Archive | November 2015

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.

Europeans are becoming more aware of the city air around them

Guest post written by Tom Cole-Hunter, researcher at the CREAL. Photos by Raül Torán.

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In the months of September and October, the Centre for Research in Environmental Epidemiology (CREAL, an ISGlobal centre) collaborated with the Institute of Photonic Sciences (ICFO) as partners in the iSPEX-EU project. The essence of this project is to capitalize on large-scale, citizen contributions to science (‘citizen science’) such as observations of their environment with simple tools that compliment their existing way-of-life.

CREAL, identified by ICFO as now prominent in local citizen science activities due to leading roles in projects such as CITI-SENSE, was approached to assist in the recruitment of citizens. To participate in the project, citizens had to download an application and clip-on an ‘add-on’ to their smartphone to make an objective observation of the atmospheric air. The add-on, pictured above attached to a smartphone, works on the principle that aerosols (tiny liquid or solid particles, such as sea salt, soot and sand) interact with light in that they scatter and absorb it changing its intensity and polarization – this way the add-on, technically a spectropolarimeter, measures the amount, the size and the type of aerosols.

Volunteers using the device to measure aerosols

Volunteers using the device to measure aerosols

Although the idea is simple and the method fun, several challenges were presented for the recruitment of participants in iSPEX-EU. The first main challenge was that the associated smartphone application and add-on were only compatible with iPhone 4/4s/5/5s. The second was that clear weather and indirect sun were needed to make a measurement. Other challenges included limited time for being on the street recruiting. All of these challenges meant that we were not able to recruit as many participants as we had hoped. A lesson learned is that more inter-compatible products should be considered and developed if possible to allow the maximum participation of citizens.

Air quality and citizenship empowerment

It is imperative to involve the public in these types of campaigns as air quality has an impact on us all; it affects our health, our air transport system and the climate. Knowing the distribution of aerosol/particle sizes and types helps to inform regulation of air quality and policy decision-making. Some particles are small enough to bypass our natural filtration system in the nose and throat and reach deep into the lungs. The smallest of them may pass through the lungs through the circulatory and even nervous system and be found in organs such as the heart and even the brain causing serious health effects. Larger particles emitted with industrial processes like generating electricity with coal-fired power plants play an important, detrimental role in climate change. Additionally, natural disasters such as forest fires and volcanic eruptions can dramatically reduce visibility and may even stop air traffic due to the risk of crashing posed by engines being clogged and malfunctioning.

While natural disasters mostly cannot be prevented, acting to reduce traffic and industrial emissions can. CREAL’s involvement in the CITI-SENSE project is to help empower citizens with environmental health information so as to identify and move to improve air quality issues through awareness, education and services enabling change. One such service is the CityAir smartphone application, available for both Android and iOS, which enables citizens to make observations of the environmental quality of the places where they are based on their perceptions. These perceptions are anonymised, collected and shown on a public platform to identify areas of concern. This information can then be used to make a case for improving local, if not global, conditions.

CITI-SENSE is a four-year Collaborative Project partly funded by the EU FP7-ENV-2012 under grant agreement No 308524, started in October 2012. iSPEX-EU is part of LIGHT2015, a project funded through the European Union’s Horizon 2020 research and innovation programme under grant agreement No 644964.

 

Challenging the model: transcription without the canonical histone marks

A guest post written by Silvia Perez Lluch, from Roderic Guigó’s laboratory at the CRG. You can find more about her career and work here.

Image used for the cover of the journal Nature Genetics. Illustration by Luisa Lens, inspired by the results of the Catalan teams and by a Salvador Dali painting.

Image used for the cover of the journal Nature Genetics. Illustration by Luisa Lens, inspired by the results of the Catalan teams and by a Salvador Dali painting.

Transcription is a process that depends on many elements such as transcription factors, DNA methylation and chromatin structure. Histones are essential for the proper regulation of transcription, and the posttranslational modifications on their tails have been related both to activation (H3K4me3, H3K9ac and H3K36me3) and silencing (H3K27me3 and H3K9me3) of gene expression.

Using the fruit fly as model organism, in our lab at the CRG and in collaboration with Montserrat Corominas’ lab in the Universitat de Barcelona, we have found a set of genes (defined as developmentally regulated genes by their restricted expression to a short period of time) that are expressed without the canonical histone marks associated to activation of transcription. These findings have been published in the October’s issue of Nature Genetics, the cover of which also refers to our work and to Dalí’s butterflies –designed by Luisa Lente and Hagen Tilgner.

Why these developmentally regulated genes show a different pattern of histone modifications is not known, but we speculate that the need of rapid activation–deactivation of gene expression during development may be easier to achieve in absence of the histone posttranslational modifications. In this context, transcription factors would play a more important role. This hypothesis is reinforced by the fact that the binding of transcription factors is different between developmentally regulated and stable genes (those expressed throughout development).

There are previous reports claiming that some genes are transcribed in the absence of the canonical histone marks for gene expression (Hödl and Basler –2012–, Chen and collaborators –2013– and Zhang and collaborators –2014–), but our main contribution to the field is that we have seen that the lack of chromatin marks is a general feature of genes that are expressed for a short period of time, being the expression of these genes likely to be regulated mainly by the action of transcription factors.

We are often asked how come nobody had described these patterns before. Actually, the answer is probably because our approach was different from the beginning. When we started the project our main goal was to analyze the chromatin marks and the splicing of tissue- and time-specific genes in the fruit fly. The settings used to define the tissue- and time-specific genes were, then, very astringent, being our developmentally regulated genes only expressed in one time point throughout development. However, to our surprise, these particular genes did not show the expected histone marks when they were expressed. It was then that we focused our attention in these particular genes.

This work was presented in the 11th Transcription and Chromatin Conference (2014) at the EMBL in Heidelberg – where they were already introduced as being controversial- and was afterwards highlighted in the EpiGenie webpage and in the Epigenetics journal, in both cases by Sascha H. C. Duttke.

As we knew that these results are controversial and somehow challenge the classical association of histone marks with transcription, we put a great deal of effort in generating and analyzing all available data to produce as solid results as possible to demonstrate that our observations do not arise from a detection artifact. Besides, we think that with this work we open a new line of research as the results, so far observed in fly and worm, need to be further validated in mammalian systems. In this sense, our results so far with the ENCODE mouse tissues and human cell lines point out that this lack of chromatin marks in regulated genes may be a general feature along metazoans.

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