The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain:Bridging within and among Host Evolutionary Rates

Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially transmit or establish new infections upon reactivation.status: publishe

Statistical and Sensory Differences Among Special Bottle Refermented Beers of a Same Type

Some countries such as Belgium, Germany, and the United Kingdom are notable for the large quantities of special beer they produce and sell worldwide. When these special beers are classified by type, some classes may include as many as eighty labels. Our aim was to propose a method for detecting the organoleptic specificity of beers by physicochemical analysis. We thus selected eigtheen parameters, independent of beer aging, which characterize a product's visual aspect, aroma, taste, and mouthfeel. The results were analyzed statistically to allow an evaluation of process reproducibility and a comparison of mean values. We conclude that despite relatively poor process reproducibility, the four beers studied here present sufficient distinctive features to make them different. This finding was corroborated by sensory analysis

Extract for the refermentation of beer in bottles

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Study of characteristic parameters of traditional process in the production of “Boganda”, a brandy of Congo

“Boganda” is an appreciated traditional distilled alcoholic beverage in Congo. It brings an interesting income to producers though its quality is extremely variable from a workshop to another. The production is based on three stages: malting of corn, fermentation and distillation. The corn used initially undergoes, during 5 days, an uncontrolled germination in medium quickly becoming anaerobic, with an increase in temperature up to about 49 ± 3 °C; that causes death of majority of corn germs and formation of various flavours. The obtained fermented malt is distilled without column. The distillate is collected empirically in fractions of volume according to the alcoholic amount corresponding to little distinct stages of temperature up to 98 °C. The final distilled alcoholic beverage has an alcoholic degree of approximately 24.2 ± 3 °GL, the volume of collected distillate being extremely variable. The study of physicochemical characteristics reveals a very great dispersion of parameters of manufacturing process and quality of product. Keywords: Brandy, ethanol, optimization, “Boganda”. Int. J. Biol. Chem. Sci. Vol. 2 (3) 2008: pp. 258-27