The four battlefronts in the war against Antibiotic Resistance

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The World Antibiotic Awareness Week took place last 14-20 November, and the Antibiotic Resistance Initiative ISGlobal team took the chance to explain to the world what are the main difficulties on the fight against antibiotic resistance – a serious problem that threatens our ability to treat infectious diseases and poses a serious risk to the progress made in global health in the past decades. They summarise the issues in four battlefronts:

1- New antibiotics
2- Diagnosis
3- Mechanisms of antibiotic resistance
4- Surveillance

You can read the whole report here.

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.

 

Pervasive translation of lncRNAS

Ribosome profiling is a sequencing technique that detects regions in mRNAs that are being translated. Using this technique, researchers have observed mysterious patterns of translation in many transcripts believed to be non-coding (lncRNAs, or long non-coding RNAs). The patterns are very similar to those observed in protein-coding genes but the translated proteins are generally smaller. Aside from their sequence, we know nothing about these peptides. Are they functional? Do they reflect some background noise of the translation machinery?

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You can get some insights from a a recent study published in bioRxiv by the group led by Mar Albà at the IMIM. Read the whole post on her group’s blog here.

See you soon, Computational Oncogenomics lab!

Núria López-Bigas started her lab on Computational Oncogenomics at the GRIB, within the PRBB, ten years ago. After a very successful decade, we are sad to see her leaving. We wish her all the best in her lab’s new adventure, and we hope the very fruitful interactions she has started with the different groups at the park will continue to prosper.

In her last post on her blog, Núria says thanks to the GRIB, the UPF, the PRBB community and the PRBB Intervals programme… We want to say, thanks to you Núria, for the great research you have done and for being such an open, collaborative and supportive person, both within the scientific community at the park and with outreach events for the general public! You will be missed. Good luck and see you soon!

PhD Thesis from the Computational Oncogenomics group at the PRBB during the last 10 years

PhD Thesis from the Computational Oncogenomics group at the PRBB during the last 10 years

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

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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!

 

 

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