and the way in which populations use space. The state-space modelling framework outlined in Chapter 11 can, in principle, be extended to capture all of these features although work on this is still in its infancy. Description: Final Report to the Joint Industry Project of the International Association of Oil & Gas Producers on contract JIP22 07_20

An investigation of the ABAD-Aβ interaction as a potential therapeutic target for the treatment of Alzheimer’s disease

2012-04-09T13:57:03Z

Abstract: Alzheimer’s disease (AD) is the leading cause of dementia but despite being identified over a century ago, current treatments remain limited. To date, no disease-modifying therapies are available. Soluble, intracellular forms of β-amyloid (Aβ), a protein associated with AD, have been identified and intracellular targets of Aβ are being investigated as potential targets for new drugs. Amyloid binding alcohol dehydrogenase (ABAD) was previously identified as a mitochondrial target of Aβ and is known to be up-regulated in AD. This interaction results in production of reactive oxygen species and cell death. Using a small peptide, known as the “decoy peptide”, disruption of this interaction has been shown to reverse biochemical and behavioural symptoms in an AD mouse model. The work reported in this thesis describes the approaches taken to develop methods for in vitro and ex vivo study of the interaction between ABAD and Aβ. A fluorogenic assay for measuring the intracellular activity of ABAD in living cells was developed and using this technique, the intracellular inhibition of ABAD by Aβ was observed for the first time. Surface plasmon resonance was used to measure binding between ABAD and Aβ and also showed the first quantitative analysis of direct binding of the decoy peptide to Aβ42. In order to synthesise small molecule inhibitors of ABAD activity with the aim of developing a molecular probe of the enzyme’s activity, compounds were identified by screening a fragment-based library. Subsequent optimisation of the compound structure led to a 10-fold improvement in the IC50 and has resulted in a lead compound for future development. A similar screening strategy was employed to identify potential small molecule inhibitors of the ABAD-Aβ interaction. This research has resulted in a range of tools and methods for studying ABAD activity and interactions, which will greatly benefit future work on developing compounds that inhibit the ABAD-Aβ interaction to provide a novel method for treating Alzheimer’s disease. Description: Electronic version does not contain associated previously published material

2A peptides provide distinct solutions to driving stop-carry on translational recoding

2013-05-12T04:09:47Z

Abstract: Expression of viral proteins frequently includes non-canonical decoding events (‘recoding’) during translation. ‘2A’ oligopeptides drive one such event, termed ‘stop-carry on’ recoding. Nascent 2A peptides interact with the ribosomal exit tunnel to dictate an unusual stop codon-independent termination of translation at the final Pro codon of 2A. Subsequently, translation ‘reinitiates’ on the same codon, two individual proteins being generated from one open reading frame. Many 2A peptides have been identified, and they have a conserved C-terminal motif. Little similarity is present in the N-terminal portions of these peptides, which might suggest that these amino acids are not important in the 2A reaction. However, mutagenesis indicates that identity of the amino acid at nearly all positions of a single 2A peptide is important for activity. Each 2A may then represent a specific solution for positioning the conserved C-terminus within the peptidyl-transferase centre to promote recoding. Nascent 2A peptide:ribosome interactions are suggested to alter ribosomal fine structure to discriminate against prolyl-tRNAPro and promote termination in the absence of a stop codon. Such structural modifications may account for our observation that replacement of the final Pro codon of 2A with any stop codon both stalls ribosome processivity and inhibits nascent chain release.

Generation and characterization of a recombinant Rift Valley fever virus expressing a V5 epitope-tagged RNA-dependent RNA polymerase

2013-05-12T04:09:45Z

Abstract: The viral RNA-dependent RNA polymerase (RdRp; L protein) of Rift Valley fever virus (RVFV; family Bunyaviridae) is a 238 kDa protein that is crucial for the life cycle of the virus, as it catalyses both transcription of viral mRNAs and replication of the tripartite genome. Despite its importance, little is known about the intracellular distribution of the polymerase or its other roles during infection, primarily because of lack of specific antibodies that recognize L protein. To begin to address these questions we investigated whether the RVFV (MP12 strain) polymerase could tolerate insertion of the V5 epitope, as has been previously demonstrated for the Bunyamwera virus L protein. Insertion of the 14 aa epitope into the polymerase sequence at aa 1852 resulted in a polymerase that retained functionality in a minigenome assay, and we were able to rescue recombinant viruses that expressed the modified L protein by reverse genetics. The L protein could be detected in infected cells by Western blotting with anti-V5 antibodies. Examination of recombinant virus-infected cells by immunofluorescence revealed a punctate perinuclear or cytoplasmic distribution of the polymerase that co-localized with the nucleocapsid protein. The generation of RVFV expressing a tagged RdRp will allow detailed examination of the role of the viral polymerase in the virus life cycle.

Innate sensing of HIV-infected cells

2013-05-12T04:09:35Z

Abstract: Cell-free HIV-1 virions are poor stimulators of type I interferon (IFN) production. We examined here how HIV-infected cells are recognized by plasmacytoid dendritic cells (pDCs) and by other cells. We show that infected lymphocytes are more potent inducers of IFN than virions. There are target cell-type differences in the recognition of infected lymphocytes. In primary pDCs and pDC-like cells, recognition occurs in large part through TLR7, as demonstrated by the use of inhibitors and by TLR7 silencing. Donor cells expressing replication-defective viruses, carrying mutated reverse transcriptase, integrase or nucleocapsid proteins induced IFN production by target cells as potently as wild-type virus. In contrast, Env-deleted or fusion defective HIV-1 mutants were less efficient, suggesting that in addition to TLR7, cytoplasmic cellular sensors may also mediate sensing of infected cells. Furthermore, in a model of TLR7-negative cells, we demonstrate that the IRF3 pathway, through a process requiring access of incoming viral material to the cytoplasm, allows sensing of HIV-infected lymphocytes. Therefore, detection of HIV-infected lymphocytes occurs through both endosomal and cytoplasmic pathways. Characterization of the mechanisms of innate recognition of HIV-infected cells allows a better understanding of the pathogenic and exacerbated immunologic events associated with HIV infection.

A transient homotypic interaction model for the influenza A virus NS1 protein effector domain

2013-05-12T04:09:34Z

Abstract: Influenza A virus NS1 protein is a multifunctional virulence factor consisting of an RNA binding domain (RBD), a short linker, an effector domain (ED), and a C-terminal 'tail'. Although poorly understood, NS1 multimerization may autoregulate its actions. While RBD dimerization seems functionally conserved, two possible apo ED dimers have been proposed (helix-helix and strand-strand). Here, we analyze all available RBD, ED, and full-length NS1 structures, including four novel crystal structures obtained using EDs from divergent human and avian viruses, as well as two forms of a monomeric ED mutant. The data reveal the helix-helix interface as the only strictly conserved ED homodimeric contact. Furthermore, a mutant NS1 unable to form the helix-helix dimer is compromised in its ability to bind dsRNA efficiently, implying that ED multimerization influences RBD activity. Our bioinformatical work also suggests that the helix-helix interface is variable and transient, thereby allowing two ED monomers to twist relative to one another and possibly separate. In this regard, we found a mAb that recognizes NS1 via a residue completely buried within the ED helix-helix interface, and which may help highlight potential different conformational populations of NS1 (putatively termed 'helix-closed' and 'helix-open') in virus-infected cells. 'Helix-closed' conformations appear to enhance dsRNA binding, and 'helix-open' conformations allow otherwise inaccessible interactions with host factors. Our data support a new model of NS1 regulation in which the RBD remains dimeric throughout infection, while the ED switches between several quaternary states in order to expand its functional space. Such a concept may be applicable to other small multifunctional proteins. Description: Work in St. Andrews was supported by the Medical Research Council, UK (RER and RJR), and the Scottish Funding Council (RJR).

Universal scaling rules predict evolutionary patterns of myogenesis in species with indeterminate growth

2013-05-12T04:09:17Z

Abstract: Intraspecific phenotypic variation is ubiquitous and often associated with resource exploitation in emerging habitats. For example, reduced body size has evolved repeatedly in Arctic charr (Salvelinus alpinus L.) and threespine stickleback (Gasterosteus aculeatus L.) across post-glacial habitats of the Northern Hemisphere. Exploiting these models, we examined how body size and myogenesis evolve with respect to the 'optimum fibre size hypothesis', which predicts that selection acts to minimize energetic costs associated with ionic homeostasis by optimizing muscle fibre production during development. In eight dwarf Icelandic Arctic charr populations, the ultimate production of fast-twitch muscle fibres (FN(max)) was only 39.5 and 15.5 per cent of that in large-bodied natural and aquaculture populations, respectively. Consequently, average fibre diameter (FD) scaled with a mass exponent of 0.19, paralleling the relaxation of diffusional constraints associated with mass-specific metabolic rate scaling. Similar reductions in FN(max) were observed for stickleback, including a small-bodied Alaskan population derived from a larger-bodied oceanic stock over a decadal timescale. The results suggest that in species showing indeterminate growth, body size evolution is accompanied by strong selection for fibre size optimization, theoretically allowing resources saved from ionic homeostasis to be allocated to other traits affecting fitness, including reproduction. Gene flow between small- and large-bodied populations residing in sympatry may counteract the evolution of this trait.

Sex differences in impulsivity : a meta-analysis

2013-05-12T04:09:06Z

Abstract: Men are overrepresented in socially problematic behaviors, such as aggression and criminal behavior, which have been linked to impulsivity. Our review of impulsivity is organized around the tripartite theoretical distinction between reward hypersensitivity, punishment hyposensitivity, and inadequate effortful control. Drawing on evolution try, criminological, developmental, and personality theories, we predicted that sex differences would be most pronounced in risky activities with men demonstrating greater sensation seeking, greater reward sensitivity, and lower punishment sensitivity. We predicted a small female advantage in effortful control. We analyzed 741 effect sizes from 277 studies, including psychometric and behavioral measures. Women were consistently more punishment sensitive (d = -0.33), but men did not show greater reward sensitivity (d = 0.01). Men showed significantly higher sensation seeking on questionnaire mea lures (d = 0.41) and on a behavioral risk-taking task (d = 0.36). Questionnaire measures of deficits in effortful control showed a very modest effect size in the male direction (d = 0.08). Sex differences were not found on delay discounting or executive function tasks. The results indicate a stronger sex difference in motivational rather than effortful or executive forms of behavior control. Specifically, they support evolutionary and biological theories of risk taking predicated on sex differences in punishment sensitivity. A clearer understanding of sex differences in impulsivity depends upon recognizing important distinctions between sensation seeking and impulsivity, between executive and effortful forms of control, and between impulsivity as a deficit and as a trait. Description: Supplemental materials: http://dx.doi.org/10.1037/a0021591.supp

A comparative investigation of the cognitive and social factors underlying a capacity for cumulative culture

2011-12-23T11:39:46Z

Abstract: Human culture has been proposed to uniquely exhibit a ‘ratchet effect’, with beneficial modifications being made to cultural traits over many generations. This is widely thought to have allowed an accumulation of technology and knowledge over time, and to be of central importance to the remarkable ecological and demographic success of humans. Whilst many researchers argue that the roots of human culture lie in social learning, a process widespread in nature, the exact cognitive capacities that set humans apart are not known. To provide a comparative assessment of nine separate hypotheses regarding different social and cognitive factors that may underlie a capacity for cumulative culture, in this thesis a cumulative puzzlebox was presented to three species. Groups of capuchins, chimpanzees and children were provided with the opportunity to solve the puzzlebox to three sequential levels to retrieve rewards of increasing desirability. Higher level solutions spread only in the children. Evidence was found for the occurrence of teaching, imitation, complex communication and prosociality in groups of children, but not in groups of capuchins and chimpanzees. Furthermore, these processes were positively correlated with the performance of individuals within the groups of children which was the only species to show evidence of cumulative cultural learning. Five further hypotheses focussed on alternative social and cognitive factors were not supported by the evidence from this experiment.

Lipidomic analysis of bloodstream and procyclic form Trypanosoma brucei

2013-05-12T03:32:58Z

Abstract: The biological membranes of Trypanosonza brucei contain a complex array of phospholipids that are synthesized de novo from precursors obtained either directly from the host, or as catabolised endocytosed lipids. This paper describes the use of nanoflow electrospray tandem mass spectrometry and high resolution mass spectrometry in both positive and negative ion modes, allowing the identification of similar to 500 individual molecular phospholipids species from total lipid extracts of cultured bloodstream and procyclic form T. brucei. Various molecular species of all of the major subclasses of glycerophospholipids were identified including phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol as well as phosphatidic acid, phosphatidylglycerol and cardolipin, and the sphingolipids sphingomyelin, inositol phosphoceramide and ethanolamine phosphoceramide. The lipidomic data obtained in this study will aid future biochemical phenotyping of either genetically or chemically manipulated commonly used bloodstream and procyclic strains of Trypanosoma brucei. Hopefully this will allow a greater understanding of the bizarre world of lipids in this important human pathogen.

Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales

2013-05-19T04:31:14Z

Abstract: Single-stranded DNA binding proteins (SSBs) based on the OB-fold are considered ubiquitous in nature and play a central role in many DNA transactions including replication, recombination and repair. We demonstrate that the thermoproteales, a clade of hyperthermophilic crenarchaea, lack a canonical SSB. Instead, they encode a distinct ssDNA-binding protein that we term "ThermoDBP", exemplified by protein Ttx1576 from Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. The crystal structure of Ttx1576 reveals a unique fold and mechanism for ssDNA binding, consisting of an extended cleft lined with hydrophobic phenylalanine residues and flanked by basic amino acids. Two ssDNA-binding domains are linked by a coiled-coil leucine zipper. ThermoDBP appears to have displaced the canonical SSB during the diversification of the thermoproteales – a highly unusual example where a “ubiquitous” protein has been lost in evolution.

Female mating decisions in the rose bitterling (Rhodeus ocellatus)

2011-12-14T14:56:25Z

Abstract: The aim of this study was to obtain an understanding of the basis to female mating decisions in the Chinese rose bitterling (Rhodeus ocellatus). Bitterling have a resource-based mating system that involves the female laying her eggs inside the gills of a freshwater mussel. Male bitterling perform elaborate courtship behaviour and are territorial and aggressively guard mussels in their territory from other territory holders and non-territorial males. Using a series of laboratory experiments it was shown in this study that females were choosy over the males they mated with, but females were not congruent in their preferences. Female mate preferences correlated positively with offspring growth rates and survival during early development. Female mate choice did not correspond with male dominance, and there may be an intersexual conflict between female mate preferences and male dominance as a result. Females tended to prefer males with functionally dissimilar MHC alleles. MHC alleles may influence male odour cues, and females showed a preference for mussels in which the sperm of multiple males had been released, possibly indicating that females use odour cues associated with sperm release in mating decisions. Bitterling show an innate preference for the colour red in a foraging context and there may be a receiver bias for red nuptial colouration in female mating preferences. Despite a significant role for mate preferences, direct (oviposition) mating preferences were shown to be more important in the mating system. Choice of oviposition sites has both immediate (survival) consequences for offspring, as well as longer-term fitness effects.

PCNA stimulates catalysis by structure-specific nuclease using two distinct mechanisms : substrate targeting and catalytic step

2013-05-12T02:05:13Z

Abstract: The sliding clamp Proliferating Cell Nuclear Antigen (PCNA) functions as a recruiter and organizer of a wide variety of DNA modifying enzymes including nucleases, helicases, polymerases and glycosylases. The 5-flap endonuclease Fen-1 is essential for Okazaki fragment processing in eukaryotes and archaea, and is targeted to the replication fork by PCNA. Crenarchaeal XPF, a 3-flap endonuclease, is also stimulated by PCNA in vitro. Using a novel continuous fluorimetric assay, we demonstrate that PCNA activates these two nucleases by fundamentally different mechanisms. PCNA stimulates Fen-1 by increasing the enzymes binding affinity for substrates, as suggested previously. However, PCNA activates XPF by increasing the catalytic rate constant by four orders of magnitude without affecting the K-M. PCNA may function as a platform upon which XPF exerts force to distort DNA substrates, destabilizing the substrate and/or stabilizing the transition state structure. This suggests that PCNA can function directly in supporting catalysis as an essential cofactor in some circumstances, a new role for a protein that is generally assumed to perform a passive targeting and organizing function in molecular biology. This could provide a mechanism for the exquisite control of nuclease activity targeted to specific circumstances, such as replication forks or damaged DNA with pre-loaded PCNA. Description: This work was supported by the Biotechnology and Biological Sciences Research Council [grants BBD0014391 and BBE0146741]

The impact of microbial extracellular polymeric substances on sediment stability

2012-08-07T14:07:36Z

Abstract: The main objective of this thesis is to investigate the impact of microbial extracellular polymeric substances (EPS) on sediment stability and the related factors which influence “biogenic stabilisation” as a basis to the prediction of sediment erosion and transport. The ability to make direct and sensitive measurements of the physical properties of the biofilm is a critical demand to further understanding of the overall biostabilisation processes.Therefore, attention has been focused on developing a new technique, Magnetic Particle Induction (MagPI) for measuring the adhesive properties of the biofilm. MagPI determines the relative adhesive properties or “stickiness” of the test surface, whether a biofilm, a sediment or other submerged material. The technique may have future applications in physical, environmental and biomedical research. Newly developed Magnetic Particle Induction(MagPI) and traditional techniques Cohesive Strength Meter (CSM) for the determination of the adhesion/cohesion of the substratum were used to assess the biostabilisation capacity of aquatic microorganisms. Whilst these devices determine slightly different surface properties of the bed, they were found to complement each other, increasing the range of measurements that could be made and presented a strong correlation in the overlapping portion of the data. It is recognized that microorganisms inhabiting natural sediments significantly mediate the erosive response of the bed (“ecosystem engineers”) through the secretion of naturally adhesive organic material (EPS: extracellular polymeric substances). Interactions between main biofilm consortia microalgae, cyanobacteria and bacteria in terms of their individual contribution to the EPS pool and their relative functional contribution to substratum stabilisation were investigated. The overall stabilisation potential of the various assemblages was impressive, as compared to controls. The substratum stabilisation by estuarine microbial assemblages was due to the secreted EPS matrix, and both EPS quality (carbohydrates and proteins) and quantity (concentration) were important in determining stabilisation. Stabilisation was significantly higher for the bacterial assemblages than for axenic microalgal assemblages. The peak of engineering effect was significantly greater in the mixed assemblage as compared to the bacterial and axenic diatom culture. This work confirmed the important role of heterotrophic bacteria in “biostabilisation” and highlighted the interactions between autotrophic and heterotrophic biofilm components of the consortia. An additional approach, to investigate the impact of toxins on biostabilisation capacity of aquatic organism was performed on cultured bacterial and natural freshwater biofilm.The data suggest a different mode of triclosan (TCS) action ranging from suppressing metabolisms to bactericidal effects depending on the TCS concentration. The inhibitory effect of triclosanon bacterial and freshwater biofilms was confirmed. This information contributes to the conceptual understanding of the microbial sediment engineering that represents an important ecosystem function and service in aquatic habitats.

Range-wide analysis of the spatial distribution and genetic diversity of Delonix s.l. (Leguminosae) in Madagascar : enhancing herbarium-based conservation assessments

2011-12-08T14:28:25Z

Abstract: Despite their ecological and economic importance, the majority of plant species and their conservation status are poorly known. Only 4% of plants have been assessed globally and listed on the IUCN Red List of Threatened Species; and without plant conservation assessments, many plant species will not feature in conservation planning. Herbarium collection information can significantly increase the number of plant conservation assessments. Thus, the aims of this thesis were: (1) to investigate how the quality of herbarium-based conservation assessments can be optimised; (2) to assess the extent to which herbarium-based conservation assessments reflect the reality on the ground; and (3) to scientifically validate genetic and spatial underpinning of IUCN criteria. Preliminary range-based assessments of the Leguminosae of Madagascar achieved a result consistent with the final conservation rating for over 95% of species when using up to fifteen herbarium specimens. Bioclimatic modelling of range shifts based on future climate change predicted that, in the worst case scenario, up to one third of endemic Leguminosae in Madagascar will be threatened with extinction over the next 100 years. An analysis of the population structure of species of Delonix s.l. (Leguminosae) showed that combining spatial analysis with population genetic data provides a more complete picture of landscape-level population dynamics and the impacts on conservation status. Moreover, range-wide genetic analysis of AFLP markers for four species of Delonix demonstrated a genetic basis for IUCN categories distinguishing between threatened and non-threatened species. Although genetic data are currently not often incorporated in conservation assessments, they are crucial in making accurate management decisions and creating effective action plans for conservation. Only by using all available scientific resources can informed conservation decisions be made and the survival of plants and their associated ecosystems be ensured.

Selection of reference genes for expression studies with fish myogenic cell cultures

2013-05-12T04:08:55Z

Abstract: Background: Relatively few studies have used cell culture systems to investigate gene expression and the regulation of myogenesis in fish. To produce robust data from quantitative real-time PCR mRNA levels need to be normalised using internal reference genes which have stable expression across all experimental samples. We have investigated the expression of eight candidate genes to identify suitable reference genes for use in primary myogenic cell cultures from Atlantic salmon (Salmo salar L.). The software analysis packages geNorm, Normfinder and Best keeper were used to rank genes according to their stability across 42 samples during the course of myogenic differentiation. Results: Initial results showed several of the candidate genes exhibited stable expression throughout myogenic culture while Sdha was identified as the least stable gene. Further analysis with geNorm, Normfinder and Bestkeeper identified Ef1 alpha, Hprt1, Ppia and RNApolII as stably expressed. Comparison of data normalised with the geometric average obtained from combinations of any three of these genes showed no significant differences, indicating that any combination of these genes is valid. Conclusion: The geometric average of any three of Hprt1, Ef1 a, Ppia and RNApolII is suitable for normalisation of gene expression data in primary myogenic cultures from Atlantic salmon.

Transcriptional regulation of the IGF signaling pathway by amino acids and insulin-like growth factors during myogenesis in Atlantic salmon

2013-02-03T05:31:15Z

Abstract: The insulin-like growth factor signalling pathway is an important regulator of skeletal muscle growth. We examined the mRNA expression of components of the insulin-like growth factor (IGF) signalling pathway as well as Fibroblast Growth Factor 2 (FGF2) during maturation of myotubes in primary cell cultures isolated from fast myotomal muscle of Atlantic salmon (Salmo salar). The transcriptional regulation of IGFs and IGFBP expression by amino acids and insulin-like growth factors was also investigated. Proliferation of cells was 15% d(-1) at days 2 and 3 of the culture, increasing to 66% d(-1) at day 6. Three clusters of elevated gene expression were observed during the maturation of the culture associated with mono-nucleic cells (IGFBP5.1 and 5.2, IGFBP-6, IGFBP-rP1, IGFBP-2.2 and IGF-II), the initial proliferation phase (IGF-I, IGFBP-4, FGF2 and IGF-IRb) and terminal differentiation and myotube production (IGF2R, IGF-IRa). In cells starved of amino acids and serum for 72 h, IGF-I mRNA decreased 10-fold which was reversed by amino acid replacement. Addition of IGF-I and amino acids to starved cells resulted in an 18-fold increase in IGF-I mRNA indicating synergistic effects and the activation of additional pathway(s) leading to IGF-I production via a positive feedback mechanism. IGF-II, IGFBP-5.1 and IGFBP-5.2 expression was unchanged in starved cells, but increased with amino acid replacement. Synergistic increases in expression of IGFBP5.2 and IGFBP-4, but not IGFBP5.1 were observed with addition of IGF-I, IGF-II or insulin and amino acids to the medium. IGF-I and IGF-II directly stimulated IGFBP-6 expression, but not when amino acids were present. These findings indicate that amino acids alone are sufficient to stimulate myogenesis in myoblasts and that IGF-I production is controlled by both endocrine and paracrine pathways. A model depicting the transcriptional regulation of the IGF pathway in Atlantic salmon muscle following feeding is proposed.

Targeted rapid amplification of cDNA ends (T-RACE)-an improved RACE reaction through degradation of non-target sequences

2013-05-12T04:04:49Z

Abstract: Amplification of the 5' ends of cDNA, although simple in theory, can often be difficult to achieve. We describe a novel method for the specific amplification of cDNA ends. An oligo-dT adapter incorporating a dUTP-containing PCR primer primes first-strand cDNA synthesis incorporating dUTP. Using the Cap finder approach, another distinct dUTP containing adapter is added to the 3' end of the newly synthesized cDNA. Second-strand synthesis incorporating dUTP is achieved by PCR, using dUTP-containing primers complimentary to the adapter sequences incorporated in the cDNA ends. The double-stranded cDNA-containing dUTP serves as a universal template for the specific amplification of the 3' or 5' end of any gene. To amplify the ends of cDNA, asymmetric PCR is performed using a single gene-specific primer and standard dNTPs. The asymmetric PCR product is purified and non-target transcripts containing dUTP degraded by Uracil DNA glycosylase, leaving only those transcripts produced during the asymmetric PCR. Subsequent PCR using a nested gene-specific primer and the 3' or 5' T-RACE primer results in specific amplification of cDNA ends. This method can be used to specifically amplify the 3' and 5' ends of numerous cDNAs from a single cDNA synthesis reaction.

PCNA and XPF cooperate to distort DNA substrates

2013-05-12T03:03:51Z

Abstract: XPF is a structure-specific endonuclease that preferentially cleaves 3' DNA flaps during a variety of repair processes. The crystal structure of a crenarchaeal XPF protein bound to a DNA duplex yielded insights into how XPF might recognise branched DNA structures, and recent kinetic data have demonstrated that the sliding clamp PCNA acts as an essential cofactor, possibly by allowing XPF to distort the DNA structure into a proper conformation for efficient cleavage to occur. Here, we investigate the solution structure of the 3'-flap substrate bound to XPF in the presence and absence of PCNA using intramolecular Forster resonance energy transfer (FRET). We demonstrate that recognition of the flap substrate by XPF involves major conformational changes of the DNA, including a 90 degrees kink of the DNA duplex and organization of the single-stranded flap. In the presence of PCNA, there is a further substantial reorganization of the flap substrate bound to XPF, providing a structural basis for the observation that PCNA has an essential catalytic role in this system. The wider implications of these observations for the plethora of PCNA-dependent enzymes are discussed.

Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei

2013-05-12T03:31:38Z

Abstract: Background: Trypanosomes undergo extensive developmental changes during their complex life cycle. Crucial among these is the transition between slender and stumpy bloodstream forms and, thereafter, the differentiation from stumpy to tsetse-midgut procyclic forms. These developmental events are highly regulated, temporally reproducible and accompanied by expression changes mediated almost exclusively at the post-transcriptional level. Results: In this study we have examined, by whole-genome microarray analysis, the mRNA abundance of genes in slender and stumpy forms of T. brucei AnTat1.1 cells, and also during their synchronous differentiation to procyclic forms. In total, five biological replicates representing the differentiation of matched parasite populations derived from five individual mouse infections were assayed, with RNAs being derived at key biological time points during the time course of their synchronous differentiation to procyclic forms. Importantly, the biological context of these mRNA profiles was established by assaying the coincident cellular events in each population (surface antigen exchange, morphological restructuring, cell cycle re-entry), thereby linking the observed gene expression changes to the well-established framework of trypanosome differentiation. Conclusion: Using stringent statistical analysis and validation of the derived profiles against experimentally-predicted gene expression and phenotypic changes, we have established the profile of regulated gene expression during these important life-cycle transitions. The highly synchronous nature of differentiation between stumpy and procyclic forms also means that these studies of mRNA profiles are directly relevant to the changes in mRNA abundance within individual cells during this well-characterised developmental transition.

Biochemical characterization of the initial steps of the Kennedy pathway in Trypanosoma brucei : the ethanolamine and choline kinases

2013-05-12T02:34:15Z

Abstract: Ethanolamine and choline are major components of the trypanosome membrane phospholipids, in the form of GPEtn (glycero-phosphoethanolamine) and GPCho (glycerophosphocholine). Ethanolamine is also found as an integral component of the GPI (glycosylpliosphatidylinositol) anchor that is required for membrane attachment of cell-surface proteins, most notably the variant-surface glycoproteins. The de novo synthesis of GPEtn and GPCho starts with the generation of phosphoethanolamine and phosphocholine by ethanolamine and choline kinases via the Kennedy pathway. Database mining revealed two putative C/EKs (choline/ethanolamine kinases) in the Trypanosoma brucei genome, which were cloned, overexpressed, purified and characterized. TbEK 1 (T brucei ethanolamine kinase 1) was shown to be catalytically active as an ethanolamine-specific kinase, i.e. it had no choline kinase activity. The K values for ethanolamine and ATP were found to be 18.4 +/- 0.9 and 219 29 mu M respectively. TbC/EK2 (T brucei choline/ethanolamine kinase 2), on the other hand, was found to be able to phosphorylate both ethanolamine and choline, even though choline was the preferred substrate, with a K-m 80 times lower than that of ethanolamine. The K. values for choline, ethanolamine and ATP were 31.4 +/- 2.6 mu M, 2.56 +/- 0.31 mu M and 20.6 +/- 1.96 mu M respectively. Further substrate specificity analysis revealed that both TbEK1 and TbC/EK2 were able to tolerate various modifications at the amino group, with the exception of a quaternary amine for TbEK1 (choline) and a primary amine for TbC/EK2 (ethanolamine). Both enzymes recognized analogues with substituents oil C-2, but substitutions oil C-1 and elongations of the carbon chain were not well tolerated.

Identifying social learning in animal populations : A new ‘option-bias’ method

2013-05-12T02:31:34Z

Abstract: Studies of natural animal populations reveal widespread evidence for the diffusion of novel behaviour patterns, and for intra- and inter-population variation in behaviour. However, claims that these are manifestations of animal ‘culture’ remain controversial because alternative explanations to social learning remain difficult to refute. This inability to identify social learning in social settings has also contributed to the failure to test evolutionary hypotheses concerning the social learning strategies that animals deploy. We present a solution to this problem, in the form of a new means of identifying social learning in animal populations. The method is based on the assumption that social learning will generate greater homogeneity in behaviour between animals than expected in its absence. Our procedure compares the observed level of homogeneity to a bootstrapped sampling distribution utilizing randomization and other procedures. We illustrate the method on data from groups of monkeys provided with novel two-option extractive foraging tasks, demonstrating that social learning can indeed be distinguished from unlearned processes and asocial learning, and revealing that the monkeys only employed social learning for the more difficult tasks. The method is further validated against published datasets and through simulation, and exhibits higher statistical power than conventional inferential statistics.

Studies on influenza A virus PB1-F2 protein

2012-04-27T11:49:09Z

Abstract: The influenza A virus genome codes for up to 12 proteins. Segment 2 encodes three proteins, the polymerase subunit PB1, a small protein PB1-F2 and an N-terminally truncated version of PB1 called N40. Different functions have been reported for PB1-F2 such as induction of apoptosis, regulation of the viral polymerase activity, enhancement of secondary bacterial infections and modulation of the innate immune system. So far, no function has been ascribed to N40. To study PB1-F2 in more detail, its coding sequence was deleted from its original position and inserted downstream of the PB1 (segment 2), NA (segment 6) or M (segment 7) open reading frames (ORF) employing different strategies, including the use of an overlapping Stop-Start cassette, a duplicated promoter sequence and the self-cleaving 2A peptide derived from foot-and-mouth disease virus. Viruses with bicistronic segments were rescued and tested for their ability to express PB1-F2. Whereas no expression of PB1-F2 was detected from bicistronic segments 2 and 7, expression of PB1-F2 from segment 6 was observed in high levels. However, the phenotype of all these viruses was similar to that of viruses lacking PB1-F2 which made mutational analysis of PB1-F2 not worthwhile. Previously, the function of PB1-F2 was mainly studied using a virus deficient in PB1-F2 production but showing increased N40 expression. In the present study, recombinant WSN viruses lacking either PB1-F2 or N40, or both proteins were engineered and the effects of these mutations on the viral life cycle were examined. Viruses deficient for PB1-F2 that overexpressed N40 showed the most attenuated phenotype, whereas the loss of PB1-F2 alone did not obviously affect virus replication. Reduced viral polymerase activity was observed for viruses lacking N40, however attenuation in vivo was only seen in combination with the loss of PB1-F2. Neither the loss of PB1-F2 nor N40 alone had a great impact, but changes in the expression level of both proteins were disadvantageous for the virus. Increased levels of N40 shifted the polymerase activity towards replication, suggesting a new function for N40. Thus, it was shown that the segment 2 gene products and their expression level influence viral replication and pathogenicity, and a careful design of mutant recombinant viruses is vital for determining the experimental outcome.

Virus and interferon : a fight for supremacy : comparison of the mechanisms of influenza A viruses and parainfluenza virus 5 in combatting a pre-existing IFN-induced antiviral state

2011-12-19T15:53:05Z

Abstract: The Interferon (IFN) family of cytokines are produced in direct response to virus infection and they constitute the first line of defence against virus infection by inducing hundreds of interferon stimulated genes (ISGs) which act in concert to establish the so-called “antiviral state”. Influenza A viruses and parainfluenza virus type 5 (PIV5) are both small negative strand RNA viruses that must circumvent their hosts’ interferon (IFN) response for replication. However, the ways in which these viruses interact with the IFN system are very different. Although PIV5 replication is initially severely impaired in cells in a pre-existing IFN-induced antiviral state, it manages to overcome the antiviral state by targeting an essential component of type I IFN signalling, STAT1, for degradation. Thus the cells cannot maintain the antiviral state indefinitely without continuous signalling. Consequently, the virus resumes its normal replication pattern after 24-48 hours post-infection. In clear contrast, influenza virus fails to establish its replication in the majority of infected cells (90-95%) with a pre-existing IFN-induced antiviral state, although a few cells are still able to produce viral antigens. To further investigate how influenza virus interacts with cells in a pre-existing IFN-induced antiviral state, I have used in situ hybridization to follow the fate of input and progeny genomes in cells that have, or have not, been treated with IFN prior to infection. Here I show for the first time that IFN pre-treatment blocks the nuclear import of influenza A virus genome, which prevents the establishment of virus replication, but this can be overcome by increasing multiplicities of infection. Of those IFN-induced antiviral molecules, human MxA is an essential component of the IFN-induced antiviral state in blocking influenza virus genome import, as this block can be abolished by lentivirus-mediated knockdown of MxA. I also show that in cells constitutively expressing MxA the viral genome still manages to be transported into the nucleus, indicating that MxA might require an unidentified IFN-induced factor to block nuclear import of the influenza virus genome. These results reveal that IFN exerts its action at an early stage of virus infection by inducing MxA to interfere with the transport of viral genome into the nucleus, which is the factory for viral RNA production.

Complex Region Spatial Smoother (CReSS)

2012-12-12T10:18:54Z

Abstract: Conventional smoothing over complicated coastal and island regions may result in errors across boundaries, due to the use of Euclidean distances to represent inter-point similarity. The new Complex Region Spatial Smoother (CReSS) method presented here, uses estimated geodesic distances, model averaging and a local radial basis function to provide improved smoothing over complex domains. CReSS is compared, via simulation, to recent related smoothing techniques, Thin Plate Splines (TPS, Harder and Desmarais, 1972), geodesic low rank TPS [Wang and Ranalli, 2007] and the Soap film smoother [Wood et al., 2008]. The GLTPS method cannot be used in areas with islands and SOAP can be hard to parameterize. CReSS is comparable with, if not better than, all considered methods on a range of simulations. Supplementary materials for this article are available online.

Bird species richness and diversity at montane Important Bird Area (IBA) sites in south-eastern Nigeria

2013-05-12T02:31:32Z

Abstract: The mountains of south-eastern Nigeria are a western extension of the Cameroon mountain range, which is classified as an endemic bird area (EBA). Unlike its eastern extension in Cameroon, most of the ornithological surveys in the western extension of the Cameroon highlands in Nigeria have produced only limited checklists and inventories. There is a clear need for quantitative baseline data so that conservation problems can be identified. Twenty line transects covering a total transect length of 28.8 km were used to survey five sites (Afi Mountain Wildlife Sanctuary, Oban and Okwangwo Division of Cross River National Park, Sankwala Mountains and Mbe Mountains) in the westernmost extension of the Cameroon Mountains EBA in south western Nigeria. Vegetation measurements were taken to control for the potential confounding effect of variation in vegetation density and structure on detectability of birds between sites. The 193 bird species recorded in Afi, 158 in Sankwala, 124 in Oban, 100 in Mbe and 73 in Okwangwo Division included most of the Cameroon highlands restricted range species. The results show that the mountains of south-eastern Nigeria are important parts of the Cameroon EBA, particularly the Afi Mountain Wildlife Sanctuary. However these sites are threatened by fire and livestock grazing on the hilltops, shifting agriculture on the hillsides and lowlands, and logging for timber in some parts, as well as wildlife hunting for bush meat.

Characteristics of the Ascophyllum nodosum stands and their associated diversity along the coast of Brittany, France

2013-05-12T04:08:22Z

Abstract: The present study aimed at estimating the characteristics of the Ascophyllum nodosum stands along the coast of Brittany, France. Although both an ecologically and economically important macroalga on sheltered rocky shores of the North Atlantic, no study has simultaneously dealt with the variability of the densities, lengths and biomasses of A. nodosum together with a description of its associated algal and animal diversity. There were significant differences in mean lengths and variations in the length–population structures between sites. However, the biomasses and densities showed no significant differences. The biomasses are amongst the highest ones estimated over the entire species distribution. The algal and animal assemblages were typical of A. nodosum zones, but only the identity composition of the algal communities seemed to reflect site differences in environmental forces. The biomasses measured in the present study should help improve future macroalgae biomass and metabolism estimates on regional or global scales. Finally, the data will provide a reference state for future studies on the responses of fucoid canopies to environmental changes.

Technical Note: Animal-borne CTD-Satellite Relay Data Loggers for real-time oceanographic data collection

2013-05-19T04:31:09Z

Abstract: The increasing need for continuous monitoring of the world oceans has stimulated the development of a range of autonomous sampling platforms. One novel addition to these approaches is a small, relatively inexpensive data-relaying device that can be deployed on marine mammals to provide vertical oceanographic profiles throughout the upper 2000 m of the water column. When an animal dives, the CTD-Satellite Relay Data Logger (CTD-SRDL) records vertical profiles of temperature, conductivity and pressure. Data are compressed once the animal returns to the surface where it is located by, and relays data to, the Argos satellite system. The technical challenges met in the design of the CTD-SRDL are the maximising of energy efficiency and minimising size, whilst simultaneously maintaining the reliability of an instrument that cannot be recovered and is required to survive its lifetime attached to a marine mammal. The CTD-SRDLs record temperature and salinity with an accuracy of better than 0.005 degrees C and 0.02 respectively. However, due to the limited availability of reference data, real-time data from remote places are often associated with slightly higher errors. The potential to collect large numbers of profiles cost-effectively makes data collection using CTD-SRDL technology particularly beneficial in regions where traditional oceanographic measurements are scarce or even absent. Depending on the CTD-SRDL configuration, it is possible to sample and transmit hydrographic profiles on a daily basis, providing valuable and often unique information for a real-time ocean observing system. Description: Funded by NERC grants NE/E018289/1 and NER/D/S/2002/00426

Integrated holographic system for all-optical manipulation of developing embryos

2013-05-12T04:04:48Z

Abstract: We demonstrate a system for the combined optical injection and trapping of developing embryos. A Ti:sapphire femtosecond laser in tandem with a spatial light modulator, is used to perform fast and accurate beam-steering and multiplexing. We show successful intracellular delivery of a range of impermeable molecules into individual blastomeres of the annelid Pomatoceros lamarckii embryo by optoinjection, even when the embryo is still enclosed in a chorion. We also demonstrate the ability of the femtosecond laser optoinjection to deliver materials into inner layers of cells in a well-developed embryo. By switching to the continuous wave mode of the Ti:sapphire laser, the same system can be employed to optically trap and orient the 60 μm sized P. lamarckii embryo whilst maintaining its viability. Hence, a complete all-optical manipulation platform is demonstrated paving the way towards single-cell genetic modification and cell lineage mapping in emerging developmental biology model species.

Inhibition of Amyloid-beta (A beta) peptide-binding alcohol dehydrogenase-A beta interaction reduces A beta accumulation and improves mitochondrial function in a mouse model of Alzheimer's disease

2013-05-12T04:03:50Z

Abstract: Amyloid- beta (A beta) peptide-binding alcohol dehydrogenase (ABAD), an enzyme present in neuronal mitochondria, exacerbates A beta-induced cell stress. The interaction of ABAD with A beta exacerbates A beta-induced mitochondrial and neuronal dysfunction. Here, we show that inhibition of the ABAD-A beta interaction, using a decoy peptide (DP) in vitro and in vivo, protects against aberrant mitochondrial and neuronal function and improves spatial learning/memory. Intraperitoneal administration of ABAD-DP [fused to the transduction of human immunodeficiency virus 1-transactivator (Tat) protein and linked to the mitochondrial targeting sequence (Mito) (TAT-mito-DP) to transgenic APP mice (Tg mAPP)] blocked formation of ABAD-A beta complex in mitochondria, increased oxygen consumption and enzyme activity associated with the mitochondrial respiratory chain, attenuated mitochondrial oxidative stress, and improved spatial memory. Similar protective effects were observed in Tg mAPP mice overexpressing neuronal ABAD decoy peptide (Tg mAPP/mito-ABAD). Notably, inhibition of the ABAD-A beta interaction significantly reduced mitochondrial A beta accumulation. In parallel, the activity of mitochondrial A beta-degrading enzyme PreP (presequence peptidase) was enhanced in Tg mAPP mitochondria expressing the ABAD decoy peptide. These data indicate that segregating ABAD from A beta protects mitochondria/neurons from A beta toxicity; thus, ABAD-A beta interaction is an important mechanism underlying A beta-mediated mitochondrial and neuronal perturbation. Inhibitors of ABAD-A beta interaction may hold promise as targets for the prevention and treatment of Alzheimer's disease.

Darwin in mind : new opportunities for evolutionary psychology

2013-05-12T04:06:13Z

Abstract: Evolutionary Psychology (EP) views the human mind as organized into many modules, each underpinned by psychological adaptations designed to solve problems faced by our Pleistocene ancestors. We argue that the key tenets of the established EP paradigm require modification in the light of recent findings from a number of disciplines, including human genetics, evolutionary biology, cognitive neuroscience, developmental psychology, and paleoecology. For instance, many human genes have been subject to recent selective sweeps; humans play an active, constructive role in co-directing their own development and evolution; and experimental evidence often favours a general process, rather than a modular account, of cognition. A redefined EP could use the theoretical insights of modern evolutionary biology as a rich source of hypotheses concerning the human mind, and could exploit novel methods from a variety of adjacent research fields.

Annelid Distal-less/Dlx duplications reveal varied post-duplication fates

2013-05-12T04:06:28Z

Abstract: Background: Dlx (Distal-less) genes have various developmental roles and are widespread throughout the animal kingdom, usually occurring as single copy genes in non-chordates and as multiple copies in most chordate genomes. While the genomic arrangement and function of these genes is well known in vertebrates and arthropods, information about Dlx genes in other organisms is scarce. We investigate the presence of Dlx genes in several annelid species and examine Dlx gene expression in the polychaete Pomatoceros lamarckii. Results: Two Dlx genes are present in P. lamarckii, Capitella teleta and Helobdella robusta. The C. teleta Dlx genes are closely linked in an inverted tail-to-tail orientation, reminiscent of the arrangement of vertebrate Dlx pairs, and gene conversion appears to have had a role in their evolution. The H. robusta Dlx genes, however, are not on the same genomic scaffold and display divergent sequences, while, if the P. lamarckii genes are linked in a tail-to-tail orientation they are a minimum of 41 kilobases apart and show no sign of gene conversion. No expression in P. lamarckii appendage development has been observed, which conflicts with the supposed conserved role of these genes in animal appendage development. These Dlx duplications do not appear to be annelid-wide, as the polychaete Platynereis dumerilii likely possesses only one Dlx gene. Conclusions: On the basis of the currently accepted annelid phylogeny, we hypothesise that one Dlx duplication occurred in the annelid lineage after the divergence of P. dumerilii from the other lineages and these duplicates then had varied evolutionary fates in different species. We also propose that the ancestral role of Dlx genes is not related to appendage development. Description: Additional files can be viewed at http://www.biomedcentral.com/1471-2148/11/241/additional/

Education research as a route to collaborative work practice in HE

2012-07-24T09:28:56Z

Habitat-specific morphological variation among threespine sticklebacks (Gasterosteus aculeatus) within a drainage basin

2013-05-12T04:06:17Z

Abstract: Habitat-specific morphological variation, often corresponding to resource specialization, is well documented in freshwater fishes. In this study we used landmark based morphometric analyses to investigate morphological variation among threespine sticklebacks (Gasterosteus aculeatus L.) from four interconnected habitat types within a single lowland drainage basin in eastern England. These included the upper and lower reaches of the river, the estuary, a connected ditch network and a coastal salt marsh. We found significant habitat-specific differences in morphology, with three axes of variation describing differences in orbit diameter, body depth, caudal peduncle shape and pectoral fin positioning as well as variation in relative dorsal and pelvic spine size. Interestingly, the ditch system, an artificial and heavily managed habitat, is populated by sticklebacks with a characteristic morphology, suggesting that human management of habitats can in some circumstances lead to morphological variation among the animals that inhabit them. We discuss the mechanisms that conceivably underlie the observed morphological variation and the further work necessary to identify them. Finally, we consider the implications of habitat-specific body shape variation for the behavioural ecology of this ecologically generalist species.

Ensuring each student reaches their potential : (2) transferability issues

2012-12-12T09:11:50Z

Abstract: Isolation of knowledge within disciplines, or for students, within the confines of single taught modules, diminishes the learner’s richness of understanding. Whilst flexible degree programmes are attractive to prospective students, there is a need to ensure that such programmes do not situate understanding within narrow contexts. The curriculum must provide both incentive and structure for students to develop transferability in their knowledge and skills. Transferability of skills is dependent upon transfer of both principles and dispositions. Teaching to maximise the former requires active development of student understanding of generalisable principles, this being a minimum aim of any educator. However, transfer of dispositions, for example towards critical thinking, is more problematic, particularly within the higher education (HE) sector where individual students are exposed to varied tutors and lecturers, each of whom has built a career upon arguing the uniqueness of their thoughts and approaches. In the University of St Andrews School of Biology, introduction of core skills teaching has facilitated and integrated learning across modules and from co-curricular activities. This structure has been successful in establishing transfer of both principles and dispositions. This reflexive analysis reviews the strategies and successes of this programme in relation to transfer conditions.