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.

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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Why virtual sponsorship is valuable

Since the start of the COVID-19 pandemic, most events have been hosted entirely virtually. Companies looking to achieve their marketing objectives by means of events sponsorship have now been faced with the question of whether or not to invest in virtual events.

Virtual Booth Image

The major challenge that we have observed is that many companies expect the same outcome from their virtual event sponsorship as from an in-person meeting. We often hear that while in-person conferences offer possibilities for networking and casual talks, the virtual format is difficult and less efficient in this respect. At our in-person meetings, for example, exhibition booths with big banners are placed in the hall, right next to the catering area. Participants have enough time to walk around and strike a spontaneous conversation with sponsors during the breaks. The virtual format, however, is different. Participants usually attend virtual conferences from their home, often juggling work and family duties. They are more selective about the kind of content they access and prefer to schedule their interactions.

At first glance, this focused approach to attending virtual conferences may not seem as beneficial for sponsors. At the same time, however, there are several ways in which virtual meetings can lend themselves well to providing opportunities for sponsors.

🌎 Wider reach

The number of participants at virtual conferences is normally much higher than at in-person meetings due to them being more affordable and more accessible. The sponsors’ brands could therefore reach wider and more diverse audiences.

💸 Lower cost

Similar to the registration fees, the cost of virtual sponsorship is lower. In addition, companies save on the usual costs associated with sponsoring or exhibiting at a conference such as travel and accommodation for staff, booth design and set-up and shipping. With all this budget left unused, companies have the opportunity to invest in producing content that is relevant and engaging for participants.

📣 More diverse advertising formats

Sponsoring a virtual conference also means making use of all digital content formats available in the virtual venue – banners, videos, flyers, white papers, polls and webinars can all be used to further engage with participants. Digital booths give participants the opportunity to access at the time that is suitable for them, browse material, chat with booth staff, or have a video call to quickly get the answer of a pressing question about the company’s products they are using.

🗓 Extended exposure of branded material

Participants are generally given access to our virtual venues for an average of 4 weeks. In this way, sponsors get extended exposure for their brands and products and have the option to follow up with participants after the end of the meeting is over.

📈 Campaign insights

Contrary to physical conferences, measuring the success of your marketing efforts and the ROI of your sponsorship is much easier at virtual meetings. The built-in tools of the virtual conference software we use provide valuable insights on the performance of your individual marketing campaigns and help you assess your approach in the future.

Virtual sponsorship is a relatively new concept and one that many companies are still hesitant about. With all of EMBL’s events staying virtual until the end of 2021 and the possibility of hosting hybrid events once we go back on-site, it is now clear that virtual sponsorship is here to stay. It is therefore important to understand that it not only offers opportunities for companies to reach their target audiences in times where face-to-face interaction is limited but it also helps them stay connected with the scientific community.

Interested in supporting an EMBL conference as a virtual sponsor? Get in touch with us at sponsorship@embl.de!

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Friend or Foe: Transcription and RNA Meet DNA Replication and Repair

Event Report by Apoorva Baluapuri, University of Würzburg, Germany

RNA and DNA were first described by the Swiss biologist Friedrich Miescher in 1868. About 150 years later, we stand at crossroads of the two disciplines which have arisen as a result of dedicated research on both molecules. The first EMBL symposium on the connections between transcription and DNA replication/repair research was a major step forward in combining the progress from wide ranging topics, thus generating a consensus on how gene expression and DNA transactions cooperate.

The symposium, which was the second one from EMBL this year,  was scheduled just a day after International Women’s Day, and that aligned very well with the equally represented line-up of speakers and organisers!

The titular opening session was dedicated to transcription-associated genomic instability where all aspects of R-loops and ribonucleotide excision repair in transcription coupled DNA double strand break repair were covered. For example, GaĂ«lle Legube (CNRS – University of Toulouse, France) expanded in great detail on the influence of DSB-induced chromatin conformation and the strong potential of 3C-based technologies, while Elodie Hatchi (Dana Farber Cancer Institute, Boston, USA) explained about her recent publication in Nature concerning the impact of BRCA1, RAD52 and PALB2 on small RNA-driven DNA repair.

Eventually, we switched over to a more translational theme with Rushad Pavri (IMP, Vienna, Austria) who spoke about the relation between DNA replication timing and frequency of oncogenic translocations.

This time around, the poster presentation sessions were equally dynamic with topics being covered from role of RBMX in RNA processing (Sara Luzzi, University of Newcastle) to role of MYCN in reconciling elevated transcription levels with DNA replication (Dimitrios Papadopoulos, University of WĂĽrzburg, Germany).

To end the first day, Philippe Pasero (CNRS, France) tried to answer the old question of the chicken or the egg in terms of toxic R-loops, if they are the cause or consequences of DNA replication stress, while Andrew Deans (St. Vincent’s Institute of Medical Research, Australia) explained about fork re-modellers as a general mechanism of R-loop removal.

The second day started out on a high note by a talk on the consequences of DNA damage and heat shock on Pol II from Jesper Svejstrup. Prof Svejstrup recently moved his lab from the Francis Crick Institute in London to the University of Copenhagen (Faculty of Health and Medical Sciences).

To make things even more exciting at the symposium, Martin Eilers (University of WĂĽrzburg, Germany) spoke about conflict resolution by MYCN between “friends and foes”, i.e. Pol II and replication fork. This was followed by talk by Marco Foiani (University of Milan, Italy) who showed the role of ATR in nuclear integrity.

In between the breaks, the participants eagerly shared their setup of how they were joining the virtual conference:

Not only were the home setups on display, but we also got a glimpse of “add-on” participants at the conference:

https://twitter.com/luzzi_s/status/1369373077394644997

Along with this fun, the second day’s poster session continued with equally interesting topics as the previous day. The virtual conference platform provided by Engagez came across as a handy tool in coming as close as possible to the in-person poster presentations.

Frédéric Chédin (University of California, Davis, USA) closed the day by talking about interplay between splicing and R-loops.

In the next two days, a wide variety of topics and methods were covered. For example,  Nick Proudfoot (University of Oxford, UK) dazzled with correlation between R-loops and antisense transcription while Petra Beli (IMB, Mainz, Germany) moved the focus from genomics to proteomics with èlan. She spoke about a method called “RDProx” which maps R-loop proximal proteome in a native chromatin environment.

Also, junior group leaders like Marco Saponaro (University of Birmingham, UK) answered what happens to replication when it encounters transcription and Madzia Crossley (Stanford University, USA) showed CytoDRIP-blots to probe RNA-DNA hybrids on gels which showed that SETX and BRCA1 loss, along with splicing inhibition, results accumulation of RNA-DNA hybrids in cytoplasm!

All along the talks, whichever questions (which, by the way, were in majority from younger researchers) didn’t get answered, were posted and responded to in the “Forum” section: this actually became a valuable summary of quite a few topics.

The networking options were also in abundance, be it the Virtual Bar mixer, or Meet the Editors session on the online platform. Given that editors from elite journals like EMBO, PLoS Biology etc. were present, it gave a nice opportunity for the researchers to gauge where their next big story could find a good home.

In summary, the symposium gave the feeling of being cozy without being too small and specific in terms of the topics covered, and benefited both the experienced and young researchers in an equal way. It was a common understanding and expectation among the participants that this symposium would perhaps be held in person next time if possible.

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Looking back on a year of organising virtual events

Exactly one year ago, the Covid-19 pandemic hit Europe. All on-site events had to be cancelled and we had to rethink our entire program. Our Course and Conference Officers worked really hard to create a virtual equivalent of EMBL’s on-site training offering.  We successfully launched our first virtual conference and many more followed. 

The learning curve was steep and so was the stress level. But when the going gets tough, the tough get going. Two of our Conference Officers, Nathalie and Diah, share with us their experience from being in the eye of the storm, the lessons they have learned and some tips for organising a virtual meeting.

Conference Officers Nathalie and Diah
Conference Officers Nathalie (left) and Diah

How does organising a virtual event compare to organising an on-site event?

Diah: “It is a different world, but equally fun! Organising a virtual event is harder than people think and often more challenging. Not getting to see anyone in person and mastering all sorts of virtual platforms can be quite tough.”

Nathalie: “Some of the milestones we have are the same, for example: preparing the website, programme, opening registration, emails with participants and invited speakers, abstract review and selection… But a huge bulk of the work is totally different: instead of booking buses and ordering catering, we are setting up Zoom webinars and populating the virtual platform.

The massive change has been adapting to the new tasks we have to do and how we should do them consistently for all our events. In our team we have numerous working groups looking at areas of event organisation and creating guidelines, procedures and templates that will help us all. It really is a whole team effort!”

Read: Why do we charge fees for virtual events?

What kind of feedback do you get from participants, speakers and organisers?

Nathalie: “The feedback I have received from speakers and participants has been great: they are so happy we converted our event to virtual instead of cancelling/postponing it. Initially a few speakers were disappointed for the event to turn virtual but the same people commented afterwards that they were impressed with how well it went. What is wonderful is that it is still so beneficial for them in their continued research.”

Diah: “Very humbling! Many agree that onsite face-to-face events are somehow irreplaceable but at the same time they are amazed at the number of benefits virtual events offer too! They give you more flexibility: you don’t have to travel across the world. Also, some people feel more comfortable asking questions in the virtual format. ”

What is the most important lesson you have learned about organising virtual events?

Nathalie: “It’s been necessary for us to turn to virtual events but the lessons we have learned are that virtual events are effective, valuable and have many advantages! We’ve noticed that participants feel more comfortable asking questions during Q&A, that virtual talks have had a wonderful response, that virtual networking works well and you can meet different people from all over the world just at your desk!

On a bigger scale, virtual events mean less travel and a lower carbon footprint and they are more inclusive as they allow some people to participate who couldn’t have done so before. This is hugely important and is a very positive outcome of this difficult situation and it will have an impact on how events are organised in the future.”

What do you miss most about on-site events?

Diah: “The buzz when everyone arrives and the ATC is full of people is very exciting – after all the planning, everyone is there! And my favourite moment is the end of the conference: everyone is smiling and happy and you wave goodbye to the buses that leave EMBL. That sense of relief and accomplishment at the same time. I miss that!”

Nathalie: “Parties! One of the best things about the onsite events is meeting the speakers and participants you’ve been in touch with for months and when it comes to the conference party, it is really fun to see everyone let their hair down and enjoy themselves! And taking silly pictures at the Photobooth with people is something I loved and a really cute memento of the conference. That is a small thing I miss too!”

What in your opinion makes virtual events better than on-site events?

Nathalie: “The inclusiveness: more participants can take part as there is not the same financial barrier (travel, accommodation) and people can join from anywhere in the world.”

Diah: “Virtual events are resilient. There is no need to cancel an event because of the weather or a disaster. Participants can attend the event from anywhere!”

Conference Officer Diah wearing a face mask in an empty auditorium during a virtual event
Conference Officer Diah working a shift in an empty Auditorium

A common criticism is that networking doesn’t work well in the virtual world. What is your experience with virtual social events?

Nathalie: “I think it is great to see how Zoom breakout rooms allow people to mix in small groups or 1-to-1. Particularly the speed networking translates very well.”

Diah: “It’s my favorite part of the programme and I am amazed at how well it has been accepted and running so far. We have had live-streamed concerts and participants love it. At one conference some of the scientific organisers even stayed for the whole duration of the social session and wanted to continue mingling even after it had finished.”

Read our blog on virtual speednetworking.

Top tips to keep in mind while organising a virtual event?

Nathalie: “First of all – be open-minded. There are so many new technologies out there and different things you can try!

Have clear guidelines and templates: you use so many different apps and systems that saving time when setting things up can be a lifesaver!”

Diah: “I would also say: Test, test and test. Glitches are always likely to happen, so be prepared and stay calm.”

Read our blog for more tips on how to organise a virtual event

How do you see the future of EMBL Events?

Nathalie: “I hope we will embrace this new world of virtual events and have effective hybrid events in the future: allowing for face-to-face interaction for those who want to come on-site, but also giving the opportunity for those who prefer to join virtually and get the benefit of being part of the event without having to leave their home!”

Diah: “I think hybrid events will take a central place in the format of EMBL Events in the future. But whatever the format will be, we will keep improving and finding the best way to support the scientific community.”

Looking back in general, what are your thoughts?

Diah and Nathalie: “It has been very rewarding during the last year to see how we at EMBL have been able to adapt to the situation we have found ourselves in and been able to ensure that we can still provide a platform for scientific exchange. The aim of EICAT is to provide excellent training to scientists, and, despite the challenges, this is being achieved virtually for the first time! We are really proud of being able to provide opportunities for this exchange of knowledge and research.

Personally, this time has also been one of continuous learning for all of us on the team. We have developed our skills and experience in a number of ways and massively increased our knowledge of online platforms and tools! It has truly been a time of teamwork as we have adapted into the virtual event world and we are grateful to everyone involved: our marketing team, our Photolab technicians, designers and scientific organisers. It has been a challenging but very valuable learning experience!”

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Best Poster Awards – In Situ Structural Biology Workshop

The EMBO Workshop: In Situ Structural Biology: From Cryo-EM to Integrative Modelling was our final virtual conference of 2020, but there was no trace of Zoom fatigue amongst the 466 participants who joined us from 6 – 8 December!

80 international researchers presented their posters during the two posters sessions on the following topics:

  • Biophysical analysis in cells
  • COVID-19
  • Imaging across scales
  • Integrative modelling
  • Molecular sociology
  • Structural analysis in situ
  • Structural biology

Each of the participants had the chance to vote for their favourite poster, resulting in two posters winning the Best Poster Award kindly sponsored by EMBO Press.  Here are the winners:

New insights on the catalytic mechanism of arsenite oxidase

PHOTO: Filipa Engrola

Authors: Filipa Engrola, Márcia Correia, Teresa Santos-Silva, Maria Romao, (UCIBIO@FCT-NOVA, Portugal)

Arsenic (As) and antimony (Sb) are two metalloids that, due to anthropogenic and natural causes, pose an environmental  threat, considered as priority pollutants by the World Health Organisation and the United States Environmental Protection Agency. Although the safety guards recommend a maximum of 10 ÎĽg/L of As and Sb in drinking water, these values are exceeded in many regions worldwide, with no remediation approach that is simultaneously effective, clean and economically sustainable [1,2]. The ancient bioenergetic enzyme arsenite oxidase (Aio), from microorganisms Rhizobium sp. NT-26 (NT-26 Aio) and Alcaligenes faecalis (A.f. Aio), is currently being studied for its use as a biosensor and in bioremediation processes. Both Aio enzymes contain a large subunit (AioA) that harbours a molybdenum centre and a [3Fe-4S] cluster, and a small subunit (AioB) that possess a Rieske [2Fe-2S] cluster and have demonstrated to oxidise AsIII, as well as SbIII, into the easier to remove and less toxic forms of AsV and SbV, respectively [3,4]. Aiming to elucidate the catalysis mechanism of the enzymes, a combination of expression and purification of the proteins, crystallisation, structural analysis, enzyme kinetics and affinity tests were conducted. X-ray structures of the ligand-free form of the enzyme had been previously determined (PDB: 4AAY, 5NQD and 1G8K [3,5,6]). In our work, Aio crystals in complex with two different forms of the substrate analogue – Sb oxyanions, with a reaction kinetic 6500 times slower than AsIII [6] – diffracted up to ca 1.8 Ă… resolution. The structures show the reaction intermediates bound at the active site, with a ÎĽ-oxo bridge binding Sb to the Mo atom. Analysis of bond lengths and geometry of the ligands at the Mo active site allowed us to revisit the catalytic mechanism of As oxidation [7], contributing to the understanding and future biotechnological application of this family of enzymes in water treatment.

View poster


Allosteric hotspot in the main protease of SARS-CoV-2

PHOTO: Léonie Ströhmich

Authors: Léonie Strömich, Sophia N Yaliraki, (Imperial College London, UK)

Since the beginning of 2020 we have seen the coronavirus SARS-CoV-2 causing a global pandemic with almost 34 million cases and over 1 million deaths worldwide [as of 01.10.2020] [1.] As a result, we have seen a surge in research efforts to develop effective treatments for the underlying disease, COVID-19. One approach is to target the main protease (Mpro) of SARS-CoV-2 as it is essential for virus replication in an early step of the viral life cycle [2.] Most efforts are centred on inhibiting the orthosteric binding site of the enzyme. However, considering allosteric sites on the protein allows for more selective drug design and widens the chemical search space. Here, we report an allosteric hotspot in the SARS-CoV-2 Mpro dimer by using novel atomistic graph theoretical methods: Markov transient analyses follow the propagation of a random walker on a graph and have been shown to successfully identify allosteric communication in catalytic proteins [3.] We further score the so identified allosteric hotspots against random sites in similar distances and thus identify a statistically significant putative allosteric site in the SARS-CoV-2 Mpro. We then simulate a binding event at this hotspot region using data from a recent XChem fragment screen by the Diamond Light Source [4.] which provides a starting point for rational drug design. This study uses highly efficient network theoretical models to shed light on allosteric communication and uncovers putative allosteric sites in the SARS-CoV-2 main protease. This provides a valuable contribution to the ongoing efforts to find a cure against COVID-19 by broadening the horizon for drug discovery efforts.

Image: Léonie Ströhmich

References:
[1.] Official World Health Organization COVID-19
dashboard: https://covid19.who.int (Accessed: 01.10.2020).
[2.] Hilgenfeld, R. (2014). FEBS Journal, 281(18), 4085-4096.
[3.] Amor, B., Yaliraki, S. N., Woscholski, R., & Barahona, M. (2014) Molecular BioSystems, 10(8), 2247-2258.
[4.] Douangamath, A., Fearon, D., Gehrtz, P., Krojer, T., Lukacik, P., Owen, C. D., … Walsh, M. A. (2020) Nature Communications, 11, 5047.

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Working on your own conference poster? Then check out these 8 tips for preparing a digital poster that stands out from the crowd.

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