Coev2Net: a computational framework for boosting confidence in high-throughput protein-protein interaction datasets

ABSTRACT: Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false positive and false negative rates. Coev2Net is easily applied to thousands of binary protein interactions and has superior predictive performance over existing methods. We experimentally validate selected high-confidence predictions in the human MAPK network and show that predicted interfaces are enriched for cancer-related or damaging SNPs. Coev2Net can be downloaded at http://struct2net.csail.mit.edu/     

The effect of fucoidan from brown seaweed Sargassum wightii on WSSV resistance and immune activity in shrimp Penaeus monodon (Fab)

The polysaccharide-fucoidan was extracted from brown seaweed Sargassum wightii and characterized through FT-IR and ¹³C & ¹H NMR analysis. The extracted fucoidan was supplemented with pellet diets at three different concentrations (0.1, 0.2 and 0.3%). The fucoidan supplemented diets were fed to Penaeus monodon for 45 days, then challenged with WSSV and the mortality percentage was recorded daily up to 21 days. During the challenge test, the control group showed 100% mortality within 10 days, but in the experimental groups, the mortality percentage (51-72% within 21 days) was decreased considerably (P < 0.05) with respect to the concentrations of fucoidan. The reduction in mortality percentage of experimental groups over control group was ranged from 50.81 to 68.06%. During challenge experiment, the immunological parameters such as THC, prophenoloxidase activity, respiratory burst activity, superoxide dismutase activity and phagocytic activity were measured before injection of WSSV (0 day) and after the injection of WSSV on 10th and 21st days, respectively. All the immunological parameters of experimental groups were significantly (P < 0.05) increased than control group. RT-PCR analysis confirmed the considerable reduction of WSSV DNA copy numbers with respect to the concentration of fucoidan. It was concluded that P. monodon fed with fucoidan of S. wightii supplemented diet had enhanced the innate immunity and increased resistance against WSSV infection.     

HIPPIE: Integrating protein interaction networks with experiment based quality scores

Protein function is often modulated by protein-protein interactions (PPIs) and therefore defining the partners of a protein helps to understand its activity. PPIs can be detected through different experimental approaches and are collected in several expert curated databases. These databases are used by researchers interested in examining detailed information on particular proteins. In many analyses the reliability of the characterization of the interactions becomes important and it might be necessary to select sets of PPIs of different confidence levels. To this goal, we generated HIPPIE (Human Integrated Protein-Protein Interaction rEference), a human PPI dataset with a normalized scoring scheme that integrates multiple experimental PPI datasets. HIPPIE's scoring scheme has been optimized by human experts and a computer algorithm to reflect the amount and quality of evidence for a given PPI and we show that these scores correlate to the quality of the experimental characterization. The HIPPIE web tool (available at http://cbdm.mdc-berlin.de/tools/hippie) allows researchers to do network analyses focused on likely true PPI sets by generating subnetworks around proteins of interest at a specified confidence level.     

Genomic and proteomic analysis of the Alkali-Tolerance Response (AlTR) in <Emphasis Type="Italic">Listeria monocytogenes</Emphasis> 10403S

Background  

Information regarding the Alkali-Tolerance Response (AlTR) in Listeria monocytogenes is very limited. Treatment of alkali-adapted cells with the protein synthesis inhibitor chloramphenicol has revealed that the AlTR is at least partially protein-dependent. In order to gain a more comprehensive perspective on the physiology and regulation of the AlTR, we compared differential gene expression and protein content of cells adapted at pH 9.5 and un-adapted cells (pH 7.0) using complementary DNA (cDNA) microarray and two-dimensional (2D) gel electrophoresis, (combined with mass spectrometry) respectively.     

DNA interaction of some polymer-copper(II) complexes containing 2,2'-bipyridyl ligand and their antimicrobial activities

The water soluble polymer-copper(II) complex samples, [Cu(bpy)(2)(BPEI)]Cl(2).4H(2)O (bpy=2,2'-bipyridine, BPEI=branched polyethyleneimine), with varying degrees of copper(II) chelates content in the polymer chain, were prepared by ligand substitution method in water-ethanol medium and characterized by Infra-red, UV-visible, EPR spectral and elemental analysis methods. The interaction of these polymer-copper(II)-bipyridyl complex samples with calf thymus DNA has been explored by using electronic absorption spectroscopy, emission spectroscopy and gel electrophoresis techniques. The observed changes in the physico-chemical features of the polymer-copper(II) complex on binding to DNA suggest that the complex binds to DNA with electrostatic interaction mode. A sample of polymer-copper(II) complex was tested for its antibacterial and antifungal activity and it was found to have good antibacterial and antifungal activities.     

Co-encapsulation of lactic acid bacteria and prebiotic with alginate-fenugreek gum-locust bean gum matrix: Viability of encapsulated bacteria under simulated gastrointestinal condition and during storage time

The aim of this study was to enhance the viability of probiotic strains Pediococcus pentosaceus KID7, Lactobacillus plantarum KII2, Lactobacillus fermentum KLAB6 and Lactobacillus helveticus KII13 in gastrointestinal transit, freeze-drying condition and during storage time by microencapsulation using a combination of alginate, fenugreek gum and locust bean gum. The microcapsules were prepared using various ratio of alginate to fenugreek gum to locust bean gum and tested for its dissolution in colonic fluid. The combination that efficiently dissolved in colonic fluid was selected for co-encapsulation of the probiotic strains and prebiotics to produce synbiotic microcapsules. Further, we observed that the bacteria encapsulated with alginate-fenugreek gum-locust bean gum (AFL) matrix tolerated gastrointestinal condition efficiently compared to non-encapsulated bacteria. The encapsulated bacterial cells retained higher viability than non-encapsulated cells during freeze-drying condition and subsequent storage for 3 months at 4°C. These results show the utility of AFL matrix in microencapsulation of probiotics for use in food industry.     

H4R activation utilizes distinct signaling pathways for the production of RANTES and IL-13 in human mast cells

Context: The histamine H4 receptor functionally expressed on human mast cells and their signaling pathways for the production of IL-13 and RANTES have never been analyzed side by side in a directly comparable manner.

Objective: Therefore, the aim of the study was to investigate signaling transduction pathways of H4R via ERK1/2, Akt and NFκB leading to the induction of inflammatory cytokine expression.

Materials and methods: In the present study, HMC-1 cells and CBMCs were pretreated individually with H4R antagonist JNJ7777120, H1R antagonist mepyramine and signaling molecule inhibitors PD 98059, LY294002, Bay 117082 followed by stimulation was done with or without histamine or 4-MH. Furthermore, the siRNA mediated H4R gene silencing effects are studied at the H4R protein expression level and also signal transduction level.

Results: We found that the pretreatment with JNJ7777120 and H4R gene silencing decreased histamine, 4-MH induced phosphorylation of ERK1/2, Akt and NFκB-p65. Moreover, PD 98059, LY294002 and Bay 117082, which respectively inhibited the histamine and 4-methylhistamine induced phosphorylation of ERK1/2, Akt and NFκB-p65 respectively. We also found that the activation of H4R caused the release of IL-13 and RANTES on human mast cells. The MEK inhibitor PD98059 blocked H4R mediated RANTES/CCL5 production by 20.33?pg/ml and inhibited IL-13 generation by 95.71?pg/ml. In contrast, PI3 kinase inhibitor LY294002 had no effect on 4-MH induced RANTES/CCL5 production but blocked IL-13 generation by 117.58?pg/ml.

Discussion and conclusion: These data demonstrate that the H4R activates divergent signaling pathways to induce cytokine and chemokine production in human mast cells.     

Abundance and diversity of macroinvertebrates and fish in the Tamiraparani river, South India

Occurrence of macroinvertebrates and fish was studied at 11 stations along the course of a tropical river, Tamiraparani, South India. Monthly variations in macroinvertebrate density were studied during 1991. Among macroinvertebrates, hemipterans were the dominant group at all sites, except site 2. Using an ordination technique, density and occurrence of macroinvertebrates were correlated with dissolved oxygen, biological oxygen demand and chemical oxygen demand. A total of 36 species of fish was recorded and their diversity in undisturbed and disturbed regions of the river was compared on a spatial scale. Different diversity indices were calculated to assess fish response to pollution and to determine species richness and composition.     

Biotransformation of progesterone to 14 alpha-hydroxypregna-1,4-diene-3,20-dione, a novel fungal metabolite, by Colletotrichum antirrhini

The fermentation of progesterone by Colletotrichum antirrhini SC 2144 was examined. Instead of 15 alpha-hydroxyprogesterone, the reported product, this fungus converted progesterone to androst-4-ene-3,17-dione, androsta-1,4-diene-3,17-dione, 14 alpha-hydroxyandrosta-1,4-diene-3,17-dione, 11 alpha-hydroxypregn-4-ene-3,20-dione, 14 alpha-hydroxypregn-4-ene-3,20-dione, and a hitherto undescribed compound, 14 alpha-hydroxypregna-1,4-diene-3,20-dione.