Tara sails to Ostia

by Sara Formichetti

It took me a while to metabolise the last two days I spent at the Porto Turistico of Ostia, close to Rome (the city where I was born and raised). We – Italian-speaking volunteers from EMBL Rome – took part in an outreach event organised by the educational association Adamas Scienza and EMBL Rome on the occasion of the Italian stopover of the boat Tara. Why is this boat so special? Because it’s a private boat at the service of the international scientific community. The crew of researchers are studying the global oceanic ecosystem and the impacts of ongoing climate change and plastic pollution.

My role as a volunteer was to guide organised tours of the boat (which were fully booked a month in advance!) for the general public. I will explain some of the reasons why this experience was so motivating for me – both as a scientist and as a citizen of the world.

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EMBL vs. EMBO – What’s the difference?

This is one of the most frequently asked questions I hear, so I thought there should be a place on the web to explain. The European Molecular Biology Laboratory (EMBL) runs six research sites across Europe where it carries out fundamental research and service in molecular biology. The European Molecular Biology Organization (EMBO) is an academy for the life sciences, provides funding, and publishes five scientific journals. In short, EMBL is a research institute, while EMBO is an academy, funder and publisher. Admittedly, the organizations are related. Both are international organizations funded by member states. Both have their headquarters on the same site in Heidelberg, Germany. Just to complicate things, the Director of EMBO has a lab at EMBL and is considered part of the Director’s Research Unit of EMBL, even though the organizations are administratively and legally separate.

In short, EMBL is a research institute, while EMBO is an academy, funder and publisher

The birth of a beer: EMB aLe

Mukkeller Brewery

The 20th anniversary celebration of EMBL Rome will be soon upon us and the preparations have already begun! On the 16th of May, Alex Young and I traveled with our collaborator for this project, Valentino Roccia, to the Italian brewery Mukkeller, located approximately 275 kilometers from Rome in Sant’Elpidio, just south of Ancona.  The next morning we started brewing at 8:00, finishing around 17:00. I designed this beer to be in the style of a Belgian Pale Ale: characterized as an easy-drinking, moderately malty, somewhat fruity, copper-colored Belgian ale. The bitterness should be moderate and complementary to the malt and fruitiness. Using a traditional Belgian yeast adds a bit of spiciness which we blended with some freshly ground coriander. I chose to add some lemon peel to accent the citrusy fruitiness from the citra hops we used. The beer will be around 6.5% alcohol.  In summary, a full flavored and interesting beer, but well balanced – good for a hot Roman summer day!

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EMBL Rome featured on Italian television program Leonardo

 

Phil Avner speaking to Leonardo

EMBL Rome was recently featured on the nightly prime-time Italian science television program Leonardo. Head of Unit Phil Avner and Group Leaders Cornelius Gross and Jamie Hackett were interviewed about the mission of the Epigenetics & Neurobiology Unit and EMBL’s role in supporting research and scientific training in Europe (see link starting at minute 6:18).

Turning peer review upside down

We recently hosted Mark Patterson, Executive Director of eLife, as part of the Science & Society Program at EMBL Rome. In case you’re not familiar with eLife, it’s a journal supported by four major Life Science research funding bodies: the Howard Hughes Medical Institute, Wellcome, the Max-Planck Society, and the Wallenberg Foundation, with a mission to explore a more responsible selective peer review system. It’s been a surprising success. Although eLife follows DORA guidelines and formally asked not to be listed by Thompson Reuters, the ascribed Impact Factor is already 7.9. It is widely regarded as a top journal in the Life Sciences on par with the Nature specialty series.

Mark Patterson is Executive Director of eLife

As promised, eLife has been experimenting, and the highlight of Mark’s talk were the results of a recent trial in which they turned peer review upside down (see this paper from Bodo Stern and Erin O’Shea for the origins of the trial). For a limited time, manuscripts sent to eLife were accepted BEFORE being sent out for review. Sounds crazy – I know. No need to respond to the reviews if you don’t like them – your paper is already accepted! The hitch, however…

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EMBL Rome 20th Anniversary – Name that Beer Contest!

EMBL Rome is celebrating its first 20 years on 8 July 2019. As part of the celebration, I am brewing a large batch of beer in collaboration with Valentino at Pork’N’Roll, a Roman brewpub. We will be brewing this beer at the award winning Italian brewery, Mukkeller. The beer will be served at the anniversary party July 8 and hopefully you will be taking some home as well. It’s a Belgian Pale Ale featuring light spiciness and a twist of lemon for freshness on a hot summer day. How can you be part of this? You can help name the beer! The contest is open to current staff or anyone who previously worked at EMBL Rome. To participate send an email with your name, when you worked at EMBL Rome, and your suggested beer name. Keep in mind that the name needs to fit nicely on a bottle label.

—- Entries are due by 17:00 on May 10 —-

The following week all staff and participants will be asked to vote for their favorite entry. What’s in it for the winner? 1) Your name featured on the EMBL Rome 20th Anniversary Beer label (pretty cool!), 2) special prize to be determined (might be way more cool?). Get your entries in now!

Stunning science: Neurons that control defence

By Irene Ayuso Jimeno

This video shows neurons (in green) that control instinctive behaviours such as defence. They are located in the periaqueductal grey or PAG: an area in the midbrain with an important role in behavioural responses to stressors like threats or pain.

Credit: Irene Ayuso Jimeno (Gross group) / EMBL

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On big data in biology

by Nicolas Descostes

In recent years, big data is a term that invaded the media and that the public has been exposed to. From finance to social networks, data are collected to infer trends and sometimes to manipulate opinions as it has been observed during recent elections. However, the public is less aware of the big data revolution that is occurring in biology. In this post, I would like to begin by explaining how big data is used in biology, and more specifically in genomics, and end by sharing some thoughts on how big data is currently shaping research.

In the early 2000’s, a battle opposed J. Craig Venter and the International Human Genome Sequencing Consortium to publish the first sequencing data of the human genome. The race produced two articles published in Science and Nature but more importantly, opened an intellectual revolution giving new possibilities to explore the 3 billion base-pair DNA sequence of the human genome in its entirety. Even if sequencing was used a long time before, sequencing the human genome opened the door to sequencing the genome of many other species.

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Staying up to date and organised with scientific literature

By Santiago Rompani

Biological research has never been more vibrant and interesting, but the flipside is an ever-increasing number of studies to keep track of. Gone are the days when the ponderous intellectual could leaf through the latest journals while twirling a goblet of brandy or smouldering pipe. Therefore, I had to come up with other ways to keep up with the scientific literature.

The first is to spend a few minutes to learn how pubmed searches work, watch a tutorial here. Then register for “My NCBI”, which is free and allows you to setup automated pubmed searches and have the website output any new results every day via email. I have searches setup for specific scientists I wish follow, like “gross cornelius[Author]” (use without the quotation marks). I also have more complex searches for keywords in particular journals such as “(Lateral Geniculate) AND (“Nature”[Journal] OR “Science (New York, N.Y.)”[Journal] OR “elife”[Journal])” (the list of journals in my actual search is very long, again, don’t include the quotation marks, but keep the square brackets).

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Taste is King

Jim Sawitzke running Beer 101

We recently had out first Beer 101 course for staff members. International beer judge and Head of our Genetic and Viral Engineering Facility, Jim Sawitzke, first challenged us to a blind tasting and then a tour of major beer varieties. Take home messages were: “if you like it, it’s a good beer” and “if it doesn’t come in a brown bottle, it’s skunked!” – which left me wondering why I kind of like Heineken. Apparently Heineken tried to change their green bottle color at some point, but were forced to relent by popular demand. Find a scientific explanation for the skunk effect here. The tour ended with us sipping beers with names like ‘Arrogant Bastard Ale’ and ‘Rauchbier’ (trans. Smoke Beer) – both dreadful! Unless of course you’re at the higher levels of beer appreciation. Can’t wait for the advanced course.