Molecular biology and clinical implication of hepatitis C virus

Hepatitis C virus (HCV) was first described in 1989 as the putative viral agent of non-A non-B hepatitis. It is a member of the Flaviviridae family and has been recognized as the major causative agent of chronic liver disease, including chronic active hepatitis, cirrhosis and hepatocellular carcinoma. HCV is a positive RNA virus with a genome containing approximately 9500 nucleotides. It has an open reading frame that encodes a large polyprotein of about 3000 amino acids and is characterized by extensive genetic diversity. HCV has been classified into at least 6 major genotypes with many subtypes and circulates within an infected individual as a number of closely related but distinct variants known as quasispecies. This article reviews aspects of the molecular biology of HCV and their clinical implication.

The Role of Second Generation Antiretroviral Drugs in HIV-1 Subtype B and non-B Variants Harboring Natural Polymorphisms and Drug Resistance Mutations.

Cette thèse traite de la résistance du VIH-1 aux antirétroviraux, en particulier de l'activité antivirale de plusieurs inhibiteurs non nucléosidiques de la transcriptase inverse (INNTI) ainsi que des inhibiteurs de protéase (IP). Nous avons exploré l’émergence et la spécificité des voies de mutations qui confèrent la résistance contre plusieurs nouveaux INNTI (étravirine (ETR) et rilpivirine (RPV)) (chapitres 2 et 3). En outre, le profil de résistance et le potentiel antirétroviral d'un nouvel IP, PL-100, est présenté dans les chapitres 4 et 5. Pour le premier projet, nous avons utilisé des sous-types B et non-B du VIH-1 pour sélectionner des virus résistants à ETR, et ainsi montré que ETR favorise l’émergence des mutations V90I, K101Q, E138K, V179D/E/F, Y181C, V189I, G190E, H221H/Y et M230L, et ce, en 18 semaines. Fait intéressant, E138K a été la première mutation à émerger dans la plupart des cas. Les clones viraux contenant E138K ont montré un faible niveau de résistance phénotypique à ETR (3,8 fois) et une diminution modeste de la capacité de réplication (2 fois) par rapport au virus de type sauvage. Nous avons également examiné les profils de résistance à ETR et RPV dans les virus contenant des mutations de résistance aux INNTI au début de la sélection. Dans le cas du virus de type sauvage et du virus contenant la mutation unique K103N, les premières mutations à apparaître en présence d’ETR ou de RPV ont été E138K ou E138G suivies d’autres mutations de résistance aux INNTI. À l’inverse, dans les mêmes conditions, le virus avec la mutation Y181C a évolué pour produire les mutations V179I/F ou A62V/A, mais pas E138K/G. L'ajout de mutations à la position 138 en présence de Y181C n'augmente pas les niveaux de résistance à ETR ou RPV. Nous avons également observé que la combinaison de Y181C et E138K peut conduire à un virus moins adapté par rapport au virus contenant uniquement Y181C. Sur la base de ces résultats, nous suggérons que les mutations Y181C et E138K peuvent être antagonistes. L’analyse de la résistance au PL-100 des virus de sous-type C et CRF01_AE dans les cellules en culture est décrite dans le chapitre 4. Le PL-100 sélectionne pour des mutations de résistance utilisant deux voies distinctes, l'une avec les mutations V82A et L90M et l'autre avec T80I, suivi de l’addition des mutations M46I/L, I54M, K55R, L76F, P81S et I85V. Une accumulation d'au moins trois mutations dans le rabat protéique et dans le site actif est requise dans chaque cas pour qu’un haut niveau de résistance soit atteint, ce qui démontre que le PL-100 dispose d'une barrière génétique élevée contre le développement de la résistance. Dans le chapitre 5, nous avons évalué le potentiel du PL-100 en tant qu’inhibiteur de protéase de deuxième génération. Les virus résistants au PL-100 émergent en 8-48 semaines alors qu’aucune mutation n’apparaît avec le darunavir (DRV) sur une période de 40 semaines. La modélisation moléculaire montre que la haute barrière génétique du DRV est due à de multiples interactions avec la protéase dont des liaison hydrogènes entre les groupes di-tétrahydrofuranne (THF) et les atomes d'oxygène des acides aminés A28, D29 et D30, tandis que la liaison de PL-100 est principalement basée sur des interactions polaires et hydrophobes délocalisées à travers ses groupes diphényle. Nos données suggèrent que les contacts de liaison hydrogène et le groupe di-THF dans le DRV, ainsi que le caractère hydrophobe du PL-100, contribuent à la liaison à la protéase ainsi qu’à la haute barrière génétique contre la résistance et que la refonte de la structure de PL-100 pour inclure un groupe di-THF pourrait améliorer l’activité antivirale et le profil de résistance.

Functional studies of the deubiquitinating enzymes USP19, USP4 and UCH-L1

El marcaje de proteínas con ubiquitina, conocido como ubiquitinación, cumple diferentes funciones que incluyen la regulación de varios procesos celulares, tales como: la degradación de proteínas por medio del proteosoma, la reparación del ADN, la señalización mediada por receptores de membrana, y la endocitosis, entre otras (1). Las moléculas de ubiquitina pueden ser removidas de sus sustratos gracias a la acción de un gran grupo de proteasas, llamadas enzimas deubiquitinizantes (DUBs) (2). Las DUBs son esenciales para la manutención de la homeostasis de la ubiquitina y para la regulación del estado de ubiquitinación de diferentes sustratos. El gran número y la diversidad de DUBs descritas refleja tanto su especificidad como su utilización para regular un amplio espectro de sustratos y vías celulares. Aunque muchas DUBs han sido estudiadas a profundidad, actualmente se desconocen los sustratos y las funciones biológicas de la mayoría de ellas. En este trabajo se investigaron las funciones de las DUBs: USP19, USP4 y UCH-L1. Utilizando varias técnicas de biología molecular y celular se encontró que: i) USP19 es regulada por las ubiquitin ligasas SIAH1 y SIAH2 ii) USP19 es importante para regular HIF-1α, un factor de transcripción clave en la respuesta celular a hipoxia, iii) USP4 interactúa con el proteosoma, iv) La quimera mCherry-UCH-L1 reproduce parcialmente los fenotipos que nuestro grupo ha descrito previamente al usar otros constructos de la misma enzima, y v) UCH-L1 promueve la internalización de la bacteria Yersinia pseudotuberculosis.

Proportions of A1, A2, B and C β-casein protein variants in retail milk in the UK

The A1 variant protein of the β-casein family has been implicated in various disease states although much evidence is weak or contradictory. The primary objective was to measure, for the first time, the proportions of the key β-casein variant proteins in UK retail milk over the course of one year. In total, 55 samples of semi-skimmed milk were purchased from five supermarkets over the course of a year and the proportions of the A1, A2, B and C casein variant proteins were measured, using high resolution HPLC-MS. The results showed that β-casein in UK retail milk comprises approximately 0.58, 0.31, 0.07 and 0.03 A2, A1, B and C protein variants, respectively. The proportion of A2 is higher than some early studies would predict although the reasons for this and any implications for health are unclear

1,8-Cineol inhibits nuclear translocation of NF-κB p65 and NF-κB-dependent transcriptional activity

Natural plant-derived products are commonly applied to treat a broad range of human diseases, including cancer as well as chronic and acute airway inflammation. In this regard, the monoterpene oxide 1,8-cineol, the active ingredient of the clinically approved drug Soledum®, is well-established for the therapy of airway diseases, such as chronic sinusitis and bronchitis, chronic obstructive pulmonary disease and bronchial asthma. Although clinical trials underline the beneficial effects of 1,8-cineol in treating inflammatory diseases, the molecular mode of action still remains unclear. Here, we demonstrate for the first time a 1,8-cineol-depending reduction of NF-κB-activity in human cell lines U373 and HeLa upon stimulation using lipopolysaccharides (LPS). Immunocytochemistry further revealed a reduced nuclear translocation of NF-κB p65, while qPCR and western blot analyses showed strongly attenuated expression of NF-κB target genes. Treatment with 1,8-cineol further led to increased protein levels of IκBα in an IKK-independent matter, while FRET-analyses showed restoring of LPS-associated loss of interaction between NF-κB p65 and IκBα. We likewise observed reduced amounts of phosphorylated c-Jun N-terminal kinase 1/2 protein in U373 cells after exposure to 1,8-cineol. In addition, 1,8-cineol led to decreased amount of nuclear NF-κB p65 and reduction of its target gene IκBα at protein level in human peripheral blood mononuclear cells. Our findings suggest a novel mode of action of 1,8-cineol through inhibition of nuclear NF-κB p65 translocation via IκBα resulting in decreased levels of proinflammatory NF-κB target genes and may therefore broaden the field of clinical application of this natural drug for treating inflammatory diseases.

Prevalence of hepatitis B and C serological markers among first-time blood donors in Brazil: A multi-center serosurvey

Little data are available on the seroprevalence of, and risk factors for hepatitis B and C viruses (HBV and HCV) infection in Latin American countries. A multi-center serosurvey was conducted among 3,598 first-time blood donors (65% men) from Sao Paulo, Salvador and Manaus in Brazil. The gender-specific seroprevalences of antibodies against hepatitis B core antigen (anti-HBc) and of the hepatitis B surface antigen (HBsAg) in anti-HBc-positive sera were measured, and risk factors analyzed by gender. The gender-specific seroprevalences of antibodies against HCV (anti-HCV) were measured, but risk factors for HCV were not determined. Anti-HBc and HBsAg seroprevalences were not significantly different in men [101/2,341 (4.31%) and 4/2,229 (0.18%), respectively] and women [65/1,237 (5.25%) and 8/ 1,169 (0.68%), respectively], whereas the seroprevalence of anti-HCV was higher in women (12/1,238 [0.97%] vs. 9/2,353 [0.38%]; odds ratio [OR] = 2.49; 95% confidence interval [Cl]: 1.0-6.0). No significant difference for HBV infection was found across the three study sites or by ethnic group. The seroprevalence of anti-HBc increased with age, but decreased with education level in both genders. Lifetime number of sexual partners was associated with anti-HBc prevalence among men (OR = 1.95; 95% Cl: 1.2-3.1), but not women. The seroprevalence of HBV and HCV was low among Brazilian blood donors, and exposure increased with age in both genders.

Active and exo-site inhibition of human factor Xa: Structure of des-Gla factor Xa inhibited by NAP5, a potent nematode anticoagulant protein from Ancylostoma caninum

Hookworms are hematophagous nematodes capable of growth, development and subsistence in living host systems such as humans and other mammals. Approximately one billion, or one in six, people worldwide are infected by hookworms causing gastrointestinal blood loss and iron deficiency anemia. The hematophagous hookworm Ancylostoma caninum produces a family of small, disulfide-linked protein anticoagulants (75-84 amino acid residues). One of these nematode anticoagulant proteins, NAP5, inhibits the amidolytic activity of factor Xa (fXa) with K-i = 43 pM, and is the most potent natural fXa inhibitor identified thus far. The crystal structure of NAP5 bound at the active site of gamma-carboxyglutamic acid domainless factor Xa (des-fXa) has been determined at 3.1 angstrom resolution, which indicates that Asp189 (fXa, S1 subsite) binds to Arg40 (NAP5, P1 site) in a mode similar to that of the BPTI/trypsin interaction. However, the hydroxyl group of Ser39 of NAP5 additionally forms a hydrogen bond (2.5 angstrom) with His57 NE2 of the catalytic triad, replacing the hydrogen bond of Ser195 OG to the latter in the native structure, resulting in an interaction that has not been observed before. Furthermore, the C-terminal extension of NAP5 surprisingly interacts with the fXa exosite of a symmetry-equivalent molecule forming a short intermolecular beta-strand as observed in the structure of the NAPc2/fXa complex. This indicates that NAP5 can bind to fXa at the active site, or the exosite, and to fX at the exosite. However, unlike NAPc2, NAP5 does not inhibit fVIIa of the fVIIa/TF complex. (c) 2007 Elsevier Ltd. All rights reserved.

Antimicrobial effects of ozonated water on the sanitization of dental instruments contaminated with E. coli, S. aureus, C. albicans, or the spores of B. atrophaeus

Objectives: Ozone has been used as an alternative method for the decontamination of water, food, equipment and instruments. The objective of this study was to evaluate the antimicrobial effects of ozonated water on the sanitization of dental instruments that were contaminated by Escherichia coli, Staphylococcus aureus, Candida albicans and the spores of Bacillus atrophaeus. Methods: A total of one hundred and twenty standardized samples of diamond dental burs were experimentally contaminated with E. coli (ATCC 25922), S. aureus (ATCC 6538) and C. albicans (ATCC 18804) and the spores of B. atrophaeus (ATCC 6633) for 30min. After the contamination, the samples were exposed to ozonated water (10mg/L O3) for 10 or 30min. The control group was composed of samples that were exposed to distilled water for 30min. After the exposure to the ozonated water, 0.1mL aliquots were seeded onto BHI agar to count the colony-forming units per milliliter (CFU/mL) of E. coli, S. aureus, and B. atrophaeus. Sabouraud dextrose agar was used to count the CFU/mL of C. albicans. The results were subjected to an analysis of variance and the Tukey test. Results: For all of the microorganisms studied, the ozonated water reduced the number of CFU/mL after 10 and 30. min of sanitization, and this microbial reduction was dependent on the duration of the exposure to the ozonated water. E. coli exhibited the greatest reduction in CFU/mL (2.72-3.78. log) followed by S. aureus (2.14-3.19. log), C. albicans (1.44-2.14. log) and the spores of B. atrophaeus (1.01-1.98. log). Conclusion: The ozonated water was effective in reducing the CFU of E. coli, S. aureus, C. albicans and B. atrophaeus spores, suggesting that ozonated water can be used for the sanitization of dental instruments. © 2012 King Saud Bin Abdulaziz University for Health Sciences.

Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Role of Coulomb and nuclear breakups in the interaction of B-8 with C-12

We investigate the breakup of the proton halo B-8 projectile in the presence of the light target C-12 at near barrier energies. Our calculations show that the effect of the breakup on the elastic scattering angular distributions is negligible. We also investigate the relative importance of Coulomb and nuclear breakups for this system. We compare the results of our calculations with those for the He-6 + C-12 and B-8 Ni-58 systems. (C) 2012 Elsevier B.V. All rights reserved.

Cellular Infiltrates and NF kappa B Subunit c-Rel Signaling in Kidney Allografts of Patients With Clinical Operational Tolerance

Background. Nuclear factor kappa B (NF kappa B) plays a potential role in tolerance by orchestrating onset and resolution of inflammation and regulatory T cell differentiation through subunit c-Rel. We characterized cellular infiltrates and expression of NF kappa B1, c-Rel and its upstream regulators phosphatidylinositol 3-kinase/RAC-alpha serine/threonine kinase, in allograft biopsies from patients with spontaneous clinical operational tolerance (COT). Methods. Paraffin-fixed kidney allograft biopsies from 40 patients with COT (n=4), interstitial rejection (IR; n=12), borderline changes (BC; n=12), and long-term allograft function without rejection (NR; n=12) were used in the study. Cellular infiltrates and immunohistochemical expression of key proteins of the NF kappa B pathway were evaluated in the cortical tubulointerstitium and in cellular infiltrates using digital image analysis software. Results were given as mean +/- SEM. Results. Biopsies from patients with COT exhibited a comparable amount of cellular infiltrate to IR, BC, and NR (COT, 191 +/- 81; IR, 291 +/- 62; BC, 178 +/- 45; and NR, 210 +/- 42 cells/mm(2)) but a significantly higher proportion of forkhead box P3-positive cells (COT, 11%+/- 1.7%; IR, 3.5%+/- 0.70%; BC, 3.4%+/- 0.57%; and NR, 3.7%+/- 0.78% of infiltrating cells; P=0.02). c-Rel expression in cellular infiltrates was significantly elevated in IR, BC, and NR when analyzing the number of positive cells per mm(2) (P=0.02) and positive cells per infiltrating cells (P=0.04). In contrast, tubular PI3K and c-Rel expression were significantly higher in IR and BC but not in NR compared with COT (P=0.03 and P=0.006, respectively). With RAC-alpha serine-threonine kinase, similar tendencies were observed (P=0.2). Conclusions. Allografts from COT patients show significant cellular infiltrates but a distinct expression of proteins involved in the NF kappa B pathway and a higher proportion of forkhead box P3-positive cells.

Mitochondrial localization and structure-based phosphate activation mechanism of Glutaminase C with implications for cancer metabolism

Glutamine is an essential nutrient for cancer cell proliferation, especially in the context of citric acid cycle anaplerosis. In this manuscript we present results that collectively demonstrate that, of the three major mammalian glutaminases identified to date, the lesser studied splice variant of the gene gls, known as Glutaminase C (GAC), is important for tumor metabolism. We show that, although levels of both the kidney-type isoforms are elevated in tumor vs. normal tissues, GAC is distinctly mitochondrial. GAC is also most responsive to the activator inorganic phosphate, the content of which is supposedly higher in mitochondria subject to hypoxia. Analysis of X-ray crystal structures of GAC in different bound states suggests a mechanism that introduces the tetramerization-induced lifting of a "gating loop" as essential for the phosphate-dependent activation process. Surprisingly, phosphate binds inside the catalytic pocket rather than at the oligomerization interface. Phosphate also mediates substrate entry by competing with glutamate. A greater tendency to oligomerize differentiates GAC from its alternatively spliced isoform and the cycling of phosphate in and out of the active site distinguishes it from the liver-type isozyme, which is known to be less dependent on this ion.

Mechanisms of resistance of tumor cells in response to treatment with the vacuolar H+-ATPase inhibitor archazolid B

Resistance of cancer cells towards chemotherapy is the major cause of therapy failure. Hence, the evaluation of cellular defense mechanisms is essential in the establishment of new chemotherapeutics. In this study, classical intrinsic and acquired as well as new resistance mechanisms relevant in the cellular response to the novel vacuolar H+-ATPase inhibitor archazolid B were investigated. Archazolid B, originally produced by the myxobacterium Archangium gephyra, displayed cytotoxicity in the low nanomolar range on a panel of cancer cell lines. The drug showed enhanced cytotoxic activity against nearly all cancerous cells compared to their non-cancerous pendants. With regards to ABC transporters, archazolid B was identified as a moderate substrate of ABCB1 (P-glycoprotein) and a weak substrate of ABCG2 (BCRP), whereas hypersensitivity was observed in ABCB5-expressing cells. The cytotoxic effect of archazolid B was shown to be independent of the cellular p53 status. However, cells expressing constitutively active EGFR displayed significantly increased resistance. Acquired drug resistance was studied by establishing an archazolid B-resistant MCF-7 cell line. Experiments showed that this secondary resistance was not conferred by aberrant expression or DNA mutations of the gene encoding vacuolar H+-ATPase subunit c, the direct target of archazolid B. Instead, a slight increase of ABCB1 and a significant overexpression of EGFR as well as reduced proliferation may contribute to acquired archazolid B resistance. For identification of new resistance strategies upon archazolid B treatment, omics data from bladder cancer and glioblastoma cells were analyzed, revealing drastic disturbances in cholesterol homeostasis, affecting cholesterol biosynthesis, uptake and transport. As shown by filipin staining, archazolid B led to accumulation of free cholesterol in lysosomes, which triggered sterol responses, mediated by SREBP-2 and LXR, including up-regulation of HMGCR, the key enzyme of cholesterol biosynthesis. Furthermore, inhibition of LDL uptake as well as impaired LDLR surface expression were observed, indicating newly synthesized cholesterol to be the main source of cholesterol in archazolid B-treated cells. This was proven by the fact that under archazolid B treatment, total free cholesterol levels as well as cell survival were significantly reduced by inhibiting HMGCR with fluvastatin. The combination of archazolid B with statins may therefore be an attractive strategy to circumvent cholesterol-mediated cell survival and in turn potentiate the promising anticancer effects of archazolid B.

Molecular signals in B lymphocyte activation: The role of intracellular calcium ion concentration, protein kinase C activation, and autocrine interleukin-2

Calcium ionophore, ionomycin, and phorbol myristate acetate (PMA) were used to activate rabbit peripheral blood B cells to study the role of increased intracellular calcium ion concentration ( (Ca$\sp2+\rbrack\sb{\rm i}$), protein kinase C (PKC) activation, and autocrine interleukin (IL-2) in inducing cell cycle entry and maintaining activation to DNA synthesis. When stimulated with a combination of ionomycin and PMA the B cells produced a soluble factor that supported the IL-2 dependent cell line, CTLL-2. The identity of the factor was established as IL-2 and its source was proved to be B cells in further experiments. Absorption studies and limiting dilution analysis indicated that IL-2 produced by B cells can act as an autocrine growth factor. Next, the effect of complete and incomplete signalling on B lymphocyte activation leading to cell cycle entry, IL-2 production, functional IL-2 receptor (IL-2R) expression, and DNA synthesis was examined. It was observed that cell cycle entry could be induced by signals provided by each reagent alone, but IL-2 production, IL-2R expression, and progression to DNA synthesis required activation with both reagents. Incomplete activation with ionomycin or PMA alone altered the responsiveness of B cells to further stimulation only in the case of ionomycin, and the unresponsiveness of these cells was apparently due to a lack of functional IL-2R expression on these cells, even though IL-2 production was maintained. The requirement of IL-2 for maintenance of activation to DNA synthesis was then investigated. The hypothesis that IL-2, acts in late G$\sb1$ and is required for DNA synthesis in B cells was supported by comparing IL-2 production and DNA synthesis in peripheral blood cells and purified B cells, kinetic analysis of these events in B cells, effects of anti-IL-2 antibody and PKC inhibitors, and by the response of G$\sb1$ B cells. Additional signals transduced by the interaction of autocrine IL-2 and functional IL-2 receptor on rabbit B cells were found to be necessary to drive these cells to S phase, after initial activation caused by simultaneous increase in (Ca$\sp2+\rbrack\sb{\rm i}$ and PKC activation had induced cell cycle entry, IL-2 production, and functional IL-2 receptor expression. ^