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  • 1
    Publication Date: 2016-06-21
    Description: Persistent hepatitis C virus (HCV) infection leads to chronic hepatitis C (CHC), which often progresses to liver cirrhosis (LC) and hepatocellular carcinoma (HCC). The molecular mechanisms that establish CHC and cause its subsequent development into LC and HCC are poorly understood. We have identified a cytoplasmic double-stranded RNA binding protein, Stau1, which is crucial for HCV replication. In this study, Stau1 specifically interacted with the variable-stem-loop region in the 3' NTR and domain IIId of the HCV-IRES in the 5' NTR, and promoted HCV replication and translation. Stau1 coimmunoprecipitates HCV NS5B and a cell factor, protein kinase R (PKR), which is critical for interferon-induced cellular antiviral and antiproliferative responses. Like Stau1, PKR displayed binding specificity to domain IIId of HCV-IRES. Stau1 binds to PKR and strongly inhibits PKR-autophosphorylation. We demonstrated that the transport of HCV RNA on the polysomes is Stau1-dependent, being mainly localized in the monosome fractions when Stau1 is downregulated and exclusively localized in the polysomes when Stau1 is overexpressed. Our findings suggest that HCV may appropriate Stau1 to its advantage to prevent PKR-mediated inhibition of eIF2α, which is required for the synthesis of HCV proteins for translocation of viral RNA genome to the polysomes for efficient translation and replication.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2016-04-01
    Description: A thin layer of fresh water from summer monsoon rain and river runoff in the Bay of Bengal (BoB) has profound influence on air-sea interaction across the south Asian region, but the mechanisms that sustain the low-salinity layer are as yet unknown. Using the first long time series of high-frequency observations from a mooring in the north BoB and satellite salinity data, we show that fresh water from major rivers is transported by large-scale flow and eddies, and shallow salinity stratification persists from summer through winter. The moored observations show frequent 0.2-1.2 psu salinity jumps with time scales of 10 minutes to days, due to O(1-10) km sub-mesoscale salinity fronts moving past the mooring. In winter, satellite sea surface temperature shows 10 km-wide filaments of cool water, in line with moored data. Rapid salinity and temperature changes at the mooring are highly coherent, suggesting slumping of salinity-dominated fronts. Based on these observations, we propose that sub-mesoscale fronts may be one of the important drivers for the persistent fresh layer in the north BoB.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
    Publication Date: 2015-07-12
    Description: We propose a novel mechanism of gene regulation in Mycobacterium tuberculosis where the protein Rv1222 inhibits transcription by anchoring RNA polymerase (RNAP) onto DNA. In contrast to our existing knowledge that transcriptional repressors function either by binding to DNA at specific sequences or by binding to RNAP, we show that Rv1222-mediated transcription inhibition requires simultaneous binding of the protein to both RNAP and DNA. We demonstrate that the positively charged C-terminus tail of Rv1222 is responsible for anchoring RNAP on DNA, hence the protein slows down the movement of RNAP along the DNA during transcription elongation. The interaction between Rv1222 and DNA is electrostatic, thus the protein could inhibit transcription from any gene. As Rv1222 slows down the RNA synthesis, upon expression of the protein in Mycobacterium smegmatis or Escherichia coli , the growth rate of the bacteria is severely impaired. The protein does not possess any significant affinity for DNA polymerase, thus, is unable to inhibit DNA synthesis. The proposed mechanism by which Rv1222 inhibits transcription reveals a new repertoire of prokaryotic gene regulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 4
    Publication Date: 2015-09-26
    Description: Oncostatin-M (OSM) is a patho-physiologically important pleiotropic, multifunctional cytokine. OSM mRNA sequence analysis revealed that its 3'UTR contains three highly conserved GC-rich cis -elements (GCREs) whose role in mRNA stability is unidentified. In the present study, the functional role of the proximal GC-rich region of osm 3'-UTR (GCRE-1) in post-transcriptional regulation of osm expression in U937 cells was assessed by transfecting construct containing GCRE-1 at 3' end of a fairly stable reporter gene followed by analysis of the expression of the reporter. GCRE-1 showed mRNA destabilizing activity however, upon PMA treatment the reporter message containing GCRE-1 was stabilized. This stabilization is owing to a time dependent progressive binding of trans -factors (atleast five proteins) to GCRE-1 post PMA treatment. Nucleolin was identified as one of the proteins in the RNP complex of GCRE-1 with PMA treated U937 cytosolic extracts by oligo-dT affinity chromatography of poly-adenylated GCRE-1. Immuno-blot revealed time dependent enhancement of nucleolin in the cytoplasm which in turn directly binds GCRE-1. RNA co-immunoprecipitation confirmed the GCRE-1-nucleolin interaction in-vivo . To elucidate the functional role of nucleolin in stabilization of osm mRNA, nucleolin was overexpressed in U937 cells and found to stabilize the intrinsic osm mRNA, where co-transfection with the reporter containing GCRE-1 confirms the role of GCRE-1 in stabilization of the reporter mRNA. Thus in conclusion, the results asserted that PMA treatment in U937 cells leads to cytoplasmic translocation of nucleolin that directly binds GCRE-1, one of the major GC-rich instability elements, thereby stabilizing the osm mRNA. This article is protected by copyright. All rights reserved
    Electronic ISSN: 0091-7419
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Wiley
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  • 5
    Publication Date: 2016-02-20
    Description: Somatic mosaicism refers to the existence of somatic mutations in a fraction of somatic cells in a single biological sample. Its importance has mainly been discussed in theory although experimental work has started to emerge linking somatic mosaicism to disease diagnosis. Through novel statistical modeling of paired-end DNA-sequencing data using blood-derived DNA from healthy donors as well as DNA from tumor samples, we present an ultra-fast computational pipeline, LocHap that searches for multiple single nucleotide variants (SNVs) that are scaffolded by the same reads. We refer to scaffolded SNVs as local haplotypes (LH). When an LH exhibits more than two genotypes, we call it a local haplotype variant (LHV). The presence of LHVs is considered evidence of somatic mosaicism because a genetically homogeneous cell population will not harbor LHVs. Applying LocHap to whole-genome and whole-exome sequence data in DNA from normal blood and tumor samples, we find wide-spread LHVs across the genome. Importantly, we find more LHVs in tumor samples than in normal samples, and more in older adults than in younger ones. We confirm the existence of LHVs and somatic mosaicism by validation studies in normal blood samples. LocHap is publicly available at http://www.compgenome.org/lochap .
    Keywords: Polymorphism/mutation detection
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 6
    Publication Date: 2016-02-27
    Description: : Riboswitches are non-coding RNA located in the 5' untranslated regions where they bind a target metabolite used to specify the riboswitch class and control the expression of associated genes. Accurate identification of riboswitches is the first step towards understanding their regulatory and functional roles in the cell. In this article, we describe a new web application named Riboswitch Scanner which provides an automated pipeline for pHMM-based detection of riboswitches in partial as well as complete genomic sequences rapidly, with high sensitivity and specificity. Availability and implementation: Riboswitch Scanner can be freely accessed on the web at http://service.iiserkol.ac.in/~riboscan/ . Contact: mukherjee.sumit89@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 7
    Publication Date: 2016-02-26
    Description: ABSTRACT Transforming growth factor-β signaling exerts divergent effects on normal and cancer cells, although mechanism underlying this differential behavior remains unclear. In this study, expression of ninety-four genes pertaining to the TGF-β signaling pathway was compared between tumor and benign tissue samples from the human prostate gland to identify major discriminators driving prostate carcinogenesis. E2F5 was identified as one of the most deregulated genes in prostate cancer tissues, predominantly in samples with Gleason-score 6. Expression of other deregulated components of TGF-β signaling was examined by qRT-PCR, western blot and immune-staining. Function of E2F5 and p38 in prostate cancer was investigated using siRNA-treatment of PC3 cell-line followed by analyses of associated components and cell cycle. Observations revealed that E2F5 overexpression was accompanied by significantly higher phosphorylation of SMAD3 at Ser-208 in the linker region (pSMAD3L) and p38 in tumor tissue. A striking difference in SMAD3 phosphorylation, marked by preponderance of pSMAD3L and pSMAD3C (Ser-423 and 425) in tumor and benign tissues, respectively was noted. Co-localization of E2F5 with pSMAD3L in the nuclei of tumor and PC3 cells indicated a functional interface between the proteins. Downregulation of E2F5 and p38 in PC3 cells resulted in marked reduction of phosphorylation of SMAD3 and perturbation of cell cycle with an arrest of cells in G 1 . Our findings unearthed that E2F5/p38 axis played a cardinal role in uncontrolled cellular proliferation in prostate cancer through pSMAD3L activation. It also underscores a strong potential for E2F5 to be incorporated as a tool in early detection of prostate cancer. This article is protected by copyright. All rights reserved
    Electronic ISSN: 1097-4652
    Topics: Biology , Medicine
    Published by Wiley
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  • 8
    Publication Date: 2019
    Description: Abstract Microbial dynamics drive the biotic machinery of early soil evolution. However, integrated knowledge of microbial community establishment, functional associations, and community assembly processes in incipient soil is lacking. This study presents a novel approach of combining microbial phylogenetic profiling, functional predictions, and community assembly processes to analyze drivers of microbial community establishment in an emerging soil system. Rigorous submeter sampling of a basalt‐soil lysimeter after 2 years of irrigation revealed that microbial community colonization patterns and associated soil parameters were depth dependent. Phylogenetic analysis of 16S rRNA gene sequences indicated the presence of diverse bacterial and archaeal phyla, with high relative abundance of Actinomyceles on the surface and a consistently high abundance of Proteobacteria (Alpha, Beta, Gamma, and Delta) at all depths. Despite depth‐dependent variation in community diversity, predicted functional gene analysis suggested that microbial metabolisms did not differ with depth, thereby suggesting redundancy in functional potential throughout the system. Null modeling revealed that microbial community assembly patterns were predominantly governed by variable selection. The relative influence of variable selection decreased with depth, indicating unique and relatively harsh environmental conditions near the surface and more benign conditions with depth. Additionally, community composition near the center of the domain was influenced by high levels of dispersal, suggesting that spatial processes interact with deterministic selection imposed by the environment. These results suggest that for oligotrophic systems, there are major differences in the length scales of variation between vertical and horizontal dimensions with the vertical dimension dominating variation in physical, chemical, and biological features.
    Print ISSN: 2169-8953
    Electronic ISSN: 2169-8961
    Topics: Biology , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
    Publication Date: 2019
    Description: Abstract Retarding potential analyzers are frequently flown on small satellites as in situ ion probes, from which can be derived a number of ion plasma parameters from a current‐voltage relationship (I‐V curve). The traditional method of analyzing retarding potential analyzer data produces inaccuracies in derived estimates when there is significant noise present in the instrument measurements. In this study we investigate the dependencies between parameters that produce uncertainties in noisy I‐V curves. It is found that multiple combinations of ion velocity and spacecraft floating potential can produce I‐V curves that lie within the noise envelope, which renders it difficult for a traditional curve fitting technique to objectively and accurately estimate parameters from a noisy I‐V curve. In this paper we propose BATFORD—a bootstrap resampling‐based technique to improve the accuracies of parameter estimates. It is particularly useful when signal‐to‐noise ratios are low. The algorithm is tested against a traditional curve fitting method for a simulated data set comprising I‐V curves for the middle‐ and low‐latitude ionosphere at low Earth orbit altitudes around 450 km, where O+ is the predominant species. BATFORD is found to provide more robust and reliable estimates assuming generalized noise distribution characteristics. As further validation, the algorithm is applied to satellite data from an orbit with deep plasma bubbles and hence low signal levels.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
    Publication Date: 2019
    Description: Abstract The high temporal variability of the soil‐to‐atmosphere CO2 flux (soil respiration, RS) has been studied at hourly to multiannual timescales, but remains less well understood than RS spatial variability. How RS fluxes vary and are auto‐correlated at various time lags has practical implications for sampling, and more fundamentally for our understanding of its abiotic and biotic underlying mechanisms. We examined the variability, correlation, and sampling requirements of RS over a wide range of temporal scales in a temperate deciduous forest in eastern Maryland, USA, using both automated (temporally continuous, N = 30,036 over ten months) and survey (spatially diverse, temporally sparse, N = 1,912 over 17 months) data. Data from a global RS database were also used to examine interannual variability in comparable forests. The coefficient of variability of successive measurements generally varied from the minute (median CV 16%) to hourly and daily (11‐12%) timescales. Successive RS values measured at a given collar exhibited a strong hour‐to‐hour correlation (r = 0.931), and a moderate correlation at a two‐hour lag (0.289); day‐to‐day (i.e., 24 hour lag) hourly observations were uncorrelated. Daily RS means were well correlated at a one‐day lag (r = 0.856), but not at any further time lag. In a linear mixed‐effects model predicting RS, soil temperature and moisture exerted consistently strong effects regardless of timescale, and model coefficient of variability was generally high (〉80%). These results provide new opportunities to explore the drivers and variability of RS fluxes, quantify sampling requirements, and improve error propagation.
    Print ISSN: 2169-8953
    Electronic ISSN: 2169-8961
    Topics: Biology , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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