From an online interview to running my first virtual course

Iva Gavran joined the EMBL Course and Conference Office in December 2020.

We asked Iva Gavran, who recently joined the team as a Course and Conference Officer, to give us her newcomer’s insights about the very first virtual course she organised (EMBO Practical Course: Drosophila Genetics and Genomics, 11 – 15 January 2021), held in the EMBL virtual learning platform – eCampus.

It was December 2020 and after a 5-day quarantine and a PCR test I had started working at EMBL. It was just one month before the EMBO Practical Course: Drosophila Genetics and Genomic was scheduled to take place. A virtual course, of course.

In fact, my job interview at EMBL was held virtually as well and I had seen the EMBL ATC building and the city itself only in pictures prior to relocating to Heidelberg (and oh, both are stunning).

A lot of things for the course were pretty much arranged by then, but I was still baffled about how one could organise a virtual practical course. The answer may well lie in the EMBL Advanced Training Centre building’s architecture that resembles the DNA’s double helix and reminds us that adaptation is the key. We have fully adapted the face-to-face training’s structure and interaction to a new, online format.

Virtual platform

What really helps is that there is a whole learning platform dedicated to our courses, called eCampus. A clean slate at first, it was soon populated with all kinds of learning materials, videos, articles and other input sent by the speakers and trainers.

The EMBL virtual learning management platform eCampus was launched in 2020 and is used as a collaboration and networking tool by the virtual course participants.

Course materials and programme

I would say there are three main pillars of eCampus: the pre-course materials, the interaction options and the daily programme. The pre-course materials are a proper little treasure trove of knowledge with pre-recorded videos, quizzes, articles and assignments. If you have any questions, just go straight to the Forum and ask away, or chat with another participant or trainer. The programme is always up-to-date with all the links you need and it also has a nice feature where you can adapt it to your time zone. If a live session has some pre-course materials that need to be watched or read, it will be hyperlinked in the programme or the material will be added below, which is pretty cool and very convenient.

Networking

Networking is a crucial part of every event, whether it’s a conference or a course, but it is hard to replicate in a virtual environment. I remember how it was for me to virtually meet my colleagues, and trust me, it’s definitely odd, but somehow at the same time it also felt normal. After all, we share the same work experience and it’s the same when attending a course. Well, not exactly the same if you are a work-from-home parent, but EMBL has amazing childcare grants to help you with that.

The Drosophila course started off on a Monday with an ice breaker event, where all participants shared a few slides to introduce themselves, their hobbies and their career path. It was a full display of lockdown life with cooking, baking and Netflix all over the slides (mine included). There were also networking activities like speed networking, student presentations, a discussion panel and a quiz which fostered interactions between participants and trainers and helped create a really nice group dynamic.

Course modules and learning process

The course was designed in a way that required some pre-course work.  The platform contained a lot of pre-course materials, papers and videos which the participants needed to go through before attending the full 5-day course with about 4-5 course hours per day.

I remember some participants were a bit unsure if they needed to watch them before the course. The idea (and I really liked this) was that participants watch the pre-recorded videos in advance, so that when the speakers and trainers joined live during the course, participants could ask as many questions as possible and thus learned even more from the discussion. This was actually the true benefit of the virtual course – a more thorough discussion and full understanding of the topic compared to the standard format of live lectures followed by 5 min of Q&As. And judging by the participants’ feedback, this format was quite a success.

Some of the interactive sessions of the course were designed in a similar way. For example, participants were assigned tasks that they had to complete before the course. During the course, they received feedback, could ask questions and go over the rest of the tasks with the trainers. To let this all sink in properly and to give them a chance to reflect on what they had learned, participants were able to access all the materials and live recordings for two weeks after the course. As some pointed out, this was amazing for a virtual event and I agree completely.

For me, the best part of the Drosophila course was watching the lively interactions and discussions between participants and trainers, and especially among participants during their presentations of their current research. I found it inspiring and rewarding to see their curiosity and ideas. There it was, 20 people sitting in their homes in different parts of the world, talking about one tiny fly with top experts in the field. How amazing is that!

Events Iva is organising or co-organising:

EMBL Course: Advanced Fluorescence Imaging Techniques, 23 – 27 August 2021

EMBL Course: Gene Expression at Spatial Resolution, 30 Aug – 2 Sep 2021.

EMBO | EMBL Symposium: Seeing is Believing – Imaging the Molecular Processes of Life, 5 – 8 Oct 2021.

EMBL Science and Society Conference: One Health: Integrating Human, Animal and Environmental Health, 3 Dec 2021.

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Take a sneak peek at EMBL’s courses and conferences for 2022

Download our 2022 preview poster

Following a year and a half of virtual events, many of you are probably looking forward to attending in-person courses and conferences. So are we! Based on the current trajectory of the COVID-19 pandemic, things are looking brighter for 2022 and we are making plans to return to providing you with onsite training and opportunities to meet and connect with each other as early in the year as possible. Naturally, we’ll have back-up plans in place should coronavirus pandemic disruption strike again, but for now most of our events next year are planned to take place face-to-face.

Our 2022 Course and Conference Programme is now live and features a large variety of exciting new scientific topics. Here are some of the highlights of the programme.

Download our 2022 poster here!
To see the full list of upcoming events, visit our events website.

Conferences

We begin the year with a virtual talent search conference that will allow the next generation of infection biologists to present their work and expertise to EMBL and a large number of participating institutes. This new format is especially interesting for postdoctoral fellows and young researchers working in infection biology.

In April, a symposium will shed light on the biological relationship between microbial infections and human cancer. While for many tumour viruses the causality is firmly established, the biological links for bacterial infections are still under research. This symposium will provide a stimulating platform for young scientists and students to present their research, network and develop further this new interdisciplinary field.

Another exciting and innovative topic will be addressed in “Phenotypic Plasticity Across Scales”, a meeting that focuses on the ability of organisms to adapt their form, physiology or behaviour to environmental cues and changes. The conference will highlight molecular mechanisms underlying plasticity and links to the environment. The meeting will also address the role of plasticity in driving evolutionary novelty and biological diversity.

Courses

In 2022 EMBL will also offer hands-on practical courses on the latest laboratory and computational technologies. Microscopy image analysis has become a key technology in research. The advanced EMBL virtual course on “Deep learning for Image Analysis” will teach the utilisation of neural networks to answer crucial biological questions.

Two courses will present methods and tools on how to integrate multi-omics data sets. The EMBL Course “Analysis and Integration of Transcriptome and Proteome Data” will teach wet-lab scientists the basics in data analysis and integration, while the advanced EMBO Practical Course on “Integrative Analysis of Multi-Omics Data” will equip computational scientists with state-of-the-art integration tools like multi-omics factor analysis.

Many of our hands-on practical courses address complete workflows from sample collection, through wet-lab experiments to computational data analysis. One of them is the EMBO Practical Course “Methods for Analysis of circRNAs: From Discovery to Function”. This course will teach cutting-edge methods to identify and study this class of non-coding RNAs.

On-demand training

Our open access bioinformatics training offerings are more popular than ever. Here you also have the option to learn at your own pace with our online tutorials and webinars to make sure you stay up-to-date with the latest scientific techniques!

If you’d like to keep up-to-date with the latest news from the EMBL Course and Conference Office, please sign up to our mailing list. You can also follow us on TwitterInstagramLinkedIn or Facebook.

 

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Metagenomics and Ribosome Profiling Smartly Explained

The science behind molecular biology is advancing fast and scientists are eager to create and share new content. But the more content is being created, the harder it is to reach the desired audience. Therefore, the scientific community has had to come up with new attractive formats to help spread valuable scientific content.

One format that is currently popular is explainer videos, which combine both, audio and visual elements to untangle a topic. It has been proved that when one sense is activated we keep part of the information, but with the activation of multiple senses we can process and store far more.

We have therefore created explainer videos as part of our e-learning series.

“It was a great experience working on this project for our virtual courses. We are very fortunate to have Daniel Krüger, a former PhD student creating the graphics for these videos. This immensely improved the communication between the scientific advisers and the graphic designer because they speak the same language,” said EMBL Training Lab Manager Yvonne Yeboah, who came up with the idea of creating the explainer videos and led their production.

The first explainer video we are introducing deals with metagenomics, the genomic analysis of microbes by direct extraction and cloning of DNA, that allows studying communities of organisms directly in their natural environment.

“Our metagenomics course encompasses many different in silico and experimental approaches to understand and gain insights into microbial communities. Therefore, we thought that the visualisation of a video would provide students with an attractive overview that helps to connect and integrate all the aspects covered in the course,” explained José Eduardo González-Pastor, who organised the EMBO Practical Course: Microbial Metagenomics: A 360° Approach and acted as scientific advisor for the videos.

The second explainer video deals with the topic of ribosome profiling, a method that allows researchers to quantitatively analyse translation genome-wide and with high resolution. The video gives a comprehensive overview on how this technique works, what ribosome protected fragments (RPFs) are and what information we can obtain from them.

“Ribosome profiling is still an emerging technology. Therefore, it is great to have a concise summary that explains the method to students. I will certainly use the video for lectures and on my website,” said Sebastian Leidel and Jan Medenbach, both organisers of the EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling and scientific advisors for the video.

Visit EMBL’s YouTube channel to find more exciting scientific content.

 

 

 

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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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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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