SCHOOLSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY NEWSLETTER

VOLUME 1 ISSUE 2 NOVEMBER 2013

In this issue

Breast Cancer Research Gap Analysis 2013

Irish Cancer Society Launches National Collaborative Research Centre BREAST-PREDICT

PhD Scholars Programme Hosts Cork Adult Flute Ensemble for Breast Cancer Charity Evening

Draft Governance Structure for School of Biochemistry and Cell Biology

Science Week 2013

UCC Open Day. 12th October 2013

Biochemistry and Biotechnology Society Annual General Meeting

People

Upcoming Events and Seminars

Postgraduate Annual Reviews

Hot off the Press! Recent publications

Message from Head of SchoolYou are very welcome to this second edition of the School Newsletter.

This month we focus in particular on our ongoing contributions to cancer research, Science Week and the School’s draft governance structure.

You will also find news about upcoming seminars, events and people in our School.

Professor David Sheehan

CANCERBreast Cancer Research Gap Analysis 2013On October 1st, a paper entitled “Critical research gaps and translational priorities for the successful prevention and treatment of breast cancer” was published in the international open access journal, Breast Cancer Research.

This analysis supported by the leading UK Breast Cancer Campaign was a collaboration between more than one hundred internationally-recognised scientists, clinicians and healthcare professionals who identified

10 gaps in breast cancer research demonstrating what is needed to “overcome - prevent, cure and outlive - breast cancer by 2050”.

http://www.breastcancercampaign.org/documents/ga-2013/help-us-find-the-cures.pdf

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October was breast cancer awareness month and the School has been active in a number of important international, national and local breast cancer initiatives

Curing Cancer: A Dream Worth Fighting ForProfessor Tom Cotter delivered a Keynote lecture: “Curing Cancer: A Dream Worth Fighting For” at the National Conference for Cancer Survivorship in the Aviva Conference centre in Dublin in late September.

The conference was attended by circa 800 people and sponsored by the Irish Cancer Society.

Professor Rosemary O’Connor, School of Biochemistry and Cell Biology, UCC is one of the authors who contributed to the analysis and is a former member of the scientific advisory board of the Breast Cancer Campaign (2008-2012).

NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

BREAST CANCER AWARENESS MONTH PAGE 2

CANCERIrish Cancer Society launch nationally collaborative research centre BREAST-PREDICTThe Irish Cancer Society has funded the first national collaborative research centre focused on Breast cancer which launches in October. This virtual research centre has nine principal investigators from diverse disciplines including oncology, cancer biology, bioinformatics and systems biology coming from most academic institutions in Ireland and collaborates with international cancer centres. The overall objective is to use information derived from breast cancer patients across Ireland to design better therapies and track prognosis and therapy responses in a personalized way. http://thecorknews.ie/articles/ucc-part-world-first-cancer-research-11946

Professor Rosemary O’Connor is one of the principal investigators and her team in the School of Biochemistry and Cell Biology will participate in research on the Insulin-like system and new proteins associated with breast cancer progression.

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October was breast cancer awareness month and the School has been active in a number of important international, national and local breast cancer initiatives

BREAST-PREDICT NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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CANCERPhD Scholars Programme hosts Cork Adult Flute Ensemble for breast cancer charity eveningOn Friday 18th October, Dr. Kellie Dean and Ms. Fionola Fogarty hosted the Cork Adult Flute Ensemble for a charity concert at the Aula Maxima. The ensemble was founded in 2011 and has a mixture of professional and amateur flute players from Cork city. For the concert, the ensemble played a selection of pieces arranged specifically for a flute choir. The ensemble was joined by several other musicians on piano and violin. Ms. Orla Fogarty (Fionola’s sister) is a member of the Cork Adult Flute Ensemble and sang three solo pieces with piano accompaniment.

The event was expertly compered by Mr. Ronan O’Riordan and attended by a diverse group of patrons from within and outside UCC. The event raised €850 Irish Cancer Society “Get the Girls” campaign from donations collected at the door and online. Online donations can still be made at http://www.mycharity.ie/event/phd_scholars_getthegirlsconcert

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October was breast cancer awareness month and the School has been active in a number of important international, national and local breast cancer initiatives

Above image purchased at http://www.123rf.com/photo_19600197_pink-ribbon-with-womens.html

BREAST CANCER CHARITY EVENING NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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SCHOOLDraft Governance Structure for School of Biochemistry and Cell Biology

A presentation on the draft governance structure for this School was made by Prof David Sheehan, Head of School on Thursday 24th October.

This features a School Assembly to meet twice yearly, a School Executive Management Committee to meet monthly and four standing committees (Research, Graduate Studies, Teaching and Learning, Health and Safety) to meet in a manner synching with SEFS College committees. In addition, student representatives will form a Students Council chaired by the Head of School to report directly to the Executive Management Committee.

Professor Sheehan commented: “The purpose of this structure is to ensure free flow of information into and out of the School, to support participation by key constituencies, not just academic staff and to improve transparency and efficiency in how we do our business.” Nominations have been requested for membership of the committees envisaged in this structure by November 1st and the first meeting of the Executive Management Committee is scheduled for Thursday, November 7th.

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Science Week 2013Science week is a national event that the Science Society has been trying to bring onto UCC’s campus for the past number of years.

By hosting a range of events over the course of the week, we aim to reach all aspects that science covers, from geology to astrophysics and provide information for budding scientists at UCC. This years theme is all about exploring the extra-ordinary, which we hope to achieve this year with our on campus events and guest speakers such as Gavin Ryan’s career workshop and our very own UCC lecturers Professor Tom Cotter and Professor David Sheehan, Head of School of Biochemistry and Cell Biology.

UCC’s Science Society Science Week begins on Monday 11th Nov this year on the theme Exploring the Ordinary.

Some talks from our School include:

* Science at Interfaces: Research Opportunities for Making Tomorrow’s World. Monday, 11th November Professor David Sheehan.

* How Lazy Thinking Leads to Strange Beliefs. Tuesday 12th November Professor Tom Cotter.

“The purpose of this structure is to ensure free flow of information into and out of the School, to support participation by key constituencies, not just academic staff and to improve transparency and efficiency in how we do our business.”

GOVERNANCE STRUCTURE FOR SCHOOL NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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OPEN DAY

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DayUCC Open Day

UCC Open day was held on the 12th October 2013. Professor Dave Sheehan, Professor Tommie McCarthy and Dr Ken Nally from the School of Biochemistry and Cell Biology were on hand to answer queries relating to Biological and Chemical Sciences and the Biochemistry Degree outlet. In addition, Dr Paul Young, Dr Sinéad Kerins and Dr John Morgan (School of Microbiology), provided information and dealt with student queries regarding the joint UCC/CIT Biomedical Science degree programme.

Prospective students attended presentations from Professor Dave Sheehan and Dr Sinéad Kerins on Biological and Chemical Sciences/Biochemistry and Biomedical Science, respectively.

Biochemistry graduates, Jamie Byrne and Niamh Barry provided tours of the undergraduate teaching laboratories in the School of Biochemistry and Cell Biology and demonstrated various Molecular Biology techniques to the students. The students also got some hands-on on experience in loading agarose and SDS-PAGE gels. They really enjoyed this and were very impressed with the teaching facilities.

The Open Day at UCC was a highly successful event attended by over 5,000 potential students and Professor Dave Sheehan would like to thank the academic staff, technical staff and past Biochemistry graduates for making our participation in this event such a success.

Dr Tanya Mulcahy, College of Science, Engineering and Food Science (SEFS) and Professor David Sheehan, Head of School of Biochemistry and Cell Biology at UCC Open Day

As part of the tours of the Undergraduate laboratory in the School of Biochemistry and Cell Biology, Biochemistry graduate, Jamie Byrne, helped Open Day participants to load a gel

Professor Tommie McCarthy, School of Biochemistry and Cell Biology talking to prospective students at UCC Open Day

The Open Day at UCC was a highly successful event attended by over 5,000 potential students.

UCC OPEN DAY NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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SOCIETYSo

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yBiochemistry and Biotechnology Society Annual General MeetingOur AGM was held on 17th October, at which the 2013/2014 committee was elected.

2013-14 Committee MembersAuditor Joan LenihanSecretary Anita MurphyTreasurer Ian Mc DermottPRO Evan Gilman-BurkePostgraduate Rep Caroline VaughanMSc Biotechnology Rep Niamh BarryMSc Biotechnology Rep Rachel Divilly4th Year Class Rep Mary Murphy3rd Year Class Rep Linda Hearn3rd Year Class Rep David O’Sullivan3rd Year Class Rep Julie O’Sullivan3rd Year Class Rep Byran Savage3rd Year Class Rep Aine Stanton

2012-13 Committee Members The Society would like to thank most sincerely the outgoing 2012-13 Committee Members:

Auditor Joan LenihanSecretary Caroline VaughanTreasurer Anita MurphyPRO Kay MuldowneyPostgraduate Rep Arthur CoakleyMSc Biotechnology Rep Sinead CreminMSc Biotechnology Rep Amit Tomar4th Year Class Rep Kiera Deane4rd Year Class Rep Liz Hinchy4th Year Class Rep Sharon McMahon3rd Year Class Rep Mirinda Tattan3rd Year Class Rep Stephen Dennehy3rd Year Class Rep Lara Farmer3rd Year Class Rep Mattie O’ Sullivan

The outgoing Biochemistry and Biotechnology Society committee would like to thank you all for your support during 2012/2013 and the current committee is looking forward to meeting you at their upcoming events.

Biochemistry and Biotechnology SocietyThe Biochemistry and Biotechnology Society was established in 2006 to organise scientific and social events for the Biochemistry Department (now School of Biochemistry and Cell Biology) on behalf of undergraduate and postgraduate students.

Over the past seven years the society has held interesting seminars, research days, table quizzes etc.

http://biochem.uccsocieties.com/

The Biochemistry and Biotechnology Society has held many interesting seminars, research days, table quizzes over the past seven years

BIOCHEMISTRY AND BIOTECHNOLOGY SOCIETY NEWSLETTER

SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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EVENTSEv

entsUpcoming Research Seminars

Wednesday, 13th November Professor Richard Cogdell FRSHooker Chair of Botany, University of Glasgow. How purple photosynthetic bacteria harvest light energy. 12.00 p.m. in WGB 4.05.

Thursday 14th November Professor Anton NekrutenkoDepartment of Biochemistry and Molecular Biology, Penn State University and founder of Galaxy Project. http://galaxyproject.org/Enacting a sustainable ecosystem for data-intensive biomedical research.Venue and time to be announced.

Tuesday 19th NovemberDr Andrey ZinovievComputational Systems Biology of Cancer group, Institut Curie. https://sysbio.curie.fr/Looking at big data in cancer biology: make it simpler.1.00 p.m. in WGB G01.

Tuesday 26th NovemberProfessor Tom CotterSchool of Biochemistry and Cell BiologyOncogene-driven redox cell survival mechanisms.1.00 p.m. in WGB G01.

EVERYBODY IS WELCOME TO ATTEND.

Public PresentationWednesday, 13th NovemberAudrey Michel-Mannion, School of Biochemistry and Cell Biology, viva will start with a public presentation:Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation.10.00 a.m. in WGB G05.

Upcoming Events

The Virtual Institute of Bioinformatics and Evolution (VIBE) meeting will take place on the 15th of November in Galway. http://www.maths.nuigalway.ie/~tim/VIBE-2013/

Alzheimer Society of Ireland (Cork Branch), meeting of the Saturday Club, 9th Nov. 2013, Bessboro Day Care Centre (2-4pm). Live music featuring THE BRADLEY SISTERS. Light refreshments provided. FREE ADMISSION.

All Welcome (contact 021 4972504).

Dr Kellie Dean organises our School seminar programme.

UPCOMING EVENTS NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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PEOPLEPe

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Dr. Jillian CaseyDr Jillian Casey (UCC graduate in Genetics) was recently profiled in Nature Jobs (17th October 2013) for her PhD work (UCD) on anophthalmia, a genetic condition where babies are born without eyes (Casey et al., Human Mutation 2011, 32, 1417-1426).

Jillian used single nucleotide polymorphism arrays and next-generation sequencing to track down genes responsible for this condition and to aid in genetic diagnosis. She is currently a postdoc with the National Children’s Research Centre at Our Lady’s Hospital Crumlin and an associated Researcher with the recently-established UCD Academic Centre on Rare Diseases where she continues to look for genes responsible for rare disorders in families.

Professor Richard Cogdell Professor Richard Cogdell FRS will deliver the annual British Biophysical Society lecture as part of the BBS lecture tour organised by Professor David Sheehan. The lecture will be in Western Gateway Building (WGB 405) at 12 Noon on Wed. 13th Nov.

Prof Cogdell took his primary (BSc 1970) and PhD degrees (1973) at University of Bristol, England. Postdoctoral work followed at Cornell (1973-4) and University of Washington (1974-5). He has been at the Department of Botany, University of Glasgow since 1975 and was appointed to the Hooker chair of Botany in 1993. He is currently also Director of the Institute of Molecular, Cell & Systems Biology and Deputy Head, College of Medical, Veterinary and Life Sciences University of Glasgow. He was elected fellow of the Royal Society of Edinburgh in 1991, FRS in 2007 and a Fellow of the Royal Society of Arts in 2009.

Since the early 1970’s, Richard has been involved in research on bacterial photosynthesis. His work has increasingly focused on the early events of photosynthesis - light harvesting and energy transfer - and the structure / function of the pigment-protein complexes involved in these processes (see: McDermott et al. Crystal structure of an integral membrane light-harvesting complex from photosynthetic bacteria. Nature (1995) 374, 517-521; Ostroumov et al. Broadband 2D electronic spectroscopy reveals a carotenoid dark state in purple bacteria. Science (2013) 340, 52-56.

PEOPLE IN THE NEWS

Dr. Kate FoleyIn 2007, Kate graduated from University College Cork with a BSc Honours Degree in Biomedical Science. She subsequently obtained Membership of the Academy of Medical Laboratory Science following completion of Clinical Laboratory Placement at the Bon Secours Hospital in Cork.

In 2008 she was part of the first group of students to join the PhD Scholars Programme in Cancer Biology funded by the Health Research Board. She conducted her PhD project under the supervision of Dr Paul Young. Her work was published earlier this year in the Biochemical Journal.

Kate graduated with a PhD in Cancer Biology last June. She recently began working as an Assay Development Scientist with Radisens Diagnostics.

Professor Dmitri Papkovsky Professor Dmitri Papkovsky has been appointed as Associated Editor of Sensors & Actuators. B. Chemical journal (from October 2013).

Professor Dmitri Papkovsky was recently invited to speak at a seminar at the Institute of Physiology, University of Zurich, October 17th, 2013. Professor Papkovsky presented a talk on ‘‘New family of phosphorescent probes for imaging tissue oxygen”.

PEOPLE NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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PEOPLEPe

opleDr Aoife Corcoran

Dr Aoife Corcoran (PhD in Cancer Biology, supervised by Prof Tom Cotter) will be starting a post-doctoral position at Dana Farber/Harvard Cancer Center in Boston, USA. She is joining the laboratory of Dr Keith Ligon, whose research focuses on transcriptional networks controlling stem/progenitor cell growth in normal cells and neurologic cancers like gliomas. http://research4.dfci.harvard.edu/ligon/index.html

Dr Kate Foley Dr Kate Foley (PhD in Cancer Biology, supervised by Dr Paul Young) has started a position as an assay development scientist with Radisens Diagnostics, a start-up company based in Cork. http://www.radisens.com/

Dean Rowe Dean Rowe (MSc in Molecular Cell Biology with Bioinnovation class of 2012-13) accepted a position as a QC chemist with Genzyme based in Waterford. http://www.genzyme.ie/

Claire Donohue Claire Donohue completed M.Sc. in Bioinformatics with Systems Biology.

Audrey MichelAudrey Michel’s viva voce examination will be on the 13th of November and the viva includes a public presentation at 10 am WGB G05. See Events page.

Siobhan ClearySiobhan Cleary is returning from a year-long secondment to Almac Diagnostics to a PhD project under the supervision of Professor Rosemary O’Connor and Dr Pavel Baranov

Christopher SchultzChristopher Schultz, MSc, a visiting scientist from the University of Lund, Sweden will join the Biophysics and Bioanalysis Lab supervised by Professor Dmitri Papkovsky. Three month secondment (Oct-Dec 2013) under the Marie Curie ITN project ‘Chebana’.

Emilie Tresse (and Erin)Emilie Tresse started maternity leave at the beginning of October with her second baby due any minute.

A baby shower complete with games and quizzes held in the BSI was hosted by Milan Bustamante Garrido and Barbara Adarrio.

Emilie is now back home with little Erin Marie Sylvie who was born on Wednesday 23rd. She is of course beautiful, 54cm and 4.090kg, and has 2 beautiful teeth! Everybody is fine and Tristan is very proud to be a big brother.

Biophysics and Bioanalysis lab (from left to right): James Jenkins, PhD1; Dr. Alexander Zhdanov; Dr. Ruslan Dmitriev; Prof. Dmitri Papkovsky; Alina Kondrashina, PhD3; Alicia Waters, PhD3; Christopher Schultz (visiting scientist, Lund); Dr. Claudio Toncelli; Caroline Kelly, PhD1.

PEOPLE NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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REVIEWSRe

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The School’s Graduate Studies Committee would like to thank all who participated, and particularly our external reviewer Dr Aideen Long. Aideen has made an extremely valuable contribution to this review process as external reviewer for the last four years. Aideen is now Dean of Graduate Studies in TCD, and with the extremely busy schedule this will be her last year reviewing the programme.

The annual post-graduate PhD reviews were held on 21st and 22nd of October organised by Dr. Cora O’ Neill, Chair of School Graduate Studies Committee, with the expert administrative assistance of Olive Cosgrave. It was a very enjoyable and informative two days of research presentations by the post-graduate PhD students at the end of year 1, 2 and 3 of their PhD programme.

Dr Aideen Long, Dean of Graduate Studies in TCD was external examiner for the review process and each presentation was additionally reviewed by two members of academic staff. All were impressed by the PhD students who presented their work to a very high standard. Support and interaction at the review was also added to by post-docs, newly commenced PhD students and other researchers who attended.

The School’s Graduate Studies Committee would like to thank all who participated, and particularly our external reviewer Dr Aideen Long.

POSTGRADUATE ANNUAL REVIEWS NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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PUBLICATIONS

Any material for inclusion in the next newsletter (December 1st) should be sent to the editor, Professor David Sheehan

Email hosbcandcb@ucc.ie

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O’Neill C. PI3K/Akt/mTOR signalling: importance of on/off switches in aging, cognitive decline and Alzheimer’s disease. Exp. Gerontol. (2013) 48, 647-653.

Long-Smith CM, Manning S, McClean PL, Coakley MF, O’Halloran DJ, Holscher C, O’ Neill C. The diabetes drug liraglutide ameliorates aberrant insulin receptor localisation and signalling in parallel with decreasing both amyloid-b plaque and glial pathology in a mouse model of Alzheimer’s disease. Neuromolecular Med. (2013) 15, 102-14.

Fogarty F, O’Keeffe J, Zhadanov A, Papkovsky DP, Ayllon V, and O’Connor R. HRG-1 enhances cancer cell invasive potential and couples glucose metabolism to cytosolic/extracellular pH gradient regulation by the Vacuolar H+ ATPase. Oncogene. (2013) Advance online publication October 21st.

Dwane S, Durack E, O’Connor R, Kiely PA. RACK1 promotes neurite outgrowth by scaffolding AGAP2 to FAK. Cell Signal. (2013) 29, 9-18 (online Sept 19).

Fig. 2 from Dwane, Durack, O’Connor and Kiely paper. RACK1 and FAK colocalise in differentiated PC12 cells. PC12 cells were seeded on laminin coated coverslips and differentiated for 4 days with 100 nM NGF. The cells were fixed with 4% PFA, permeabilised with PHEM/0.1% Triton X, blocked with PHEM/5% goat serum and co-stained with RACK1 (red) and FAK (green). All images were acquired sequentially and images merged using ImageJ. Growth cones in differentiated cells had high level of RACK1/FAK colocalisation (arrowheads). Level of colocalisation measured using Pearson’s coefficient: undifferentiated = 0.455 ± 0.05, differentiated = 0.897 ± 0.06. Change in level of colocalisation is statistically significant, p < 0.001.

Ron D, Adams DR, Baillie GS, Long A, O’Connor R, Kiel PA. RACK1 to the future-a historical perspective. Cell Commun. Signal. (2013) (online 13th August)

Vanoirbeek E, Eelen G, Verlinden L, Carneliet G, Mathieu C, Roger G, O’Connor R, Xiao G, Verstuyf A. PDLIM2 expression is driven by vitamin D and is involved in the pro-adhesion and anti-migration and -invasion activity of vitamin D. Oncogene (2013) 1-8.

Abreu CM, Kumar R, Hamilton D, Dawdy AW, Creavin K, et al.) Site-specific phosphorylation of the DNA damage response mediator Rad9 by cyclin-dependent kinases regulates activation of checkpoint kinase 1. PLoS One Genet (2013) 9, 1003310.

Papkovsky DB, Dmitriev RI, Biological detection by optical oxygen sensing (Invited Review), Chem Soc Rev (2013) DOI:10.1039/C3CS60131E.

Dmitriev RI, Zhdanov AV, Nolan YM, Papkovsky DB, Imaging of neurosphere oxygenation with phosphorescent probes, Biomaterials (2013) 34, 9307-9317.

Zhdanov AV, Dmitriev RI, Golubeva AV, Gavrilova SA, Papkovsky DB, Chronic hypoxia leads to a glycolytic phenotype and suppressed HIF-2a signalling in PC12 cells, Biochim Biophys Acta - General Subjects (2013) 1830, 3553-69.

Zhdanov AV, Waters A, Golubeva AV, Dmitriev RI, Papkovsky DB, Availability of the key metabolic substrates dictates the respiratory response of cancer cells to the mitochondrial uncoupling in cancer cells, BBA – Bioenergetics (2013) 1837, 51–62.

Kondrashina A, Papkovsky DB, Dmitriev RI, Measurement of cell oxygenation and OCR in commercial microchamber biochips by means of phosphorescent probes, Analyst (2013) 138, 4915-21.

Troppens DM, Dmitriev RI, Papkovsky DB, O’Gara F, Morrissey JP: Genome-wide investigation of cellular targets and mode of action of the antifungal bacterial metabolite 2,4-diacetylphloroglucinol in Saccharomyces cerevisiae. FEMS Yeast Research (2013) 13, 322-334.

HOT OFF THE PRESS! RECENT PUBLICATIONS NEWSLETTERSCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY

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