Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces

16S rRNA-targeted oligonucleotide probes were designed for butyrate-producing bacteria from human feces. Three new cluster-specific probes detected bacteria related to Roseburia intestinalis, Faecalibacterium prausnitzii, and Eubacterium hallii at mean populations of 2.3, 3.8, and 0.6%, respectively, in samples from 10 individuals. Additional species-level probes accounted for no more than 1%, with a mean of 7.7%, of the total human fecal microbiota identified as butyrate producers in this study. Bacteria related to E. hallii and the genera Roseburia and Faecalibacterium are therefore among the most abundant known butyrate-producing bacteria in human feces.     

Animal models of anxiety and their molecular dissection

Genetic approaches to psychiatric illness need appropriate animal models both for investigating how genetic variants give rise to behavioural disorder and for identifying genes that may be important in human conditions. Yet the relevance of many animal models to psychiatric illness is often not clear. Here I discuss how genetic approaches can be used to validate animal models of anxiety, an approach which is applicable to other animal models. One drawback of genetic validation is the difficulty inherent in identifying the molecular variants that influence the phenotype. I review genetic approaches that have the potential to overcome this problem.     

Survival of nonspecific porin-deficient mutants of Escherichia coli in black sea water

AIMS: The aim of this study was to investigate the links between survival of Escherichia coli in sea water microcosms in the laboratory and the presence of porins in the outer membrane. The E. coli strains studied were a wild-type strain and a series of outer membrane protein (omp) mutants. METHODS AND RESULTS: Bacteria were suspended in natural or filtered-autoclaved sea water microcosms and numbers determined over an incubation period by plate count and by count of cells capable of respiration. CONCLUSIONS: The type of omp mutation has a significant impact in bacterial survival. The double OmpC-OmpF mutant and the OmpR mutant (which was incapable of synthesizing OmpC and OmpF) survived poorly compared with single omp mutants and the wild-type strain. This suggests that these proteins are important in determining the entry of E. coli into the survival mode. The EnvZ mutant, which lacks the protein by which the cell senses some changes in the environment, survived as well as the wild-type strain when compared by plate counts and by respiring cell count. The loss of the EnvZ protein has no effect on survival but it could prevent the organism sensing the changes in the environment through which entry into the survival state is triggered. SIGNIFICANCE AND IMPACT OF THE STUDY: This work is another piece in the puzzle as to how bacteria survive stress conditions.     

c-Src and HSP72 interact in ATP-depleted renal epithelial cells

Disruption of cell contact sites during ischemiacontributes to the loss of organ function in acute renal failure.Because prior heat stress protects cell contact sites in ATP-depleted renal epithelial cells in vitro, we hypothesized that heat shock protein 72 (HSP72), the major inducible cytoprotectant in mammalian cells, interacts with protein kinases that regulate cell-cell andcell-matrix interactions. ATP depletion increased the content ofTyr⁴¹⁶ Src, the activated form of this kinase. c-Srcactivation was associated with an increase in the tyrosinephosphorylation state of -catenin, paxillin, and vinculin, threec-Src substrate proteins that localize to and regulate cell contactsites. Prior heat stress inhibited c-Src activation and decreased thedegree of tyrosine phosphorylation of all three Src substrates duringATP depletion and/or early recovery. HSP72 coimmunoprecipitated withc-Src only in cells subjected to heat stress. ATP depletion markedlyincreased the interaction between HSP72 and c-Src, supporting thehypothesis that HSP72 regulates Src kinase activity. These resultssuggest that alterations in the tyrosine phosphorylation state ofproteins located at the cell-cell and cell-matrix interface mediate, at least in part, the functional state of these structures during ATPdepletion and may be modulated by interactions between HSP72 and c-Src.

     

Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide

We have identified in the Streptococcus pneumoniae genome sequence a two-component system (TCS13, Blp [bacteriocin-like peptide]) which is closely related to quorum-sensing systems regulating cell density-dependent phenotypes such as the development of genetic competence or the production of antimicrobial peptides in lactic acid bacteria. In this study we present evidence that TCS13 is a peptide-sensing system that controls a regulon including genes encoding Blps. Downstream of the Blp TCS (BlpH R) we identified open reading frames (blpAB) that have the potential to encode an ABC transporter that is homologous to the ComA/B export system for the competence-stimulating peptide ComC. The putative translation product of blpC, a small gene located downstream of blpAB, has a leader peptide with a Gly-Gly motif. This leader peptide is typical of precursors processed by this family of transporters. Microarray-based expression profiling showed that a synthetic oligopeptide corresponding to the processed form of BlpC (BlpC*) induces a distinct set of 16 genes. The changes in the expression profile elicited by synthetic BlpC* depend on BlpH since insertional inactivation of its corresponding gene abolishes differential gene induction. Comparison of the promoter regions of the blp genes disclosed a conserved sequence element formed by two imperfect direct repeats upstream of extended -10 promoter elements. We propose that BlpH is the sensor for BlpC* and the conserved sequence element is a recognition sequence for the BlpR response regulator.     

Metabolic Dysfunction in Familial, but Not Sporadic, Amyotrophic Lateral Sclerosis

Abstract: Autosomal dominant familial amyotrophic lateral sclerosis (FALS) is associated with mutations in the gene encoding Cu/Zn superoxide dismutase (SOD1). Previous studies have implicated the involvement of metabolic dysfunction in ALS pathogenesis. To further investigate the biochemical features of FALS and sporadic ALS (SALS), we examined SOD activity and mitochondrial oxidative phosphorylation enzyme activities in motor cortex (Brodmann area 4), parietal cortex (Brodmann area 40), and cerebellum from control subjects, FALS patients with and without known SOD mutations, SALS patients, and disease controls (Pick's disease, progressive supranuclear palsy, diffuse Lewy body disease). Cytosolic SOD activity, predominantly Cu/Zn SOD, was decreased ∼50% in all regions in FALS patients with SOD mutations but was not significantly altered in other patient groups. Marked increases in complex I and II–III activities were seen in FALS patients with SOD mutations but not in SALS patients. We also measured electron transport chain enzyme activities in a transgenic mouse model of FALS. Complex I activity was significantly increased in the forebrain of 60-day-old G93A transgenic mice overexpressing human mutant SOD1, relative to levels in transgenic wild-type animals, supporting the hypothesis that the motor neuron disorder associated with SOD1 mutations involves a defect in mitochondrial energy metabolism.     

A web server to locate periodicities in a sequence

Summary : FT is a tool written in C++, which implements the Fourier analysis method to locate periodicities in aminoacid or DNA sequences. It is provided for free public use on a WWW server with a Java interface. Availability : The server address is http://o2.db. uoa.gr/FT Contact : shamodr@atlas.uoa.gr      

Divergent post‐breeding distribution and habitat associations of fledgling and adult Black‐footed Albatrosses Phoebastria nigripes in the North Pacific

Past tracking studies of marine animals have primarily targeted adults, biasing our understanding of at‐sea habitat use toward older life stages. Anthropogenic threats persist throughout the at‐sea ranges of all life stages and it is therefore of interest to population ecologists and managers alike to understand spatiotemporal distributions and possible niche differentiation between age‐classes. In albatrosses, particularly little is known about the juvenile life stage when fledglings depart the colonies and venture to sea with no prior experience or parental guidance. We compared the dispersal of 22 fledgling Black‐footed Albatross Phoebastria nigripes between 2006 and 2008 using satellite telemetry and 16 adults between 2008 and 2009 using geolocaters from Midway Atoll National Wildlife Refuge, Northwest Hawaiian Islands. Following tag deployment, all fledglings spent several days within the calm atoll waters, then travelled northward until reaching 750–900 km from the colony. At this point, fledgling distributions approached the productive North Pacific Transition Zone (NPTZ). Rather than reaching the high chlorophyll a densities on the leading edge of this zone, however, fledglings remained in areas of low productivity in the subtropical gyre. In contrast, adult albatrosses from the same breeding colony did not utilize the NPTZ at this time of year but rather ranged throughout the highly productive northern periphery of the Pacific Ocean Basin among the shelf regions off Japan and the Aleutian Islands. The dichotomy in habitat use between fledglings and adults from Midway Atoll results in complete spatial segregation between age‐classes and suggests ontogenetic niche separation in this species. This research fills a large knowledge gap in at‐sea habitat use during a little known yet critical life stage of albatrosses, and contributes to a more comprehensive understanding of differential mortality pressure between age‐classes and overall conservation status for the vulnerable Black‐footed Albatross.