Best Poster Awards – EMBO|EMBL Symposium: New Approaches and Concepts in Microbiology

It’s a well known fact that EMBL conferences present the most top-class science from around the world, not only from established researchers but also up-and-coming scientists. In this brand new series we will feature some of the award-winning posters from recent EMBL conferences and symposia. 

We begin with 4 of the poster prize winners at the EMBO|EMBL Symposium: New Approaches and Concepts in Microbiology (10-13 July 2019). 

De novo selection of peptides that confer antibiotic resistance

Michael Knopp is currently a PostDoc at the University of Uppsala and will join the Typas group at EMBL Heidelberg in October 2019.

Authors: Michael Knopp (1), Jonina Gudmundsdottir (1), Tobias Nilsson (2), Finja König (2), Omar Warsi (1), Fredrika Rajer (1), Pia Ädelroth (2), Dan Andersson (1)

The origin of novel genes and proteins is a fundamental question in evolutionary biology. New genes can originate from different mechanisms including horizontal gene transfer, duplication-divergence and de novo from non-coding DNA sequences. Comparative genomics has generated strong evidence for de novo emergence of genes in various organisms but experimental demonstration of this process has been limited to localized randomization in pre-existing structural scaffolds. This is bypassing the basic requirement of de novo gene emergence, i.e. lack of an ancestral gene. We constructed highly diverse plasmid libraries encoding randomly generated open reading frames and expressed them in Escherichia coli to identify peptides that could confer a beneficial and selectable phenotype in vivo. Selections on antibiotic-containing agar plates resulted in the identification of three inserts that increased aminoglycoside resistance up to 48-fold. Combining genetic and functional analyses, we show that the peptides are highly hydrophobic and that they insert into the membrane, reduce membrane potential, decrease aminoglycoside uptake and thereby confer high-level resistance. This study demonstrates that randomized DNA sequences can encode peptides that confer selective benefits, and illustrates how expression of random sequences could spark the origination of new genes.

View PDF Poster

(1) Uppsala University, Sweden;  (2) Stockholm University, Sweden


Combinatoria genetics approach to prevent and disrupt biofilm-associated infection

Irina Afonina is a postdoctoral associate at the Singapore-MIT Alliance for Research and Technology (SMART).

Authors: Irina Afonina (1), Kimberly Kline (2), Timothy Lu (3)

Enterococci are opportunistic bacterial pathogens that cause a variety of infections including life-threatening endocarditis, chronic wounds, medical device and urinary tract infections. All of these infections are biofilm-associated, which are intrinsically more tolerant to antimicrobial clearance, and which therefore pose a major challenge in treating these infections. Biofilm formation is multifactorial, requiring multiple factors, which can vary depending on the environment or niche where the bacteria reside. Therefore, to understand the complexity of interactions and factors that contribute to enterococcal biofilms, we are combining CRISPRi technology with rapid DNA assembly to identify gene pairs involved in biofilm formation in different infection niches. We established a dual-vector inducible CRISPRi system for Enterococcus faecalis that targets planktonic and biofilm cells with efficiency resembling that of a gene knock out. We have shown that CRISPRi targeting of constitutively expressed gfp gene on the bacterial chromosome, fully quenches GFP signal within planktonic, early and late biofilm cells. Additionally, we have shown that silencing of the croR gene, required for bacitracin resistance, mimics a croR in-frame deletion phenotype, and both CRISPRi croR and croR show reduced minimal inhibitory concentration to bacitracin compared to uninduced or wild type strains. We are creating combinatorial libraries to identify pairs and quartets of genes of all of the two-component signal transduction systems encoded in E. faecalis, to address the hypothesis that different signals will drive unique biofilm programs in different environmental conditions. This research serves as a platform to rapidly identify combinations of genes involved in enterococcal pathogenesis, including antimicrobial resistance, virulence, and immune invasion.

View PDF Poster

(1) SMART, Singapore; (2) Nanyang Technological University, Singapore; (3) Massachusetts Institute of Technology, USA


A conserved RNA seed-pairing domain directs small RNA-mediated stress resistance in enterobacteria

Nikolai Peschek is a PhD student in Prof. Dr. Kai Papenfort’s lab in the Department of Biology at the Ludwig-Maximilians-University of Munich, Germany.

Authors: Nikolai Peschek (1), Mona Hoyos (1), Roman Herzog (1), Konrad U. Förstner (2), Kai Papenfort (1)

Small regulatory RNAs (sRNAs) are crucial components of many stress response systems. The envelope stress response (ESR) of Gram-negative bacteria is a paradigm for sRNA-mediated stress management and involves, among other factors, the alternative sigma factor E (σE) and one or more sRNAs. In this study, we identified the MicV sRNA as a new member of the σE regulon in Vibrio cholerae. We show that MicV acts redundantly with another sRNA, VrrA, and that both sRNAs share a conserved seed-pairing domain to regulate multiple target mRNAs. V. cholerae lacking σE displayed increased sensitivity towards antimicrobial substances and overexpression of either of the sRNAs suppressed this phenotype. Laboratory selection experiments using a library of synthetic sRNA regulators revealed that the seed-pairing domain of σE-dependent sRNAs is strongly enriched under membrane-damaging conditions and that repression of OmpA is key for sRNA-mediated stress relief. Together, our work shows that MicV and VrrA act as global regulators in the ESR of V. cholerae and provides evidence that bacterial sRNAs can be functionally annotated by their seed-pairing sequences.

View PDF Poster

Peschek, N. et al. A conserved RNA seed‐pairing domain directs small RNA‐mediated stress resistance in enterobacteria. The EMBO Journal (2019) DOI:10.15252/embj.2019101650

(1) Ludwig-Maximilians-Universität München, Germany;  (2) TH Köln, ZB MED, Germany


The interaction between replication factor DiaA and primary metabolite sedoheptulose-7- phosphate directly regulates DNA replication in Escherichia coli

Joanna Morcinek-Orłowska is a PhD Student at the University of Gdańsk, Poland.

Authors: Joanna Morcinek-Orlowska (1), Aleksandra Bebel (1), Justyna Galinska (1), Torsten Wladminghaus (2), Anna Zawilak-Pawlik (3), Monika Glinkowska (1)

To proliferate, bacterial cells duplicate their genomes and this process is coordinated with cell growth and division. During the last few decades, various biochemical mechanisms controlling initiation of DNA replication in the model bacterium Escherichia coli have been characterized in detail. However, it remains elusive what constitutes a signal for the growing cell to initiate the next round of chromosomal DNA replication. Here we present evidence that a primary metabolite sedoheptulose 7-phosphate (S7P) binds to a replication factor DiaA and regulates its activity in promoting oligomerization of the DnaA initiator protein. Furthermore, our results show that the cellular level of S7P and the ability of DiaA to interact with the metabolite both influence DNA replication in vivo. S7P is an intermediate in the pentose phosphate pathway, providing building blocks for synthesis of nucleotides and a starting point for production of the outer membrane components. Consequently, we propose a mechanism which links DNA replication with cell growth through primary metabolism.

View PDF Poster

(1) University of Gdansk, Poland;  (2) LOEWE Center for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Germany; (3) Polish Academy of Sciences, Poland


Working on your own conference poster? Then check out 10 tips to create a scientific poster people want to stop by .

No more browser restrictions!

For those of you who have been coming to EMBL for scientific training over the years, you may have noticed that we recently (finally?!) have a new and improved registration and abstract submission software, with a brand new look and feel.

We have moved to an HTML5 software solution, which offers an enhanced customer experience, meaning that we now no longer have browser restrictions or preferred browsers. The interface is fully responsive for submitters and evaluators alike, and is user-friendly on all devices. YAAAAAAY!!!!

The new software is pretty self-explanatory, but just in case you get stuck, here are a couple of how-to videos for abstract and motivation letter submission.

How to submit an abstract – for EMBL conferences and symposia

 

How to submit a motivation letter – for EMBL courses

 

Meet the Trainer – Anna Kreshuk

PHOTO: EMBL/Marietta Schupp

Meet Dr. Anna Kreshuk, a group leader in the EMBL Cell Biology and Biophysics unit, whose group uses machine learning to develop automated methods to help biologists speed up image analysis. Anna joined EMBL in 2018 and has since been very active in building up training opportunities in her research field.

What is your research focus and why did you choose to become a scientist?

My research is concerned with developing new machine learning-based methods of the analysis of biological images. I enjoy doing science, both for the thrill of finding new things and the joy of seeing others do that in their domain with the help of our tools.

Where do you see this field heading in the future?

I hope to see most of the routine image analysis automated in the future. This will hopefully raise new research questions in biology which can only be answered by imaging at scale, creating, in its turn, more exciting research questions for us.

How has training influenced your career?

We develop software for end users without computational expertise, who want to solve biological problems we don’t quite understand. Participating in training has provided a lot of insight to the user side of things, brought new collaborations and even new research directions for me and for my group.

What is your number one tip for people looking for scientific training?

A one-week course can be a great start, however, it’s important to find out how you can get support with the new technology in your everyday work. Try to stay in contact with your course buddies, but also look for online communities. For image analysis, for example, there is a great forum connecting all the popular tools.

If you weren’t a scientist, what would you be?

My 7-year-old recently asked: “you say I can become anything I want to be, but then why didn’t you become an astronaut?”. Seriously though, I’d probably be a programmer, I love automating things.

You are organising the EMBL Course: Deep Learning for Image Analysis (20 – 24 January 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

Deep learning has brought an enormous advance in computer vision. We can now analyse microscopy images in ways no one thought possible just 10 years ago. While the technology is getting more accessible every year, it’s still difficult even for computationally savvy biologists to apply state-of-the-art methods to their image analysis problems. This is exactly the gap we intend to close.

Fostering friendly collaborations across organisations

Guest blog post by Jürgen Deka, Head of External Scientific Training, EMBL

The International Day of Friendship (annually on 30th July) got me thinking about our friends in the scientific training field, and our collaborations with them which enable us all to deliver our high-level scientific conferences and courses.

It’s important to have a goal to work towards, and at EMBL Events we generally benchmark ourselves against Cold Spring Harbor Laboratory and Keystone Symposia in the US, and the Wellcome Genome Campus in the UK. A bit of healthy competition is good for the soul, and I think we all thrive on challenges! It allows all four of us to provide top-class training to benefit as many scientists as possible throughout the world, and in this sense we all have the same aim.

“Competition has been shown to be useful up to a certain point and no further, but cooperation, which is the thing we must strive for today, begins where competition leaves off.”    

Franklin D. Roosevelt

If you are looking to establish and foster friendly collaborations in scientific training, here are 6 tips that can help you achieve your goal:

  1. Keep in regular contact
  2. Align your goals with each other
  3. Be aware of what the other organisations are doing and talk to them openly so you can adapt your plans accordingly
  4. Don’t arrange meetings with the same audiences too close together. If people are going to attend both meetings – either as speakers, participants or sponsors – there needs to be some space in between
  5. Find ways to work together in order to highlight and complement your strengths
  6. Learn from each other, but don’t try to be like the others – work on developing your own strengths

Here’s how we work with our counterparts to allow us all to offer the best science possible worldwide:

  • Cold Spring Harbor Laboratory: With the Cold Spring Harbor Laboratory we have very close ties. We alternate one of our most popular conferences with our friends at CSHL, the EMBO Workshop ‘Protein Synthesis and Translational Control’. We align our programme plans in order to provide added value for our scientific community. Discussion and exchange between the programme heads and other members of staff takes place on a regular basis.
  • Keystone Symposia: As with the other research institutes, EMBL’s collaboration with Keystone Symposia is a long-standing one. We exchange our thoughts and ideas and align our conference programmes once per year. Our friends at Keystone Symposia have been particularly open and collaborative with regards to the alignment of their symposia taking place in Europe.

10 questions to ask journal editors at conferences

From guest blogger Céline Carret
Senior Editor EMBO Molecular Medicine,
EMBO Press,  
@EMBOMolMed

 

At last! You’ve made it to the conference you’ve been waiting so long to attend. It’s going to be perfect – 4 days of great science, poster presentations, socialising and networking opportunities galore. There’s even a ‘Meet the Editors’ session – surely the editors can give you some tips on how to get that paper published that you’ve been working on?

To make sure you get the most out of the opportunity, here are 10 of the best questions I’ve been asked as an editor over the years:

  1. What do you think of my paper?

It’s true – we want to know what you’re working on! Be prepared to pitch your paper to the editor. Bring print-outs or even show them your paper on your computer. We may not be able to give you the same detailed feedback as in a normal review process, but we can definitely let you know if it’s interesting for the journal or what the missing experiment is that would make your paper stand out.

  1. Does your journal respect the request for specific referee exclusion?

If there is a conflict of interest with another scientist or you would like to exclude someone as a reviewer for personal reasons, you’ll want to make sure that your dream journal will respect your wish. Depending on the policies of the journal the editor can give you advice regarding how best to approach the issue, and what the chances are of your request being taken into account.

  1. What is your acceptance rate? 

Although the acceptance rate of a journal generally varies from month to month, it’s good to get an idea of your chances of being accepted. In general, competition is high, and perhaps you’d prefer to go for a “safer” journal with a lower impact but higher acceptance rate. The final decision, of course, is yours.

  1. Do you offer blind submissions so referees don’t see the author’s names?

The idea behind blind submissions is to reduce any chance of possible bias from a reviewer. The practice is becoming increasingly common, and rightfully so! Some journals offer this practice, and some are still to catch on, so it’s worth asking about the policies of the specific journals you’re interested in publishing in.

  1. What types of studies do you publish?

This question is quite broad, but it gives editors the chance to give you an overview of the various kinds of options you have if you want to submit to their journal, and maybe they’ll give you some new ideas that you hadn’t considered as options previously.

  1. What do you think of pre-prints and open science?

There are varying opinions on pre-prints and open science publishing, and whether these are really beneficial for the field as a whole. It’s definitely worth talking to an experienced editor to find out their views and tips on whether you should rather wait until the review process is complete or submit your article to a pre-print server at the same time.

  1. Is your journal open-access?

Theoretically you should have done your research and should know the answer to this beforehand, but perhaps there are some editors at the conference you weren’t expecting. Remember that there are several ways of getting a paper open access, so feel free to ask this to find out what your submission options are.

  1. How do you handle research integrity issues?

Unfortunately issues relating to research integrity do still exist, and it’s important to find out how the journal deals with these issues should they arise. Editors are generally quite open about this, so don’t be afraid to ask specifics!

  1. What’s the coolest paper you’ve published this year?

Although they perhaps shouldn’t admit it, editors will have a favourite paper that they are generally more than happy to go on…and on…and on about! So if you want to get them talking, this is the question to ask!

  1. How can I become an editor?

This career question is one that we are more than happy to answer! Although many editors may have taken different paths to end up where they are, we are all scientists and can provide insight into what life is really like as an editor, and how you can make your way into the field.

 

So don’t be afraid to approach the editors – we are always happy to give you some tips, and would love to talk to you to find out more!

Meet the editors at EMBL and EMBO upcoming conferences!