The importance of being a highly conserved non-coding region

Yesterday Gill Bejerano (Stanford University) gave a talk at the PRBB in which he advocated the key role of highly conserved non-coding regions, in particular in the context of evolution. He explained there are only about 20,000 human genes, but more than 1,000,000 genome ‘switches’, short DNA regions which control which genes are expressed and at what levels. And the so-called ‘gene deserts’, areas of the genome with very few genes in them, are actually very rich in these conserved non-coding elements which act as cis-regulators of gene expression. So, as he said, perhaps more than gene deserts they should be … Continue reading The importance of being a highly conserved non-coding region

Molecular and healthcare information, a necessary marriage

The first keynote speaker at the XI Bioinformatics Symposium was Søren Brunak, director of the Centre for Biological Sequence Analysis (CBS) in Denmark. He gave an interesting overview on the need to integrate the very detailed molecular information we have with the phenotypic data we can get from the healthcare sector. He explained the best source of this type of data are the electronic patient records (EPR or EMR – for medical records), which are very well established in his country as well as other small European countries such as the Netherlands, but not at all in bigger countries such … Continue reading Molecular and healthcare information, a necessary marriage

Challenges and limitations of Bioinformatics: XI Bioinformatics Symposium at the PRBB

More than 225 people registered to the XI Bioinformatics Symposium, co-organised by the Spanish Institute of Bioinformatics (INB) and the Portuguese Bioinformatics Network and hosted by the PRBB. From yesterday, January 23 and until tomorrow, Jan 25 they will enjoy the talks of three keynote speakers and another 31 scientists, as well as more than 100 scientific posters. Alfonso Valencia, director of the INB – and who had recently been at the PRBB for another bioinformatics meeting – explained at the inauguration that the aim of the conference, organized jointly with the Portuguese community for the last three years, was to stimulate collaborations between both countries … Continue reading Challenges and limitations of Bioinformatics: XI Bioinformatics Symposium at the PRBB

The challenges of engineering zinc-finger nucleases

Artificial zinc-finger DNA-binding proteins (ZFPs) have been engineered for quite some time now, and can be very useful in molecular biology. Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. These structural motifs are involved in a broad range of biological activities including DNA binding, DNA and RNA recognition, as well as coordinating protein-protein interactions. One use of ZFPs is the creation of a sequence-specific nuclease, which can be used, for example, to mutate chromosomal targets, via a double-stranded DNA break, or to integrate foreign DNA into a locus. These are called zinc finger nucleases (ZFNs). Even though a … Continue reading The challenges of engineering zinc-finger nucleases

Computer simulations with pharmacological interest

Computer simulations with pharmacological interest In this image by Ignasi Buch, from the Computational Biochemistry and Biophysics Laboratory of the GRIB (IMIM/UPF), we can see a simulation of the union of a drug with its target. The small hexagonal molecule represents the benzamidine drug, an inhibitor of tripsine, which is represented by the 3D grey molecule. Tripsine is an enzyme which cuts proteins. Its binding to benzamidine makes it impossible for it to connect to other proteins that it should cut. This dynamic simulation of the inhibition shows how benzamidine first interacts with several regions of tripsine which help the … Continue reading Computer simulations with pharmacological interest

A new type of neutrophils with a role in antibody production

Following on a previous post on a review on the regulation of mucosal IgA responses by Andrea Cerutti, we are back with this IMIM researcher, who has now published a paper in Nature Immunology. His group, in collaboration with scientists in Mount Sinai in New York, has just discovered the presence of neutrophils in the marginal zone (MZ) of the spleen, a B cell area positioned at the interface between the circulation and the immune system. The presence of these cells is constant, even in the absence of infection. The authors obtained lymphoid organs from people with no inflammation or infection. … Continue reading A new type of neutrophils with a role in antibody production

Phosphorylase kinase PhKG1, a new target for anti-angiogenesis therapies

A team of researchers from the CMRB directed by Juan Carlos Izpisúa Belmonte has discovered two novel inhibitors of the phosphorylase kinase subunit G1 (PhKG1) that has been identified for the first time to be involved in angiogenesis in vivo. Furthermore, they found that PhKG1 mRNA levels are elevated by more than two-fold in the majority of human tumors (breast, colon, kidney, lung, liver and thyroid), except in prostate cancer. The study was published in Oncogene. Pathological angiogenesis, the growth of microvessels from existing vasculature, is associated with tumor progression and is a pre-requisite of tumor growth and metastasis. Therefore, inhibitors … Continue reading Phosphorylase kinase PhKG1, a new target for anti-angiogenesis therapies

Environmental stress responses can protect individuals from inherited mutations

Mutations often have consequences that vary across individuals. A study published in Science by Ben Lehner, head of the Genetic Systems Group at the CRG, shows that the stimulation of a stress response can reduce mutation penetrance in Caenorhabditis elegans. Moreover, this induced mutation buffering varies across isogenic individuals because of interindividual differences in stress signaling. This variation has important consequences in wild-type animals, producing some individuals with higher stress resistance but lower reproductive fitness and other individuals with lower stress resistance and higher reproductive fitness. In the experimental setting they used a transgene to overexpress the heat shock factor … Continue reading Environmental stress responses can protect individuals from inherited mutations