A densely interconnected genome-wide network of microRNAs and oncogenic pathways revealed using gene expression signatures

MicroRNAs (miRNAs) are important components of cellular signaling pathways, acting either as pathway regulators or pathway targets. Currently, only a limited number of miRNAs have been functionally linked to specific signaling pathways. Here, we explored if gene expression signatures could be used to represent miRNA activities and integrated with genomic signatures of oncogenic pathway activity to identify connections between miRNAs and oncogenic pathways on a high-throughput, genome-wide scale. Mapping >300 gene expression signatures to >700 primary tumor profiles, we constructed a genome-wide miRNA-pathway network predicting the associations of 276 human miRNAs to 26 oncogenic pathways. The miRNA-pathway network confirmed a host of previously reported miRNA/pathway associations and uncovered several novel associations that were subsequently experimentally validated. Globally, the miRNA-pathway network demonstrates a small-world, but not scale-free, organization characterized by multiple distinct, tightly knit modules each exhibiting a high density of connections. However, unlike genetic or metabolic networks typified by only a few highly connected nodes ("hubs"), most nodes in the miRNA-pathway network are highly connected. Sequence-based computational analysis confirmed that highly-interconnected miRNAs are likely to be regulated by common pathways to target similar sets of downstream genes, suggesting a pervasive and high level of functional redundancy among coexpressed miRNAs. We conclude that gene expression signatures can be used as surrogates of miRNA activity. Our strategy facilitates the task of discovering novel miRNA-pathway connections, since gene expression data for multiple normal and disease conditions are abundantly available.     

Complete killing of Caenorhabditis elegans by Burkholderia pseudomallei is dependent on prolonged direct association with the viable pathogen

Background

Burkholderia pseudomallei is the causative agent of melioidosis, a disease of significant morbidity and mortality in both human and animals in endemic areas. Much remains to be known about the contributions of genotypic variations within the bacteria and the host, and environmental factors that lead to the manifestation of the clinical symptoms of melioidosis.

Methodology/Principal Findings

In this study, we showed that different isolates of B. pseudomallei have divergent ability to kill the soil nematode Caenorhabditis elegans. The rate of nematode killing was also dependent on growth media: B. pseudomallei grown on peptone-glucose media killed C. elegans more rapidly than bacteria grown on the nematode growth media. Filter and bacteria cell-free culture filtrate assays demonstrated that the extent of killing observed is significantly less than that observed in the direct killing assay. Additionally, we showed that B. pseudomallei does not persistently accumulate within the C. elegans gut as brief exposure to B. pseudomallei is not sufficient for C. elegans infection.

Conclusions/Significance

A combination of genetic and environmental factors affects virulence. In addition, we have also demonstrated that a Burkholderia-specific mechanism mediating the pathogenic effect in C. elegans requires proliferating B. pseudomallei to continuously produce toxins to mediate complete killing.     

Influence of substrate supply on cardiac efficiency, as measured by pressure-volume analysis in ex vivo mouse hearts

In the present study, we tested the reliability of measurements of pressure-volume area (PVA) and oxygen consumption (MVo(2)) in ex vivo mouse hearts, combining the use of a miniaturized conductance catheter and a fiber-optic oxygen sensor. Second, we tested whether we could reproduce the influence of increased myocardial fatty acid (FA) metabolism on cardiac efficiency in the isolated working mouse heart model, which has already been documented in large animal models. The hearts were perfused with crystalloid buffer containing 11 mM glucose and two different concentrations of FA bound to 3% BSA. The initial concentration was 0.3 +/- 0.1 mM, which was subsequently raised to 0.9 +/- 0.1 mM. End-systolic and end-diastolic pressure-volume relationships were assessed by temporarily occluding the preload line. Different steady-state PVA-MVo(2) relationships were obtained by changing the loading conditions (pre- and afterload) of the heart. There were no apparent changes in baseline cardiac performance or contractile efficiency (slope of the PVA-MVo(2) regression line) in response to the elevation of the perfusate FA concentration. However, all hearts (n = 8) showed an increase in the y-intercept of the PVA-MVo(2) regression line after elevation of the palmitate concentration, indicating an FA-induced increase in the unloaded MVo(2). Therefore, in the present model, unloaded MVo(2) is not independent of metabolic substrate. This is, to our knowledge, the first report of a PVA-MVo(2) relationship in ex vivo perfused murine hearts, using a pressure-volume catheter. The methodology can be an important tool for phenotypic assessment of the relationship among metabolism, contractile performance, and cardiac efficiency in various mouse models.     

The complete nucleotide sequence and gene organization of the mitochondrial genome of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae)

The complete nucleotide sequences of the mitochondrial genome (mitogenome) of the oriental mole cricket, Gryllotalpa orientalis (Orthoptera: Gryllotalpidae), were determined. The 15,521-bp-long G. orientalis mitogenome contains typical gene complement, base composition, and codon usage found in metazoan mitogenomes. The G. orientalis mitogenome contains the third lowest A+T content (70.5%) among the complete insects mt genome sequences. The initiation codon for the G. orientalis COI gene appears to be ATG, instead of the tetranucleotides, which have been postulated to act as initiation codon for Locusta migratoria and some lepidopteran COI genes. The initiation codon for ND2 appears to be GTG, which is rare, but has been designated as an initiator of Tricholepidion gertschi ND2. All anticodons of G. orientalis tRNAs were identical to Drosophila yakuba and L. migratoria. The tRNA(Ser)(AGN) could not form a stable stem loop structure in the DHU arm as shown in many other insect tRNA(Ser)(AGN). Phylogenetic analysis of nucleotide sequence information from all mt genes supported a monophyletic Diptera, a monophyletic Lepidoptera, a monophyletic Coleoptera, a monophyletic Mecopterida (Diptera+Lepidoptera), and a monophyletic Endopterygota (Diptera+Lepidoptera+Coleoptera), suggesting that the complete insect mitogenome sequence has a resolving power to the diversification events within Endopterygota. However, the relationships of ancient insect orders were unstable, indicating the limited use of mitogenome information at deeper phylogenetic depth.     

Effect of natural zeolite on methane production for anaerobic digestion of ammonium rich organic sludge

The effect of an inorganic additive on the methane production from NH(4+)-rich organic sludge during anaerobic digestion was investigated using different kinds of inorganic adsorbent zeolites (mordenite, clinoptilolite, zeolite 3A, zeolite 4A), clay mineral (vermiculite), and manganese oxides (hollandite, birnessite). The additions of inorganic materials resulted in significant NH4+ removals from the natural organic sludge ([NH4+]=1, 150 mg N/l), except for the H-type zeolite 3A and birnessite. However, an enhanced methane production was only achieved using natural mordenite. Natural mordenite also enhanced the methane production from the sludge with a markedly high NH4+ concentration (4500 mg N/l) during anaerobic digestion. Chemical analyses of the sludge after the digestion showed considerable increases in the Ca2+ and Mg2+ concentrations in the presence of natural mordenite, but not with synthetic zeolite 3A. The effect of Ca2+ or Mg2+ addition on the methane production was studied using Na(+)-exchanges mordenite and Ca2+ or Mg(2+)-enriched sludge. The simultaneous addition of Ca2+ ions and Na(+)-exchanged mordenite enhanced the methane production; the amount of produced methane was about three times greater than that using only the Na(+)-exchanged mordenite. In addition, comparing the methane production by the addition of natural mordenite or Ca2+ ions, the methane production with natural mordenite was about 1.7 times higher than that with only Ca2+ ions. The addition of 5% and 10% natural mordenite were suitable condition for obtaining a high methane production. These results indicated that the Ca2+ ions, which are released from natural mordenite by a Ca2+/NH4+ exchange, enhanced the methane production of the organic waste at a high NH4+ concentration. Natural mordenite has a synergistic effect on the Ca2+ supply as well on the NH4+ removal during anaerobic digestion, which is effective for the mitigation of NH4+ inhibition against methane production.     

Some of the properties of flame retardant medium density fiberboard made from rubberwood and recycled containers containing aluminum trihydroxide

The flame retardancy of medium density fiberboard (MDF) made from mixture of rubberwood fibers and recycled old corrugated containers was studied. Aluminum trihydroxide (ATH) was used as a fire retardant additive and mixed with the fibers to manufacture experimental MDF panels using wet process. Phenol formaldehyde (PF) resin in liquid, 2% based on oven dry weight of fibers, was used along with 0%, 10%, 15% and 20% of ATH. The flame retardant test was done using the limiting oxygen index (LOI) test. The other properties investigated include internal bond strength, thickness swelling and water absorption. The results showed that ATH loading increased as the LOI of MDF increased. This demonstrated that ATH could improved the fire retardant property of MDF at sufficient loading. An increase in concentration of ATH showed an increase in the IB values of MDF made without resin. MDF panels made without resin showed a progressive increase in internal bond as the composition of recycled old corrugated containers fiber increased. Addition of resin improved internal bond strength and reduced thickness swelling, and water absorption. Thickness swelling of panel increased as the composition of recycled old corrugated containers fiber increased. Scanning electron microscopy (SEM) and energy dispersive X-ray analysis (EDAX) showed that there is indication of ATH and resin filling the void space in between fibers.     

Purification and characterization of a vaterite-inducing peptide, pelovaterin, from the eggshells of Pelodiscus sinensis (Chinese soft-shelled turtle)

Proteins play a crucial role in the biomineralization of hard tissues such as eggshells. We report here the purification, characterization, and in vitro mineralization studies of a peptide, pelovaterin, extracted from eggshells of a soft-shelled turtle. It is a glycine-rich peptide with 42 amino acid residues and three disulfide bonds. When tested in vitro, the peptide induced the formation of a metastable vaterite phase. The floret-shaped morphology formed at a lower concentration ( approximately 1 microM) was transformed into spherical particles at higher concentrations (>500 microM). The solution properties of the peptide are investigated by circular dichroism (CD), fluorescence emission spectroscopy, and dynamic light scattering (DLS) experiments. The conformation of pelovaterin changed from an unordered state at a low concentration to a beta-sheet structure at high concentrations. Fluorescence emission studies indicated that the quantum yield is significantly decreased at higher concentrations, accompanied by a blue shift in the emission maximum. At higher concentrations a red-edge excitation shift was observed, indicating the restricted mobility of the peptide. On the basis of these observations, we discuss the presence of a peptide concentration-dependent monomer-multimer equilibrium in solution and its role in controlling the nucleation, growth, and morphology of CaCO(3) crystals. This is the first peptide known to induce the nucleation and stabilization of the vaterite phase in solution.     

Evaluation of sulfated fungal beta-glucans from the sclerotium of Pleurotus tuber-regium as a potential water-soluble anti-viral agent

Six water-insoluble fractions of fungal beta-glucans extracted by hot alkali (TM8-1 to TM8-6) from the sclerotia of Pleurotus tuber-regium (PTR) having different molecular weights (M(w)) were sulfated to give their corresponding water-soluble derivatives (S-TM8-1 to S-TM8-6) with the degree of sulfation (DS) ranging from 1.14 to 1.74. The in vitro anti-viral activities of the native beta-glucans (TM8s) and their sulfated derivatives (S-TM8s) were evaluated by the cytopathic effect assay (CPE) and the plaque reduction assay (PRA) against four kinds of viruses, including herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), respiratory syncytial virus (RSV), and influenza A virus (Flu A). Although TM8s were inactive in inhibiting the viral replication in cell cultures, the S-TM8 fractions with the defined M(w) range had potent anti-viral activity against HSV-1 and HSV-2 as shown by the CPE assay. The PRA results suggested that S-TM8 fractions seemed to exert their anti-viral effect by binding to the viral particles, preventing the latter from infecting the host cells. It was plausible that the negative charges on the polymer chain of S-TM8 could interact with the positively charged glycoproteins on the surface of HSV, minimizing the interaction between the HSV and the negatively charged host cells. The anti-viral activity of the S-TM8s might also be explained by their more extended chain conformation in solution due to an increase in one of their molecular parameter, persistence length (q), as compared to the native TM8s. The potential use of S-TM8s as a water-soluble anti-HSV agent is discussed.