RIKEN and JSPS visits, sharing coral genomes, grants for Europe visits: EMBL Australia in October

EMBL Australia

In this month’s newsletter:

Posted on behalf of Nadia Rosenthal, Scientific Head, EMBL Australia

  • What can we learn from the Japanese science system? Hear from the Executive Director of the JSPS in Melbourne today and Canberra tomorrow
  • Creating research links with RIKEN – next week in Melbourne
  • How can young researchers add European experience to their CV? Grants open
  • Maths – the key to effective healthcare and global sustainability – talks in Sydney and Melbourne

Welcome to my EMBL Australia report for October.

We’re in the middle of our Japan month – bringing leaders from RIKEN, the Japan Society for the Promotion of Science (JSPS), The University of Tokyo, and Sony Computer Science Laboratories to Australia.

This week we’re hosting Dr Makoto Asashima, Executive Director at the JSPS, in Melbourne and Canberra.

He is presenting two public seminars during his visit:

  • In Melbourne this afternoon (2 October) at 3:30pm at Monash University he will talk about “Developmental biology and regenerative medicine in recent years”
  • In Canberra he will give a public lecture on “Research and policy trends in life sciences in Japan” at Questacon tomorrow (3 October) at 4:15pm

Next Tuesday 8 October we host the first ever Nature Café outside Japan at Monash University. It features panellists from RIKEN, Sony Computer Science Laboratories, Nature, the Australian Academy of Science and more. The topic, Internationalising your research, is EMBL Australia’s main raison d’être. The next day we hold an invite-only reception for Australian researchers with strong links to Japan.

And we’re sharing coral genomes in Queensland on 11 October with Guy Cochrane, from EMBL-EBI. He’s also visiting Melbourne.

Later in the month US data visualisation guru Scooter Morris will contribute to a protein sequence analysis workshop in Sydney and a Cytoscope workshop in Melbourne.

All this and more below including a profile on Hiroki Ueda and his ideas on temporal medicine and circadian rhythms.

Finally, my congratulations to Jennifer Zenker, a post-doc in Nicolas Plachta’s group, for receiving the Prix Amicitia for her doctoral thesis and to Nicolas for receiving a Monash Interdisciplinary Grant. It’s great to see EMBL Australia attracting such outstanding young scientists. I look forward to the work of our new research teams in South Australia.

EMBL Australia’s Japan month – delegates coming to Melbourne, Canberra and Sydney

This week we’re hosting Dr Makoto Asashima, Executive Director at the Japan Society for the Promotion of Science (JSPS), in Melbourne and Canberra.

He will be presenting two public seminars during his visit:

  • In Melbourne he will be presenting a seminar this afternoon (2 October) at 3:30pm at Monash University entitled “Developmental Biology and Regenerative Medicine in Recent Years”.
  • In Canberra he will be presenting a public lecture on “Research and policy trends in life sciences in Japan” at Questacon tomorrow (3 October) at 4:15pm.

Next week, the RIKEN delegation arrives in Melbourne to engage in a series of meetings aimed at building stronger Melbourne- Japan partnerships and collaborations in systems biology and other fields including metagenomics (intestinal biology), immuno-cancer therapy, iPS, integrative genomics.

The delegation will also be joined in Melbourne by Professor Hiroaki Kitano, who is visiting Australia in his role as Ambassador for Maths of Planet Earth and is presenting public lectures in Sydney and Melbourne sbiaustralia.org/news/mope

The RIKEN delegation will take part in the first Australian Nature Café, which will be presented in partnership by Monash University and EMBL Australia on Tuesday 8 October. It’s an informal forum for invited research leaders and in this first session we’ll discuss the challenge of internationalising Australian science – learning from the achievements of our guests.

You can find more information about the delegation and other visitors on the EMBL Australia website:www.emblaustralia.org/About_us/Events.aspx

Sharing Great Barrier Reef coral genomes with the world

The Australian Bioinformatics Resource building links with our partners in Europe

BRAEMBL is working to build systems to manage and share coral reef genome data generated by the Sea-quence project, as part of a wider effort to introduce this iconic Australian data into global public databases.

“The goal is, in collaboration with the EBI, to polish data of key interest to Australia to a high shine using our own efforts, as often these data would not float up the priority stack of the global databases,” says BRAEMBL director Graham Cameron. “By doing this we will make those data optimally useful and ensure that they are a credit to Australian science.”

To develop this partnership, Guy Cochrane from EMBL EBI will be visiting Australia to meet with participants in the Sea-quence project – a collaboration between Bioplatforms Australia, Rio Tinto and the ReFuGe 2020 consortium, to sequence and compare ten coral species from the Great Barrier Reef and the Red Sea, in order to better understand coral reef genetics, coral resilience, and how these unique marine ecosystems respond to climate change.

Whilst he’s in Australia, Guy will also be presenting seminars at:

  • University of Queensland on Friday 11 October at 10 am
  • VLSCI in Melbourne on Monday 14 October (TBC)

For more details on these events go to: www.emblaustralia.org/About_us/Events/Guy_Cochrane_visit.aspx

You can find more information about Guy’s work at www.ebi.ac.uk/about/people/guy-cochrane and about the tools available European Nucleotide Archive (ENA) herewww.ebi.ac.uk/ena/about/cram_toolkit

How do neurones make decisions?

An international prize and an interdisciplinary grant for the Victorian node

Dr Jennifer Zenker, a post-doc in the Plachta Group, has been awarded the Prix Amicitia Excellence Prize in recognition of outstanding scientific research in neuroscience. The prize, worth CHF7500, was awarded for her PhD thesis at the University of Lausanne in collaboration with the Lemanic Neuroscience Doctoral School. The aim of the prize, which is awarded once a year at the Lemanic Neuroscience Annual Meeting, is to support graduates who are continuing their scientific career at an international academic institution.

Jennifer is currently establishing imaging technologies to understand how neuronal cells make decisions at the single-cell level. In collaboration with computational modelling experts, she hopes to reveal how dynamic molecular processes control the ability of neurons to communicate and extend long axons to connect with each other in the mammalian body.

Nicolas Plachta has also been awarded a Monash Interdisciplinary Grant to investigate how cells choose their positions in living mouse embryos. The grant, worth $35,000, provides seed funding for a collaboration between the Plachta group and Monash University’s Laboratory of Dynamic Imaging, headed by Associate Professor Andreas Fouras.

Using image analysis tools developed by the Fouras Lab, Nico and his team will quantitatively study how cells change their shape and position as they form the first tissue structures, using non-invasive imaging to visualize the cells moving and interacting with each other in intact embryos.

“We have developed new genetic tools to fluorescently label the membrane of the cells in the embryos to better understand how cell morphology changes as the embryos develop,” says Nico. “We also plan to develop label-free methods to monitor cell shape in real time to predict normal embryogenesis.”

Applications open for PhD travel grants to EMBL in 2014

Do you or one of your students need support to set up collaboration in Europe?

Our program of student grants for 2014 have been announced. Applications for the first round of European travel grants are now open and close Friday 8 November 2013. You can find out more and submit your application now at www.emblaustralia.org/students/grants/travelgrants1

With an EMBL Australia PhD travel grant you could take a short course, attend a conference or work alongside some of the young researchers at EMBL’s five facilities: Heidelberg and Hamburg in Germany; Grenoble in France; Hinxton in England; or Monterotondo in Italy.

Up to $3,500 is available for short trips, less than six weeks. Or you can apply for up to $7,500 for a longer visit, up to 6 months.

For more information on all our student grant programs visit www.emblaustralia.org/students.aspx  or like us on Facebook www.facebook.com/EMBLaustralia

Hiro Ueda – Using synthetic biology to understand life

Talks in Melbourne and Adelaide by EMBL Australia’s first “Japan month” visitor

Dr Hiroki (Hiro) Ueda is interested in the meaning of life, how it forms, how it works, and what we can change. He liked the idea of using natural sciences to understand himself, but he soon discovered that biology is complicated. He turned to the research areas of systems and synthetic biology to assist him understands the complex systems of nature.

During his recent visit to Australia, Hiro spoke to audiences at Monash University, SAHMRI/University of Adelaide, and the Baker IDI about how he’s used systems biology to understand mammalian circadian rhythms. And how, once he understood the systems he and his team used synthetic biology to manipulate them – changing the sleep/wake cycles.

In his new position at the University of Tokyo, Hiro is hoping to move this work from the cellular level to the whole organism. Disease tends to be caused by the interaction between cells and affect the organism, rather than being a molecular level issue. We understand molecules and how they interact with cells through our work with genomics, but there is no comparable technique or platform for research at the cellular level. This is Hiro’s next challenge.

At the age of 38 Hiro is a medical doctor and holds a PhD in Pharmacology. He was also recently appointed a professor in the Department of Pharmacology of the School of Medicine at the University of Tokyo, after many years as a senior researcher in the Center for Developmental Biology of Japan’s national research organisation, RIKEN, where he developed a prestigious funding base.

In September, Hiro visited EMBL nodes in Victoria and South Australia. He was one of the first international visitors to the SA node of EMBL Australia, which will be officially opening its doors at the South Australian Health and Medical Institute (SAHMRI) in 2014. And he’ll be back in Melbourne next year for the international conference on systems biology.

You can find information about Hiro’s visit at http://sbiaustralia.org/news/ueda

Events and meetings around the country

Visualising biological data with Scooter – classes in Sydney and Melbourne

Biocomputing expert John “Scooter” Morris will be in Australia to teach at two workshops in Melbourne and Sydney later this month.

Scooter is based at the University of California, San Francisco, where he is the executive director of the Resource for Biocomputing, Visualization, and Informatics. His research focuses on the visualization of diverse biological data in ways that can communicate important properties about underlying properties.

The major vehicle for that visualization has been Cytoscape, an open source platform for integration and visualisation of biological data-particularly biological data that can be mapped onto networks of various different kinds.

While in Australia, Scooter will teach at two workshops:

  • The EMBL Australia Master Class on Protein Sequence Analysis, 21-25 October, Garvan Institute of Medical Research (NSW)
  • Cytoscape Workshop hosted by SBI Australia, 28 October, Monash University (VIC)

You can find more information and register at: sbiaustralia.org/training/cytoscape

An introduction to bioinformatics: BioInfoSummer registration open

BioInfoSummer, an annual summer school in bioinformatics held by the Australian Mathematical Sciences Institute, introduces students, researchers and others working in related areas to bioinformatics.

This year’s BioInfoSummer will be held at the University of Adelaide from 2 to 6 December.

The program features:

  • Introduction to Biology and Bioinformatics
  • Evolutionary Biology
  • Systems Biology
  • Next Generation Sequencing
  • Coding and Algorithms for Bioinformatics

Early bird registration closes on 25 October. For further details, including invited speakers, visit the website: www.maths.adelaide.edu.au/biosummer2013/index.html

Hiroaki Kitano: Maths of Planet Earth lectures in Sydney and Melbourne

In the same way that systems biology uses mathematics to model biological systems, mathematics can help us understand economic systems, climate change and medicine, and design intelligent systems which can respond to unpredictable environments.

Hiroaki Kitano, Director and President of Japan’s Systems Biology Institute will be back in Australia in October in his role as a Maths of Planet Earth Ambassador and he’ll present two public lectures on the topicAct Beyond Borders.

Hiroaki’s talk illustrates how mathematics is the key to questions of healthcare and global sustainability, and why mathematics should feed into strategic and policy decisions.

Upcoming events and deadlines

Upcoming events and deadlines 
If you have events to add to the EMBL Australia events calendar, drop us a note on info@emblaustralia.org with the details and a link for more information.

11 October – Guy Cochrane, Brisbane


20 November – Next Generation Sequencing Bioinformatics, Sydney
21 to 23 November – EMBL PhD Symposium, Competition in Biology: The Race for Survival from Molecules to Systems, Heidelberg, Germany
25 November – Next Generation Sequencing Bioinformatics, Brisbane

Australia’s membership of EMBL

EMBL – the European Molecular Biology Laboratory – is Europe’s flagship for the life sciences. The Australian government joined EMBL as an Associate Member in 2008.

EMBL Australia was created to maximise the benefits of Australia’s associate membership of EMBL. It creates opportunities for:
  • internationalising Australian research
  • empowering and training our best early career researchers/research leaders
  • embedding powerful new enabling tools such as bioinformatics and systems biology in Australian life science.

EMBL Australia comprises:

  • Victorian node at Monash University, with two research groups and SBI Australia (Systems Biology Institute)
  • South Australian node at SAHMRI, opening in 2013 with three research groups
  • Queensland node at the University of Queensland with the Bioinformatics Resource Australia and plans for future research groups
  • NSW node at the University of Sydney with one research group (currently based in Europe) and plans for future research groups
  • Australian Bioinformatics Network, based at CSIRO
  • A node will be developed at the University of Western Australia as funds and opportunities arise.

EMBL Australia is an unincorporated joint venture between members of the Group of Eight universities and the CSIRO, supported by the Australian government.

Read more about EMBL Australia at: www.emblaustralia.org

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