FEMS Affiliates Letter June 2013

June 2013

A F F I L I AT E S L E T T E R The official newsletter for FEMS Affiliates

Successful FEMS Advanced Fellowship on evolution of adhesins Also in this issue: Grants Corner FEMS Meeting Attendance Grants Publications Page Publish your ‘omics in PAD for free News on FEMS congress • Preliminary program of FEMS 2013 • Download the FEMS congress app now!

Deadlines FEMS-Sponsored Meetings Microbiology TidBits

Jack Leo , FEMS Advanced Fellow 2011 - 2013. Photograph: Martin Schueckel

For the last two years, molecular microbiologist Jack Leo was a FEMS Advanced Fellow at the Department of Protein Evolution of the Max Planck Institute for Developmental Biology. Until now, already three high-interest publications are the result. Leo himself is looking back happily as well.

‘This department is a world leader in the area of my interest.’

In 2011, FEMS decided to grant the promising young Finnish-British scientist Jack Leo, who had just finished his PhD thesis at the Department of Structural Biology of the University of Helsinki, a FEMS Advanced Fellowship (FAF) for the period from April 2011 until March 2013. This FAF implied a substantial amount of € 24,000.-, to be spent on a postdoc

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position at the Department of Protein Evolution of the Max Planck Institute for Developmental Biology in the German city of Tübingen.

Bigger perspective Leo was already specialized in a specific type of bacterial adhesins called trimeric autotransporters through his PhD research. These outer membrane proteins, only found in Gramnegative bacteria, secrete their own N-terminus, called the passenger domain, to the cell surface across the outer membrane. The passenger domains are adhesins, which allow the infection of host cells.

Continue reading on page 2.

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Continuation of page 1. host. It is a process also referred to as the Red Queen hypothesis in evolutionary biology.

Working as a FAF postdoc in Tübingen, Leo further studied the evolution of protein structures under the supervision of Dirk Linke. It became a successful cooperation, as Leo published a review article in the Philosophical Transactions of the Royal Society B already in 2012. In this study, he put the details known on the mechanism of single autotransporters from different classes and organisms into a bigger perspective. In the same article, he discussed recently discovered classes of autotransporters. Leo also contributed to publications in PLOS One and Cellular Microbiology and is planning to submit a new manuscript by the end of this year.

Through an email interview, Leo explains to us what receiving the FAF has meant to his scientific development.

Excellent models ‘Why I wanted to work at the Department of Protein Evolution? It has had a long lasting interest in bacterial adhesins. The approach taken by the department is to look at the evolution of protein structures. Bacterial adhesins and other surface proteins of pathogens are excellent models for this as their evolution is accelerated by the constant need to avoid immune responses of the

‘Joining the group of Dirk Linke was a natural choice for me. He is interested in the trimeric autotransporters that I had studied for my PhD thesis. However, he also studies other outer membranes and their biogenesis. In Linke’s group I got the chance to learn more about these proteins, about biophysical techniques and about structural bioinformatics. The Department of Protein Evolution is a world leader on these subjects.

No need to change fields ‘The FEMS Advanced Fellowship made it possible for me to move to Germany and pursue research in my preferred field, the biochemistry of bacterial adhesion. In general, funding is very tight. The only fallback option I had, would have meant that I would essentially have needed to change fields.

In this sense, the FAF has allowed me to continue in the field of the biochemistry of bacterial adhesion.

‘Receiving the FAF has given me the chance to deepen my previous areas of expertise and to attend several meetings. Due to fruitful collaborations with nearby institutions, I was given access to methods that are not part of the usual, biochemically and biophysically oriented methods that I was used to.’

For the time being, Jack Leo was one of the last recipients of a FEMS Advanced Fellowship. This grant is no longer available. FEMS will inform you if and when it will be made available again.

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FEMS Meeting Attendance Grants 1 September is the deadline for the Meeting Attendance Grants. These are grants awarded to young European Scientists wishing to attend microbiology meetings that are not supported by a FEMS Meeting Grant.

Grant description

Application checklist

Meeting Attendance Grants may support attendance at meetings worldwide but preference will be given for meetings within the European area.

FEMS Meeting Attendance Grants regulations apply to each application for the FEMS Meeting Attendance Grants. The requirements consist of, but are not limited to, the following:

The maximum amount of a FEMS Meeting Attendance Grant is € 600.- while the minimum is € 250.-.

We are calling on young scientists, who wish to apply for a Meeting Attendance Grant, to first familiarize themselves with the regulations governing FEMS Meeting Attendance Grants.

Complete applications should be received by FEMS Central Office by: • 1 September 2013, for attending meetings that open between 1 October 2013 and 30 April 2014.

• 1 April 2014, for attending meetings that open between 1 May and 30 September 2014.

• You are a member of a FEMS Society.

• You are not above 36 years of age at the closing date of the meeting.

• You are an active microbiologist.

• You include an abstract for which you are the presenting author.

• The meeting that you are attending is not awarded a FEMS Meeting Grant.

• You have read the regulations for your application and you fulfill all requirements.

• You have read the application form.

The regulations and application forms are available online. Please read them carefully and check the list at the right before contacting the FEMS Central Office.

• You have completely filled in the application form.

• The following should be submitted along with your application form: • Your curriculum vitae including a list of publications.

• One letter of recommendation.

• The abstract including a letter confirming its acceptance by the meeting organizers.

• A passport photograph of yourself.

Send the complete application to grants@ fems-microbiology.org before the deadline of 1 September 2013.

G R AN T S CO R N ER

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Publish your ‘omics in PAD for free Our journal “Pathogens and Disease“ is presenting a new section called Shortomics. In Shortomics, you can publish your ‘omic studies, ranging from ‘omic announcements to short communications in ‘omics and system’s biology.

Because your low hanging fruits should be harvested now!

‘Omics refer to the study of certain themes in biological sciences, like genomics, metabolomics and proteomics. Scientists active in an ‘omic field often gather many data in a short period of time.

They can either do two things with their data: save them for possible use in the future or publish them in our journal Pathogens and Disease.

Shortomics The new PAD section Shortomics aims to provide a platform for the rapid publication of large ‘omic datasets. There are primarily two reasons for this.

Firstly, such a platform could make datasets available to the research community soon after their production.

Secondly, it could provide a rapidly published overview of the more remarkable features of an ‘omic dataset. All submissions to PAD will be handled at editorial level.

THE advantages of publishing your ‘omic announcements in Pathogens and Disease, FEMS Microbiology Letters or FEMS Yeast Research 1. There will be no page charges.

However, the on-line open option will be available.

2. Authors will include information on why the sequence is interesting microbiologically.

3. You may include one or two figures plus tables.

4. Your announcement will be processed by our extra-fast route to publication.

P U B L I C AT I O N S PA G E

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‘Omics are like fruit trees at harvest time An ‘omic dataset is very much like a fruit tree at harvest time. Consider a transcriptomic dataset as an example. The transcriptome of any cell type can usually be divided into multiple subsets, the branches of a tree, depending of the level of up or down regulation of specific genes and pathways, respectively the smaller and larger branches.

And just like a branch of a tree, a pathway will often divide into smaller branches or will network with other pathways, for example low versus high branches.

Hungry scientists simply can’t wait From this results a complexity that is as beautiful to our mind’s eye as it is undecipherable to our

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regular eye. The human eye in fact sees a fruit tree, less for its complex beauty, and more for the fruits themselves.

Just as it will take many people, machines and time to harvest all the fruits of a tree, it will take many people armed with sophisticated computers and not days, but perhaps years, to harvest all the fruits of an ‘omic dataset. To the hungry researcher, this may seem an eternity…

Harvest the low hanging fruits!

What the hungry scientist can do however is to go for the ‘low hanging fruits’: those features of a dataset that are readily observable with just a cursory look at the dataset. Low hanging fruits from ‘omic datasets are the juicy fruits the shortomics basket aims to harvest!

Want to publish your ‘omic announcement? Any of the following dataset features are suitable: • Conserved gene or gene family.

• New plasmid.

• New pathogenicity island, from a comparative genomic dataset.

• A previously unsuspected virulence regulon or a small RNA family from a transcriptomic dataset.

• Conserved protein post-translational modification from a proteomic dataset.

• New or revealing class of metabolites from a glycomic, lipidomic or metabolomic dataset.

Source: Crazy-Frankenstein.com

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Preliminary program of FEMS 2013 The scientific program of the FEMS congress in Leipzig next month is going to be a diverse one. Internationally renowned microbiologists will share their insights on highly relevant topics. From Sunday, 21 July until Thursday, 25 July, you can take part in numerous sessions.

Check all plenary lectures below and go to the congress website or download the app on the next page to see what else you can expect.

Sunday, 21 July

Tuesday, 23 July

15:30 – 16:00 Opening session

8:30 – 9:25 Antje Boetius

16:00 – 16:50

The microbes that came in from the cold – microbial communities of the changing arctic

Nobel prize winner Harald zur Hausen Infectious causes of human cancers

16:50 – 17:40 Kristala Jones Prather Exploiting the synthetic capacity of microbes for the production of novel value-added biochemicals

Wednesday, 24 July 8:30 – 9:25 Johan Leveau Turning over a new leaf in phyllosphere microbiology

Monday, 22 July

Thursday, 25 July

8:30 – 9:25

8:30 – 9:25

Rudolf Aebersold

Wolfgang Buckel

The quantitative proteome of microbial cells and its control

Electron bifurcation – a new paradigm in microbial energy metabolism

17:00 – 18:00

12:00 – 13:15

Anne Glover, Chief Scientific Adviser of the European Commission

Closing lecture

Policy – Should it be based on fact or fiction?

N E WS O N FEMS CO N G R E SS

Lwoff Award followed by Awards and Closing Ceremony

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Download the FEMS congress app now!

Wiley Blackwell has created an app especially for the FEMS congress. Download it to your smartphone, tablet or laptop now and don’t miss a thing.

• Create your own agenda.

• Make your personal attendee profile.

• Access speaker profiles.

• Read the congress abstracts online.

• Find information about the venue and the city of Leipzig.

• Get updated with alerts, news and polls during the congress.

N E WS O N FEMS CO N G R E SS

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DEADLINES 1 September 2013 1 April 2014 FEMS Meeting Attendance Grants

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MICROBIOLOGY TIDBITS Asian tigers subject to CDV What has happened to African lions about twenty years ago is now happening to Asian tigers. They are being affected by the canine distemper virus (CDV), a relative of measles.

According to Wildlife Vets International, this virus has probably killed 30 percent of all Serengeti lions in the mid-nineties. Symptoms vary from respiratory problems like pneumonia to neurological ones, resulting in somehow losing their fear of people. Veterinarians in Indonesia have already observed tigers entering villages. Human-tiger conflicts and vulnerability to poachers could be the consequence of this new behaviour.

1 December 2013 FEMS - ASM Mäkelä - Cassell Grant 1 December 2013 15 June 2014 FEMS Research Fellowships 15 December 2013 1 June 2014 FEMS National & Regional Congresses Grants 1 March 2014 FEMS Meeting Grants (for meetings to be held in 2015)

How computational biology can help find tumour cells

FEMS-Sponsored Meetings, Spring/Summer 2013 2 9 A u g u s t - 3 S e p t e m b e r 2 013 26th International Conference on Yeast Genetics and Molecular Biology, Frankfurt/M, Germany.

7 - 11 September 2013 14th International Conference on Pseudomonas, Lausanne, Switzerland.

8 - 13 September 2013 Symposium on Aquatic Microbial Ecology, SAME13, Stresa, Italy.

8 - 13 September 2013 Thermophiles 2013, Regensburg, Germany.

22 - 25 September 2013 1st European Conference on Natural Products: Research and Applications, Frankfurt/M, Germany.

The FEMS Affiliates Letter is a production of the Federation of European Microbiological Societies

Although it is currently possible to determine whole genomes quickly, deciphering them still provides scientists with problems of a different order. Identifying specific types of cancer DNA therefore usually is a long and patient journey.

Early June, a group of computational biologists published an article in PNAS that could be the solution. They are making use of so-called cores, small repetitive intervals. In their analysis, the number of recurrent cores determines their significance, separating them from noisy data.

Guide to discovering a new antibiotic Increase your chances to discover a new antibiotic with this blog in the Guardian. It only takes seven things to think about and they are supposedly based on historical evidence.

As two of the recommendations are ‘Buy your vegetables locally’ and ‘Get lucky’, it seems that a world-shaking scientific breakthrough both depends on scientific and trivial success!

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