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Proteins bound to DNA impair Nucleotide Excision Repair

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Congratulations to Núria López-Bigas at the GRIB (UPF-IMIM) for her lab’s latest paper in Nature describing why there’s an increased mutation rate in Transcription Factor Binding Sites (TFBS) in melanomas and lung tumors!!!!

You can read more about the experience publishing this paper in this post from her lab’s blog, where she explains how, after a long process of reviewing, they felt they “had the responsibility to describe our finding as soon as possible to the community”, and decided to publish the manuscript in bioRxiv. Later on, the paper was accepted and published by Nature.

Here’s for this success story!

You can read the paper here:

Radhakrishnan Sabarinathan, Loris Mularoni, Jordi Deu-Pons, Abel Gonzalez-Perez & Núria López-Bigas. Nucleotide excision repair is impaired by binding of transcription factors to DNA. Nature 532, 264–267 (14 April 2016) doi:10.1038/nature17661

Bad times, slimmer children?

On January 21, Judit Vall Castelló from the Centre for Research in Health and Economics (Pompeu Fabra University) gave a conference at the PRBB invited by the CREAL. She talked about her last study on the effect of business cycle conditions on children’s weight.

She explained that the majority of the research connecting recessions with body-weight has so far focused on adults or babies. In adults, most of the literature finds a link between better economy and weight increase, which would suggest that recessions are “good” for adult’s health. But, is it the same for children?

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Spain is one of the ten countries of the OECD with a higher prevalence of infant overweight – about 25% of children aged 5 to 17.  Children’s obesity rates represent an important public policy issue as a number of short-term adverse effects and risks have been associated with obesity in the early stages of life. For example, obese children have a greater risk of being bullied and they are more likely to stay obese into adulthood, therefore having a higher probability of suffering certain chronic diseases later in life.

The relationship between the business cycle conditions and children’s weight is not in the political agenda of Spanish politicians, it’s an unexplored topic on the scientific literature about children, and it has relevant consequences in the short and long-term. These were the main motivations for Vall Castello’s research.

Her team used data from 8 waves (1987-2012) of the Spanish National Health Survey. The pooled sample contained 37,562 observations of children between the ages of 2 and 15 years old.

She explained to an attentive audience how their strategy takes advantage of the variation in the unemployment rate across regions and survey years to look for potential effects. They used the regional unemployment rate as a proxy for the business cycle phase at the local level.

The researchers found that an increase in the unemployment rate is associated with lower obesity incidence, especially for children under 6 years old and over 12 years old – similarly to what was known in adults. A decrease in obesity is actually good news, but what happens to the other extreme of the population, the ones that were already underweight when the economy was good?

They found that negative economic conditions increased the prevalence of infant underweight, particularly for those under 6. So, an increase in the unemployment rate shifts the entire weight distribution to the left, decreasing the probability of suffering obesity and overweight but at the same time increasing the probability of being underweight for children under 6 and children over 12.

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There is a positive correlation between unemployement and the prevalence of infant underweight

Vall Castello was also interested in the possible channels through which the economy could be impacting infant underweight and obesity, such as changes in the nutritional composition of the children’s diet or in the frequency of exercise.

Their results suggest that an increase in the local unemployment rate may be linked to a decrease in the probability of following a Mediterranean Diet, which is considered as one of the healthiest dietary options. More worryingly, this negative correlation was most significant for children under 6 years old.

Since compulsory education starts at age 6 in Spain – and, for most children, it includes lunch at school – this research seems to point out just how important it is to ensure that all children, regardless of their parents’ economic situation, have at least one balanced meal a day, and the key role schools play in this.

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A report by Mari Carmen Cebrián 

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)

 

 

 

A successful EMBO Practical Course on targeted proteomics at the PRBB

Different targeted strategies have recently emerged in the field of proteomics that enable the detection and quantification of a predetermined subset of proteins with a high degree of sensitivity and reproducibility across many samples. Major advances have been achieved in the targeted proteomics workflow, including advances in instrumentation, the generation of thousands of publicly available targeted assays, and the development of multiple computational tools for convenient data analysis.

This field is known as targeted proteomics and although it has successfully been applied in several research projects of molecular biology, systems biology and translational medicine, there is still a strong gap between theory and real application.

To address this mismatch and boost the applications of targeted proteomics, the PRBB held a new edition of the 6-day long EMBO Practical Course “Targeted proteomics: Experimental design and data analysis” co-organised by Eduard Sabidó, head of the CRG/UPF Proteomics Unit and Ruedi Aebersold from the ETH in Zurich.

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Twenty-five participants coming from 20 countries from all continents attended the course, which offered a combination of keynotes, practical demonstrations and tutorials to provide the participants with the required knowledge and skills to design and analyse their own targeted proteomic experiments using the most advanced and state-of-the-art methods.

Each day started with a keynote open to all PRBB residents by different renowned proteomics researchers that reviewed the latest achievements in the field of targeted proteomics and introduced the “topic of the day”. The students also attended to several practical session to master the complete workflow associated to targeted proteomics, thus filling the gap between theory and the actual implementation of targeted proteomics experiments. During the practical sessions the students generated, refined and optimized targeted proteomics methods for a set of selected proteins of interest, and automated manual data analysis by reviewing concepts such as peak picking, quality assessment, and statistics for accurate protein quantitation. The program was complemented with poster sessions and several social events to foster informal scientific discussions and to adapt the technology to each participant’s particular interests.

The participants, ranging from PhD students to postdocs and senior researchers, gave a very positive feedback on the course, with an overall score of 4’75 on a scale from 0 to 5 and very encouraging comments:

“Very motivating meeting with very interesting researchers from very different fields but same interest in proteomics, and high quality seminars and tutorials that made me want to continue research in proteomics”

“I feel confident to start my own experiments now”

“Informative and engaging with strong relevance to my research”

“The most useful course so far and also great to share knowledge and tips between us!”

“Excellent speakers, plenty usufull, practical informations, nice atmosphere it is shortest description of the course”

“A wonderful course instructed by cutting edge and innovative field leading scientists whom together have passed on the necessary tools to enable me to design and implement successful targeted proteomic workflows”

This course disseminated the know-how present at the CRG/UPF Proteomics Unit to a broader scientific community and strengthened the interdisciplinary exchange of knowledge and ideas. Thus, by transferring the expertise on experimental design and data analysis for targeted proteomics, the CRG/UPF Proteomics Unit aims to facilitate a wider and more routine application of targeted proteomics among non-proteomic laboratories worldwide.

For those who could not attend this year, the EMBO Practical Course “Targeted proteomics: Experimental design and data analysis” will take place again at the PRBB in November 2016. You will soon be able to access this website to register for the 2016 edition – do not miss this opportunity!

You can see the videos of the 2015 edition here.

 

Course instructors that participated in the 2015 edition

Abersold, Ruedi; ETH Zürich, Switzerland
Altelaar, Maarten; Utrecht University, The Netherlands
Borràs, Eva; CRG-UPF Proteomics Unit, Spain
Bensimon, Ariel; ETH Zürich, Switzerland
Chiva, Cristina; CRG-UPF Proteomics Unit, Spain
Guillet, Ludovic; ETH Zürich, Switzerland
Ludwig, Christina; ETH Zürich, Switzerland
MacCoss, Michael; University of Washington, USA
MacLean, Brendan; University of Washington, USA
Reiter, Lukas; Biognosys GmbH, Switzerland
Sabidó, Eduard; CRG-UPF Proteomics Unit, Spain
Vitek, Olga; Northeastern University, USA

 

 

First in Europe: one of the most precise Mass Spectrometers in the world

 

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A couple of months ago, the CRG-UPF Proteomics Unit at the PRBB – run by the Centre for Genomic Regulation (CRG) and the Pompeu Fabra University (UPF) – announced the installation of one of the most precise mass spectrometers in the world, marketed as Orbitrap Fusion Lumos, becoming the first place in Europe and the third in the world to have this tribrid instrument.

You can read more about this innovative mass spectrometer – which can achieve simultaneous analysis and quantification of more than 10,000 proteins from ten different samples in a single day! – in a post entitled “The CRG Becomes the First European Centre to Have One of the Most Precise Mass Spectrometers in the World” and published on September 29th in Biocores – a directory of the core facilities, technological platforms, and scientific services in Barcelona.

You can also read an article published in Ellipse – the monthly newspaper of the PRBB – in which Eduard Sabidó, head of the Proteomics Unit, tells us about how mass spectrometry-based proteomics is helping to solve complex problems of molecular biology and translational research (see page 6 of this months’ edition of the Ellipse).

 

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.

A new tool to analyze bipartite networks in community networks

A new study in which Sergi Valverde, from the Complex Systems Lab  at DCEXS-UPF has collaborated, provides an open source MATLAB package to study the structure of bipartite ecological networks inspired by real problems in microbiology and with broader applications.

 

Bipartite networks are a special type of ecological network where individuals of a certain species interact with individuals of different species. They are ubiquitous in community ecology, such as the relation between phages (viruses that infect bacteria) and their bacterial hosts.

You can read more about this tool, called BiMat, at the group’s blog.

Science at PRBB: Jordi Garcia Ojalvo’s Dynamical Systems Biology lab (CEXS-UPF)

In this sort video the physicist Jordi Garcia-Ojalvo, at the Department of Health and Experimental Sciences of the University Pompeu Fabra – located at the PRBB in Barcelona – talks about his group’s studies on circadian rhythms and other biochemical oscillations at a systems biology level.

Video produced by the Barcelona Biomedical Research Park www.prbb.org

 

In-silico selection of targeted anti-cancer therapies

The Biomedical Genomics group led by Núria López-Bigas at the Pompeu Fabra Unviersity have recently published a paper in Cancer Cell describing the landscape of anti-cancer targeted therapeutic opportunities across a cohort of patients of twenty eight of the most prevalent cancers. They first looked for all the driver mutations (mutations that ’cause’ the cancer) for each individual cancer, then collected information on all the existing therapeutic agents that target those mutations, and finally, combining both datasets, came up with anti-cancer targeted drugs that could potentially benefit each patient. You can read more about this paper on their blog post.

Coinciding with the publication of that paper, the lab has crafted a new IntOGen interface which presents the results of this analysis. You can see it and learn more about it here.

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!

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