Tag Archive | cell biology

Female sex control: a third way

Females have an extra X chromosome as compared to males, and this can mean trouble – think of what happens when someone has an extra copy of any other chromosome, 21 being the most (in)famous! Dosage compensation is therefore essential, and there’s different ways of dealing with it. In humans, women inactivate one of their X chromosomes, while in the fruifly the opposite happens: males overactivate their only copy of X.

The complex in charge of doing so is called MSL and male-specific-lethal-2 (msl2) is one of its subunits. Female flies must inhibit this gene in order to survive, and Sex-lethal (SXL) is the protein which orchestrates this repression. So far, it was known that SXL binds to the 5′ and 3′ untranslated regions (UTRs) of the msl2 mRNA, inhibiting splicing in the nucleus and subsequent translation in the cytoplasm.

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But Fatima Gebauer and colleagues at the CRG have now found a third way SXL can repress msl2: by inhibition of nucleocytoplasmic transport of msl2 mRNA.

To identify SXL cofactors in msl2 regulation, the researchers from the Regulation of Protein Synthesis in Eukaryotes group devised a two-step purification method termed GRAB (GST pull-down and RNA affinity binding) and identified Held-Out-Wings (HOW) as a component of the msl2 5′ UTR-associated complex.

Their experiments showed that HOW directly interacts with SXL and binds to two sequence elements in the msl2 5′ UTR. Depletion of HOW reduced the capacity of SXL to repress the expression of msl2 reporters without affecting SXL-mediated regulation of splicing or translation. Instead, HOW was required for SXL to retain msl2 transcripts in the nucleus.

These results, published in Genes & Development uncover a novel function of SXL in (msl2) nuclear mRNA retention – a third way for female control of sex-specific gene expression.

Reference:
Graindorge A, Carré C, Gebauer F. Sex-lethal promotes nuclear retention of msl2 mRNA via interactions with the STAR protein HOW. Genes Dev. 2013 Jun 15;27(12):1421-33

Manuel Mendoza and chromosome segregation

Basic cell division mechanisms are still a huge mystery, says Manuel Mendoza, head of the Cytokinesis and chromosome segregation group at the CRG. His lab is trying to understand how do chromosomes condense and segregate, and he explains why this is important in this short video.

Horses with spots and giraffes with stripes

Shigeru Kondo (Institute of Frontier Biosciences, Osaka University, Japan) gave one of the last talks at the “Computational approaches to networks, cells and tissues” meeting that took place this week  at the PRBB Auditorium.

Co-organised by James Sharpe (CRG) and Hernán López-Schier (HZM), the meeting was supported by QuanTissue, a collaborative European network to bridge the gap between the traditional developmental cell biology, biophysics and systems biology. And so it did!

Most of the nearly 200 participants were physicysts or mathematicians, as one could tell from their presentations and posters full of complicated mathematical formulae. But the subjects they studied were all related to the development of tissues and organs within organisms.

Kondo, for example, talked about the pigmentation pattern of zebrafish and how the Turing model could explain it.

Although his lab found there is no actual diffusion of any molecules, they showed that the interaction between the two types of pigment cells that define the skin patterns in the fish can still be explained by the Turing reaction-diffusion model. Melanophores, one of the cell types, elongate long projections towards xanthophores, the other cell type, and the effect of this is mathematically equivalent to the classical Turing model. Interestingly, he showed how, changing one single gene his lab was able to generate fish with skin patterns resembling most of those present in nature, from leopards and jaguars to zebras. Hence, the title of this posts, with which he finished his talk: “If you want horses with spots or giraffes with stripes, I can make it!”.

The meeting is still going on – another two hours of good science if you rush!

A report by Maruxa Martinez, Scientific Editor at the PRBB

Pedro Carvalho (CRG) explains the role of ER in protein control and lipid homeostasis

Pedro Carvalho, from the CRG tries to understand how the cell uses its quality control mechanisms to get rid of proteins that are not functional. He also studies lipid homeostasis. Both functions take place at the Endoplasmic Reticulum (ER). Check out this video to hear him explain his research.

How stress dictates cell expression

Stress causes a general down-regulation of gene expression in cells, together with the induction of a set of stress-responsive genes. How do cells know which specific genes to activate when they are silencing most of the others? The (yeast) answer is called Hog1, as shown in a recent paper published in Genome Biology by the Cell Signalling research group at the UPF.

The authors, led by Francesc Posas, used yeast as a model organism to study the response to osmostress, and they focused on Hog1, a stress-activated protein kinase which is related to p38. Using chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-Seq) they did genome-wide localization studies of RNA polymerase II (RNA Pol II) and Hog1. The results show that upon stress, RNA Pol II localization shifts toward stress-responsive genes relative to housekeeping genes, and that this relocalization required Hog1, which also localized to stress-responsive loci.

Posas and colleagues also looked at the re-organization of nucleosomes by micrococcal nuclease followed by sequencing (MNase-Seq). The analysis showed that, even though chromatin structure was not significantly altered at a genome-wide level in response to stress, there was pronounced chromatin remodeling at stress-responsive loci, which displayed Hog1 association.

The authors conclude that Hog1 serves to bypass the general down-regulation of gene expression that occurs in response to osmostress, and does so both by targeting RNA Pol II machinery and by inducing chromatin remodeling at stress-responsive loci.

Reference:

Nadal-Ribelles M, Conde N, Flores O, Gonzalez-Vallinas J, Eyras E, Orozco M, de Nadal E, Posas F. Hog1 bypasses stress-mediated down-regulation of transcription by RNA polymerase II redistribution and chromatin remodeling. Genome Biol. 2012 Nov 18;13(11):R106

“Healthy criticism is essential for change and success”

An interview published in Ellipse, the monthly magazine of the PRBB.
vivek malhotra (CRG)

Vivek Malhotra was born in India 50 years ago and received his formal education in England. After graduating from Oxford, he went to the US as a postdoc at Stanford. He was a professor at the University of California in San Diego where he has spent most of his life. Married to a Basque biologist, in 2008 he came to the PRBB where he coordinates the Cell and Developmental Biology programme of the CRG.

What differences are there between here and the US? 

Americans are goal oriented and very driven. They want to solve problems whatever the cost. They are aggressive and critical. And that’s how they have managed to advance so much. I have the feeling that in Spain people are scared of criticising. Consequently they cannot deal with criticism very well. Healthy criticism is essential for change and success.

Are we talking about science? 
Criticism is essential in all aspects of life, but especially important for science. As the Greek philosopher Thales said, biology, unlike maths, is not complete, accurate, and permanent. It is open to interpretation, today’s proposal may need to be revised later on based on new knowledge and one should be willing to accept that.

Why did you come to Barcelona? 
After 23 years in California I was bored. And even though I took a salary cut I am very happy here. At the CRG, I am able to do science at the same level I used to. I can see myself staying here for the rest of my career. The only thing that scares me is the general ’laissez faire’ attitude to the long-term potential of basic science. Spain needs to invest more in education, long-term and at all levels: school, university and research centres. There are now good research centres in Spain, but far too few. Jordi Camí deserves a lot of credit for building up the PRBB. If we had 2 or 3 more Jordis who could build 2 or 3, or even one more centre like this in the next 5 years, it would be terrific.

What is the best advice you have ever received? 
“Work on something you think you might be able to solve in your lifetime”. I have followed this suggestion and focused on key aspects of protein secretion. We have made significant discoveries, some of which could lead to the development of therapeutics for chronic obstructive pulmonary diseases. Drug development, however, is not for me. I dislike the corporate aspect of science.

What is a normal day for you? 
I walk to work, which takes about 25 minutes. This gives me time to focus on the key issues for the day. When I get to work I talk to the people in my lab, and in fact I keep on doing that all day. On average every 10 mins I abandon the computer and walk around the lab and my floor, and generally bother people by repeatedly asking if they have anything new. Most people hide when they see me coming but the brave and passionate ones take the bait and we have fun talking. I do not have a set routine but I try to communicate regularly with my friends both here and in the US. My iPhone is always on. If I am awake at 3am and come up with a useful idea I send an email right away to my lab members. So there is no time limit for work. However, I am learning to keep my evenings free for my family.

Anniversary CRG Symposium: from genomics to cell biology

Next October 18 and 19, the CRG will be celebrating its annual Symposium. This year it is especially relevant, since this research centre is celebrating its 10th Anniversary.

The symposium will focus on the latest and most important advances in genomics but also in genetics, molecular and cell biology, or biotechnology. Several scientists in the international arena, such as Angus LAMOND (Wellcome Trust Centre for Gene Regulation and Expression, Dundee, UK), Tom MANIATIS (Columbia University, New York, US), or Iain MATTAJ (EMBL Heidelberg, Germany) will showcase the achievements of the CRG in the last 10 years in these fields. You can check here the full program.

Registration is free of charge, but finishes next Oct 8, so hurry up!

“Our translational research makes us compulsive collaborators”

The Molecular physiology and channelopaties research group from the CEXS-UPF is formed by several PhD students, postdocs, a technician and a couple of principal researchers with teaching duties. Miguel Angel Valverde leads the group since 1999, when he came to Barcelona from King’s College in London.

The aim of the group is two-fold. On the one hand, they try to understand how the ionic channels are activated, how they sense the physical or chemical signals that tell them to open or close. The second goal is to understand what happens when these channels don’t work correctly.

Ca2+ and its role in disease

Different types of ion channels are present in all cells, but they all have a unique, essential function: to modify the electric potential of the cell with the ultimate goal of regulating the intracellular Ca2+ concentration. Indeed, Ca2+ is not only an ion itself, but also a signalling molecule involved in many processes, such as muscle contraction, neurotransmitter release, or even gene transcription. This is why, when its concentration is deregulated, problems as diverse, common and complex as cardiovascular, respiratory or neuronal pathologies can arise. And these are precisely the channelopaties that the group studies.

Hypertension is one of the most important predictors of cardiovascular diseases. And one of the causes of hypertension is the contraction of the arteries, which makes their diameter smaller. This contraction is started by the Ca2+ signalling in the vascular smooth muscle. Ca2+ concentrations are also crucial for the immune system response, which explains why the group is interested in asthma, an inflammatory pathology. Finally, migraine is caused by a hyper excitability of the brain cortex, which in its turn is caused by an increase in the activation of synaptic transmission. Again, we find the usual suspect, an increase in Ca2+ levels, at the beginning of the chain of events that lead to migraine.

A multidisciplinary approach 

role of ion channels in these channelopaties is studied at the genetic, molecular, cellular and physiological level. The group collects population samples, either by themselves or in collaboration with clinical or epidemiological groups. They sequence some candidate genes to find any genetic variations (called polymorphisms) that may be linked to the pathology. Once there is a polymorphism that represents a clear risk or beneficial factor, the group studies why this change in the genome is associated with the disease. “We don’t just link a gene to a disease. Instead we want to understand the whole process: how this gene affects the protein structure, and how that change in structure affects the function of the channel and the Ca2+ concentration”, explains Valverde.

They introduce the genetic changes under study in cells in culture and they analyse how the Ca2+ concentration varies by fluorescent microscopy, or do electrophysiology studies to look at the electrical activity of a single channel.
Such a multidisciplinary work requires lots of collaborations, and the laboratory has found many of them within the PRBB. They have worked with researchers at the IMIM and with neurologists and pediatricians at the Hospital del Mar for the cardiovascular and asthma studies; with groups at the CRG and other colleagues at the UPF and the GRIB for some genetic, biochemical and computer modelling aspects of the studies. “We do truly translational research, and are compulsive collaborators”, concludes Valverde with a smile.

This article was published in the El·lipse publication of the PRBB.

Postdoc position on cell and molecular biology at the CRG

A postdoctoral position is available in the group of Pedro Carvalho at the CRG. The Organelle biogenesis and homeostasis lab studies the molecular mechanisms by which misfolded secretory and membrane proteins are detected and eliminated from cells. The succesful candidate will work on protein quality control.

Application deadline is February, 29, 2012. Starting date would be no later than May 2012.

Details: Postdoc position

A new factor in non-centrosomal microtubule assembly

Chromosome segregation requires the formation of K-fibres, microtubule bundles that attach sister kinetochores to spindle poles. Most K-fibre microtubules originate around the chromosomes through a non-centrosomal RanGTP-dependent pathway and become oriented with the plus ends attached to the kinetochore and the minus ends focused at the spindle poles. The capture and stabilization of microtubule plus ends at the kinetochore has been extensively studied but very little is known on how their minus-end dynamics are controlled.

Here Isabelle Verno’s lab at the CRG shows that MCRS1 is a RanGTP-regulated factor essential for non-centrosomal microtubule assembly. MCRS1 localizes to the minus ends of chromosomal microtubules and K-fibres, where it protects them from depolymerization. Their data reveal the existence of a mechanism that stabilizes the minus ends of chromosomal microtubules and K-fibres, and is essential for the assembly of a functional bipolar spindle.

Reference:
Meunier S, Vernos I. K-fibre minus ends are stabilized by a RanGTP-dependent mechanism essential for functional spindle assembly. Nat Cell Biol. 2011 Nov 13;

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