September Ellipse edition

Again with a delay... I'm actually about to post the October issue! But first, take a look at the September one - I'm sure you'll find something of interest there!

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Millions of our cells die through apoptosis every day. That’s what the group profile of Gabriel Gil (IMIM) tells us in this new issue of Ellipse. Common patterns of virus infections, common origins of genetic diseases and a more efficient cell reprogramming are other of the discoveries announced this month. You can also learn how cycling saves lives, how a simple analysis can help predict cardiovascular risk or which gene has been found to be responsible for the rare but very serious Bohring-Opitz syndrome. Also, check out the pictures of the PRBB summer party and beach volleyball championship!!

Ellipse d'estiu / Summer Ellipse

Forgot to post the summer issue of Ellipse before going on holidays.. here it is!

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The Institute of Evolutionary Biology (IBE: UPF-CSIC) has officially joined the PRBB. Also, the CRG, another of the centres at our biomedical research park, has a new director, Luis Serrano. The ex-director Miguel Beato expresses his farewell in the editorial of this month's El•lipse. Other news include a new drug against hepatitis C, the deciphering of the chronic lymphocytic leukaemia genome, the role of CB1 receptors in learning and advances in drug design thanks to computer simulations. Enjoy!

Weekly meetings for runners

After the success of the "5 years 5 km" initiative last May 30, many of the runners of the PRBB decided they didn´t have enough. So now four weekly meetings have been scheduled for anyone who wants to go for a run with some colleagues.


Every Monday at 6pm and at 7pm
Every Thursday at 6pm and at 7pm

The starting point is the inner square, where "runners" can meet and warm up.

Thanks to all who participated on May 30, and let's keep on running!!!

New edition of El·lipse, June 2011: "Five years, five kilometres"

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In the June issue of the Ellipse, the monthly newspaper of the PRBB, you can learn how about 100 residents of the PRBB met to run 5km to celebrate 5 years since the park creation. In addition, Toni Gabaldón, from the CRG, explains his research in comparative genomics; UPF researchers publish in Science the relationship between DNA compaction and the stress cell response; several studies from the IMIM help the benefits of olive oil to be recognized by the European Food Safety Authority; Audrey de Nazelle, from CREAL, reveals the utility of smartphones for epidemiological studies; and scientists from the CMRB show how the LSD1 enzyme helps stem cells to decide between renewal or differentiation. You can also discover who has won the PRBB award or how statistics can support research, among many other things. Enjoy it!

Premi Ellipse sobre la biologia de la memoria

Recordad, ya podeis enviar vuestros trabajos (escritos o gràficos) para participar en el premio Ellipse. La única condición es que traten sobre la biologia de la memoria. Estan en juego 1000 euros!

Ànimos!

Mas información aquí:
http://bit.ly/hEhQkF

New Ellipse edition (May 2011)

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The PRBB celebrates its 5th anniversary! Check out what we have been up to these five years.

An EMBO workshop at the park, the largest European research project on child health or a 'scientific competition' to find the best solution to the problems of DNA assembly are other of the subjects you will find in this May edition of El•lipse, the PRBB monthly newspaper. What do the PRBB researchers think about the new Spanish Science Law?

Last but not least, you will find information on the III Ellipse Award for science popularisation. We encourage you to participate!

You can read the El·lipse here or check our multimedia version here.

El premi El·lipse del PRBB s'apropa a la biologia de la memòria | Biocat – Biociències i innovació

El premi El·lipse del PRBB s'apropa a la biologia de la memòria | Biocat – Biociències i innovació

The PRBB runner's club

The runner's club
Cargado originalmente por PRBB

Many of the PRBB residents go running regularly, and now we have T-shirts to identift them!

If you want to be part of the 'runner's club', come and get your T-shirt at the 4th floor!

El·lipse d'abril: El cervell, aquest gran desconegut

El cervell, aquest gran desconegut, protagonitza la portada de l’edició d’abril de l’El·lipse.

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També hi trobareu articles sobre nous avenços en la nostre comprensió de l’envelliment prematur i l’infart de miocardi, sobre la predicció d’efectes secundaris de fàrmacs, la compactació de l’ADN, la regeneració de teixits i òrgans, l’origen de l’Homo sapiens, el virus de l’hepatitis C... i molt més!

L’estudi del càncer de pròstata és l’objectiu del grup de recerca que analitzem aquest mes, i en l’apartat de ‘ciència al descobert’ entendrem com funciona la citometria de flux.

En l’entrevista, David Searls, ex-vicepresident de la secció de bioinformàtica de GlaxoSmithKline ens explica com n’és d’important aquesta disciplina per les grans farmacèutiques i per la medicina del futur. I parlant de futur, quatre investigadors dels centres del PRBB imaginen quins desenvolupament tecnològic els seria útil per la seva recerca.

Desitgem que us agradi!

The biology of memory - what do YOU have to say about it for 1000€?

Literature and arts get close to science for the third consecutive year with the Ellipse Award organised by the Barcelona Biomedical Research Park (PRBB).

This award started three years ago by initiative of a group of young researchers of the park, and it is aimed at anyone interested in biomedical research - whatever their training and profession. It gives them the opportunity to explain a particular concept related to biomedicine using, amongst other genres, a fictional story, a poem, an essay, a theatrical script or any form of graphical work.

In the spirit of reaching as many people as possible, the texts can be written in Catalan, Spanish or English.

Under the Alzheimer International 2011 initiative, the prize this year will be awarded to the best works that address any aspect related to the biology of memory from a scientific perspective (e.g. the biochemistry of memory, its physiological conditions, the diseases that cause its alteration or the potential treatments to restore it).

The prize is 1000 Euros for the winning entry in each category: graphics and written, and the deadline for sending your work is July 15, 2011. For more information: premi-ellipse.prbb.org

Good luck!!

Cis-regulation and genome architecture during development, evolution and genetic diseases

That's the title of today's PRBB-CRG conference by José Luís Gómez-Skamerta. I learned many things, but here’s two interesting ones:

1-3C (Chromosome Conformation Capture), a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell. In particular, it allows one to check whether two very distant DNA regions interact with each other via cross-linking, digestion and re-ligation. I had heard about it before, but had forgotten, and it’s quite cool, isn´t it?

2-How the 3D structure of the genome (and particularly, the formation of loops on the DNA) can add a new level of complexity to gene regulation. Gómez-Skamerta showed us how the same collection of genes and the same collection of enhancers can have a very different result through evolution (in different organisms) and through development (at different stages), and one way of achieving this is via the DNA loops. How? Using the example of the Iroquois genes (Irx), which he originally cloned, he showed how keeping two promoters (and several enhancers) within one same loop facilitated the fact that these two genes are activated by the same enhancers. It also explains why those enhancers in the loop have more difficulty to activate a gene outside the loop.

And that’s my very brief summary :)

Evolutionary medicine - understanding malaria drug resistance

Forgetting for a minute their use of complicated mathematical formulae, scientists are, really, like children. They ask: why? And when they have the answer, ask again: but why? And once a satisfactory explanation has been found they wonder, but why? And on and on and on…

But this stubbornness pays off. Daniel Hartl, from Harvard University, gave us an example today of how this relentless questioning actually helps come up with interesting and useful explanations about how things are the way they are.

In his talk at the PRBB Conference Hal, Hartl talked about the evolution of drug resistance in the malaria parasite. He pointed out how the different existing treatments for malaria that have existed have been effective for less and less years each, before resistance appeared.

He focused on his analysis of DHFR, a parasite enzyme which is the target of the antimalaria drug pyrimethamine. There are 4 aa changes that can be combined following 24 potential evolutionary pathways. Hartls simulations and laboratory experiments (using E.coli) showed that only three of those account for most of the outcomes. When he checked the ‘real world’ and looked at all the polymorphisms that exist for DhFR he found that, indeed, there were few that were common, and these coincided with those he found to be more successful in the lab.

Now come the questions :)

Hartl found that a particular polymorphism very common in South East Asia (which contained all four aa changes, let’s call it 1111) was not present in Africa. Why?, he asked (especially since he found some resistant strains found in Africa had their origin in East Asia). Well, he found that the fourth mutation had a high fitness cost associated (the enzyme was less efficient), so it was not very good. ..

But then (second why) why was that mutation present in Asia to begin with? Well, because in Asia those 1111 strains had high copy numbers of a gene linked to the 1111allele which coded for the enzyme substrate, and those high copies resulted in high levels of the enzyme substrate, which meant that having a less efficient enzyme was not that bad.

But then (yes, a third one!) why was that CNV not present in Africa? Well, it turns out that while in Asia people are usually only bitten once, in Africa a person can be infected by several parasites at the same time. That means that recombination takes place between the different parasites, and therefore the CNV and the 1111 allele are easily separated. Therefore, having a 1111 is bad, and it’s not compensated by high copy numbers of the CNV, because they are not linked.

Interesting, eh? If you (or your 3-year old child) can think of any other whys don’t be shy, contact Daniel Hartl who, I am sure, will be delighted to keep on investigating…

Of sex and death

Why does sex exist? And why having sex with another organism instead of oneself? These are two of the questions that Patrick Phillips, from the Unviersity of Oregon, tried to answer in his talk at the PRBB last week.

The biologist uses the nematode C.elegans for his research, which consists primarily in recreating evolution in the lab. How does that work? It basically consists of two steps: artificial selection+adaptation to the laboratory conditions. That is, he creates a novel environment, generates mutations in the worms, and sees which ones adapt and which ones die. Cruel? Not more than reality…

The advantages of these evolutionary experiments in the lab is that they are controlled and can be replicated. The problems are that they are limited in time (while real evolution takes 1000s of years) and there’s also a limited population size, which means that rare events (as in rare mutations) won’t be seen. Regardless of these inconveniences, Phillips managed to convince the audience that these experiments can prove that sex is good – to get rid of deleterious mutations and to increase genetic variation, which provides a better adaptation to the changing environment.

According to the scientist, one reason C. elegans is good for studying evolution is that they can be frozen. When you are doing the kind of experiments he does, if you freeze worms from different generations along the experiment, you have the equivalent to a ‘fossil register’ that allows you to compare the organisms at the ‘beginning’ and the ‘end’ of the evolution phase you are studying. Isn´t that cool?

Apart from sex, Phillips also talked about death – or why we age. Again, the elegans nematode plays an important role in ageing research: actually some mutants can live up to 10 times their usual lifespan. That is the equivalent of a human living 1000 years!

His experiment consisted in breading the worms for 323 generations by selecting only one worm in each generation to spread the population. As a consequence, the population size went dooooown and the worms were very sick (ah, the lack of genetic variation!). He then, playing God, saved the species by letting a higher number of worms reproduce for another 60 generations. When he compared the genome of the sick (thanks to his ‘fossil record’) and the recovered worms he found very few changes: only about 10 nucleotides! He went back in history to check when each change had taken place – again, thanks to the frozen worms (amazing, eh?). What he found is that the ‘recovery’ mutations were not the result of ‘mutating back’ to the original sequence, but rather they were compensatory mutations.

All in all, he showed us what he called an ‘emerging paradigm in evolutionary biology’, a new way of studying evolution: create a perturbation (mutation); propagate the species for 50-100 generations to let them recover fitness; sequence the genome to find out which changes have occurred; use genetics to confirm the results.

Voilà! Now you can try it at home :)

February issue of El.lipse - new format!

New issue of El.lipse, and new look - check it out!!!!

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Life at its physical limits

“What cannot be measured properly, is not science”, sentences Matthieu Louis when he introduces William Bialek’s talk at the PRBB. There’s a packed room of close to 100 people, many of them left standing, others sitting on the floor.

There’s always a silence, longer than average, before Bill answers any question directed to him. You are left to wonder whether he has heard you. But he has. It’s just that, unlike many people, he actually thinks before he speaks.

And he obviously knows he’s talking about complex issues, too complex for the average human brain to grasp easily (not that the brains in this room are average, though). So his discourse is slow-paced, as if there’s a conscious thought before every single word he says. He stops and looks at the ceiling while reflecting, takes his glasses out and runs his hand through his face and dense beard before continuing.

With a green pen he writes formulae on a whiteboard with as easy a flow as if he was using words. Mathematics is his language and he thinks, as did Galileo Galilei, that it is also the language in which Nature is written.

He starts his talk with a Calvin and Hobbes Cartoon (one of his favourites) about how mathematics allow us to make predictions about the way things work, and throughout the seminar he gives some sharp and crisp examples of ‘life at its best’, i.e. of how Nature gets very close to its physical limits, such as the workings of the compound eye of a fly.

“The default assumption that evolution is sloppy and imprecise is probably not fair”, concludes the physicist from Princeton University. He leaves us with a question: are all these examples of optimization of information transmission just independent cases or can they all be connected to a general theory? Here’s some food for thought.

New Ellipse edition (January 2011)

Should scientist publish their negative results? Four researchers from the PRBB centres give their opinion in the latest Ellipse’s debate.

In this issue you can also find more about the PRBB Intervals programme, which offers free workshops for interdisciplinary learning and reflection for scientists at the PRBB centres and celebrates its 3rd anniversary.

How scientists have created a living computer system, how benign tumors can help understand malign cancers, or how researchers have found out there was (female) contact between America and Europe before Columbus are only some more of the things you can read here!