Best short talk winners at New Approaches and Concepts in Microbiology

The popular symposium “New Approaches and Concepts in Microbiology” took place virtually this year. 598 people from across the globe joined from their own time zone. Two presenters impressed the crowd with their short talks, even though the local time for one of them was 4.50 am (that doesn’t count as morning yet, does it?).

Jordi van Gestel and Nitzan Tal were the well-deserved winners. Read about their research below.

Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities

Jordi van Gestel, University of California, San Francisco, USA

Presenter: Jordi van Gestel, University of California, San Francisco (UCSF), USA

Introduction: I am a Postdoc in the laboratory of Carol Gross at UCSF. Being trained as an evolutionary biologist, I was introduced to the fascinating world of microbiology during my PhD and have been working at the interface of both fields ever since. My research focuses on the organisation and evolution of bacterial cell collectives.

Abstract
Inside bacterial communities, cells often communicate through the release and detection of small diffusible molecules, a process termed quorum-sensing.

In general, signal molecules are thought to broadly diffuse in space; yet, paradoxically, cells often employ quorum-sensing to regulate traits that strictly depend on the local community composition, such as conjugative transfer. This raises the question if and how nearby cells in the community can be detected.

Here, we employ a microfluidic platform to determine how diverse quorum-sensing systems, differing in their regulatory design, impact the range of communication. While some systems indeed support long-range communication, we show that other systems support a novel form of highly localized communication.

In these systems, signal molecules propagate no more than a few microns away from signalling cells, due to the irreversible uptake of these signal molecules from the environment. This enables cells to accurately detect micron scale changes in the community composition and engage in local cell-to-cell communication.

Intriguingly, several mobile genetic elements, including conjugative elements and phages, employ short-range communication to specifically assess the fraction of susceptible host cells in their vicinity and adaptively trigger horizontal gene transfer in response. Our results underscore the complex spatial biology of bacteria, where cells both communicate and interact at widely different spatial scales.

https://twitter.com/EvolvedBiofilm/status/1413103744649203719?s=20

Antiviral defense via nucleotide depletion in bacteria

Nitzan Tal, Department of Molecular Genetics, Weizmann Institute of Science, Israel

Presenter: Nitzan Tal, Department of Molecular Genetics, Weizmann Institute of Science, Israel

Introduction: I am a PhD student in the lab of Professor Rotem Sorek at the Weizmann Institute of Science. For the past few years I’ve been studying the interactions between bacteria and their viruses (bacteriophages), and how both adapt to ever changing conditions in order to survive. My research focuses on identifying novel anti-viral defense systems and on understanding the extremely diverse arsenal of microbial immunity.

Abstract

DNA viruses and retroviruses need to consume large quantities of deoxynucleotides (dNTPs) when replicating within infected cells. The human antiviral factor SAMHD1 takes advantage of this vulnerability in the viral life cycle, and inhibits viral replication by degrading dNTPs into their constituent deoxynucleosides and inorganic phosphate.

In this study, we report that bacteria employ a similar strategy to defend against phage infection. We found a family of defensive dCTP deaminase proteins that, in response to phage infection, convert dCTP into deoxy-uracil nucleotides. A second family of phage resistance genes encode dGTPase enzymes, which degrade dGTP into phosphate-free deoxy-guanosine (dG) and are distant homologs of the human SAMHD1.

Our results show that the defensive proteins completely eliminate the specific deoxynucleotide (either dCTP or dGTP) from the nucleotide pool during phage infection, thus starving the phage of an essential DNA building block and halting its replication. Our study demonstrates that manipulation of the deoxynucleotide pool is a potent antiviral strategy shared by both prokaryotes and eukaryotes.

For tips and tricks on how to give a good scientific talk, watch this video

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Best Poster Awards — Chromatin and Epigenetics

The 10th edition of the EMBL Conference: Chromatin and Epigentics took place virtually this year. We welcomed more than 800 participants, from which 3 were selected best poster award winners prior to the meeting and who gave a short talk on the last day of the conference. Get a glimpse of their research.

Sequence-dependent surface condensation of pioneer transcription factor on DNA

Sina Wittmann, Max Planck Institute for Molecular Cell Biology and Genetics, Germany
Presenter: Sina Wittmann, Max Planck Institute for Molecular Cell Biology and Genetics, Germany

Abstract: Biomolecular condensates are dense assemblies of proteins that are dynamic and provide distinct biochemical compartments without being surrounded by a membrane. Some, such as P granules and stress granules, behave as droplets, have many millions of molecules, and are well described by a classic phase separation picture. Others, such as transcriptional condensates are thought to form on surfaces such as DNA, are small and contain thousands of molecules. However, the correct physical description of small condensates on DNA surfaces is still under discussion. Here we investigate this question using the pioneer transcription factor Klf4. We show that Klf4 can phase separate on its own at concentrations that are above physiological, but that at lower concentrations, Klf4 only forms condensates on DNA. Analysis using optical tweezers shows that these Klf4 condensates form on DNA by a switch-like transition from a thin adsorbed layer to a thick condensed layer that is well described as a prewetting transition on a heterogeneous substrate. Condensate formation of Klf4 on DNA is thus a form of surface condensation mediated by and limited to the DNA surface. Furthermore, we are investigating how Klf4 condensation is regulated by the property of the surface such as through DNA methylation. We speculate that the prewetting transition orchestrated by pioneer transcription factors underlies the formation of transcriptional condensates in cells and provides robustness to transcription regulation.

View poster.

Single-cell profiling of histone post-translational modifications and transcription in mouse and zebrafish differentiation systems

Presenter: Kim de Luca,  Hubrecht Institute, The Netherlands
Presenter: Kim de Luca,  Hubrecht Institute, The Netherlands

Abstract: During organism development and cellular differentiation, gene expression is carefully regulated at many levels. To that end, various epigenetic mechanisms translate cell-intrinsic and -extrinsic cues into activation and repression of the relevant parts of the genome. One of the most studied and versatile forms of epigenetic regulation is the post-translational modification (PTM) of the histone proteins around which DNA is wrapped. Histone PTMs affect the surrounding DNA by forming a binding platform for a range of effector proteins, as well as by directly modulating the biophysical properties of the chromatin. Hence, histone PTMs play a crucial role in priming, establishing, and maintaining transcriptional output and cell state. Many techniques used to study histone PTMs require thousands to millions of cells, and consequently mask the heterogeneity inherent to complex biological systems. To understand the nuanced relationship between chromatin context and transcription, single-cell and multi-modal approaches are necessary. We have previously developed a method to simultaneously measure transcriptional output and DNA-protein contacts by single-cell sequencing (scDam&T). This multi-modal method is particularly suitable for studying systems containing many transient cellular states. Here, we apply scDam&T to measure chromatin modifications by expressing the E. coli DNA adenine methyltransferase (Dam) fused to a domain that specifically recognizes a histone PTM. First, we validate this approach in population and single-cell samples by comparing the resulting data to orthogonal state-of-the-art techniques. Next, using mouse embryoid bodies as an in vitro differentiation system, we apply our method to deconvolve the lineage-specific regulation of Polycomb chromatin. Finally, we study the role of H3K9me3-marked heterochromatin in the developing zebrafish embryo.

Poster not available due to unpublished data, however, you can watch a short talk presentation here.

 

Presenter: Moushumi Das, University of Bern, Switzerland
Presenter: Moushumi Das, University of Bern, Switzerland

Poster and abstract not available due to unpublished data.

 

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8 tips for preparing a digital poster that stands out from the crowd

Virtual meetings are rapidly gaining popularity, due largely to the necessity of continuing knowledge exchange during the social isolation brought on by the Corona pandemic.

Even before the pandemic, EMBL´s Course and Conference Office was already exploring options to improve our services and the event experience on-site, including the option of digital poster presentations.

Our software provider iPosterSessions comes with easy to use WYSIWYG templates. Users can display high-resolution images, videos & animations, and the content can be updated at any time right throughout the conference – allowing poster presenters to present their research digitally and dynamically.

If you are presenting a digital poster at an upcoming (virtual!) meeting, here are eight tips to help you on your way:

  1. Download the official template from the software provider

Most digital software providers have an official template that you can download – use it! This will reduce the risk of glitches, resolution problems and sizing issues in the final product, and you know from the outset what you have to work with.

  1. Check out the tutorials

No two digital poster tools are the same, so take the time to browse through the online tips and tutorials to make sure you are comfortable with the software before starting. It will save you a lot of frustration in the long run!

  1. Make your design eye-catching – it should stand out from the crowd

This is the same principle as creating a printed scientific poster – there are so many of them, so make sure yours stands out! It should be eye-catching and visually appealing. Include clear data representations, and make sure the text is to the point. It should grab attention but not explain every little thing about your results – that’s your job during the discussion.

  1. Use media – images, sounds, video. Check that they work and display properly

Graphics and media can express details more quickly and memorably than paragraphs of text, so have a think about how you can present your work in this way and put some time into it. Be sure to check that the media files work with the software, and test every file to make sure they display or play properly.

  1. Link to external resources

Digital posters differ from printed posters in that you can generally link to other pages online – so if there is a great external paper or online source you want to link to in order to explain your point in more detail, do it! Your audience will be grateful to have further reading handed to them on a plate if they want to find out more after the poster session.

  1. Check your work

This should really be a no-brainer. Check your work is complete, correct and final before publishing your poster! Silly mistakes only show that you haven’t put as much time and effort into the work as you probably should have, so get someone else to go over your poster before you release it to the conference community.

  1. Practice your presentation

Yes, it’s a digital poster presentation, and no, you won’t be talking face-to-face with your audience as you normally would, but you still need to practice your presentation beforehand and know exactly what you want to say and how you want to say it. It may feel strange online, so try presenting the poster online with a colleague or your boss (e.g. with Skype, Zoom, Google Hangouts) and get them to give you feedback and pointers.

  1. Stick to the publishing deadline

There are deadlines for a reason, so please stick to them! You don’t want to risk your poster being excluded from the poster presentation because of tardiness. Give yourself plenty of time in case of any issues that may arise with uploading or compatibility (this shouldn’t be an issue if you followed the template and guidelines, but sometimes computers have a mind of their own!).

So why not check out our list of upcoming virtual events to see where you can try out your digital poster presentation skills!

For general pointers about creating posters, see 10 tips to create a scientific poster people want to stop at.

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How to become a better scientific presenter

Presenting your work to your colleagues and peers is an integral part of being a scientist. However, sometimes presentation nerves can get the better of you. Never fear – you are not alone! 9 out of 10 people suffer from presentation nerves. If you’re in this majority, read on for some tips to help you become a better scientific presenter.

  1. Breathe

To overcome nerves, the best thing you can do is breathe. Breathe in to a slow count of 5, and then out to the same slow count of 6, and you will feel your pulse gentling, you’ll feel yourself getting calmer and the world will seem a better place.

  1. Pay attention to your audience

Don’t worry about yourself. If things go wrong – which they may do – just make it okay for the audience. As long as they’re sitting there thinking, ‘well that happened to me last Thursday’, you haven’t got a problem. If they’re sitting there worrying about you, then you do have a problem.

  1. Don’t be predictable

At the beginning of a presentation it’s best not to give your audience a boring and predictable introduction. If, for example, you get a set of results and you try and hit them with a whole bunch of data, they won’t remember it. If you tell them about the moment you got those results and how they thrilled or frustrated you, let them share your excitement or frustration. Then they’ll remember.

  1. Give them the shiny bits

Audiences are like magpies – they like shiny things. Any kind of bling is good. Those are the bits that get taken back to their nests. It doesn’t matter how good you are, if you bombard your audience with mountains of data and expect them to remember it, they won’t. Give them little shiny polished messages, stories, analogies, anecdotes, case histories, specific examples, powerful pictures – those are the shiny bits that will go back to their nests.

  1. Look forward

There are so many presenters who seem to think the audience wants to see the back of their head, or possibly their right ear because they’re pointing or talking to the screen behind them. Big mistake. You want to be talking to your audience. Look forward, make eye contact (or at least appear to do so) with all your audience (not the one smiling, nodding person in the front row)!

  1. You have a face – use it

If you smile, the audience can hear it. If you are surprised, your eyebrows go up and your voice goes up with it. If you’re in despair, everything sags and your voice goes down with it. Facial expressions and voice work as one, so use them to your advantage.

  1. Don’t over-practice

One of the biggest mistakes is over-practicing. If you’re writing a script and trying to stick to it slavishly, you put yourself in a kind of straightjacket. If you do use notes that’s fine – but be obvious about it – don’t pretend you’re not using them!

  1. Keep it simple

With an academic paper people can read it as many times as they like over as many cups of coffee as they need.  Over time they’ll get it. With a presentation you have to get them on the first pass – they have to understand it straight away. So keep it really, really simple, even to the point it might mildly offend you – it won’t offend them!

  1. Three bullets

If you must use bullet points, three is the magic number. Never use more than three per slide – we’re pre-programmed to remember things in threes. If you are doing bullet points keep them tight and really short. Better still give them bullets (see shiny bits above).

  1. Avoid using a pointer

If you need to use a pointer there’s something wrong with the slide – it’s too busy. You can pre-select what you want the audience to see – circle things, draw boxes around them, highlight them. If you’re waving your pointer around manically – which happens a lot of the time – the audience may or may not bother to look at where you’re pointing. If you tell them where to look, they’ll look there.

  1. Finish with a bang

If you can leave the audience with a big idea – something to take home – that’s a good thing, but please don’t tell them “this is your take-home message”. It makes your audience very grumpy and makes them determined to take home any message except the one you’ve told them to.

  1. Have fun

Above all, enjoy yourself. If you enjoy yourself, the audience will have enjoyed your talk.

Original video with Media and Presentation Trainer Ali Sargent, UK

 

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