In silico secretome analysis approach for next generation sequencing transcriptomic data

<p>Abstract</p> <p>Background</p> <p>Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel therapeutic strategies against parasitic infections. However, none of transcriptomic studies have extensively covered ES protein prediction for identifying novel therapeutic targets, especially as parasites adopt non-classical secretion pathways.</p> <p>Results</p> <p>We developed a semi-automated computational approach for prediction and annotation of ES proteins using transcriptomic data from next generation sequencing platforms. For the prediction of non-classically secreted proteins, we have used an improved computational strategy, together with homology matching to a dataset of experimentally determined parasitic helminth ES proteins. We applied this protocol to analyse 454 short reads of parasitic nematode, <it>Strongyloides ratti</it>. From 296231 reads, we derived 28901 contigs, which were translated into 20877 proteins. Based on our improved ES protein prediction pipeline, we identified 2572 ES proteins, of which 407 (1.9%) proteins have classical N-terminal signal peptides, 923 (4.4%) were computationally identified as non-classically secreted while 1516 (7.26%) were identified by homology to experimentally identified parasitic helminth ES proteins. Out of 2572 ES proteins, 2310 (89.8%) ES proteins had homologues in the free-living nematode <it>Caenorhabditis elegans</it> and 2220 (86.3%) in parasitic nematodes. We could functionally annotate 1591 (61.8%) ES proteins with protein families and domains and establish pathway associations for 691 (26.8%) proteins. In addition, we have identified 19 representative ES proteins, which have no homologues in the host organism but homologous to lethal RNAi phenotypes in <it>C. elegans</it>, as potential therapeutic targets.</p> <p>Conclusion</p> <p>We report a comprehensive approach using freely available computational tools for the secretome analysis of NGS data. This approach has been applied to <it>S. ratti</it> 454 transcriptomic data for <it>in silico</it> excretory/secretory proteins prediction and analysis, providing a foundation for developing new therapeutic solutions for parasitic infections.</p

Study on role of rural health training centre (RHTC) as a supporting component to a primary health care system for NRHM programme in district Muzaffarnagar (UP)

Background:The role of RHTC set up under MCI requirement of medical colleges is rising in implementation of NRHM phase 2 programme (2012 onwards); as private medical colleges are expanding in India and they can be an important supporter in public-private partnership for national health programmes.Objective of current study was to assess the role of rural health training centre as a supporting component to a primary health care system for NRHM programme.Methods:The present study was carried out by comparative evaluation of the rural health and training centre of a private medical college with a sub-centre (Muzaffarnagar) on key RCH services of NRHM: a) Family planning materials distribution, b) ANC services and c) Immunization services. Inclusion criteria: Proper ethical approval from both primary health care system and private medical college authorities were obtained for the study. Study design: Prospective evaluation based study on ANM in SC & SN in RHTC in NRHM programme for 1 year duration from 1st January 2013 to 31st December 2013. Data analysis: The statistical data was analysed by Epi-info version 7.1.3.  Results:The ANC services, family planning services and immunization services delivered under NRHM programme was found to statistically significantly contributed (P <0.05) by SN of RHTC as compared to ANM of SC in area of Bilaspur, Muzaffarnagar (Uttar Pradesh).Conclusion:RHTC of a private medical college in Muzaffarnagar (UP) is significantly contributing and supporting in RCH services of NRHM programme for primary health care system. RHTC of medical colleges can be an asset for public private partnership in NRHM programme.

Nexus between environmental, social and economic development in South Asia: evidence from econometric models

This study investigates the impact of various economic, social and environmental indicators on economic growth in South Asian countries. Using the data throughout 1990–2017, a panel data estimation method is adopted with sophisticated econometric approaches. The obtained results indicate a long-term positive effect of biological capacity, financial development, human development index, income inequality on economic growth while the effect of energy use is the opposite. The findings of the study suggest that governments and associated bodies must promote financial development, human development, and biocapacity to not only attain economic growth in the long-run and but dissuade ecological footprint, and income inequality at the same time while matching the energy consumption with the bio-capacity of each economy

The Transcriptome Analysis of Strongyloides stercoralis L3i Larvae Reveals Targets for Intervention in a Neglected Disease

BackgroundStrongyloidiasis is one of the most neglected diseases distributed worldwide with endemic areas in developed countries, where chronic infections are life threatening. Despite its impact, very little is known about the molecular biology of the parasite involved and its interplay with its hosts. Next generation sequencing technologies now provide unique opportunities to rapidly address these questions.Principal FindingsHere we present the first transcriptome of the third larval stage of S. stercoralis using 454 sequencing coupled with semi-automated bioinformatic analyses. 253,266 raw sequence reads were assembled into 11,250 contiguous sequences, most of which were novel. 8037 putative proteins were characterized based on homology, gene ontology and/or biochemical pathways. Comparison of the transcriptome of S. strongyloides with those of other nematodes, including S. ratti, revealed similarities in transcription of molecules inferred to have key roles in parasite-host interactions. Enzymatic proteins, like kinases and proteases, were abundant. 1213 putative excretory/secretory proteins were compiled using a new pipeline which included non-classical secretory proteins. Potential drug targets were also identified.ConclusionsOverall, the present dataset should provide a solid foundation for future fundamental genomic, proteomic and metabolomic explorations of S. stercoralis, as well as a basis for applied outcomes, such as the development of novel methods of intervention against this neglected parasite

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis

Search for heavy resonances decaying to two Higgs bosons in final states containing four b quarks

A search is presented for narrow heavy resonances X decaying into pairs of Higgs bosons (H) in proton-proton collisions collected by the CMS experiment at the LHC at root s = 8 TeV. The data correspond to an integrated luminosity of 19.7 fb(-1). The search considers HH resonances with masses between 1 and 3 TeV, having final states of two b quark pairs. Each Higgs boson is produced with large momentum, and the hadronization products of the pair of b quarks can usually be reconstructed as single large jets. The background from multijet and t (t) over bar events is significantly reduced by applying requirements related to the flavor of the jet, its mass, and its substructure. The signal would be identified as a peak on top of the dijet invariant mass spectrum of the remaining background events. No evidence is observed for such a signal. Upper limits obtained at 95 confidence level for the product of the production cross section and branching fraction sigma(gg -> X) B(X -> HH -> b (b) over barb (b) over bar) range from 10 to 1.5 fb for the mass of X from 1.15 to 2.0 TeV, significantly extending previous searches. For a warped extra dimension theory with amass scale Lambda(R) = 1 TeV, the data exclude radion scalar masses between 1.15 and 1.55 TeV