2024-03-28T17:12:46Zhttps://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
00925njm 22002777a 4500
dc
Swiatek, Agnieszka
author
MacNeill, Stuart Andrew
author
2010-04-12
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.
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
QH301 Biology
The archaeo-eukaryotic GINS proteins and the archaeal primase catalytic subunit PriS share a common domain
oai:research-repository.st-andrews.ac.uk:10023/43112024-02-29T00:41:43Zcom_10023_175com_10023_39com_10023_48com_10023_16com_10023_879com_10023_878col_10023_176col_10023_49col_10023_880
00925njm 22002777a 4500
dc
Caie, Peter David
author
Schuur, Klaas
author
Oniscu, Anca
author
Mullen, Peter
author
Reynolds, Paul Andrew
author
Harrison, David James
author
2013-12
Histopathology, the examination of an architecturally artefactual, two dimensional, static image remains a potent tool allowing diagnosis and empirical expectation of prognosis. Considerable optimism exists that the advent of molecular genetic testing and other biomarker strategies will improve or even replace this ancient technology. A number of biomarkers add considerable value for prediction of whether a treatment will work. This short review argues that a systems medicine approach to pathology will not seek to replace traditional pathology, but rather augment it. Systems approaches need to incorporate quantitative morphological, protein, mRNA and DNA. A significant challenge for clinical implementation of systems pathology is how to optimise information available from tissue, which is frequently sub-optimal in quality and amount, and yet generate useful predictive models which work. The transition of histopathology to systems pathophysiology and the use of multiscale datasets ushers in a new era in diagnosis, prognosis and prediction based on analysis of human tissue.
Caie , P D , Schuur , K , Oniscu , A , Mullen , P , Reynolds , P A & Harrison , D J 2013 , ' Human tissue in systems medicine ' , FEBS Journal , vol. 280 , no. 23 , pp. 5949–5956 . https://doi.org/10.1111/febs.12550
1742-464X
https://hdl.handle.net/10023/4311
10.1111/febs.12550
Histopathology
Human disease
Predictive models
Systems biology
Systems medicine
RB Pathology
SDG 3 - Good Health and Well-being
Human tissue in systems medicine
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
00925njm 22002777a 4500
dc
Giroux, Xavier
author
MacNeill, Stuart
author
2015-12-22
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.
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
DNA repair
Sliding clamp
Double-strand breaks
PCNA
Archaea
QR Microbiology
BDC
A novel archaeal DNA repair factor that acts with the UvrABC system to repair mitomycin C-induced DNA damage in a PCNA-dependent manner
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
00925njm 22002777a 4500
dc
Garcia, JS
author
Baranovskiy, AG
author
Knatko, EV
author
Gray, FC
author
Tahirov, TH
author
MacNeill, Stuart Andrew
author
2009-08-17
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.
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
QH426 Genetics
Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis
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
00925njm 22002777a 4500
dc
He, Xu
author
Pierce, Owen
author
Haselhorst, Thomas
author
Kolarich, Daniel
author
Packer, Nicolle H.
author
Gloster, Tracey
author
Vocadlo, David J.
author
Qian, Yi
author
Brooks, Doug
author
Kermode, Allison R.
author
2013-12
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.
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
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
Characterization and downstream mannose phosphorylation of human recombinant α-L-iduronidase produced in Arabidopsis complex glycan-deficient (cgl) seeds
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
00925njm 22002777a 4500
dc
Mücke, Katrin
author
Paulus, Christina
author
Bernhardt, Katharina
author
Gerrer, Katrin
author
Schön, Kathrin
author
Fink, Alina
author
Sauer, Eva-Maria
author
Asbach-Nitzsche, Alexandra
author
Harwardt, Thomas
author
Kieninger, Bärbel
author
Kremer, Werner
author
Kalbitzer, Hans Robert
author
Nevels, Michael
author
2014-01-15
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.
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
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
Human cytomegalovirus major immediate early 1 protein targets host chromosomes by docking to the acidic pocket on the nucleosome surface
oai:research-repository.st-andrews.ac.uk:10023/98622023-04-19T00:41:20Zcom_10023_175com_10023_39com_10023_126com_10023_31com_10023_879com_10023_878col_10023_176col_10023_128col_10023_880
00925njm 22002777a 4500
dc
Murawski, Caroline
author
Elschner, Chris
author
Lenk, Simone
author
Reineke, Sebastian
author
Gather, Malte Christian
author
2016-11-14
Thin films of the phosphorescent emitters Ir(ppy)3 and Ir(ppy)2(acac) are investigated by GIXRD and GIWAXS. Both molecules form crystalline grains and exhibit a preferred orientation that is pertained even when doped into a host.
Murawski , C , Elschner , C , Lenk , S , Reineke , S & Gather , M C 2016 , Orientation of OLED emitter molecules revealed by XRD . in Proceedings, Light, Energy and the Environment . , SSW2D.7 , Solid-State Lighting , Optical Society of American (OSA) , OSA Light, Energy and the Environment Congress , Leipzig , Germany , 14/11/16 . https://doi.org/10.1364/SSL.2016.SSW2D.7
conference
9780960038046
PURE: 247838032
PURE UUID: 7e5e585d-bf9d-4ab1-b0cf-d518a94f1d4f
Scopus: 85019528159
ORCID: /0000-0002-4857-5562/work/47136442
http://hdl.handle.net/10023/9862
https://doi.org/10.1364/SSL.2016.SSW2D.7
703387
Thin films, optical properties
Organic materials
Fluorescent and luminescent materials
QC Physics
T Technology
NDAS
Orientation of OLED emitter molecules revealed by XRD
oai:research-repository.st-andrews.ac.uk:10023/122362023-04-19T00:45:49Zcom_10023_175com_10023_39com_10023_126com_10023_31com_10023_879com_10023_878col_10023_176col_10023_128col_10023_880
00925njm 22002777a 4500
dc
Morton, Andrew
author
Murawski, Caroline
author
Gather, Malte Christian
author
2016-12-01
With the advent of optogenetics, numerous functions in cells have been rendered responsive to the experimental delivery of light. The most common implementation of this technique features neurons genetically modified to express light-sensitive ion channel proteins, which open specifically in response to pulses of blue light, triggering electrical impulses in neurons. Optogenetics now has matured to a point where in addition to answering fundamental questions about the function of the brain, scientists begin to consider clinical applications. Further progress in this field however will require new ways of delivering light. One of these involves the use of organic light-emitting diodes (OLEDs), a display technology increasingly common in modern-day smart phones, for the optical stimulation of cells.
Morton , A , Murawski , C & Gather , M C 2016 , ' Carpe lucem : harnessing organic light sources for optogenetics ' The Biochemist , vol. 38 , no. 6 , pp. 4-7 . < http://www.biochemist.org/bio/03806/0004/038060004.pdf >
0954-982X
PURE: 248134956
PURE UUID: 85b5641a-042c-4d11-9d3a-aa3901bd4a87
ORCID: /0000-0002-4857-5562/work/47136443
Scopus: 85011961333
http://hdl.handle.net/10023/12236
http://www.biochemist.org/bio/03806/0004/038060004.pdf
QC Physics
QH426 Genetics
RC0321 Neuroscience. Biological psychiatry. Neuropsychiatry
T Technology
Carpe lucem: harnessing organic light sources for optogenetics
oai:research-repository.st-andrews.ac.uk:10023/132742024-03-27T00:42:37Zcom_10023_175com_10023_39com_10023_126com_10023_31com_10023_879com_10023_878col_10023_176col_10023_128col_10023_880
00925njm 22002777a 4500
dc
Fröbel, Markus
author
Schwab, Tobias
author
Kliem, Mona
author
Lenk, Simone
author
Leo, Karl
author
Reineke, Sebastian
author
Gather, Malte C.
author
2017
A device concept for highly efficient OLEDs is introduced that allows to tune the emission color of the device over a broad range of the CIE color gamut. The approach exploits the different polarities of the positive and negative half-cycles of an alternating current driving signal to independently address two vertically stacked emission units with complementary color. Ultrathin metal electrodes fabricated by a wetting layer approach are used to achieve good electrical contact to each stack with minimal impact on optical performance.
Fröbel , M , Schwab , T , Kliem , M , Lenk , S , Leo , K , Reineke , S & Gather , M C 2017 , ' 3-2: Invited paper: Color on Demand - Color-tunable OLEDs for lighting and displays ' , SID Symposium Digest of Technical Papers , vol. 48 , no. 1 , pp. 5-8 . https://doi.org/10.1002/sdtp.11558
0097966X
crossref: 10.1002/sdtp.11558
ORCID: /0000-0002-4857-5562/work/47136515
https://hdl.handle.net/10023/13274
10.1002/sdtp.11558
PCIG12-GA-2012-334407
OLED
Color tuning
White
Stacked
Ultrathin metal electrode
Alternating current driving
Lighting
Display
QC Physics
QD Chemistry
T Technology
NDAS
3-2: Invited paper: Color on Demand - Color-tunable OLEDs for lighting and displays
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
00925njm 22002777a 4500
dc
Leeming, Gail H
author
Kipar, Anja
author
Hughes, David J
author
Bingle, Lynne
author
Bennett, Elaine
author
Moyo, Nathifa A
author
Tripp, Ralph A
author
Bigley, Alison L
author
Bingle, Colin D
author
Sample, Jeffery T
author
Stewart, James P
author
2015-06
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.
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
QH301 Biology
NDAS
Gammaherpesvirus infection modulates the temporal and spatial expression of SCGB1A1 (CCSP) and BPIFA1 (SPLUNC1) in the respiratory tract
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
00925njm 22002777a 4500
dc
Pérez-Moreno, J J
author
Bischoff, M
author
Martín-Bermudo, M D
author
Estrada, B
author
2014-07
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.
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
Myogenesis
Muscle
Myofibril
Sarcomere
Integrin
Chondroitin sulfate proteoglycan
Perdido
Kon-tiki
CSPG4
MCSP
AN2
NG2
QR Microbiology
The conserved transmembrane proteoglycan Perdido/Kon-tiki is essential for myofibrillogenesis and sarcomeric structure in Drosophila
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
00925njm 22002777a 4500
dc
Constantinescu Aruxandei, Diana
author
Petrovic-Stojanovska, Biljana
author
Schiemann, Olav
author
Naismith, Jim
author
White, Malcolm F
author
2015-12-10
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.
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
QH301 Biology
NDAS
Taking a molecular motor for a spin : helicase mechanism studied by spin labelling and PELDOR
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
00925njm 22002777a 4500
dc
Smith, Terry K
author
2015-01
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.
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
QH301 Biology
Lipidomic analysis of fats and oils – a lot more than just omega-3
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
00925njm 22002777a 4500
dc
Akman, Goekhan
author
MacNeill, Stuart Andrew
author
2009-02-19
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.
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
QH301 Biology
MCM-GINS and MCM-MCM interactions in vivo visualised by bimolecular fluorescence complementation in fission yeast
oai:research-repository.st-andrews.ac.uk:10023/52412022-04-12T14:30:25Zcom_10023_175com_10023_39com_10023_51com_10023_18com_10023_879com_10023_878col_10023_176col_10023_52col_10023_880
00925njm 22002777a 4500
dc
Perni, S.
author
Hackett, L.
author
Goss, R.J.M.
author
Simmons, M.J.
author
Overton, T.W.
author
2013-11-04
Engineered biofilms comprising a single recombinant species have demonstrated remarkable activity as novel biocatalysts for a range of applications. In this work, we focused on the biotransformation of 5-haloindole into 5-halotryptophan, a pharmaceutical intermediate, using Escherichia coli expressing a recombinant tryptophan synthase enzyme encoded by plasmid pSTB7. To optimise the reaction we compared two E. coli K-12 strains (MC4100 and MG1655) and their ompR234 mutants, which overproduce the adhesin curli (PHL644 and PHL628). The ompR234 mutation increased the quantity of biofilm in both MG1655 and MC4100 backgrounds. In all cases, no conversion of 5-haloindoles was observed using cells without the pSTB7 plasmid. Engineered biofilms of strains PHL628 pSTB7 and PHL644 pSTB7 generated more 5-halotryptophan than their corresponding planktonic cells. Flow cytometry revealed that the vast majority of cells were alive after 24 hour biotransformation reactions, both in planktonic and biofilm forms, suggesting that cell viability was not a major factor in the greater performance of biofilm reactions. Monitoring 5-haloindole depletion, 5-halotryptophan synthesis and the percentage conversion of the biotransformation reaction suggested that there were inherent differences between strains MG1655 and MC4100, and between planktonic and biofilm cells, in terms of tryptophan and indole metabolism and transport. The study has reinforced the need to thoroughly investigate bacterial physiology and make informed strain selections when developing biotransformation reactions.
Perni , S , Hackett , L , Goss , R J M , Simmons , M J & Overton , T W 2013 , ' Optimisation of engineered Escherichia coli biofilms for enzymatic biosynthesis of L-halotryptophans ' , AMB Express , vol. 3 , pp. 1-10 . https://doi.org/10.1186/2191-0855-3-66
2191-0855
PURE: 143502194
PURE UUID: 43c28864-5e57-4027-92b4-d0a16dec383f
Scopus: 84891446993
http://hdl.handle.net/10023/5241
https://doi.org/10.1186/2191-0855-3-66
http://www.scopus.com/inward/record.url?eid=2-s2.0-84891446993&partnerID=8YFLogxK
BB/I008713/2
E. coli
Biofilm
Biotransformation
Haloindole
Halotryptophan
QD Chemistry
Optimisation of engineered Escherichia coli biofilms for enzymatic biosynthesis of L-halotryptophans
oai:research-repository.st-andrews.ac.uk:10023/98612024-03-02T00:39:41Zcom_10023_175com_10023_39com_10023_126com_10023_31com_10023_130com_10023_32com_10023_879com_10023_878col_10023_176col_10023_128col_10023_131col_10023_880
00925njm 22002777a 4500
dc
Murawski, Caroline
author
Morton, Andrew
author
Samuel, Ifor David William
author
Pulver, Stefan
author
Gather, Malte Christian
author
2016-11-14
Optogenetics is an emerging method in biology that enables controlling neurons with light. We use organic light-emitting diodes to stimulate neurons in Drosophila larvae and investigate subsequent behavioral changes at different light intensities.
Murawski , C , Morton , A , Samuel , I D W , Pulver , S & Gather , M C 2016 , Organic light-emitting diodes for optogenetic stimulation of Drosophila larvae . in Proceedings, Light, Energy and the Environment . , JW4A.9 , Fourier Transform Spectroscopy , Optical Society of American (OSA) , OSA Light, Energy and the Environment Congress , Leipzig , Germany , 14/11/16 . https://doi.org/10.1364/FTS.2016.JW4A.9
conference
9780960038046
ORCID: /0000-0002-4857-5562/work/47136417
ORCID: /0000-0001-5170-7522/work/69463441
https://hdl.handle.net/10023/9861
10.1364/FTS.2016.JW4A.9
RGY0074/2013
EP/J01771X/1
703387
Medical optics and biotechnology – lllumination design
Thin film devices and applications
Organic materials
QB Astronomy
QC Physics
T Technology
NDAS
Organic light-emitting diodes for optogenetic stimulation of Drosophila larvae
oai:research-repository.st-andrews.ac.uk:10023/33032024-02-17T00:40:25Zcom_10023_175com_10023_39com_10023_48com_10023_16com_10023_126com_10023_31com_10023_879com_10023_878col_10023_176col_10023_49col_10023_128col_10023_880
00925njm 22002777a 4500
dc
Balagopal, Bavishna
author
Ashok, Praveen Cheriyan
author
Mazilu, Michael
author
Riches, Andrew Clive
author
Herrington, C Simon
author
Dholakia, Kishan
author
2012-07-09
In the field of biomedical optics, Raman spectroscopy is a powerful tool for probing the chemical composition of biological samples. In particular, fiber Raman probes play a crucial role for in vivo and ex vivo tissue analysis. However, the high-fluorescence background typically contributed by the auto fluorescence from both a tissue sample and the fiber-probe interferes strongly with the relatively weak Raman signal. Here we demonstrate the implementation of wavelength-modulated Raman spectroscopy (WMRS) to suppress the fluorescence background while analyzing tissues using fiber Raman probes. We have observed a significant signal-to-noise ratio enhancement in the Raman bands of bone tissue, which have a relatively high fluorescence background. Implementation of WMRS in fiber-probe-based bone tissue study yielded usable Raman spectra in a relatively short acquisition time (∼30 s), notably without any special sample preparation stage. Finally, we have validated its capability to suppress fluorescence on other tissue samples such as adipose tissue derived from four different species.
Balagopal , B , Ashok , P C , Mazilu , M , Riches , A C , Herrington , C S & Dholakia , K 2012 , ' Fluorescence suppression using wavelength modulated Raman spectroscopy in fiber-probe-based tissue analysis ' , Journal of Biomedical Optics , vol. 17 , no. 7 , 077006 . https://doi.org/10.1117/1.JBO.17.7.077006
1083-3668
https://hdl.handle.net/10023/3303
10.1117/1.JBO.17.7.077006
502011.K501/NG
Biophotonics
Bone tissue studies
Raman probe
Raman spectroscopy
Tissues
QC Physics
QD Chemistry
Fluorescence suppression using wavelength modulated Raman spectroscopy in fiber-probe-based tissue analysis
oai:research-repository.st-andrews.ac.uk:10023/9562019-04-01T08:50:44Zcom_10023_175com_10023_39com_10023_48com_10023_16col_10023_176col_10023_49
00925njm 22002777a 4500
dc
Stewart, AJ
author
Mukherjee, J
author
Roberts, SJ
author
Lester, D
author
Farquharson, C
author
2005
Phosphoinositol (PhoIns)-specific phospholipase C enzymes (PLCs) are central to the inositol lipid signaling pathways and contribute to intracellular Ca2+ release and protein kinase C activation. Five distinct classes of PhoIns-specific PLCs are known to exist in mammals, which are activated by membrane receptor-mediated events. Here we have identified a sixth class of PhoIns-specific PLC with a novel domain structure, which we have termed PLC-eta. Two putative PLC-eta enzymes were identified in humans and in mice. Sequence analysis revealed that residues implicated in substrate binding and catalysis from other PhoIns-specific PLCs are conserved in the novel enzymes. PLC-eta enzymes are most closely related to the PLC-delta class and share a close evolutionary relationship with other PLC isozymes. EST analysis and RT-PCR data suggest that PLC-eta enzymes are expressed in several cell types and, by analogy with other mammalian PhoIns-specific PLCs, are likely to be involved in signal transduction pathways.
Stewart, A.J., Mukherjee, J., Roberts, S.J., Lester, D. and Farquharson, C. (2005). Identification of a novel class of mammalian phosphoinositol-specific phospholipase C enzymes. International Journal of Molecular Medicine 15: 117-121
1107-3756
StAndrews.ResExp.Output.OutputID.29367
http://www.spandidos-publications.com/ijmm/index.jsp?full=yes
http://hdl.handle.net/10023/956
Ca2+ Signaling
Phosphatidylinositol
Phospholipase C-eta
Protein Kinase C
Receptor-Mediated Signaling
Signal Transduction
Identification of a novel class of mammalian phosphoinositol-specific phospholipase C enzymes.
oai:research-repository.st-andrews.ac.uk:10023/55182023-04-25T23:37:33Zcom_10023_45com_10023_17com_10023_175com_10023_39com_10023_879com_10023_878col_10023_46col_10023_176col_10023_880
00925njm 22002777a 4500
dc
Luke, Garry Alec
author
Ryan, Martin Denis
author
2013-10
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.
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
PURE: 71028375
PURE UUID: 87f6131f-c4cc-4136-9da1-ca97f2c98821
Scopus: 84884224657
ORCID: /0000-0002-0012-0614/work/47136059
http://hdl.handle.net/10023/5518
https://doi.org/10.2217/fvl.13.82
http://www.futuremedicine.com/loi/fvl
BB/H007849/1
G0901002
SDG 3 - Good Health and Well-being
The protein coexpression problem in biotechnology and biomedicine : virus 2A and 2A-like sequences provide a solution
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
00925njm 22002777a 4500
dc
Boe, Cathrine A.
author
Garcia, Ignacio
author
Pai, Chen-Chun
author
Sharom, Jeffrey R.
author
Skjolberg, Henriette C.
author
Boye, Erik
author
Kearsey, Stephen
author
MacNeill, Stuart Andrew
author
Tyers, Michael D.
author
Grallert, Beata
author
2008-05-05
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.
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
QH301 Biology
Rapid regulation of protein activity in fission yeast
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
00925njm 22002777a 4500
dc
Edwards, Thomas E.
author
Cekan, Pavol
author
Reginsson, Gunnar Widtfeldt
author
Shelke, Sandip A.
author
Ferre D'Amare, Adrian R.
author
Schiemann, Olav
author
Sigurdsson, Snorri
author
2011-05
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.
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
DNA
Crystallographic analysis
Deoxyguanosine
Oxazine linkage
DAS
Crystal structure of a DNA containing the planar, phenoxazine-derived bi-functional spectroscopic probe Ç
oai:research-repository.st-andrews.ac.uk:10023/61582022-04-14T11:30:29Zcom_10023_175com_10023_39com_10023_126com_10023_31com_10023_879com_10023_878col_10023_176col_10023_128col_10023_880
00925njm 22002777a 4500
dc
Fuchs, C.
author
Schwab, T.
author
Wieczorek, M.
author
Gather, M.C.
author
Hofmann, S.
author
Leo, K.
author
Scholz, R.
author
2014
We report on the enhanced light outcoupling efficiency of monochrome top-emitting organic light-emitting diodes (OLEDs). These OLEDs incorporate a hole transport layer (HTL) material with a substantially lower refractive index (∼ 1:5) than the emitter material or the standard HTL material (∼ 1:8) of a reference device. This low-index HTL is situated between the opaque bottom metal contact (anode) and the active emission layer. Compared to an HTL with common refractive index, the dispersion relation of the surface plasmon polariton (SPP) mode from the opaque metal contact is shifted to smaller in-plane wavenumbers. This shift enhances the outcoupling efficiency as it reduces the total dissipated power of the emitter. Furthermore, the excitation of the coupled SPPs at the thin transparent metal top contact (cathode) is avoided by using an ultrathin top electrode. Hence, the coupling of the electroluminescence from the emitter molecules to all non-radiative evanescent modes, with respect to the emitter material, is reduced by at least a factor of two, additionally increasing the outcoupling efficiency. Furthermore, for sufficiently high refractive index contrast the shift of the SPP at the anode/organic interface can lead to in-plane wavenumbers smaller than the wavenumber within the organic emitter layer and outcoupling of all excited modes by high index light extraction structures, e.g. microlens, seems feasible. In accordance to optical simulations, the external quantum efficiency is enhanced by about 20% for monochrome green emitting OLEDs with low refractive index HTL compared to a reference sample.
Fuchs , C , Schwab , T , Wieczorek , M , Gather , M C , Hofmann , S , Leo , K & Scholz , R 2014 , Surface plasmon polariton modification in top-emitting organic light-emitting diodes for enhanced light outcoupling . in F So (ed.) , Organic Light Emitting Materials and Devices XVIII . vol. 9183 , Proceedings of SPIE , vol. 9183 , SPIE , Organic Light Emitting Materials and Devices XVIII , San Diego , United Kingdom , 17/08/14 . https://doi.org/10.1117/12.2061585
conference
9781628412109
0277-786X
PURE: 172276634
PURE UUID: bb278344-8ed1-4124-b8a0-e7b257fdbd8e
Scopus: 84922765275
ORCID: /0000-0002-4857-5562/work/47136460
http://hdl.handle.net/10023/6158
https://doi.org/10.1117/12.2061585
QC Physics
Surface plasmon polariton modification in top-emitting organic light-emitting diodes for enhanced light outcoupling
oai:research-repository.st-andrews.ac.uk:10023/47362023-04-18T09:44:02Zcom_10023_175com_10023_39com_10023_48com_10023_16com_10023_126com_10023_31com_10023_879com_10023_878col_10023_176col_10023_49col_10023_128col_10023_880
00925njm 22002777a 4500
dc
Ploschner, Martin
author
Mazilu, Michael
author
Cizmar, Tomas
author
Dholakia, Kishan
author
2011-07-06
We explore the passive optical sorting of plasmon nanoparticles and investigate the optimal wavelength and optimal beam shape of incident field. The condition for optimal wavelength is found by maximising the nanoparticle separation whilst minimising the temperature increase in the system. We then use the force optical eigenmode (FOEi) method to find the beam shape of incident electromagnetic field, maximising the force difference between plasmon nanoparticles. The maximum force difference is found with respect to the whole sorting region. The combination of wavelength and beam shape study is demonstrated for a specific case of gold nanoparticles of radius 40 nm and 50 nm respectively. The optimum wavelength for this particular situation is found to be above 700 nm. The optimum beam shape depends upon the size of sorting region and ranges from plane-wave illumination for infinite sorting region to a field maximising gradient force difference in a single point. (C) 2011 Optical Society of America
Ploschner , M , Mazilu , M , Cizmar , T & Dholakia , K 2011 , ' Numerical investigation of passive optical sorting of plasmon nanoparticles ' , Optics Express , vol. 19 , no. 15 , pp. 13922-13933 . https://doi.org/10.1364/OE.19.013922
1094-4087
PURE: 14284262
PURE UUID: 9b560061-10b5-4ecf-a439-caf369a9d853
Scopus: 79960517695
http://hdl.handle.net/10023/4736
https://doi.org/10.1364/OE.19.013922
http://www.opticsinfobase.org/abstract.cfm?URI=oe-19-15-13922
EP/G029733/1
QC Physics
Numerical investigation of passive optical sorting of plasmon nanoparticles
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
00925njm 22002777a 4500
dc
Van Knippenberg, Ingeborg Christine
author
Carlton-Smith, Charles
author
Elliott, Richard Michael
author
2010-04
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.
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
QR Microbiology
The N-terminus of Bunyamwera orthobunyavirus NSs protein is essential for interferon antagonism
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
00925njm 22002777a 4500
dc
Rudhall, Andrew Peter
author
Antkowiak, Maciej
author
Tsampoula, Xanthi
author
Mazilu, Michael
author
Metzger, N Klaus
author
Gunn-Moore, Frank J
author
Dholakia, Kishan
author
2012
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.
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
Ultrashort femtosecond pulsed lasers
Membrane permeabilisation
Mammalian cells
Q Science
Exploring the ultrashort pulse laser parameter space for membrane permeabilisation in mammalian cells.
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
00925njm 22002777a 4500
dc
MacNeill, Stuart
author
2014-12-19
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.
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
9-1-1 complex
sliding clamp
kinetoplastid
QH301 Biology
Identification of a candidate Rad1 subunit for the kinetoplastid 9-1-1 (Rad9-Hus1-Rad1) complex
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
00925njm 22002777a 4500
dc
Michelmore, Richard
author
Coaker, Gitta
author
Bart, Rebecca
author
Beattie, Gwyn
author
Bent, Andrew
author
Bruce, Toby
author
Cameron, Duncan
author
Dangl, Jeff
author
Dinesh-Kumar, Savithramma
author
Edwards, Rob
author
Eves-van den Akker, Sebastian
author
Gassmann, Walter
author
Greenberg, Jean
author
Hanley-Bowdoin, Linda
author
Harrison, Richard
author
He, Ping
author
Harvey, Jagger
author
Huffaker, Alisa
author
Hulbert, Scot
author
Innes, Roger
author
Jones, Jonathan
author
Kaloshian, Isghouhi
author
Kamoun, Sophien
author
Katagiri, Fumiaki
author
Leach, Jan
author
Ma, Wenbo
author
McDowell, John
author
Medford, June
author
Meyers, Blake
author
Nelson, Rebecca
author
Oliver, Richard
author
Qi, Yiping
author
Saunders, Diane
author
Shaw, Michael
author
Smart, Christine
author
Subudhi, Prasanta
author
Torrance, Lesley
author
Tyler, Brett
author
Valent, Barbara
author
Walsh, John
author
2017-07
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.
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
QH301 Biology
SB Plant culture
T-NDAS
SDG 2 - Zero Hunger
SDG 3 - Good Health and Well-being
SDG 13 - Climate Action
Foundational and translational research opportunities to improve plant health
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
00925njm 22002777a 4500
dc
Mitchell, C.A.
author
Kalies, S.
author
Cizmár, T.
author
Heisterkamp, A.
author
Torrance, L.
author
Roberts, A.G.
author
Gunn-Moore, F.J.
author
Dholakia, K.
author
2013-11-14
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.
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
Pulsed laser beam
Cell membrane permeability
Photoporation
Femtosecond optical injection
Tobacco BY-2 cells
Q Science
Femtosecond optoinjection of intact tobacco BY-2 cells using a reconfigurable photoporation platform