We’ve proved it, biologists can also program

“Like punning, programming is a play on words.” Alan J. Perlis.

You don’t have to be a programmer to have programming skills. Writing code is an essential part of being a programmer (duh!), but is also a vital component of being a scientific developer, software developer or computer scientist. You can utilise computer programs to automate tedious and repetitive tasks, extract results from experimental data, apply models to solve your research questions or purely have fun with your own projects.

Today is Programmers’ Day (yay!🥳) and we want to recognise all those who submerge themselves in the deepest mysteries of code (especially their own) and aim to automate the future.

If you’re looking to start venturing into the programming world or embark on your next project, get some inspiration from some scientists who are helping out at our EMBL Events’ courses.

Florian Huber PHOTO: Marietta Schupp/EMBL

“What do I love about programming? It allows me to go from zero to one: gaining new biological insights from data.” Florian Huber (Postdoctoral Fellow, at the Typas Group in EMBL Heidelberg and the Beltrao Group at EMBL–EBI in Hinxton).

 

 

 

 

Ullrich Köthe PHOTO: Ullrich Köthe

“Automated image analysis has always been an interesting and fun field of research, but thanks to the deep learning revolution and the wide availability of wonderful neural network libraries, we can now actually solve hard practical problems.” Ullrich Köthe (Group Leader in the Visual Learning Lab Heidelberg).

 

 

Valentyna Zinchenko PHOTO: Carolina Cuadras/EMBL

“Programming skills allow you to automate the routineparts of your job and focus more on the exciting ones. At some moment you just have so much data, that you would not want to process it manually. You would not wash your clothes by hand if you have a washing machine, would you? Then why analyzing your data manually, when you can have it done by a machine as well?” Valentyna Zinchenko (Predoctoral Fellow in the Kreshuk Group).

 

Adrian Wolny PHOTO: Carolina Cuadras/EMBL

“Whenever I build something, be it a new machine learning model or my pet project, I always try to make it easy to understand and generic enough so that other people could use it in their work. I try to open source my projects whenever I can and contribute back to the community. There is nothing more rewarding than seeing your little piece of software used by others to find answers to their own research questions.” Adrian Wolny (Visiting Researcher at EMBL and PhD candidate at Heidelberg University).

 

Pavel Baranov PHOTO: Pavel Baranov

“The relationship between computer science and modern biology is akin to that between mathematics and physics.” Pavel Baranov (Professor of Biomolecular Informatics, University College Cork, Ireland)

 

 

 

 

It’s no secret that managing biological data efficiently can be overwhelming and feel impossible. If you’re a biologist who’s interested in learning how to process, analyse, organise and interpret your almost innumerable data sets – preferably with the most suitable and state-of-the-art techniques and tools out there – EMBL Events has got you covered.

EMBL Course: Deep Learning for Image Analysis, Apply by 20 September 2019

EMBL Course: Exploratory Analysis of Biological Data: Data Carpentry, Apply by 5 November 2019

EMBL Course: Analysis and Integration of Transcriptome and Proteome Data, Apply by 10 November 2019

EMBL Course: Immune Profiling of Single Cells, Apply by 10 November 2019

EMBO Practical Course: Microbial Metagenomics: A 360º Approach, Apply by 27 January 2020

EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling, Apply by 9 February 2020

14 tips for a smooth conference experience

The date of your first EMBL conference in Heidelberg is fast approaching. You are excited, have already bookmarked interesting abstracts in the conference app and are ready to make your travel arrangements. Here are 14 tips that will help you stay out of trouble and focus on the science.

1. Don’t try to book a flight to Heidelberg

Although it is one of the most popular tourist destinations in Germany, Heidelberg does not have an airport. The closest airports are Frankfurt International Airport, Stuttgart Airport and Airport Karlsruhe/Baden-Baden. More information on how to reach Heidelberg is available here.

2. Make sure you read the final logistical email (FLE) we send you

The information provided in this email is vital for your travel plans and conference schedule and will be your bible for the days you spend at the conference. It provides important attachments such as the programme, the onsite handout and the poster listing.

3. Try not to miss the shuttle bus

The EMBL campus is located on a hill outside of Heidelberg which makes it a beautiful and inspiring place to visit, away from the hustle and bustle of downtown Heidelberg. However, it also makes it more difficult to reach by public transport. Although efforts have been made to improve the public transport connection to the campus, there is still the need of conference shuttle busses that operate on a strict schedule (included in the FLE). So if you miss the shuttle bus, your only way up the hill may be by taxi. Please note that there are no UBER services in Heidelberg.

Our team has prepared an onsite handout with pictures of all bus stops so that you don’t miss the bus because you don’t know where the correct stop is. This information is provided in the FLE.

4. Get the app instead of the abstract book

When you register online, you will be asked if you would like to receive a printed copy of the abstract book. If you click yes, you will get your copy onsite, but make sure that you don’t lose it as this is the only copy you will get. Many participants diligently take notes in the abstract book during the sessions, only to go home one day realising they have lost their copy.

One way to avoid that is by using the app instead. It includes everything contained in the printed abstract book and more, and it also allows you to review the abstracts ahead of the conference and offers the option to export your notes directly to your email.

5. Share your dietary requirements

The EMBL canteen makes a special effort to cater to everyone’s needs by providing fresh food every day and appropriate substitutes for participants on vegetarian, vegan, lactose-free or gluten-free diets. In our registration system you have the option to indicate your preferences, but should you have special requirements based on food allergies or intolerances, please do not hesitate to reach out to us, so we can ensure you are well fed.

6. Send your flash talk slides well in advance

If you are presenting a flash talk, make sure to send us your slides well in advance to make sure they are looped on the screen in time. You will have only 2 minutes to present your poster in the flash talk, so you don’t want to waste any second with technical difficulties.

For some more tips on how to give a flash talk, watch this video.

7. Avoid asking for a certificate of participation during the registration

As much as we’d like to help you out, registration is not the best time to ask for a certificate of participation. These are normally sent out after the end of the event via email.

8. Hold on to your badge

Your badge is your access card to the conference venue and your coupon for the lunch and dinner buffets, so make sure you don’t lose it or leave it in your hotel room.

9. No cash policy on the EMBL Campus

If you arrive on campus outside of the conference times and you would like to get something to eat or drink, it might not be possible. EMBL has a no cash policy on its campus and the only way to purchase something from the cafeteria or canteen is via a special guest credit card. Therefore, it would be a good idea to grab something to eat on your way to the campus, especially for breakfast as we normally only have coffee available in the mornings.

10. Do not ask us for medicine

As much as we would like to help you with your headache or cold symptoms, we are not authorised to hand out any medicine. However, we have a list of pharmacies that are close to the conference venue which we are happy to share with you.

11. When you sign up for a social event, show up!

Most conference social events like dinners, lunches, parties take place in the EMBL Advanced Training Centre (ATC) and are open to all conference participants without prior registration. In the case that there are organised social events taking place outside of the conference venue such as tours or downtown dinners, these are usually restricted to a limited number of participants, and prior registration is necessary.

All the logistics are meticulously coordinated with the service providers and very often there are waiting lists for these events, so if you are unable to attend, please inform us, so that we can give your spot to someone who can.

12. Stay on the paths in the woods

The EMBL Heidelberg Campus is surrounded by a beautiful forest which offers a great opportunity for lunch-time walks or runs. However, before you set on exploring the woods, please familiarise yourself with the paths so that you easily find your way back. In the app you will find 4 different walking routes of various lengths.

13. Take down your poster on the last day

You have put in so much work in your poster that it is a shame to leave it with us. Make sure you take it down on the last day of the event as you may end up needing it for another conference.

14. Stay away from red push buttons on the emergency exit doors

Not all exit doors in the ATC Foyer may be opened. Look out for a silver button with a key on it to open the door without activating the emergency exit alarm.

Meet the Trainer – Imre Gaspar

Meet Dr. Imre Gaspar, Senior Research Assistant in the Kikuë Tachibana Group at the Institute of Molecular Biotechnology in Vienna, Austria, which focuses on understanding how chromatin is spatially reorganised in totipotent cells.

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

I’m interested in the central dogma, that is how gene expression is regulated on the transcriptional and post-transcriptional levels and how these regulations allow development of an organism.

I became a scientist because I always fancied solving riddles – and as a scientist you get to work on solving the ultimate riddle that interests us, humans.

Where do you see this field heading in the future?

Right now, there is a boom of high-throughput and omics techniques in studying gene expression allowing us to create predictive quantitative models of regulatory networks, which will allow us to get mechanistic understanding of the processes underlying development, homeostasis and pathogenesis. Microscopy analysis is already essential for the latter and is also gaining importance also in the omics studies with the advent of high-throughput hybridisation techniques.

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

Being a microscopist, it was absolutely essential for my career to receive training in state-of-the-art imaging and image analysis technologies. Courses are important, of course, but I find that the best source of training a scientist can receive is core facilities, internal trainings, and of course close colleagues in the lab.

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

I have a degree in medicine, so I probably would have become a medical software developer – that profession is closest to the work of a scientist and having a background in medicine would allow me to contribute to the development of medical instrumentation.

You are organising the EMBO Practical Course ”FISHing for RNAs: Classical to Single Molecule Approaches” (15 – 20 March 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?

We are at the onset of quantitative analysis in biology: many labs have already implemented corresponding work-flows, but this principle should be spread widely, especially in the fields working on the understanding of gene expression. I expect that the single molecule techniques we will cover during the course will serve as mind-changers to help people embrace the concept of quantitative biology.

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