www.fems-microbiology.org

The official newsletter for FEMS Affiliates

A F F I L I AT E S L E T T E RJune 2013

Also in this issue:

Grants CornerFEMS Meeting Attendance Grants

Publications PagePublish 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

For the last two years, molecu-lar 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 publi-cations 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 sci-entist Jack Leo, who had just finished his PhD thesis at the Department of Structural Biology of the University of Helsinki, a FEMS Advanced Fel-lowship (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

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 spe-cific type of bacterial adhesins called trimeric autotransporters through his PhD research. These outer mem-brane proteins, only found in Gram-negative bacteria, secrete their own N-terminus, called the passenger domain, to the cell surface across the outer membrane. The passenger do-mains are adhesins, which allow the infection of host cells.

Continue reading on page 2.

Successful FEMS Advanced Fellowshipon evolution of adhesins

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

www.fems-microbiology.orgwww.fems-microbiology.org

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

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.

Continuation of page 1.

Working as a FAF postdoc in Tübingen, Leo fur-ther studied the evolution of protein structures under the supervision of Dirk Linke. It became a successful cooperation, as Leo published a re-view 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 publica-tions 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 scien-tific development.

Excellent models

‘Why I wanted to work at the Department of Protein Evolution? It has had a long lasting inter-est 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 mod-els for this as their evolution is accelerated by the constant need to avoid immune responses of the

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

‘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 mem-branes and their biogenesis. In Linke’s group I got the chance to learn more about these proteins, about biophysical techniques and about struc-tural 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 bacte-rial 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 adhe-sion.

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

www.fems-microbiology.orgwww.fems-microbiology.org

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

G R A N T S CO R N E R

Grant description

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

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.

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.

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.

Application checklist

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:

• 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.

• You have completely filled in the application form.

• The following should be submitted along with your application form:

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

• 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.

www.fems-microbiology.orgwww.fems-microbiology.org

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

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

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 commu-nications 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 avail-able 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 han-dled 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 pro-cessed by our extra-fast route to publication.

www.fems-microbiology.orgwww.fems-microbiology.org

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

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

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 data-set.

• New or revealing class of metabo-lites from a glycomic, lipidomic or metabolomic dataset.

‘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 sub-sets, 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 net-work 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

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 comput-ers 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 shor-tomics basket aims to harvest!

Source: Crazy-Frankenstein.com

www.fems-microbiology.orgwww.fems-microbiology.org

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

Preliminary program of FEMS 2013The 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

15:30 – 16:00

Opening session

16:00 – 16:50

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

Monday, 22 July

8:30 – 9:25

Rudolf Aebersold

The quantitative proteome of microbial cells and its control

17:00 – 18:00

Anne Glover, Chief Scientific Adviser of the European Commission

Policy – Should it be based on fact or fiction?

Tuesday, 23 July

8:30 – 9:25

Antje Boetius

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

Wednesday, 24 July

8:30 – 9:25

Johan Leveau

Turning over a new leaf in phyllosphere microbiology

Thursday, 25 July

8:30 – 9:25

Wolfgang Buckel

Electron bifurcation – a new paradigm in microbial energy metabolism

12:00 – 13:15

Closing lecture

Lwoff Award followed by Awards and Closing Ceremony

N E W S O N F E M S CO N G R E S S

www.fems-microbiology.orgwww.fems-microbiology.org

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

N E W S O N F E M S CO N G R E S S

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.

Download the FEMS congress app now!

• 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.

www.fems-microbiology.org

The voice of microbiology in Europe.We advance and unify microbiology knowledge.

Keverling Buismanweg 4, 2628 CL Delft, The NetherlandsT: 0031 15 269 3920 | F: 0031 15 269 3921 | E: fems@fems-microbiology.org The FEMS Affiliates Letter

is a production of the Federation of European Microbiological Societies

F E M S A F F I L I A T E S L E T T E R , J U N 2 0 1 3

DEADLINES1 September 2013

1 April 2014FEMS Meeting Attendance Grants

1 December 2013FEMS - ASM Mäkelä - Cassell Grant

1 December 201315 June 2014

FEMS Research Fellowships

15 December 20131 June 2014

FEMS National & Regional Congresses Grants

1 March 2014 FEMS Meeting Grants

(for meetings to be held in 2015)

2 9 A u g u s t - 3 S e p t e m b e r 2 0 1 3 26th International Conference on Yeast Ge-netics and Molecular Biology, Frankfurt/M, Germany.

7 - 11 September 201314th International Conference on Pseudomonas, Lausanne, Switzerland.

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

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

22 - 25 September 20131st European Conference on NaturalProducts: Research and Applications, Frankfurt/M, Germany.

FEMS-Sponsored Meetings, Spring/Summer 2013

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 pneumo-nia to neurological ones, resulting in somehow losing their fear of people. Veterinarians in In-donesia have already observed tigers entering villages. Human-tiger conflicts and vulnerability to poachers could be the consequence of this new behaviour.

How computational biology can help find tumour cells

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 biolo-gists 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!