Record attendance at New Approaches and Concepts in Microbiology

Written by event reporter Magdalena Wutkowska.

This year’s EMBO|EMBL Symposium: New Approaches and Concepts in Microbiology took place 7-9 July 2021. For the first time in its history, the meeting was held virtually, with a record of over 650 attendees from all over the world. The three day programme featured six sessions, 36 talks, discussion panels and countless posters showcasing the newest scientific advances in the field.

This was my second time reporting during a virtual conference organised by EMBL, the first one being the EMBO Workshop: Molecular Mechanisms in Evolution and Ecology. It is interesting to note, even though the two meetings started with quite different scopes and aims, over time they began to resemble one another. Both meetings welcomed topics in microbiology that use cutting-edge techniques to disentangle and unravel microorganisms’ intricate worlds. The two meetings followed a similar format, which included a fairly intuitive online platform with links to presentations, posters, chats and a variety of other information prepared by the organisers.

A table with a laptop, a thermos with coffee or tea and a notebook on a desk.
My setup for the symposium

Pre-symposium sessions

As part of New Approaches and Concepts in Microbiology, three special pre-symposium sessions explored transitioning to starting a lab, the nooks and crannies of publishing presented from the editor’s perspective and the future of scientific meetings in a post-pandemic world. The panelists shared many insightful ideas distilled from decades of experience in their work, and usually this type of knowledge is not so readily available, especially to early-career scientists.

From my personal perspective, the pre-symposium session on the future of scientific meetings was one of the most interesting, and is also a topic that will affect everyone in the scientific community. Gerlind Wallon representing EMBO shared results of a recent survey in which scientists were asked what they expected from meetings in the future and how did they perceive the online meetings that became a sudden reality for the scientific community, since the onset of the pandemic.

Scientific sessions

The scientific programme of the conference was fully packed with impressive and wide-ranging talks tackling most of the ‘big’ areas and pressing topics in microbiology. The first day was dedicated to systems biology, followed by the environment and antibiotics. The presentations on the second day dealt with regulation, signalling, protein machines and cell biology. The final day’s sessions covered novel approaches to study pathogenesis, infection, and microbiomes.

A common and reoccurring theme in many talks was the role of viruses in microbial systems and processes. The importance of that topic was strongly emphasised during the 1st day’s panel discussion on phage-microbe interactions, which  highlighted some new and exciting perspectives on viruses.

The highlights from the conference have been instantly reported on Twitter using #EESMicrobiology. If the data presented during a talk has already been published, there is usually a link to the associated paper(s) in the tweet.

Onsite to virtual to hybrid?

Pandemics brought many tragic events, but on the other hand, it gave us a chance to rethink many issues and come up with alternatives for our actions. Virtual meetings are perhaps one of the broadly acquired tools, which in my opinion should further be used to make science more available for people and lower our impact on the environment. Will the next “New Approaches and Concepts in Microbiology” be held in a hybrid format?

Unexpected perks of attending online meetings from a favourite place!

This blogpost was written by Magdalena Wutkowka, Postdoc in Anne Daebeler’s Group, Soil and Water Research Infrastructure, Biology Centre CAS, České Budějovice (CZ).

Learn more on how to become an event reporter for EMBL Events.

 

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Zooming into the PhD Symposium: “It’s about different scales of life, and not even just life on earth.”

Each year, a bunch of PhD students from EMBL join forces to organise a large symposium for their fellow PhD students across the globe. This year’s (virtual) PhD symposium is the 23rd of its kind. The Big Picture: Zooming into Life is taking place from 16 -17 December.

Around 30 first year PhD students are part of the organising committee for the symposium. Amandine and Dewi, both in Heidelberg, are two of the main organisers. Amandine is a joint PhD student at the University of Heidelberg (Kuner lab) and EMBL (Alexandrov lab)  on neuroinvasive cancer, and Dewi is working at EMBL in the Steinmetz lab, where she is working on developing a CRISPR/Cas9 screen in primary immune cells.

Dewi Moonen
Amandine Prats

How did the team come up with the theme of this symposium?

Amandine: “We wanted to have an interdisciplinary topic that is interesting for a lot of people. We all have such different research backgrounds, but it should be interesting for everyone. We tried to include more than just biology.”

Dewi: “I really like that this topic is about different scales of life, and not even just life on earth, we also have a talk about astrobiology.”

Amandine: “It is a very broad topic, but the talks themselves are not general. They are accessible, but they will be in-depth and connected to the bigger picture at the same time. We are hoping the talks will spark ideas and new collaborations.”

What are you personally excited about?

Dewi: “For the talks, amongst others, I am looking forward to Christoph Bock. His group performs interdisciplinary research at the interface of immunology, cancer and precision medicine, and develops new technologies to support this. This technology development is especially an interest of mine.”

Amandine: “We selected really great speakers for this symposium. Not just because of the research topics, but also because they are really good at giving talks. I am very enthusiastic about the astrobiologist Dr. Lynn Rothschild. It is not my field at all, and I never thought about it before, but I am very curious to find out more about bringing life to other planets.”

You are calling for abstracts for short talks and posters. What topics are you looking for?

Dewi: “This symposium is really made by and for PhD students, so we are giving PhD students the opportunity to share their research. We will have a virtual poster session and selected short talks, divided into different categories. It can be about any topic related to life science, but it would be great if you are able to place your research into the bigger picture.”

Can you tell us a little bit more about the programme elements?

Dewi: “We want the symposium to be interactive, so besides the talks, we are organising different workshops and social activities, like virtual lunches and coffee breaks. Because the organisers are all PhD students, the workshops reflect our interests. We have a career workshop and a scientific workshop on imaging. We also have a workshop on mental health that I am looking very much forward to.”

Amandine: “With regard to the workshop on mental health: it can be hard being a PhD-student, as we can be under a lot of stress. Not just due to the current pandemic, but also just in general. The pandemic just made it more visible.”

What was your experience with organising this virtual symposium?

Amandine: “In the beginning, we had to figure out a lot. Most of us have never met each other in real life due to the pandemic. We’ve never organised a large-scale event like this before. But it feels really good now that it is all coming together.”

Dewi: “I think working together in teams is going really well. We have eight different committees, but there is also overlap between them, so we stay connected and up to date.”

A group picture taken on Zoom, with the organisers of this years PhD Symposium. Around 20 people are on screen, with the visual of the symposium as their background.
The PhD Symposium Organising Committee

You have put a lot of effort and time into organising this symposium. When do you think it will be a success?

Dewi: “For me, it will be a success if the participants are actively engaged, and not just having their computers open and listening to the talks. We want to organise a truly interactive meeting.”  

Amandine: “I am hoping that people will talk to each other and make some longer-term connections, and maybe even collaborations.” 

The Big Picture – Zooming into Life takes place on 16 – 17 December 2021.
Submit your abstract by 10 October

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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 – BioMalPar XVII

This year,  the BioMalPar conference took place for the 17th time, but the second time virtually. Three poster presenters stunned their peers with their visually attractive digital posters, presentations and research insights. Out of 90 posters, they received the best poster award by popular vote. Meet the winners!

Sex-specific genetic screens identify hundreds of Plasmodium fertility genes essential for the transmission of malaria parasites

Claire Sayers, Umea University, Sweden

Abstract

Sexual reproduction of malaria parasites is essential for their transmission by mosquitoes. Biological processes required for Plasmodium fertility include the formation of gametocytes, their transformation into gametes in response to signals from the mosquito, fertilisation in the bloodmeal, meiosis, and the formation of an invasive ookinete. Stage-specific gene expression data suggest that hundreds of parasite genes are uniquely required for sexual reproduction, but previous gene knockout studies have merely scratched the surface of this important aspect of parasite biology. We have mutagenised P. berghei lines that make only fertile male or only fertile female gametocytes, with barcoded PlasmoGEM vectors to screen >1200 targetable genes for sex-specific phenotypes. Our screens identify hundreds of genes with sex-specific roles. The data recapitulate existing knowledge of Plasmodium fertility and assign functions to previously unannotated genes. For the first time, we are gaining an unbiased picture of the molecular mechanisms of Plasmodium fertility at genome-scale, which will lead to a deeper understanding of this novel biology that could serve as targets for transmission blocking drugs or vaccines.

View Claire Sayers’ poster

ABCI3 confers pleiotropic drug resistance to antimalarial compounds

Emma Carpenter, Wellcome Sanger Institute, UK

Abstract

Understanding the mechanisms available to the malaria parasite for acquiring multidrug resistance will be important for predicting which genes may become important for clinical resistance in the future.
ABC transporters are an important protein family with roles in drug resistance across a variety of organisms, and mutations in PfMDR1 modulate sensitivity to multiple antimalarials. Several other ABC transporters are encoded in the Plasmodium genome, and we have identified mutations in ABCI3 that confer resistance to several experimental antimalarial compounds.
Using in vitro drug selection regimes with a set of four chemically related compounds (SY4, 10, 11, 13), we isolated 12 drug resistant lines that were subjected to whole genome sequencing. All contained either single nucleotide variants (SNVs) or copy number amplifications of abci3. The point mutations were located in or near predicted transmembrane domains, consistent with a role in modifying the substrate specificity of the transporter, and testing of these lines against other compounds chemically-unrelated to the SY series identified a subset to which sensitivity is also affected.

In addition, natural variants of ABCI3 are observed at or near to these putative resistance SNVs, and preliminary evidence indicates differing sensitivities to the SY compounds among field isolates and common lab strains that may be driven by variation in ABCI3.

This work suggests abci3 should be among the genes monitored for changes in prevalence in longitudinal sampling of field isolates.

View  Emma Carpenters’ Poster

Characterization of a new malaria vaccine candidate against Plasmodium vivax using genetically modified rodent malaria parasites

Diana Moita, Instituto de Medicina Molecular João Lobo Antunes, Portugal

Abstract

Malaria, a mosquito-borne disease caused by Plasmodium parasites, is the most prevalent parasitic infection worldwide. Despite considerable efforts, there is still no effective vaccine against human-infective Plasmodium parasites, of which P. falciparum (Pf) and P. vivax (Pv) are the clinically most significant. Whole-sporozoite (Wsp) vaccines, which induce efficient immune responses against the pre-erythrocytic (PE) stages of Plasmodium parasites, are among the most promising immunization strategies so far. Although most malaria vaccine research has focused on Pf infection, Pv continues to be the most widespread of the human-infective Plasmodium species, imposing significant health and economic burdens on affected countries. Importantly, Pv can originate dormant parasitic liver forms – hypnozoites – which may cause malaria relapses long after mosquito transmission. Recently, our lab developed a new Wsp based on the use of transgenic rodent P. berghei (Pb) parasites as a platform to deliver immunogens of human-infective Plasmodium parasites. Since our in silico studies predict that >60% of CD8+ T cell epitopes encoded in both the Pv and Pb proteomes are shared between these two parasites, we generated a new genetically modified Pb expressing the highly immunogenic circumsporozoite (CS) protein from Pv (PvCS), in addition to its endogenous CS, Pb(PvCS@UIS4), to be used as a vaccine candidate against Pv malaria. Our immunofluorescence microscopy studies confirmed that both the endogenous PbCS and the inserted PvCS are expressed during the PE stages of this transgenic parasite, and that its infectivity is similar to that of its wild-type (WT) counterpart. Specifically, the ability of Pb(PvCS@UIS4) to infect Anopheles stephensi mosquitoes, as measured by the number of oocysts or sporozoites formed, as well as its ability to infect and develop normally in mouse hepatocytes and red blood cells showed no significant differences from those observed for WT parasites. Subsequent studies showed that mice immunization with Pb(PvCS@UIS4) elicits the production of anti-PvCS antibodies that efficiently recognize and bind to Pv sporozoites. Considering the lack of efficient strategies to tackle Pv, this study represents a crucial step on the development of a new Wsp vaccine candidate against this parasite.

View Diana Moita’s poster

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Lazy Fur upgrades virtual conference experience with live music

Meet Ira and Tom – a newly-wed couple from Heidelberg and band members of Lazy Fur – a music duo that have been performing live for participants of numerous virtual EMBL conferences and symposia.

Tom and Ira of Lazy Fur. Ira holding a mic, Tom playing the guitar
Tom and Ira of Lazy Fur

“It feels good that we can bring joy and help provide even a better conference experience with a little bit of live music.”

Who is Lazy Fur?

Tom is a Research Staff Scientist in Matthias Hentze’s and Wolfgang Huber’s labs at EMBL Heidelberg and Ira is an executive assistant in a real estate company.

Both of them grew up with music. Ira started singing when she was little and now also plays the piano and bass guitar.

“I used to play the keyboard but discovered my calling as a guitarist in my PostDoc time at EMBL.” Tom shares.

They bonded over their passion for music and started playing acoustic covers of pop and rock songs and singer/songwriter style music. Ira is inspired by Walk Off The Earth, a Canadian group of friends who do spectacular covers of pop songs. And Tom is generally fascinated by buskers in Dublin he met during his PhD.

Virtual concert setup

Virtual conferences are great for many things, but it is very hard to organise entertainment. Lazy Fur found a way to give a live music performance and interact with participants.

Tom had to put in quite some effort to get it right:

“The technical side was quite challenging at first, but now we are very happy that we can provide high-quality streams. We can interact with the viewers who appreciate the live aspect of our performance. ”

What is it like to perform for a virtual audience?

Onsite, you can easily tell which songs the audience likes and if they like the show. In front of a virtual audience, it is more difficult, because you can not see and hear them. Tom and Ira did find a way to interact with the audience.

“The audience can communicate with us either via the YouTube or conference platform chat displayed on the TV in front of us.” Tom says. 

Ira: “We are extremely happy about all the positive responses we got in the chat or comments people sent us after the show.”

Tom: “We have had heart-warming messages from participants about how they enjoyed it. They wrote that this was a very unique and uplifting experience that reminded them of past conferences at the EMBL Heidelberg site.”

And after Covid-19?

Tom: “Performing live is just an amazing experience. EMBL has a great appreciation for live music at their events and it is wonderful to connect with people on that level. So yes, definitely looking forward to that as well!”

Lazy Fur will be performing at the virtual EMBO Workshop: Predicting Evolution, 14 – 16 June 

Check out the website of Lazy Fur
Check the Lazy Fur YouTube channel

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