Newsletter 007 June 2014 - University College Cork
Transcription
Newsletter 007 June 2014 - University College Cork
VOLUME 1 ISSUE 7 JUNE 2014 SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY NEWSLETTER Message from Head of School You are very welcome to the June edition of our School e-Newsletter, the final issue for academic year 2013 2014. to the first issue of academic year 2014-15 which will be available in September. In this issue Student wins best poster award UCC enters iGEM Competition Professor David Sheehan Class of BSc in Biochemistry 2014 PhD Conferrings SCHOOL This has been a very busy period as we finalised examining this year’s BSc (Biochemistry) graduating class and also graduated one of the largest cohorts of PhDs when 12 students graduated recently in the Summer conferrings. The latter was the occasion for the first “selfie” by an Irish University president which has attracted in excess of 23,000 views on twitter last week. You can find out more about these happy events elsewhere in this issue. The continuing excellence of our researchers is emphasised by a best-poster award to Caroline Vaughan (Dr Justin McCarthy’s lab) and travel awards to Dr Ruslan Dmitriev, Alicia Waters and Alina Kondrashina (Professor Dmitri Papkovsky’s lab). I hope that you enjoy this newsletter and I look forward A Modelling invitation for you! People in the News People on the Move Upcoming Events Research Highlights Hot Off the Press! Recent Publications Summer 2014 Barbeque PEOPLE IN THE NEWS School of Biochemistry and Cell Biology Student Wins Best Poster Award at Biomedica 2014 On the 29th -30th April, the Academy of Medical Laboratory Science (A.M.LS) in the year of its 40th anniversary hosted Biomedica 2014. This is a unique, biennial forum where Medical Scientists, Clinicians, academic researchers and diagnostic partners from industry are invited to come together, exchange and share research ideas and to explore the latest technological and scientific solutions on offer. The event was held in Dublin’s RDS exhibition hall. Caroline Vaughan, School of Biochemistry and Cell Biology This year’s exhibition attracted in excess of 800 delegates and a scientific poster competition formed part of the programme. From the poster entries four finalists were selected and each invited NEWSLETTER PAGE 2 to give a 5-minute talk to the judges about their research. The School of Biochemistry and Cell Biology was represented by 2nd year PhD student Caroline Vaughan (pictured here with the president of the A.M.L.S., Mr Patrick Mullane) who claimed 1st prize for the presentation of her work on a role for Presenilin 2 in the human innate immune response. This forms part of her PhD work under the supervision of Dr Justin McCarthy. Second year PhD student, Caroline Vaughan, claimed 1st prize for the poster and presentation of her work on a role for Presenilin 2 in the human innate immune response. People in the news STUDENT WINS BEST POSTER AWARD SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY PEOPLE IN THE NEWS that exhibit some exciting properties: the fibres are 10 times stronger than nylon, but are 100 times thinner than a human hair; they are antimicrobial and can form a hydrogel. Potential novel applications include the use of the biopolymer as a suture in delicate surgeries, fabric for the textile industry, or an antimicrobial aerosol for surgical instruments and implants, to name but a few. Benthic Labs are hoping to commercialise some of these products. ACADEMIC MENTORS AND STUDENT MEMBERS OF THE UCC IGEM 2014 TEAM Back: Professor Tommie McCarthy, Leanne O’Sullivan, Gavin King, Cian Scannell, Russell Banta, Selma Bouanane, Shama Chilakwad, Patrick Xie and Dr Paul Young. Front: Cian O’ Donnell, Timothy O’Flynn, Daniel Collins, Ian Valentine McDermott, Carolina Cordero. UCC Leads the Way in Synthetic Biology Students awarded venture capital to form SynBio start-up, compete in international competition This month, a group of UCC students will begin a research project that they will enter in the International Genetically Engineered Machine (iGEM) competition. They will be the first Irish team to compete in this prestigious event. In addition to participating in the iGEM competition, they have set up a company, Benthic Labs, which has successfully secured a place on the SynBio axlr8r programme. SynBio axlr8r offers start-ups expert mentoring, lab space, access to state-of-the-art facilities and 30,000 USD in funding. This funding will support the team’s bid at the iGEM competition in Boston, Massachusetts, this November. The iGEM competition sees student teams given a kit of biological parts at the beginning of the summer. Working at their own universities, the teams use these biological parts, and new parts of their own design, to build biological systems and operate them in living cells. The UCC team aims to run two innovative synthetic biology projects over the summer, the results of which will form the basis of their iGEM entry. The first project aims to synthesise a novel biopolymer. By engineering hagfish genes into bacterial cells, the team hopes to produce and purify the proteins that constitute hagfish slime (a gooey substance used by the hagfish for self-defence). These hagfish slime proteins form fibres The second project will involve engineering bacteria to detect specific DNA sequences. In this way, it is hoped that the bacteria could be used to detect pathogenic viruses, for example. This would have applications as an ultra-low cost diagnostic technology. The interdisciplinary group is made up of students from UCC’s College of Science, Engineering NEWSLETTER and was initiated by Dr Paul Young and Professor Tommie McCarthy from the School of Biochemistry and Cell Biology, who will act as the main academic mentors. The iGEM summer competition, which began with five teams in 2004, has grown enormously over the past ten years. This year, 245 teams from the world’s leading universities will take part. The competition is run by the iGEM Foundation, an independent, non-profit organisation dedicated to inspiring education and competition, advancing synthetic biology, and developing an open community with collaboration among students. SynBio axlr8r is backed by venture capital firm SOSventures and focuses on entrepreneurs building technologies relating to the field of synthetic biology. The programme is sponsoring six start-ups through a three-month period in UCC. The UCC team aims to run two innovative synthetic biology projects over the summer, the results of which will form the basis of their iGEM entry. and Food Science (SEFS), each with a different focus – Genetics, Chemistry, Biochemistry, Biomedical Science, Mathematics, Physics and Engineering. The team’s entry in iGEM is supported by UCC’s College of SEFS PAGE 3 For more information, please contact Dr Paul Young ([email protected]; 087-7408586) or Shama Chilakwad ([email protected]; 0894946998). igem competition UCC ENTERS IGEM COMPETITION SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY BSC IN BIOCHEMISTRY 2014 SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY NEWSLETTER PAGE 4 UPCOMING Congratulations to the fourth year Biochemistry students who completed their final exams in May and received their examination results in June. These students will graduate in October 2014, of which nine students will graduate with a first class honours Biochemistry degree, twenty one students will graduate with a second class honours grade 1 degree and seven students will graduate with a second class honours grade 2 degree. BSc in Biochemistry 2014 BSc in Biochemistry: Class of 2013-2014 EVENTS The staff in the School of Biochemistry and Cell Biology would like to wish them all well in their future careers and thank them for their interest in the programme and diligence over the past four years. The staff in the School of Biochemistry and Cell Biology would also like to thank the Biochemistry external examiner, Professor Adrian Harwood for his feedback and support regarding the curriculum and teaching of the BSc Biochemistry degree programme and for the positive manner in which he engaged with the students. Professor Adrian Harwood is a professor in the School of Biosciences at Cardiff University and was appointed as external examiner of the Biochemistry programme in 2012, and will remain as external examiner of this programme until 2015. PEOPLE IN THE NEWS NEWSLETTER PHD CONFERRINGS IN THE SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY Back: Dr Jyoti Chibber, Dr Maura Hannon, Dr Janina Berghoff, Dr Will Landry, Dr Abrar Ahmed, Dr Zhenfei Ning, Dr Ronan O’Riordan, Dr Kathy Barriscale, Dr Finola Fogarty and Dr Meghan Coakley. Front: Dr Ken Nally, Dr Cora O’Neill, Professor Tommie McCarthy, Professor Rosemary O’Connor, Dr Michael Murphy, Professor David Sheehan, Dr Justin McCarthy, Dr Kellie Dean and Dr Tom Moore. PhD Conferrings in June On 12 June 2014, five students in the PhD Scholars Programme in Cancer Biology were conferred with a PhD in Cancer Biology from UCC. The conferring marks the completion of the first two cohorts of PhD students in the PhD Scholars Programme in Cancer Biology with nine students earning PhD in Cancer Biology from UCC. Eight more students are due to complete in 2016. This Programme was established in 2008 with a €4.3 million award from Dr Finola Fogarty and Professor Rosemary O’Connor the Health Research Board to develop PhD training with an underlying focus on cell signalling systems and gene regulation. The Scholars Programme is directed by Professor Rosemary O’Connor, with additional leadership and management provided by a Steering Committee comprising: Professor John Atkins, Professor Tom Cotter, and Professor Tommie McCarthy, School of Biochemistry and Cell Biology; Professor Noel Caplice, Department of Medicine; and Professor Paul Redmond, Department of Surgery. The Programme has also benefitted from input and advice from an External Advisory Board consisting of Professor Gerard Evan, University of Cambridge; Dr Helke Hillebrand, EMBL; and Professor Donald McDonnell, Duke University. Dr Kellie Dean, Training Coordinator for the PhD Scholars Programme, has facilitated and monitored the progress of the students through the programme and provided ongoing support and mentorship to the PhD Scholars. story continues on next page... PAGE 5 phd Conferrings PHD CONFERRINGS SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY PEOPLE IN THE NEWS Dr Justin McCarthy and Dr Jyoti Chibber Dr Maura Hannon and Professor Tommie McCarthy story continued from previous page This was one of the first, 4-year structured PhD programmes in UCC. The programme follows a “1+3” model that included one year of laboratory rotation projects, taught elements and general scientific training, with a focus on the biological and clinical aspects of cancer. In year 2 of the programme, the students selected a project and supervisor for their PhD research. Throughout the programme, they had research seminars with national and international speakers and It’s a lovely day! On 12 June 2014, five students in the PhD Scholars Programme in Cancer Biology were conferred with a PhD in Cancer Biology from UCC. advanced training workshops. With support from the Programme and Eli Lilly, some PhD Scholars have presented their work at international conferences including Gordon Research Conferences, the American Association for Cancer Research annual meetings, Cold Spring Harbor Laboratory meetings, and EMBO/EMBL Symposia. To date, students in the PhD Scholars Programme in Cancer Biology have authored 14 publications in various journals including Oncogene, Blood, Cancer Research, PLoS One, PNAS, Biochemistry Journal, Analytical NEWSLETTER Dr Will Landry Biochemistry, FEBS Journal, and RNA Biology. Students conferred on 12 June with PhD in Cancer Biology include: • Abrar Ahmed, supervised by Dr Ruaidhri Carmody • Kathy Barriscale, supervised by Professor Tommie McCarthy • Janina Berghoff, supervised by Dr Justin McCarthy • Fionola Fogarty, supervised by Professor Rosemary O’Connor • Ronan O’Riordan, supervised by Dr Tom Moore. Dr Kathy Barriscale-Walsh and Professor Tommie McCarthy PAGE 6 Phd Conferrings PHD CONFERRINGS SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY A MODELLING INVITATION FOR YOU! PEOPLE IN THE NEWS It has been an exciting time for Dr Meghan Coakley, recent PhD graduate (Dr Cora O’ Neill’s lab). The week after her PhD graduation ceremony at UCC, Meghan was a featured exhibitor at the White House Maker Faire in Washington DC as part of the official launch of the NIH 3D Print Exchange. Press Release at http://www.nih.gov/news/health/ jun2014/niaid-18.htm Meghan is a Scientific Program Analyst in the Bioinformatics and Computation Biosciences Branch at the National Institute of Allergy and infectious Diseases (NIAID), US National Institutes of Health (NIH). She began working there while completing her PhD thesis at home in the US, after enjoyable years as a PhD and MSc (Applied Biotechnology) graduate student in the School of Biochemistry and Cell Biology, where she worked on projects in Alzheimer’s Disease and Neurodegeneration. In her new role, Meghan and her Dr Meghan Coakley shows off a 3D-printed model of the hemagglutinin receptor on the influenza virus. colleagues developed the NIH 3D Print Exchange, where she is a colead on the project. This is a public website that enables users to share and download 3D print files related to health and science. The files can be used, for example, to print models of cells, bacteria, human anatomy and customised laboratory equipment. NIH Director Francis Collins, M.D., NEWSLETTER planning interactions with her former supervisor, Dr Cora O’ Neill, using this platform. Meghan would especially love to interact with the School of Biochemistry and Cell Biology in the future, to see models and hear feedback from former colleagues and current staff and students at UCC. For more information, contact Meghan. For researchers, the most exciting part is the collection of free tools built into the site, which eliminate the need for any 3D modeling design experience: For example, a registered user can upload a CT scan, molecular structure file, or volumetric data, such as a microscopy image stack, and in minutes the site generates files that are ready to download and compatible with 3D printers. To help new users, the site also features video tutorials on 3D modeling software, and a discussion forum to promote collaboration. Meghan and her colleagues are eager to grow the community of users on the Exchange and she is Using a 3D-printed model of the hemagglutinin receptor on the influenza virus, researchers at NIAID were able to identify a previously-unseen binding groove in the trimer structure, and that discovery was a breakthrough into research on a universal flu vaccine. PAGE 7 Dr Meghan Coakley (left) and Dr Darrell Hurt (right) of the NIH 3D Print Exchange, with NIH Director Dr Francis Collins (centre), at the White House Maker Faire on 18 June 2014. 3d-Modelling Ph.D., says: “3D printing is a potential game changer for medical research”. The mission of the NIH 3D Print Exchange site is to provide users – scientists, educators, students, DIYbio and 3D print enthusiasts – with high-quality, scientifically accurate models of molecules, bacteria, cells, and anatomy, and more which can be utilized for scientific visualization and discovery. Dr Meghan Coakley, a recent PhD graduate from this School invites you to use the NIH 3D Print Exchange! SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY PEOPLE IN THE NEWS Laying down markers for future cancer treatments Professor Rosemary O’Connor was interviewed for a story on the BioMARKERIGF project to mark February 4th, World Cancer Day. The interview has been published on the Horizon 2020 website, in the “Projects Stories” section at https:// ec.europa.eu/programmes/horizon2020/en/news/ laying-down-markers-future-cancer-treatments Professor Rosemary O’Connor, School of Biochemistry and Cell Biology NEWSLETTER SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY Professor Rosemary O’Connor interviewed to mark World Cancer Day, February 4th. NEWSLETTER PAGE 8 PLoS Publication from Professor David Sheehan’s lab Ms Sidra Ilyas, a PhD Scholar at the University of the Punjab, Lahore, Pakistan was funded by the Pakistani Government to spend eightmonths in the lab of Professor David Sheehan during 2012- 2013. She is investigating the biochemical basis of an unusual metal-resistance in a fungus isolated from industrial effluent in Lahore, Pakistan. This turned out to be Trichosporon asahii, an emerging pathogen increasingly implicated in nosocomial infections, fatal opportunistic infections and in a condition called summertype hypersensitivity pneumonitis. Sidra discovered that this fungus could be successfully cultured in very high levels of heavy metals such as arsenic and cadmium. People in the news PEOPLE IN THE NEWS SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY She came to UCC to compare proteome profiles between metal-exposed and control fungi. Taking advantage of the availability of two recently-sequenced T. asahii genomes and using redox proteomics approaches, she was able to show that Arsenic had specific oxidative effects on key enzymes involved in amino acid metabolism. Her study has just been accepted for publication in PLoS One (Ilyas et al., 2014). PEOPLE ON THE MOVE People on the Move Professor Dmitri Papkovsky welcomes the following new lab members: • Dr Irina Okkelman - Research Assistant, from March 2014 • Dr Swagata Banjeree, PhD – Postdoctoral Researcher, from May 1, 2014 • as well as visiting PhD students from the University of Tartu, Estonia - Mrs Kadri Ligi, MSc and Mrs Marie Kriisa, MSc - who will be here in UCC for the period June-July 2014. Dr Dmitry Andreev from Moscow State University is visiting Dr Pasha Baranov’s lab at the end of July. Emily Power and Shauna O’Donnovan joined his lab for the Summer to work on their MSc research projects Dr Swagata Banjeree Dr Kathy Barriscale Walsh is joining Dr Tom Moore’s lab on an SFI TIDA award in collaboration with Dr Jim Clover, recently-appointed plastic surgeon. The project aims to develop a novel wound healing therapy. Departures We say farewell with best wishes to Dr Claudio Toncelli who left in February 2014 to work at the University of Heraklion (Greece). NEWSLETTER SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY Dr Kathy Barriscale Walsh Professor David Sheehan has been elected by SEFS academics to represent the College on the University’s Academic Board. NEWSLETTER PAGE 9 Professor David Sheehan to represent SEFS on Academic Board Professor David Sheehan Professor David Sheehan has been elected by SEFS academics to represent the College on the University’s Academic Board. People on the Move PEOPLE ON THE MOVE SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY This is the senior Academic Council standing committee and makes many of the key decisions later ratified by AC or Governing Body. SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY UPCOMING EVENTS NEWSLETTER PAGE 10 UPCOMING British Biophysical Society Biennial Conference The British Biophysical Society biennial conference is taking place July 9th-11th in Warwick, UK. Bursaries are available for early-stage researchers to attend. • Professor Sir John Walker FRS (MRC Mitochondrial Biology Unit) • Professor Gabriel Waksman FRS (University College London) • Professor Ernst Bamberg (Max Planck Institute of Biophysics, Hamburg) • Professor Wolfgang Baumeister (Max-Planck-Institute of Biochemistry, Martinsried) Further details on the conference can be found at http://www2.warwick.ac.uk/fac/sci/wcas/events/bbs2014 EBSA Biophysics Course The European Biophysical Society Association is continuing its very successful Advanced Courses on Biophysics with a workshop on Membranes and Lipid-protein Interactions in September 2014 to be held at Le Grande Motte, near Montpelier, France. nced a v d A : e ours C s c i s pidy i L h p d o n i a B s EBSA rane b m e M n course o Interactions protein Upcoming Events EVENTS The conference features keynotes from: PEOPLE IN THE NEWS Grant awards and Research presentations Dr Dmitriev, Alicia Waters and Alina Kondrashina – all received travel awards to facilitate their attending the forthcoming Experimental Biology conference, San Diego, April 21-26, 2014. They will be making the following poster presentations: 1. Ruslan Dmitriev, Sergey Borisov, Alina Kondrashina, Janelle Pakan, Dmitri Papkovsky, Real-time monitoring of oxygenation in cultured organotypic brain slices, FASEB J, 2014, 28:1180.20. 2. Alicia Waters, Alexander Zhdanov, Dmitri Papkovsky, Regulation of pyruvate dehydrogenase phosphorylation by hypoxia, FASEB J, 2014, 28:572.4. Dr Ruslan Dmitriev (Professor Dmitri Papkovsky’s lab) has been awarded a Science Foundation Ireland Starting Investigator research grant. Dr Ruslan Dmitriev, School of Biochemistry and Cell Biology Dr Ruslan Dmitriev (Professor Dmitri Papkovsky’s lab) has been awarded a Science Foundation Ireland Starting Investigator research grant for a project: Development of bionic sensor materials for metabolic imaging in regenerative medicine - Sep 2014 –Aug 2018, Total: €517k. NEWSLETTER SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY NEWSLETTER PAGE 11 Talk given at workshop on Advanced Multiphoton and Fluorescence Lifetime Imaging Techniques People in the news RESEARCH HIGHLIGHTS IN APRIL-MAY SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY Professor Dmitri Papkovsky recently gave the following invited talk: Imaging of tissue oxygen Professor Dmitri Papkovsky by means of cell-penetrating phosphorescent probes and TCSPCFLIM, 9th Workshop on Advanced Multiphoton and Fluorescence Lifetime Imaging Techniques, Saarbrucken, Germany, May 27-28, 2014. HOT OFF THE PRESS! RECENT PUBLICATIONS SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY NEWSLETTER PAGE 12 Dmitriev RI, Kondrashina AV, Koren K, Klimant I, Pakan J, McDermott K, Zhdanov AV, Papkovsky DB (2014) Small molecule phosphorescent probes for O2 imaging in 3D tissue models, Biomater. Sci., 2, 853-866. Deevi RK, Cox, OT, O’Connor R (2014) Essential function for PDLIM2 in cell polarization in three-dimensional cultures by feedback regulation of the β1-integrin-RhoA signaling axis. Neoplasia pii: S14765586(14)00045-1. doi: 10.1016/j.neo.2014.04.006. [Epub ahead of print] RECENT Publications HOT OFF THE Recent Research Publications from this School Toncelli C, Arzhakova O, Dolgova A, Kerry JP, Papkovsky DB (2014) Oxygen-sensitive phosphorescent nanomaterials produced from high density polyethylene films by local solvent-crazing, Anal Chem 86, 1917-23. PRESS Zhdanov AV, Dmitriev RI, Hynes J, Papkovsky DB (2014) Kinetic analysis of local oxygenation and respiratory responses of mammalian cells using intracellular oxygen-sensitive probes and time-resolved fluorescence plate reader, In: Conceptual Background and Bioenergetic/Mitochondrial Aspects of Oncometabolism, Eds.L. Galluzzi, G. Kroemer, Methods in Enzymology vol. 542, p. 183-207. (book chapter). Kondrashina A, Dmitriev R, Papkovsky D (2014) Comparison of different techniques for monitoring of mammalian cell respiration FASEB J 28, 960.4. Dmitriev R, Kondrashina A, Foley T, Papkovsky D (2014), Imaging of molecular oxygen at subcellular resolution in mammalian cell culture: from 2D to 3D models FASEB J 228, 764.1. Jenkins J, Dmitriev RI, Papkovsky DB (2014) TCSPC-PLIM imaging of cell oxygenation in 3D porous scaffold, 9th Workshop on Advanced Multiphoton and Fluorescence Lifetime Imaging Techniques, Saarbruecken, Germany, May 27-28,. (poster) Papkovsky DB (2014) Imaging of tissue oxygenation with phosphorescent oxygen (nano)sensors, European Conference on Optical Chemical Sensors and Biosensors, April 12-16, , Athens, Greece (poster). Kelly C, Toncelli C, Kerry JP, Papkovsky DB (2014) Phosphorescent O2 sensors based on the non-woven polyolefine fabric materials, J. Mater. Chem. C, 2, 2169-2174. Sharma V, Prere MF, Canal I, Firth AE, Atkins JF, Baranov PV, Favet O (2014) Nucleic Acids Research 42, 7210-7225. Ilyas S., Rehman A., Coelho Varela A., Sheehan D. (2014) 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. PLoS One IN PRESS. n o i s u l c n i r o f l a i r r e e t t t a e l m s Any e next new o the editor, in th d be sent t heehan. shoulssor David S ucc.ie Profe osbcandcb@ h : L I A M E SUMMER 2014 BARBEQUE – THE ANGLER’S REST SCHOOL OF BIOCHEMISTRY AND CELL BIOLOGY NEWSLETTER PAGE 13 people in the news UPCOMING EVENTS Some 35 staff attended the 2014 Summer barbeque at the Angler’s Rest in Carrigrohane. A great night was had by all!
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