Predicting gene ontology from a global meta-analysis of 1-color microarray experiments.

Background: Global meta-analysis (GMA) of microarray data to identify genes with highly similar co-expression profiles is emerging as an accurate method to predict gene function and phenotype, even in the absence of published data on the gene(s) being analyzed. With a third of human genes still uncharacterized, this approach is a promising way to direct experiments and rapidly understand the biological roles of genes. To predict function for genes of interest, GMA relies on a guilt-by-association approach to identify sets of genes with known functions that are consistently co-expressed with it across different experimental conditions, suggesting coordinated regulation for a specific biological purpose.

High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses.

Background: Microarray experiments are becoming increasingly common in biomedical research, as is their deposition in publicly accessible repositories, such as Gene Expression Omnibus (GEO). As such, there has been a surge in interest to use this microarray data for meta-analytic approaches, whether to increase sample size for a more powerful analysis of a specific disease (e.g.

Olfactomedin 4 defines a subset of human neutrophils.

OLFM4 was identified initially as a gene highly induced in myeloid stem cells by G-CSF treatment. A bioinformatics method using a global meta-analysis of microarray data predicted that OLFM4 would be associated with specific granules in human neutrophils. Subcellular fractionation of peripheral blood neutrophils demonstrated complete colocalization of OLFM4 with the specific granule protein NGAL, and stimulation of neutrophils with PMA resulted in corelease of NGAL and OLFM4, proving that OLFM4 is a genuine constituent of neutrophil-specific granules.

GenomeRunner: automating genome exploration.

Motivation: One of the challenges in interpreting high-throughput genomic studies such as a genome-wide associations, microarray or ChIP-seq is their open-ended nature-once a set of experimentally identified regions is identified as statistically significant, at least two questions arise: (i) besides P-value, do any of these significant regions stand out in terms of biological implications? (ii) Does the set of significant regions, as a whole, have anything in common genome wide? These issues are difficult to address because of the growing number of annotated genomic features (e.g. single nucleotide polymorphisms, transcription factor binding sites, methylation peaks, etc.

Iron oxyhydroxide nanoparticles formed by forced hydrolysis: dependence of phase composition on solution concentration.

Nanoparticles of single-phase lepidocrocite (γ-FeOOH) and goethite (α-FeOOH) have been synthesized by forced hydrolysis of ferric nitrate with no other additives, and the particles have been characterized by XRD, FT-IR and TEM. At low Fe(NO(3))(3) concentrations the hydrolysis product is predominantly γ-FeOOH, while at high concentrations it is α-FeOOH. These particles are nanometers in size and fall within narrow particle size distributions.

Novel protein ADTRP regulates TFPI expression and function in human endothelial cells in normal conditions and in response to androgen.

Thrombosis and cardiovascular disease (CVD) represent major causes of morbidity and mortality. Low androgen correlates with higher incidence of CVD/thrombosis. Tissue Factor Pathway Inhibitor (TFPI) is the major inhibitor of tissue factor-factor VIIa (TF-FVIIa)-dependent FXa generation.

CO2 induced seawater acidification impacts sea urchin larval development I: elevated metabolic rates decrease scope for growth and induce developmental delay.

Anthropogenic CO(2) emissions are acidifying the world's oceans. A growing body of evidence is showing that ocean acidification impacts growth and developmental rates of marine invertebrates. Here we test the impact of elevated seawater pCO(2) (129 Pa, 1271 μatm) on early development, larval metabolic and feeding rates in a marine model organism, the sea urchin Strongylocentrotus purpuratus.

Effect of gamma irradiation on gas-ionic liquid and water-ionic liquid interfacial stability.

The effect of γ-radiation on gas-ionic liquid (IL) and water-IL interfacial stability was investigated. Three phosphonium-based ILs, which vary considerably in their viscosity, conductivity and miscibility with water, were examined. The gas phase above the IL samples (headspace gas) was analyzed using gas chromatography with a mass spectrometer detector while the changes in the IL and aqueous phases were followed by conductivity measurements and Raman spectroscopy.

Long-term γ-radiolysis kinetics of NO3(-) and NO2(-) solutions.

Radiolysis kinetics in NO(3)(-) and NO(2)(-) solutions during γ-irradiation were studied at an absorbed dose rate of 2.1 Gy·s(-1) at room temperature. Air- or argon-saturated nitrate or nitrite solutions at pH 6.

Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus.

Systemic lupus erythematosus is a chronic-relapsing autoimmune disease of incompletely understood etiology. Recent evidence strongly supports an epigenetic contribution to the pathogenesis of lupus. To understand the extent and nature of dysregulated DNA methylation in lupus T cells, we performed a genome-wide DNA methylation study in CD4 (+) T cells in lupus patients compared to normal healthy controls.

Iron oxyhydroxide colloid formation by gamma-radiolysis.

Gamma-irradiation of deaerated aqueous solutions containing FeSO(4) leads to the formation of uniform-sized colloidal particles of γ-FeOOH. At short irradiation times, or in solutions with a low initial [Fe(2+)](0), spherical particles with a size less than 10 nm are formed. These primary particles grow to form a dendritic structure upon longer irradiation, and the final size of the large particles is ∼60 nm with a very narrow size distribution.

Aggregation of [Au(CN)4]- anions: examination by crystallography and 15N CP-MAS NMR and the structural factors influencing intermolecular Au···N interactions.

To investigate the factors influencing the formation of intermolecular Au···NC interactions between [Au(CN)(4)](-) units, a series of [cation](n+)[Au(CN)(4)](n) double salts was synthesized, structurally characterized and probed by IR and (15)N{(1)H} CP-MAS NMR spectroscopy. Thus, [(n)Bu(4)N][Au(CN)(4)], [AsPh(4)][Au(CN)(4)], [N(PPh(3))(2)][Au(CN)(4)], [Co(1,10-phenanthroline)(3)][Au(CN)(4)](2), and [Mn(2,2';6',2''-terpyridine)(2)][Au(CN)(4)](2) show [Au(CN)(4)](-) anions that are well-separated from one another; no Au-Au or Au···NC interactions are present. trans-[Co(1,2-diaminoethane)(2)Cl(2)][Au(CN)(4)] forms a supramolecular structure, where trans-[Co(en)(2)Cl(2)](+) and [Au(CN)(4)](-) ions are found in separate layers connected by Au-CN···H-N hydrogen-bonding; weak Au···NC coordinate bonds complete octahedral Au(III) centers, and support a 2-D (4,4) network motif of [Au(CN)(4)](-)-units.

Application of physiologically based modelling and transcriptomics to probe the systems toxicology of aldicarb for Caenorhabditis elegans (Maupas 1900).

The toxicity of aldicarb on movement, life cycle, population growth rate and resource allocation, and the gene expression changes underpinning these effects, were investigated for Caenorhabditis elegans. A clear effect of aldicarb on nematode movement was found suggesting that this pesticide acts as a neurotoxicant. Aldicarb also had an effect on life cycle traits including low concentration life-span extension; high concentration brood size reduction and a high concentration extension of time to first egg.

Elevated AKR1C3 expression promotes prostate cancer cell survival and prostate cell-mediated endothelial cell tube formation: implications for prostate cancer progression.

Background: Aldo-keto reductase (AKR) 1C family member 3 (AKR1C3), one of four identified human AKR1C enzymes, catalyzes steroid, prostaglandin, and xenobiotic metabolism. In the prostate, AKR1C3 is up-regulated in localized and advanced prostate adenocarcinoma, and is associated with prostate cancer (PCa) aggressiveness. Here we propose a novel pathological function of AKR1C3 in tumor angiogenesis and its potential role in promoting PCa progression.

Cross-resistance relationships between neonicotinoids and pymetrozine in Bemisia tabaci (Hemiptera: Aleyrodidae).

Background: Although cross-resistance between compounds in the same insecticide group is a frequently observed phenomenon, cross-resistance between groups that differ in structural and functional characteristics can be extremely unpredictable. In the case of controlling the whitefly, Bemisia tabaci Gennadius, neonicotinoids and the pyridine azomethine antifeedant pymetrozine represent independent lines of discovery that should be suited for alternation to avoid prolonged selection for the same resistance mechanism. Reports of an association between responses to neonicotinoids and pymetrozine were investigated by resistance profiling of seven B.

Hypoxia tolerance in animals: biology and application.

Many invertebrates and ectothermic vertebrates successfully cope with a fluctuating supply of ambient oxygen-and consequently, a highly variable tissue oxygenation-through increasing their antioxidant barriers. During chronic deprivation of oxygen, however, the hypometabolic defense mode of the fruit fly Drosophila, the hypoxia-induced behavioral hypothermia of the crayfish Pacifastacus leniusculus, and the production of ethanol during anoxia by the crucian carp Carassius carassius all indicate that these animals are also capable of utilizing a suite of genetic and physiological defenses to survive otherwise lethal reductions in tissue oxygenation. Normally, much of an organism's gene response to hypoxia is orchestrated via the hypoxia-inducible transcription factor HIF.

Identifying duplicate content using statistically improbable phrases.

Motivation: Document similarity metrics such as PubMed's 'Find related articles' feature, which have been primarily used to identify studies with similar topics, can now also be used to detect duplicated or potentially plagiarized papers within literature reference databases. However, the CPU-intensive nature of document comparison has limited MEDLINE text similarity studies to the comparison of abstracts, which constitute only a small fraction of a publication's total text. Extending searches to include text archived by online search engines would drastically increase comparison ability.

DNA methylome in human CD4+ T cells identifies transcriptionally repressive and non-repressive methylation peaks.

DNA methylation is an epigenetic mark that is critical in determining chromatin accessibility and regulating gene expression. This epigenetic mechanism has an important role in T-cell function. We used genome-wide methylation profiling to characterize the DNA methylome in primary human CD4+ T cells.

Linking toxicant physiological mode of action with induced gene expression changes in Caenorhabditis elegans.

Background: Physiologically based modelling using DEBtox (dynamic energy budget in toxicology) and transcriptional profiling were used in Caenorhabditis elegans to identify how physiological modes of action, as indicated by effects on system level resource allocation were associated with changes in gene expression following exposure to three toxic chemicals: cadmium, fluoranthene (FA) and atrazine (AZ).

Results: For Cd, the physiological mode of action as indicated by DEBtox model fitting was an effect on energy assimilation from food, suggesting that the transcriptional response to exposure should be dominated by changes in the expression of transcripts associated with energy metabolism and the mitochondria. While evidence for effect on genes associated with energy production were seen, an ontological analysis also indicated an effect of Cd exposure on DNA integrity and transcriptional activity.

Limitations of the ristocetin cofactor assay in measurement of von Willebrand factor function.

Background: Type 2M von Willebrand disease (VWD) is characterized by a qualitative defect in von Willebrand factor (VWF) and diagnosed by a disproportionate decrease in VWF ristocetin cofactor activity (VWF:RCo) as compared with VWF antigen (VWF:Ag).

Objective: We report here on the spurious diagnosis of VWD in a patient with a sequence variation in the ristocetin-binding domain of VWF.

Patients/methods: The index case had a VWF:RCo of 11 IU dL(-1), with VWF:RCo/VWF:Ag ratio of 0.