Research

Research Overview

The School of Biochemistry and Cell Biology is one of the most successful molecular life science research units in Ireland and hosts several internationally recognized research leaders. In its latest research quality review, it received a score of 4 (of 5 maximum) placing it in the front rank of UCC academic units. The School’s research laboratories are located in modern purpose-built accommodation with state of the art facilities in the Western Gateway Building (Western Rd.),  Biosciences Research Institute  and  the Analytical & Biological Chemistry Research Facility at the School of Pharmacy.

Research in the school is directed by Principal Investigator’s (PIs) on the academic staff and spans the biomedical, biotechnological and environmental science areas.  We use all of the modern tools of molecular/cellular biology, protein biochemistry, molecular genetics, signal transduction, immunology, bioinformatics and analytical biochemistry to address fundamental and applied research questions in these challenging areas.  Our principal research themes are:

The school prides itself on its high quality publication record, high level of innovation and commercialization, and its central role interfacing with a variety of other basic science and clinical schools within the University and the scientific and biotechnological community worldwide.

Our Academic Staff and their Research Collaborators

The School of Biochemistry and Cell Biology Academic Staff and their Research Collaborators is listed below.

The list of our collaborators is also available for you to download as a PDF document: Research Collaborators.

Professor John Atkins

Internal

Pavel V. Baranov, University College Cork, Ireland

Joseph Eustace, University College Cork, Ireland

Louise Kenny, University College Cork, Ireland

John Mackrill, University College Cork, Ireland

Douwe van Sinderen, University College Cork, Ireland

External

Mark Borodovsky, Georgia Institute of Technology, US

Raymond F. Burk, Vanderbilt University, US

Mario Capecchi, University of Utah, US

Eric Cascales, Aix-Marseille University, France

Lynn Cooley, Yale University, us

Thomas Dever, NIH, US

Olivier Fayet, University Paul Sabatier-Toulouse, France

Marc Ferrer, National Institutes of Health, US

Andrew E. Firth, University of Cambridge, UK

Vadmim Gladyshev, Harvard University, USA

Michael Howard, University of Utah, US

Ivaylo, Ivanov, NIH, US

Michael Kashlev, National Cancer Institute, USA

Maniolis Kellis, Massachusetts Institute of Technology, US

Alexander Mankin,  University of Illinois, us

Olivier Namy, IGM, Orsay, France

Elizabeth Rieder, United States Department of Agriculture, Agriculture Research Service, US

Marina Rodnina, Max Planck Institute for Biophysical Chemistry, Germany

Matthew Sachs, Texas A & M University, us

Jonathan S. Weissman, University of California, Berkeley, US

Sen Wu, China Agricultural University, China

Dr Pasha Baranov

Internal

Professor John Atkins, University College Cork, Ireland

Dmitri Papkovsky, University College Cork, Ireland

Gregory Provan, University College Cork, Ireland

Douwe van Sinderen, University College Cork, Ireland

External

Mark Borodovsky, Georgia Institute of Technology, USA

Joseph Curran, University of Geneva, Switzerland

Olivier Fayet, University of Touluse, France

Andrew Firth, Cambridge University, United Kingdom

Vadmim Gladyshev, Harvard University, USA

Des Higgins, University College Dublin, Ireland

Nicholas Ingolia, Berkley University, USA

Michael Kashlev, National Cancer Institute, USA

Manolis Kellis, Massachusetts Institute of Technology, USA

Victoria Kolupaeva, University of New York, USA

Antea Letsou, University of Utah, USA

Robbie Loewith, University of Geneva, Switzerland

Gerard Manning, University of California in San Diego, USA

Derek Morris, Trinity College Dublin, Ireland

Ronan O'Sullivan, National Children's Research Centre, Ireland

Dmitri Rachinskii, The University of Texas at Dallas, USA

Robert Reenan, Brown University, USA

Ivan Shatsky, Moscow state University, Russia

Paul Walsh, Cork Institute of Technology, Ireland

Jonathan Weissman, University of California in San Francisco, UCSF

Industrial

Nsilico

Thompson Reuters 

Professor Tom Cotter

Internal

Professor Paul Redmond, University College Cork, Ireland

External

Professor Chris Chang, University Berkeley, California USA

Professor Nicolas Cuenca, University Alicante Spain

Professor Enrique de la Rosa, University Madrid Spain

Professor Angel Messeguer, CSIC Barcelona, Spain

Professor Colm O’Brien, University College Dublin, Ireland

Dr Kellie Dean

Internal

John Atkins, University College Cork, Ireland

Pasha Baranov, University College Cork, Ireland

Paul Young, University College Cork, Ireland

External

Nancy Kedersha, Harvard University, Boston, MA, USA

Jack Keene, Duke University, Durham, NC, USA

Ruslan Dmitriev (Research Fellow (SFI Investigator)

Internal

Dmitri B. Papkovsky, University College Cork, Ireland

External

Ingo Klimant, Graz University of Technology, Austria

Dr Eoin Fleming

Internal

Dr Gerard O’Keeffe, Anatomy and Neuroscience, University College Cork, Ireland

Professor Mary McCaffrey, School of Biochemistry and Cell Biology, University College Cork, Ireland

External

Professor Timothy Wang, Columbia University, New York 

Professor James Heffron

Internal

Dr Ashley Allshire, Pharmacology, University College Cork, Ireland

Professor Tommie McCarthy, Biochemistry, University College Cork, Ireland

Professor John Sodeau, Chemistry, University College Cork, Ireland

Dr Frank van Pelt, Pharmacology, University College Cork, Ireland

External

Dr Thierry Girard, University of Basel, Switzerland

Dr R.J.A. Heffron, University of Leeds, United Kingdom

Dr Werner Klingler, University of Ulm, Germany

Professor Frank Lehmann-Horn, University of Ulm, Germany

Professor Catherine McDermott, Bond University, Robina, Australia

Professsor Vincent McLoughlin, Physiology, Trinity College Dublin, Ireland

Professor V. Sorrentino, University of Sienna, Sienna, Italy

Professor V. Teggazin, University of Padua, Italy

Professor Mary McCaffrey

Internal

Dr Eoin Fleming, Biochemistry and Pharmacy, University College Cork, Ireland

Dr Paul Young, Biochemistry, University College Cork, Ireland

External

Anton Bennett, Yale University, USA

Paul Digard, The Roslin Institute, United Kingdom

Terje Espevik & Harald Husebye, The Norwegian University of Sciences & Technology, Norway

Clare Futter, Universtiy College London, United Kingdom

Bruno Goud, Institut Curie, France

Clare Jolly, University College London, United Kingdom

Amir Khan, Trinity College, Ireland

Yuichiro Nakatsu & Makota Takeda, National Institute of Infectious Diseases, Japan

Jim Norman, Beatson Institute for Cancer Research, United Kingdom

Graca Raposo, Institu Curie, France

Trina Schroer, Johns Hopkins Univeristy, USA

Jeremy Tavare, University of Bristol, United Kingdom

Industrial

Farfield Inc., United Kingdom

Dr Justin McCarthy

Internal

Dr Niamh Birmingham, Neuropathologist, Cork University Hospital, Ireland

Dr Eric Downer, University College Cork, Ireland

Dr Gerard McGlacken, University College Cork, Ireland

External

Professor Bart De Strooper, KUL Leuven, Belgium

Professor Andreas Ludwig, Aachen University, Germany

Professor Albert Shaw, Yale University, USA

Professor Tommie McCarthy

Internal

Professor Ted Dinan, Department of Psychiatry, University College Cork, Ireland

Dr Paul Galvin, Tyndall National Institute, University College Cork, Ireland

External

Dr Linda Giblin, Teagasc, Moorepark, Fermoy, Ireland

Dr Karen Keeshan, Paul O’Gorman Institute, Glasgow, Scotland

Professor Susan Walsh, Purdue University,  Indianapolis, USA

Professor Alan Wright, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland

Dr Tom Moore

Internal

Professor Noel Caplice, Medicine, University College Cork, Ireland

Dr Patrick Harrison, Physiology, University College Cork, Ireland

Dr Conor O’Mahony, Tyndall, University College Cork, Ireland

Professor Paul O’Toole, Microbiology, University College Cork, Ireland

External

Professor John Aplin, University of Manchester, UK

Dr Jim Clover, HSE consultant plastic surgeon

Professor Stipan Jonjic, Croatia

Dr Robert Kammerer, Institute of Immunology, Tubingen

Dr Vincent Kelly, Trinity College Dublin, Ireland

Dr Bernhard Singer, University of Essen, Germany

Professor Wolfgang Zimmermann, Tumor Immunology Laboratory, Munich

Dr Ken Nally

Internal

Professor John Cryan, University College Cork, Ireland

Professor Rosemary O’Connor, University College Cork, Ireland

Professor Fergus Shanahan, University College Cork, Ireland

Dr Silvia Melgar, APC, University College Cork, Ireland

Professor Paul O’Toole, University College Cork, Ireland

Professor Douwe Van Sinderen, University College Cork, Ireland

Dr John MacSharry, University College Cork, Ireland

Dr Aileen Houston, University College Cork, Ireland

Dr Beth Brint, University College Cork, Ireland

Dr Ian Jeffery, University College Cork, Ireland

Dr Marcus Claesson, University College Cork, Ireland

External

Professor Jeremy Simpson, University College Dublin, Ireland

Professor Grant McFadden, University of Florida, USA

Dr Christian Riedel, University of Ulm, Germany

Dr Laurens Kruidenier, GlaxoSmithKline UK, United Kingdom

Dr Norma O’Donovan, Dublin City University, Ireland

Dr Rab Prinjha, GlaxoSmithKline UK, United Kingdom

Professor Rosemary O’Connor

Internal

Dr Cora O’Neill, University College Cork, Ireland

Dr Ken Nally, University College Cork, Ireland

Professor Dmitri Papkovsky University College Cork, Ireland

Professor Fergal O’Gara, University College Cork, Ireland

Dr Michael Clarkson, Cork University Hospital, Ireland

Professor Noel Caplice, Centre for Research and Cardiovascular Biology, School of Medicine, University College Cork, Ireland

External

Dr Nancy L. Kedersha, Harvard University, Boston, USA

Professor David Adams Heriot Watt University, Edinburgh, UK

Professor George Baille, University of Glasgow, UK

Dr Patrick Kiely, University of Limerick, Ireland

Professor Richard Kennedy, Professor Paul Harkin and Dr Karen Keating, Almac Diagnostics, Craigavon, Northern Ireland

Professor Stephen D Hursting, University of North Carolina, USA

Professor Marek Brzozowski, University of York, UK

Professor Alexander Marx, University of Heidelberg, Germany

Professor Michael Forgac, Tufts University, Boston, USA

Professor William Gallagher and PIs in BreastPredict at University Colege Dublin, Royal College of Surgeons, University College Dublin and Trinity College Dublin

Dr Cora O’Neill

Internal

Dr Suzanne Timmons, Gerontology and Rehabilitation, University College Cork, Ireland

Professor Will Molloy, Gerontology and Rehabilitation, University College Cork, Ireland

Professor Rosemary O’Connor, Biochemistry and Cell Biology, University College Cork, Ireland

Dr Aideen Sullivan, Anatomy and Neuroscience, University College Cork, Ireland

Dr Eric Downer, Anatomy and Neuroscience, University College Cork, Ireland

Professor Paul O’Toole, Microbiology and APC, University College Cork, Ireland

Dr Sean O’Sullivan, Neurology, University College Cork, Ireland

Dr Barry Boland, Pharmacology, University College Cork, Ireland

Members of Cork NeuroScience Centre, University College Cork, Ireland

External

Professor Bart De Strooper KU Leuven, Belgium

Dr Vanessa Morais, KU Leuven, Belgium

Professor Wolfgang Wurst, Helmhotz Centre, Munich, Germany

Netherland’s Brain Bank

Professor Maria Ankarkrona, Karolinska Institute, Sweden

Professor Christian Holscher, Lancaster University, UK

Irish Network for Biomarkers in Neurodegenerative disease, (INBIND) members

EU BIOMARKAPD grant  team

National team

Professor Brian Lawlor, TCIN, Trinity College Dublin, Dublin, Ireland

Professor Orla Hardiman TCIN, Trinity College Dublin, Dublin, Ireland

Professor Mike Rowan TCIN, Trinity College Dublin, Dublin, Ireland

Professor Roseanne Kenny TILDA, Trinity College Dublin, Dublin, Ireland

Professor Marina Lynch TCIN, , Trinity College Dublin, Dublin, Ireland

Professor Michael Farrell, RCSI, Beaumont Hospital, Dublin, Ireland

Professor Dmitri Papkovsky

Internal

Professor John Cryan, Anatomy and Neuroscience, University College Cork, Ireland

Professor Ken O’Halloran, Physiology, University College Cork, Ireland

Dr Peter O’Brien, Dr Vladimir Ogurtsov, Tyndall Institute, University College Cork, Ireland

Professor Noel Caplice, Centre for Cardiovascular Biology, Cork University Hospital, Cork, Ireland

Dr Yvonne Nolan, Anatomy and Neuroscience, University College Cork, Ireland

Dr Neill Hyland, Pharmacology Department, University College Cork, Ireland

External

Professors Ingo Klimant & Sergey Borisov, Department of Analytical Chemistry, Graz University of Technology, Austria

Dr Karl Morten, Department of Obsterics and Gynecology, University of Oxford, UK

Professor Joachim Fandrey, University of Essen, Germany

Professor Cormac Taylor, Conway Institute, University College Dublin, Ireland 

Professor Ulla Knaus, University College Dublin, Ireland

Professor Jochen Prehn, Department Physiology, Royal College of Surgeons in Ireland

Professor Colm O’Brien, Mater Hospital, University College Dublin

Professor Gelii Ponomarev, Institute of Biomedical Chemistry, Moscow, Russia

Professor Kenneth Smith, University College London

Vassiliy Tsytsarev, University of Maryland, USA

Professor David Sheehan

Internal

Professor Ed Johns and Professor Ken O’Halloran, Physiology, University College Cork, Cork, Ireland

Dr Hugh Doyle, Tyndall National Institute, University College Cork, Cork, Ireland

Professor Sarah Cullotty, Environmental Research Institute, University College Cork, Cork, Ireland

External

Professor Carmel Mothersill, McMaster University, Canada

Professor Maria Bebianno, University of the Algarve, Portugal

Professor Ana Varela Coelho, ITQB, New University of Lisbon, Portugal

Professor Antonio Barcena, University of Cordoba, Spain

Professor Julian Blasco, CSIC, Cadiz, Spain

Professor Kenneth Dawson, University College Dublin, Dublin, Ireland

Professor Andrea Binelli, University of Milan, Italy

Professor S. Olga Cacciola, University of Catania, Italy

Professor Ashkan Madadlou, University of Teheran, Iran

Dr Paul Young

Internal

Professor John Cryan, University College Cork, Ireland

Professor Mary McCaffrey, University College Cork, Ireland

External

Professor Susan Dmecki, Department of Genetics, Harvard University, USA

Professor Guoping Feng, MIT, Boston, USA

Manolis Fanto, Kings College, London, United Kingdom

Our Academic Staff and Conference Organisation

Since 2008, nine members of our Academic staff (Professors Atkins, O’Connor, Papkovsky, Sheehan and McCaffrey and Drs O’Neill, Fleming, Young and Baranov) were the organisers or co-organisers of several conferences and symposia. 

8th Neuroscience Ireland Conference 2013

International conferences

Recoding: Reprogramming genetic decoding 2014

http://events.embo.org/14-recoding/

 

Biochemical Society: Membrane, Morphology and Function 2014

http://www.biochemistry.org/TabId/379/MeetingNo/SA156/view/Conference

Conference participants at the Biochemistry Society conference

 

17th Pollution Research in Marine Organisms (PRIMO) Meeting 2013

http://www.cima.ualg.pt/primo17/

 

28th Congress: European Society for Comparative Physiology & Biochemistry 2012

http://www.sciencedirect.com/science/journal/10956433/163/supp/S

https://www.deepdyve.com/lp/elsevier/congress-committee-teYrZ97dxm

http://www.sebc.es/varios/28thESCPB_1st_announcement.pdf

Bags of Biochemistry! Biochemistry Society conference

 

Biochemical Society: Rab GTPases and their interacting proteins in health and disease

http://www.biochemistry.org/TabId/379/MeetingNo/SA138/view/Conference

Professor Mary McCaffrey delivers the welcoming speech at Biochemistry Society conference: Rab GTPases and their interacting proteins in health and disease. The conference was hosted in the Western Gateway building in University College Cork between 11-13 June 2012.

Professor Mary McCaffrey of this School delivers the welcoming speech at the Biochemistry Society conference "Rab GTPases and their interacting proteins in health and disease", hosted in the Western Gateway building in University College Cork between 11-13 June 2012. Photo by Tomas Tyner, UCC.

 

Bruno Goud, CNRS, Institut Curie, France speaking at the Biochemistry Society conference

Bruno Goud, CNRS, Institut Curie, France speaking at the Biochemistry Society conference "Rab GTPases and their interacting proteins in health and disease", hosted in the Western Gateway building in University College Cork between 11-13 June 2012. Photo by Tomas Tyner, UCC.

 

 Roger Goody and Alan Hall at the Biochemistry Society conference

Roger Goody and Alan Hall at the Biochemistry Society conference "Rab GTPases and their interacting proteins in health and disease", hosted in the Western Gateway building in University College Cork between 11-13 June 2012. Photo by Tomas Tyner, UCC.

 

Jennifer Timoney, Niamh Irwin and Sylvia O'Sullivan (all of University College Cork) at the Biochemistry Society conference

Jennifer Timoney, Niamh Irwin and Sylvia O'Sullivan (all of University College Cork) at the Biochemistry Society conference "Rab GTPases and their interacting proteins in health and disease", hosted in the Western Gateway building in University College Cork between 11-13 June 2012. Photo by Tomas Tyner, UCC.

 

Conor Horgan and Sara Hanscom, School of Biochemistry and Cell Biology photographed during the Biochemistry Society conference

Conor Horgan and Sara Hanscom, School of Biochemistry and Cell Biology photographed during the Biochemistry Society conference "Rab GTPases and their interacting proteins in health and disease", hosted in the Western Gateway building in University College Cork between 11-13 June 2012. Photo by Tomas Tyner, UCC.

 

Advanced Study Course on Optical Chemical Sensors 2011

http://www.ascos.org/

http://members.aon.at/ascos/ascos2011.html

 

Gordon Research Conference: Insulin-like Growth factors in Physiology & Disease 2011

https://www.grc.org/programs.aspx?id=13156

 

27th Congress: European Society of Comparative Physiology & Biochemistry 2010

http://disav.unipmn.it/index.php?page=27escpb&hl=en_US

 

5th International Congress of the GRS-IGF Society 2010

http://rop.gu.se/news-events/news/news-details/meeting--5th-international-congress-of-the-grs-igf-society.cid948427

 

Biochemical Society: The Dynamic Cell 2009       

http://www.jointbscbbs2009.org

Poster problems at the Biochemistry Society conference

 

National Conferences/Symposia 

Irish Network for Biomarkers in Neurodegeneration Symposium 2014

http://www.tcd.ie/research/inbind/news/inbind%20symposium.php

 

Biochemical Society (Irish Area Section) 8th Neuroscience Ireland Conference 2013 - Brain Disorders Across the Lifespan: Translational Neuroscience From Molecule to Man

http://www.biochemistry.org/events/AllConferences/tabid/379/MeetingNo/IND109/view/Conference/Default.aspx

http://neuroscienceireland.com/nsi-conference/2013conference/

http://www.ucc.ie/en/nsi-iasbs-joint-meeting/

 

Symposium of the Microscopy Society of Ireland 2012

http://microscopy.ie/Society.php

http://symposium.microscopy.ie/MSI2012/

 

VIBE Bioinformatics Conference 2010

http://www.ucc.ie/en/news/newsarchive/2010pressreleases/fullstory-106477-en.html

Conference participants at the Biochemistry Society conference

Our Academic Staff and Selected Research Publications

Our Academic Staff and a selection of their research publications from the period 2008  to 2014 are listed and linked to the research PDF's below.

This list is also available to download: 2015-Selected Research Publications.

 

Professor John F. Atkins

Books

RNA worlds: From life’s origins to diversity in gene regulation.

Atkins, J. F., Gesteland, R. F., & Cech, T. (Eds.). (2011).  
New York;: Cold Spring Harbor Laboratory Press.
ISBN:  978-0-879699-46-8.

Recoding: Expansion of Decoding rules enriches gene expression.

J.F. Atkins and R.F. Gesteland.  (2010). 
New York: Springer Science+Business Media, LLC.
ISBN: 978-0-387-89381-5.
DOI: 978-0-387-89382-2.

 

Journal Articles

An overlapping protein-coding region in influenza A virus segment 3 modulates the host response.

Jagger, B. W., H. M. Wise, J. C. Kash, K. A. Walters, N. M. Wills, Y. L. Xiao, R. L. Dunfee, L. M. Schwartzman, A. Ozinsky, G. L. Bell, R. M. Dalton, A. Lo, S. Efstathiou, J. F. Atkins, A. E. Firth, J. K. Taubenberger and P. Digard (2012). 
Science 337(6091): 199-204. 
DOI: 10.1126/science.1222213. (1,442kB)

uORFs with unusual translational start codons autoregulate expression of eukaryotic ornithine decarboxylase homologs.

Ivanov, I. P., G. Loughran and J. F. Atkins (2008). 
Proc Natl Acad Sci U S A 105(29): 10079-10084. 
DOI: 10.1073/pnas.0801590105. (765kB)

Translational bypassing without peptidyl-tRNA anticodon scanning of coding gap mRNA.

Wills, N. M., M. O'Connor, C. C. Nelson, C. C. Rettberg, W. M. Huang, R. F. Gesteland and J. F. Atkins (2008). 
EMBO J 27(19): 2533-2544. 
DOI: 10.1038/emboj.2008.170. (314kB)

 

Dr Pasha V. Baranov

GWIPS-viz: development of a ribo-seq genome browser.

Michel, A. M., G. Fox, M. K. A, C. De Bo, P. B. O'Connor, S. M. Heaphy, J. P. Mullan, C. A. Donohue, D. G. Higgins and P. V. Baranov (2014). 
Nucleic Acids Res 42(Database issue): D859-864. 
DOI: 10.1093/nar/gkt1035. (341kB)

Observation of dually decoded regions of the human genome using ribosome profiling data.

Michel, A. M., K. R. Choudhury, A. E. Firth, N. T. Ingolia, J. F. Atkins and P. V. Baranov (2012). 
Genome Res 22(11): 2219-2229. 
DOI: 10.1101/gr.133249.111. (2,410kB)

A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.

Sharma, V., A. E. Firth, I. Antonov, O. Fayet, J. F. Atkins, M. Borodovsky and P. V. Baranov (2011). 
Mol Biol Evol 28(11): 3195-3211. 
DOI: 10.1093/molbev/msr155. (1,290kB)

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences.

Ivanov, I. P., A. E. Firth, A. M. Michel, J. F. Atkins and P. V. Baranov (2011). 
Nucleic Acids Res 39(10): 4220-4234. 
DOI: 10.1093/nar/gkr007. (1,411kB)

DARNED: a DAtabase of RNa EDiting in humans.

Kiran, A. and P. V. Baranov (2010). 
Bioinformatics 26(14): 1772-1776. 
DOI: 10.1093/bioinformatics/btq285. (486kB)

 

Professor Thomas G. Cotter

Recent advances in reactive oxygen species measurement in biological systems.

Woolley, J. F., J. Stanicka and T. G. Cotter (2013). 
Trends Biochem Sci 38(11): 556-565. 
DOI: 10.1016/j.tibs.2013.08.009. (1,092kB)

H2O2 production downstream of FLT3 is mediated by p22phox in the endoplasmic reticulum and is required for STAT5 signalling.

Woolley, J. F., R. Naughton, J. Stanicka, D. R. Gough, L. Bhatt, B. C. Dickinson, C. J. Chang and T. G. Cotter (2012). 
PLoS One 7(7): e34050. 
DOI: 10.1371/journal.pone.0034050. (652kB)

Inhibition of protein-tyrosine phosphatase 1B (PTP1B) mediates ubiquitination and degradation of Bcr-Abl protein.

Alvira, D., R. Naughton, L. Bhatt, S. Tedesco, W. D. Landry and T. G. Cotter (2011). 
J Biol Chem 286(37): 32313-32323. 
DOI: 10.1074/jbc.M111.249060. (4,069kB)

Apoptosis and cancer: the genesis of a research field.

Cotter, T. G. (2009). 
Nat Rev Cancer 9(7): 501-507.
DOI: 10.1038/nrc2663. (387kB) 

Redox survival signalling in retina-derived 661W cells.

Mackey, A. M., N. Sanvicens, G. Groeger, F. Doonan, D. Wallace and T. G. Cotter (2008). 
Cell Death Differ 15(8): 1291-1303. 
DOI: 10.1038/cdd.2008.43. (543kB)

 

Dr Ruslan I. Dmitriev

Imaging of neurosphere oxygenation with phosphorescent probes.

Dmitriev, R. I., A. V. Zhdanov, Y. M. Nolan and D. B. Papkovsky (2013). 
Biomaterials 34(37): 9307-9317. 
DOI: 10.1016/j.biomaterials.2013.08.065. (2,903kB)

Biological detection by optical oxygen sensing.

Papkovsky, D. B. and R. I. Dmitriev (2013). 
Chem Soc Rev 42(22): 8700-8732. 
DOI: 10.1039/c3cs60131e. (3,759kB)

Assessment of cellular oxygen gradients with a panel of phosphorescent oxygen-sensitive probes.

Dmitriev, R. I., A. V. Zhdanov, G. Jasionek and D. B. Papkovsky (2012). 
Anal Chem 84(6): 2930-2938. 
DOI: 10.1021/ac3000144. (465kB)

A Phosphorescent Nanoparticle-Based Probe for Sensing and Imaging of (Intra)Cellular Oxygen in Multiple Detection Modalities.

Kondrashina, A. V., R. I. Dmitriev, S. M. Borisov, I. Klimant, I. O'Brien, Y. M. Nolan, A. V. Zhdanov and D. B. Papkovsky (2012). 
Advanced Functional Materials 22(23): 4931-4939. 
DOI: 10.1002/adfm.201201387. (1,672kB)

Cell-penetrating conjugates of coproporphyrins with oligoarginine peptides: rational design and application for sensing intracellular O2.

Dmitriev, R. I., H. M. Ropiak, G. V. Ponomarev, D. V. Yashunsky and D. B. Papkovsky (2011). 
Bioconjug Chem 22(12): 2507-2518. 
DOI: 10.1021/bc200324q. (678kB)

 

Dr (Eoin) John V. Fleming

The human ubiquitin conjugating enzyme UBE2J2 (Ubc6) is a substrate for proteasomal degradation.

Lam, S. Y., C. Murphy, L. A. Foley, S. A. Ross, T. C. Wang and J. V. Fleming (2014). 
Biochemical and Biophysical Research Communications 451(3): 361-366. 
DOI: 10.1016/j.bbrc.2014.07.099. (664kB)

Differential processing of mammalian L-histidine decarboxylase enzymes.

Fennell, L. M. and J. V. Fleming (2014). 
Biochemical and Biophysical Research Communications 445(2): 304-309. 
DOI: 10.1016/j.bbrc.2014.01.178. (613kB)

N-Glycosylation is important for the correct intracellular localization of HFE and its ability to decrease cell surface transferrin binding.

Bhatt, L., C. Murphy, L. S. O'Driscoll, M. Carmo-Fonseca, M. W. McCaffrey and J. V. Fleming (2010). 
Febs Journal 277(15): 3219-3234. 
DOI: 10.1111/j.1742-4658.2010.07727.x. (1,502kB)

 

Professor James J.A. Heffron

Functional and genetic characterization of clinical malignant hyperthermia crises: a multi-centre study.

Klingler, W., S. Heiderich, T. Girard, E. Gravino, J. J. A. Heffron, S. Johannsen, K. Jurkat-Rott, H. Ruffert, F. Schuster, M. Snoeck, V. Sorrentino, V. Tegazzin and F. Lehmann-Horn (2014). 
Orphanet Journal of Rare Diseases 2014, 9:8. 
DOI: 10.1186/1750-1172-9-8. (1,226kB)

Toxicity of Industrially Relevant Chlorinated Organic Solvents In Vitro.

McDermott, C. and J. J. A. Heffron (2013). 
International Journal of Toxicology 32(2): 136-145. 
DOI: 10.1177/1091581813482006.

Genotoxicity of imidacloprid in relation to metabolic activation and composition of the commercial product.

Costa, C., V. Silvari, A. Melchini, S. Catania, J. J. Heffron, A. Trovato and R. De Pasquale (2009). 
Mutat Res 672(1): 40-44. 
DOI: 10.1016/j.mrgentox.2008.09.018. (300kB)

n-Hexane toxicity in Jurkat T-cells is mediated by reactive oxygen species.

McDermott, C., M. H. O'Donoghue and J. J. A. Heffron (2008). 
Archives of Toxicology 82(3): 165-171. 
DOI: 10.1007/s00204-008-0286-x. (380kB)

In vitro exposure of Jurkat T-cells to industrially important organic solvents in binary combination: Interaction analysis.

McDermott, C., A. Allshire, F. van Pelt and J. J. A. Heffron (2008). 
Toxicological Sciences 101(2): 263-274. 
DOI: 10.1093/toxsci/kfm274. (160kB)

 

Professor Mary W. McCaffrey

Identification and characterization of multiple novel Rab-myosin Va interactions.

Lindsay, A. J., F. Jollivet, C. P. Horgan, A. R. Khan, G. Raposo, M. W. McCaffrey and B. Goud (2013). 
Mol Biol Cell 24(21): 3420-3434. 
DOI: 10.1091/mbc.E13-05-0236. (10,925kB)

Rab30 is required for the morphological integrity of the Golgi apparatus.

Kelly, E. E., F. Giordano, C. P. Horgan, F. Jollivet, G. Raposo and M. W. McCaffrey (2012). 
Biol Cell 104(2): 84-101. 
DOI: 10.1111/boc.201100080. (871kB)

Rab11-FIP3 links the Rab11 GTPase and cytoplasmic dynein to mediate transport to the endosomal-recycling compartment.

Horgan, C. P., S. R. Hanscom, R. S. Jolly, C. E. Futter and M. W. McCaffrey (2010). 
J Cell Sci 123(Pt 2): 181-191. 
DOI: 10.1242/jcs.052670. (5,275kB)

Class I Rab11-family interacting proteins are binding targets for the Rab14 GTPase.

Kelly, E. E., C. P. Horgan, C. Adams, T. M. Patzer, D. M. Ni Shuilleabhain, J. C. Norman and M. W. McCaffrey (2010). 
Biology of the Cell 102(1): 51-62. 
DOI: 10.1042/Bc20090068.. (1,428kB)

Rab-coupling protein coordinates recycling of α5β1 integrin and EGFR1 to promote cell migration in 3D microenvironments.

Caswell, P. T., M. Chan, A. J. Lindsay, M. W. McCaffrey, D. Boettiger and J. C. Norman (2008). 
J Cell Biol 183(1): 143-155. 
DOI: 10.1083/jcb.200804140. (6,736kB)

 

Dr Justin V. McCarthy

Presenilins are novel substrates for TRAF6-mediated ubiquitination.

Yan, R., S. Farrelly and J. V. McCarthy (2013). 
Cell Signal 25(9): 1769-1779. 
DOI: 10.1016/j.cellsig.2013.05.015. (1,113kB)

Semagacestat, a γ-secretase inhibitor, activates the growth hormone secretagogue (GHS-R1a) receptor.

Schellekens, H., O. McNamara, T. G. Dinan, J. V. McCarthy, G. P. McGlacken and J. F. Cryan (2013). 
J Pharm Pharmacol 65(4): 528-538. 
DOI: 10.1111/jphp.12010. (866kB)

TRAF6 promotes ubiquitination and regulated intramembrane proteolysis of IL-1R1.

Twomey, C., S. Qian and J. V. McCarthy (2009). 
Biochem Biophys Res Commun 381(3): 418-423. 
DOI: 10.1016/j.bbrc.2009.02.051. (531kB)

Association between Presenilin-1 and TRAF6 modulates regulated intramembrane proteolysis of the p75NTR neurotrophin receptor.

Powell, J. C., C. Twomey, R. Jain and J. V. McCarthy (2009). 
J Neurochem 108(1): 216-230. 
DOI: 10.1111/j.1471-4159.2008.05763.x. (1,443kB)

Interleukin-1 receptor type 1 is a substrate for γ-secretase-dependent regulated intramembrane proteolysis.

Elzinga, B. M., C. Twomey, J. C. Powell, F. Harte and J. V. McCarthy (2009). 
J Biol Chem 284(3): 1394-1409. 
DOI: 10.1074/jbc.M803108200. (1,374kB)

 

Professor Tommie V. McCarthy

A single secreted luciferase-based gene reporter assay.

Barriscale, K. A., S. A. O'Sullivan and T. V. McCarthy (2014). 
Anal Biochem 453: 44-49. 
DOI: 10.1016/j.ab.2014.02.019. (548kB)

Characterization of the bovine innate immune response in milk somatic cells following intramammary infection with Streptococcus dysgalactiae subspecies dysgalactiae.

Beecher, C., M. Daly, R. P. Ross, J. Flynn, T. V. McCarthy and L. Giblin (2012). 
J Dairy Sci 95(10): 5720-5729. 
DOI: 10.3168/jds.2012-5338. (300kB)

Polymorphisms in bovine immune genes and their associations with somatic cell count and milk production in dairy cattle.

Beecher, C., M. Daly, S. Childs, D. P. Berry, D. A. Magee, T. V. McCarthy and L. Giblin (2010). 
BMC Genet 11: 99. 
DOI: 10.1186/1471-2156-11-99. (214kB)

Administration of a live culture of Lactococcus lactis DPC 3147 into the bovine mammary gland stimulates the local host immune response, particularly IL-1β and IL-8 gene expression.

Beecher, C., M. Daly, D. P. Berry, K. Klostermann, J. Flynn, W. Meaney, C. Hill, T. V. McCarthy, R. P. Ross and L. Giblin (2009). 
J Dairy Res 76(3): 340-348. 
DOI: 10.1017/S0022029909004154. (118kB)

'Shotgun immunological' approach for analysis of a complex subcellular system.

Mackrill, J. J., K. England, B. E. Flucher and T. V. McCarthy (2009). 
Int J Mol Med 23(3): 399-405.
DOI: 10.3892/ijmm_00000144. (288kB)

 

Dr Tom Moore

Psg22 expression in mouse trophoblast giant cells is associated with gene inversion and co-expression of antisense long non-coding RNAs.

Williams, J. M., M. Ball, A. Ward and T. Moore (2015). 
Reproduction 149(1): 125-137. 
DOI: 10.1530/REP-14-0390.

Pregnancy-specific glycoproteins: complex gene families regulating maternal-fetal interactions.

Moore, T. and G. S. Dveksler (2014). 
Int J Dev Biol 58(2-4): 273-280. 
DOI: 10.1387/ijdb.130329gd. (1,587kB)

Pregnancy-specific glycoproteins bind integrin αIIbβ3 and inhibit the platelet-fibrinogen interaction.

Shanley, D. K., P. A. Kiely, K. Golla, S. Allen, K. Martin, R. T. O'Riordan, M. Ball, J. D. Aplin, B. B. Singer, N. Caplice, N. Moran and T. Moore (2013). 
PLoS One 8(2): e57491. 
DOI: 10.1371/journal.pone.0057491. (2,534kB)

Maternal-fetal resource allocation: co-operation and conflict.

Fowden, A. L. and T. Moore (2012). 
Placenta 33 Suppl 2: e11-15. 
DOI: 10.1016/j.placenta.2012.05.002. (254kB)

Expression of pleiotrophin and its receptors in human placenta suggests roles in trophoblast life cycle and angiogenesis.

Ball, M., M. Carmody, F. Wynne, P. Dockery, A. Aigner, I. Cameron, J. Higgins, S. D. Smith, J. D. Aplin and T. Moore (2009). 
Placenta 30(7): 649-653. 
DOI: 10.1016/j.placenta.2009.05.001. (686kB)

 

Dr Ken Nally

Natural killer cells protect mice from DSS-induced colitis by regulating neutrophil function via the NKG2A receptor.

Hall, L. J., C. T. Murphy, A. Quinlan, G. Hurley, F. Shanahan, K. Nally and S. Melgar (2013). 
Mucosal Immunol 6(5): 1016-1026. 
DOI: 10.1038/mi.2012.140. (2,839kB)

The sphingosine-1-phosphate analogue FTY720 impairs mucosal immunity and clearance of the enteric pathogen Citrobacter rodentium.

Murphy, C. T., L. J. Hall, G. Hurley, A. Quinlan, J. MacSharry, F. Shanahan, K. Nally and S. Melgar (2012). 
Infect Immun 80(8): 2712-2723. 
DOI: 10.1128/IAI.06319-11. (2,722kB)

Differential intestinal M-cell gene expression response to gut commensals.

Lapthorne, S., J. Macsharry, P. Scully, K. Nally and F. Shanahan (2012). 
Immunology 136(3): 312-324. 
DOI: 10.1111/j.1365-2567.2012.03581.x. (957kB)

Technical Advance: Function and efficacy of an α4-integrin antagonist using bioluminescence imaging to detect leukocyte trafficking in murine experimental colitis.

Murphy, C. T., G. Moloney, J. Macsharry, A. Haynes, E. Faivre, A. Quinlan, P. G. McLean, K. Lee, L. O'Mahony, F. Shanahan, S. Melgar and K. Nally (2010). 
J Leukoc Biol 88(6): 1271-1278. 
DOI: 10.1189/jlb.0909627. (1,665kB)

Use of bioluminescence imaging to track neutrophil migration and its inhibition in experimental colitis.

Murphy, C. T., G. Moloney, L. J. Hall, A. Quinlan, E. Faivre, P. Casey, F. Shanahan, S. Melgar and K. Nally (2010). 
Clin Exp Immunol 162(1): 188-196. 
DOI: 10.1111/j.1365-2249.2010.04234.x. (775kB)

 

Professor Rosemary O’Connor

PDLIM2 regulates transcription factor activity in epithelial-to-mesenchymal transition via the COP9 signalosome.

Bowe, R. A., O. T. Cox, V. Ayllon, E. Tresse, N. C. Healy, S. J. Edmunds, M. Huigsloot and R. O'Connor (2014). 
Mol Biol Cell 25(1): 184-195. 
DOI: 10.1091/mbc.E13-06-0306. (1,011kB)

Serine phosphorylation of the insulin-like growth factor I (IGF-1) receptor C-terminal tail restrains kinase activity and cell growth.

Kelly, G. M., D. A. Buckley, P. A. Kiely, D. R. Adams and R. O'Connor (2012). 
J Biol Chem 287(33): 28180-28194. 
DOI: 10.1074/jbc.M112.385757. (3,012kB)

Mitochondrial pyrimidine nucleotide carrier (PNC1) regulates mitochondrial biogenesis and the invasive phenotype of cancer cells.

Favre, C., A. Zhdanov, M. Leahy, D. Papkovsky and R. O'Connor (2010). 
Oncogene 29(27): 3964-3976. 
DOI: 10.1038/onc.2010.146. (1,086kB)

Heme-binding protein HRG-1 is induced by insulin-like growth factor I and associates with the vacuolar H+-ATPase to control endosomal pH and receptor trafficking.

O'Callaghan, K. M., V. Ayllon, J. O'Keeffe, Y. Wang, O. T. Cox, G. Loughran, M. Forgac and R. O'Connor (2010). 
J Biol Chem 285(1): 381-391. 
DOI: 10.1074/jbc.M109.063248. (3,078kB)

Phosphorylation of RACK1 on tyrosine 52 by c-Abl is required for insulin-like growth factor I-mediated regulation of focal adhesion kinase.

Kiely, P. A., G. S. Baillie, R. Barrett, D. A. Buckley, D. R. Adams, M. D. Houslay and R. O'Connor (2009). 
J Biol Chem 284(30): 20263-20274. 
DOI: 10.1074/jbc.M109.017640. (3,874kB)

 

Dr Cora O’Neill

The Parkinson's gene PINK1 regulates cell cycle progression and promotes cancer-associated phenotypes.

O'Flanagan, C. H., V. A. Morais, W. Wurst, B. De Strooper and C. O'Neill (2014). 
Oncogene 0. 
DOI: 10.1038/onc.2014.81. (3,893kB)

The diabetes drug liraglutide ameliorates aberrant insulin receptor localisation and signalling in parallel with decreasing both amyloid-β plaque and glial pathology in a mouse model of Alzheimer's disease.

Long-Smith, C. M., S. Manning, P. L. McClean, M. F. Coakley, D. J. O'Halloran, C. Holscher and C. O'Neill (2013). 
Neuromolecular Med 15(1): 102-114. 
DOI: 10.1007/s12017-012-8199-5. (3,018kB)

Defects in IGF-1 receptor, insulin receptor and IRS-1/2 in Alzheimer's disease indicate possible resistance to IGF-1 and insulin signalling.

Moloney, A. M., R. J. Griffin, S. Timmons, R. O'Connor, R. Ravid and C. O'Neill (2010). 
Neurobiol Aging 31(2): 224-243. 
DOI: 10.1016/j.neurobiolaging.2008.04.002. (7,019kB)

Akt signal transduction dysfunction in Parkinson's disease.

Timmons, S., M. F. Coakley, A. M. Moloney and C. O'Neill (2009). 
Neurosci Lett 467(1): 30-35. 
DOI: 10.1016/j.neulet.2009.09.055. (4,003kB)

Understanding BACE1: essential protease for amyloid-β production in Alzheimer's disease.

Stockley, J. H. and C. O'Neill (2008). 
Cell Mol Life Sci 65(20): 3265-3289. 
DOI: 10.1007/s00018-008-8271-3. (2,090kB)

 

Professor Dmitri B. Papkovsky

Journal Articles

Imaging of neurosphere oxygenation with phosphorescent probes.

Dmitriev, R. I., A. V. Zhdanov, Y. M. Nolan and D. B. Papkovsky (2013). 
Biomaterials 34(37): 9307-9317. 
DOI: 10.1016/j.biomaterials.2013.08.065. (2,903kB)

A Phosphorescent Nanoparticle-Based Probe for Sensing and Imaging of (Intra)Cellular Oxygen in Multiple Detection Modalities.

Kondrashina, A. V., R. I. Dmitriev, S. M. Borisov, I. Klimant, I. O'Brien, Y. M. Nolan, A. V. Zhdanov and D. B. Papkovsky (2012). 
Advanced Functional Materials 22(23): 4931-4939. 
DOI: 10.1002/adfm.201201387. (1,672kB)

Intracellular O2 sensing probe based on cell-penetrating phosphorescent nanoparticles.

Fercher, A., S. M. Borisov, A. V. Zhdanov, I. Klimant and D. B. Papkovsky (2011). 
ACS Nano 5(7): 5499-5508. 
DOI: 10.1021/nn200807g. (1,048kB)

Comparative bioenergetic assessment of transformed cells using a cell energy budget platform.

Zhdanov, A. V., C. Favre, L. O'Flaherty, J. Adam, R. O'Connor, P. J. Pollard and D. B. Papkovsky (2011). 
Integr Biol (Camb) 3(11): 1135-1142. 
DOI: 10.1039/c1ib00050k.

Book

Phosphorescent Oxygen-Sensitive Probes. 

Papkovsky DB, Zhdanov AV, Fercher A, Dmitriev RI, Hynes J. (2012). 
Springer Briefs in Biochemistry and Molecular Biology. 
ISBN 978-3-0348-0524-7. 
DOI: 10.1007/978-3-0348-0525-4.

 

Professor David Sheehan

Toxicity of copper oxide nanoparticles in the blue mussel, Mytilus edulis: a redox proteomic investigation.

Hu, W., S. Culloty, G. Darmody, S. Lynch, J. Davenport, S. Ramirez-Garcia, K. A. Dawson, I. Lynch, J. Blasco and D. Sheehan (2014). 
Chemosphere 108: 289-299. 
DOI: 10.1016/j.chemosphere.2014.01.054. (2,072kB)

Redox proteomics changes in the fungal pathogen Trichosporon asahii on arsenic exposure: identification of protein responses to metal-induced oxidative stress in an environmentally-sampled isolate.

Ilyas, S., A. Rehman, A. C. Varela and D. Sheehan (2014). 
PLoS One 9(7): e102340. 
DOI: 10.1371/journal.pone.0102340. (3,054kB)

Proteomic evaluation of citrate-coated silver nanoparticles toxicity in Daphnia magna.

Rainville, L. C., D. Carolan, A. C. Varela, H. Doyle and D. Sheehan (2014). 
Analyst 139(7): 1678-1686. 
DOI: 10.1039/c3an02160b. (671kB)

Redox proteomics in study of kidney-associated hypertension: new insights to old diseases.

Sheehan, D., L. C. Rainville, R. Tyther and B. McDonagh (2012). 
Antioxid Redox Signal 17(11): 1560-1570. 
DOI: 10.1089/ars.2012.4705.

Oxidative stress and toxicity of gold nanoparticles in Mytilus edulis.

Tedesco, S., H. Doyle, J. Blasco, G. Redmond and D. Sheehan (2010). 
Aquat Toxicol 100(2): 178-186. 
DOI: 10.1016/j.aquatox.2010.03.001. (796kB)

 

Dr Paul Young

Tight, cell type-specific control of LNX expression in the nervous system, at the level of transcription, translation and protein stability.

Lenihan, J. A., O. Saha, L. M. Mansfield and P. W. Young (2014). 
Gene 552(1): 39-50. 
DOI: 10.1016/j.gene.2014.09.011. (2,028kB)

An analysis of splicing, actin-binding properties, heterodimerization and molecular interactions of the non-muscle α-actinins.

Foley, K. S. and P. W. Young (2013). 
Biochem J 452(3): 477-488. 
DOI: 10.1042/BJ20121824. (1,066kB)

Efficient inducible Pan-neuronal cre-mediated recombination in SLICK-H transgenic mice.

Heimer-McGinn, V. and P. Young (2011). 
Genesis 49(12): 942-949. 
DOI: 10.1002/dvg.20777. (2,180kB)

Molecular evolution of the LNX gene family.

Flynn, M., O. Saha and P. Young (2011). 
BMC Evol Biol 11: 235. 
DOI: 10.1186/1471-2148-11-235. (3,975kB)

Single-neuron labeling with inducible Cre-mediated knockout in transgenic mice.

Young, P., L. Qiu, D. Wang, S. Zhao, J. Gross and G. Feng (2008). 
Nat Neurosci 11(6): 721-728. 
DOI: 10.1038/nn.2118. (488kB)

 

 

Strategic Plan 2015 - 2020 (including Research Strategy)

150429-1537-Research Policy 2015-2020

School of Biochemistry and Cell Biology

University College Cork, Western Road, Cork.

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