Data merging for integrated microarray and proteomic analysis.

The functioning of even a simple biological system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will facilitate the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is the extraction of the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modelling of cell and tissue responses. Given the apparent difficulty in defining the correspondence between gene expression and protein abundance measured in several systems to date, how do we make sense of these data and design the next experiment? In this review, we highlight current approaches and challenges associated with integration and analysis of heterogeneous data sets, focusing on global analysis obtained from high-throughput technologies.     

Long‐term changes in the feeding of Pollachius virens on the Scotian Shelf: responses to a dynamic ecosystem

The diet and feeding ecology of pollock Pollachius virens from the Scotian Shelf and Bay of Fundy in the north‐west Atlantic changed over the last few decades, which was associated with decreases in euphausiid abundance. Stomach contents data for 2078 pollock collected during the 1958–1967 period and for 1230 pollock collected during the 1996–2002 period indicated that pollock diet contained fewer euphausiids and feeding activity decreased. During the early period, euphausiids were present in 65% of the pollock stomachs that contained food and only 9% of these stomachs in the recent period. The decrease of euphausiids was not wholly offset by an increase in piscivory, since there was little increase in the frequency of fish prey in the diet or in the fullness index for this prey type. Empty stomachs were significantly more common in the recent period during both the winter and summer. The decreased occurrence of euphausiids in stomach samples coincided with a significantly decreased abundance of this prey, suggesting that the near‐absence of euphausiids in recently collected pollock stomachs reflected prey abundance. Concurrent with changes in diet and feeding intensity, the condition or 'plumpness' of pollock significantly declined from the early to the late sampling periods.     

Tissue factor activity is increased in human endothelial cells cultured under elevated static pressure

We tested the hypothesis that elevated blood pressure, a knownstimulus for vascular remodeling and an independent risk factor for thedevelopment of atherosclerotic disease, can modulate basal andcytokine-induced tissue factor (TF; CD 142) expression in culturedhuman endothelial cells (EC). Using a chromogenic enzymatic assay, wemeasured basal and tumor necrosis factor- (TNF-; 10 ng/ml, 5 h)-induced TF activities in human aortic EC (HAEC) and vena cava EC(HVCEC) cultured at atmospheric pressure and at 170 mmHg imposedpressure for up to 48 h. Basal TF activities were 22 ± 10 U/mgprotein for HAEC and 14 ± 9 U/mg protein for HVCEC and wereupregulated in both cell types >10-fold by TNF-. Exposure topressure for 5 h induced additional elevation of basal TF activity by47 ± 16% (P < 0.05, n = 6) for HAEC and 17 ± 5%(P < 0.05, n = 3) for HVCEC. Pressurization alsoenhanced TF activity in TNF--treated cells from 240 ± 28 to 319 ± 32 U/mg protein in HAEC (P < 0.05, n = 4) and from 148 ± 25 to179 ± 0.8 U/mg protein (P < 0.05, n = 3) in HVCEC. Cytokinestimulation caused an ~100-fold increase in steady-state TF mRNAlevels in HAEC, whereas pressurization did not alter either TF mRNA orcell surface antigen expression, as determined by quantitative RT-PCRmethodology and ELISA. Elevated pressure, however, modulated the ECplasma membrane organization and/or permeability as inferred from theincreased cellular uptake of the fluorescent amphipathic dyemerocyanine 540 (33 ± 7%, P < 0.05). Our data suggest that elevated static pressure modulates thehemostatic potential of vascular cells by modifying the molecular organization of the plasma membrane.

     

Approaches for Integrated Risk Assessment

Recognizing the need to enhance the effectiveness and efficiency of risk assessments globally, the World Health Organization's International Programme on Chemical Safety, the U.S. Environmental Protection Agency, the European Commission, and the Organization for Economic Cooperation and Development developed a collaborative partnership to foster integration of assessment approaches used to evaluate human health and ecological risks. The objectives of this effort included: improving understanding of the benefits of integration, identifying obstacles to the integration process, and engaging key agencies, organizations, and scientific societies to promote integration. A framework with supporting documentation was developed to describe an approach for integration. Four case studies were constructed to illustrate how integrated risk assessments might be conducted for chemical and nonchemical stressors. The concepts and approaches developed in the project were evaluated in an international workshop. The goal of this effort was international acceptance of guidance for integrated risk assessment.     

Facility-Based Delivery during the Ebola Virus Disease Epidemic in Rural Liberia: Analysis from a Cross-Sectional,Population-Based Household Survey

BackgroundThe Ebola virus disease (EVD) epidemic has threatened access to basic health services through facility closures, resource diversion, and decreased demand due to community fear and distrust. While modeling studies have attempted to estimate the impact of these disruptions, no studies have yet utilized population-based survey data.ConclusionsWe detected a 30% decreased odds of FBD after the start of EVD in a rural Liberian county with relatively few cases. Because health facilities never closed in Rivercess County, this estimate may under-approximate the effect seen in the most heavily affected areas. These are the first population-based survey data to show collateral disruptions to facility-based delivery caused by the West African EVD epidemic, and they reinforce the need to consider the full spectrum of implications caused by public health emergencies.     

Evolution of alcohol dehydrogenase genes in peonies (Paeonia): phylogenetic relationships of putative nonhybrid species

Alcohol dehydrogenase genes were amplified by PCR, cloned, and sequenced from 11 putative nonhybrid species of the angiosperm genus Paeonia. Sequences of five exons and six intron regions of the Adh gene were used to reconstruct the phylogeny of these species. Two paralogous genes, Adh1A, and Adh2, were found; an additional gene, Adh1B, is also present in section Moutan. Phylogenetic analyses of exon sequences of the Adh genes of Paeonia and a variety of other angiosperms imply that duplication of Adh1 and Adh2 occurred prior to the divergence of Paeonia species and was followed by a duplication resulting in Adh1A and Adh1B. Concerted evolution appears to be absent between these paralogous loci. Phylogenetic analysis of only the Paeonia Adh exon sequences, positioning the root of the tree between the paralogous genes Adh1 and Adh2, suggests that the first evolutionary split within the genus occurred between the shrubby section Moutan and the other two herbaceous sections Oneapia and Paeonia. Restriction of Adh1B genes to section Moutan may have resulted from deletion of Adh1B from the common ancestor of sections Oneapia and Paeonia. A relative-rate test was designed to compare rates of molecular change among lineages based on the divergence of paralogous genes, and the results indicate a slower rate of evolution within the shrubby section Moutan than in section Oneapia. This may be responsible for the relatively long branch length of section Oneapia and the short branch length between section Moutan and the other two sections found on the Adh, ITS (nrDNA), and matK (cpDNA) phylogenies of the genus. Adh1 and Adh2 intron sequences cannot be aligned, and we therefore carried out separate analyses of Adh1A and Adh2 genes using exon and intron sequences together. The Templeton test suggested that there is not significant incongruence among Adh1A, ITS, and matK data sets, but that these three data sets conflict significantly with Adh2 sequence data. A combined analysis of Adh1A, ITS, and matK sequences produced a tree that is better resolved than that of any individual gene, and congruent with morphology and the results of artificial hybridization. It is therefore considered to be the current best estimate of the species phylogeny. Paraphyly of section Paeonia in the Adh2 gene tree may be caused by longer coalescence times and random sorting of ancestral alleles.      

Intraspecific phylogeography of the Cape galaxias from South Africa: evidence from mitochondrial DNA sequences

Mitochondrial cytochrome b gene sequences were obtained from representatives of five populations of the Cape galaxias Galaxias zebratus . Four highly distinct genotypes were revealed, with sequence divergence values ranging from 5.8 to 13.8%. Some of the pairwise divergences are the highest yet reported for cytochrome b within a fish species, and are more typical of interspecific and intergeneric comparisons. In contrast, the low genetic divergence (0.3%) between two recently recorded populations from the Krom and Gamtoos (Kouga) Rivers indicates recent gene flow. Parsimony analysis consistently produced a tree with the population from the Olifants River on the west coast as ancestral and eastern populations as progressively more derived. Estimated divergence times for the Olifants population range from 4.4 to 6.6 million years ago. The findings suggest that another detailed revision is required to determine whether these divergent populations represent a single species or a species complex.     

Secretory protein translocation in a yeast cell-free system can occur posttranslationally and requires ATP hydrolysis

We describe an in vitro system with all components derived from the yeast Saccharomyces cerevisiae that can translocate a yeast secretory protein across microsomal membranes. In vitro transcribed prepro-alpha-factor mRNA served to program a membrane-depleted yeast translation system. Translocation and core glycosylation of prepro-alpha-factor were observed when yeast microsomal membranes were added during or after translation. A membrane potential is not required for translocation. However, ATP is required for translocation and nonhydrolyzable analogues of ATP cannot serve as a substitute. These findings suggest that ATP hydrolysis may supply the energy required for translocation of proteins across the endoplasmic reticulum.     

Alloantigenic sites on class I major histocompatibility complex antigens: 61-69 region in the first domain of the H-2Kb molecule induces specific antibody and T cell responses

The most polymorphic residues in the first domain of class I major histocompatibility complex (MHC) molecules are in the 61-69 region. We have chosen the H-2Kb molecule for determining the role of this region in the induction of alloimmune responses. A synthetic peptide, Glu-Arg-Glu-Thr-Gln-Lys-Ala-Lys-Gly corresponding to this region was synthesized. T cells enriched from the lymph nodes of allostrain mice that were previously primed with H-2Kb containing cells or with the synthetic peptide in complete Freund's adjuvant undergo extensive in vitro proliferation in response to the synthetic (61-69)H-2Kb peptide. The response was dependent on the presentation of the (61-69)H-2Kb peptide by the syngeneic antigen-presenting cells and was blocked by anti-class II MHC monoclonal antibodies. This peptide fragment of class I MHC molecule activates only helper/inducer type T cells that are involved in the primary responses but not the effector cytotoxic T cells. When coupled to a carrier protein, (61-69)H-2Kb peptide induced antibodies in allostrain mice that bind to intact H-2Kb molecule. No antibodies or T cell responses could be induced in syngeneic H-2b mice. The antigenic site on the H-2Kb molecule recognized by two H-2Kb-specific monoclonal antibodies B8 X 3 X 24 and Y-25 was also mapped in the 61-69 region by direct binding to the synthetic peptide. Therefore the 61-69 region on the H-2Kb molecule represents the first defined sequence on a class I molecule that is directly involved in the induction of alloimmune responses.