Flavour distribution and release from gelatine-starch matrices

© 2020 The Authors Microstructure design of protein-polysaccharide phase separated gels has been suggested as a strategy to nutritionally improve food products. Varying the phase volumes of a phase separated matrix may affect texture and overall flavour balance of the final product, which are both important for consumer acceptance. The aims of this study were to investigate how modifying the phase volumes of a gelatine-starch biphasic mixture affected aroma release, and how addition of sucrose affects phase separation, flavour distribution and aroma release. Biphasic gels of different microstructures with the same effective concentration of gelatine and starch in each phase were developed. Microstructure significantly affected aroma release in vitro but not in vivo when panellists (n = 5) chewed and swallowed the sample. Addition of sucrose (0–60%) to the biphasic mixture significantly reduced water activity, affected the microstructure and affected aroma distribution in each phase and subsequent release rates depending on the physicochemical properties of the aroma volatile. In general, affinity for the gelatine phase for the less hydrophobic, more volatile compounds was not significantly affected by sucrose concentration. Whereas an increased affinity for the starch phase for the more hydrophobic, less volatile compounds was observed with increased sucrose as the starch phase becomes more dispersed at sucrose concentrations between 40 and 60%. The results of this study may be of interest to researchers and industry to enable prediction of how reformulation, such as reduction of sucrose, to meet nutritional guidelines may affect the overall aroma balance of a phase separated food matrix

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans

One major expectation from the transcriptome in humans is to characterize the biological basis of associations identified by genome-wide association studies. So far, few cis expression quantitative trait loci (eQTLs) have been reliably related to disease susceptibility. Trans-regulating mechanisms may play a more prominent role in disease susceptibility. We analyzed 12,808 genes detected in at least 5% of circulating monocyte samples from a population-based sample of 1,490 European unrelated subjects. We applied a method of extraction of expression patterns—independent component analysis—to identify sets of co-regulated genes. These patterns were then related to 675,350 SNPs to identify major trans-acting regulators. We detected three genomic regions significantly associated with co-regulated gene modules. Association of these loci with multiple expression traits was replicated in Cardiogenics, an independent study in which expression profiles of monocytes were available in 758 subjects. The locus 12q13 (lead SNP rs11171739), previously identified as a type 1 diabetes locus, was associated with a pattern including two cis eQTLs, RPS26 and SUOX, and 5 trans eQTLs, one of which (MADCAM1) is a potential candidate for mediating T1D susceptibility. The locus 12q24 (lead SNP rs653178), which has demonstrated extensive disease pleiotropy, including type 1 diabetes, hypertension, and celiac disease, was associated to a pattern strongly correlating to blood pressure level. The strongest trans eQTL in this pattern was CRIP1, a known marker of cellular proliferation in cancer. The locus 12q15 (lead SNP rs11177644) was associated with a pattern driven by two cis eQTLs, LYZ and YEATS4, and including 34 trans eQTLs, several of them tumor-related genes. This study shows that a method exploiting the structure of co-expressions among genes can help identify genomic regions involved in trans regulation of sets of genes and can provide clues for understanding the mechanisms linking genome-wide association loci to disease

Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1,395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; and 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared with information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known nonpathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Large scale multifactorial likelihood quantitative analysis of BRCA1 and BRCA2 variants: An ENIGMA resource to support clinical variant classification

Abstract The multifactorial likelihood analysis method has demonstrated utility for quantitative assessment of variant pathogenicity for multiple cancer syndrome genes. Independent data types currently incorporated in the model for assessing BRCA1 and BRCA2 variants include clinically calibrated prior probability of pathogenicity based on variant location and bioinformatic prediction of variant effect, co-segregation, family cancer history profile, co-occurrence with a pathogenic variant in the same gene, breast tumor pathology, and case-control information. Research and clinical data for multifactorial likelihood analysis were collated for 1395 BRCA1/2 predominantly intronic and missense variants, enabling classification based on posterior probability of pathogenicity for 734 variants: 447 variants were classified as (likely) benign, and 94 as (likely) pathogenic; 248 classifications were new or considerably altered relative to ClinVar submissions. Classifications were compared to information not yet included in the likelihood model, and evidence strengths aligned to those recommended for ACMG/AMP classification codes. Altered mRNA splicing or function relative to known non-pathogenic variant controls were moderately to strongly predictive of variant pathogenicity. Variant absence in population datasets provided supporting evidence for variant pathogenicity. These findings have direct relevance for BRCA1 and BRCA2 variant evaluation, and justify the need for gene-specific calibration of evidence types used for variant classification. This article is protected by copyright. All rights reserved.Peer reviewe

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P = 9.2 x 10(-20)), ER-negative BC (P = 1.1 x 10(-13)), BRCA1-associated BC (P = 7.7 x 10(-16)) and triple negative BC (P-diff = 2 x 10(-5)). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P = 2 x 10(-3)) and ABHD8 (PPeer reviewe

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Conditionnement et fonctionnalisation de la surface du nitrure de silicium

Covalent grafting of organic molecules on glass can modify its surface physico-chemical properties or improve the adhesion of a coating. Such a functionalization usually relies on a silanisation reaction, bonding molecules to the surface through Si-O-Si bonds. Unfortunately, the resulting molecular layers do not exhibit long-term stability due to the hydrolysis of siloxane groups. One solution would consist in depositing a silicon nitride layer on glass, allowing the glass surface to be functionalized through more stable bonds N-C or Si-C. Silicon nitride layers are frequently used in glass industry. They are well-known for their durability properties and are often used as a protective layer against glass corrosion.The aim of this project is to characterize and control the non-oxidized silicon nitride surface, then to optimize and understand the surface modification by covalent grafting of organic molecules.When silicon nitride is exposed to atmosphere, an oxynitride layer is formed on its surface. Several efficient ways to remove this native oxynitride are first studied and optimized. The quantitative characterization and control of the surface chemical composition provide a reliable starting point for the functionalization step. The surface chemical composition is quantitatively investigated by combining Attenuated Total Reflection InfraRed spectroscopy (ATR-IR), X-ray photoelectron spectroscopy (XPS) and chemical dosing. The etching in HF-based solutions efficiently removes the oxynitride layer and leads to a surface mainly covered with Si-F bonds and smaller amounts of Si-OH and N-H bonds. The surface composition can be modified by a H2 plasma treatment performed after the wet etching or by changing the silicon nitride layer composition (silicon enrichment), leading in either case to the formation of Si-H bonds on surface. An etching mechanism is suggested from these experimental observations.The second part of this work is focused on the grafting of the alkyl chains on the silicon nitride surface. The surface is reacted with a 1-alkene, using photochemical or thermal activation. The grafting efficiency depends on the surface composition and the activation conditions. The presence of surface Si-H bonds and the effect of Si enrichment are considered in details. In a final part, in an applicative view, functional hydrophobic molecules are grafted on the silicon nitride surface.La fonctionnalisation de la surface du verre par des molécules organiques permet de modifier son énergie de surface ou d’améliorer l’adhésion d’un revêtement. La méthode classique de fonctionnalisation directe du verre repose sur une réaction de silanisation, via la formation de ponts siloxanes Si O Si. Ces ponts ont tendance à s’hydrolyser en milieu salin ou alcalin, entrainant la perte de la fonctionnalité du verre. Une solution envisagée consiste à déposer une couche de nitrure de silicium (SixN4) sur le verre, permettant de greffer des molécules organiques via des liaisons covalentes robustes : Si C ou N C. Le nitrure de silicium présente l’avantage d’être un matériau très souvent utilisé dans l’industrie verrière en raison de sa capacité à bloquer la diffusion des ions sodium et de protéger ainsi le verre de la corrosion.L’objectif de ce travail de thèse est de caractériser et contrôler la surface du nitrure de silicium, puis d’optimiser et de comprendre la modification de sa surface par le greffage covalent de molécules organiques.Lorsque le nitrure de silicium est exposé à l’air, une couche d’oxynitrure est formée en surface. L’optimisation et la compréhension du décapage de cette couche d’oxynitrure natif en milieu liquide est l’objet de la première phase de ce travail. La composition chimique de la surface est finement caractérisée et quantifiée en combinant des mesures de spectroscopie infrarouge en mode de réflexion totale atténuée (IR-ATR), de spectroscopie de photoélectrons X (XPS) et des dosages chimiques de surface. Le décapage dans des solutions fluorées (HF et NH4F) permet de retirer efficacement la couche d’oxynitrure et laisse majoritairement en surface des liaisons Si-F et dans une moindre mesure des liaisons N H et Si OH. La composition chimique de la surface peut toutefois être modifiée pour former des groupements Si H, soit en enrichissant la couche du SixN4 en silicium, soit en soumettant la surface à un traitement par plasma d’hydrogène à l’issue du décapage. A partir des observations expérimentales, une proposition décrivant les mécanismes mis en jeu lors du décapage est présentée.Dans la seconde partie de la thèse, la surface du nitrure de silicium est modifiée par l’immobilisation de molécules organiques, plus spécifiquement par la réaction d’un 1 alcène sous activation thermique ou photochimique. La composition chimique de la surface et les conditions d’activation de la réaction modifient la réaction de greffage et la densité des couches organiques. En particulier, la présence de liaisons Si-H et l’enrichissement de la couche en silicium sont étudiés en détail. Dans une dernière partie, dans une visée plus applicative, des couches denses fluorées présentant un caractère hydrophobe naturel sont greffées sur la surface du nitrure de silicium

Control and functionalization of silicon nitride surface

La fonctionnalisation de la surface du verre par des molécules organiques permet de modifier son énergie de surface ou d’améliorer l’adhésion d’un revêtement. La méthode classique de fonctionnalisation directe du verre repose sur une réaction de silanisation, via la formation de ponts siloxanes Si O Si. Ces ponts ont tendance à s’hydrolyser en milieu salin ou alcalin, entrainant la perte de la fonctionnalité du verre. Une solution envisagée consiste à déposer une couche de nitrure de silicium (SixN4) sur le verre, permettant de greffer des molécules organiques via des liaisons covalentes robustes : Si C ou N C. Le nitrure de silicium présente l’avantage d’être un matériau très souvent utilisé dans l’industrie verrière en raison de sa capacité à bloquer la diffusion des ions sodium et de protéger ainsi le verre de la corrosion.L’objectif de ce travail de thèse est de caractériser et contrôler la surface du nitrure de silicium, puis d’optimiser et de comprendre la modification de sa surface par le greffage covalent de molécules organiques.Lorsque le nitrure de silicium est exposé à l’air, une couche d’oxynitrure est formée en surface. L’optimisation et la compréhension du décapage de cette couche d’oxynitrure natif en milieu liquide est l’objet de la première phase de ce travail. La composition chimique de la surface est finement caractérisée et quantifiée en combinant des mesures de spectroscopie infrarouge en mode de réflexion totale atténuée (IR-ATR), de spectroscopie de photoélectrons X (XPS) et des dosages chimiques de surface. Le décapage dans des solutions fluorées (HF et NH4F) permet de retirer efficacement la couche d’oxynitrure et laisse majoritairement en surface des liaisons Si-F et dans une moindre mesure des liaisons N H et Si OH. La composition chimique de la surface peut toutefois être modifiée pour former des groupements Si H, soit en enrichissant la couche du SixN4 en silicium, soit en soumettant la surface à un traitement par plasma d’hydrogène à l’issue du décapage. A partir des observations expérimentales, une proposition décrivant les mécanismes mis en jeu lors du décapage est présentée.Dans la seconde partie de la thèse, la surface du nitrure de silicium est modifiée par l’immobilisation de molécules organiques, plus spécifiquement par la réaction d’un 1 alcène sous activation thermique ou photochimique. La composition chimique de la surface et les conditions d’activation de la réaction modifient la réaction de greffage et la densité des couches organiques. En particulier, la présence de liaisons Si-H et l’enrichissement de la couche en silicium sont étudiés en détail. Dans une dernière partie, dans une visée plus applicative, des couches denses fluorées présentant un caractère hydrophobe naturel sont greffées sur la surface du nitrure de silicium.Covalent grafting of organic molecules on glass can modify its surface physico-chemical properties or improve the adhesion of a coating. Such a functionalization usually relies on a silanisation reaction, bonding molecules to the surface through Si-O-Si bonds. Unfortunately, the resulting molecular layers do not exhibit long-term stability due to the hydrolysis of siloxane groups. One solution would consist in depositing a silicon nitride layer on glass, allowing the glass surface to be functionalized through more stable bonds N-C or Si-C. Silicon nitride layers are frequently used in glass industry. They are well-known for their durability properties and are often used as a protective layer against glass corrosion.The aim of this project is to characterize and control the non-oxidized silicon nitride surface, then to optimize and understand the surface modification by covalent grafting of organic molecules.When silicon nitride is exposed to atmosphere, an oxynitride layer is formed on its surface. Several efficient ways to remove this native oxynitride are first studied and optimized. The quantitative characterization and control of the surface chemical composition provide a reliable starting point for the functionalization step. The surface chemical composition is quantitatively investigated by combining Attenuated Total Reflection InfraRed spectroscopy (ATR-IR), X-ray photoelectron spectroscopy (XPS) and chemical dosing. The etching in HF-based solutions efficiently removes the oxynitride layer and leads to a surface mainly covered with Si-F bonds and smaller amounts of Si-OH and N-H bonds. The surface composition can be modified by a H2 plasma treatment performed after the wet etching or by changing the silicon nitride layer composition (silicon enrichment), leading in either case to the formation of Si-H bonds on surface. An etching mechanism is suggested from these experimental observations.The second part of this work is focused on the grafting of the alkyl chains on the silicon nitride surface. The surface is reacted with a 1-alkene, using photochemical or thermal activation. The grafting efficiency depends on the surface composition and the activation conditions. The presence of surface Si-H bonds and the effect of Si enrichment are considered in details. In a final part, in an applicative view, functional hydrophobic molecules are grafted on the silicon nitride surface