Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Study of enzymatic and non-enzymatic browning of mango during the drying process using a reconstituted model matrix approach

Le séchage est un procédé de transformation largement répandu dans le monde qui permet d'augmenter significativement la durée de conservation des denrées alimentaires et d'apporter une valeur ajoutée aux produits. Le traitement thermique appliqué lors de cette opération peut causer des modifications physiques, chimiques et biochimiques aboutissant à des altérations des qualités nutritionnelles et organoleptiques des produits séchés. La couleur est le premier attribut perçu par le consommateur et est généralement corrélé à une représentation de la qualité globale du produit. La maîtrise du brunissement est donc capitale pour préserver le potentiel commercial des produits alimentaires. La filière mangue séchée biologique du Burkina Faso constitue le cadre d'étude de ces travaux de thèse axés sur la compréhension des phénomènes impliqués dans le brunissement des mangues au cours de l'opération de séchage et pendant le stockage. L'objectif principal est d'identifier les paramètres majeurs influant sur le brunissement enzymatique et non-enzymatique afin de proposer des voies d'amélioration de la qualité du produit pertinentes. Une approche expérimentale permettant d'étudier les effets spécifiques de la température et de l'activité de l'eau indépendamment des autres paramètres nous a permis d'identifier les points critiques du procédé induisant des altérations de la couleur.Drying is a world common transformation process which significantly increase the food shelf-life and the added value of the products. The heat treatment applied during this operation can provoke physical, chemical and biochemical modifications resulting to alterations in nutritional and organoleptic properties of dried products. Color is the first property perceived by the consumer and is generally correlated with a global representation of product quality. Browning knowledge is essential to conserve the commercial potential of food. Dried mango sector in Burkina Faso constitute a part of my course thesis based on the understanding of phenomena involved in the mango browning during drying process and then during the storage. The global objective is to identify the main parameters affecting the enzymatic and non-enzymatic browning in order to propose optimized technological ways improving the final quality of the dried mango products. Experimental approach offering possibility to study temperature and water activity specifics effects independently to other parameters allowed us to identify critical points of the process occurring color variations

Heat inactivation of polyphenol oxidase and peroxidase as a function of water activity : a case study of mango drying

An innovative method was developed to study the specific uncoupled effect of temperature and water activity (Aw) during mango drying. Thermal treatment of reconstituted lyophilized mango powder at targeted Aw enabled evaluation of the inactivation of polyphenol oxidase and peroxidase activity in a range 0.98-0.6 Aw and a time-temperature range of 1-4h and 50-60 degrees C. We established that thermal treatment of the enzymatic extract was not the same as the inactivation phenomena that occurred in the mango matrix, mainly due to differences in the pH of the buffer extract (6.4) and reconstituted food matrix (3.8). Even if the inactivation of these two enzymes was directly correlated with the temperature of the treatment, this behavior was also strongly linked to the Aw. A two-step change in the fruit was observed at high Aw (i.e., at 0.98 in fresh fruit), polyphenol oxidase (PPO) was shown to be more thermostable than peroxidase (POD), whereas when evaporation reduced the Aw to around 0.6, the opposite behavior was observed. As a consequence, enzymatic inactivation during drying should be considered as the result of the coupled effects of time-temperature and water activity

Operationalizing circular economy. Reflections on a by-product upcycling value chain construction in the brewing sector

The concept of a circular economy has arisen in response to the problems related to the limits of the dominant linear economic system in contemporary societies and of the finite resources of our planet. The transition from waste status to a raw material by reusing it makes it possible to modify its value for future users and thus to redistribute this value. This article focuses on the case of spent grain to illustrate the role of the circular economy in food transition. Bases on a series of interviews, the paper discusses business modeling to operationalize sustainable development in the food sector and presents a discussion and conclusion on the advantages and limitations of the deployment of the circular economy in the brewing industry, taking into account and understanding the interests and constraints of various stakeholders