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.

 

 

 

Follow us:

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.

 

Follow us:

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

Follow us:

EMBL-EBI Training – 1 Year of Virtual Courses

A year ago today, we kicked off our first virtual course; Starting single cell RNA-seq analysis. This course was originally planned to take place onsite at EMBL-EBI Hinxton however, due to the pandemic we swiftly had to move this to virtual. Little did we know that virtual courses would still be going a year on. We have successfully hosted just over 18 virtual courses. Looking ahead to next year, we are hoping to continue with a virtual aspect of our programme. Below we hear from three team members on virtual events and their experiences.

PHOTO: Group photo from the starting single cell RNA-seq analysis course.

 

PHOTO: Sarah Morgan

Sarah Morgan 

Sarah has been the Scientific Training Coordinator since 2012, she manages the EMBL-EBI external user training programme, and leads our team of Scientific Training Officers. As you can imagine a year ago was a very busy time for Sarah moving a full programme of courses to virtual. She tells us her thoughts and experiences of virtual courses

How did you manage the team moving into a virtual environment? 

The first thing I did was check that all my team were fine working from home and getting to know their home situation – juggling children, partners, parents, pets, they had lots to deal with alongside trying to find new ways to keep delivering our programme! The move to home working was incredibly quick, so there was lots to deal with. Trying to get regular catch-ups across the team was incredibly important – I missed my daily catch-ups with our Events manager Charlotte Pearton (who I normally share an office with), and we needed to be in contact very often in those early days.

How did you manage moving an onsite course to virtual within a couple of months? 

We were lucky in that we had some experience of delivering training virtually, but not to the extent that we have done over the past year. We quickly set up a small task force to plan out how we could approach delivering the courses, thinking about what platforms to use, how we would give trainees compute access, what additional support they might need; and how to encourage and support our trainers to do their job in this new environment. We spent a lot of time communicating with participants, trainers and colleagues across EMBL in the early days, and were generally met with very positive responses. The team as a whole worked brilliantly to bring those first few courses online. The support and enthusiasm from everyone is what enabled us to move so quickly, along with fantastic ways to bring the virtual training alive.

How has your job changed with the team moving to virtual courses? 

I think I re-worked our training calendar about once a month from March onwards last year! Many parts of the job have not really changed that much – I still work closely with my training officers and the rest of the training team to get our courses up and running, monitoring how the courses are running and looking to improve where we can. What has changed is the travel and meeting with colleagues from across the world – though I don’t miss airports at the moment!

What do you miss most about on-site courses? 

Getting a chance to see the trainees in one big group and hearing the buzz of a course in action. When courses are running in our building at Hinxton there is always a nice hum of activity at coffee and lunch breaks with people chatting and getting to know each other. I miss seeing that and getting a chance to pop down and say hello.

What is something that can never be as good as during on-site courses, in your opinion?

Dinners at Hinxton Hall (and the tea-time biscuits with afternoon coffee!).

How do you see the future of EMBL-EBI Training courses? What are your hopes and thoughts? 

I would like to see a return to on-site training, but virtual courses are very definitely here to stay. We have seen some major advantages of running virtual courses, and I think looking ahead the EMBL-EBI programme will definitely be a mixture of both approaches.

 

PHOTO: Marina Pujol
PHOTO: Marina Pujol

Marina Pujol 

Marina joined the team in June 2018 as one of our Events Organisers. Her focus is on our onsite and virtual training courses as well as assisting with the delivery of events for the CABANA project. Marina was paramount in the planning and delivery of the Starting single-cell RNA-seq analysis course in 2020 and below she shares her experiences, lessons learned, and tips for organising a virtual course.

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

The first few months that we were organising virtual courses I thought that there wasn’t much difference between an onsite and a virtual course, however looking back at what has now been now 1 year, I have come to realise that it’s a completely different world.

Back when we worked on face-to-face courses we would deal with the logistics and organisation outside the training room, now we are sitting with them during the training too. This means our role has evolved and we have had the chance to understand and help to improve the trainers and trainees’ needs during that part of the course as well.

Events’ Organisers in the EMBL-EBI Training Team are nowadays working hand in hand, more than ever with the Scientifics Training Organisers. We are now invited to participate in the pre-organisation meetings with trainers and can provide advice thanks to our vast experience on virtual courses during the last year.

Overall, I believe this experience has enriched our job and is definitely something I would love to be part of in the future despite going back to face-to-face courses.

Top 3 tips to keep in mind while organising a virtual course?

  • Make the instructions on how to access the course are as clear and easy as possible, for example, zoom links, handbook link and programme information.
  • If possible, have at least two big screens to work like a pro, a speedy mouse, and a nice audio setting. Events’ Organisers have to juggle with at least 3 different platforms while hosting a course.
  • Surround yourself with amazing colleagues and team players that can give you a hand whenever you need it. And don’t forget to have something to drink and snacks available.

What is the biggest lesson you learned about organising virtual courses?

How grateful people are to be able to access training without having to travel, which would have resulted in higher costs for them meaning they might not be able to attend.

When we have delegates that are in a completely different time zone, and you can see the effort they are making to be awake and participate during the course – this makes me realise the importance that our training has for them and that we are lucky to contribute and help, even in the smallest part.

The one thing that you wished someone had told you before organising your first virtual course? 

How exhausting it could be! Especially during the first courses, when everything is new and you still don’t have the hang of it. I remember being really nervous at the beginning, a lot of new information was in our heads. Now it has become the norm and it’s nice to see the progress we have made.

How does the contact with speakers, organisers, and participants differ from on-site courses? 

The contact before the course is more or less the same, as we usually contact them only by email. However, once the course is running the dynamic changes quite a bit. You no longer can have that random conversation with them on their arrival or during coffee breaks, which I miss.

What is something that in your opinion is better about virtual courses?

The fact that our training can reach people from all over the world now, offering cheaper fees and even sometimes free courses that have been streamed live online. An ideal future would be to have both, virtual courses and face-to-face courses available, so more people could benefit from our training.

What do you miss most about on-site courses?

I miss the interactivity with trainers and trainees. Knowing how they are feeling daily, being able to help them with any query during the day, and having that personal contact. Although we offer a range of virtual networking activities we can never replace in-person interaction. It is also nice to see the relationships created at each course with the delegates, I believe good friendships have started in our courses.

How do you see the future of EMBL-EBI Training courses? What are your hopes and thoughts?

I would love to be able to offer both, on-site courses and virtual courses, so you have the opportunity to visit us onsite and have that face-to-face interaction but also you can choose to stay at home and have a great learning opportunity at less cost.

Hybrid at the moment is an unknown type of course for me, however,  something that we are exploring in the team.

 

Alexandra Holinski

PHOTO: Alexandra Holinski

Alexandra (Alex) joined the team in 2017 as a Scientific Training Officer and is responsible for designing, developing, and delivering several on-site and virtual courses. Alex together with experts from the BioModels team ran the Mathematics of life: Modelling molecular mechanisms virtually in October 2020 which, was the first edition of this course. This is running again in September and is open for applications until July, find out more here.

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

Organising a virtual course is different from organising an on-site course, a virtual course allows for more flexibility as far as the delivery of training is concerned. An example of this is the talks during a course, these can be pre-recorded and provided to course participants ahead of the course, watched during the course, or delivered live. The practicals can be run synchronously or asynchronously. This can be both exciting and an organisational challenge, especially as not one format perfectly suits all participants & trainers, and works for the content we deliver. The “how-to” has to be considered carefully ahead of the course so that the participants can have the most efficient virtual learning experience and both participants and trainers feel comfortable in the virtual setting.

How does the contact with speakers, organisers, and participants differ from on-site courses? 

In a virtual course, we are missing out on the informal chats with participants and trainers over coffee, lunch, and dinner. These have always been helpful in an on-site course, to get immediate feedback about the training from participants and therefore identify challenges and reacting to these. In a virtual course, we are contactable via Slack, Zoom, and email but it is more challenging to notice certain issues.

How has your role changed with moving to virtual courses?

The overall role has not changed immensely, I still develop training programmes together with scientific experts and support trainers in developing and delivering their training. However, of course, the focus and how we do things has changed. Also, I am getting more involved in delivering training on my own, and I quite enjoy this in a virtual setting.

How does the course programme differ from onsite courses?

During a virtual course, we start the days with short morning challenges like quizzes, so that the participants start working and chatting with each other and not feeling isolated in front of their screens. In an on-site course, this happens automatically over morning coffee. Instead of an on-site poster session, we have flash talks that allow the participants to present their research and network with each other. Also, I have realised it is important to ensure that breaks are long enough for everyone to get away from the screen and stretch – this is similar to an on-site course but I feel breaks are even more important in a virtual setting.

What is the biggest challenge of virtual courses?

A virtual course is more challenging to create a sense of community, which encourages efficient collaborative learning and networking. In a virtual setting, there is often the danger that participants might get lost and feel isolated. However, there are ways that we can work to avoid this. In the virtual Mathematics of Life course in 2020, we ran group projects, in which we organised participants in small groups into breakout rooms and gave them a project to work on during the week. These groups were supported by trainers who jumped in and out of the breakout rooms. At the end of the course, the groups presented their results to all of the course participants. The participants worked very collaboratively and highly appreciated the group work, which was reflected in the feedback survey. We have also learnt that some participants continued working on their projects after the course had finished. In addition, we also ran morning challenges that participants were asked to work on together in breakout rooms. The flash talks during the week enabled scientific networking.

What is something that in your opinion is better about virtual courses?

Virtual courses can be more inclusive than on-site courses. We can easily reach people worldwide, including scientists from low-to-middle-income countries (LMIC). Virtual courses can also be easier to attend for scientists with family or caring responsibilities.

Also, since we moved to virtual courses, I have delivered more training on my own and enjoy this. I feel very comfortable with delivering virtual training and love being creative and developing training activities like discussions and quizzes using a range of interactive virtual tools.

What do you miss most about on-site courses?

I am missing the non-virtual informal chats with participants and trainers. It is great to get to know so many people from all around the world and chat with them in person.

How do you see the future of EMBL-EBI Training courses? What are your hopes and thoughts? 

I am sure we will return to on-site training courses, but I do not think that virtual courses will disappear. By running both virtual and on-site courses we will be able to satisfy the diverse learning preferences of our trainees and allow more researchers to access our training.

Interested in joining one of our virtual courses, check out our upcoming courses here. 

Follow us: