An adaptive bin framework search method for a beta-sheet protein homopolymer model

Background  

The problem of protein structure prediction consists of predicting the functional or native structure of a protein given its linear sequence of amino acids. This problem has played a prominent role in the fields of biomolecular physics and algorithm design for over 50 years. Additionally, its importance increases continually as a result of an exponential growth over time in the number of known protein sequences in contrast to a linear increase in the number of determined structures. Our work focuses on the problem of searching an exponentially large space of possible conformations as efficiently as possible, with the goal of finding a global optimum with respect to a given energy function. This problem plays an important role in the analysis of systems with complex search landscapes, and particularly in the context of ab initio protein structure prediction.     

The <Emphasis Type="Italic">Yersinia enterocolitica</Emphasis> type three secretion chaperone SycO is integrated into the Yop regulatory network and binds to the Yop secretion protein YscM1

Background  

Pathogenic yersiniae (Y. pestis, Y. pseudotuberculosis, Y. enterocolitica) share a virulence plasmid encoding a type three secretion system (T3SS). This T3SS comprises more than 40 constituents. Among these are the transport substrates called Yops (Yersinia outer proteins), the specific Yop chaperones (Sycs), and the Ysc (Yop secretion) proteins which form the transport machinery. The effectors YopO and YopP are encoded on an operon together with SycO, the chaperone of YopO. The characterization of SycO is the focus of this study.     

eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

Background  

Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships between multiple genomic regions and multiple expressional profiles. There is a need for informative bioinformatics tools to assist the visualization and interpretation of these mapping results.     

Habitat utilization by sympatric European mink<Emphasis Type="Italic">Mustela lutreola</Emphasis> and polecats<Emphasis Type="Italic">Mustela putorius</Emphasis> in south-western France

The European minkMustela lutreola Linnaeus, 1761 and the European polecatMustela putorius Linnaeus, 1758 are related species sympatric in southwestern France. The European mink is rapidly disappearing whereas the polecat maintains good populations. Seasonal habitat use of both species was compared in the Landes de Gascogne region to identify if some vulnerability factors of the European mink were associated with habitats occupied by this mustelid. Potential habitats were mapped using a satellite picture and 12 main types of habitats were defined. Animal locations were recorded by radiotracking 9 European mink and 14 polecats from March 1996 to August 1999. Resting animals were located by triangulation, and, when possible, resting places were described. Animals in activity were tracked by continuous monitoring. Data collected revealed a strong preference of European mink for flooded habitats, particularly open marshes, flooded woodlands and moorlands. They seldom left the corridor of the riparian forest and their resting places were mainly in flooded environments, above ground (under herbs or bushes) or in cavities between tree roots. European polecats were less tightly linked to wetlands. Most of their locations were in the pine forests outside the valleys and their resting places were mainly in burrows. The strong specialisation of European mink in aquatic habitats is probably one of the main reasons for its decline because wetlands suffer drastic damages throughout all of its range. Maintaining adequate water levels is crucial for satisfying habitat requirements of mink.     

Prediction and preliminary validation of oncogene regulation by miRNAs

Background  

MicroRNAs (miRNAs) are one of the most abundant groups of regulatory genes in multicellular organisms, playing important roles in many fundamental cellular processes. More than four hundred miRNAs have been identified in humans and the deregulation of miRNA expression has been also shown in many cancers. Despite the postulated involvement of miRNAs in tumourigenesis, there are only a few examples where an oncogene or a tumour suppressor has been identified as a miRNA target.     

GATA elements control repression of cardiac troponin I promoter activity in skeletal muscle cells

Background  

We reported previously that the cardiac troponin I (cTnI) promoter drives cardiac-specific expression of reporter genes in cardiac muscle cells and in transgenic mice, and that disruption of GATA elements inactivates the cTnI promoter in cultured cardiomyocytes. We have now examined the role of cTnI promoter GATA elements in skeletal muscle cells.