Sparkling Scientific Ideas, Lovely People and Food – EDBC 2019

By June, Predoctoral Fellow at Sharpe Lab:

How to combine sparkling scientific ideas, lovely people and food? Throw a conference in Alicante. The European Developmental Biology Congress 2019 was exactly that.

Six of us from EMBL Barcelona overcame a long journey consisting of cancelled train and a delayed flight, right in time for the first plenary lecture given by Nipam Patel (Woodshole, USA), on Hox conservation and butterfly patterns.

EMBL suffering through the longest queue in Sants station

The conference overall addressed exciting biological questions, such as:

How are the cell identity/fate determined and regulated? How do individuals cells ‘know’ their organ shape? How do biological patterns regenerate in robust manner?

To the first question, Meryem Baghdadi (Institute Pasteur, France) suggested that quiescent stem cells, which are the cells that no longer stay in the cell cycle, is not a ‘passive’ state but maintaining its own niche through Notch-regulated microRNAs.

To the second question, James Sharpe (Head of EMBL Barcelona 🙌) discussed how convergent extension, the concept that involves both cell migration and cell intercalation, elegantly explains the shape of the limb bud.

Yonatan Stelzer (Weizmann institute, Israel) presented exciting single-cell RNA sequencing methodology, which incorporates fine spatial and temporal information during gastrulation stage. The team achieved high temporal resolution by assigning individual embryos with molecular indexes, followed by cell type & transcriptional similarity analyses.

The highlight of the session came when James Cotterell, a postdoc of the Sharpe Lab, gave a short talk under the title of “Endogenous CRISPR arrays for scalable whole organism lineage tracing”.

James Cotterell, during his talk on CRISPR

And the poster session followed – EMBL had six posters: Four from Sharpe lab, One from Ebisuya lab and one from Trivedi lab.

Some of us found a time for a tiny excursion to the heart of the city, as you could see from the refreshing view from Castell de la Santa Barbara.

The last night of the conference was accompanied by the Michelin star winning-chef’s vegetarian Paella – as keen EMBLers, we were able to get a special photo with her, and a few signed bottles of the finest quality olive oil. I’ll open one when I want to revisit the memories of Alicante!

 

New beginnings: Scary adventures that end up being the best decision you made

A day to remember

On a not so particularly special Wednesday in December of 2017, I received a little email from EMBL confirming that I had been accepted for the position of Purchase and Budget Officer, needless to say from that moment onwards it became special as this meant a complete change in my life. What this meant was packing up and leaving my town, my country, starting all over from zero in a different country, city and culture and a completely different field of work. As exciting as it sounded, I admit it was equally scary.

After reading and re-reading the email and telling my family and rejoicing…..came the questions: “what now?”, “what am I doing?”, “is this the right thing for me?”, “what if I don’t fit in?”, “what if the city is too much?” To be very honest it was like that the rest of the month, going from the excitement of starting something new to the fear of the exact same thing. Luckily, it got a lot easier and smoother once I started talking to my future admin colleagues asking for help and tips on accommodation and life in Barcelona so I got to relax a bit.

But then…..

My first days and first contacts with Barcelona and EMBL

I remember it was a raining and slightly cold February day when I arrived to Barcelona, and I was trying to get to two oversized bags (that later turned into 4) to get to my temporary accommodation. What an adventure that was. From that moment on, I had 2 months to learn how the real estate market works in Barcelona, find a place I liked and could afford and move….

It all sounds easy, straightforward and organized right? Well…..not so much so in a very dynamic city as Barcelona. Here I found that even if you´re not convinced by the flat, but you kinda like it, you should either way scream “I´ll take it”, “hit” the real estate agency with piles of documents attesting your capacity to afford the place, because then… if not it gets taken by someone else.

Stressful? Yes, very much so, but I like to look at the positive side of things and so took it as a challenge to get used to the city, experience its neighbourhoods, its little streets and alleys. During the two months of real estate investigation, I got to enjoy the city, find favourite spots (where I still go to), restaurants, bars and found that Barcelona is a vibrant and alive city.

The people here also helped me feel like welcomed and included, from the colleagues at EMBL to the people I interact with everyday buying fruits and veggies to post office and neighbours.

The best thing though are the colleagues I met here who are always more than happy to show me a bit of what they’re doing, of their (simplest) experiments, lab terminology, to explain what each equipment that they need to buy is doing and why the need it. And who also, unknowing my non-existent talent for beach volleyball, have included me in the unit team which has been a blast.

Beach Volleyball Tournament 2019

A year and half of EMBL and Barcelona

Decorated Streets during Festa Major de Gracia 2019 (Grumpy Broccoli)

Well over a year passed since I first came here, I am more settled. I believe I am beginning to feel Barcelona as home.

I experienced normal flat related issues (flooding, appliances not working, electricity going out), normal lab related adventures (suppliers not delivering what we requested, not communicating when they deliver large equipment, importing bureaucracy mayhem and many more).

At work, as an admin member of staff, I very much still need guidance from my colleagues with lab related issues, but I am happy to have all of them here to ask for help, but things are going a lot more smoothly.

Outside work, I am thankful for every single day  in which I am be able to enjoy what Barcelona and Catalunya have to offer from neighbourhood parties (Festes Majors) and flower festivals (Girona) to competitions of Castellers (in Tarragona).

It has been a great journey so far and what I feel like is only lucky that I am getting to have this experience. I don´t think I fully grasped what it would mean to move to a different country with my work until I actually did it, I think I didn´t fully understand what it would be like to work for a research institution until I actually started it, but it is all worth it and even if it was very scary in the beginning it did end up to be one of the best decisions made.

 

Andra

Barcelona hosts the Limb Development and Regeneration Biennial

Two years have passed since last Limb meeting, which took place in Edinburgh. This year’s conference was hosted by EMBL Barcelona, located in the Barcelona Biomedical Research Park. James Sharpe (EMBL Barcelona) together with Marian Ros (CSIC-SODERCAN) and Miguel Torres (CNIC) organized a four-day meeting bringing together experts in the field of Limb Development.

The conference was divided in five specialized areas (Gene Regulation, Patterning and Regeneration, Morphogenesis and Modelling, Growth and Evolution), and hosted almost fifty talks and two poster sessions (including 64 posters).

Miguel Torres and Marian Ros announcing the poster and flash talk winners

Gene Regulation

Thanks to genome editing (CRISPR/CAS9), human mutations can be introduced in mice to understand the molecular interactions that give rise to limb-related diseases such as polydactyly or Nail-Patella Syndrome (NPS). Len Pennacchio and Kerby Oberg presented their work on this topic.

Single cell transcriptomics techniques are being used to investigate cell fate determination and differentiation in a spatio-temporal fashion during limb development and regeneration.

James Sharpe, Head of EMBL Barcelona, presenting LIMB-NET project to the audience

Patterning and Regeneration

During development, diffusible signals (morphogens) are known to generate gradients that pattern cells along embryonic axes. Nevertheless, since cells from the limb are in constant rearrangement over space and time during development and regeneration, the signalling pathways coupled with morphogen interactions are not completely understood at every embryological stage. Irene Delgado (CNIC, Madrid), Malcom Logan (King’s College London, UK) and Elly Tanaka (Research Institute of Molecular Pathology, Austria) gave some insights on this topic.

Morphogenesis and Modelling

During limb development, cells are exposed to constant molecular signalling but also cell interactions, tissue rearrangements, movement and mechanics. Thanks to improved imaging techniques and computer modelling, we have a better understanding of how cells interact with each other in order to shape the limb. Highlighted talks by Paula Murphy (Trinity College Dublin, Ireland), Jerome Gros (Institute Pasteur, France) and Miquel Marin-Riera (EMBL, Spain) summarized perfectly this section.

Growth

Cell proliferation and organisation are involved in tissue growth in order to pattern and shape bigger structures such as organs and later on full organisms. How proportions are maintained during these processes is still unknown.

Hanh Nguyen (CNRS, France) talked about using imaging techniques to achieve cell linage reconstruction of pectoral fin from Zebrafish at very early stages (28 to 48 hours post fertilization), exactly when embryos grow from 2D to 3D tissues during development.

Neil Vargesson giving his talk about Thalidomide effects on vascular system

Neil Vargesson (University of Aberdeen, UK) talked about how Thalidomide, a drug used to deal with nauseas in pregnant women during 1957 that produced limb malformations (phocomedia) to new-borns,  affects limb development by avoiding the proper formation of the vascular system during limb development.

Evolution

Fin to limb transition it has always been an intriguing question from an evolutionary point of view. Joost Woltering (University of Konstanz, Germany) investigates genetic markers for the anterior-posterior and proximo-distal axis of the lung fish fins, which are anatomically very different from the ray-finned fish and closer to the tetrapods.

Karen Sears talking about limb morphology and diversity in bats

Other scientists such as Karen Sears (University of California, Los Angeles) and Kimberly Cooper (University of California, San Diego) focused their research in using mammals with different limb morphologies such as bats and bipedal jerboa Jaculus jaculus to understand the regulatory changes in the genome of these species in the evolution of gene expression and limb morphology.

Poster session

The poster sessions were a success and around 20 scientists presented their research in flash talks.

Scientific atmosphere at poster sessions

Science is evolving fast thanks to new techniques and this year’s Limb meeting was at the forefront of it discussing projects related to CRISPR/Cas9, single cell transcriptomics and live imaging.

 

A Zebrafish Fairy Tale

(Science Communication from the very beginning) 

 

Mom:  Uff… that was tough! I was running to set up those fish crosses for the experiment to be able to get to the school bus stop on time to pick up my kid. I have just beaten my record, 15 minutes by bike, not bad! Sometimes it is just so difficult to distinguish between the female and male fish… especially when I’m in a hurry… Anyway, let me see if I have the dinner ready… ah, there she is! Tonight, if she doesn’t ask for Little Red Riding Hood I will explain her about my fish, she will love it. 

 Mom:  Come on Sweetheart, it’s time to go to bed.

Kid:  Mummy, first you have to explain a fairy tale!

Mom:  Why don’t you explain what you have done at school today?

Kid:  Hmmm… we went to swim. Now it’s your turn, what have you done at your school?

Mom:  I was with my fish again.

Kid:  The ones with the black and white stripes!

Mom:  Yes, the zebrafish.

Kid:  Were you playing with them?

Mom:  Actually yes, we were playing Mom and Dad. I selected couples; I put one girl and one boy into a hotel room. During all night, they will be close to each other and tomorrow morning, probably they will have babies.

Kid:  I was playing that with my friends today!

Mom:  And how many babies did you have?

Kid:  One, I was giving her baby food.

Mom:  So just imagine, those fish can have up to 200 babies!

Kid:  Wow, they must eat a lot! Do you give them food?

Mom:  It’s not me who is giving the food, but a colleague of mine. He knows a lot about what they like to eat. He gives the adults shrimps.

Kid:  Oh, I like shrimps! Do they suck their head as we do?

Mom:  Hahaha, they just eat them as a whole. And just imagine, they call this food Artemia.

Kid:  Is it Hungarian?

Mom:  I know it’s a difficult word, but it’s not Hungarian. Going back to the babies, they don’t eat shrimps on the first days! Their Moms prepare them a bag full of baby food and they eat it alone. Wait, I can show you some pictures I have done of them!

Kid:  Why are they green or red?

Mom:  Mmm… at my school we made some part of these fish fluorescent, so we can see them in the dark, just like in medusas.

Kid:  Like the star-stickers on my ceiling! When you switch of the lights, they shine!

Mom:  Yes babe, you are such a clever girl!

Kid:  Mummy, I want to have a Zebrafish at home, may I?

Mom:  Dear, we already have a cat. Besides that, these fish are not originally from here, they might not be happy in our flat. They were brought here from far away, from India, for example.

Kid:  Isn’t it where your teacher comes from?

Mom:  Yes.

Kid:  Did he bring them here?

Mom:  No. Other people brought them here.

Kid:  Mom, I want to see your fish! May I go with you tomorrow to your school? Pleeease…

Mom:  No dear, it’s impossible. Actually, you have seen several fish in your life. Do you remember when we went to the Aquarium with the grandparents? And during summer holiday when we went snorkeling? Or on the weekends when we go to the market to buy some for lunch?

Kid:  But those are dead! That lady cuts their fins off!

Mom:  Well, at my school we do that as well and they are alive.

Kid:  What?

Mom:  We just cut a tiny little piece and it grows back in 3 weeks. This is the only way to take blood from Zebrafish because they are much smaller than the ones you see at the market. Sometimes it is needed, like when you go to the doctor.

Kid:  Tomorrow I will explain all this to my friends, they will be amazed!

Mom:  That’s a good idea! You can even prepare a drawing. But for that now you should sleep and rest a bit. Close your eyes, have a nice dream! Good night!

Celebrating HOLI: A blend of cultures @EMBL Barcelona

 

Photo credit: Joan Gorro and Montse Coll Llado

In its nascent stage, our rapidly growing EMBL site in Barcelona consists of people from 13 different nationalities, speaking a multitude of languages. We often find ourselves curious about each other’s cultures, so we thought – what could be better than celebrating festivals together in the most authentic way?! On April 6th, 2019, we came together to celebrate the Indian festival of Holi (marking the beginning of spring) in the beautiful town of Begues, situated in the Garraf massif, south-west of Barcelona.

According to legends, Holi signifies the victory of good over evil. However, in modern times, it is a symbol of inclusiveness, friendliness, love and unbound joy.

Amidst the uncertainty of weather prediction, people joined with their families and young kids with great enthusiasm. With a mix of traditional and bollywood music, Indian food and vibrant colors, we enjoyed ourselves to the fullest! While this was a first Holi experience for most of us in the unit, in the coming years, we look forward to many such cultural events inspired by traditions across the globe!

Illustration by Aina

The festive spirit left a lasting impression on each one of us, an example is this cute drawing made by Aina (daughter of Krisztina Arató), explaining holi to her friends at school.

 

Video Credit: Joan Gorro and Montse Coll Llado

Thank you one and all for making it a memorable experience!

Gopi Shah
Project Manager, Mesoscopic Imaging Facility (EMBL Barcelona)

 

A journey through Germany: limbs, modelling and a bunch of Barcelonan scientists

EMBL Barcelona is now up and running for more than a year and, believe it or not, despite these first busy months of transition we’ve also managed to continue doing science. To prove that, is there a better opportunity than to present our work at a conference? Well actually, yes; to decide to do it in two consecutive meetings!

Different conferences and workshops attract different members of EMBL Barcelona according to specific topics during the year. However, last March, two conferences seemed to be specifically tailored for the whole Barcelona unit, and in particular for James Sharpe’s group (which also includes myself). So, I packed my suitcase, and joined the majority of the group for a scientific trip.

First stop Dresden, Max Planck Institute for the Physics of Complex Systems, to attend the inaugural workshop on “Image-based Modelling and Simulation of Morphogenesis” organised by Kyle I. S. Harrington (University of Idaho, Moscow, ID USA) and Ivo F. Sbalzarini (Centre for Systems Biology Dresden, Germany).

I left a sunny and vernal Barcelona and arrived to a rainy and cold Dresden on March 12th for this four-day meeting. Thankfully, the warm welcome by the organisers and exciting science made up for the weather.  Indeed, some of the leading minds from different fields and expertise gathered in the valley of the River Elbe to discuss how computer modelling and bio-image analysis can improve our understanding of biological morphogenesis.

EMBL Barcelona was probably one of the major contributors, since James Sharpe was one of the keynote speakers and three members of the lab were selected to give a presentation: M. Marin-Riera, A. Matyjaszkiewicz and myself.

James Sharpe presented an overview on how we combine theoretical and experimental work to mechanistically explain limb bud morphogenesis in mice. Regarding myself, I had the opportunity to show in more detail one piece of the puzzle talking about some of the latest results of my current project: creating an evolution in space and time of a mouse limb bud using 3D volumetric images.

Not much time to rest and visit the beautiful Dresden at the end of the conference, since we had just one day to catch a train heading south to our next destination: Heidelberg, where other members of James Sharpe’s and Miki Ebisuya’s group were already waiting for us. We crossed all of Germany to be ready on March 17th to take part in the EMBO-EMBL symposium: “Synthetic Morphogenesis: From Gene Circuits to Tissue Architecture” in EMBL headquarters.

This meeting, organised by Stefano de Renzis (EMBL Heidelberg), Miki Ebisuia (EMBL Barcelona), Wendell Lim (University of California, San Francisco and Howard Hughes Medical Institute, USA) and James Sharpe (EMBL Barcelona), was particularly important not only for the eminent speakers, but also because this was the first time that we were, as a group, visiting EMBL’s main site since the site in Barcelona was born.

The symposium focused on “Synthetic Morphogenesis”, a novel field that brings together different scientific communities from developmental biologists to chemists and material scientists. This new area aims to understand how cells/tissues/organs can be built de novo starting from isolated components. Being part of the discussion of a new field is nothing short of exciting.

Attending two conferences in a row was quite intense but it ended in new ideas, suggestions and collaborations that will certainly improve my current research. Moreover, in addition to discussing and contributing to groundbreaking science with experts from all over the world, there is always a chance to meet old friends, find new ones and strengthen the bond with colleagues. Not many jobs allow these privileges, and that is why I enjoy being a scientist.

Giovanni Dalmasso

Postdoctoral Fellow (James Sharpe’s group)

My experience at EMBL Barcelona: the wonder of going through the different stages of its life

 

I still remember how, the day I joined EMBL – one of the world’s leading research institutions – as a legal advisor, I was informed that its Council of Member States wanted to open a new site in Spain, and I would be responsible for its legal set-up. For a specialist in international law, being so fortunate to participate in the establishment of a brand new site of an intergovernmental organisation is a rare gift.

Only a few days later, my colleagues and I were already in Madrid negotiating with the Ministry. Over time, the Host Site Agreement was approved, and I finalized a complex set of agreements for the use of the premises and for the collaboration with other on-site institutes. Of course, that was not the end, there was plenty left to plan and prepare before the day when the international treaty establishing EMBL Barcelona was published in the Spanish Official Gazette!

That happened on 12th May 2017 and EMBL Barcelona was officially born. The site started a new phase, and so did my career. I was charged, as the first Head of Administration and Senior Legal Advisor of EMBL Barcelona, with turning the plans we set on paper into a reality – and to deal with every challenge that could come along the way.

This is how one day I left the busy EMBL Heidelberg headquarters to arrive to an empty basement in Barcelona. I was alone, with just a table, a chair and an office, not even a working phone line yet. I was looking forward to work with the beautiful sea views of the PRBB building, but the refurbishment was still in progress. And yet, my makeshift workspace somehow contributed to the feeling of adventure.

With the invaluable advice of my colleagues at EMBL and at other international organisations, I started planning the administrative strategy and team composition, networking with national authorities and research institutions, making sure that EMBL’s legal status as an international organization was correctly implemented. I delved on everything from legal topics, human resources, budgets, purchases, new grants, ethics… even helped follow up the refurbishment of the site!

Little by little, EMBL Barcelona was taking shape. James Sharpe, the Head of Unit, and his group, joined in October 2017 and we started to grow together as a team, as a site. Researchers and administration working together towards the same goal, with a true interest in what the other was doing, supporting each other and with this feeling of purpose that one could sense in the air. We set our sights high and made every effort to achieve the goal of establishing a collaborative and pioneering scientific site.

EMBL Barcelona now has three research groups and an imaging facility up-and-running, two more to arrive during this year, and two more to be recruited next year. We still encounter new set-up challenges, but now we also have to meet the needs of an operating site that is ramping up very fast. Getting here would have been simply be impossible without my fantastic administration team, who capably deals with those unexpected challenges that every day brings and reliably manages our day-to-day needs.

I am still filled with excitement, and a myriad of ideas and initiatives for the future of EMBL Barcelona. Seeing it growth and getting progressively embedded with the national scientific and institutional landscape has become a great source of personal satisfaction, team pride, and motivation to keep on developing it.

When I stop and look at it, I realise that, someday soon, this embryo that grew so fast into an adult will be key in contributing to unveil the unknown processes behind how tissues and organs function and develop, in health and disease. Everyone who directly or even obliquely participated in the creation of EMBL Barcelona should be proud; I know I am.

Amaranta Amador Bernal

Head of Administration EMBL Barcelona / Senior Legal Advisor

 

 

EMBL Barcelona: Lab-warming Party!!

It’s 7 months since we moved into our new spaces here at the PRBB in Barcelona. Although I must say that it feels a lot more! Maybe it seems a bit late for a lab-warming party, but believe me – we’ve been busy during those months…

Our new EMBL Barcelona lab spaces were completed by June of last year, and my own group moved in during July. Eerily empty spaces at that time, but they’re looking much more lived in by now – we’re rapidly growing: The admin team – headed by Amaranta Amador – has been our key to success from day 1, and has grown during the year into a wonderful team of 4, running everything from purchasing to PR. Last July our first newly recruited Group Leader arrived – Miki Ebisuya, from the RIKEN Center for Biosystems Dynamics Research in Kobe. She’s been bringing her group across gradually – two more members of the lab will be arriving here in a couple of months. A few months later (October) our next group leader started – Vikas Trivedi, arriving from his post-doc in Cambridge. Both groups have been recruiting staff, and we also welcomed EMBL Barcelona’s first 3 new PhD students!

At the same time the Mesoscopic Imaging Facility got seriously underway – Jim Swoger (head of the facility) recruited 2 more staff, so the unit has a full complement of 4 (with a diverse array of backgrounds from physics to biology) – they’re ready and waiting to scan your favorite tissue, embryo or organoid.

This period has been both challenging and exciting. Trouble-shooting the new labs, getting our purchasing system up-and-running, testing and installing new equipment – and getting to know each other. One of the key biological features we’re studying is self-organisation of multicellular systems. This is a great metaphor for how we ourselves are functioning! Like a true “self-organizing system” everyone is pitching in, helping each other, working as a team, so that together this great new project is rapidly emerging into reality. Happy Lab Warming!

James Sharpe (Head of EMBL Barcelona)