A tutorial on Burrows-Wheeler indexing methods

Guillaume Filion’s latest post is aimed at those wanting to understand the details of how the Burrows–Wheeler transform (an algorithm used in data compression) works. It may be of particular interest to those genomics researchers working on alignments, since, Filion says, the Burrows-Wheeler indexing is used to perform the seeding step of the DNA alignment problem, and it’s exceptionally well adapted to indexing the human genome.

For those of you who are not afraid of the small mathematical details, you can see this “The grand locus” post here.

Contact With Natural Spaces Improves the Health of the Population

park in the city 2

 

In this recent post by the HealthISglobal blog, Margarita Triguero, a PhD student at CREAL (now part of ISGLobal), gives us an overview about some recent studies showing the effects of natural spaces – mostly green spaces, both big and small – on health. As she says, blue spaces, such as lakes, rivers, or the sea, have been much less studied so far, but that’s about to change with a new international project called “BlueHealth Project“, which is led from the UK and in which the CREAL/ISGlobal researchers are involved.

Looking forward to hear more about this new project, which started earlier this year and will run until 2020! For the time being, you can read Margarita’s post here!

 

Open Science: not only a matter of outcomes, but also of processes

Post written by Toni Hermoso, bioinformatician at the CRG.

 

Image by Mari Carmen Cebrián

It’s been almost a decade since the term “Open Science” first appeared in Wikipedia. The page was created by Aaron Swartz and initially redirected to the “Open Access” entry. Some years later this young activist committed suicide as a result of the pressure from the judicial charges against him after having uploaded many privative licensed articles to the Internet.

Parallel to these events, Creative Commons licenses, a set of recommendations intended to foster sharing in the digital world, became increasingly popular, and many novel publishing initiatives took advantage of them for promoting open access to scientific literature.

At the same time, more and more government agencies started to demand that the benefactors of their funding should provide their publication results openly within a certain period of time. So, if research was not published originally in an open-access journal (golden road) it should be eventually uploaded in an institutional repository (green road). Furthermore, preprints, an already common practice in Physical Sciences, started to become widespread in Biosciences after the creation of portals such as BioRxiv.

However, despite the bloom of Open-Access (OA) journals and the introduction of a more favouring legislation, there are still strong concerns regarding the future of open access in science. This is mostly due to the fact that the publishing sector is effectively controlled by very few parties, which often provide pay walled content. A reaction to this situation is evidenced by initiatives such as Sci-Hub, which is defiantly providing free-access to those restricted articles.

In any case, there is more to Open Science than Open Access. We could highlight at least two other major facets: Open Data and Open Methodology. These are the indispensable two pilars for making reproducibility in modern science actually possible. In general terms, they may be the initial and raw data (straight from machines or sensors) or the final outcomes such as chart images or spreadsheets. The recent data flood has made necessary the birth of established public open repositories (e.g. Sequence Read Archive or the European Variant Archive) so researchers could freely reuse and review existing material.

It is also a common requirement from these repositories that data must be available in an open format, so other researchers may process them with different tools or versions than the ones originally used. This latter aspect is intimately associated to Open Source, which is also essential for ensuring a reproducible methodology. As a consequence, an increasing number of journals are requiring submitters to provide both data and program code so reviewers may assess by themselves that results are those that are claimed to be.

The present challenge is how to transfer those good practices -which originated in the software engineering world and later permeated into computational sciences- to the wide scientific community, where subject systems may be far less controllable (e.g., organisms or population samples). In order to help on this, there is an increasing effort in training scientists on technologies such as control version systems (e.g. GitHub), wikis or digital lab notebooks. All these kind of systems can enable collaboration of several different parties in an open and traceable way.

Even though there are some practices in everyday scientific activity, such as peer review, that are still under experimentation within the open umbrella, hopefully we may expect that in the future more and more of the key points we commented above will be just taken for granted. At that stage we might not even need to distinguish Open Science from simply SCIENCE anymore.

Science for All and All for Air Quality

Citizen Science is blooming. There’s a growing number of examples of research projects in which the general population can participate. In this post at the blog Health ISGlobal, the researcher Irene Eleta (CREAL) talks about some of these projects which are related to air pollution and that scientists at CREAL /ISGlobal are leading, such as CITI-SENSE.

CITI-SENSE sensor in Barcelona

CITI-SENSE sensor in Barcelona

 

 

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

Did Mendel fake his results?

jacinta lluch valero (CC BY-SA 2.0)

“You went to high school and you learned genetics. You heard about a certain Gregor Mendel who crossed peas and came up with the idea that there is a dominant and a recessive allele. You did not particularly like the guy because there would always be a question about peas with recessive and dominant alleles at the exam. But you grew up, became wiser and just as you started to like him, you heard from someone that he faked his data….”

Did he or didn’t he?

You can read Guillaume Filion’s latest blog entry about the father of Mendelian genetics and statistics – but you will have to choose by yourself!

 

 

Senior female researchers, still too few

This post should perhaps have been published on March 8th. But then, achieving gender equality in science is not something that can be concentrated on a single day; it’s an unresolved and impending issue that we need to think about constantly.

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A group of the female group leaders at the PRBB

On December 2015, the United Nations General Assembly proclaimed the 11th of February as the International Day of Women and Girls in Science. As the UNESCO Director-General Irina Bokova said on the occasion of the first observance of this day, “the world needs science and science needs women”. Yet, women are still underrepresented in the sciences, especially in high-level, decision-making positions. With differences in countries and disciplines, a general trend arises, with only 28 percent of researchers across the world being female, according to the most recent UNESCO Science Report.

At the PRBB, we are not foreign to this problem. Even though about 60% of the total scientific staff working at the park are women, they only represent 30% of the positions at the group leader level. Also, our flagship series of conferences, the PRBB-CRG conferences taking place twice a week, is also skewed with only about 13% of the invited speakers being female scientists (average from 2011 to 2014).

Positive action is needed to change this, and the PRBB and its centres are starting to make this a priority. In 2015, 12 of the 63 (19%) PRBB-CRG speakers were women. Albeit still clearly too low, this represents a 4% increase from the average of the previous four years, and we aim to increase this percentage even more this year: out of the 37 PRBB-CRG talks planned so far for 2016, 13 are by women (about 30%). This percentage may change along the year, as more talks are organised, but it’s undeniable a beginning far better than any other year.

All centres at the PRBB are also working hard at improving conditions for their female staff as well as encouraging the hiring of more female scientists.

The CRG’s Gender Balance Committee was created in 2013 following the centres’ distinction with the HR Excellence in Research’ logo from the European Commission. Its mission is “to promote equal opportunities for men and women at the centre and foment women’s advancement in scientific career”. Chaired by Isabelle Vernos, it is formed by women and men from both administration and scientific backgrounds and ranging from PhD and technicians to PIs. The CRG is also leading the European Project LIBRA: Leading Innovative Measures to Reach Gender Balance in Research, awarded within the H2020 program and with the participation of ten European research institutes, all members of the EU-LIFE alliance. Its goal is to implement Gender Equality Plans in all institutes addressing four key areas, from recruitment policies and career development, to work-life balance and even the sex and gender dimension of research. Further to this ‘good intentions’ the CRG has taken specific action by organising some seminars related to the Women in Science topic, and with a Women Scientists Support Grant with two calls per year for young female scientists (PhD or postdoc level) with maternity responsibilities.

Similarly, the CEXS-UPF, recently awarded a “Maria de Maetzu” distinction, has also a Gender Action Plan that includes grants to support talented young female scientists with maternity responsibilities in their scientific career development. The Gender Action Plan also envisages other measures such as ensuring that at least 30% of the members of committees at the centre are female, or improving work-life balance conditions.

The IBE (CSIC-UPF) is a younger centre, and an ‘Equality commission’ was created just last summer which is raising awareness about the issue. They are working on creating an ‘Equality plan’ and trying to set up a mentoring program for PhD students and postodcs. They already have managed to tip the balance of their external evaluating committee, formerly composed by six male members, to three men and three women. Now, they aim to reach a 40% female rate in their invited speakers. “We are just starting, but we believe gender balance in science is a key issue, and we try to attract people’s attention to this subject. Every time we find something of interest – material, studies or any kind of documentation – we circulate it to the whole institute” says Elena Casacuberta, one of the instigators of the commission.

The CREAL, the CMRB and the IMIM are the three PRBB centres that have the most balanced men-women ratio amongst their staff, with 54%, 50% and 45%, respectively, of their senior researchers being women. But they also keep this issue in mind, and continue doing some actions to avoid this delicate balance to be upset.

At CREAL, with their committee for equity and the management of diversity formed by representatives from all stages, they don’t stop at the men-women issue, but they aim to consider all other collectives which may be in minority. In 2015, they created an Equity Plan and are taking actions, such as news in the intranet about women and research every fortnight, an online course on the topic, or talks about experts on flexible policies to achieve work-family balance.

The CMRB has an Equality Committee, formed in 2014, which has prepared a series of documents such as guides with non-sexist language, a protocol for a fair staff selection or an anti-bullying protocol. Some of the specific actions they have taken are the setting up, about five years ago, of a room for breast-feeding mothers, open to all women at the PRBB, or some changes in the recruiting protocols, for example asking job applicants not to include any personal data, such as marital status, in their CVs. Also, last year they had an awareness campaign with an online course on gender equality compulsory for all staff.

The IMIM has also guides for non-sexist language –  and the institution is revising all their web content and other documents to ensure they all abide by these rules –  and protocols against sexual bullying included in their Equality Plan (2013-2016).

We have done a lot, but a lot more remains to be done. The road for female scientists is long and winding, as the Beatles said; but it must be walked until we managed to cross that door.

 

Report by Maruxa Martínez-Campos, scientific editor at the PRBB.

Odour-guided behaviours in mice

On March 11th, Venkatesh Murthy from the Department of Molecular and Cellular Biology of Harvard University, US, gave a conference at the PRBB invited by the CRG. He explained his study “An olfactory cocktail party: figure-ground segregation of odorants in rodents”, which was the cover of Nature Neuroscience in September 2014. After a brief introduction to the anatomy of the olfactory system of rodents, he explained that many odours are complex mixtures: different chemicals combine and then we can smell a particular object. His main question was: how well can a mouse pick out an individual odorant from a mixture?

nature-neuroscience_cover-w-captionThey wanted the mice to pick a single ingredient within an odour cocktail. In order to do that, mice were trained to recognize target odorants embedded in unpredictable and variable background mixtures. They used 14 different chemicals, so there were more than 16.000 possible mixtures. It was impossible for the mice to memorize the combination; they had to recognize the single odorant. The test used was the go/no go, in which stimuli, in this case smell, are presented in a continuous stream and mice perform a binary decision on each stimulus. One of the outcomes (the correct smell) requires mice to make a motor response (go) in order to receive the reward, whereas the other requires mice to withhold a response (no-go). Accuracy and reaction time are measured for each event.

Mice could learn this task in a few days, they performed it well, but performance dropped with increasing number of background odours. To understand why, the researchers first had to overcome a problem particular to olfaction.

While the relationship among different visual stimuli is relatively simple – differences in colour can be described as differences in wavelength of light – there is not a simple explanation for describing how odours relate to each other. Instead, the researchers tried to describe scents according to how they activate neurons in the brain. They used optical imaging and computational models to relate behavioural performance to the combinatorial neural representation of odorants in odour receptors.

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Using fluorescent proteins, they created images that showed how each of 14 different odours stimulated neurons in the olfactory bulb. Each odour gave rise to a particular spatial pattern of neural responses. When the spatial pattern of the background odours overlapped with the target odour, the ability of mice to identify the target was diminished. Therefore, the difficulty of picking out a particular smell among a cocktail of other odours depends on how much the background interferes with the target smell.

All in all, it was a very interactive session, with the public discussing several issues all through the talk, especially about methodology, so both the speaker and the public got new ideas!

 

A report by Mari Carmen Cebrián 

European Code Against Cancer. 12 ways to reduce your cancer risk

Manolis Kogevinas, Codirector of CREAL, one of the centres within the PRBB, has written this post recently in the “Health is Global” blog about how external factors play a major role in most cancers. He also talks about the new edition of the European Code Against Cancer, published by the International Agency for Research on Cancer (IARC)  and addressed to all European citizens.

ECAC2

If you want to know more about the European Code against Cancer and the workings behind it, you can read the interview to Joachim Schüz, head of the environment and radiation section at the IARC and one of the principal investigators involved in its updating. He visited the PRBB a few months ago, and you will find the interview here, in page 4 of the Ellipse newspaper – the monthly publication at the PRBB.

Enjoy it!

 

 

 

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.

bad times

 

A report by Mari Carmen Cebrián 

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