H-NS mediates the silencing of laterally acquired genes in bacteria

Histone-like nucleoid structuring protein (H-NS) is a modular protein that is associated with the bacterial nucleoid. We used chromatin immunoprecipitation to determine the binding sites of H-NS and RNA polymerase on the Salmonella enterica serovar Typhimurium chromosome. We found that H-NS does not bind to actively transcribed genes and does not co-localize with RNA polymerase. This shows that H-NS principally silences gene expression by restricting the access of RNA polymerase to the DNA. H-NS had previously been shown to preferentially bind to curved DNA in vitro. In fact, at the genomic level we discovered that the level of H-NS binding correlates better with the AT-content of DNA. This is likely to have evolutionary consequences because we show that H-NS binds to many Salmonella genes acquired by lateral gene transfer, and functions as a gene silencer. The removal of H-NS from the cell causes un-controlled expression of several Salmonella pathogenicity islands, and we demonstrate that this has deleterious consequences for bacterial fitness. Our discovery of this novel role for H-NS may have implications for the acquisition of foreign genes by enteric bacteria.     

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

The shape of human gene family phylogenies

Background  

The shape of phylogenetic trees has been used to make inferences about the evolutionary process by comparing the shapes of actual phylogenies with those expected under simple models of the speciation process. Previous studies have focused on speciation events, but gene duplication is another lineage splitting event, analogous to speciation, and gene loss or deletion is analogous to extinction. Measures of the shape of gene family phylogenies can thus be used to investigate the processes of gene duplication and loss. We make the first systematic attempt to use tree shape to study gene duplication using human gene phylogenies.     

Constructing Alzheimer's: Narratives of Lost Identities,Confusion and Loneliness in Old Age

This paper is a qualitative study based on retrospective, unstructured, qualitative interviews with Mrs. Jones and other African-American, Chinese-American, Irish-American and Latino family caregivers in the Boston area. A narrative approach is used to show how family caregivers draw on their cultural and personal resources to create stories about the nature and meaning of illness and to ask how ethnic identity may influence the kinds of stories family caregivers tell. Three different story types are identified and described, each with a distinctive configuration of illness meanings and overarching theme, or storyline: a subset of African-American, Irish-American, and Chinese-American caregivers told us stories about Alzheimer's as a disease that erodes the core identity of a loved one and deteriorates their minds; a subset of Chinese caregivers narrated stories that emphasized how families managed confusion and disabilities, changes ultimately construed as an expected part of growing old; a subset of Puerto Rican and Dominican families, while using the biomedical label of Alzheimer's disease or dementia, placed the elder's illness in stories about tragic losses, loneliness, and family responsibility. To construct their stories, caregivers drew upon both biomedical explanations and other cultural meanings of behavioral and cognitive changes in old age. Their stories challenge us to move beyond the sharp contrast between ethnic minority and non-ethnic minority views of dementia-related changes, to local clinics and hospitals as sites where biomedical knowledge is interpreted, communicated, discussed, and adapted to the perspectives and lived realities of families.     

Ceramide-induced apoptosis: role of catalase and hepatocyte growth factor

The aim of this study was to elucidate cellular mechanisms involved in ceramide-induced apoptosis and its attenuation by hepatocyte growth factor (HGF). Human retinal pigmented epithelial cells (RPE) incubated with C2 ceramide accumulated reactive oxygen species (ROS) in mitochondria and underwent apoptosis in a dose-dependent manner. Ceramide-treated cells showed increased caspase-3 activation and an increase in mitochondrial membrane permeability transition (MPT). Low doses of H2O2 (100 microM) alone induced negligible apoptosis; however, ceramide-induced apoptosis was significantly enhanced by co-incubation with H2O2 (100 microM). Furthermore, ceramide treatment significantly decreased catalase enzymatic activity and protein expression. HGF pretreatment (20 ng/ml) significantly inhibited ceramide-induced apoptosis and reduced the accumulation of ROS, the activation of caspase-3, and the increase in MPT and prevented the reduction in catalase activity and expression. Together, the data suggest that ceramide induces apoptosis in RPE cells by increasing ROS production, MPT, and caspase-3 activation. The ceramide effect is potentiated by H2O2 and associated with a reduction in catalase activity, suggesting that catalase plays a central role in regulating this apoptotic response. The ability of HGF to attenuate these effects demonstrates its effectiveness as an antioxidant growth factor.     

A purified subfragment of yeast Atp11p retains full molecular chaperone activity

Atp11p is a molecular chaperone of the mitochondrial matrix that participates in the biogenesis pathway to form F1, the catalytic unit of the ATP synthase. Affinity tag pull-down assays and yeast two-hybrid screens have shown that Atp11p binds to free beta subunits of F1 (Wang, Z. G., and Ackerman, S. H. (2000) J. Biol. Chem. 275, 5767-5772). This binding action prevents the beta subunit from associating with itself in non-productive complexes and fosters the formation of a (alpha beta)3 hexamer. Following the premise that Atp11p action is mediated primarily through a surface (as opposed to specific amino acids, as in an enzyme active site), solving its three-dimensional structure so that we may learn how the shape of the protein influences its function is a high priority. Recombinant yeast Atp11p has proven refractory for such analysis because of the presence of a disordered region in the protein. In this article, we show that removal of 67 residues from the amino terminus of recombinant Atp11p yields a subfragment of the protein (called Atp11pTRNC) that retains molecular chaperone function as determined in vitro with both a surrogate substrate (reduced insulin) and the natural substrate (F1 beta). Moreover, preliminary 15N-1H heteronuclear single quantum coherence spectra obtained with Atp11pTRNC indicate that the truncated protein is well ordered and amenable to structure determination by nuclear magnetic resonance.     

Sources and flowpaths of dissolved organic carbon during storms in two forested watersheds of the Precambrian Shield

Dissolved organic carbon (DOC) concentrations and export were studied in two small catchments in central Ontario to examine DOC sources and to assess the hypothesis that organic matter adjacent to the stream is a significant contributor of DOC during storms. Different DOC dynamics and exports were observed according to the depth of the riparian water table. In Harp 4-21, riparian flowpaths were predominantly through A and upper B soil horizons and riparian soils contributed between 73 and 84% of the stream DOC export during an autumn storm. In Harp 3A, riparian flowpaths were predominantly through lower B horizons. Consequently, riparian soils were less important and hillslopes contributed more than 50% of the stream DOC export in subcatchments without wetlands during storms. Wetlands and adjacent soils contributed significantly to DOC export in Harp 3A; 8% of the total catchment area exported 32 to 46% of the storm runoff DOC. DOC export dynamics in wetlands and riparian soils were distinctly different. In wetlands, transport was affected by leaching and flushing of DOC at the wetland surface leading to lower DOC concentrations with successive storms. In riparian soils, groundwater flowpaths were more important and stronger positive relationships between discharge and DOC concentration were observed. Precipitation, throughfall and stemflow were minor sources of stream DOC during storms and contributed less than 20% of the total export.     

Two Mutators and Their Suppressors in DROSOPHILA ANANASSAE

Assays of seven mutant stocks exposed a ten-fold range in spontaneous Minute mutation frequencies. Genetic analysis of the difference between the px (0.0006 Minutes) and bri (0.0042 Minutes) stocks revealed that each of these stocks lacks one of two complementary, autosomally transmitted, maternally expressed, dominant suppressors of a dominant 3-linked mutator present in the bri stock. Analysis of the ca; stw stock (0.0013 Minutes) with respect to the former two indicated the presence of the autosomal suppressor functions in addition to a maternally expressed, extrachromosomally transmitted, suppressor of a paternal chromosome-breaking mutator, which is also extra-chromosomally transmitted. The lesions induced by the two mutators in male carriers are probably different, but both kinds are subject to modification by the maternal suppressors soon after fertilization. The existence of these diverse controls of mutability is viewed as confirmation of Sturtevant's (1937) argument that natural selection invokes a variety of devices to minimize mutation rates while retaining mutational potential.