miRegulome: a knowledge-base of miRNA regulomics and analysis

miRNAs regulate post transcriptional gene expression by targeting multiple mRNAs and hence can modulate multiple signalling pathways, biological processes, and patho-physiologies. Therefore, understanding of miRNA regulatory networks is essential in order to modulate the functions of a miRNA. The focus of several existing databases is to provide information on specific aspects of miRNA regulation. However, an integrated resource on the miRNA regulome is currently not available to facilitate the exploration and understanding of miRNA regulomics. miRegulome attempts to bridge this gap. The current version of miRegulome v1.0 provides details on the entire regulatory modules of miRNAs altered in response to chemical treatments and transcription factors, based on validated data manually curated from published literature. Modules of miRegulome (upstream regulators, downstream targets, miRNA regulated pathways, functions, diseases, etc) are hyperlinked to an appropriate external resource and are displayed visually to provide a comprehensive understanding. Four analysis tools are incorporated to identify relationships among different modules based on user specified datasets. miRegulome and its tools are helpful in understanding the biology of miRNAs and will also facilitate the discovery of biomarkers and therapeutics. With added features in upcoming releases, miRegulome will be an essential resource to the scientific community. Availability:http://bnet.egr.vcu.edu/miRegulome

Effective detoxification of Abrus precatorius Linn. seeds by Shodhana

Ayurveda, which is one of the traditional systems of medicine of India, reports the seeds of Abrus precatorius (family: Fabaceae) can be used therapeutically after shodhana process, which removes the toxin. The main objective was to scientifically study the shodhana process by evaluating the safety and efficacy of A. precatorius seeds. Aqueous extract (A1) and detoxified extract (A2) of the seeds were prepared by a process described in Ayurvedic pharmacopoeia. Thin-layer chromatography (TLC) method was developed for the two extracts using different solvent systems. Identical spots were obtained in A1 with reference values (Rf) 0.27, 0.47, and 0.79, whereas A2 showed the absence of spot having Rf value 0.47, which could possibly be the toxin found in the intact seed. A1 and A2 were evaluated for their safety and efficacy. The acute toxicity studies for A1 and A2 revealed that A1 was toxic, whereas A2 was safe at the dose of 2 g/kg. Absence of toxicity in the detoxified extract suggests removal of toxic material in processed seeds. The results obtained for hair growth activity of both the extracts were comparable to that of the standard. However, A2 showed better results in comparison to A1. Thus, the shodhana process described in Ayurveda helps in removing the toxin, while retaining the efficacy at the same time. The statistical analysis was done using one-way analysis of variance

Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in <em>Vibrio cholerae</em> Targeted by <em>Piper betel</em> Derived Compounds

<div><p><em>Vibrio cholerae</em> is the causal organism of the cholera epidemic, which is mostly prevalent in developing and underdeveloped countries. However, incidences of cholera in developed countries are also alarming. Because of the emergence of new drug-resistant strains, even though several generic drugs and vaccines have been developed over time, <em>Vibrio</em> infections remain a global health problem that appeals for the development of novel drugs and vaccines against the pathogen. Here, applying comparative proteomic and reverse vaccinology approaches to the exoproteome and secretome of the pathogen, we have identified three candidate targets (<em>ompU</em>, <em>uppP</em> and <em>yajC</em>) for most of the pathogenic <em>Vibrio</em> strains. Two targets (<em>uppP</em> and <em>yajC</em>) are novel to <em>Vibrio</em>, and two targets (<em>uppP</em> and <em>ompU</em>) can be used to develop both drugs and vaccines (dual targets) against broad spectrum <em>Vibrio</em> serotypes. Using our novel computational approach, we have identified three peptide vaccine candidates that have high potential to induce both B- and T-cell-mediated immune responses from our identified two dual targets. These two targets were modeled and subjected to virtual screening against natural compounds derived from <em>Piper betel</em>. Seven compounds were identified first time from <em>Piper betel</em> to be highly effective to render the function of these targets to identify them as emerging potential drugs against <em>Vibrio</em>. Our preliminary validation suggests that these identified peptide vaccines and <em>betel</em> compounds are highly effective against <em>Vibrio cholerae</em>. Currently we are exhaustively validating these targets, candidate peptide vaccines, and <em>betel</em> derived lead compounds against a number of <em>Vibrio</em> species.</p> </div

Pepitope analysis of identified T-cell epitopes for their exomembrane topology (colored in red) within the corresponding folded proteins.

<p>A) The “VTSGEPVHS” epitope of <i>uppP</i>, B) the “VTETNAAKY” epitope of <i>ompU</i>, and C) the “YNNAETAKK” epitope of <i>ompU</i>.</p

Protein-protein and host-pathogen interactions among ten preliminary identified <i>Vibrio</i> targets.

<p>The interactions demonstrate that the finally selected three targets (<i>ompU</i>, <i>yajC</i>, and <i>uppP</i>) are involved in <i>Vibrio</i> pathogenesis and modulate host response (immunity and apoptosis) by interacting with the host protein PDCD6.</p

3D models of <i>Vibrio</i> targets constructed using threading approaches.

<p>A) Front view of <i>ompU</i>, B) Side view of <i>ompU</i>, and C) Front view of <i>uppP</i>.</p

The best seven <i>Piper betel</i> compounds that may render activities of <i>Vibrio</i> targets <i>ompU</i> and <i>uppP</i>.

<p>GOLD fitness and Moldock scores were considered to select the compounds. Guineesine, Pinoresinol, and Piperdardine inhibit both targets. Dehydropipernonaline and Piperrolein B are effective on <i>ompU</i>. Chlorogenic acid and Eugenyl acetate are good ligands for <i>uppP</i>.</p

Anti-<i>Vibrio</i> activity of Piperdardine.

<p>A). Growth inhibition effects Piperdardine, Ampicillin, and Chloranphenicol on <i>V. Cholerae O1 Inaba</i> growth as per the disk diffusion method. 1) 100 mM, 2) 200 mM, and 3) 300 mM Piperdardine; 4) water; 5) Ampicillin (10 µg); and 6) Chloranphenicol (30 µg). The zones of inhibition (mm) around disks containing Piperdardine are concentration-dependent: 1) 19.3±0.03; 2) 26.23±0.1; 3) 28.65±0.16. Controls: 4) 0±0; 5) 18.51±0.16; and 6) 29.47±0.16. B). Effects on Piperdardine and Chloranphenicol on <i>V. Cholerae O1 Inaba</i> growth as per the Colony-forming units (CFU/ml) assay. As per the method described in the text, 60 mM of Piperdardine (squares) shows anti-<i>Vibrio</i> effect similar to 100 µg/ml of Chloramphenicol (triangles).</p

Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

In this work, we report the complete genome sequence of a Corynebacterium pseudotuberculosis PAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium