Hepatitis B virus preS2Δ38-55 variants: A newly identified risk factor for hepatocellular carcinoma.

BACKGROUND & AIMS: Although HBV is a major cause of death in Africa, its genetic variability has been poorly documented. This study aimed to address whether HBV genotype and surface gene variants are associated with HBV-related liver disease in The Gambia. METHODS: We conducted a case-control study nested in the Prevention of Liver Fibrosis and Cancer in Africa programme. Consecutive treatment-naive patients with chronic HBV infection and detectable viral load were recruited: 211 controls with no significant liver disease and 91 cases (56 cirrhosis and 35 HCC cases). HBV genotypes and surface gene variants were determined by Sanger sequencing or next-generation sequencing (NGS) in serum DNA. Aflatoxin B1 (AFB1)-specific codon 249 TP53 mutation was determined by NGS in circulating cell-free plasma DNA. RESULTS: In phylogenetic analysis, 85% of individuals carried HBV genotype E, 14% genotype A, and 1% A/E recombinant viruses. Surface gene variants were more frequently observed in cases (43% and 57% in cirrhosis and HCC cases, respectively) than controls (25%; p 2,000 IU/ml (OR 22.7 [8.0-64.9]), HBsAg levels <10,000 IU/ml (OR 19.0 [5.5-65.3]), and AFB1 exposure (OR 29.3 [3.7-230.4]) on HCC risk. CONCLUSIONS: This study identified a hotspot for HBV preS2 deletions as a strong independent factor for HCC in The Gambia, with HBV genotypes and AFB1 exposure contributing to the high liver cancer risk. LAY SUMMARY: Although HBV-related liver disease is highly prevalent in sub-Saharan Africa, the associated virological characteristics are poorly studied. Using clinical data from African patients chronically infected with HBV, an assessment of the virological variability (genotypes and mutations) and exposure to AFB1, a toxin often contaminating food, was carried out. Our results show that HBV genotypes, the presence of a highly prevalent mutant form of HBV, and AFB1 exposure contribute to the high liver cancer risk in this population

Development of new oenological yeast strains with reduced ethanol yield, by using a combination of various approaches based on adaptative evolution

Il existe une forte demande de l'industrie pour des technologies permettant de réduire la teneur en alcool des vins. Bien que des levures à faible rendement alcool aient été développées par ingénierie génétique, les approches non-OGM sont aujourd'hui largement privilégiées. Nous avons mis en œuvre et comparé différentes stratégies d'évolution adaptative, à partir d'une souche œnologique commerciale, afin de réorienter le flux carboné vers la formation de glycérol aux dépens de l'éthanol. Après 200 générations en conditions de stress salin, nous avons obtenu des souches évoluées présentant une augmentation de la production de glycérol de 50 à 70 %, capables de diminuer de 0,45 à 0,80 % (v/v) la teneur en alcool de vins naturels ou synthétiques. Cette réorientation s'accompagne d'une accumulation de succinate et de 2,3-butanediol et d'une réduction de la vitesse fermentaire. Les mutants ont une survie accrue en conditions de stress salin et carence en glucose. Afin d'identifier les mécanismes sous-jacents, nous avons réalisé des analyses du transcriptome, du métabolome (exo- et endo-) et du génome des souches évoluées. Nous avons montré que le phénotype des mutants n'est pas dû à une dérégulation ou à des mutations des gènes de la voie de synthèse du glycérol mais à de larges modifications du métabolisme carboné, énergétique et redox. Le génome des souches évoluées présente des pertes d'hétérozygotie qui pourraient contribuer au phénotype observé. L'étude génétique d'une souche évoluée montre une origine multigénique des traits métaboliques. Une analyse de cartographie de QTL en utilisant une approche « bulk sequencing » a été initiée pour identifier les mutations impliquées dans le caractère fort glycérol/faible éthanol. Ces travaux ont ainsi permis de développer et caractériser des souches œnologiques faibles productrices d'alcool et de fournir un cadre pour l'identification des bases moléculaires impliquées.Mots-clefs : S. cerevisiae, fermentation œnologique, évolution adaptative, éthanol, glycérol, transcriptome, métabolome, génome.There is a strong demand from the industry for technologies to reduce the alcohol content of wine. Although low-alcohol yield yeasts have been developed by genetic engineering, GMO-free approaches are now widely preferred. We have implemented and compared different strategies for adaptive evolution to redirect the carbon flux towards glycerol formation at the expense of ethanol. After 200 generations salt stress conditions, we obtained evolved strains with glycerol production increased by 50 to 70%, able to decrease from 0.45 to 0.80% (v/v) the alcohol content of natural or synthetic wines. This shift is accompanied by an accumulation of succinate and 2,3-butanediol and a reduced fermentation rate. Mutants also exhibit a better survival under salt stress and glucose restriction conditions. To identify the underlying mechanisms, we analysed the transcriptome, metabolome (endo- and exo-) and genome of the evolved strains. We showed that the evolved phenotype is not due to deregulation or mutations of genes of involved in the glycerol synthesis pathway but to major changes in carbon, energy and redox metabolism. The genome of the evolved strains revealed loss of heterozygosity which could contribute to the observed phenotype. The genetic study of an evolved strain shows that the metabolic traits are under multigenic control. A QTL mapping analysis using a "bulk sequencing" approach was initiated to identify mutations involved in the high glycerol/low ethanol trait. This work has enabled the development and characterization of low alcohol wine yeast strains and has provided a framework for the identification of the underlying molecular bases.Key-words: S. cerevisiae, wine fermentation, adaptative evolution, ethanol, glycerol, transcriptome, metabolome, genome

Reduction of ethanol yield and improvement of glycerol formation by adaptive evolution of the wine yeast Saccharomyces cerevisiae under hyperosmotic conditions

There is a strong demand from the wine industry for methodologies to reduce the alcohol content of wine without compromising wine's sensory characteristics. We assessed the potential of adaptive laboratory evolution strategies under hyperosmotic stress for generation of Saccharomyces cerevisiae wine yeast strains with enhanced glycerol and reduced ethanol yields. Experimental evolution on KCl resulted, after 200 generations, in strains that had higher glycerol and lower ethanol production than the ancestral strain. This major metabolic shift was accompanied by reduced fermentative capacities, suggesting a trade-off between high glycerol production and fermentation rate. Several evolved strains retaining good fermentation performance were selected. These strains produced more succinate and 2,3-butanediol than the ancestral strain and did not accumulate undesirable organoleptic compounds, such as acetate, acetaldehyde, or acetoin. They survived better under osmotic stress and glucose starvation conditions than the ancestral strain, suggesting that the forces that drove the redirection of carbon fluxes involved a combination of osmotic and salt stresses and carbon limitation. To further decrease the ethanol yield, a breeding strategy was used, generating intrastrain hybrids that produced more glycerol than the evolved strain. Pilot-scale fermentation on Syrah using evolved and hybrid strains produced wine with 0.6% (vol/vol) and 1.3% (vol/vol) less ethanol, more glycerol and 2,3-butanediol, and less acetate than the ancestral strain. This work demonstrates that the combination of adaptive evolution and breeding is a valuable alternative to rational design for remodeling the yeast metabolic network

The Stringent Response Promotes Antibiotic Resistance Dissemination by Regulating Integron Integrase Expression in Biofilms

Class 1 integrons are genetic systems that enable bacteria to capture and express gene cassettes. These integrons, when isolated in clinical contexts, most often carry antibiotic resistance gene cassettes. They play a major role in the dissemination of antibiotic resistance among Gram-negative bacteria. The key element of integrons is the integrase, which allows gene cassettes to be acquired and shuffled. Planktonic culture experiments have shown that integrase expression is regulated by the bacterial SOS response. In natural settings, however, bacteria generally live in biofilms, which are characterized by strong antibiotic resilience and by increased expression of stress-related genes. Here, we report that under biofilm conditions, the stringent response, which is induced upon starvation, (i) increases basal integrase and SOS regulon gene expression via induction of the SOS response and (ii) exerts biofilm-specific regulation of the integrase via the Lon protease. This indicates that biofilm environments favor integron-mediated acquisition of antibiotic resistance and other adaptive functions encoded by gene cassettes

ASPICov: An automated pipeline for identification of SARS-Cov2 nucleotidic variants

ASPICov was developed to provide a rapid, reliable and complete analysis of NGS SARS-Cov2 samples to the biologist. This broad application tool allows to process samples from either capture or amplicon strategy and Illumina or Ion Torrent technology. To ensure FAIR data analysis, this Nextflow pipeline follows nf-core guidelines and use Singularity containers. Pipeline is implemented and available at https://gitlab.com/vtilloy/aspicov

Des avancées dans le développement de levures à faible rendement en alcool

Des avancées dans le développement de levures à faible rendement en alcool. 7. Journées scientifiques de la vigne et du vi

Des avancées dans le développement de levures à faible rendement en alcool

Des avancées dans le développement de levures à faible rendement en alcool. 7. Journées scientifiques de la vigne et du vi

Comprehensive Genomic Characterization of Antibiotic Resistance, Virulence, and Clonality in Salmonella Isolates from Wild Animals in Algeria

International audienceThis study investigated Salmonella spp. in wild animals in Algeria, focusing on their prevalence, serotypes, antibiotic resistance, and virulence profiles. From fecal samples collected between May 2021 and June 2022, 1.9% showed Salmonella shedding. The identified serotypes included S. Bredeney, S. Enteritidis, S. Altona, and S. Virchow. Except for S. Altona, all isolates were resistant to quinolones, with S. Bredeney strains, exhibiting multidrug resistance. Whole-genome sequencing revealed various resistance genes and mutations in gyrA or parC genes. Additionally, plasmids IncX1 and ColpVC were detected in several isolates. A comprehensive analysis identified 201 virulence genes. These findings contribute to understanding Salmonella in wild animal populations and their potential impact on public health

Evolutionnary and reverse engineering of commercially important metabolic traits in wine yeast

Evolutionnary and reverse engineering of commercially important metabolic traits in wine yeast. 31. International Specialised Symposium on Yeas