2024-03-29T13:27:06Zhttps://research-repository.st-andrews.ac.uk/oai/requestoai:research-repository.st-andrews.ac.uk:10023/10472024-02-26T00:40:45Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain
Swiatek, Agnieszka
MacNeill, Stuart Andrew
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH301 Biology
QH301
This work was funded by the Scottish Universities Life Sciences Alliance (SULSA).
Primase and GINS are essential factors for chromosomal DNA replication in eukaryotic and archaeal cells. Here we describe a previously undetected relationship between the C-terminal domain of the catalytic subunit (PriS) of archaeal primase and the B-domains of the archaeo-eukaryotic GINS proteins in the form of a conserved structural domain comprising a three-stranded antiparallel beta-sheet adjacent to an alpha-helix and a two-stranded beta-sheet or hairpin. The presence of a shared domain in archaeal PriS and GINS proteins, the genes for which are often found adjacent on the chromosome, suggests simple mechanisms for the evolution of these proteins.
Peer reviewed
2010-04-12
2010-10-20T11:04:31Z
2010-10-20T11:04:32Z
Journal article
1751910
912ee3a4-5038-4bb8-9bc8-7f145d364564
77950637780
Swiatek , A & MacNeill , S A 2010 , ' The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain ' , Biology Direct , vol. 5 , no. 1 , pp. 17 . https://doi.org/10.1186/1745-6150-5-17
1745-6150
ORCID: /0000-0002-0555-0007/work/39107844
https://hdl.handle.net/10023/1047
10.1186/1745-6150-5-17
http://www.scopus.com/inward/record.url?scp=77950637780&partnerID=8YFLogxK
http://www.biology-direct.com/content/5/1/17
eng
Biology Direct
6
1817798
application/pdf
oai:research-repository.st-andrews.ac.uk:10023/107262023-04-25T23:48:52Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_792com_10023_879com_10023_878col_10023_46col_10023_182col_10023_795col_10023_880
Contrasting migratory responses of two closely-related seabirds to long-term climate change
Grecian, W. James
Taylor, Graeme A.
Loh, Graeme
McGill, Rona A. R.
Miskelly, Colin M.
Phillips, Richard A.
Thompson, David R.
Furness, Robert W.
University of St Andrews. School of Biology
University of St Andrews. Sea Mammal Research Unit
University of St Andrews. Scottish Oceans Institute
Biologging
Conservation
Migration
Moult
Movement
Non-breeding behaviour
Seamounts
Stable isotopes
Upwelling zones
QH301 Biology
NDAS
SDG 13 - Climate Action
SDG 14 - Life Below Water
QH301
Many marine predators migrate between breeding and non-breeding areas to target resources that are seasonal but spatio-temporally predictable, and so are vulnerable to climate-induced changes in prey phenology and abundance. In the Southern Ocean, small petrels are major consumers, but perturbations in the ecosystem through ocean warming are altering food-web structure and have been linked to poleward shifts in the distribution of their cold-water zooplankton prey. In this study, we focused on 2 small congeneric petrels: the broad-billed prion Pachyptila vittata and the Antarctic prion P. desolata. Both are planktivorous, but the broad-billed prion specialises in feeding on large copepods. We investigated historical trends in non-breeding distribution by analysing feather stable isotope ratios from a time-series dating back to 1926, and examined contemporary non-breeding distributions of broad-billed prions tracked using miniaturised geolocation-immersion loggers. After controlling temporally for the Suess effect, we found that the δ13C signatures of Antarctic prions, but not broad-billed prions, declined during the study period. This suggests a southward shift in Antarctic prion non-breeding distribution over the last century. Both species exhibited significant declines in δ15N during the same period, indicative of long-term decreases in marine productivity in their moulting areas, or changes in the trophic structure of prey communities. Tracked broad-billed prions migrated ca. 1000 km to an area east of the breeding colony where the Louisville seamount chain bisects the subtropical front. Topographically driven upwellings are stable and predictable features and may be crucial in aggregating plankton. Targeting seamounts could therefore mitigate the impact of climate-induced prey shifts by providing refugia for the broad-billed prion.
Publisher PDF
Peer reviewed
2016-11-09
2017-05-08T16:30:09Z
2017-05-08T16:30:09Z
2016-11-09
Journal article
Grecian , W J , Taylor , G A , Loh , G , McGill , R A R , Miskelly , C M , Phillips , R A , Thompson , D R & Furness , R W 2016 , ' Contrasting migratory responses of two closely-related seabirds to long-term climate change ' , Marine Ecology Progress Series , vol. 559 , pp. 231-242 . https://doi.org/10.3354/meps11875
0171-8630
PURE: 249951353
PURE UUID: df960e08-4f87-43ea-b2f3-60a3a18e743e
Scopus: 84994756758
ORCID: /0000-0002-6428-719X/work/32706772
http://hdl.handle.net/10023/10726
https://doi.org/10.3354/meps11875
http://eprints.gla.ac.uk/123065/
eng
Marine Ecology Progress Series
© The Authors 2016. Open Access under Creative Commons by Attribution Licence. Use, distribution and reproduction are unrestricted. Authors and original publication must be credited.
12
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oai:research-repository.st-andrews.ac.uk:10023/34722024-02-20T00:40:13Zcom_10023_45com_10023_17com_10023_184com_10023_39com_10023_879com_10023_878col_10023_46col_10023_185col_10023_880
Development of a contact call in black-capped chickadees (Poecile atricapillus) hand-reared in different acoustic environments
Guillette, Lauren
Bloomfiled, Laurie
Batty, Emily
Dawson, Michael
Sturdy, Chris
University of St Andrews. School of Biology
University of St Andrews. Centre for Social Learning & Cognitive Evolution
QL Zoology
QL
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.
Peer reviewed
2011
2013-04-06T20:31:01Z
2013-04-06T20:31:01Z
Journal article
49562541
add1dcc8-af05-48db-8922-a675438c1cd0
82255163970
Guillette , L , Bloomfiled , L , Batty , E , Dawson , M & Sturdy , C 2011 , ' Development of a contact call in black-capped chickadees ( Poecile atricapillus ) hand-reared in different acoustic environments ' , Journal of the Acoustical Society of America , vol. 130 , no. 4 , pp. 2249-2256 . https://doi.org/10.1121/1.3628343
0001-4966
https://hdl.handle.net/10023/3472
10.1121/1.3628343
eng
Journal of the Acoustical Society of America
232522
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oai:research-repository.st-andrews.ac.uk:10023/94242023-04-18T10:02:29Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner
Giroux, Xavier
MacNeill, Stuart
University of St Andrews. Biomedical Sciences Research Complex
University of St Andrews. School of Biology
DNA repair
Sliding clamp
Double-strand breaks
PCNA
Archaea
QR Microbiology
BDC
QR
This work was supported by the USAF Office of Scientific Research under award number FA9550-10-1-0421.
The sliding clamp PCNA plays a vital role in a number of DNA repair pathways in eukaryotes and archaea by acting as a stable platform onto which other essential protein factors assemble. Many of these proteins interact with PCNA via a short peptide sequence known as a PIP (PCNA interacting protein) motif. Here we describe the identification and functional analysis of a novel PCNA interacting protein NreA that is conserved in the archaea and which has a PIP motif at its C-terminus. Using the genetically tractable euryarchaeon Haloferax volcanii as a model system, we show that the NreA protein is not required for cell viability but that loss of NreA (or replacement of the wild-type protein with a truncated version lacking the C-terminal PIP motif) results in an increased sensitivity to the DNA damaging agent mitomycin C (MMC) that correlates with delayed repair of MMC-induced chromosomal DNA damage monitored by pulsed-field gel electrophoresis (PFGE). Genetic epistasis analysis in Hfx. volcanii suggests that NreA works together with the UvrABC proteins in repairing DNA damage resulting from exposure to MMC. The wide distribution of NreA family members implies an important role for the protein in DNA damage repair in all archaeal lineages.
Postprint
Peer reviewed
2015-12-22
2016-09-04T23:33:10Z
2016-09-04T23:33:10Z
2016-09-04
Journal article
Giroux , X & MacNeill , S 2015 , ' A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner ' , Molecular Microbiology , vol. 99 , no. 1 , pp. 1-14 . https://doi.org/10.1111/mmi.13210
0950-382X
PURE: 214045682
PURE UUID: c4b5df8d-e195-405c-8446-cbcf1eedc2f3
Scopus: 84955179044
ORCID: /0000-0002-0555-0007/work/39107857
WOS: 000369157900001
http://hdl.handle.net/10023/9424
https://doi.org/10.1111/mmi.13210
eng
Molecular Microbiology
© 2015 John Wiley & Sons Ltd. This work is made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at: https://dx.doi.org/10.1111/mmi.13210. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving (http://olabout.wiley.com/WileyCDA/Section/id-820227.html#terms)
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oai:research-repository.st-andrews.ac.uk:10023/33632023-04-18T09:45:14Zcom_10023_45com_10023_17com_10023_2323com_10023_39com_10023_879com_10023_878col_10023_46col_10023_2324col_10023_880
Genetic analysis of life-history constraint and evolution in a wild ungulate population
Morrissey, Michael Blair
Walling, Craig
Wilson, Alastair
Pemberton, Josephine
Clutton-Brock, Tim
Kruuk, Loeske
University of St Andrews. School of Biology
University of St Andrews. Centre for Biological Diversity
Life history
Quantitative genetics
Natural selection
Constraint
Projection model
Sensitivity
Red deer
Cervus elaphus
QH Natural history
QH
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.
Publisher PDF
Peer reviewed
2012-04
2013-02-24T00:21:59Z
2013-02-24T00:21:59Z
2013-02-24
Journal article
Morrissey , M B , Walling , C , Wilson , A , Pemberton , J , Clutton-Brock , T & Kruuk , L 2012 , ' Genetic analysis of life-history constraint and evolution in a wild ungulate population ' , American Naturalist , vol. 179 , no. 4 , pp. E97-E114 . https://doi.org/10.1086/664686
0003-0147
PURE: 20353286
PURE UUID: d3f96f7d-5fff-4cbb-b141-7155aa13f9b3
Scopus: 84858785923
http://hdl.handle.net/10023/3363
https://doi.org/10.1086/664686
eng
American Naturalist
© 2012 by The University of Chicago.
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oai:research-repository.st-andrews.ac.uk:10023/46272024-03-22T00:39:35Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis
Garcia, JS
Baranovskiy, AG
Knatko, EV
Gray, FC
Tahirov, TH
MacNeill, Stuart Andrew
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH426 Genetics
QH426
JSG was supported by a BBSRC Research Committee studentship, EVK by the Darwin Trust of Edinburgh, and FCG and SAM by a Wellcome Trust Senior Research Fellowship in Basic Biomedical Sciences. AGB and THT research was supported by UNMC Eppley Cancer Center Pilot Project LB595 to THT.
Background: DNA polymerase delta plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol delta is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol d comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results: To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion: In the absence of a three-dimensional structure of the entire Pol d complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.
Peer reviewed
2009-08-17
2014-04-28T11:01:01Z
2014-04-28T11:01:01Z
Journal article
459175
5700f52c-e80f-4c10-91e5-cd294548f646
69549121822
Garcia , JS , Baranovskiy , AG , Knatko , EV , Gray , FC , Tahirov , TH & MacNeill , S A 2009 , ' Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis ' , BMC Molecular Biology , vol. 10 , 82 . https://doi.org/doi:10.1186/1471-2199-10-82
1471-2199
standrews_research_output: 31443
ORCID: /0000-0002-0555-0007/work/39107862
https://hdl.handle.net/10023/4627
doi:10.1186/1471-2199-10-82
http://www.scopus.com/inward/record.url?scp=69549121822&partnerID=8YFLogxK
http://www.biomedcentral.com/1471-2199/10/82
eng
BMC Molecular Biology
13
2061054
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oai:research-repository.st-andrews.ac.uk:10023/20422022-04-22T11:30:05Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Characteristics of the Ascophyllum nodosum stands and their associated diversity along the coast of Brittany, France
Gollety, Claire
Thiébaut, Eric
Davoult, Dominique
University of St Andrews. School of Biology
University of St Andrews. Sediment Ecology Research Group
University of St Andrews. Marine Alliance for Science & Technology Scotland
Length
Biomass
Species richness
Rocky intertidal community
QH Natural history
QH
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.
Publisher PDF
Peer reviewed
2011-05
2011-11-17T09:29:01Z
2011-11-17T09:29:01Z
Journal article
Gollety , C , Thiébaut , E & Davoult , D 2011 , ' Characteristics of the Ascophyllum nodosum stands and their associated diversity along the coast of Brittany, France ' , Journal of the Marine Biological Association of the United Kingdom , vol. 91 , no. 3 , pp. 569-577 . https://doi.org/10.1017/S0025315410000901
0025-3154
PURE: 15679822
PURE UUID: 5a50a2f9-5bbc-41c4-a882-92593572a650
Scopus: 80055057130
http://hdl.handle.net/10023/2042
https://doi.org/10.1017/S0025315410000901
eng
Journal of the Marine Biological Association of the United Kingdom
(c) Marine Biological Association of the United Kingdom, 2010
9
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oai:research-repository.st-andrews.ac.uk:10023/76522023-04-18T10:03:14Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1
Wregglesworth, Kristin
Barker, Daniel
University of St Andrews. School of Biology
Chlorobium tepidum TLS
Pelodictyon phaeoclathratiforme BU-1
Chlorobiaceae
Protein families
Comparative genomics
OrthoMCL
Ortholog
Paralog
Raspberry Pi
QH301 Biology
QA75 Electronic computers. Computer science
QH301
QA75
Date of Acceptance: 30/09/2015
Background: Chlorobium tepidum and Pelodictyon phaeoclathratiforme are organisms within the green sulphur bacteria family, Chlorobiaceae, occupying very different habitats. It has recently been proposed that the genera Chlorobium and Pelodictyon are synonymous. Findings: To investigate generic boundaries for the two species, protein families were predicted computationally based on sequence similarity across the genome-wide protein sets of Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1. The distribution of the resulting protein families across the two species was summarized. The largest number of families exhibited 1:1 putative orthology between the two species (1468 families). Of families unique to one of the species, the largest number was unique to P. phaeoclathratiforme (113 families), of which the largest family contained pentapeptide repeat proteins (16 proteins). Families unique to P. phaeoclathratiforme also included a family of gas vesicle synthesis proteins (four proteins). Although only 7 families were identified as containing paralogous proteins in both species (with two or more proteins in each species), this group included families of major biochemical importance. One such family, with three members in each species, contained magnesium chelatase, an enzyme involved in the chlorophyll biosynthetic pathway. Conclusion: The unique protein family groups in both C. tepidum and P. phaeoclathratiforme mirror the occupancy of different environments, while key shared family groups provide evidence for a common origin for the species, as previously suggested in the literature. The current study only uses sequence similarity-based protein families for the two species. This, alone, does not permit a firm conclusion to be drawn on the taxonomic question, of whether the two species belong in one genus or two.
Publisher PDF
Peer reviewed
2015-10-14
2015-10-14T16:10:02Z
2015-10-14T16:10:02Z
Journal article
Wregglesworth , K & Barker , D 2015 , ' A comparison of the protein-coding genomes of two green sulphur bacteria, Chlorobium tepidum TLS and Pelodictyon phaeoclathratiforme BU-1 ' , BMC Research Notes , vol. 8 , 565 . https://doi.org/10.1186/s13104-015-1535-8
1756-0500
PURE: 220802549
PURE UUID: d733ec61-8833-4cfa-8571-ecd46fb89b41
Scopus: 84944048700
http://hdl.handle.net/10023/7652
https://doi.org/10.1186/s13104-015-1535-8
http://www.biomedcentral.com/1756-0500/8/565#sec5
eng
BMC Research Notes
© 2015 Wreggelsworth and Barker. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
5
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oai:research-repository.st-andrews.ac.uk:10023/4912019-03-29T10:18:33Zcom_10023_45com_10023_17col_10023_46
Coda vocalizations recorded in breeding areas are almost entirely produced by mature female sperm whales (Physeter macrocephalus)
Marcoux, M
Whitehead, H
Rendell, L
We investigated the use and function of coda communication by sperm whales (Physeter macrocephalus L., 1758 (=Physeter Catodon L., 1758)) Codas are stereotyped patterns of clicks often made by sperm whales in social contexts. We used the pulsed structure of coda clicks recorded from socializing female/immature groups to estimate the bodylength distribution of the animals producing the codas. Ninety-five percent of the 10653 codas that we measured were produced by whales measuring from 9 to 11 m. This size range corresponds to the length of mature females. We compared these data to a length distribution calculated from photographic measurements of individuals from the same groups encountered during the same studies. There were more whales shorter than 8.5 m (10.0%)and longer than 12.5 m (2.7%) in the photographic length distribution than in that of the coda producers (0.30% and 0.08% respectively). Since males leave their natal group when they are shorter than 9 m and return to breeding areas when they measure 13 m or more, our data shows that the codas were produced almost entirely by mature females. We suggest that coda communication serves several functions, including social bonding.
Publisher PDF
2006
2008-05-23T12:04:42Z
2008-05-23T12:04:42Z
Journal article
Marcoux, M., Whitehead, H. and Rendell, L. (2006). Coda vocalizations recorded in breeding areas are almost entirely produced by mature female sperm whales (Physeter macrocephalus). Canadian Journal of Zoology 84(4): 609-614
00084301
StAndrews.ResExp.Output.OutputID.16276
http://pubs.nrc-cnrc.gc.ca/eng/home.html
http://hdl.handle.net/10023/491
en
Canadian Journal of Zoology
Copyright of NRC Research Press. Copyright notice at http://pubs.nrc-cnrc.gc.ca/cgi-bin/rp/rp2_copy_e?copyright_e.html
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Identifying the "demon whale-biter" : patterns of scarring on large whales attributed to a cookie-cutter shark Isistius sp
Best, Peter B.
Photopoulou, Theoni
University of St Andrews. School of Biology
University of St Andrews. Centre for Research into Ecological & Environmental Modelling
QH301 Biology
Biochemistry, Genetics and Molecular Biology(all)
Agricultural and Biological Sciences(all)
DAS
SDG 14 - Life Below Water
QH301
The presence of crater-like wounds on cetaceans and other large marine vertebrates and invertebrates has been attributed to various organisms. We review the evidence for the identity of the biting agent responsible for crater wounds on large whales, using data collected from sei (Balaenoptera borealis), fin (B. physalus), inshore and offshore Bryde's (B. brydeii sp) and sperm whales (Physeter macrocephalus) examined at the Donkergat whaling station, Saldanha Bay, South Africa between March and October 1963. We then analyse the intensity and trends in its predation on large whales. Despite the scarcity of local records, we conclude that a cookie-cutter shark Isistius sp is the most likely candidate. We make inferences about the trends in (1) total counts of unhealed bitemarks, and (2) the proportion of unhealed bitemarks that were recent. We use day of the year; reproductive class, social grouping or sex; depth interval and body length as candidate covariates. The models with highest support for total counts of unhealed bitemarks involve the day of the year in all species. Depth was an important predictor in all species except offshore Bryde's whales. Models for the proportion of recent bites were only informative for sei and fin whales. We conclude that temporal scarring patterns support what is currently hypothesized about the distribution and movements of these whale species, given that Isistius does not occur in the Antarctic and has an oceanic habitat. The incidence of fresh bites confirms the presence of Isistius in the region. The lower numbers of unhealed bites on medium-sized sperm whales suggests that this group spends more time outside the area in which bites are incurred, providing a clue to one of the biggest gaps in our understanding of the movements of mature and maturing sperm males.
Peer reviewed
2016-04-07
2018-04-11T09:30:13Z
2018-04-11T09:30:13Z
Journal article
252783133
2c8601a7-1071-429b-baba-921980feeee0
84963570240
27055057
Best , P B & Photopoulou , T 2016 , ' Identifying the "demon whale-biter" : patterns of scarring on large whales attributed to a cookie-cutter shark Isistius sp ' , PLoS ONE , vol. 11 , no. 4 , e0152643 . https://doi.org/10.1371/journal.pone.0152643
1932-6203
ORCID: /0000-0001-9616-9940/work/44748884
https://hdl.handle.net/10023/13113
10.1371/journal.pone.0152643
eng
PLoS ONE
20
1237003
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oai:research-repository.st-andrews.ac.uk:10023/39602023-07-25T10:30:02Zcom_10023_45com_10023_17com_10023_184com_10023_39com_10023_879com_10023_878col_10023_46col_10023_185col_10023_880
Reverberlocation in chickadees?
Mercado, Eduardo
Wisniewski, Matthew
Guillette, Lauren
McIntosh, Brittany
Sturdy, Christopher
University of St Andrews. School of Biology
University of St Andrews. Centre for Social Learning & Cognitive Evolution
Chickadee song
Amplitude
Frequency
Reverberation
Auditory distance
Spectral energy
Signal energy
Auditory filter bandwidth
Chickadee songs provide conspecifics with information about the locations of singers. Song amplitude, frequency, and reverberation all vary with distance, and it is thought that chickadees use such cues to estimate distance. The current study examined transmission of chickadee songs in an open field to assess whether other cues such as relative changes in inter-note timing or relative differences in spectral energy might also provide useful information about a singer's location. Surprisingly, the difference between direct signal energy and reverberant spectral energy provided clear indications of how far a song had traveled. Preliminary analyses suggest that this cue may be robust to variations in source level, note duration, note frequency, and transmission loss. If chickadees use this cue to judge auditory distance, then this may explain why they maintain specific spectral ratios between the notes within their songs. Specifically, the spectral spacing of notes within songs appears to be directly related to chickadee auditory filter bandwidth. We describe ranging of a singing chickadee based on the spectral profile of its songs as reverberlocation (construed as an instance of passive echolocation) because it involves comparisons between a direct signal and echoes of a signal.
Publisher PDF
2013-06
2013-08-14T08:31:01Z
2013-08-14T08:31:01Z
Conference item
Mercado , E , Wisniewski , M , Guillette , L , McIntosh , B & Sturdy , C 2013 , Reverberlocation in chickadees? in Proceedings of Meetings on Acoustics . vol. 19 , Acoustical Society of America (ASA) , Melville, NY , The 21st International Congress on Acoustics , Montreal , Canada , 2/07/13 . https://doi.org/10.1121/1.4799208
conference
1939-800X
PURE: 55875283
PURE UUID: 976845e1-7134-471d-a17e-1968d83edfb3
Scopus: 84878959812
http://hdl.handle.net/10023/3960
https://doi.org/10.1121/1.4799208
eng
Proceedings of Meetings on Acoustics
© 2013 Acoustical Society of America. Proceedings of Meetings on Acoustics (POMA) is an online open-access journal published by the Acoustical Society of America.
application/pdf
Acoustical Society of America (ASA)
oai:research-repository.st-andrews.ac.uk:10023/39032023-04-18T09:46:23Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_792com_10023_879com_10023_878col_10023_46col_10023_182col_10023_795col_10023_880
Wintertime water mass modification near an Antarctic Ice Shelf front
Arthun, Marius
Nicholls, Keith
Boehme, Lars
NERC
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Sea Mammal Research Unit
Antarctica
Continental shelf/slope
Sea ice
Southern Ocean
Mixed layer
In situ oceanic observations
GC Oceanography
GC
Under ice measurements by seals carrying a miniaturized conductivity–temperature–depth (CTD) instrument fill an important gap in existing observations. Here we present data from an instrumented Weddell seal that spent 8 consecutive months (February–September) for aging in close proximity to Filchner Ice Shelf, thus providing detailed information about the evolution of mixed layer hydrography during the austral autumn and winter. The resultant time series of hydrography shows strong seasonal water mass modification, dominated by an upper–ocean (0–300 m) salinity increase of 0.31, corresponding to 3.1 m sea ice growth, and the development of a 500 m thick winter mixed layer. Observations furthermore highlight a gradual salinity increase in a slow (3–5 cms−1 ) southward flow on the continental shelf, to wards the site, and suggest that the inferred ice production is better considered as a regional average rather than being purely local. No clear seasonality is observed in the properties of the underlying Ice Shelf Water.
Publisher PDF
Peer reviewed
2013-02
2013-08-01T23:50:04Z
2013-08-01T23:50:04Z
2013-08-02
Journal article
Arthun , M , Nicholls , K & Boehme , L 2013 , ' Wintertime water mass modification near an Antarctic Ice Shelf front ' , Journal of Physical Oceanography , vol. 43 , no. 2 , pp. 359-365 . https://doi.org/10.1175/JPO-D-12-0186.1
0022-3670
PURE: 27672043
PURE UUID: e6a3f07c-cc81-42f9-98bb-c4cc9bcb93d1
Scopus: 84875549662
http://hdl.handle.net/10023/3903
https://doi.org/10.1175/JPO-D-12-0186.1
http://journals.ametsoc.org/doi/full/10.1175/JPO-D-12-0186.1
NE/G014833/1
eng
Journal of Physical Oceanography
© 2013 American Meteorological Society
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oai:research-repository.st-andrews.ac.uk:10023/39102024-02-27T00:41:32Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Characterization and downstream mannose phosphorylation of human recombinant α-L-iduronidase produced in Arabidopsis complex glycan-deficient (cgl) seeds
He, Xu
Pierce, Owen
Haselhorst, Thomas
Kolarich, Daniel
Packer, Nicolle H.
Gloster, Tracey
Vocadlo, David J.
Qian, Yi
Brooks, Doug
Kermode, Allison R.
The Wellcome Trust
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
Arabidopsis cgl mutant
Mucopolysaccharidosis I
Human α-L-iduronidase
Mannose-6-phosphate recognition marker
N-glycosylation
QK Botany
QH426 Genetics
SDG 3 - Good Health and Well-being
QK
QH426
This work was supported by a Wellcome Trust award to TMG.
Mucopolysaccharidosis (MPS) I is a lysosomal storage disease caused by a deficiency of α-L-iduronidase (IDUA) (EC 3.2.1.76); enzyme replacement therapy is the conventional treatment for this genetic disease. Arabidopsis cgl mutants are characterized by a deficiency of the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of hybrid and complex N-glycan biosynthesis. To develop a seed-based platform for the production of recombinant IDUA for potential treatment of MPS I, cgl mutant seeds were generated to express human IDUA at high yields and to avoid maturation of the N-linked glycans on the recombinant human enzyme. Enzyme kinetic data showed that cgl-IDUA has similar enzymatic properties to the commercial recombinant IDUA derived from cultured Chinese hamster ovary (CHO) cells (AldurazymeTM). The N-glycan profile showed that cgl-derived IDUA contained predominantly high-mannose-type N-glycans (94.5%), and the residual complex/hybrid N-glycan-containing enzyme was efficiently removed by an additional affinity chromatography step. Furthermore, purified cgl-IDUA was amenable to sequential in vitro processing by soluble recombinant forms of the two enzymes that mediate the addition of the mannose-6-phosphate (M6P) tag in mammalian cells—UDP-GlcNAc:lysosomal enzyme N−acetylglucosamine (GlcNAc)−1−phosphotransferase—and GlcNAc−1−phosphodiester α−N−acetylglucosaminidase (the ‘uncovering enzyme’). Arabidopsis seeds provide an alternative system for producing recombinant lysosomal enzymes for enzyme replacement therapy; the purified enzymes can be subjected to downstream processing to create the M6P, a recognition marker essential for efficient receptor-mediated uptake into lysosomes of human cells.
Peer reviewed
2013-12
2013-08-05T14:01:07Z
2013-08-05T14:01:07Z
Journal article
62940362
ae658d84-9878-4323-a023-d7c7e25a5ba7
84888136369
He , X , Pierce , O , Haselhorst , T , Kolarich , D , Packer , N H , Gloster , T , Vocadlo , D J , Qian , Y , Brooks , D & Kermode , A R 2013 , ' Characterization and downstream mannose phosphorylation of human recombinant α-L-iduronidase produced in Arabidopsis complex glycan-deficient (cgl) seeds ' , Plant Biotechnology Journal , vol. 11 , no. 9 , pp. 1034–1043 . https://doi.org/10.1111/pbi.12096
1467-7644
https://hdl.handle.net/10023/3910
10.1111/pbi.12096
095828/Z/11/Z
eng
Plant Biotechnology Journal
323766
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oai:research-repository.st-andrews.ac.uk:10023/30222022-04-07T08:30:34Zcom_10023_45com_10023_17com_10023_792com_10023_39com_10023_879com_10023_878col_10023_46col_10023_795col_10023_880
Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates
Tinti, Michele
Johnson, Catherine
Toth, Rachel
Ferrier, David Ellard Keith
MacKintosh, Carol
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
Branchiostoma
Ciona
Hereditary spastic paraplegia
RAB3GAP1
RAB3GAP2
QH301 Biology
QH301
This work was supported by the UK Medical Research Council via a Developmental Pathway Funding Scheme award and a Research Councils UK fellowship in marine biology.
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.
Publisher PDF
Peer reviewed
2012-07
2012-07-25T15:31:02Z
2012-07-25T15:31:02Z
Journal article
Tinti , M , Johnson , C , Toth , R , Ferrier , D E K & MacKintosh , C 2012 , ' Evolution of signal multiplexing by 14-3-3-binding 2R-ohnologue protein families in the vertebrates ' , Open Biology , vol. 2 , 120103 . https://doi.org/10.1098/rsob.120103
2046-2441
PURE: 24998691
PURE UUID: 184c6da7-dc5b-4bfa-8b87-b6460a87c92e
Scopus: 84873901523
ORCID: /0000-0003-3247-6233/work/36423827
http://hdl.handle.net/10023/3022
https://doi.org/10.1098/rsob.120103
eng
Open Biology
© 2012 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.
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oai:research-repository.st-andrews.ac.uk:10023/148712022-07-05T10:30:02Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surface
Mücke, Katrin
Paulus, Christina
Bernhardt, Katharina
Gerrer, Katrin
Schön, Kathrin
Fink, Alina
Sauer, Eva-Maria
Asbach-Nitzsche, Alexandra
Harwardt, Thomas
Kieninger, Bärbel
Kremer, Werner
Kalbitzer, Hans Robert
Nevels, Michael
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
Amino acid sequence
Binding sites
Chromosomes, human
Cytomegalovirus
Cytomegalovirus infections
Histones
Humans
Immediate-early proteins
Models, molecular
Molecular sequence data
Nucleosomes
Protein binding
Protein structure, tertiary
QH301 Biology
BDY
R2C
QH301
The 72-kDa immediate early 1 (IE1) protein encoded by human cytomegalovirus (hCMV) is a nuclearly localized promiscuous regulator of viral and cellular transcription. IE1 has long been known to associate with host mitotic chromatin, yet the mechanisms underlying this interaction have not been specified. In this study, we identify the cellular chromosome receptor for IE1. We demonstrate that the viral protein targets human nucleosomes by directly binding to core histones in a nucleic acid-independent manner. IE1 exhibits two separable histone-interacting regions with differential binding specificities for H2A-H2B and H3-H4. The H2A-H2B binding region was mapped to an evolutionarily conserved 10-amino-acid motif within the chromatin-tethering domain (CTD) of IE1. Results from experimental approaches combined with molecular modeling indicate that the IE1 CTD adopts a β-hairpin structure, docking with the acidic pocket formed by H2A-H2B on the nucleosome surface. IE1 binds to the acidic pocket in a way similar to that of the latency-associated nuclear antigen (LANA) of the Kaposi's sarcoma-associated herpesvirus. Consequently, the IE1 and LANA CTDs compete for binding to nucleosome cores and chromatin. Our work elucidates in detail how a key viral regulator is anchored to human chromosomes and identifies the nucleosomal acidic pocket as a joint target of proteins from distantly related viruses. Based on the striking similarities between the IE1 and LANA CTDs and the fact that nucleosome targeting by IE1 is dispensable for productive replication even in "clinical" strains of hCMV, we speculate that the two viral proteins may serve analogous functions during latency of their respective viruses.
Postprint
Peer reviewed
2014-01-15
2018-07-03T16:30:28Z
2018-07-03T16:30:28Z
Journal article
Mücke , K , Paulus , C , Bernhardt , K , Gerrer , K , Schön , K , Fink , A , Sauer , E-M , Asbach-Nitzsche , A , Harwardt , T , Kieninger , B , Kremer , W , Kalbitzer , H R & Nevels , M 2014 , ' Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surface ' , Journal of Virology , vol. 88 , no. 2 , pp. 1228-1248 . https://doi.org/10.1128/JVI.02606-13
0022-538X
PURE: 173809775
PURE UUID: ff54ae23-309b-49e8-b91c-8a937ad68f22
PubMed: 24227840
Scopus: 84891707336
ORCID: /0000-0002-7115-407X/work/28624008
ORCID: /0000-0002-4123-5629/work/47136648
http://hdl.handle.net/10023/14871
https://doi.org/10.1128/JVI.02606-13
eng
Journal of Virology
© 2014, American Society for Microbiology. This work has been made available online in accordance with the publisher’s policies. This is the author created accepted version manuscript following peer review and as such may differ slightly from the final published version. The final published version of this work is available at https://doi.org/10.1128/JVI.02606-13
21
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oai:research-repository.st-andrews.ac.uk:10023/162532024-03-09T00:43:37Zcom_10023_45com_10023_17com_10023_165com_10023_39com_10023_181com_10023_792com_10023_879com_10023_878col_10023_46col_10023_166col_10023_182col_10023_795col_10023_880
Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal
Schuert, Courtney
Pomeroy, Patrick
Twiss, Sean
University of St Andrews. School of Biology
University of St Andrews. Sea Mammal Research Unit
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Centre for Research into Ecological & Environmental Modelling
Accelerometer
Grey seal
Maternal behaviour
Breeding behaviour
Machine learning
Classification
QH301 Biology
NDAS
NERC
QH301
Funding for this work was provided by the Durham Doctoral Studentship scheme at Durham University and supported by Natural Environment Research Council’s core funding to the Sea Mammal Research Unit at the University of St. Andrews.
Background: Classifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus). Results: Using random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species. Conclusions: At this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.
Peer reviewed
2018-10-16
2018-10-17T10:30:11Z
2018-10-17T10:30:11Z
Journal article
255932668
0f248f59-9a4c-4bc1-8658-1e384fc9de41
85054869267
Schuert , C , Pomeroy , P & Twiss , S 2018 , ' Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal ' , Animal Biotelemetry , vol. 6 , 14 . https://doi.org/10.1186/s40317-018-0158-y
2050-3385
ORCID: /0000-0003-1603-5630/work/49580160
https://hdl.handle.net/10023/16253
10.1186/s40317-018-0158-y
eng
Animal Biotelemetry
17
1340526
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oai:research-repository.st-andrews.ac.uk:10023/60042024-03-26T00:41:48Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Gammaherpesvirus infection modulates the temporal and spatial expression of SCGB1A1 (CCSP) and BPIFA1 (SPLUNC1) in the respiratory tract
Leeming, Gail H
Kipar, Anja
Hughes, David J
Bingle, Lynne
Bennett, Elaine
Moyo, Nathifa A
Tripp, Ralph A
Bigley, Alison L
Bingle, Colin D
Sample, Jeffery T
Stewart, James P
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH301 Biology
NDAS
QH301
This work was supported by a Royal Society (London) University Research Fellowship (to JPS), by Biotechnology and Biological Sciences Research Council (UK) grants BB/K009664/1 (to JPS, AK, and GHL) and BB/K009737/1 (CDB and LB), US Public Health Service grant CA090208, the Penn State Hershey Cancer Institute, and a Biotechnology and Biological Sciences Research Council studentship (to GHL).
Murine γ-herpesvirus 68 (MHV-68) infection of Mus musculus-derived strains of mice is an established model of γ-herpesvirus infection. We have previously developed an alternative system using a natural host, the wood mouse (Apodemus sylvaticus), and shown that the MHV-68 M3 chemokine-binding protein contributes significantly to MHV-68 pathogenesis. Here we demonstrate in A. sylvaticus using high-density micro-arrays that M3 influences the expression of genes involved in the host response including Scgb1a1 and Bpifa1 that encode potential innate defense proteins secreted into the respiratory tract. Further analysis of MHV-68-infected animals showed that the levels of both protein and RNA for SCGB1A1 and BPIFA1 were decreased at day 7 post infection (p.i.) but increased at day 14 p.i. as compared with M3-deficient and mock-infected animals. The modulation of expression was most pronounced in bronchioles but was also present in the bronchi and trachea. Double staining using RNA in situ hybridization and immunohistology demonstrated that much of the BPIFA1 expression occurs in club cells along with SCGB1A1 and that BPIFA1 is stored within granules in these cells. The increase in SCGB1A1 and BPIFA1 expression at day 14 p.i. was associated with the differentiation of club cells into mucus-secreting cells. Our data highlight the role of club cells and the potential of SCGB1A1 and BPIFA1 as innate defense mediators during respiratory virus infection.
Peer reviewed
2015-06
2015-01-15T11:31:10Z
2015-01-15T11:31:10Z
Journal article
160454581
67cd6bd9-0874-4b1c-bd2c-d3973969c23f
25531566
84930033074
Leeming , G H , Kipar , A , Hughes , D J , Bingle , L , Bennett , E , Moyo , N A , Tripp , R A , Bigley , A L , Bingle , C D , Sample , J T & Stewart , J P 2015 , ' Gammaherpesvirus infection modulates the temporal and spatial expression of SCGB1A1 (CCSP) and BPIFA1 (SPLUNC1) in the respiratory tract ' , Laboratory Investigation , vol. 95 , pp. 610-624 . https://doi.org/10.1038/labinvest.2014.162
0023-6837
ORCID: /0000-0002-0090-5710/work/39632381
https://hdl.handle.net/10023/6004
10.1038/labinvest.2014.162
eng
Laboratory Investigation
15
831462
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oai:research-repository.st-andrews.ac.uk:10023/50402024-03-22T00:41:02Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
The conserved transmembrane proteoglycan Perdido/Kon-tiki is essential for myofibrillogenesis and sarcomeric structure in Drosophila
Pérez-Moreno, J J
Bischoff, M
Martín-Bermudo, M D
Estrada, B
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
Myogenesis
Muscle
Myofibril
Sarcomere
Integrin
Chondroitin sulfate proteoglycan
Perdido
Kon-tiki
CSPG4
MCSP
AN2
NG2
QR Microbiology
QR
M.B. was funded by a Wellcome Trust Senior Investigator Award to P. Lawrence (WT096645MA).
Muscle differentiation requires the assembly of high-order structures called myofibrils, composed of sarcomeres. Even though the molecular organization of sarcomeres is well known, the mechanisms underlying myofibrillogenesis are poorly understood. It has been proposed that integrin-dependent adhesion nucleates myofibril at the periphery of the muscle cell to sustain sarcomere assembly. Here, we report a role for the gene perdido (perd, also known as kon-tiki, a transmembrane chondroitin proteoglycan) in myofibrillogenesis. Expression of perd RNAi in muscles, prior to adult myogenesis, can induce misorientation and detachment of Drosophila adult abdominal muscles. In comparison to controls, perd-depleted muscles contain fewer myofibrils, localized at the cell periphery. These myofibrils are detached from each other and display a defective sarcomeric structure. Our results demonstrate that the extracellular matrix receptor Perd has a specific role in the assembly of myofibrils and in sarcomeric organization. We suggest that Perd acts downstream or in parallel to integrins to enable the connection of nascent myofibrils to the Z-bands. Our work identifies the Drosophila adult abdominal muscles as a model to investigate in vivo the mechanisms behind myofibrillogenesis.
Peer reviewed
2014-07
2014-07-18T16:31:01Z
2014-07-18T16:31:01Z
Journal article
123097998
e3b2afe1-bfe4-4068-991a-9fd92aea61e7
24794494
84904291881
Pérez-Moreno , J J , Bischoff , M , Martín-Bermudo , M D & Estrada , B 2014 , ' The conserved transmembrane proteoglycan Perdido/Kon-tiki is essential for myofibrillogenesis and sarcomeric structure in Drosophila ' , Journal of Cell Science , vol. 127 , pp. 3162-3173 . https://doi.org/10.1242/jcs.150425
0021-9533
ORCID: /0000-0002-0737-6321/work/41120271
https://hdl.handle.net/10023/5040
10.1242/jcs.150425
eng
Journal of Cell Science
6817816
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oai:research-repository.st-andrews.ac.uk:10023/6442010-12-07T15:30:02Zcom_10023_45com_10023_17col_10023_46
Is all learning innovation?
Rendell, L
Hoppitt, W
Kendal, J
Open peer commentary on "Animal innovation defined and operationalized" Grant Ramsey, Meredith L. Bastian and Carel van Schaik
Behavioral and Brain Sciences , Volume 30, Issue 04, August 2007, pp 393-407
Research on animal innovation is an underdeveloped field, and for this reason we welcome the efforts Ramsey and colleagues have made to stimulate its study in wild populations. However, we feel that in attempting to find an operational definition the authors have overstretched the idea of what we should consider innovation in some areas and over-restricted it in others.
Publisher PDF
2007
2009-04-06T14:58:37Z
2009-04-06T14:58:37Z
Journal article
Rendell, L., Hoppitt, W. and Kendal, J. (2007). Is all learning innovation? Behavioral and Brain Sciences 30(4): 421-422
0140525X
StAndrews.ResExp.Output.OutputID.24569
http://dx.doi.org/10.1017/S0140525X0700252X
http://hdl.handle.net/10023/644
en
Behavioral and Brain Sciences
Copyright of Cambridge University Press
560908 bytes
2541 bytes
application/pdf
text/plain
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421-422
oai:research-repository.st-andrews.ac.uk:10023/79262023-04-18T10:04:50Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_51com_10023_18com_10023_879com_10023_878col_10023_46col_10023_176col_10023_52col_10023_880
Taking a molecular motor for a spin : helicase mechanism studied by spin labelling and PELDOR
Constantinescu Aruxandei, Diana
Petrovic-Stojanovska, Biljana
Schiemann, Olav
Naismith, Jim
White, Malcolm F
The Wellcome Trust
BBSRC
University of St Andrews. School of Chemistry
University of St Andrews. EaSTCHEM
University of St Andrews. Biomedical Sciences Research Complex
University of St Andrews. School of Biology
QH301 Biology
NDAS
QH301
Welcome Trust programme grant [WT091825MA to M.F.W., J.H.N.]; Wellcome Trust multi-user equipment grant [099149/Z/12/Z]. Royal Society Wolfseon Merit Award (to M.F.W., J.H.N.). Funding for open access charge: Wellcome Trust [WT091825MA].
The complex molecular motions central to the functions of helicases have long attracted attention. Protein crystallography has provided transformative insights into these dynamic conformational changes, however important questions about the true nature of helicase configurations during the catalytic cycle remain. Using pulsed EPR (PELDOR or DEER) to measure interdomain distances in solution, we have examined two representative helicases: PcrA from superfamily 1 and XPD from superfamily 2. The data show that PcrA is a dynamic structure with domain movements that correlate with particular functional states, confirming and extending the information gleaned from crystal structures and other techniques. XPD in contrast is shown to be a rigid protein with almost no conformational changes resulting from nucleotide or DNA binding, which is well described by static crystal structures. Our results highlight the complimentary nature of PELDOR to crystallography and the power of its precision in understanding the conformational changes relevant to helicase function.
Publisher PDF
Peer reviewed
2015-12-10
2015-12-22T20:40:04Z
2015-12-22T20:40:04Z
Journal article
Constantinescu Aruxandei , D , Petrovic-Stojanovska , B , Schiemann , O , Naismith , J & White , M F 2015 , ' Taking a molecular motor for a spin : helicase mechanism studied by spin labelling and PELDOR ' , Nucleic Acids Research , vol. Advance Access . https://doi.org/10.1093/nar/gkv1373
0305-1048
PURE: 236138592
PURE UUID: 4938570e-a43a-4b48-9b61-251db030a21a
Scopus: 84966263778
ORCID: /0000-0003-1543-9342/work/47136123
WOS: 000371266000047
http://hdl.handle.net/10023/7926
https://doi.org/10.1093/nar/gkv1373
091825/Z/10/Z
BB/H017917/1
eng
Nucleic Acids Research
Copyright (c) The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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oai:research-repository.st-andrews.ac.uk:10023/129942023-04-18T23:45:54Zcom_10023_45com_10023_17com_10023_2323com_10023_39com_10023_879com_10023_878col_10023_46col_10023_2324col_10023_880
Professional medical writing support and the reporting quality of randomized controlled trial abstracts among high-impact general medical journals
Mills, Ira
Sheard, Catherine
Hays, Meredith
Douglas, Kevin
Winchester, Christopher C.
Gattrell, William T.
University of St Andrews. School of Biology
University of St Andrews. Centre for Biological Diversity
R Medicine
DAS
R
Background : In articles reporting randomized controlled trials, professional medical writing support is associated with increased adherence to Consolidated Standards of Reporting Trials (CONSORT). We set out to determine whether professional medical writing support was also associated with improved adherence to CONSORT for Abstracts. Methods : Using data from a previously published cross-sectional study of 463 articles reporting randomized controlled trials published between 2011 and 2014 in five top medical journals, we determined the association between professional medical writing support and CONSORT for Abstracts items using a Wilcoxon rank-sum test. Results : The mean proportion of adherence to CONSORT for Abstracts items reported was similar with and without professional medical writing support (64.3% vs 66.5%, respectively; p=0.30). Professional medical writing support was associated with lower adherence to reporting study setting (relative risk [RR]; 0.40; 95% confidence interval [CI], 0.23–0.70), and higher adherence to disclosing harms/side effects (RR 2.04; 95% CI, 1.37–3.03) and funding source (RR 1.75; 95% CI, 1.18–2.60). Conclusions : Although professional medical writing support was not associated with increased overall adherence to CONSORT for Abstracts, important aspects were improved with professional medical writing support, including reporting of adverse events and funding source. This study identifies areas to consider for improvement.
Publisher PDF
Peer reviewed
2017-09-23
2018-03-22T10:30:08Z
2018-03-22T10:30:08Z
Journal article
Mills , I , Sheard , C , Hays , M , Douglas , K , Winchester , C C & Gattrell , W T 2017 , ' Professional medical writing support and the reporting quality of randomized controlled trial abstracts among high-impact general medical journals ' , F1000Research , vol. 6 , 1489 . https://doi.org/10.12688/f1000research.12268.2
2046-1402
PURE: 252359840
PURE UUID: e904e441-25ab-4d5c-863d-88029419a629
crossref: 10.12688/f1000research.12268.2
Scopus: 85030674147
http://hdl.handle.net/10023/12994
https://doi.org/10.12688/f1000research.12268.2
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5615774/
eng
F1000Research
© 2017 Mills I et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
12
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oai:research-repository.st-andrews.ac.uk:10023/107752023-04-25T23:48:54Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_792com_10023_879com_10023_878col_10023_46col_10023_182col_10023_795col_10023_880
Inter- and intra-year variation in foraging areas of breeding kittiwakes (Rissa tridactyla)
Robertson, G. S.
Bolton, M.
Grecian, W. J.
Monaghan, P.
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Sea Mammal Research Unit
University of St Andrews. School of Biology
QH301 Biology
Aquatic Science
Ecology, Evolution, Behavior and Systematics
Ecology
SDG 14 - Life Below Water
QH301
This work was supported by the National Environment Research Council (award number NE/I528369/1) and the Royal Society for the Protection of Birds through a CASE studentship to the University of Glasgow.
While seabird conservation efforts have largely focused on protection from threats at the colony (e.g. reducing disturbance and predation), attention is increasingly being given to implementing protection measures for foraging areas at sea. For this to be effective, important foraging areas must be identified. Although numerous studies have examined seabird foraging behaviour, information is still lacking on the variability in area utilisation within and among breeding seasons. GPS devices were attached to adult black-legged kittiwakes breeding at an expanding North Sea colony (55°20′N, 1°32′W) during both incubation and chick-rearing in 2012 and during chick-rearing in 2011, to determine whether foraging areas remained consistent and to identify the oceanographic characteristics of areas used for foraging. The type and size of prey items consumed at different stages of the breeding cycle was also examined. During incubation (April-May 2012), kittiwakes foraged substantially further from the colony and fed on larger sandeels than when feeding chicks, and there was significant inter-annual variation in foraging areas used during the chick-rearing period (June-July 2011 and 2012). Foraging areas were characterised by cooler sea surface temperatures and areas of high chlorophyll a concentration, although association with specific oceanographic features changed within the breeding season and between years. These results emphasise the importance of considering how foraging areas and reliance on specific oceanographic conditions change over time when seeking to identify important marine areas for seabirds.
Publisher PDF
Peer reviewed
2014-09
2017-05-15T14:30:13Z
2017-05-15T14:30:13Z
Journal article
Robertson , G S , Bolton , M , Grecian , W J & Monaghan , P 2014 , ' Inter- and intra-year variation in foraging areas of breeding kittiwakes ( Rissa tridactyla ) ' , Marine Biology , vol. 161 , no. 9 , pp. 1973-1986 . https://doi.org/10.1007/s00227-014-2477-8
0025-3162
PURE: 249954407
PURE UUID: 81d1a8a6-e6df-482c-b57d-e40af2d7bc02
Scopus: 84907596371
ORCID: /0000-0002-6428-719X/work/32706782
http://hdl.handle.net/10023/10775
https://doi.org/10.1007/s00227-014-2477-8
eng
Marine Biology
© The Author(s) 2014. This article is published with open access at Springerlink.com. This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s) and the source are credited.
14
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oai:research-repository.st-andrews.ac.uk:10023/92432023-04-18T10:00:30Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Lipidomic analysis of fats and oils – a lot more than just omega-3
Smith, Terry K
European Commission
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH301 Biology
QH301
TKS research is supported in part by the Wellcome Trust, SUSLA, BBSRC and the European Community’s Seventh Framework Programme under grant agreement No. 602773 (Project KINDReD)
Edible oils and fats are among the most abundant cooking ingredients in the world, and are an important part of a healthy balanced diet, especially if they are high in omega-6 and omega-3 polyunsaturated fatty acids. Rather than just the total fatty acid compositions, the analysis of individual lipid species within these oils and fats has become increasingly important. Within the past decade several mass spectrometric lipidomics methods have been adapted and applied to the analysis of edible oils and fats. These methodologies are vital for the analysis of a plethora of lipid species that will be important for numerous health and sustainability issues in the future.
Postprint
Peer reviewed
2015-01
2016-08-02T12:30:05Z
2016-08-02T12:30:05Z
Journal article
Smith , T K 2015 , ' Lipidomic analysis of fats and oils – a lot more than just omega-3 ' , Lipid Technology , vol. 27 , no. 1 , pp. 7–10 . https://doi.org/10.1002/lite.201400061
PURE: 194604021
PURE UUID: ef7e4308-c3d9-4fc8-b721-1a3088c9022a
Scopus: 84920989243
http://hdl.handle.net/10023/9243
https://doi.org/10.1002/lite.201400061
602773
eng
Lipid Technology
© 2016, WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. This work is made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at onlinelibrary.wiley.com / https://dx.doi.org/10.1002/lite.201400061
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oai:research-repository.st-andrews.ac.uk:10023/46282023-04-18T09:40:07Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
MCM-GINS and MCM-MCM interactions in vivo visualised by bimolecular fluorescence complementation in fission yeast
Akman, Goekhan
MacNeill, Stuart Andrew
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH301 Biology
QH301
Background: Each of the three individual components of the CMG complex (Cdc45, MCM and GINS) is essential for chromosomal DNA replication in eukaryotic cells, both for the initiation of replication at origins and also for normal replication fork progression. The MCM complex is a DNA helicase that most likely functions as the catalytic core of the replicative helicase, unwinding the parental duplex DNA ahead of the moving replication fork, whereas Cdc45 and the GINS complex are believed to act as accessory factors for MCM. Results:To investigate interactions between components of the CMG complex, we have used bimolecular fluorescence complementation (BiFC) in the fission yeast Schizosaccharomyces pombe for the first time, to analyse protein-protein interactions between GINS and MCM subunits expressed from their native chromosomal loci. We demonstrate interactions between GINS andMCM in the nuclei of exponentially-growing fission yeast cells and on chromatin in binucleate S-phase cells. In addition we present evidence of MCM-MCM interactions in diploid fission yeast cells. As with GINS-MCM interactions, MCM-MCM interactions also occur on chromatin in S-phase cells. Conclusion: Bimolecular fluorescence complementation can be used in fission yeast to visualise interactions between two of the three components of the CMG complex, offering the prospect that this technique could in the future be used to allow studies on replication protein dynamics in living S. pombe cells.
Publisher PDF
Peer reviewed
2009-02-19
2014-04-28T12:01:01Z
2014-04-28T12:01:01Z
Journal article
Akman , G & MacNeill , S A 2009 , ' MCM-GINS and MCM-MCM interactions in vivo visualised by bimolecular fluorescence complementation in fission yeast ' , BMC Cell Biology , vol. 10 , 12 . https://doi.org/10.1186/1471-2121-10-12
1471-2121
PURE: 436168
PURE UUID: 8968fdf5-1e9b-4d71-a8f5-c43eef214fd5
standrews_research_output: 29594
Scopus: 62349139846
ORCID: /0000-0002-0555-0007/work/39107883
http://hdl.handle.net/10023/4628
https://doi.org/10.1186/1471-2121-10-12
http://www.scopus.com/inward/record.url?scp=62349139846&partnerID=8YFLogxK
http://www.biomedcentral.com/1471-2121/10/12
eng
BMC Cell Biology
© 2009 Akman and MacNeill; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
7
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oai:research-repository.st-andrews.ac.uk:10023/76512023-04-18T10:02:57Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer
Robson, James
Barker, Daniel
University of St Andrews. School of Biology
Chlamydia
Protochlamydia
Chlamydiae
parasite
endosymbiont
bioinformatics
comparative genomics
protein families
Raspberry Pi
QH301 Biology
QH301
Background: To demonstrate the bioinformatics capabilities of a low-cost computer, the Raspberry Pi, we present a comparison of the protein-coding gene content of two species in phylum Chlamydiae: Chlamydia trachomatis, a common sexually transmitted infection of humans, and Candidatus Protochlamydia amoebophila, a recently discovered amoebal endosymbiont. Identifying species-specific proteins and differences in protein families could provide insights into the unique phenotypes of the two species. Findings: Using a Raspberry Pi computer, sequence similarity-based protein families were predicted across the two species, Chlamydia trachomatis and Protochlamydia amoebophila, and their members counted. Examples include nine multi-protein families unique to C. trachomatis, 132 multi-protein families unique to P. amoebophila and one family with multiple copies in both. Most families unique to C. trachomatis were polymorphic outer-membrane proteins. Additionally, multiple protein families lacking functional annotation were found. Predicted functional interactions suggest one of these families is involved with the exodeoxyribonuclease V complex. Conclusion: The Raspberry Pi computer is adequate for a comparative genomics project of this scope. The protein families unique to P. amoebophila may provide a basis for investigating the host-endosymbiont interaction. However, additional species should be included; and further laboratory research is required to identify the functions of unknown or putative proteins. Multiple outer membrane proteins were found in C. trachomatis, suggesting importance for host evasion. The tyrosine transport protein family is shared between both species, with four proteins in C. trachomatis and two in P. amoebophila. Shared protein families could provide a starting point for discovery of wide-spectrum drugs against Chlamydiae.
Publisher PDF
Peer reviewed
2015-10-13
2015-10-14T16:10:00Z
2015-10-14T16:10:00Z
Journal article
Robson , J & Barker , D 2015 , ' Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer ' , BMC Research Notes , vol. 8 , 561 . https://doi.org/10.1186/s13104-015-1476-2
1756-0500
PURE: 218610472
PURE UUID: 9e5a318d-aac4-4fef-90c0-48655ed5d596
Scopus: 84943811337
http://hdl.handle.net/10023/7651
https://doi.org/10.1186/s13104-015-1476-2
http://www.biomedcentral.com/1756-0500/8/561/additional
eng
BMC Research Notes
© 2015 Robson and Barker. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
6
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oai:research-repository.st-andrews.ac.uk:10023/42302023-04-18T09:39:51Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Actin turnover is required for myosin-dependent mitochondrial movements in Arabidopsis root hairs
Zheng, Maozhong
Beck, Martina
Muller, Jens
Wang, Xiaohua
Wang, Qinli
Baluska, Frantisek
Logan, David
Samaj, Jozef
Lin, Jinxing
University of St Andrews. School of Biology
Actins
Mitochondria
Arabidopsis thaliana
Root hairs
Q Science
Q
Background: Previous studies have shown that plant mitochondrial movements are myosin-based along actin filaments, which undergo continuous turnover by the exchange of actin subunits from existing filaments. Although earlier studies revealed that actin filament dynamics are essential for many functions of the actin cytoskeleton, there are little data connecting actin dynamics and mitochondrial movements. Methodology/Principal Findings: We addressed the role of actin filament dynamics in the control of mitochondrial movements by treating cells with various pharmaceuticals that affect actin filament assembly and disassembly. Confocal microscopy of Arabidopsis thaliana root hairs expressing GFP-FABD2 as an actin filament reporter showed that mitochondrial distribution was in agreement with the arrangement of actin filaments in root hairs at different developmental stages. Analyses of mitochondrial trajectories and instantaneous velocities immediately following pharmacological perturbation of the cytoskeleton using variable-angle evanescent wave microscopy and/or spinning disk confocal microscopy revealed that mitochondrial velocities were regulated by myosin activity and actin filament dynamics. Furthermore, simultaneous visualization of mitochondria and actin filaments suggested that mitochondrial positioning might involve depolymerization of actin filaments on the surface of mitochondria. Conclusions/Significance: Base on these results we propose a mechanism for the regulation of mitochondrial speed of movements, positioning, and direction of movements that combines the coordinated activity of myosin and the rate of actin turnover, together with microtubule dynamics, which directs the positioning of actin polymerization events.
Publisher PDF
Peer reviewed
2009-06
2013-12-02T10:01:01Z
2013-12-02T10:01:01Z
Journal article
Zheng , M , Beck , M , Muller , J , Wang , X , Wang , Q , Baluska , F , Logan , D , Samaj , J & Lin , J 2009 , ' Actin turnover is required for myosin-dependent mitochondrial movements in Arabidopsis root hairs ' , PLoS ONE , vol. 4 , no. 6 , e5961 . https://doi.org/10.1371/journal.pone.0005961
1932-6203
PURE: 406956
PURE UUID: 5b77df04-587c-4009-8bed-37bc15330bf3
standrews_research_output: 23629
Scopus: 67650099504
http://hdl.handle.net/10023/4230
https://doi.org/10.1371/journal.pone.0005961
http://www.scopus.com/inward/record.url?scp=67650099504&partnerID=8YFLogxK
eng
PLoS ONE
© 2009 Zheng et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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oai:research-repository.st-andrews.ac.uk:10023/166362023-04-18T23:47:32Zcom_10023_45com_10023_17com_10023_2323com_10023_39com_10023_301com_10023_792com_10023_879com_10023_878col_10023_46col_10023_2324col_10023_303col_10023_795col_10023_880
BayesPiles : visualisation support for Bayesian network structure learning
Vogogias, Athanasios
Kennedy, Jessie
Archambault, Daniel
Bach, Benjamin
Smith, V Anne
Currant, Hannah
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Centre for Biological Diversity
Visualisation
Graphs
Bioinformatics
QA75 Electronic computers. Computer science
QA76 Computer software
QH301 Biology
NDAS
QA75
QA76
QH301
We address the problem of exploring, combining, and comparing large collections of scored, directed networks for understanding inferred Bayesian networks used in biology. In this field, heuristic algorithms explore the space of possible network solutions, sampling this space based on algorithm parameters and a network score that encodes the statistical fit to the data. The goal of the analyst is to guide the heuristic search and decide how to determine a final consensus network structure, usually by selecting the top-scoring network or constructing the consensus network from a collection of high-scoring networks. BayesPiles, our visualisation tool, helps with understanding the structure of the solution space and supporting the construction of a final consensus network that is representative of the underlying dataset. BayesPiles builds upon and extends MultiPiles to meet our domain requirements. We developed BayesPiles in conjunction with computational biologists who have used this tool on datasets used in their research. The biologists found our solution provides them with new insights and helps them achieve results that are representative of the underlying data.
Postprint
Peer reviewed
2018-11
2018-12-06T16:30:08Z
2018-12-06T16:30:08Z
2018-11-28
Journal article
Vogogias , A , Kennedy , J , Archambault , D , Bach , B , Smith , V A & Currant , H 2018 , ' BayesPiles : visualisation support for Bayesian network structure learning ' , ACM Transactions on Intelligent Systems and Technology , vol. 10 , no. 1 , 5 . https://doi.org/10.1145/3230623
2157-6904
PURE: 252830854
PURE UUID: e1b4c0c9-92ce-409a-9494-3bf1f97f11a6
Scopus: 85057586933
ORCID: /0000-0002-0487-2469/work/51470191
WOS: 000458017400005
http://hdl.handle.net/10023/16636
https://doi.org/10.1145/3230623
eng
ACM Transactions on Intelligent Systems and Technology
© 2018, Association for Computing Machinery. This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://doi.org/10.1145/3230623
23
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oai:research-repository.st-andrews.ac.uk:10023/40542023-04-25T23:37:32Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Abundance and survival of Pacific humpback whales in a proposed critical habitat area
Ashe, Erin
Wray, Janie
Picard, Christopher R.
Williams, Robert
University of St Andrews. School of Biology
QL Zoology
SDG 3 - Good Health and Well-being
QL
This research was funded through grants to Cetacealab and Gitga’at First Nation from Julie Walters and Sam Rose, and Fisheries and Oceans Canada (Cetacean Research Program, Species at Risk Program). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Humpback whales (Megaptera novaeangliae) were hunted commercially in Canada's Pacific region until 1966. Depleted to an estimated 1,400 individuals throughout the North Pacific, humpback whales are listed as Threatened under Canada's Species at Risk Act (SARA) and Endangered under the US Endangered Species Act. We conducted an 8-year photo-identification study to monitor humpback whale usage of a coastal fjord system in British Columbia (BC), Canada that was recently proposed as candidate critical habitat for the species under SARA. This participatory research program built collaborations among First Nations, environmental non-governmental organizations and academics. The study site, including the territorial waters of Gitga'at First Nation, is an important summertime feeding destination for migratory humpback whales, but is small relative to the population's range. We estimated abundance and survivorship using mark-recapture methods using photographs of naturally marked individuals. Abundance of humpback whales in the region was large, relative to the site's size, and generally increased throughout the study period. The resulting estimate of adult survivorship (0.979, 95% CI: 0.914, 0.995) is at the high end of previously reported estimates. A high rate of resights provides new evidence for inter-annual site fidelity to these local waters. Habitat characteristics of our study area are considered ecologically significant and unique, and this should be considered as regulatory agencies consider proposals for high-volume crude oil and liquefied natural gas tanker traffic through the area. Monitoring population recovery of a highly mobile, migratory species is daunting for low-cost, community-led science. Focusing on a small, important subset of the animals' range can make this challenge more tractable. Given low statistical power and high variability, our community is considering simpler ecological indicators of population health, such as the number of individuals harmed or killed each year by human activities, including ship strikes and entanglement in fishing gear.
Publisher PDF
Peer reviewed
2013-09-11
2013-09-16T08:31:01Z
2013-09-16T08:31:01Z
Journal article
Ashe , E , Wray , J , Picard , C R & Williams , R 2013 , ' Abundance and survival of Pacific humpback whales in a proposed critical habitat area ' , PLoS One , vol. 8 , no. 9 , e75228 . https://doi.org/10.1371/journal.pone.0075228
1932-6203
PURE: 69971802
PURE UUID: 5e40311b-ba55-41cf-9a1d-b8e30d483f79
Scopus: 84907299902
http://hdl.handle.net/10023/4054
https://doi.org/10.1371/journal.pone.0075228
eng
PLoS One
© 2013 Ashe et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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oai:research-repository.st-andrews.ac.uk:10023/41432023-04-18T09:45:23Zcom_10023_45com_10023_17com_10023_792com_10023_39com_10023_879com_10023_878col_10023_46col_10023_795col_10023_880
Female rose bitterling prefer MHC-dissimilar males : experimental evidence
Reichard, Martin
Spence, Rowena Grace Alison
Bryjova, Anna
Bryja, Pepa
Smith, Carl
University of St Andrews. School of Biology
University of St Andrews. Fish Behaviour and Biodiversity Research Group
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
Female mate choice
Sexual selection
Major Histocompatibility Complex (MHC) alleles
Q Science
Q
The role of genetic benefits in female mate choice remains a controversial aspect of sexual selection theory. In contrast to “good allele” models of sexual selection, “compatible allele” models of mate choice predict that females prefer mates with alleles complementary to their own rather than conferring additive effects. While correlative results suggest complementary genetic effects to be plausible, direct experimental evidence is scarce. A previous study on the Chinese rose bitterling (Rhodeus ocellatus) demonstrated a positive correlation between female mate choice, offspring growth and survival, and the functional dissimilarity between the Major Histocompatibility Complex (MHC) alleles of males and females. Here we directly tested whether females used cues associated with MHC genes to select genetically compatible males in an experimental framework. By sequentially pairing females with MHC similar and dissimilar males, based on a priori known MHC profiles, we showed that females discriminated between similar and dissimilar males and deposited significantly more eggs with MHC dissimilar males. Notably, the degree of dissimilarity was an important factor for female decision to mate, possibly indicating a potential threshold value of dissimilarity for decision making, or of an indirect effect of the MHC.
Publisher PDF
Peer reviewed
2012-07-18
2013-11-04T11:31:01Z
2013-11-04T11:31:01Z
Journal article
Reichard , M , Spence , R G A , Bryjova , A , Bryja , P & Smith , C 2012 , ' Female rose bitterling prefer MHC-dissimilar males : experimental evidence ' , PLoS One , vol. 7 , no. 7 , e40780 . https://doi.org/10.1371/journal.pone.0040780
1932-6203
PURE: 21240026
PURE UUID: 1d723748-b33e-4eda-8e8f-0d1c2175fb52
Scopus: 84864012521
ORCID: /0000-0003-3285-0379/work/47136202
http://hdl.handle.net/10023/4143
https://doi.org/10.1371/journal.pone.0040780
eng
PLoS One
© 2012 Reichard et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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oai:research-repository.st-andrews.ac.uk:10023/122662022-07-31T11:30:24Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_792com_10023_879com_10023_878col_10023_46col_10023_182col_10023_795col_10023_880
Sex-related differences in the postmolt distribution of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea
Langley, Izzy
Fedak, Mike
Nicholls, Keith
Boehme, Lars
NERC
University of St Andrews. Sea Mammal Research Unit
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
Weddell seal
Leptonychotes weddellii
Postmolt distribution
Sex-related differences
CTD-SRDL
State-space model
Resident state
Weddell Sea
GC Oceanography
QH301 Biology
NDAS
BDC
GC
QH301
Funding: NERC grants NE/G014833/1 (MF) and NE/G014086/1 (KWN).
The population of Weddell seals (Leptonychotes weddellii) in the southern Weddell Sea is in a unique position on the continental shelf edge, with vast shelf waters to the south, and deep Southern Ocean to the north. We describe sex-related differences in the winter distribution of this population, from data collected by 20 conductivity-temperature-depth satellite relay data loggers deployed in February 2011 at the end of the annual molt. The regional daily speed was calculated, and a state-space model was used to estimate behavioral states to positions along individuals’ tracks. GLMMs estimated that males and smaller individuals, diving in shallower water, traveled less far per day of deployment (males 14.6 ± 2.26 km/d, females 18.9 ± 2.42 km/d), and males were estimated to dive in shallower water (males 604 ± 382 m, females 1,875 ± 1,458 m). Males and smaller individuals were also estimated to be more resident; males spent an average 83.4% ± 7.7% of their time in a resident behavioral state, compared to females at 74.1% ± 7.1%. This evidence that male and female Weddell seals in the southern Weddell Sea are adopting different strategies has not been shown elsewhere along their circumpolar distribution.
Publisher PDF
Peer reviewed
2018-04
2017-12-06T10:30:11Z
2017-12-06T10:30:11Z
Journal article
Langley , I , Fedak , M , Nicholls , K & Boehme , L 2018 , ' Sex-related differences in the postmolt distribution of Weddell seals ( Leptonychotes weddellii ) in the southern Weddell Sea ' , Marine Mammal Science , vol. 34 , no. 2 , pp. 403-419 . https://doi.org/10.1111/mms.12461
1748-7692
PURE: 248865290
PURE UUID: 3180ed44-822f-41a1-ad34-3f3a446973e3
Scopus: 85037664828
ORCID: /0000-0002-9569-1128/work/47136252
WOS: 000430918200008
ORCID: /0000-0002-8957-1373/work/116598365
http://hdl.handle.net/10023/12266
https://doi.org/10.1111/mms.12461
NE/G014833/1
eng
Marine Mammal Science
© 2017 The Authors. Marine Mammal Science published by Wiley Periodicals, Inc. on behalf of Society for Marine Mammalogy. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
17
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oai:research-repository.st-andrews.ac.uk:10023/71822023-04-25T23:41:04Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Experimental evidence for the effect of small wind turbine proximity and operation on bird and bat activity
Minderman, J.
Pendlebury, C.J.
Pearce-Higgins, J.W.
Park, K.J.
University of St Andrews. School of Biology
QH301 Biology
SDG 7 - Affordable and Clean Energy
QH301
This research was funded by a research grant from the Leverhulme Trust (a U.K. based independent charity) to Dr. Kirsty Park, grant no. F/00 241/L. This grant has now expired.
The development of renewable energy technologies such as wind turbines forms a vital part of strategies to reduce greenhouse gas emissions worldwide. Although large wind farms generate the majority of wind energy, the small wind turbine (SWT, units generating <50 kW) sector is growing rapidly. In spite of evidence of effects of large wind farms on birds and bats, effects of SWTs on wildlife have not been studied and are likely to be different due to their potential siting in a wider range of habitats. We present the first study to quantify the effects of SWTs on birds and bats. Using a field experiment, we show that bird activity is similar in two distance bands surrounding a sample of SWTs (between 6–18 m hub height) and is not affected by SWT operation at the fine scale studied. At shorter distances from operating turbines (0–5 m), bat activity (measured as the probability of a bat ‘‘pass’’ per hour) decreases from 84% (71–91%) to 28% (11–54%) as wind speed increases from 0 to 14 m/s. This effect is weaker at greater distances (20–25 m) from operating turbines (activity decreases from 80% (65–89%) to 59% (32–81%)), and absent when they are braked. We conclude that bats avoid operating SWTs but that this effect diminishes within 20 m. Such displacement effects may have important consequences especially in landscapes where suitable habitat is limiting. Planning guidance for SWTs is currently lacking. Based on our results we recommend that they are sited at least 20 m away from potentially valuable bat habitat.
Publisher PDF
Peer reviewed
2012-07-30
2015-08-11T12:10:02Z
2015-08-11T12:10:02Z
Journal article
Minderman , J , Pendlebury , C J , Pearce-Higgins , J W & Park , K J 2012 , ' Experimental evidence for the effect of small wind turbine proximity and operation on bird and bat activity ' , PLoS One , vol. 7 , no. 7 , e41177 . https://doi.org/10.1371/journal.pone.0041177
1932-6203
PURE: 174255979
PURE UUID: 1db7fa10-dea3-4dcd-a9fa-6f1e00a3129e
Scopus: 84864430840
http://hdl.handle.net/10023/7182
https://doi.org/10.1371/journal.pone.0041177
eng
PLoS One
Copyright 2012 Minderman et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
7
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oai:research-repository.st-andrews.ac.uk:10023/117652023-04-25T23:46:33Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_879com_10023_878col_10023_46col_10023_182col_10023_880
Physiological constraints and energetic costs of diving behaviour in marine mammals : a review of studies using trained Steller sea lions diving in the open ocean
Rosen, David
Hindle, Allyson
Fahlman, Andreas
Gerlinsky, Carling
Goundie, Elizabeth
Hastie, Gordon Drummond
Volpov, Beth
Trites, Andrew
University of St Andrews. School of Biology
University of St Andrews. Sea Mammal Research Unit
Diving physiology
Stellar sea lions
Metabolism
Foraging
QH301 Biology
T-NDAS
SDG 14 - Life Below Water
QH301
The research was funded through a number of sources, including grants provided by the Natural Sciences and Engineering Research Council (Canada) and from the US National Oceanic and Atmospheric Administration to the North Pacific Universities Marine Mammal Research Consortium through the North Pacific Marine Science Foundation.
Marine mammals are characterized as having physiological specializations that maximize the use of oxygen stores to prolong time spent under water. However, it has been difficult to undertake the requisite controlled studies to determine the physiological limitations and trade-offs that marine mammals face while diving in the wild under varying environmental and nutritional conditions. For the past decade, Steller sea lions (Eumetopias jubatus) trained to swim and dive in the open ocean away from the physical confines of pools participated in studies that investigated the interactions between diving behaviour, energetic costs, physiological constraints, and prey availability. Many of these studies measured the cost of diving to understand how it varies with behaviour and environmental and physiological conditions. Collectively, these studies show that the type of diving (dive bouts or single dives), the level of underwater activity, the depth and duration of dives, and the nutritional status and physical condition of the animal affect the cost of diving and foraging. They show that dive depth, dive and surface duration, and the type of dive result in physiological adjustments (heart rate, gas exchange) that may be independent of energy expenditure. They also demonstrate that changes in prey abundance and nutritional status cause sea lions to alter the balance between time spent at the surface acquiring oxygen (and offloading CO2 and other metabolic by-products) and time spent at depth acquiring prey. These new insights into the physiological basis of diving behaviour further our understanding of the potential scope for behavioural responses of marine mammals to environmental changes, the energetic significance of these adjustments, and the consequences of approaching physiological limits.
Postprint
Peer reviewed
2017-01
2017-09-29T23:32:14Z
2017-09-29T23:32:14Z
2017-09-29
Journal article
Rosen , D , Hindle , A , Fahlman , A , Gerlinsky , C , Goundie , E , Hastie , G D , Volpov , B & Trites , A 2017 , ' Physiological constraints and energetic costs of diving behaviour in marine mammals : a review of studies using trained Steller sea lions diving in the open ocean ' , Journal of Comparative Physiology B: Biochemical, Systems, and Environmental Physiology , vol. 187 , no. 1 , pp. 29-50 . https://doi.org/10.1007/s00360-016-1035-8
0174-1578
PURE: 245970582
PURE UUID: 06a0f05e-0297-4e7a-b6df-252385cb654a
Scopus: 84989159472
ORCID: /0000-0002-9773-2755/work/54819218
http://hdl.handle.net/10023/11765
https://doi.org/10.1007/s00360-016-1035-8
eng
Journal of Comparative Physiology B: Biochemical, Systems, and Environmental Physiology
© Springer-Verlag Berlin Heidelberg 2016. This work has been made available online in accordance with the publisher’s policies. This is the author created accepted version manuscript following peer review and as such may differ slightly from the final published version. The final published version of this work is available at: https://doi.org/10.1007/s00360-016-1035-8
22
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oai:research-repository.st-andrews.ac.uk:10023/10342024-03-05T00:40:33Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_792com_10023_879com_10023_878col_10023_46col_10023_182col_10023_795col_10023_880
Assessing the effectiveness of conservation measures : resolving the "wicked" problem of the Steller sea lion
Boyd, Ian Lamont
University of St Andrews. School of Biology
University of St Andrews. Sea Mammal Research Unit
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
Wicked
Extinction
Risk
Viability
Population
Ecology
Alaska
Pacific
Mammal
Marine
Policy
Conservation
Problem
QH301 Biology
SDG 14 - Life Below Water
QH301
“Wicked” problems are those that are complex and that change when solutions are applied. Many conflicts in conservation fall in to this category. The study approached the problem of how to constrain the apparent wickedness of a problem in the conservation management of a species by using simple empirical indicators to carry out iterative assessment of the risk to a population and to document how this risk evolves in relation to the addition of new data and the implementation of management actions. Effects of high levels of uncertainty within data and also concerning population structure were examined through stochastic simulation and by exploration of scenarios. Historical trends in the example used, the Steller sea lion, showed rapid declines in abundance in some regions during the 1980s. The current total population is 130,000-150,000 Steller sea lions through Alaska and British Columbia and this number has been stable since about 1990 in spite of regional differences in population dynamics. Regional differences in the sequence of changes in the number of pups and non-pups, suggested that an internal re-distribution of juveniles could have happened between 1980 and 1990. Current productivity also appears close to the long term mean. Stochastic population projection using various scenarios showed that, based upon this history, the risk of extinction for the population has declined and is below reasonable thresholds for considering the population to be endangered.
Peer reviewed
2010-07
2010-10-19T10:16:17Z
2010-10-19T10:16:18Z
Journal article
486687
88c35ba3-da86-4864-b6c6-d7c5ab7d3e52
77954814411
Boyd , I L 2010 , ' Assessing the effectiveness of conservation measures : resolving the "wicked" problem of the Steller sea lion ' , Biological Conservation , vol. 143 , no. 7 , pp. 1664-1674 . https://doi.org/10.1016/j.biocon.2010.04.006
0006-3207
standrews_research_output: 32820
https://hdl.handle.net/10023/1034
10.1016/j.biocon.2010.04.006
http://www.scopus.com/inward/record.url?scp=77954814411&partnerID=8YFLogxK
eng
Biological Conservation
11
915810
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oai:research-repository.st-andrews.ac.uk:10023/55182024-03-28T00:41:20Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
The protein coexpression problem in biotechnology and biomedicine : virus 2A and 2A-like sequences provide a solution
Luke, Garry Alec
Ryan, Martin Denis
BBSRC
Medical Research Council
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
SDG 3 - Good Health and Well-being
The authors acknowledge the support of the UK Biotechnology and Biological Sciences Research Council (BBSRC), the Wellcome Trust and the UK Medical Research Council (MRC).
Synthetic biology enables us to create genes virtually at will. Ensuring that multiple genes are efficiently co-expressed within the same cell – to assemble multimeric complexes, to transfer biochemical pathways, to transfer ‘traits’, is more problematic. Viruses such as picornaviruses accomplish exactly this task: they generate multiple, different, proteins from a single open reading frame. The study of how foot-and-mouth disease virus (FMDV) controls it’s protein biogenesis lead to the discovery of a short oligopeptide sequence, ‘2A’, that is able to mediate a co-translational ‘cleavage’ between proteins. 2A and ‘2A-like’ sequences (from other viruses and cellular sequences) can be used to concatenate multiple gene sequences into a single gene, ensuring their co-expression within the same cell. These sequences are now being used in the treatment of cancer, in the production of pluripotent stem cells, to create transgenic plants and animals amongst a host of other biotechnological and biomedical applications.
Peer reviewed
2013-10
2014-09-30T23:01:37Z
2014-09-30T23:01:37Z
2014-10-01
Journal article
71028375
87f6131f-c4cc-4136-9da1-ca97f2c98821
84884224657
Luke , G A & Ryan , M D 2013 , ' The protein coexpression problem in biotechnology and biomedicine : virus 2A and 2A-like sequences provide a solution ' , Future Virology , vol. 8 , no. 10 , pp. 983-996 . https://doi.org/10.2217/fvl.13.82
1746-0794
ORCID: /0000-0002-0012-0614/work/47136059
https://hdl.handle.net/10023/5518
10.2217/fvl.13.82
http://www.futuremedicine.com/loi/fvl
BB/H007849/1
G0901002
eng
Future Virology
14
615574
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oai:research-repository.st-andrews.ac.uk:10023/46482022-04-14T15:30:36Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Improving classification in protein structure databases using text mining
Koussounadis, Antonis
Redfern, Oliver
Jones, David
University of St Andrews. School of Biology
QH301 Biology
QA75 Electronic computers. Computer science
QH301
QA75
AK was funded by BBSRC grant BBC5072531 and the BioSapiens Network of Excellence (funded by the European Commission within its FP6 programme, under the thematic area Life Sciences, Genomics and Biotechnology for Health), grant number: LSHG-CT-2003-503265
BACKGROUND: The classification of protein domains in the CATH resource is primarily based on structural comparisons, sequence similarity and manual analysis. One of the main bottlenecks in the processing of new entries is the evaluation of 'borderline' cases by human curators with reference to the literature, and better tools for helping both expert and non-expert users quickly identify relevant functional information from text are urgently needed. A text based method for protein classification is presented, which complements the existing sequence and structure-based approaches, especially in cases exhibiting low similarity to existing members and requiring manual intervention. The method is based on the assumption that textual similarity between sets of documents relating to proteins reflects biological function similarities and can be exploited to make classification decisions. RESULTS: An optimal strategy for the text comparisons was identified by using an established gold standard enzyme dataset. Filtering of the abstracts using a machine learning approach to discriminate sentences containing functional, structural and classification information that are relevant to the protein classification task improved performance. Testing this classification scheme on a dataset of 'borderline' protein domains that lack significant sequence or structure similarity to classified proteins showed that although, as expected, the structural similarity classifiers perform better on average, there is a significant benefit in incorporating text similarity in logistic regression models, indicating significant orthogonality in this additional information. Coverage was significantly increased especially at low error rates, which is important for routine classification tasks: 15.3% for the combined structure and text classifier compared to 10% for the structural classifier alone, at 10-3 error rate. Finally when only the highest scoring predictions were used to infer classification, an extra 4.2% of correct decisions were made by the combined classifier. CONCLUSION: We have described a simple text based method to classify protein domains that demonstrates an improvement over existing methods. The method is unique in incorporating structural and text based classifiers directly and is particularly useful in cases where inconclusive evidence from sequence or structure similarity requires laborious manual classification.
Publisher PDF
Peer reviewed
2009-05-05
2014-04-29T09:01:04Z
2014-04-29T09:01:04Z
Journal article
Koussounadis , A , Redfern , O & Jones , D 2009 , ' Improving classification in protein structure databases using text mining ' , BMC Bioinformatics , vol. 10 , no. 129 , pp. 638-647 . https://doi.org/10.1186/1471-2105-10-129
1471-2105
PURE: 6215264
PURE UUID: 52344b18-b696-4d32-8313-b57c28e9e192
Scopus: 66549127733
http://hdl.handle.net/10023/4648
https://doi.org/10.1186/1471-2105-10-129
http://www.ncbi.nlm.nih.gov/pubmed/19416501
eng
BMC Bioinformatics
© 2009 Koussounadis et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited
9
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oai:research-repository.st-andrews.ac.uk:10023/46292023-04-18T09:40:07Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Rapid regulation of protein activity in fission yeast
Boe, Cathrine A.
Garcia, Ignacio
Pai, Chen-Chun
Sharom, Jeffrey R.
Skjolberg, Henriette C.
Boye, Erik
Kearsey, Stephen
MacNeill, Stuart Andrew
Tyers, Michael D.
Grallert, Beata
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH301 Biology
QH301
Background: The fission yeast Schizosaccharomyces pombe is widely-used as a model organism for the study of a broad range of eukaryotic cellular processes such as cell cycle, genome stability and cell morphology. Despite the availability of extensive set of genetic, molecular biological, biochemical and cell biological tools for analysis of protein function in fissio n yeast, studies are often hampered by the lack of an effective method allowing for the rapid regulation of protein level or protein activity. Results: In order to be able to regulate protein function, we have made use of a previous finding that the hormone binding domain of steroid receptors can be used as a regulatory cassette to subject the activity of heterologous proteins to hormonal regulation. The approach is based on fusing the protein of interest to the hormone binding domain (HBD) of the estrogen receptor (ER). The HBD tag will attract the Hsp90 complex, which can render the fusion protein inactive. Upon addition of estradiol the protein is quickly released from the Hsp90 complex and thereby activated. We have tagged and characterised the induction of activity of four different HBD-tagged proteins. Here we show that the tag provided the means to effectively regulate the activity of two of these proteins. Conclusion: The estradiol-regulatable hormone binding do main provides a means to regulate the function of some, though not all, fission yeast proteins. This system may result in very quick and reversible activation of the protein of interest. Therefore it will be a powerful tool and it will open experimental approaches in fission yeast that have previously not been possible. Since fission yeast is a widely-used model organism, this will be valuable in many areas of research.
Publisher PDF
Peer reviewed
2008-05-05
2014-04-28T12:01:02Z
2014-04-28T12:01:02Z
Journal article
Boe , C A , Garcia , I , Pai , C-C , Sharom , J R , Skjolberg , H C , Boye , E , Kearsey , S , MacNeill , S A , Tyers , M D & Grallert , B 2008 , ' Rapid regulation of protein activity in fission yeast ' , BMC Cell Biology , vol. 9 , 23 . https://doi.org/10.1186/1471-2121-9-23
1471-2121
PURE: 436256
PURE UUID: 229845d6-2b63-46fe-aec0-32dc36921e80
standrews_research_output: 29597
Scopus: 44649163253
ORCID: /0000-0002-0555-0007/work/39107878
http://hdl.handle.net/10023/4629
https://doi.org/10.1186/1471-2121-9-23
http://www.scopus.com/inward/record.url?scp=44649163253&partnerID=8YFLogxK
http://www.biomedcentral.com/1471-2121/9/23
eng
BMC Cell Biology
© 2008 Bøe et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
11
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oai:research-repository.st-andrews.ac.uk:10023/42702022-04-26T10:30:07Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_802com_10023_879com_10023_878col_10023_46col_10023_176col_10023_804col_10023_880
Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe Ç
Edwards, Thomas E.
Cekan, Pavol
Reginsson, Gunnar Widtfeldt
Shelke, Sandip A.
Ferre D'Amare, Adrian R.
Schiemann, Olav
Sigurdsson, Snorri
BBSRC
University of St Andrews. School of Biology
University of St Andrews. Centre of Magnetic Resonance
University of St Andrews. Biomedical Sciences Research Complex
DNA
Crystallographic analysis
Deoxyguanosine
Oxazine linkage
DAS
Electron Paramagnetic Resonance (EPR) spectroscopy and fluorescence spectroscopy are complementary biophysical techniques used to examine the structure and dynamics of macromolecules. We have previously described the bi-functional spectroscopic probe Ç for the study of nucleic acid structure and dynamics using EPR and fluorescence spectroscopy. As with any newly designed spectroscopic probe, the utility, functionality, and the structural effects of the probe on the nucleic acid must be examined in detail. Initial EPR, fluorescence, and thermal denaturation studies indicated that the phenoxazine-derived spin-labeled deoxycytosine analog Ç forms a structurally non-perturbing base-pair with deoxyguanosine in DNA. Here we extend the analysis of the spectroscopic probe by presenting a detailed crystallographic study of this label based on small molecule crystal structures of the nucleoside base ç and its phenoxazine analog as well as a 1.7 Å resolution crystal structure of Ç within a decamer duplex A-form DNA. The DNA crystal structure confirms that the spin-labeled deoxycytosine analog forms a non-perturbing base-pair with deoxyguanosine. Interestingly, this structure and also the one of the phenoxazine base show the label in a planar conformation, whereas the structure of the free spin label base ç has a bend at the oxazine linkage. Density function theory (DFT) calculations reveal that both conformations are very close in energy and possess both the same frequency for bending at the oxazine linkage. These results are interpreted as a small degree of bending flexibility around the oxazine linkage, which may be a consequence of the antiaromaticity in this 16-pi electron ring system. Within DNA, the amplitude of the bending motion is likely to be restricted due to steric hindrance. This detailed structural analysis shows that the spin label base ç can be used with high confidence in EPR- or fluorescence-based structural and dynamics studies of oligonucleotides.
Publisher PDF
Peer reviewed
2011-05
2013-12-05T12:31:02Z
2013-12-05T12:31:02Z
Journal article
Edwards , T E , Cekan , P , Reginsson , G W , Shelke , S A , Ferre D'Amare , A R , Schiemann , O & Sigurdsson , S 2011 , ' Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe Ç ' , Nucleic Acids Research , vol. 39 , no. 10 , pp. 4419-4426 . https://doi.org/10.1093/nar/gkr015
0305-1048
PURE: 4103214
PURE UUID: ea412b71-41db-4d4e-8166-c96a1386534a
Scopus: 79961200425
http://hdl.handle.net/10023/4270
https://doi.org/10.1093/nar/gkr015
BB/F004583/1
eng
Nucleic Acids Research
© The Author(s) 2011. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
8
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oai:research-repository.st-andrews.ac.uk:10023/39612023-07-25T10:30:02Zcom_10023_45com_10023_17com_10023_184com_10023_39com_10023_879com_10023_878col_10023_46col_10023_185col_10023_880
Categories, concepts, and calls : auditory perceptual mechanisms and cognitive abilities across different types of birds.
Hahn, Allison
Guillette, Lauren
Hoeschele, Marisa
Cook, Robert
Sturdy, Christopher
University of St Andrews. School of Biology
University of St Andrews. Centre for Social Learning & Cognitive Evolution
Category perception
Concept formation
Auditory objects
Bird vocalisations
QL Zoology
QL
Although involving different animals, preparations, and objectives, our laboratories (Sturdy's and Cook's) are mutually interested in category perception and concept formation. The Sturdy laboratory has a history of studying perceptual categories in songbirds, while Cook laboratory has a history of studying abstract concept formation in pigeons. Recently, we undertook a suite of collaborative projects to combine our investigations to examine abstract concept formation in songbirds, and perception of songbird vocalizations in pigeons. This talk will include our recent findings of songbird category perception, songbird abstract concept formation (same/different task), and early results from pigeons' processing of songbird vocalizations in a same/different task. Our findings indicate that (1) categorization in birds seems to be most heavily influenced by acoustic, rather than genetic or experiential factors (2) songbirds treat their vocalizations as perceptual categories, both at the level of the note and species/whole call, (3) chickadees, like pigeons, can perceive abstract, same-different relations, and (4) pigeons are not as good at discriminating chickadee vocalizations as songbirds (chickadees and finches). Our findings suggest that although there are commonalities in complex auditory processing among birds, there are potentially important comparative differences between songbirds and non-songbirds in their treatment of certain types of auditory objects.
Publisher PDF
2013-06
2013-08-14T12:31:01Z
2013-08-14T12:31:01Z
Conference item
Hahn , A , Guillette , L , Hoeschele , M , Cook , R & Sturdy , C 2013 , Categories, concepts, and calls : auditory perceptual mechanisms and cognitive abilities across different types of birds. in Proceedings of Meetings on Acoustics . vol. 19 , Acoustical Society of America (ASA) , Melville, New York , The 21st International Congress on Acoustics , Montreal , Canada , 2/07/13 . https://doi.org/10.1121/1.4806086
conference
1939-800X
PURE: 52508657
PURE UUID: c7f6d86d-256c-4558-b05a-25bbaf1dff93
Scopus: 84878955726
http://hdl.handle.net/10023/3961
https://doi.org/10.1121/1.4806086
eng
Proceedings of Meetings on Acoustics
© 2013 Acoustical Society of America. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the Acoustical Society of America. The following article appeared in Proceedings of Meetings on Acoustics, Volume 19, and may be found at http://asadl.org/jasa/resource/1/jasman/v133/i5/p3442_s1
application/pdf
Acoustical Society of America (ASA)
oai:research-repository.st-andrews.ac.uk:10023/35662022-04-14T20:31:48Zcom_10023_45com_10023_17com_10023_184com_10023_39com_10023_879com_10023_878col_10023_46col_10023_185col_10023_880
Acoustic mechanisms of a species-based discrimination of the chick-a-dee call in sympatric black-capped (Poecile atricapillus) and mountain chickadees (P. gambeli)
Guillette, Lauren
Farrell, Tara
Hoeschele, Marisa
Sturdy, Christopher
University of St Andrews. School of Biology
University of St Andrews. Centre for Social Learning & Cognitive Evolution
Black-capped chickadee
Chick-a-dee call
Mountain chickadee
Operant conditioning
Songbird vocalization
Species discrimination
Sympatric
QL Zoology
QL
Previous perceptual research with black-capped and mountain chickadees has demonstrated that these species treat each other’s namesake chick-a-dee calls as belonging to separate, open-ended categories. Further, the terminal dee portion of the call has been implicated as the most prominent species marker. However, statistical classification using acoustic summary features suggests that all note-types contained within the chick-a-dee call should be sufficient for species classification. The current study seeks to better understand the note-type based mechanisms underlying species-based classification of the chick-a-dee call by black-capped and mountain chickadees. In two, complementary, operant discrimination experiments, both species were trained to discriminate the species of the signaler using either entire chick-a-dee calls, or individual note-types from chick-a-dee calls. In agreement with previous perceptual work we find that the D note had significant stimulus control over species-based discrimination. However, in line with statistical classifications, we find that all note-types carry species information. We discuss reasons why the most easily discriminated note-types are likely candidates to carry species-based cues.
Publisher PDF
Peer reviewed
2010
2013-05-29T12:01:02Z
2013-05-29T12:01:02Z
Journal article
Guillette , L , Farrell , T , Hoeschele , M & Sturdy , C 2010 , ' Acoustic mechanisms of a species-based discrimination of the chick-a-dee call in sympatric black-capped (Poecile atricapillus ) and mountain chickadees ( P. gambeli ) ' , Frontiers in Psychology , vol. 1 , 229 . https://doi.org/10.3389/fpsyg.2010.00229
1664-1078
PURE: 49565296
PURE UUID: c78cef60-82c1-43bc-b7e5-677cb09e01ed
Scopus: 79959606095
http://hdl.handle.net/10023/3566
https://doi.org/10.3389/fpsyg.2010.00229
http://www.frontiersin.org/comparative_psychology/10.3389/fpsyg.2010.00229/abstract
eng
Frontiers in Psychology
© 2010 Guillette, Farrell, Hoeschele and Sturdy. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
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oai:research-repository.st-andrews.ac.uk:10023/42282023-04-18T09:46:31Zcom_10023_45com_10023_17com_10023_181com_10023_39com_10023_792com_10023_879com_10023_878col_10023_46col_10023_182col_10023_795col_10023_880
Investigating annual diving behaviour by Hooded seals (Cystophora cristata) within the Northwest Atlantic Ocean
Andersen, Julie Marie
Skern-Mauritzen, Mette
Boehme, Lars
Wiersma, Yolanda F.
Rosvig-Asvid, Aqqalu
Hammill, Mike
Stenson, Garry
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Sea Mammal Research Unit
Hooded seals
Feeding migrations
Habitat use
Diving behaviour
Satellite Relay Data Loggers (SRDLs)
General Additive Models (GAMs)
First Passage Time (FPT)
This work was funded through the Atlantic Seal Research Programme, International Governance Programme (DFO), the Greenland Institute of Natural Resources, and a CFI grant to YFW. The authors also acknowledge the support of the Marine Alliance for Science and Technology for Scotland (MASTS) pooling initiative in the completion of this study. MASTS is funded by the Scottish Funding Council (grant reference HR09011) and contributing institutions. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
With the exception of relatively brief periods when they reproduce and moult, hooded seals, Cystophora cristata, spend most of the year in the open ocean where they undergo feeding migrations to either recover or prepare for the next fasting period. Valuable insights into habitat use and diving behaviour during these periods have been obtained by attaching Satellite Relay Data Loggers (SRDLs) to 51 Northwest (NW) Atlantic hooded seals (33 females and 18 males) during ice-bound fasting periods (2004−2008). Using General Additive Models (GAMs) we describe habitat use in terms of First Passage Time (FPT) and analyse how bathymetry, seasonality and FPT influence the hooded seals’ diving behaviour described by maximum dive depth, dive duration and surface duration. Adult NW Atlantic hooded seals exhibit a change in diving activity in areas where they spend >20 h by increasing maximum dive depth, dive duration and surface duration, indicating a restricted search behaviour. We found that male and female hooded seals are spatially segregated and that diving behaviour varies between sexes in relation to habitat properties and seasonality. Migration periods are described by increased dive duration for both sexes with a peak in May, October and January. Males demonstrated an increase in dive depth and dive duration towards May (post-breeding/pre-moult) and August–October (post-moult/pre-breeding) but did not show any pronounced increase in surface duration. Females dived deepest and had the highest surface duration between December and January (post-moult/pre-breeding). Our results suggest that the smaller females may have a greater need to recover from dives than that of the larger males. Horizontal segregation could have evolved as a result of a resource partitioning strategy to avoid sexual competition or that the energy requirements of males and females are different due to different energy expenditure during fasting periods.
Publisher PDF
Peer reviewed
2013-11-25
2013-11-29T17:01:03Z
2013-11-29T17:01:03Z
Journal article
Andersen , J M , Skern-Mauritzen , M , Boehme , L , Wiersma , Y F , Rosvig-Asvid , A , Hammill , M & Stenson , G 2013 , ' Investigating annual diving behaviour by Hooded seals (Cystophora cristata) within the Northwest Atlantic Ocean ' , PLoS One , vol. 8 , no. 11 , e80438 . https://doi.org/10.1371/journal.pone.0080438
1932-6203
PURE: 28385286
PURE UUID: 6c85dcb2-cd44-445e-a8ac-54d08a6a2db1
Scopus: 84894225498
http://hdl.handle.net/10023/4228
https://doi.org/10.1371/journal.pone.0080438
eng
PLoS One
© 2013 Andersen et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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oai:research-repository.st-andrews.ac.uk:10023/75812023-04-25T23:41:46Zcom_10023_45com_10023_17com_10023_301com_10023_39com_10023_181com_10023_792com_10023_309com_10023_879com_10023_878col_10023_46col_10023_303col_10023_182col_10023_795col_10023_311col_10023_880
Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur seals
Hooker, Sascha Kate
Barychka, Tatsiana
Jessopp, Mark J
Staniland, Iain J
The Royal Society
University of St Andrews. School of Biology
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. St Andrews Sustainability Institute
University of St Andrews. Sea Mammal Research Unit
Pinniped
Animal-attached camera
Sociality
Foraging
Groups
Arctocephalus gazella
QH301 Biology
SDG 14 - Life Below Water
QH301
Background: Although there have been recent advances in the development of animal-attached ‘proximity’ tags to remotely record the interactions of multiple individuals, the efficacy of these devices depends on the instrumentation of sufficient animals that subsequently have spatial interactions. Among densely colonial mammals such as fur seals, this remains logistically difficult, and interactions between animals during foraging have not previously been recorded. Results: We collected data on conspecific interactions during diving at sea using still image and video cameras deployed on 23 Antarctic fur seals. Animals carried cameras for a total of 152 days, collecting 38,098 images and 369 movies (total time 7.35 h). Other fur seals were detected in 74% of deployments, with a maximum of five seals seen at one time (n = 122 images, 28 videos). No predators other than conspecifics were observed. Detection was primarily limited by light conditions, since conspecifics were usually further from each other than the 1-m range illuminated by camera flash under low light levels. Other seals were recorded at a range of depths (average 27 ± 14.3 m, max 66 m). In terms of bouts of dives, still images of other seals were recorded in 5 single dives (of 330) and 28 bouts of dives <2 min apart (of 187). Linear mixed models suggested a relationship between conspecific observations per dive and the number of krill images recorded per dive. Using light conditions as a proxy for detectability, other seals were more likely to be observed at the bottom of dives than during descent or ascent. Seals were also more likely to be closer to each other and oriented perpendicular to each other at the bottom of dives, and in the same direction as each other during ascent. Conclusions: These results are contrary to animal-attached camera observations of penguin foraging, suggesting differing group-foraging tactics for these marine predators. Group foraging could have consequences for models linking predator behaviour to prey field densities since this relationship may be affected by the presence of multiple predators at the same patch.
Publisher PDF
Peer reviewed
2015-09-29
2015-10-01T23:12:40Z
2015-10-01T23:12:40Z
Journal article
Hooker , S K , Barychka , T , Jessopp , M J & Staniland , I J 2015 , ' Images as proximity sensors : the incidence of conspecific foraging in Antarctic fur seals ' , Animal Biotelemetry , vol. 3 , 37 . https://doi.org/10.1186/s40317-015-0083-2
2050-3385
PURE: 193890101
PURE UUID: 5e5e860f-a9b1-42aa-af33-c701de5b7611
Scopus: 85018192858
ORCID: /0000-0002-7518-3548/work/47136149
http://hdl.handle.net/10023/7581
https://doi.org/10.1186/s40317-015-0083-2
eng
Animal Biotelemetry
© 2015 Hooker et al. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
11
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oai:research-repository.st-andrews.ac.uk:10023/39972023-04-18T09:48:53Zcom_10023_45com_10023_17com_10023_792com_10023_39com_10023_879com_10023_878col_10023_46col_10023_795col_10023_880
Time is of the essence for ParaHox homeobox gene clustering.
Garstang, Myles Grant
Ferrier, David Ellard Keith
University of St Andrews. School of Biology
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Scottish Oceans Institute
ParaHox genes
Hox gene
Colinearity
ParaHox clustering
Q Science
Q
ParaHox genes, and their evolutionary sisters the Hox genes, are integral to patterning the anterior-posterior axis of most animals. Like the Hox genes, ParaHox genes can be clustered and exhibit the phenomenon of colinearity - gene order within the cluster matching gene activation. Two new instances of ParaHox clustering provide the first examples of intact clusters outside chordates, with gene expression lending weight to the argument that temporal colinearity is the key to understanding clustering.
Publisher PDF
Non peer reviewed
2013-06
2013-08-27T08:31:03Z
2013-08-27T08:31:03Z
Journal item
Garstang , M G & Ferrier , D E K 2013 , ' Time is of the essence for ParaHox homeobox gene clustering. ' , BMC Biology , vol. 11 , no. 72 , 72 . https://doi.org/10.1186/1741-7007-11-72
1741-7007
PURE: 66898552
PURE UUID: ab0860b6-6770-4c86-840a-5256ee805729
Scopus: 84879576564
http://hdl.handle.net/10023/3997
https://doi.org/10.1186/1741-7007-11-72
eng
BMC Biology
© 2013 Garstang and Ferrier; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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oai:research-repository.st-andrews.ac.uk:10023/32502023-04-18T09:43:12Zcom_10023_45com_10023_17com_10023_792com_10023_39com_10023_879com_10023_878col_10023_46col_10023_795col_10023_880
Tunicates push the limits of animal evo-devo
Ferrier, David Ellard Keith
University of St Andrews. School of Biology
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Marine Alliance for Science & Technology Scotland
QH301 Biology
QH301
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.
Publisher PDF
Peer reviewed
2011-01-20
2012-11-16T15:31:01Z
2012-11-16T15:31:01Z
Journal item
Ferrier , D E K 2011 , ' Tunicates push the limits of animal evo-devo ' , BMC Biology , vol. 9 , 3 . https://doi.org/10.1186/1741-7007-9-3
1741-7007
PURE: 5347147
PURE UUID: fc4414a0-09fd-4a1b-a4cb-9eccda5fae6f
Scopus: 78751573940
ORCID: /0000-0003-3247-6233/work/36423831
http://hdl.handle.net/10023/3250
https://doi.org/10.1186/1741-7007-9-3
eng
BMC Biology
© 2011 Ferrier; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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oai:research-repository.st-andrews.ac.uk:10023/11482023-04-18T09:42:04Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
The N-terminus of Bunyamwera orthobunyavirus NSs protein is essential for interferon antagonism
Van Knippenberg, Ingeborg Christine
Carlton-Smith, Charles
Elliott, Richard Michael
The Wellcome Trust
Medical Research Council
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QR Microbiology
QR
This work is supported by UK MRC and BBRC
Bunyamwera virus NSs protein is involved in the inhibition of cellular transcription and the interferon (IFN) response, and it interacts with the Med8 component of Mediator. A spontaneous mutant of a recombinant NSs-deleted Bunyamwera virus (rBUNdelNSs2) was identified and characterized. This mutant virus, termed mBUNNSs22, expresses a 21 aa N-terminally truncated form of NSs. Like rBUNdelNSs2, mBUNNSs22 is attenuated in IFN-deficient cells, and to a greater extent in IFN-competent cells. Both rBUNdelNSs2 and mBUNNSs22 are potent IFN inducers and their growth can be rescued by depleting cellular IRF3. Strikingly, despite encoding an NSs protein that contains the Med8 interaction domain, mBUNNSs22 fails to block RNA polymerase II activity during infection. Overall, our data suggest that both the interaction of NSs with Med8 and a novel unidentified function of the NSs N-terminus, seem necessary for Bunyamwera virus to counteract host antiviral responses.
Publisher PDF
Peer reviewed
2010-04
2010-10-27T16:04:31Z
2010-10-27T16:04:31Z
Journal article
Van Knippenberg , I C , Carlton-Smith , C & Elliott , R M 2010 , ' The N-terminus of Bunyamwera orthobunyavirus NSs protein is essential for interferon antagonism ' , Journal of General Virology , vol. 91 , no. 8 , pp. 2002-2006 . https://doi.org/10.1099/vir.0.021774-0
0022-1317
PURE: 3939425
PURE UUID: 94a44517-9d41-4763-8665-ec76e6d8fd3e
Scopus: 77955297217
http://hdl.handle.net/10023/1148
https://doi.org/10.1099/vir.0.021774-0
http://www.scopus.com/inward/record.url?scp=77955297217&partnerID=8YFLogxK
079810/Z/06/Z
G0800161
eng
Journal of General Virology
This article is published by the Society for General Microbiology under the Open Option which allows reuse for non commercial purposes.
5
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oai:research-repository.st-andrews.ac.uk:10023/39192023-04-18T09:46:20Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_301com_10023_126com_10023_31com_10023_879com_10023_878col_10023_46col_10023_176col_10023_303col_10023_128col_10023_880
Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells.
Rudhall, Andrew Peter
Antkowiak, Maciej
Tsampoula, Xanthi
Mazilu, Michael
Metzger, N Klaus
Gunn-Moore, Frank J
Dholakia, Kishan
University of St Andrews. School of Biology
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Biomedical Sciences Research Complex
University of St Andrews. School of Physics and Astronomy
Ultrashort femtosecond pulsed lasers
Membrane permeabilisation
Mammalian cells
Q Science
Q
The use of ultrashort femtosecond pulsed lasers to effect membrane permeabilisation and initiate both optoinjection and transfection of cells has recently seen immense interest. We investigate femtosecond laser-induced membrane permeabilisation in mammalian cells as a function of pulse duration, pulse energy and number of pulses, by quantifying the efficiency of optoinjection for these parameters. Depending on pulse duration and pulse energy we identify two distinct membrane permeabilisation regimes. In the first regime a nonlinear dependence of order 3.4-9.6 is exhibited below a threshold peak power of at least 6 kW. Above this threshold peak power, the nonlinear dependence is saturated resulting in linear behaviour. This indicates that the membrane permeabilisation mechanism requires efficient multiphoton absorption to produce free electrons but once this process saturates, linear absorption dominates. Our experimental findings support a previously proposed theoretical model and provide a step towards the optimisation of laser-mediated gene delivery into mammalian cells.
Publisher PDF
Peer reviewed
2012
2013-08-05T16:01:01Z
2013-08-05T16:01:01Z
Journal article
Rudhall , A P , Antkowiak , M , Tsampoula , X , Mazilu , M , Metzger , N K , Gunn-Moore , F J & Dholakia , K 2012 , ' Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells. ' , Nature Science Reports , vol. 2 , no. 858 , pp. 1-5 . https://doi.org/10.1038/srep00858
PURE: 27611994
PURE UUID: 35faf452-b6b9-48e9-90e8-fdbe5b0136dc
Scopus: 84870814873
ORCID: /0000-0003-3422-3387/work/34730443
http://hdl.handle.net/10023/3919
https://doi.org/10.1038/srep00858
eng
Nature Science Reports
© 2012 Nature Publishing Group. This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/
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oai:research-repository.st-andrews.ac.uk:10023/165322022-04-14T20:35:55Zcom_10023_45com_10023_17com_10023_879com_10023_878col_10023_46col_10023_880
Differential responses to gosling distress calls in parental and non-parental Greylag Geese
Loth, Alina
Frigerio, Didone
Kotrschal, Kurt
Szipl, Georgine
University of St Andrews. School of Biology
Greylag Geese
Anser anser
Distress calls
Vigilance behavior
Parental investment
Acoustic recognition
QH301 Biology
NDAS
QH301
GS received funding by the Austrian Science Fund (FWF) projects Y-366-B17 and W-1234-G17. AL was funded by the Austrian Federal Ministry of Science, Research and Economy (BMWFW, former BMWF) project SPA/03-005/Graugänse and DF by the Austrian Science Fund (FWF) project P-21489-B17.
The pre-fledging survival of Greylag goslings (Anser anser) is known to be influenced by parenting style and particularly parental vigilance. Visual and acoustic cues may be important in parental vigilance: if vision is blocked, for example in a highly structured habitat, acoustic recognition of the goslings by their parents would be beneficial. We confronted parental and non-parental Greylag Geese with playbacks of gosling distress calls and analyzed their behavioral responses. Parental geese showed a significant increase in their vigilance behavior during and after playbacks while geese without offspring showed increased comfort behavior. In a permutated discriminant function analysis, we found no family-specific vocal cues in gosling calls, and potential call familiarity did not have any effect on parental behavioral responses. Vigilance in families was further influenced by the number of goslings and gosling age, with increased vigilance when the number of goslings was high, and when goslings were younger. Parental females were more vigilant than parental males, suggesting differences in parental investment between males and females. We conclude that visual cues may be more important in offspring-related vigilance than calls, which elicited different behavioral responses depending on the social class of the geese.
Postprint
Peer reviewed
2018-04
2018-11-23T00:49:44Z
2018-11-23T00:49:44Z
2018-11-23
Journal article
Loth , A , Frigerio , D , Kotrschal , K & Szipl , G 2018 , ' Differential responses to gosling distress calls in parental and non-parental Greylag Geese ' , Journal of Ornithology , vol. 159 , no. 2 , pp. 401-412 . https://doi.org/10.1007/s10336-017-1521-0
2193-7192
PURE: 251740253
PURE UUID: 37a25e53-e352-4de8-b4f0-4e32a2c7c38c
Scopus: 85044732671
http://hdl.handle.net/10023/16532
https://doi.org/10.1007/s10336-017-1521-0
eng
Journal of Ornithology
© 2017, Dt. Ornithologen-Gesellschaft e.V. . This work has been made available online in accordance with the publisher’s policies. This is the author created, accepted version manuscript following peer review and may differ slightly from the final published version. The final published version of this work is available at https://doi.org/10.1007/s10336-017-1521-0
12
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oai:research-repository.st-andrews.ac.uk:10023/77352023-04-25T23:42:21Zcom_10023_45com_10023_17com_10023_165com_10023_39com_10023_181com_10023_792com_10023_879com_10023_878col_10023_46col_10023_166col_10023_182col_10023_795col_10023_880
Predicting future European breeding distributions of British seabird species under climate change and unlimited/no dispersal scenarios
Russell, Deborah Jill Fraser
Wanless, Sarah
Collingham, Yvonne C.
Huntley, Brian
Hamer, Keith C.
NERC
University of St Andrews. School of Biology
University of St Andrews. Marine Alliance for Science & Technology Scotland
University of St Andrews. Scottish Oceans Institute
University of St Andrews. Centre for Research into Ecological & Environmental Modelling
University of St Andrews. Sea Mammal Research Unit
Climate envelope modelling
Climate response surface
Conservation
Ecological niche modelling
Extinction risk
Foraging ecology
Global warming
Marine spatial planning
Sea surface temperature
Species distribution model
QH301 Biology
SDG 13 - Climate Action
SDG 14 - Life Below Water
QH301
We thank the European Bird Census Council for their data on European seabird distributions. DJFR was supported by NERC UKPopNet.
Understanding which traits make species vulnerable to climatic change and predicting future distributions permits conservation efforts to be focused on the most vulnerable species and the most appropriate sites. Here, we combine climate envelope models with predicted bioclimatic data from two emission scenarios leading up to 2100, to predict European breeding distributions of 23 seabird species that currently breed in the British Isles. Assuming unlimited dispersal, some species would be “winners” (increase the size of their range), but over 65% would lose range, some by up to 80%. These “losers” have a high vulnerability to low prey availability, and a northerly distribution meaning they would lack space to move into. Under the worst-case scenario of no dispersal, species are predicted to lose between 25% and 100% of their range, so dispersal ability is a key constraint on future range sizes. More globally, the results indicate, based on foraging ecology, which seabird species are likely to be most affected by climatic change. Neither of the emissions scenarios used in this study is extreme, yet they generate very different predictions for some species, illustrating that even small decreases in emissions could yield large benefits for conservation.
Publisher PDF
Peer reviewed
2015-11-02
2015-11-03T15:40:06Z
2015-11-03T15:40:06Z
Journal article
Russell , D J F , Wanless , S , Collingham , Y C , Huntley , B & Hamer , K C 2015 , ' Predicting future European breeding distributions of British seabird species under climate change and unlimited/no dispersal scenarios ' , Diversity , vol. 7 , no. 4 , pp. 342-359 . https://doi.org/10.3390/d7040342
1424-2818
PURE: 209437567
PURE UUID: 6e2a05dd-523b-436f-b3f5-5929b6d0363d
Scopus: 84952908445
ORCID: /0000-0002-1969-102X/work/49052054
http://hdl.handle.net/10023/7735
https://doi.org/10.3390/d7040342
Agreement R8-H12-86
eng
Diversity
© 2015 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
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oai:research-repository.st-andrews.ac.uk:10023/67042023-04-18T09:56:36Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Identification of a candidate Rad1 subunit for the kinetoplastid 9-1-1 (Rad9-Hus1-Rad1) complex
MacNeill, Stuart
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
9-1-1 complex
sliding clamp
kinetoplastid
QH301 Biology
QH301
Date of Acceptance: 12/12/2014
The trimeric 9-1-1 (Rad9-Hus1-Rad1) complex plays an important role in the eukaryotic DNA damage response by recruiting DNA repair factors and checkpoint mediators to damaged sites. Extensively characterised in mammals and yeast, evidence is now emerging that 9-1-1 function is conserved beyond the relatively narrow evolutionary range of the Opisthokonts. Kinetoplastid Rad9 and Hus1 proteins have been identified and shown to be involved in the DNA damage response but Rad1 has remained elusive. In this study, PSI-BLAST iterative database searching, phylogenetic and structural modeling techniques are used to identify and characterise candidate Rad1 proteins in kinetoplastid organisms.
Publisher PDF
Peer reviewed
2014-12-19
2015-05-28T15:10:01Z
2015-05-28T15:10:01Z
Journal article
MacNeill , S 2014 , ' Identification of a candidate Rad1 subunit for the kinetoplastid 9-1-1 (Rad9-Hus1-Rad1) complex ' , Biology , vol. 3 , no. 4 , pp. 922-927 . https://doi.org/10.3390/biology3040922
2079-7737
PURE: 162370326
PURE UUID: a22c3443-8284-4d1b-a4a5-4bb1d1bef163
Scopus: 84919438877
ORCID: /0000-0002-0555-0007/work/39107845
http://hdl.handle.net/10023/6704
https://doi.org/10.3390/biology3040922
eng
Biology
© 2014 by the authors; licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/4.0/).
6
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oai:research-repository.st-andrews.ac.uk:10023/111422023-04-25T23:49:10Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
Foundational and translational research opportunities to improve plant health
Michelmore, Richard
Coaker, Gitta
Bart, Rebecca
Beattie, Gwyn
Bent, Andrew
Bruce, Toby
Cameron, Duncan
Dangl, Jeff
Dinesh-Kumar, Savithramma
Edwards, Rob
Eves-van den Akker, Sebastian
Gassmann, Walter
Greenberg, Jean
Hanley-Bowdoin, Linda
Harrison, Richard
He, Ping
Harvey, Jagger
Huffaker, Alisa
Hulbert, Scot
Innes, Roger
Jones, Jonathan
Kaloshian, Isghouhi
Kamoun, Sophien
Katagiri, Fumiaki
Leach, Jan
Ma, Wenbo
McDowell, John
Medford, June
Meyers, Blake
Nelson, Rebecca
Oliver, Richard
Qi, Yiping
Saunders, Diane
Shaw, Michael
Smart, Christine
Subudhi, Prasanta
Torrance, Lesley
Tyler, Brett
Valent, Barbara
Walsh, John
University of St Andrews. School of Biology
University of St Andrews. Biomedical Sciences Research Complex
QH301 Biology
SB Plant culture
T-NDAS
SDG 2 - Zero Hunger
SDG 3 - Good Health and Well-being
SDG 13 - Climate Action
QH301
SB
This whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on non-sustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.
Preprint
Preprint
Peer reviewed
2017-07
2017-07-04T10:30:22Z
2017-07-04T10:30:22Z
Journal article
Michelmore , R , Coaker , G , Bart , R , Beattie , G , Bent , A , Bruce , T , Cameron , D , Dangl , J , Dinesh-Kumar , S , Edwards , R , Eves-van den Akker , S , Gassmann , W , Greenberg , J , Hanley-Bowdoin , L , Harrison , R , He , P , Harvey , J , Huffaker , A , Hulbert , S , Innes , R , Jones , J , Kaloshian , I , Kamoun , S , Katagiri , F , Leach , J , Ma , W , McDowell , J , Medford , J , Meyers , B , Nelson , R , Oliver , R , Qi , Y , Saunders , D , Shaw , M , Smart , C , Subudhi , P , Torrance , L , Tyler , B , Valent , B & Walsh , J 2017 , ' Foundational and translational research opportunities to improve plant health ' , Molecular Plant-Microbe Interactions , vol. 30 , no. 7 , pp. 515-516 . https://doi.org/10.1094/MPMI-01-17-0010-CR
0894-0282
PURE: 250026590
PURE UUID: ba338bc6-e652-478a-b0ec-a3d78ae19669
Scopus: 85021386193
http://hdl.handle.net/10023/11142
https://doi.org/10.1094/MPMI-01-17-0010-CR
eng
Molecular Plant-Microbe Interactions
© 2017, the Author(s). This work has been made available online in accordance with the publisher’s policies. This is the author created, submitted version. The final published version of this work is available at apsjournals.apsnet.org / https://doi.org/10.1094/MPMI-01-17-0010-CR
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oai:research-repository.st-andrews.ac.uk:10023/42342022-04-26T11:30:20Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_1943com_10023_24com_10023_301com_10023_48com_10023_16com_10023_126com_10023_31com_10023_879com_10023_878col_10023_46col_10023_176col_10023_1944col_10023_303col_10023_49col_10023_128col_10023_880
Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platform
Mitchell, C.A.
Kalies, S.
Cizmár, T.
Heisterkamp, A.
Torrance, L.
Roberts, A.G.
Gunn-Moore, F.J.
Dholakia, K.
EPSRC
EPSRC
University of St Andrews. School of Biology
University of St Andrews. University of St Andrews
University of St Andrews. School of Physics and Astronomy
University of St Andrews. School of Medicine
University of St Andrews. Geography & Sustainable Development
University of St Andrews. Institute of Behavioural and Neural Sciences
University of St Andrews. Biomedical Sciences Research Complex
Pulsed laser beam
Cell membrane permeability
Photoporation
Femtosecond optical injection
Tobacco BY-2 cells
Q Science
Q
A tightly-focused ultrashort pulsed laser beam incident upon a cell membrane has previously been shown to transiently increase cell membrane permeability while maintaining the viability of the cell, a technique known as photoporation. This permeability can be used to aid the passage of membrane-impermeable biologically-relevant substances such as dyes, proteins and nucleic acids into the cell. Ultrashort-pulsed lasers have proven to be indispensable for photoporating mammalian cells but they have rarely been applied to plant cells due to their larger sizes and rigid and thick cell walls, which significantly hinders the intracellular delivery of exogenous substances. Here we demonstrate and quantify femtosecond optical injection of membrane impermeable dyes into intact BY-2 tobacco plant cells growing in culture, investigating both optical and biological parameters. Specifically, we show that the long axial extent of a propagation invariant (“diffraction-free”) Bessel beam, which relaxes the requirements for tight focusing on the cell membrane, outperforms a standard Gaussian photoporation beam, achieving up to 70% optoinjection efficiency. Studies on the osmotic effects of culture media show that a hypertonic extracellular medium was found to be necessary to reduce turgor pressure and facilitate molecular entry into the cells.
Publisher PDF
Peer reviewed
2013-11-14
2013-12-02T10:31:02Z
2013-12-02T10:31:02Z
Journal article
Mitchell , C A , Kalies , S , Cizmár , T , Heisterkamp , A , Torrance , L , Roberts , A G , Gunn-Moore , F J & Dholakia , K 2013 , ' Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platform ' , PLoS One , vol. 8 , no. 11 , e79235 . https://doi.org/10.1371/journal.pone.0079235
1932-6203
PURE: 71205869
PURE UUID: eae2748c-d5e9-4cb7-92b4-718acd4e1100
Scopus: 84893643628
Scopus: 84893643628
ORCID: /0000-0003-3422-3387/work/34730434
http://hdl.handle.net/10023/4234
https://doi.org/10.1371/journal.pone.0079235
EP/H045368/1
EP/J01771X/1
eng
PLoS One
© 2013 Mitchell et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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