How can conference exhibitors and sponsors help your research?

Matthias with several participants from the EMBL Conference: Transcription and Chromatin 2018. From left to right: Adam Whisnant (University of Würzburg), Melvin Jesus Noe Gonzalez (Francis Crick Institute), Matthias Spiller-Becker (Active Motif Europe), Gabriel Villamil (Max Planck Institute for Biophysical Chemistry). PHOTO: EMBL Events

Meet Matthias Spiller-Becker, Key Account Manager at Active Motif Europe. Matthias acquired his PhD degree in Biology at the Centre for Molecular Biology Heidelberg (ZMBH) where he focused on chromatin and the regulation of the centromere in Drosophila. Now in his 7th year at the company, Matthias is one of the most familiar faces at our conferences on transcription, chromatin and epigenetics – always friendly and welcoming. The popularity of the Active Motif booth at these events has not gone unnoticed, so we asked him what the secret to this success is and what tips he can give to conference attendees when approaching exhibitors.

How many events does your company exhibit at annually? 

In general we participate in about 50+ conferences and meetings/workshops each year, globally. But it’s not only the big and medium-sized conferences that are important to us. We often try to be present at more intimate, local events. Sometimes we sponsor chromatin clubs where only a couple of students and postdocs come together to share their latest research. And we also do a lot of tech talks where we discuss cutting-edge techniques to study gene regulation.

In the era of digital advertising, why do you still choose to be physically present at conferences?

Talking to people face to face changes EVERYTHING!

I think that’s a statement of holistic truth in life! You don’t trust companies in the first place – you trust people. You don’t buy your antibodies or reagents from companies. You buy from people!

And even more: you don’t give away your scientific baby (aka outsourcing your project) to strangers – you give it to people you know and trust. Sure, it happens a lot that folks in the lab search an assay on the web and inform themselves about alternatives on the market before making their “informed” decision, but that is often not the end of the story. It turns out that students and postdocs mostly need to get in touch with us at some point during the experimental process to further discuss their project. And surprisingly often, this first interaction happens at conferences as in “hey, are you working for Active Motif…I think we used your antibody. Can I ask you something?…”. Moreover, being physically present at the conferences is the only way to stay current with cutting-edge research. We discuss with people at their posters and also join the conference sessions in order to see the latest and future trends in chromatin and gene regulation research.

Apart from presenting their newest technology and developments, what else can exhibitors offer participants?

Networking, distraction, fun, and a “Staun-Anlass” (hard to translate that word but probably a reason to positively wonder nails it). Basically, you want to be the red bean in a jar full of green beans. You want to be distinct and recognised among others, leaving a positive impression that lasts.

During my PhD, I always liked companies that didn’t come around too stiff at conferences, but were more approachable”. As a student it takes courage to cross the invisible boarder at a company booth – you don’t want to end up in the web of the sales spider. You are afraid that the company representative might talk you into buying something you never really wanted.

I know this feeling personally – so I try to avoid that when talking to people. My daily goal (whether at a conference or elsewhere) is to be able to help people a bit further. Having a chat at the conference booth can do many things. For example, you may learn that the problem you are discussing with the exhibiting company is indeed a bigger one that’s not to be solved easily. That’s great information! You may also hear that your problem is actually easy to address and solve – even better! You may get info about peers in the same boat as you => networking!

And last but not least, you may simply want to use the chance of talking to people in industry to get an idea about their journey in life & science => career chat!

I try to offer all the above to the people that get in touch with me during a conference!

The Active Motif booth at the EMBO|EMBL Symposium: Metabolism Meets Epigenetics (2019). PHOTO: EMBL Events
What tips can you give participants on how to approach exhibitors?

DON’T BE SHY! Just go and talk to them.

Of course, you need to choose your battles. Often it helps to orient yourself first. Do you already know the company? Is there an overlap between your research and them? If not, just read their banners and roll-ups. Sounds trivial but many people don’t do that. A company would hopefully try to have the most prominent and distinct features of their capabilities written or otherwise sketched out on their banners. If you don’t find any overlap there, I would not necessarily approach them.

But beware: company roll-ups can be like lab websites. Some truths are stated, and some are hidden, so even if your fancy new technique is not mentioned there, as long as the company topic seems to fit your science, go check them out.

If you just want a pen or some chocolate but otherwise, they don’t interest you – simply tell them upfront. You will still get your sweets but honestly, how many pens does a single person need?! 🙂

Can you give an example of a mutually beneficial collaboration that has arisen at your booth through your presence at a conference as an exhibitor?

There are so many examples. It frequently happens that conference participants approach me and tell me that they have an issue with a given technique, mostly Chromatin IP. It turns out that talking them through the experiment step by step often yields at least one weak spot in the setup.

A classic is that people often use the same amount of antibody for ChIP, independent of the varying targets and the respective antibody clones they may use. This is (like many protocol-related “facts” in the life sciences) a dogmatic – or nearly a religious – topic. People can be determined to use “always 2 µg of antibody”. Then you ask them “but did it work when using 2 µg?” and they may need to admit that “no, it didn’t”.

This is a good example that talking with a person outside your own lab can help you to critically re-consider an established protocol, and see things from a new angle.

Another example is that some projects can truly benefit from outsourcing parts of it. Everybody does it in academia but they mostly call it a “collaboration”.

You can take it a step further and outsource parts of your work to a company that offers paid scientific services. This “commercial relationship” can truly boost creativity and assay development. A company that does ChIP-Seq as a paid research service for years will always see more model organisms, more common and uncommon obstacles and more antibody targets than any other lab working only on their own project.

What approach do you use to get into contact with participants?

“It’s just me, myself and I” LOL…

No, it’s not 100 % like that but mostly…you need to simply engage the people!

I try to see every interaction with a person as the most important one in my life at that specific moment. I tend to call that my “Dalai Lama approach”.

How else can you do it!? At Active Motif, we often use our chromatin-related T-shirts to break the invisible barrier between conference audience and the booth. People usually like nerdy science shirts and ours are no exception to that rule. I mostly play a game where people can win the shirts or at least have some distraction from the packed conference program. Often, I implement a little quiz session: people need to give me one or two lines about their research and I create a question around it. If they can answer it, they can play the game to win a shirt. This shows them that we belong to the chromatin community and they often feel more encouraged to talk about a given experiment or planned project.

Is there anything you always wanted to try out at a conference but didn’t do yet?

YES! In a perfect world, I would want to sit in a tweed jacket in my very British armchair, a boiling tea kettle next to me…people can sit down in my little chromatin tea room called “The Nucleosome” and have a relaxed chat around gene regulation and epigenetics with me, or do some networking with others.


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7 tips to successfully deliver wet-lab-based training courses

Are you planning a wet-lab-based training course but don’t know where to start? There are so many things that could go wrong! After 6 years as a training lab manager at EMBL,  I have seen it all. Here are some tips that could save you time, nerves and wasted lab consumables.

Our final meeting with the organisers and trainers of the EMBO Practical Course: Humanized Mice, to go over the finishing touches of the lab practicals. PHOTO: EMBL Events

1. Identify your main contacts

Whilst the course organisers are the experts with regards to subject and course content, they are often very busy and trying to get hold of them can be a difficult task. Most of the time they will appoint an experienced colleague in their lab to help with the more practical and logistical aspects of organising the course. These people are the key players for my job – it is generally with them that I organise the practical set-up, because they know exactly what is needed, and when.

2. Timing is everything

Trainers are always surprised by how much longer people need in the lab for things they are doing for the first time. From my experience participants need twice as long in the lab as people who do the experiment regularly. So have this in mind when planning the schedule for a course. If possible, perform dry runs to get a better feeling of how long some experiments really take, and then double that time.

3. Back up, Back up, Back up

Not every experiment that we run during a course will be successful, but it is not the end of the world if you have prepared some back-up samples. The course days are already long enough – nobody wants to miss dinner to repeat a failed experiment, and troubleshooting is also a valuable lesson for the participants.

4. Everything clear?

Giving clear, coherent instructions is one of those things that sounds easy to do but in real life can actually be more complex, especially in a course setting. Some trainers don´t feel comfortable raising their voices to get everyone’s attention, meaning they have to repeat every single thing over and over again, which can cost valuable time.

5. Having good relationships to the main lab

You can plan a practical down to the smallest detail, but someone might still forget to tell you things like, “Oh, your incubator is actually too small to fit the instrument in there!” or “Oops! All my cells died over the weekend!”

In these situations it is key to have a good knowledge about who is doing what in the main lab and is willing and able to help out. Luckily my cheerful personality and baking skills have saved the one or other practical!

6. P p p poker face, p p poker face

As much as I love to have everything planned ahead of time, often this is not the reality when planning courses. Instructors often travel from abroad, and by the time they have arrived on-site, there are so many things that could go wrong. I refer to the first couple of days before the course starts as the “headless chicken mode”. But thanks to the experience and skill of our trainers, we always manage to overcome any difficulties that arise and are able to deliver our courses professionally – and the participants aren’t affected in the slightest!

7. Always be prepared for the unexpected

“It was working fine until this morning!”- This is one of the sentences nobody wants to hear during a course, but that is just how it is in the lab sometimes, and the training lab is no exception. You need to be a flexible thinker and be able to find a solution so the course can go on. Find a replacement instrument, shift the schedule around until the problem is solved. If there is no quick fix come up with another activity and cover the topic theoretically.

But to be honest in these cases I am so happy that I am doing this job at EMBL— because the EMBL people never let you down.

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Using chemical biology to expand the druggable proteome

Gerard Drewes
Head of Science, GSK Cellzome, Germany

In 2020 the EMBL Resource Development team and  industry partners of the EMBL Corporate Partnership Programme will bring together academic and industrial scientists with interests in chemical biology, chemogenomic libraries, pharmacology, medicinal chemistry and bioinformatics for the EMBL Conference: Expanding the Druggable Proteome with Chemical Biology (5-7 February 2020).

We spoke to co-organiser Gerard Drewes from GSK Cellzome about how chemical biology is helping to expand the druggable proteome.

How would you define the “druggable proteome”?

This is the fraction of our >20,000 human proteins that can be functionally modulated by a drug. Drugs can be small molecules or large molecules such as therapeutic antibodies. Estimates of how many proteins are “tractable” vary widely, I think there may be around 5,000. Only a subset of these 5,000 would be “druggable” which means that modulating them with a drug will also have a therapeutic benefit.

How are advances in chemical biology helping to expand the druggable proteome?

Small molecules are still the main modality for intracellular targets. Deep pockets, typical for enzymes, are more easily tractable than shallow pockets typical for protein-protein interactions. Chemical biology has developed tools to explore different types of pockets. I am excited in particular by the potential of DNA-encoded libraries, and small fragment approaches with covalent modes of action. Some of these compounds will just be “binders” but these can be made into target degraders as PROTACs.

How can these advances help our understanding of disease biology?

If we had more chemical probes, we could use these in a standardised, controlled way to interrogate target function in cell-based models, organoids, and in some cases animal models. Yes, we have gene editing now, but that is not the same as pharmacological modulation.

We also need in vitro models that translate better to in vivo. Our old immortalised cell lines won’t do, we are going to need more work in primary cells, organoids, etc.

What are the main challenges facing scientists in this field?

Lack of standardised probe sets. Bad probe compounds, e.g. with bad selectivity, are still used and wrong conclusions drawn.

Lack of translational in vitro models.

Why is it important to bring industry and academia together to discuss this topic?

Academia brings creativity, agility, fast progress of new ideas and concepts, thinking out of the box.

Industry sometimes lacks these but knows how to develop a compound into a drug, which requires a host of technologies not readily available to academia. Also, industry requires a new generation of drug targets with better validation, and historically targets are often discovered in academia. Once a target hypothesis exists, academics and industry should ideally collaborate to figure out how to drug it.

What will be the main highlight of this conference?

I see many but still hope to be surprised!

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Generating meaningful images – a report from Seeing is Believing 2019

By event reporters Liz Haynes @actin_crazy and Stephan Daetwyler @Daetwyler_St

Seeing is Believing event reporters Liz Haynes & Stephan Daetwyler, PHOTO: Liz Haynes/Stephan Daetwyler

The field of biology owes some of its most compelling discoveries to careful visual observation. From Van Leeuwenhoek’s use of new microscopes to describe microscopic “animalcules” in the late 1600s, to Ramon y Cajal’s pioneering 19th century work illustrating beautiful and complex neuronal architecture. Images inspire us, help us generate new hypotheses, and shed light into the tiny worlds yet unexplored. Indeed, these observations uniquely help us understand the structures and dynamics of life, something that would not be achievable with approaches like biochemistry alone.

The images are only as valuable as the amount of information that we can deduce from it.

Generating meaningful images, however, is not an easy task. There have always been limits to what we can observe, due to the properties of the sample or the techniques that we can apply to it. These are the boundaries that microscopists seek to push. A successful imaging experiment requires an amenable sample, a contrast agent to reveal the structures of interest, and a microscope that is capable of capturing an image at a relevant scale. Moreover, the images are only as valuable as the amount of information that we can deduce from it. Therefore, image storage, accessibility and analysis are crucial. Each one of these steps offers opportunities for optimisation and new technologies.

Co-organiser Jan Ellenberg opens the Seeing is Believing symposium, PHOTO: Liz Haynes & Stephan Daetwyler

The EMBO | EMBL Symposium “Seeing is Believing: Imaging the Molecular Processes of Life” (9-12 October 2019) presented us with exciting new developments in all of these fields, coupled with a drive to make new progress available as quickly as possible to the community through preprints, open-source initiatives, and resource sharing.

Advances in sample preparation

At the heart of every imaging approach is the sample. Even the best microscope is ineffective with dim or improperly prepared samples. At Seeing is Believing, we saw an emphasis on using expansion of samples to help overcome the resolution limits of microscopy and solve some traditionally difficult problems. In particular, we were impressed with expansion-based approaches to study centriole structure (Paul Guichard, Ultrastructural Expansion Microscopy) and resolve microtubules tightly packed within axons (Lukas C. Kapitein). By far, the biggest emphasis in sample improvement was on the development of new fluorescent probes and biosensors. Kai Johnsson presented design strategies for the improvement of live cell dyes, and introduced new MaP dyes that are SNAP and HALO compatible, and importantly require no wash to clear unbound probe. Periklis Pantazis presented a mechanosensor based on the Piezo1 stretch activated ion channel, allowing users to visualise mechanical stress within a live cell. Atsushi Miyawaki wowed the audience by meeting the challenge to “be better than a firefly” with a new variant of luciferase named AkaBLI, which his lab generated through targeted evolution. This improved luciferase allowed them to visualise neuronal activity within freely behaving mice and marmosets.

Advances in microscopy

New imaging methods on show at Seeing is Believing, PHOTO: EMBL Events

The features of our microscopes directly determine which questions we can address. Seeing is Believing highlighted exciting new development in building cutting-edge microscopy tools. Reto Fiolka presented a novel single-objective light-sheet microscope enabling imaging of live cells in microfluidics devices or 3D environments with 200 nm lateral resolution. Kevin Dean complemented novel light-sheet development by presenting an axially swept light-sheet microscope ideally suited for all clearing techniques that provides an unprecedented field of view enabling whole tissue imaging with sub-micron resolution. With her imaging approach, Alexandra Pacureanu surprised the audience with how X-ray holographic nano-tomography is capable of resolving the fine, dense and complex neuronal circuitry in large tissues or even organism providing a new route to understand how the nervous system processes information.

Nobel Prize winner Stefan Hell spoke on how to attain 1 nm resolution with super-resolution microscopy, PHOTO: Liz Haynes & Stephan Daetwyler

Further impressive advances were presented in fast volumetric imaging (Lars Hufnagel, light field imaging) and high-resolution imaging, e.g. MINFLUX by Stefan Hell, correlative EM imaging by Harald Hess and Lucy Collinson, GI-SIM/LLS-SIM by Dong Li, and 3D-STED deep in a tissue by Joerg Bewersdorf.

Advances in data analysis

All acquired data is meaningless if we cannot extract information from it. At Seeing is Believing, it became obvious how artificial neuronal networks have become important for image analysis. Applications range from segmentation to denoising an image (BGnet, W.E. Moerner and Noise2Void, A. Krull/Florian Jug). Particularly, the convolutional network architecture U-Net has become an important tool. To provide a user-friendly environment to apply those state-of-the art image analysis tools, Anna Kreshuk presented the iLastik platform as an easy to use tool. A new fundamental approach to handle, visualise and process the large amount of data coming from the microscopes was presented by Ivo Sbalzarini. Instead of using pixels to save an image, adaptive particles approximate the image content. Furthermore, Gaudenz Danuser gave a thought-provoking talk on how current perturbation-based approaches in cell biology can mislead us in our analysis. Danuser emphasised that the observed phenotype from a perturbation of a system (e.g. loss of a protein’s function) is not equal to the real function of the gene. For example, cutting a wire from the battery to the electronic board of radio would lead to the “phenotype” loss of sound. However, the function of the wire was simply to provide power to the radio, not to produce sound! As a better perturbation-free alternative, Danuser introduced a concept used in econometrics known as Granger causality.

Advances in biology

All of these new developments culminated in impressive new insights into biological processes. There were many talks on mitochondria and endoplasmic reticulum dynamics revealed by novel live-cell super-resolution techniques. Suliana Manley gave one of the most intriguing of those talks, on modes of asymmetric and symmetric mitochondrial division.

Co-organiser Jennifer Lippincott-Schwartz presents how RNA moves around the cell and is translated at different locations, PHOTO: Liz Haynes & Stephan Daetwyler

Jennifer Lippincott-Schwartz also gave a stunning presentation on how RNA granules can hitch a ride through an ANXA-11 mediated connection to lysosomes, and how ALS associated mutations in ANXA-11 break this connection. Furthermore, an intriguing new mRNA reading frame sensor (Moon and Sun tags) was presented by Sanne Boersma of the Tanenbaum lab to understand stochasticity of mRNA translation.

To conclude, the field of microscopy has grown so much that some may feel we have solved all the theoretical problems, and only engineering challenges are left – hardware improvements, new materials, new engineering solutions. At the closing dinner of the conference, however, Atsushi Miyawaki from RIKEN beautifully summarised how he felt about the future of microscopy, and of Seeing is Believing. Standing in the banquet hall of the Heidelberg Castle, he told us that castles in Japan remain unfinished. This state of incompletion is not due to any fault of the architects, but a feature of beauty, as it was believed that things that were incomplete had room to grow, and that growth is valuable. No matter how high our achievements are in the field of microscopy and image analysis, there will always be unforeseen avenues of growth. Attending Seeing is Believing has hopefully prepared us to follow those avenues, and to share what we find so we may all grow together.

For a more comprehensive summary of all talks presented at Seeing is Believing, and to get links to preprints, publications, and resources, visit our blog at https://seeingbelievingweb.wordpress.com/

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If there is no record of it, did it really happen?

World Day for Audiovisual Heritage #WDAVH, #audiovisualheritage

EMBL Archivist and guest blogger Anne-Flore Laloë, PHOTO: EMBL Photolab

Is there a sound from your childhood that just carries you back? For me, one of those is the opening credits of the Tintin animated show. That’s why I’m really grateful that I can click on a link and find it online and travel back in space and time pretty much at will.

As an archivist, though, I am acutely aware of the work that goes behind maintaining access to the world’s audiovisual heritage for future generations. Think about all those films, sound recordings, radio and TV programmes that are created everyday and capture unique records of activities, events and exchanges. But these exist in many formats, from wax cylinders to Super 8 films, .mp3 files or VHS tapes, and require specific hardware (such as VCRs, projectors, etc…) or software (like MPlayer, QuickTime media player) that can render the recordings.

In the course of its activities, and in particular its training activities undertaken by the EMBL Course and Conference Office, some audiovisual material might be created, most likely recordings of talks. This is a great way to create a trace of the meeting that can complement abstract books in an engaging format. It then also makes it easy to share these recordings and help disseminate knowledge further when some of these are made available for all to see through various channels, such at the EMBL YouTube “Keynotes @ EMBL” playlist. Even if you weren’t at the event, you can join in long after they have ended.

Nowadays, these videos are likely born-digital, straight into a format that you can watch on your laptop. But in earlier times, this is what you might have created:

Or even, earlier, this:

 

Luckily, when such things end up with me in the EMBL Archive, I can contact my colleagues in the EMBL Photolab, our in-house AV department to create digital files of these. They have the equipment that helps migrate the contents of these films into digital formats.

But whether these are born-digital or migrated, they all need to be preserved to ensure ongoing access to them. Because indeed, nothing is ever preserved – it is only ever being preserved.

Unfortunately, though, it happens that things are lost… With these discs, I have not been so fortunate and the video content contained on this CRVdisc could not be retrieved.

So, next time you are at a conference, and there’s a film crew, or when you are being interviewed on the radio – think about these traces you are leaving behind, that will traverse time so that future generations can look at your work and hear your voice in new formats, on machines we can’t yet fathom, and through these, make a connection with you as an individual presenter.

Links:

EMBL Archive: www.embl.org/archive
UN World Day for Audiovisual Heritage: https://www.un.org/en/events/audiovisualday/

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