The Role of Enterococcus faecalis Sugar Transport in Experimental Colitis

Inflammatory bowel diseases (IBDs), which afflict 1.6 million people in the United States, are chronic, relapsing and immune-mediated intestinal disorders caused in part by aggressive T-cell-mediated immune responses to intestinal microbes in genetically susceptible individuals. However, relatively little is known about how intestinal inflammation affects the function of gut microbiota. We show that Il10-/- mice colonized with a simplified, defined microbial consortium that includes Enterococcus faecalis develop immune-mediated colitis. Transcription of two putative E. faecalis phosphotransferase systems (PTS) that import sugars into the bacterium is upregulated in colitis. We identify gluconate, ribose, and glucosamine as potential substrates for these PTS. The presence of these PTS is associated with altered intestinal microbial ecology and worsened colitis, therefore suggesting a role for E. faecalis sugar metabolism in colitis development. This work highlights the complexity of host-microbial-environmental interactions underlying colitis development and could enable the development of safe and effective treatments for IBDs.Master of Scienc

Rare case of magnetic Ag3+^{3+} ion: double perovskite Cs2_{2}KAgF6_{6}

Normally $4d$ or $5d$ transition metals are in a low-spin state. Here using first-principles calculations, we report on a rare case of a high-spin $S$=1 magnetic state for the Ag$^{3+}$ ion in the double perovskite Cs$_{2}$KAgF$_{6}$. We also explored a possibility of a conventional low-spin $S$=0 ground state and find an associated tetragonal distortion to be 0.29 {\AA}. However, the lattice elastic energy cost and the Hund exchange loss exceed the e$_{g}$ crystal-field energy gain, thus making the low-spin tetragonal structure less favorable than the high-spin cubic structure. We conclude that the compact perovskite structure of Cs$_{2}$KAgF$_{6}$ is an important factor in stabilizing the unusual high-spin ground state of Ag$^{3+}$.Comment: 6 pages, 6 figures, accepted for publication in PR

Comparing One with Many -- Solving Binary2source Function Matching Under Function Inlining

Binary2source function matching is a fundamental task for many security applications, including Software Component Analysis (SCA). The "1-to-1" mechanism has been applied in existing binary2source matching works, in which one binary function is matched against one source function. However, we discovered that such mapping could be "1-to-n" (one query binary function maps multiple source functions), due to the existence of function inlining. To help conduct binary2source function matching under function inlining, we propose a method named O2NMatcher to generate Source Function Sets (SFSs) as the matching target for binary functions with inlining. We first propose a model named ECOCCJ48 for inlined call site prediction. To train this model, we leverage the compilable OSS to generate a dataset with labeled call sites (inlined or not), extract several features from the call sites, and design a compiler-opt-based multi-label classifier by inspecting the inlining correlations between different compilations. Then, we use this model to predict the labels of call sites in the uncompilable OSS projects without compilation and obtain the labeled function call graphs of these projects. Next, we regard the construction of SFSs as a sub-tree generation problem and design root node selection and edge extension rules to construct SFSs automatically. Finally, these SFSs will be added to the corpus of source functions and compared with binary functions with inlining. We conduct several experiments to evaluate the effectiveness of O2NMatcher and results show our method increases the performance of existing works by 6% and exceeds all the state-of-the-art works

Licochalcone A exerts antitumor activity in bladder cancer cell lines and mice models

Purpose: To investigate the effect of licochalcone A (LA) on the inhibition of cell proliferation and ERK1/2 phosphorylation in bladder carcinoma cell lines.Methods: Cell viability was investigated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide (MTT) assay. Dye-binding method was used to examine the concentration of proteins. Lymphocytes were extracted from mice and after surface staining were subjected to BD fixation and permeabilization for intracellular staining. Flow cytometry was used to measure cellular fluorescence.Results: MTT results revealed a significant decrease in the proliferation of UM-UC-3, J82 and HT-1197 cell lines on treatment with LA. LA also induced reduction in phosphorylation of ERK1/2 in all three carcinoma cell lines. In the mouse model, licochalcone A treatment via intraperitoneal (ip) administration induced a significant decrease in the level of regulatory T cells (Tregs). Comparison of the mouse interferon-α (IFN-α)-treated and LA-treated groups revealed that LA treatment caused enhancement of cytotoxic T lymphocyte (CTL) activity similar to that of IFN-α. Administration of UM-UC-3 cells in C3H/HeN mice resulted in marked reduction in the counts for splenocytes and CD4+ CD25+ Foxp3+ T (regulatory T cells) cell proportion in LA-treated mice compared to untreated control group.Conclusion: Licochalcone A may be of therapeutic importance for the prevention of bladder carcinoma. However, studies are required to ascertain the compound’s usefulness in this regard.Keywords: Licochalcone A, Bladder carcinoma, Splenocytes, Phosphorylation, Cell proliferation, Interfero

Evaluation of X-Inactivation Status and Cytogenetic Stability of Human Dermal Fibroblasts after Long-Term Culture

Human primary fibroblasts are a popular type of somatic cells for the production of induced pluripotent stem (iPS) cells. Here we characterized biological properties of primary fibroblasts in terms of cell-growth rate, cytogenetic stability, and the number of inactive X chromosomes during long-term passaging. We produced eight lines of female human dermal fibroblasts (HDFs) and found normal karyotype and expected pattern of X chromosome inactivation (XCI) at low passages (Passage P1-5). However, four out of the eight HDF lines at high passage numbers (≥ P10) exhibited duplicated hallmarks of inactive X chromosome including two punctuate signals of histone H3 lysine 27 trimethylation (H3K27me3) and X inactive-specific transcript (XIST) RNA signals in approximately 8.5–18.5% of the cells. Our data suggest that the copy number of inactive X chromosomes in a subset of female HDF is increased by a two-fold. Consistently, DNA fluorescent in situ hybridization (FISH) identified 3-4 copies of X chromosomes in one nucleus in this subset of cells with two inactive Xs. We conclude that female HDF cultures exhibit a higher risk of genetic anomalies such as carrying an increased number of X chromosomes including both active and inactive X chromosomes at a high passage (≥ P10)

Inflammation-Induced Acid Tolerance Genes gadAB in Luminal Commensal Escherichia coli Attenuate Experimental Colitis

ABSTRACT Dysregulated immune responses to commensal intestinal bacteria, including Escherichia coli , contribute to the development of inflammatory bowel diseases (IBDs) and experimental colitis. Reciprocally, E. coli responds to chronic intestinal inflammation by upregulating expression of stress response genes, including gadA and gadB . GadAB encode glutamate decarboxylase and protect E. coli from the toxic effects of low pH and fermentation acids, factors present in the intestinal lumen in patients with active IBDs. We hypothesized that E. coli upregulates gadAB during inflammation to enhance its survival and virulence. Using real-time PCR, we determined gadAB expression in luminal E. coli from ex-germfree wild-type (WT) and interleukin-10 (IL-10) knockout (KO) (IL-10 −/− ) mice selectively colonized with a commensal E. coli isolate (NC101) that causes colitis in KO mice in isolation or in combination with 7 other commensal intestinal bacterial strains. E. coli survival and host inflammatory responses were measured in WT and KO mice colonized with NC101 or a mutant lacking the gadAB genes (NC101Δ gadAB ). The susceptibility of NC101 and NC101Δ gadAB to killing by host antimicrobial peptides and their translocation across intestinal epithelial cells were evaluated using bacterial killing assays and transwell experiments, respectively. We show that expression of gadAB in luminal E. coli increases proportionately with intestinal inflammation in KO mice and enhances the susceptibility of NC101 to killing by the host antimicrobial peptide cryptdin-4 but decreases bacterial transmigration across intestinal epithelial cells, colonic inflammation, and mucosal immune responses. Chronic intestinal inflammation upregulates acid tolerance pathways in commensal E. coli isolates, which, contrary to our original hypothesis, limits their survival and colitogenic potential. Further investigation of microbial adaptation to immune-mediated inflammation may provide novel insights into the pathogenesis and treatment of IBDs

A novel chlorpyrifos hydrolase CPD from Paracoccus sp. TRP: Molecular cloning, characterization and catalytic mechanism

Background: Biodegradation is a reliable approach for efficiently eliminating persistent pollutants such as chlorpyrifos. Despite many bacteria or fungi isolated from contaminated environment and capable of degrading chlorpyrifos, limited enzymes responsible for its degradation have been identified, let alone the catalytic mechanism of the enzymes. Results: In present study, the gene cpd encoding a chlorpyrifos hydrolase was cloned by analysis of genomic sequence of Paracoccus sp. TRP. Phylogenetic analysis and BLAST indicated that CPD was a novel member of organophosphate hydrolases. The purified CPD enzyme, with conserved catalytic triad (Ser155-Asp251-His281) and motif Gly-Asp-Ser-Ala-Gly, was significantly inhibited by PMSF, a serine modifier. Molecular docking between CPD and chlorpyrifos showed that Ser155 was adjacent to chlorpyrifos, which indicated that Ser155 may be the active amino acid involved in chlorpyrifos degradation. This speculation was confirmed by site-directed mutagenesis of Ser155Ala accounting for the decreased activity of CPD towards chlorpyrifos. According to the key role of Ser155 in chlorpyrifos degradation and molecular docking conformation, the nucleophilic catalytic mechanism for chlorpyrifos degradation by CPD was proposed. Conclusion: The novel enzyme CPD was capable of hydrolyze chlorpyrifos and Ser155 played key role during degradation of chlorpyrifos

Chronic Intestinal Inflammation Induces Stress-Response Genes in Commensal Escherichia coli

Intestinal microbes induce homeostatic mucosal immune responses, but can also cause inappropriate immune activation in genetically susceptible hosts. While immune responses to bacterial products have been studied extensively, little is known about how intestinal inflammation affects the function of commensal luminal microbes