Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Biochemistry and mode of action of the Bacillus sphaericus toxins

Bacillus sphaericus produces at least two toxins which are highly toxic to mosquito larvae. The binary toxin, which is comprised of proteins of 51.4 and 41.9 kDa, is present in all highly insecticidal strains. The 100 kDa SSII-1 toxin is present in most highly insecticidal as well as the weakly insecticidal strains. The current status of studies on biochemistry and mode of action of these toxins is reviewed.

Intra- and interindividual variation in flank gland secretions of free-ranging shrews Crocidura russula

Individual differences in Rank gland secretions were examined among males of the monogamous shrew Crocidura russula during the breeding and nonbreeding seasons. Gas chromatography was used to measure intra- and interindividual variation of flank gland secretions of free-ranging shrews from different populations. The number of compounds detected by gas chromatographic analyses was correlated with body mass, flank gland size, and the presence of blood parasites in individual shrews. Very few compounds were detected from the Bank gland area of juvenile males. After they reached sexual maturity, however, the number of compounds detected from the Rank gland secretions increased significantly. At the beginning of the reproductive season 48 different compounds were detected from male flank gland secretions. In the middle of the breeding season 70 compounds were detected, while only 11 compounds were detected during the nonbreeding season. Few compounds were common to all males. There were more volatile compounds in the Bank gland secretions of males in the beginning of the breeding season than later in the breeding season. Males from the same population had fewer differences in the elution profile of compounds than males from different populations indicating that individuals from a distinct population have similar elution profiles of compounds and that each population has its own type of elution profile. No correlations were found between the number of compounds detected by gas chromatography for each male and the male's body mass or flank gland size. Blood parasites (trypanosomes, Trypanosoma crocidurae) were found in only three of 30 males investigated.

Insight into cross-talk between intra-amoebal pathogens.

Abstract: Background: Amoebae are phagocytic protists where genetic exchanges might take place between amoeba-resistant bacteria. These amoebal pathogens are able to escape the phagocytic behaviour of their host. They belong to different bacterial phyla and often show a larger genome size than human-infecting pathogens. This characteristic is proposed to be the result of frequent gene exchanges with other bacteria that share a sympatric lifestyle and contrasts with the genome reduction observed among strict human pathogens.Results: We sequenced the genome of a new amoebal pathogen, Legionella drancourtii, and compared its gene content to that of a Chlamydia-related bacterium, Parachlamydia acanthamoebae. Phylogenetic reconstructions identified seven potential horizontal gene transfers (HGTs) between the two amoeba-resistant bacteria, including a complete operon of four genes that encodes an ABC-type transporter. These comparisons pinpointed potential cases of gene exchange between P. acanthamoebae and Legionella pneumophila, as well as gene exchanges between other members of the Legionellales and Chlamydiales orders. Moreover, nine cases represent possible HGTs between representatives from the Legionellales or Chlamydiales and members of the Rickettsiales order.Conclusions: This study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle.

Ribonucleotide reductase genes of Bacillus prophages: a refuge to introns and intein coding sequences.

The ribonucleotide reductase gene tandem bnrdE/bnrdF in SPbeta-related prophages of different Bacillus spp. isolates presents different configurations of intervening sequences, comprising one to three of six non-homologous splicing elements. Insertion sites of group I introns and intein DNA are clustered in three relatively short segments encoding functionally important domains of the ribonucleotide reductase. Comparison of the bnrdE homologs reveals mutual exclusion of a group I intron and an intein coding sequence flanking the codon that specifies a conserved cysteine. In vivo splicing was demonstrated for all introns. However, for two of them a part of the mRNA precursor molecules remains unspliced. Intergenic bnrdE-bnrdF regions are unexpectedly long, comprising between 238 and 541 nt. The longest encodes a putative polypeptide related to HNH homing endonucleases.

Intra-articular osteoid osteoma of the knee: clinical and therapeutical particularities

The intra-articular osteoid osteoma (10-13% of the cases) is often difficult to identify. They present frequent atypical clinical signs and radiological images that eventually lead to inadequate treatment. For example, it has been observed that this pathology leads to inappropriate arthroscopies (up to 40%). Meniscal tear and then osteochondritis were initially suspected on a patient with an intra-articular osteoid osteoma at the tibia level. For the treatment, any damage of the cartilage has to be avoided. Thermoablation with radiofrequency is the treatment of choice

Analyse des cannabinoïdes par spectrométrie de masse en mode tandem = Analysis of cannabinoids by tandem mass spectrometry

Depuis quelques années, la spectrométrie de masse en tandem (MS/MS) ne cesse de gagner du terrain comme méthode d'analyse en toxicologie forensique, notamment pour le dosage des cannabinoïdes. Couplée à la chromatographie liquide (LC) ou gazeuse (GC), elle permet l'identification fiable et le dosage rapide du THC, de son précurseur acide, et de ses principaux métabolites, y compris les glucuronides. Au cours de ces dix dernières années, un nombre significatif de publications sont parues sur ce sujet. L'objectif de cet article est de passer en revue les analyses par spectrométrie de masse en tandem des cannabinoïdes dans diverses matrices biologiques. In recent years, tandem mass spectrometry (MS/MS) is gaining ground as a reference method of analysis in clinical and forensic toxicology, especially for the determination of cannabinoids. Coupled to liquid chromatography (LC) or gas chromatography (GC), it allows the definitive identification and rapid determination of THC, its acid precursor, and its major metabolites, including the glucuronides. During the past decade, several methods of analysis of cannabinoids in different matrices have appeared on this subject. The aim of this paper is to review the analysis of cannabinoids by tandem mass spectrometry methods in various biological matrices