Interplay between NS3 protease and human La protein regulates translation-replication switch of Hepatitis C virus

HCV NS3 protein plays a central role in viral polyprotein processing and RNA replication. We demonstrate that the NS3 protease (NS3(pro)) domain alone can specifically bind to HCV-IRES RNA, predominantly in the SLIV region. The cleavage activity of the NS3 protease domain is reduced upon HCV-RNA binding. More importantly, NS3(pro) binding to the SLIV hinders the interaction of La protein, a cellular IRES-trans acting factor required for HCV IRES-mediated translation, resulting in inhibition of HCV-IRES activity. Although overexpression of both NS3(pro) as well as the full length NS3 protein decreased the level of HCV IRES mediated translation, replication of HCV replicon RNA was enhanced significantly. These observations suggest that the NS3(pro) binding to HCV IRES reduces translation in favor of RNA replication. The competition between the host factor (La) and the viral protein (NS3) for binding to HCV IRES might regulate the molecular switch from translation to replication of HCV.

Advances in the Mathematical Modelling of Hepatitis C Virus Dynamics

Mathematical models have provided key insights into the pathogenesis of hepatitis C virus (HCV) in vivo, suggested predominant mechanism(s) of drug action, explained confounding patterns of viral load changes in HCV infected patients undergoing therapy, and presented a framework for therapy optimization. In this article, I present an overview of the major advances in the mathematical modeling of HCV dynamics.

Influence of Si-C bond density on the properties of a-Si(1-x)C(x) thin films

Amorphous silicon carbide (a-Si(1-x)C(x)) films were deposited on silicon (100) and quartz substrates by pulsed DC reactive magnetron sputtering of silicon in methane (CH(4))-Argon (Ar) atmosphere. The influence of substrate temperature and target power on the composition, carbon bonding configuration, band gap, refractive index and hardness of a-SiC films has been investigated. Increase in substrate temperature results in slightly decreasing the carbon concentration in the films but favors silicon-carbon (Si-C) bonding. Also lower target powers were favorable towards Si-C bonding. X-ray photoelectron spectroscopy (XPS) results agree with the Fourier Transform Infrared (FTIR), UV-vis spectroscopy results. Increase in substrate temperature resulted in increased hardness of the thin films from 13 to 17 GPa and the corresponding bandgap varied from 2.1 to 1.8 eV. (C) 2011 Elsevier B.V. All rights reserved.

Structure and mechanical properties of Ti-C films deposited using combination of pulsed DC and normal DC magnetron co-sputtering

Titanium-carbon (Ti-C) thin films of different compositions were prepared by a combination of pulsed DC (for Ti target) and normal DC (for graphite target) magnetron co-sputtering on oxidized silicon and fused quartz substrates. At 33.7 at.% of C content, pure hcp Ti transforms into fcc-TiC with a preferential orientation of (2 2 0) along with (1 1 1) and (2 0 0). A clear transformation in the preferential orientation from (2 2 0) to (1 1 1) has been observed when the C content was increased to 56 at.%. At 62.5 at.% of C, TiC precipitates in an amorphous carbon matrix whereas further increase in C leads to X-ray amorphous films. The cross-sectional scanning electron microscope images reveal that the films with low carbon content consists of columnar grains, whereas, randomly oriented grains are in an amorphous carbon matrix at higher carbon content. A dramatic variation was observed in the mechanical properties such as hardness, H, from 30 to 1 GPa and in modulus, E, from 255 to 25 GPa with varying carbon content in the films. Resistance to plastic deformation parameter was observed as 0.417 for films containing 62.5 at.% of C. Nanoscratch test reveals that the films are highly scratch resistant with a coefficient of friction ranging from 0.15 to 0.04. (C) 2012 Elsevier B.V. All rights reserved.

Theoretical and in vitro studies of a C-terminal peptide from PGKC of Leishmania mexicana mexicana

Trypanosomatids cause deadly diseases in humans. Of the various biochemical pathways in trypanosomatids, glycolysis, has received special attention because of being sequestered in peroxisome like organelles critical for the survival of the parasites. This study focuses on phosphoglycerate kinase (PGK) from Leishmania spp. which, exists in two isoforms, the cytoplasmic PGKB and glycosomal PGKC differing in their biochemical properties. Computational analysis predicted the likelihood of a transmembrane helix only in the glycosomal isoform PGKC, of approximate length 20 residues in the 62-residue extension, ending at, arginine residues R471 and R472. From experimental studies using circular dichroism and NMR with deuterated sodium dodecyl sulfate, we find that the transmembrane helix spans residues 448 +/- 2 to 476 in Leishmania mexicana PGKC. The significance of this observation is discussed in the context of glycosomal transport and substrate tunneling. (C) 2012 Elsevier B.V. All rights reserved.

A cyclic peptide mimic of an RNA recognition motif of human La protein is a potent inhibitor of hepatitis C virus

Due to limited available therapeutic options, developing new lead compounds against hepatitis C virus is an urgent need. Human La protein stimulates hepatitis C virus translation through interaction with the hepatitis C viral RNA. A cyclic peptide mimicking the beta-turn of the human La protein that interacts with the viral RNA was synthesized. It inhibits hepatitis C viral RNA translation significantly better than the corresponding linear peptide at longer post-treatment times. The cyclic peptide also inhibited replication as measured by replicon RNA levels using real time RT-PCR. The cyclic peptide emerges as a promising lead compound against hepatitis C.

Durability of Pt/C and Pt/MC-PEDOT catalysts under simulated start-stop cycles in polymer electrolyte fuel cells

A composite of mesoporous carbon (MC) with poly(3,4-ethylenedioxythiophene) (PEDOT) is studied as catalyst support for platinum nanoparticles. The durability of commercial Pt/carbon and Pt/MC-PEDOT as cathode catalyst is investigated by invoking air-fuel boundary at the anode side so as to foster carbon corrosion at the cathode side of a polymer electrolyte fuel cell (PEFC). Pt/MC-PEDOT shows higher resistance to carbon corrosion in relation to Pt/C. Electrochemical techniques such as cyclic voltammetry (CV) and impedance measurements are used to evaluate the extent of degradation in the catalyst layer. It is surmised that the resistance of MC-PEDOT as catalyst support toward electrochemical oxidation makes Pt/MC-PEDOT a suitable and stable cathode catalyst for PEFCs.

Specific Sequence of a Beta Turn in Human La Protein May Contribute to Species Specificity of Hepatitis C Virus

Human La protein is known to be an essential host factor for translation and replication of hepatitis C virus (HCV) RNA. Previously, we have demonstrated that residues responsible for interaction of human La protein with the HCV internal ribosomal entry site (IRES) around the initiator AUG within stem-loop IV form a beta-turn in the RNA recognition motif (RRM) structure. In this study, sequence alignment and mutagenesis suggest that the HCV RNA-interacting beta-turn is conserved only in humans and chimpanzees, the species primarily known to be infected by HCV. A 7-mer peptide corresponding to the HCV RNA-interacting region of human La inhibits HCV translation, whereas another peptide corresponding to the mouse La sequence was unable to do so. Furthermore, IRES-mediated translation was found to be significantly high in the presence of recombinant human La protein in vitro in rabbit reticulocyte lysate. We observed enhanced replication with HCV subgenomic and full-length replicons upon overexpression of either human La protein or a chimeric mouse La protein harboring a human La beta-turn sequence in mouse cells. Taken together, our results raise the possibility of creating an immunocompetent HCV mouse model using human-specific cell entry factors and a humanized form of La protein.

Emergent properties of the interferon-signalling network may underlie the success of hepatitis C treatment

Current interferon alpha-based treatment of hepatitis C virus (HCV) infection fails to cure a sizeable fraction of patients treated. The cause of this treatment failure remains unknown. Here using mathematical modelling, we predict treatment failure to be a consequence of the emergent properties of the interferon-signalling network. HCV induces bistability in the network, creating a new steady state where it can persist. Cells that admit the new steady state alone are refractory to interferon. Using a model of viral kinetics, we show that when the fraction of cells refractory to interferon in a patient exceeds a critical value, treatment fails. Direct-acting antivirals that suppress HCV replication can eliminate the new steady state, restoring interferon sensitivity and improving treatment response. Our study thus presents a new conceptual basis of HCV persistence and treatment response, elucidates the origin of the synergy between interferon and direct-acting antivirals, and facilitates rational treatment optimization.

Serum proteomics of hepatitis C virus infection reveals retinol-binding protein 4 as a novel regulator

Persistent infection of hepatitis C virus (HCV) can lead to liver cirrhosis and hepatocellular carcinoma, which are currently diagnosed by invasive liver biopsy. Approximately 15-20% of cases of chronic liver diseases in India are caused by HCV infection. In North India, genotype 3 is predominant, whereas genotype 1 is predominant in southern parts of India. The aim of this study was to identify differentially regulated serum proteins in HCV-infected Indian patients (genotypes 1 and 3) using a two-dimensional electrophoresis approach. We identified eight differentially expressed proteins by MS. Expression levels of one of the highly upregulated proteins, retinol-binding protein 4 (RBP4), was validated by ELISA and Western blotting in two independent cohorts. We also confirmed our observation in the JFH1 infectious cell culture system. Interestingly, the HCV core protein enhanced RBP4 levels and partial knockdown of RBP4 had a positive impact on HCV replication, suggesting a possible role for this cellular protein in regulating HCV infection. Analysis of RBP4-interacting partners using a bioinformatic approach revealed novel insights into the possible involvement of RBP4 in HCV-induced pathogenesis. Taken together, this study provided information on the proteome profile of the HCV-infected Indian population, and revealed a link between HCV infection, RBP4 and insulin resistance.

Assignment of the C-13 NMR spectrum by correlation to dipolar coupled proton-pairs and estimation of order parameters of a thiophene based liquid crystal

Materials with widely varying molecular topologies and exhibiting liquid crystalline properties have attracted considerable attention in recent years. C-13 NMR spectroscopy is a convenient method for studying such novel systems. In this approach the assignment of the spectrum is the first step which is a non-trivial problem. Towards this end, we propose here a method that enables the carbon skeleton of the different sub-units of the molecule to be traced unambiguously. The proposed method uses a heteronuclear correlation experiment to detect pairs of nearby carbons with attached protons in the liquid crystalline core through correlation of the carbon chemical shifts to the double-quantum coherences of protons generated through the dipolar coupling between them. Supplemented by experiments that identify non-protonated carbons, the method leads to a complete assignment of the spectrum. We initially apply this method for assigning the C-13 spectrum of the liquid crystal 4-n-pentyl-4'-cyanobiphenyl oriented in the magnetic field. We then utilize the method to assign the aromatic carbon signals of a thiophene based liquid crystal thereby enabling the local order-parameters of the molecule to be estimated and the mutual orientation of the different sub-units to be obtained.

On linear series and a conjecture of D. C. Butler

Let C be a smooth irreducible projective curve of genus g and L a line bundle of degree d generated by a linear subspace V of H-0 (L) of dimension n+1. We prove a conjecture of D. C. Butler on the semistability of the kernel of the evaluation map V circle times O-C -> L and obtain new results on the stability of this kernel. The natural context for this problem is the theory of coherent systems on curves and our techniques involve wall crossing formulae in this theory.

Ru (II)-Catalyzed C-H Activation: Ketone-Directed Novel 1,4-Addition of Ortho C-H Bond to Maleimides

A 1,4-addition with the nucleophilic center generated at the ortho carbon atom of an aromatic ketone in the presence of the highly reactive alpha-C-H bond, using a directing group strategy, is presented. The reaction yields pharmaceutically useful 3-arylated succinimide derivatives. In order to gain understanding of this redox neutral reaction, despite the presence of copper acetate, and to substantiate the lack of Heck-type products, DFT calculations have been carried out.