Laboratoire de Génie Chimique

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell’s regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene. A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs. These authors describe the ENCODE (Encyclopedia of DNA Elements) effort to provide a complete catalogue of primary and processed RNAs found either in specific sub-cellular compartments or throughout the cell. They show that three-quarters of the human genome can be transcribed, and provide a wealth of information about the range and levels of expression, localization, processing fates and modifications of both known and previously unannotated RNAs. Collectively, these observations suggest that the current concept of a gene should be revisited.

In the past 10-15 years, the microbial fuel cell (MFC) technology has captured the attention of the scientific community for the possibility of transforming organic waste directly into electricity through microbially catalyzed anodic, and microbial/enzymatic/abiotic cathodic electrochemical reactions. In this review, several aspects of the technology are considered. Firstly, a brief history of abiotic to biological fuel cells and subsequently, microbial fuel cells is presented. Secondly, the development of the concept of microbial fuel cell into a wider range of derivative technologies, called bioelectrochemical systems, is described introducing briefly microbial electrolysis cells, microbial desalination cells and microbial electrosynthesis cells. The focus is then shifted to electroactive biofilms and electron transfer mechanisms involved with solid electrodes. Carbonaceous and metallic anode materials are then introduced, followed by an explanation of the electro catalysis of the oxygen reduction reaction and its behavior in neutral media, from recent studies. Cathode catalysts based on carbonaceous, platinum-group metal and platinum-group-metal-free materials are presented, along with membrane materials with a view to future directions. Finally, microbial fuel cell practical implementation, through the utilization of energy output for practical applications, is described.

Ochratoxin A (OTA) is a ubiquitous mycotoxin produced by fungi of improperly stored food products. OTA is nephrotoxic and is suspected of being the main etiological agent responsible for human Balkan endemic nephropathy (BEN) and associated urinary tract tumours. Striking similarities between OTA-induced porcine nephropathy in pigs and BEN in humans are observed. International Agency for Research on Cancer (IARC) has classified OTA as a possible human carcinogen (group 2B). Currently, the mode of carcinogenic action by OTA is unknown. OTA is genotoxic following oxidative metabolism. This activity is thought to play a central role in OTA-mediated carcinogenesis and may be divided into direct (covalent DNA adduction) and indirect (oxidative DNA damage) mechanisms of action. Evidence for a direct mode of genotoxicity has been derived from the sensitive 32P-postlabelling assay. OTA facilitates guanine-specific DNA adducts in vitro and in rat and pig kidney orally dosed, one adduct comigrates with a synthetic carbon (C)-bonded C8-dG OTA adduct standard. In this paper, our current understanding of OTA toxicity and carcinogenicity are reviewed. The available evidence suggests that OTA is a genotoxic carcinogen by induction of oxidative DNA lesions coupled with direct DNA adducts via quinone formation. This mechanism of action should be used to establish acceptable intake levels of OTA from human food sources.

BACKGROUND: The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay. METHODOLOGY/PRINCIPAL FINDINGS: A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274. CONCLUSIONS/SIGNIFICANCE: Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.

Kombucha is a beverage of probable Manchurian origins obtained from fermented tea by a microbial consortium composed of several bacteria and yeasts. This mixed consortium forms a powerful symbiosis capable of inhibiting the growth of potentially contaminating bacteria. The fermentation process also leads to the formation of a polymeric cellulose pellicle due to the activity of certain strains of Acetobacter sp. The tea fermentation process by the microbial consortium was able to show an increase in certain biological activities which have been already studied; however, little information is available on the characterization of its active components and their evolution during fermentation. Studies have also reported that the use of infusions from other plants may be a promising alternative. PRACTICAL APPLICATION: Kombucha is a traditional fermented tea whose consumption has increased in the recent years due to its multiple functional properties such as anti-inflammatory potential and antioxidant activity. The microbiological composition of this beverage is quite complex and still more research is needed in order to fully understand its behavior. This study comprises the chemical and microbiological composition of the tea and the main factors that may affect its production.

We introduce a new framework for the analysis of association studies, designed to allow untyped variants to be more effectively and directly tested for association with a phenotype. The idea is to combine knowledge on patterns of correlation among SNPs (e.g., from the International HapMap project or resequencing data in a candidate region of interest) with genotype data at tag SNPs collected on a phenotyped study sample, to estimate ("impute") unmeasured genotypes, and then assess association between the phenotype and these estimated genotypes. Compared with standard single-SNP tests, this approach results in increased power to detect association, even in cases in which the causal variant is typed, with the greatest gain occurring when multiple causal variants are present. It also provides more interpretable explanations for observed associations, including assessing, for each SNP, the strength of the evidence that it (rather than another correlated SNP) is causal. Although we focus on association studies with quantitative phenotype and a relatively restricted region (e.g., a candidate gene), the framework is applicable and computationally practical for whole genome association studies. Methods described here are implemented in a software package, Bim-Bam, available from the Stephens Lab website http://stephenslab.uchicago.edu/software.html.

While the commensal bacterium Propionibacterium acnes (P. acnes) is involved in the maintenance of a healthy skin, it can also act as an opportunistic pathogen in acne vulgaris. The latest findings on P. acnes shed light on the critical role of a tight equilibrium between members of its phylotypes and within the skin microbiota in the development of this skin disease. Indeed, contrary to what was previously thought, proliferation of P. acnes is not the trigger of acne as patients with acne do not harbour more P. acnes in follicles than normal individuals. Instead, the loss of the skin microbial diversity together with the activation of the innate immunity might lead to this chronic inflammatory condition. This review provides results of the most recent biochemical and genomic investigations that led to the new taxonomic classification of P. acnes renamed Cutibacterium acnes (C. acnes), and to the better characterisation of its phylogenetic cluster groups. Moreover, the latest data on the role of C. acnes and its different phylotypes in acne are presented, providing an overview of the factors that could participate in the virulence and in the antimicrobial resistance of acne-associated strains. Overall, this emerging key information offers new perspectives in the treatment of acne, with future innovative strategies focusing on C. acnes biofilms and/or on its acne-associated phylotypes.

Gluconic acid is a mild organic acid derived from glucose by a simple oxidation reaction. The reaction is facilitated by the enzyme glucose oxidase (fungi) and glucose dehydrogenase (bacteria such as Gluconobacter). Microbial production of gluconic acid is the preferred method and it dates back to several decades. The most studied and widely used fermentation process involves the fungus Aspergillus niger. Gluconic acid and its derivatives, the principal being sodium gluconate, have wide applications in food and pharmaceutical industry. This article gives a review of microbial gluconic acid production, its properties and applications.

Data on comprehensive population-based surveillance of antimicrobial resistance is lacking. In low- and middle-income countries, the challenges are high due to weak laboratory capacity, poor health systems governance, lack of health information systems, and limited resources. Developing countries struggle with political and social dilemma, and bear a high health and economic burden of communicable diseases. Available data are fragmented and lack representativeness which limits their use to advice health policy makers and orientate the efficient allocation of funding and financial resources on programs to mitigate resistance. Low-quality data means soaring rates of antimicrobial resistance and the inability to track and map the spread of resistance, detect early outbreaks, and set national health policy to tackle resistance. Here, we review the barriers and limitations of conducting effective antimicrobial resistance surveillance, and we highlight multiple incremental approaches that may offer opportunities to strengthen population-based surveillance if tailored to the context of each country.

ABSTRACT: : Edible chitosan coatings showed anti‐ Listeria monocytogenes effect evaluated by numeration and epifluorescence methods, imparting a strong localized functional effect at the food surface by active packaging. The use of film‐forming solution in culture liquid medium showed a known flocculant phenomenon combined with bactericidal activity, keeping 20% of the initial microbial charge as viable cells in flocculant, which could develop subsequently. However, chitosan film showed 100% of L. monocytogenes inhibition for at least 8 d, completed by bactericidal activity measured by epifluorescence assays. A decrease in antibactericidal effect with time was obtained, most probably due to a decreasing availability of amino‐groups of chitosan. Latter results were validated on Emmental cheese samples using L. innocua as model strain because of its nonpathogenicity.

BACKGROUND: The growing demand for natural food preservatives in the last decade has promoted investigations on their application for preserving perishable foods. In this context, the present review is focused on discussing the prospective application of plant extracts containing phenolics or isolated plant phenolics as natural antimicrobials in foods. Plant essential oils are outside the scope of this review since utilization of their antimicrobial activity for food preservation has been extensively reviewed. RESULTS: Although the exact antimicrobial mechanisms of action of phenolic compounds are not yet fully understood, it is commonly acknowledged that they have diverse sites of action at the cellular level. Antimicrobial phenolics can be added directly to the formulation of perishable food products or incorporated into food-contact materials to release them in the immediate zone of perishable foods. Edible coatings or active food packaging materials can thus be used as carriers of plant bioactive compounds. CONCLUSION: These materials could be an interesting delivery system to improve the stability of phenolics in foods and to improve the shelf life of perishable foods. This review will thus provide an overview of current knowledge of the antimicrobial activity of phenolic-rich plant extracts and of the promises and limits of their exploitation for the preservation of perishable foods. © 2018 Society of Chemical Industry.

UNLABELLED: CAR(H)(T)A GENE: is an integrated genetic and radiation hybrid (RH) mapping tool which can deal with multiple populations, including mixtures of genetic and RH data. CAR(H)(T)A GENE: performs multipoint maximum likelihood estimations with accelerated expectation-maximization algorithms for some pedigrees and has sophisticated algorithms for marker ordering. Dedicated heuristics for framework mapping are also included. CAR(H)(T)A GENE: can be used as a C++ library, through a shell command and a graphical interface. The XML output for companion tools is integrated. AVAILABILITY: The program is available free of charge from www.inra.fr/bia/T/CarthaGene for Linux, Windows and Solaris machines (with Open Source). CONTACT: tschiex@toulouse.inra.fr.

From a green and sustainable chemistry standpoint, the current challenge in the polyurethane’s industry is to switch from petrobased polyurethanes (PUs) to biobased polyhydroxyurethanes (PHUs). This review describes the main alternative strategies being developed with a focus on PHUs from vegetable oils and derivatives. The substitution of petrobased polyols by natural oil based polyols was the first route to biobased PUs to be developed. The second strategy involves synthesis without the need of harmful isocyanate by the nucleophilic polyaddition of polyamines to polycyclic carbonates. The technological barrier to the synthesis of biobased cyclic carbonates could be overcome by the chemical transformation of epoxidized vegetable oils or by the use of glycerine carbonate-based intermediates. New families of biobased PHUs with a lower environmental footprint could be generated.

A concise review of relevant experimental observations and modeling of high-pressure trickle-bed reactors, based on recent studies, is presented. The following topics are considered: flow regime transitions, pressure drop, liquid holdup, gas−liquid interfacial area and mass-transfer coefficient, catalyst wetting efficiency, catalyst dilution with inert fines, and evaluation of trickle-bed models for liquid-limited and gas-limited reactions. The effects of high-pressure operation, which is of industrial relevance, on the physicochemical and fluid dynamic parameters are discussed. Empirical and theoretical models developed to account for the effect of high pressure on the various parameters and phenomena pertinent to the topics discussed are briefly described.

AIMS: To study the biochemical response of Yarrowia lipolytica LGAM S(7)1 during growth on raw glycerol (the main by-product of bio-diesel production units) in order to produce metabolic products of industrial significance. METHODS AND RESULTS: Yarrowia lipolytica was cultivated on raw glycerol or glucose in flasks. Although nitrogen-limited media were employed, growth was not followed by production of reserve lipid. Nitrogen limitation led to citric acid excretion. Growth and citric acid production parameters on glycerol were similar to those obtained on glucose. When high initial glycerol media were used, citric acid up to 35 g l(-1) (yield 0.42-0.44 g acid g(-1) glycerol consumed) was produced. CONCLUSIONS: Raw glycerol was an adequate substrate for Y. lipolytica. Growth was not followed by reserve lipid accumulation, but amounts of citric acid were produced. SIGNIFICANCE AND IMPACT OF THE STUDY: Raw glycerol is an industrial feedstock appearing in increasing quantities as the main by-product of bio-diesel production facilities. The present study describes an alternative way of glycerol valorization, with the production of remarkable amounts of citric acid, in addition to its main valorization way (production of 1,3-propanediol by bacteria).

Mycotoxins are secondary metabolites present worldwide in agricultural commodities and produced by filamentous fungi that cause a toxic response (mycotoxicosis) when ingested by animals. Prevention of mycotoxicoses includes pre- and post-harvest strategies. The best way to reduce the mycotoxin content in food and feed is the prevention of mycotoxin formation in the field, but this is often not sufficient, so other methods are needed. To decontaminate and/or detoxify mycotoxin-contaminated food and feed, the most prevalent approach in the feed industry is the inclusion of sorbent materials in the feed thus obtaining more or less selective removal of toxins by adsorption during passage through the gastrointestinal tract. Another reliable approach is to add enzymes or microorganisms capable of detoxifying some mycotoxins. Through a comprehensive review of published reports on the strategies for mycotoxin removal, this present work aims to update our understanding of mycotoxin removal. It provides an insight into the detoxification of mycotoxin present in food and feed. In the future, more emphasis needs to be placed on adsorption of mycotoxins in the gastrointestinal tract. Concerning the enzymatic transformation of mycotoxins, further efforts are required in understanding detoxification reactions, the toxicity of transformation products and in the characterization of enzymes responsible for transformations.

A new process was developed to fabricate electrically conducting nylon 6/graphite nanocomposites via intercalation polymerization of ϵ-caprolactam in the presence of expanded graphite. The transition from an electrical insulator to an electrical semiconductor for nylon 6 occurred when the graphite volume content was 0.75, which was much lower than that of conventional conducting polymer composites. The electrical conductivity reached 10−4 S/cm when the graphite content was 2.0 vol %. The TEM microphotographs suggested that the low percolation threshold and the great improvement of electrical conductivity could be attributed to the high aspect ratio (width-to-thickness), the high expansion ratio in c axis of the graphite sheets and the homogeneous dispersion of the nanoscale graphite particles in the nylon 6 matrix. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 1626–1633, 2000

Over 1.7 billion students around the world have had their education disrupted by the spread of the Coronavirus disease worldwide. Schools and universities have not faced this level of disruption since World War II. The COVID-19 pandemic presented a colossal challenge for teachers to urgently and massively adapt all their classes to distance learning in order to maintain educational continuity with the same quality. Even if some teachers and certain classes were ready to face the situation, a large majority had to adapt their teaching and learning in a very short time without training, with insufficient bandwidth, and with little preparation. This unexpected and rapid transition to online learning has led to a multiplication of teachers’ strategies for distance learning in lectures, tutorials, project groups, lab works, and assessments. The purpose of this paper is to present the feedback from students and teachers who participated in the lockdown semester of two different groups of a 5-year program in Chemistry, Environment and Chemical Engineering (100 students) at INSA Toulouse (France). The analysis has highlighted some great successes and some failures in the solutions proposed. Consequently, some guidelines can be given to help us all to learn the lessons of such a singular experience in order to face the unexpected future with more knowledge and more successful distance learning. Teachers have shown very strong resilience during this crisis, at the cost of significant personal commitment. They admit that they have learned more about distance education in two months than in the last 10 years.

Abstract Velocity and residence time distributions play a crucial role in the performance of microreactors for chemical synthesis. The specific features of fluid flow through multiplate microchannel reactors are examined by an approximate pressure drop model whose validity is confirmed through comparison with more detailed finite‐volume calculations. The model results allow for determination of the influence of the geometrical characteristics of the microchannel structures on the flow distributions and are used to optimize the reactor design for maximum flow uniformity.

Abstract A proposed theoretical model describes colloids deposition on a membrane surface accounting for surface interactions. A mass‐transfer equation links the deposition rate to hydrodynamic conditions (permeation and tangential flow through a boundary layer thickness, δ) and to physicochemical properties of the suspension (diffusion, D, and potential barrier between particles, V B ). This equation predicts the existence of a critical flux, J crit , for ultrafiltration, reverse osmosis, or microfiltration of large‐size colloids as: Some of the trends observed when processing protein solutions are explained by this model. Previous experimental data for various colloids or our data with a clay suspension in the presence of electrolytes are also compared to predictions of our model. It explains the “flux anomaly” for particle sizes between 10 nm and 1 μm.