newsletter department of biochemistry and molecular biology · professor robert medcalf and dr...

Newsletter Department of Biochemistry and Molecular Biology

www.med.monash.edu.au/biochem

NEWS AND EVENTS

Prof Steve Bottomley: Research Published in Cell Reports

Issue 29: October 2012

Necrosis occurs when cells in living tissue die prematurely due to external stress or injury. The body’s system for removing waste associated with necrotic cell removal was not, until now, well understood.

Professor Robert Medcalf and Dr Andre Samson, of the University’s Australian Centre for Blood Diseases (ACBD), led the research with Professor Stephen Bottomley of the Monash Department of Biochemisty and Molecular Biology. http://www.med.monash.edu.au/biochem/staff/bottomley.html

Extract and microscopic image from: www.monash.edu.au/news/show/clot-busting-enzymes-are-working-two-jobs

The Department of Biochemistry Postgraduate Research Conference will be held on the Thursday 22nd November and Friday 23rd November 2012.The conference will provide an opportunity for 3rd year PhD students to present a talk and all students to present a poster to the department – with opportunities for great prizes!

Staff and fellow students are encouraged to support the participants, so please put the dates in your diary.

2012 Postgraduate Research Conference

A fluorescence microscope image of neurons. In this experiment, Tubulin - an abundant protein that rapidly undergoes NCC - has been tagged with a blue-coloured fluorescent dye. NCC is the formation of clot-like aggregates within dead cells.

5 October 2012

The body’s blood clot-busting enzymes are much busier than previously imagined, with new research showing that they also dispose of every cell that dies prematurely from disease or trauma.

In research published today in Cell Reports, scientists from Monash University have demonstrated for the first time the enzyme t-PA, which plays a vital role in the removal of blood clots, is also a major player in the removal of necrotic, or dead, cells.

Congratulations are extended to those members of the Department who were successful in attaining NHMRC grants and fellowships.

The Department achieved a NHMRC project grant success rate of 36% (18 CIA NHMRC project grants awarded from 50 applications), which was significantly better than the national (20.5%) and Monash University (27.8%) success rates.

The Department secured almost half of all project grants awarded to the School of Biomedical Sciences (a total 41 awarded to SOBS) and $10.8mil in funding commencing in 2013.

NHMRC Grants Success

Department of Biochemistry and Molecular BiologyNewsletter: October 2012, Issue 29

Bio-Plex® MAGPIX™ Multiplex ReaderMAGPIX Multiplex plate reader is now installed and fully functional and is located in the Biochem Imaging Facility in Bld76/G58. This instrument allows you to label and read up to 50 analytes per well per 96 well plate.

All queries relating to this instrument, please contact: Irene Hatzinisiriou

How the body uses vitamin B to recognise bacterial infection - Prof Jamie RossjohnExcerpt from Press Release October 2012

An Australian research team has discovered how specialised immune cells recognise products of vitamin B synthesis that are unique to bacteria and yeast, triggering the body to fight infection.

The finding opens up potential targets to improve treatments or to develop a vaccine for tuberculosis.

The study, jointly led by the University of Melbourne and Monash University and published today in the journal Nature, has revealed for the first time that the highly abundant mucosal associated invariant T cells (MAIT cells), recognise products of vitamin B synthesis from bacteria and yeast in an early step to activating the immune system.

The research revealed how by-products of bacterial vitamin synthesis, including some derived from Folic acid or vitamin B9 and Riboflavin or vitamin B2, could be captured by the immune receptor MR1 thus fine-tuning the activity of MAIT cells.

Visit Biochem website for further details: http://www.med.monash.edu.au/biochem/

New insight into coeliac disease - Prof Jamie RossjohnExcerpt from Press Release October 2012

For the first time, scientists have visualised an interaction between gluten and T-cells of the immune system, providing insight into how coeliac disease, which affects approximately one in 133 people, is triggered.

Published in Immunity, the discovery was led by Dr Hugh Reid and Professor Jamie Rossjohn of Monash University, Professor Frits Koning of the University of Leiden and Dr Bob Anderson of biotechnology company ImmusanT Inc, based in the US.

An increasingly-diagnosed chronic inflammatory disorder, coeliac disease affects the digestive process of the small intestine. When a person with coeliac disease consumes gluten, their immune system triggers T-cells to fight the offending proteins, damaging the small intestine and inhibiting the absorption of important nutrients into the body. There are currently no treatments available apart from a diet completely free of gluten.

The researchers used the Australian Synchrotron to visually determine how T-cells of the immune system interact with gluten, a protein found in wheat, rye and barley, which causes coeliac disease, The discovery will boost attempts to produce a treatment allowing sufferers to resume a normal diet.

Visit Biochem website for further details: http://www.med.monash.edu.au/biochem/

LATEST MEMBERS OF STAFF

Lab Head New Staff Member Position

Prof Jamie Rossjohn Peter Vella RF

Prof Jamie Rossjohn Preethi Sukumar RF

Dr Ana Traven Jiyota Verma Gaur RF

Prof Tony Tiganis Vanni Caruso RF

Please visit our Departmental website www.med.monash.edu.au/biochem

Department of Biochemistry and Molecular Biology

Lab Head: Prof Kate LovelandI have a joint appointment with the Department of Anatomy and Developmental Biology and the Department of Biochemistry and Molecular Biology.

My laboratory projects are investigating the mechanisms that underpin mammalian testis development and are required for spermatogenesis. Our objective is to identify and characterise the molecular switches that regulate cell fate decisions in somatic and germline cells. To achieve this we use animal models, a wide variety of cell and organ culture approaches and human clinical specimens. Specific research areas of focus are in activin/ TGFβ superfamily, Wnts and Hedgehog signalling pathways, growth factor/hormone signalling cross-talk, and the contribution of regulated nuclear transport molecules to cellular development and stress responses.

I have active collaborations with research groups around Australia, in Denmark, the US and Japan which underpin the work of my students and postdoctoral fellows. I currently hold an NHMRC Senior Research Fellowship and was recognised by the American Society for Andrology as the 2004 Young Andrologist, their highest distinction for a developing

Setting a Fine ExamplePhillip Nagley and Gavin Higgins spent a lot of time during October cleaning out Nagley Lab material from the cold rooms on the second floor of Building 13D. Some of the stuff dated back to 1987 (long-forgotten hand-me-downs from another lab!). The bewildering array of chemicals and samples were mostly those left behind by a succession of post-docs and PhD students over the past decade. The clean-out was inspired not only by the upcoming OSHE inspection but also by Phillip’s decision to close his lab, as his retirement draws close at the end of 2012. This working bee stimulated others on the second floor of building 13D also to begin clearing disused and out-of-date materials from these cold rooms.

Photo courtesy Phillip Nagley: Phillip Nagley (foreground) after a 3-hour stint clearing his shelves in the cold room, under the watchful eye of Deputy Departmental Safety Officer (and Phillip’s research colleague), Gavin Higgins

researcher. I have been Chief Investigator and Deputy Director of the Australian Research Council Centre of Excellence in Biotechnology and Development (2003-2010). I currently head a research team at Monash University of approximately 12-15 undergraduate and postgraduate students, postdoctoral fellows and research assistants, supported by grants from the National Health and Medical Research Council and the Australian Research Council.

We have published over 115 publications that reflect my keen interest in discovering how cells change from one state of differentiation to the next.

I am currently an editor for several journals (including Biology of Reproduction, Andrology, Spermatogenesis, Reproduction), and I contribute actively to the Society of Reproductive Biology (Australia and New Zealand), the Society for the Study of Reproduction (International Members Liason Subcommittee Chair), the American Society for Andrology (Council member and Chair of ASA Basic Science Workshop) and am involved in planning for the 2014 World Congress in Reproductive Biology.

Prof Loveland’s Lab page: Testis Development and Germ Cell Differentiation Group http://www.med.monash.edu.au/biochem/staff/loveland-lab-page.html


POSTGRADUATE MATTERS

PhD GraduatesMegan Kerr Thesis: “Mechanisms of cellular binding and internalisation of the beta-amyloid protein of Alzheimer’s disease” Supervisors: Alfons Lawen, Mibel Aguilar, David Small

Greg Kowalski Thesis: “The role of inflammation and the haematopoietic system in insulin resistance” Supervisors: Mark Febbraio, Graeme Lancaster

New students:Nusrat Jahan Supervisors: Chris Mitchell and Michelle Davies

Rebecca Davies Supervisors: David Jans and Kylie Wagstaff

Link to MBio e-bulletin: http://www.med.monash.edu.au/mbio-gradschool/e-bulletin.html

All queries on Postgraduate matters: Please contact Prof Mibel Aguilar [email protected]

OHS MATTERSHOW TO TREAT PHENOL BURNS IN THE LAB (DO NOT WASH WITH WATER - ONLY PEG300)

On top of each First Aid kit there is now a Phenol Burns Module.

It contains instruction sheet and a squirt bottle of PEG300 which is to be used to wash any affected skin surface when it has come into contact with any solution containing PHENOL.

Take a few minutes to familiarize yourself in what to do, even if you do not use any phenol in your lab, someone on your floor may need your assistance one day!

2012 Post-Graduate Conference Quiz

November 23rd from 2-3 pm in Central 1

Are you:

1. Excited by trivia?

2. Fond of “amazing” your “friends” with your knowledge of the inane?

3. A repository of useless facts?

4. Keen to demonstrate your general knowledge prowess and win some great prizes?

If you answered YES to any of the above then REGISTER your team of 4-6 people (and your team name) for the 2012 Post-Graduate Conference Quiz!

Question topics range from science-related to sports to general knowledge. The format will be similar to a pub quiz. Everyone welcome to compete/watch.

Quizmaster: James Whisstock

Register with [email protected]

Environmental Sustainability At MonashAnyone concerned with any environmental issues should contact Shani Keleher ([email protected]) or visit The Office of Environmental Sustainability (TOES) http://www.fsd.monash.edu.au/environmental-sustainability.

QUICK OVERVIEW OF WHAT TO DO WHEN AN EMERGENCY ARISES:

1. Remain CALM…

2. Yell out for a First Aider (don’t go looking for one yourself, get someone else to go looking)

3. First Aiders: Read MSDS before treating any chemical injury

4. First Aiders: Call Med Centre if necessary ext. 53175

5. First Aiders: Call the Safety Officer and/or Safety Representative as soon as possible


FIRST AID PROCEDURE PHENOL EXPOSURE TO SKIN

Applies to all phenol containing solutions such as Trizol, QIAzol, Phenol:Chloroform, etc.

Always seek assistance from a First Aider and notify Deptl Safety Officer Irene Hatzinisiriou ext 29255 immediately

Dept. Biochemistry & Molecular Biology Updated on 19th Oct 2012

EYES:

• Flush with copious amounts of water for >15 mins, lifting eyelids occasionally• Remove contact lenses if easily removable• Do not interrupt flushing• Get medical attention IMMEDIATELY

INHALATION:

• Remove to fresh air• Get medical attention immediately

INGESTION:

• Do not induce vomiting• If victim is conscious and able to swallow, give ~200mls of milk or water• Get medical attention immediately• Never give anything by mouth to an unconscious person

SKIN CONTACT:

• Rapid and immediate skin decontamination is critical• First Aiders must wear PPE• Small Exposures - Remove ALL contaminated clothing - Irrigate or wipe exposed areas immediately and repeatedly PEG 300 - Treatment should be continued until there is no detectable odor of phenol - If PEG 300 is not available, use a glycerine solution - If neither available use shower for minimum of 15 mins• Large Exposures - If phenol on the skin is more than can be quickly removed by swabbing or irrigating with PEG 300 - Use Emergency Shower for >15mins - Immediately call Emergency Services 000, then call Security 333 - Keep victim under shower till Emergency arrives


RECENT PUBLICATIONS

1. Battad, J.M., D.A. Traore, E. Byres, J. Rossjohn, R.J. Devenish, S. Olsen, M.C. Wilce, and M. Prescott, A Green Fluorescent Protein Containing a QFG Tri-Peptide Chromophore: Optical Properties and X-Ray Crystal Structure. PLoS One, 2012. 7(10): p. e47331.1-14 Category: Biology Impact Factor: 4.092 Ranking: 12/85 [BCH]

2. Broughton, S.E., J. Petersen, A. Theodossis, S.W. Scally, K.L. Loh, A. Thompson, J. van Bergen, Y. Kooy-Winkelaar, K.N. Henderson, T. Beddoe, J.A. Tye-Din, S.I. Mannering, A.W. Purcell, J. McCluskey, R.P. Anderson, F. Koning, H.H. Reid, and J. Rossjohn, Biased T Cell Receptor Usage Directed against Human Leukocyte Antigen DQ8-Restricted Gliadin Peptides Is Associated with Celiac Disease. Immunity, 2012. 37(4): p. 611-621 Category: Immunology Impact Factor: 21.637 Ranking: 4/139 [BCH]

3. Ellisdon, A.M. and M. Stewart, Structural biology of the PCI-protein fold. Bioarchitecture, 2012. 2(4): p. 1-6 [BCH]

4. Gras, S., S.R. Burrows, S.J. Turner, A.K. Sewell, J. McCluskey, and J. Rossjohn, A structural voyage toward an understanding of the MHC-I-restricted immune response: lessons learned and much to be learned. Immunol Rev, 2012. 250(1): p. 61-81 Category: Immunology Impact Factor: 11.148 Ranking: 6/139 [BCH]

5. Hardy, C.L., H.A. Nguyen, R. Mohamud, J. Yao, D.Y. Oh, M. Plebanski, K.L. Loveland, C.A. Harrison, J.M. Rolland, and R.E. O’Hehir, The activin A antagonist follistatin inhibits asthmatic airway remodelling. Thorax, 2012. E-pub: p. 1-12 Category: Respiratory System Impact Factor: 6.840 Ranking: 2/48 [BCH]

6. Hayashida, M., M. Kamada, J. Song, and T. Akutsu. Predicting Protein-RNA Residue-base Contacts Using Two-dimensional Conditional Random Field. in 2012 IEEE 6th International Conference on Systems Biology (ISB). 2012. P.R.China: Curran Associates Inc [BCH]

7. Kjer-Nielsen, L., O. Patel, A.J. Corbett, J. Le Nours, B. Meehan, L. Liu, M. Bhati, Z. Chen, L. Kostenko, R. Reantragoon, N.A. Williamson, A.W. Purcell, N.L. Dudek, M.J. McConville, R.A. O’Hair, G.N. Khairallah, D.I. Godfrey, D.P. Fairlie, J. Rossjohn, and J. McCluskey, MR1 presents microbial vitamin B metabolites to MAIT cells. Nature, 2012. E-pub: p. 1-9 Category: Multidisciplinary Sciences Impact Factor: 36.280 Ranking: 1/56 [BCH]

8. Lahoud, M.H., F. Ahmet, J.G. Zhang, S. Meuter, A.N. Policheni, S. Kitsoulis, C.N. Lee, M. O’Keeffe, L.C. Sullivan, A.G. Brooks, R. Berry, J. Rossjohn, J.D. Mintern, J. Vega-Ramos, J.A. Villadangos, N.A. Nicola, M.C. Nussenzweig, K.J. Stacey, K. Shortman, W.R. Heath, and I. Caminschi, DEC-205 is a cell surface receptor for CpG oligonucleotides. Proc Natl Acad Sci U S A, 2012. 109(40): p. 16270-16275 Category: Multidisciplinary Sciences Impact Factor: 9.681 Ranking: 3/56 [BCH]

9. Linke, C., N. Siemens, S. Oehmcke, M. Radjainia, R.H. Law, J.C. Whisstock, E.N. Baker, and B. Kreikemeyer, The extracellular protein factor Epf from streptococcus pyogenes is a cell-surface adhesin that binds to cells through an N-terminal domain containing a carbohydrate-binding module. J Biol Chem, 2012. E-pub: p. 1-25 Category: Biochemistry & Molecular Biology Impact Factor: 4.773 Ranking: 66/290 [BCH]

10. Liu, X.H., H.M. Gao, F. Xu, J.P. Lu, R.J. Devenish, and F.C. Lin, REVIEW: Autophagy vitalizes the pathogenicity of pathogenic fungi. Autophagy, 2012. 8(10): p. 1415-1425 Category: Cell Biology Impact Factor: 7.453 Ranking: 30/180 [BCH]

11. Maloveste, S.M., D. Chen, E. Gostick, J.P. Vivian, R.J. Plishka, R. Iyengar, R.L. Kruthers, A. Buckler-White, A.G. Brooks, J. Rossjohn, D.A. Price, and B.A. Lafont, Degenerate Recognition of MHC Class I Molecules with Bw4 and Bw6 Motifs by a Killer Cell Ig-like Receptor 3DL Expressed by Macaque NK Cells. J Immunol, 2012. E-pub: p. 1-12 Category: Immunology Impact Factor: 5.788 Ranking: 20/139 [BCH]

12. Roeszler, K.N., C. Itman, A.H. Sinclair, and C.A. Smith, The long non-coding RNA, MHM, plays a role in chicken embryonic development, including gonadogenesis. Dev Biol, 2012. 366(2): p. 317-26 Category: Developmental Biology Impact Factor: 4.069 Ranking: 7/40 [BCH,ANT]

13. Smith, C., D. Elhassen, S. Gras, K.K. Wynn, V. Dasari, J. Tellam, S.K. Tey, S. Rehan, Y.C. Liu, J. Rossjohn, S.R. Burrows, and R. Khanna, Endogenous antigen presentation impacts on T-box transcription factor expression and functional maturation of CD8+ T cells. Blood, 2012. E-pub: p. 1-36 Category: Hematology Impact Factor: 9.898 Ranking: 2/68 [BCH]

14. Traven, A., A. Janicke, P. Harrison, A. Swaminathan, T. Seemann, and T.H. Beilharz, Transcriptional profiling of a yeast colony provides new insight into the heterogeneity of multicellular fungal communities. PLoS One, 2012. 7(9): p. e46243.1-11 Category: Biology Impact Factor: 4.092 Ranking: 12/85 [BCH]

15. Wang, H., J. Li, L. Liu, X. Li, D. Jia, G. Du, J. Chen, and J. Song, Increased production of alkaline polygalacturonate lyase in the recombinant Pichia pastoris by controlling cell concentration during continuous culture. Bioresour Technol. 124C: p. 338-346 Category: Biotechnology & Applied Microbiology Impact Factor: 4.980 Ranking: 20/158 [BCH]


RECENT PUBLICATIONS

16. Webb, C.T., E. Heinz, and T. Lithgow, REVIEW: Evolution of the beta-barrel assembly machinery. Trends Microbiol, 2012. E-pub: p. 1-9 Category: Biochemistry & Molecular Biology Impact Factor: 7.910 Ranking: 27/290 [BCH]

17. Wun, K.S., F. Ross, O. Patel, G.S. Besra, S.A. Porcelli, S.K. Richardson, S. Keshipeddy, A.R. Howell, D.I. Godfrey, and J. Rossjohn, Human and mouse type I Natural Killer T-cell antigen receptors exhibit different fine specificities for CD1d-antigen. J Biol Chem, 2012. E-pub: p. 1-17 Category: Biochemistry & Molecular Biology Impact Factor: 4.773 Ranking: 66/290 [BCH]

18. Zhu, Y., J. Song, Z. Xu, J. Sun, Y. Zhang, Y. Li, and Y. Ma, Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis. Biotechnol Bioeng, 2012. E-pub: p. 1-10 Category: Biotechnology & Applied Microbiology Impact Factor: 3.946 Ranking: 28/158 [BCH]

CONTACT US: Department of Biochemistry and Molecular Biology Monash University, Ground Floor, Building 77, Wellington Road, Clayton VIC 3800 Australia Website: www.med.monash.edu.au/biochem Tel: +61 3 990 29400 Fax: +61 3 990 29500 Content and Layout: [email protected] Photography: MNHS Multimedia Services

newsletter department of biochemistry and molecular biology · professor robert medcalf and dr...

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