Tag Archive | IBE

LabTechnician position open at the IBE

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The González lab at the Institute of Evolutionary Biology (CSIC-UPF), which focuses on understanding how organisms adapt to the environment, is seeking a lab technician to join their research team. You can read more about this position – with a starting date around February 2017 – here.

You can read a bit about the lab’s citizen science project “Melanogaster: Catch the fly!” in this post.

And here you can see a post about a recent publication of the lab where they discovered several naturally occurring independent transposable element insertions in the promoter region of a cold-stress response gene in the fruitfly Drosophila melanogaster.

 

The ERC recognises the excellence of PRBB researchers

European_Research_Council_logo.svgThe research group of Biomedical Genomics from the Research Programme on Biomedical Informatics (GRIB), led by Núria López-Bigas, has been awarded an European Research Council (ERC) Consolidator Grant. These grants are aimed at the development of innovative and excellent projects conducted by young postdoctoral researchers of a consolidated career between 7 and 12 years. The project that received the ERC, named “NONCODRIVERS” aims at identifying mutations involved in tumour development in non-coding regions. It is set to start in 2016 and to last for five years. You can read more about this here.

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Núria López-Bigas, PI at the GRIB (UPF-IMIM)

The ERC AcademiaNet Cover Teaser EN.1570463.jpg.1570468has also recognized the work of another female researcher from the PRBB, Josefa González, a PI at the IBE. She has been nominated to join AcademiaNet, an expert database for outstanding female academics. It was created in 2010 with the aim of raising the visibility of exceptional women in science and increasing their number in leadership positions.

Congratulations to both of them!

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Josefa González, PI at the IBE (UPF-CSIC)

 

 

 

Recreating the images of the mind

On “Back to the future” day, October 21st, 2015, Luís Seoane, member of the Complex Systems Lab at the IBE (UPF-CSIC) led by Ricard Solé, wrote a blog post called “Images of the mind”. In it, he discusses how much technology has advanced in the last 30 years. Our present is not quite the ‘future’ of the characters of the film directed by Robert Zemeckis, produced by Steven Spielberg and starring Michael J. Fox. But we have gone a long way.

In this post, Seoane focuses on Brain Computer Interfaces, which are bringing back motility and communication to injured patients, and on which he himself has worked prior to joining the Complex Systems Lab at the PRBB. In particular, he talks about one he came up with in 2011, which he then developed together with Stephan Gabler and Benjamin Blankertz.

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Early this morning Marty McFly has arrived to the future. It is true that cars don’t fly quite yet. Hoverboards are not available either. Households are not powered by their own nuclear reactors and clothes don’t dry and adjust automatically. Good old Marty has got reasons to be disappointed. But advances in some other directions have been astonishing during the last 30 years. Who could foresee the transformative power of the internet? Everyone is plugged to a tablet or smartphone, immediately accessing far away friends and personalized web content. Synthetic biology is taking its first, promising steps (to which we are glad to contribute) and advances in prosthetics and Brain Computer Interfaces are bringing back motility and communication to injured patients….

You can read here the whole post, published on the lab’s blog.

El·lipse: Last edition of 2013!

The 2nd CEXS-UPF Symposium on Evolutionary Biology that took place in November at the Barcelona Biomedical Research Park (PRBB) opens this edition of El·lipse, the park’s monthly newspaper.

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Also on the topic of evolution, Salvador Carranza (IBE) tells us about his research on reptile phylogeny. Other news include new findings on senescence and embryo development, lung cancer diagnosis, ‘mini-kidneys’ created from human stem cells, the benefits of long-term breastfeeding, new molecules involved in metastasis or computational models to decipher biological problems. On a more personal note, Baldomero Oliva (UPF) tells us about his scientific career and the secret to become a good scientist: patience and stubbornness. The current-affairs debate deals with a very topical question, raised by a recent article in The Economist: is there a reliability problem in science? Find out the different opinions of four researchers at the park!

You can read a multimedia version here.  To download a PDF version please click here. We hope you will enjoy this introduction to what we are doing at the PRBB!

Common causes of complex diseases between Europeans and Asians

Genome-wide association studies (GWAS) have revolutionized the field of complex disease genetics in the last six years. Many disease associations (i.e. genetic variants that increase risk for a specific disease) have been detected using this technique, but the reported variants tend to explain only small fractions of risk. Also, the causal variants that generate the associations unveiled by GWAS have not been identified. And their frequency and degree of sharing across different ethnical populations remains unknown.

Arcadi Navarro, from the Institute of Evolutionary Biology (UPF-CSIC), set out to study the degree of sharing of disease-associated variants across populations, in order to help solving these issues. Together with Urko Marigorta, they did a comprehensive survey of GWAS replicability across 28 diseases. As they report in their paper in PLOS Genetics, most loci and SNPs discovered in Europeans for these conditions had been extensively replicated using peoples of European and East Asian ancestry, while replication with individuals of African ancestry proved to be much less common.

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The authors found a strong and significant correlation across Europeans and East Asians, indicating that underlying causal variants are common and shared between the two ancestries and that they tend to map close to the associated marker SNPs.

They also observed that GWAS with larger sample sizes have detected variants with weaker effects but not with lower frequencies. This indicates that most GWAS results are due to common variants.

 

Reference:

Marigorta UM, Navarro A. High Trans-ethnic Replicability of GWAS Results Implies Common Causal Variants. PLoS Genet. 2013 Jun;9(6):e1003566

Studying how evolution has shaped our genome- Arcadi Navarro (UPF) explains

In this video you can hear Arcadi Navarro, from the Institute for Evolutionary Biology (IBE), a mixed centre from the CSIC and the Pompeu Fabra University (UPF). His group studies how evolution has shaped our genomes and those from other species.

Studying two very particular ethnic groups: from Pygmies to Basques

Pygmies, everyone knows, present the lowest height among humans – adult men grow to less than 150 cm. One can find pygmy populations not only in Africa, but also in Australia, Brazil and several countries in Asia. The fact that populations in such diverse locations all have short stature in common suggests the presence of strong selective pressures on this phenotype, but this has never been proved. David Comas and colleagues from the Institute of Evolutionary Biology (IBE: CSIC-UPF) have recently published in the journal Human Genetics the first genetic hint of adaptive evolution in the African Pygmy phenotype.

Mbuti pygmy men in Congo

They have developed a novel approach to survey the genetic architecture of phenotypes, one in which the genetic analysis also incorporated environmental variables to understand local adaptation. They have applied it to study the genomic covariation between allele frequencies and height measurements among Pygmy and non-Pygmy populations. The results show that the genomic regions that most likely participate in the genetic architecture of the phenotype, are those associated to bone homeostasis and skeletal remodeling, which could therefore be a key biological process underlying the Pygmy phenotype. They have also proved that these regions have most likely evolved under positive selection. These results are consistent with the independent emergence of the Pygmy height in other continents with similar environments, and support the putative adaptive role of the short stature of Pigmies.

David Comas’ group on Human Genome Diversity has also recently studied another very particular ethnic group, that from the Basque country in Spain. The Basque people have received considerable attention from anthropologists, geneticists and linguists during the last century due to the singularity of their language and to other cultural and biological characteristics. But any attempt to address the questions of their origin, uniqueness and heterogeneity has suffered from a weak study-design where populations were not analyzed in an adequate geographic and population context. In their last paper, published in Molecular Biology and Evolution, the group has tried to solve that by analyzing the Y chromosome and mitochondrial DNA of ∼900 individuals from 18 populations, including some where Basque is currently spoken and others where Basque might have been spoken in historical times.

The results indicate that Basque-speaking populations are similar to geographically surrounding non-Basque populations, and that their genetic uniqueness is based on a lower amount of external influences compared to other Iberians and French populations. The rough overlap of the pre-Roman tribe location and the current dialect limits supports the notion that the environmental diversity in the region has played a recurrent role in cultural differentiation at different time periods.

References:
Mendizabal I, Marigorta UM, Lao O, Comas D. Adaptive evolution of loci covarying with the human African Pygmy phenotype. Hum Genet. 2012 Mar 11

Martínez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharçabal B, Quintana-Murci L, Comas D, the Genographic Consortium. Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers. Mol Biol Evol. 2012 Mar 12;

Positive selection on the insulin signal transduction pathway across human populations

The insulin/TOR signal transduction pathway is involved in metabolic disorders such as obesity, insulin resistance and diabetes. The prevalence of such disorders is dramatically different among human populations. Therefore, applying population genetics analysis to describe how natural selection acted in different populations on the genes involved in this pathway may provide key insight into the etiology of these diseases.

A recent paper published in Molecular Biology and Evolution does just that. The authors, from Jaume Bertranpetit’s lab at the Institute of Evolutionary Biology (IBE: CSIC-UPF), have combined genotype data from nearly 1,000 individuals from 39 human populations from around the world with current knowledge of the structure and function of the insulin/TOR pathway. Their aim was to analyse the patterns of molecular evolution of 67 genes involved in that pathway.

They identified the footprint of recent positive selection in nine of the studied genes. Looking at the network position of the proteins coded by those genes, they found that positive selection (that is, a favourable selection which ensures that the affected genes/alleles will increase) preferentially targets the most central elements in the pathway. This result is in contrast to previous observations using the whole human interactome, which had found that peripheral elements of the network were more targeted by positive selection.  Therefore, the authors conclude, “the structure of the pathway influences the patterns of molecular evolution of its components”.

“We worked with a hand-curated data set, minimizing the possibility of mis-annotation interactions among proteins. We looked at polymorphisms within different populations worldwide for genes encoding proteins involved in the insulin/TOR pathway. The fact that we focussed our work at intra-specific level makes it fairly unique in the field of network evolution. This systems biology approach is a nice and robust way of understanding human diseases through the study of human evolution”, says first author Pierre Luisi.

ResearchBlogging.orgReference:
Luisi P, Alvarez-Ponce D, Dall’olio GM, Sikora M, Bertranpetit J, & Laayouni H (2011). Network-level and population genetics analysis of the insulin/TOR signal transduction pathway across human populations. Molecular Biology and Evolution PMID: 22135191

The Genographic Project confirms that humans emigrated from Africa through Arabia

Modern humans emigrated from Africa along a southerly route, via Arabia, rather than a northerly path through Egypt, as had been thought up to now. This is the main result of a study coordinated by David Comas, Francesc Calafell and Jaume Bertranpetit, from the Institute of Evolutionary 
Biology (UPF-CSIC) and published in the October online edition of Molecular Biology and Evolution. The paper, in which geneticists from the USA, the Netherlands, India, Russia and China participated, also reveals that our ancestors spread into Eurasia along a route located between Iran and India, and not through the Middle East as scholars had thought.

This study is part of the Genographic Project, funded by the National Geographic and IBM and the most extensive project to date to use genetic data from human populations. It utilised a new analytical method that infers the recombinations of the past from human DNA. The study confirmed that African populations are the most diverse on Earth and enabled calculation of the possible size of ancient human communities, which seem to have comprised a few thousand individuals each.

Reference work:

Marta Melé, Asif Javed, Marc Pybus, Pierre Zalloua, Marc Haber, David Comas, Mihai G. Netea, Oleg Balanovsky, Elena Balanovska, Li Jin, Yajun Yang, RM. Pitchappan, G. Arunkumar, Laxmi Parida, Francesc Calafell, Jaume Bertranpetit, and The Genogràfic Consortium (2011), ” Recombination gives a new insight in the effective population size and the history of the Old World human populations“, Mol Biol Evol (2011), doi:10.1093/molbev/msr213.

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