Methylation regulation of Antiviral host factors, Interferon Stimulated Genes (ISGs) and T-cell responses associated with natural HIV control

GWAS, immune analyses and biomarker screenings have identified host factors associated with in vivo HIV-1 control. However, there is a gap in the knowledge about the mechanisms that regulate the expression of such host factors. Here, we aimed to assess DNA methylation impact on host genome in natural HIV-1 control. To this end, whole DNA methylome in 70 untreated HIV-1 infected individuals with either high (>50,000 HIV-1-RNA copies/ml, n = 29) or low (<10,000 HIV-1-RNA copies/ml, n = 41) plasma viral load (pVL) levels were compared and identified 2,649 differentially methylated positions (DMPs). Of these, a classification random forest model selected 55 DMPs that correlated with virologic (pVL and proviral levels) and HIV-1 specific adaptive immunity parameters (IFNg-T cell responses and neutralizing antibodies capacity). Then, cluster and functional analyses identified two DMP clusters: cluster 1 contained hypo-methylated genes involved in antiviral and interferon response (e.g. PARP9, MX1, and USP18) in individuals with high viral loads while in cluster 2, genes related to T follicular helper cell (Tfh) commitment (e.g. CXCR5 and TCF7) were hyper-methylated in the same group of individuals with uncontrolled infection. For selected genes, mRNA levels negatively correlated with DNA methylation, confirming an epigenetic regulation of gene expression. Further, these gene expression signatures were also confirmed in early and chronic stages of infection, including untreated, cART treated and elite controllers HIV-1 infected individuals (n = 37). These data provide the first evidence that host genes critically involved in immune control of the virus are under methylation regulation in HIV-1 infection. These insights may offer new opportunities to identify novel mechanisms of in vivo virus control and may prove crucial for the development of future therapeutic interventions aimed at HIV-1 cure

Deep-sequencing reveals broad subtype-specific HCV resistance mutations associated with treatment failure

A percentage of hepatitis C virus (HCV)-infected patients fail direct acting antiviral (DAA)-based treatment regimens, often because of drug resistance-associated substitutions (RAS). The aim of this study was to characterize the resistance profile of a large cohort of patients failing DAA-based treatments, and investigate the relationship between HCV subtype and failure, as an aid to optimizing management of these patients. A new, standardized HCV-RAS testing protocol based on deep sequencing was designed and applied to 220 previously subtyped samples from patients failing DAA treatment, collected in 39 Spanish hospitals. The majority had received DAA-based interferon (IFN) a-free regimens; 79% had failed sofosbuvir-containing therapy. Genomic regions encoding the nonstructural protein (NS) 3, NS5A, and NS5B (DAA target regions) were analyzed using subtype-specific primers. Viral subtype distribution was as follows: genotype (G) 1, 62.7%; G3a, 21.4%; G4d, 12.3%; G2, 1.8%; and mixed infections 1.8%. Overall, 88.6% of patients carried at least 1 RAS, and 19% carried RAS at frequencies below 20% in the mutant spectrum. There were no differences in RAS selection between treatments with and without ribavirin. Regardless of the treatment received, each HCV subtype showed specific types of RAS. Of note, no RAS were detected in the target proteins of 18.6% of patients failing treatment, and 30.4% of patients had RAS in proteins that were not targets of the inhibitors they received. HCV patients failing DAA therapy showed a high diversity of RAS. Ribavirin use did not influence the type or number of RAS at failure. The subtype-specific pattern of RAS emergence underscores the importance of accurate HCV subtyping. The frequency of “extra-target” RAS suggests the need for RAS screening in all three DAA target regions

7th Drug hypersensitivity meeting: part two

No abstract availabl

Still not there, but on our way: thinking of urban ICT policies in European cities

In the information society, information and communication technology (ICT) is potentially an important policy tool. Especially at local levels, scholars stress the essentiality of active intervention and use of ICT tools. However, since these technologies are still new, little experience exists relative to urban ICT initiatives. This paper therefore aims to examine the way urban front-liners (both elected politicians and administrative professionals) perceive the opportunities of urban ICT policy. Using a European survey, the authors researched views and beliefs about different aspects of urban ICT policies. Following that, they tested whether there is a relationship between the activity field of the respondents and their views on ICT policies. Significant differences among urban planners and economists were established. Copyright 2003 by the Royal Dutch Geographical Society KNAG.

Effect of High-Pressure Processing on Quality and Microbiological Properties of a Fermented Beverage Manufactured from Sweet Whey Throughout Refrigerated Storage

The production of fermented beverages is a promising way to valorize by-products of dairy manufacturing. However, the shelf-life of these products is often limited by the post-acidification process that occurs during storage. In this work, we manufactured a fermented beverage from sweet whey by using the starter lactic acid bacteria (SLAB) Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. High-pressure processing (HPP) at 200 MPa for 10 min or 400 MPa for 1 min were applied after manufacturing. The aim of this study was to evaluate the effect of HPP on the quality of the beverage and on the behavior of the SLAB. Both high hydrostatic pressure treatments preserved flavor and texture attributes until 45 days post-HPP, without affecting chromatic parameters. Plate counts for both species were lower in HPP-treated beverages (HB) than in control beverages (CB), although treatment at 200 MPa maintained optimal amounts of total SLAB (6.6–7.9 log CFU/mL). Conversely, quantitative PCR (qPCR) and reverse transcription-qPCR (RT-qPCR) revealed that bacterial DNA or mRNA levels persisted after HPP (> 1.4 × 105 genome or cDNA copies/mL), even upon 400-MPa treatments. As a whole, this study indicated that HPP preserved the quality of the beverage until 45 days post-HPP, which is longer than the shelf-life of conventional fermented beverages obtained from milk. Moreover, our results obtained with these SLAB in a fermented dairy beverage upon HPP extend previous findings regarding the limitations of culture-dependent methods to assess microbial viability.Fil: Pega, Juan Franco. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Agroindustria. Instituto de Tecnología de Alimentos; ArgentinaFil: Denoya, Gabriela Inés. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Agroindustria. Instituto de Tecnología de Los Alimentos; ArgentinaFil: Castells, M.L.. Instituto Nacional de Tecnología Industrial. Centro de Investigaciones Tecnológicas de la Industria Láctea; ArgentinaFil: Sarquis, S.. Instituto Nacional de Tecnología Industrial. Centro de Investigaciones Tecnológicas de la Industria Láctea; ArgentinaFil: Aranibar, G.F.. Instituto Nacional de Tecnología Industrial. Centro de Investigaciones Tecnológicas de la Industria Láctea; ArgentinaFil: Vaudagna, Sergio Ramon. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Agroindustria. Instituto de Tecnología de Los Alimentos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Nanni, M.. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Agroindustria. Instituto de Tecnología de Los Alimentos; Argentin

Bovine astrovirus surveillance in Uruguay reveals high detection rate of a novel mamastrovirus species.

Abstract:Viral infections affecting cattle lead to economic losses to the livestock industry worldwide, but little is known about the circulation, pathogenicity and genetic diversity of enteric bovine astrovirus (BoAstV) in America. The aim of this work was to describe the prevalence and genetic diversity of enteric BoAstV in dairy cattle in Uruguay. A total of 457 fecal and 43 intestinal contents from dairy calves were collected between July 2015 and May 2017 and tested by RT-PCR, followed by sequencing and phylogenetic analyses of the polymerase and capsid regions. Twenty-six percent (128/500) of the samples were positive. Three different species within the Mamastrovirus genus were identified, including Mamastrovirus 28, Mamastrovirus 33 (3 samples each) and an unclassified Mamastrovirus species (19 samples). The unclassified species was characterized as a novel Mamastrovirus species. BoAstV circulates in Uruguayan dairy cattle with a high genetic diversity. The eventual clinicopathological significance of enteric BoAstV infection in cattle needs further investigation