A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign

The efficacy of a newly created software package for predictive modeling of developmental gene regulatory networks (GRNs) has recently been demonstrated (Peter et al., 2012). The program GeNeTool computes spatial gene expression patterns based on GRN interactions and thereby allows the direct comparison of predicted and observed spatial expression patterns. GeNeTool also permits in silico exploration of both cis- and trans- perturbations of GRN interactions. Here, we present this program, review briefly its major features and applications, and provide a detailed and accessible tutorial

Predictive computation of genomic logic processing functions in embryonic development

Gene regulatory networks (GRNs) control the dynamic spatial patterns of regulatory gene expression in development. Thus, in principle, GRN models may provide system-level, causal explanations of developmental process. To test this assertion, we have transformed a relatively well-established GRN model into a predictive, dynamic Boolean computational model. This Boolean model computes spatial and temporal gene expression according to the regulatory logic and gene interactions specified in a GRN model for embryonic development in the sea urchin. Additional information input into the model included the progressive embryonic geometry and gene expression kinetics. The resulting model predicted gene expression patterns for a large number of individual regulatory genes each hour up to gastrulation (30 h) in four different spatial domains of the embryo. Direct comparison with experimental observations showed that the model predictively computed these patterns with remarkable spatial and temporal accuracy. In addition, we used this model to carry out in silico perturbations of regulatory functions and of embryonic spatial organization. The model computationally reproduced the altered developmental functions observed experimentally. Two major conclusions are that the starting GRN model contains sufficiently complete regulatory information to permit explanation of a complex developmental process of gene expression solely in terms of genomic regulatory code, and that the Boolean model provides a tool with which to test in silico regulatory circuitry and developmental perturbations

Comparing Strategies for Coding Adjoints

This document presents and compares methodologies to generate discrete adjoint codes. These methods can be implemented when hand writing adjoints, or within Automatic Differentiation tools. Automatic differentiation has been applied successfully to industrial codes that are large and general enough to fully validate this new technology. Future AD tools will make use of some general methods presented in this paper but still not implemented within present tools. In this paper, we try to compare these strategies in terms of accuracy, execution time and memory requirement on a one dimension- al thermal-hydraulic module for two-phase flow modeling

The sizes of the exchangeable pools of selenium in elderly women and their relation to institutionalization

Exchangeable pools of Se after an intravenous injection of 74Se-enriched isotope as sodium selenite were measured in two groups (n 9) of elderly women (free-living aged 64-82 years and institutionalized aged 68-82 years), and a comparison group (n 9) of young women aged 31-40 years to evaluate the effect of age and institutionalization on Se reserves. Dietary Se intake was not different among the three groups. Plasma Se and glutathione peroxidase (EC 1.11.1.9) levels were significantly lower in the institutionalized elderly women (P < 0.05). In each of the three groups, two pools were determined from our model. The size of the first pool and the sum of the two pools were lower in the group of institutionalized elderly women than in the other two groups. The significant correlation between plasma Se level and total Se pool size (r 0.66, P < 0.01) indicated that this last variable could serve as a new marker of Se status. Finally, these data suggest that the Se status of elderly women is more related to lifestyle, in terms of institutionalization or not, than to age per s

In Subfertile Couple, Abdominal Fat Loss in Men Is Associated with Improvement of Sperm Quality and Pregnancy: A Case-Series

International audienceBackground: The impact of overweight among men of reproductive-age may affect fertility. Abdominal fat, more than body mass index, is an indicator of higher metabolic risk, which seems to be involved in decreasing sperm quality. This study aims to assess the relationship between abdominal fat and sperm DNA fragmentation and the effect of abdominal fat loss, among 6 men in subfertile couples. Methods: Sperm DNA fragmentation, abdominal fat and metabolic and hormonal profiles were measured in the 6 men before and after dietary advices. Seminal oxidative stress and antioxidant markers were determined. Results: After several months of a lifestyle program, all 6 men lost abdominal fat (patient 1: loss of 3 points of abdominal fat, patient 2: loss of 3 points, patient 3: loss of 2 points, patient 4: loss of 1 point, patient 5: loss of 4 points and patient 6: loss of 13 points). At the same time, their rate of sperm DNA fragmentation decreased: 9.5% vs 31%, 24% vs 43%, 18% vs 47%, 26.3% vs 66%, 25.4% vs 35% and 1.7% vs 25%. Also, an improvement in both metabolic (significant decrease in triglycerides and total cholesterol; p = 0.0139) and hormonal (significant increase in testosterone/oestradiol ratio; p = 0.0139) blood profiles was observed after following the lifestyle program. In seminal plasma, the amount of SOD2 has significantly increased (p = 0.0139) while in parallel carbonylated proteins have decreased. Furthermore, all spouses got pregnant. All pregnancies were brought to term. Conclusion: This study shows specifically that sperm DNA fragmentation among men in subfertile couples could be affected by abdominal fat, but improvement of lifestyle factor may correct this alteration. The effect of specific abdominal fat loss on sperm quality needs further investigation. The reduction of oxidative stress may be a contributing factor

Patrimoines gastronomiques. Définitions, typologies et enjeux de conservation

Depuis l’inscription, en novembre 2010, du repas gastronomique des Français sur la Liste représentative du Patrimoine culturel immatériel de l’humanité, l’intérêt et les questionnements autour de la gastronomie, envisagée comme fait patrimonial, n’ont cessé de croître. Cette reconnaissance internationale a de fait affirmé, avec une force incontestablement inédite, la dimension sociale, culturelle et patrimoniale de l’alimentation. Les aspects culturels et éducatifs du patrimoine gastronomique..

Un manifeste patrimonial pour la gastronomie

Si sa reconnaissance par l’Unesco, en 2010 a attiré sur le repas gastronomique des Français l’attention internationale, le fait alimentaire et culinaire dans les enjeux des politiques patrimoniales en France est plus ancien. Ce numéro de In Situ. Revue des patrimoines questionne ainsi de multiples manières, pluridisciplinaires et complémentaires, la notion même de « patrimoines gastronomiques » et la façon dont ceux-ci sont, depuis près de cinquante ans maintenant, identifiés, constitués, étudiés, conservés, protégés, valorisés et transmis. Les spécialistes du patrimoine, dans leur quotidien professionnel, se sont adaptés à l’essor sans précédent de la recherche appliquée au domaine de la gastronomie. En explorant les relations entre nourriture et patrimoine et phénomènes de patrimonialisation, les sciences du patrimoine ont profité de l’implication renouvelée des chercheurs et fait de la gastronomie un objet d’étude total, qui ne peut plus exclure aujourd’hui l’ampleur des études et des recherches menées par les professionnels des services patrimoniaux eux-mêmes. De l’objet au monument, la gastronomie, dans son acception patrimoniale, se rattache à un large éventail d’espaces spécialisés : jardins, potagers et vergers, conservatoires de plantes alimentaires et horticoles, restaurants, cafés, usines de production alimentaire, commerces de produits de bouche, cuisines, salles à manger, salles des fêtes, lieux de restauration collective…, la typologie des lieux associés, à divers titres, à la notion, est l’une des plus riches qui soit. Dans leurs spécialités respectives, les acteurs du patrimoine ont progressivement défriché le champ des pratiques culinaires, à travers l’instauration et la valorisation de jardins patrimonialisés et de conservatoires de plantes alimentaires, les études du patrimoine gastronomique conduites par les services de l’Inventaire général du patrimoine culturel, les chantiers de restauration ou de réhabilitation du cadre architectural de la gastronomie, les protections au titre des monuments historiques des lieux, des monuments et des objets mobiliers liés aux arts culinaires, la collecte de fonds spécialisés, dits parfois « fonds gourmands », par les archives et les bibliothèques et la constitution de collections d’objets par les musées, en particulier les écomusées et les musées de société. Le patrimoine culturel immatériel, qui met en valeur les pratiques, les savoirs et les savoir-faire des détenteurs de traditions vivantes, constitue l’avènement patrimonial le plus récent du champ culinaire. Ainsi, bien avant l’inscription du repas gastronomique des Français par l’Unesco, et même dès les années 1960 selon les secteurs, les professionnels du patrimoine se sont penchés sur le terrain tout matériel de la culture alimentaire et culinaire : cet intérêt pour l’infinie variété des éléments matériels de la culture alimentaire et du fait culinaire s’est développé sur tout le territoire français, hexagonal et ultramarin, à travers autant de démarches décisives pour identifier, étudier, préserver et valoriser ce patrimoine, tantôt bâti, tantôt mobilier, tantôt écrit, tantôt anthropologique. L’observation sur le temps long et la prise en compte synoptique des principaux secteurs institutionnels que propose ce numéro de In Situ. Revue des patrimoines donnent une cohérence à cette approche du domaine de la gastronomie par le patrimoine matériel et immatériel, c’est-à-dire, à l’échelle nationale, régionale ou locale, par la voie des inventaires, des protections juridiques, des collectes d’archives et d’objets d’art ou des projets scientifiques, didactiques et pédagogiques.If its recognition by UNESCO in 2010 drew international attention to the gastronomic meal of the French people, the food and culinary fact in the stakes of heritage policies in France is older. This issue of In Situ. Revue des patrimoines thus questions in multiple, multidisciplinary and complementary ways the very notion of "gastronomic heritage" and the way in which it has been identified, constituted, studied, conserved, protected, enhanced and transmitted for nearly fifty years now. Heritage specialists, in their daily professional lives, have adapted to the unprecedented growth of applied research in the field of gastronomy. By exploring the relationship between food and heritage and heritage phenomena, heritage sciences have benefited from the renewed involvement of researchers and have made gastronomy a subject of total study, which can no longer exclude the scope of studies and research carried out by heritage services professionals themselves. From objects to monuments, gastronomy, in its heritage sense, is linked to a wide range of specialized spaces: gardens, vegetable gardens and orchards, conservatories of food and horticultural plants, restaurants, cafés, food production plants, shops selling food products, kitchens, dining rooms, party rooms, collective catering places..., the typology of the places associated, in various ways, with the concept is one of the most rich. In their respective specialities, heritage actors have gradually cleared the field of culinary practices, through the establishment and enhancement of heritage gardens and food plant conservatories, studies of the gastronomic heritage conducted by the services of the General Inventory of Cultural Heritage, work to restore or rehabilitate the architectural framework of gastronomy, protection of historic monuments, monuments and movable objects related to the culinary arts, the collection of specialised funds, sometimes called "gourmet funds", by archives and libraries and the constitution of collections of objects by museums, in particular ecomuseums and social museums. The intangible cultural heritage, which highlights the practices, knowledge and skills of the holders of living traditions, is the most recent heritage development of the culinary field. Thus, well before the inclusion of the French gourmet meal by UNESCO, and even as early as the 1960s, depending on the sector, heritage professionals focused on the field of all material aspects of food and culinary culture: this interest in the infinite variety of material elements of food and culinary culture developed in France, through so many decisive steps to identify, study, preserve and enhance this heritage, sometimes built, sometimes movable, sometimes written, sometimes anthropological. Observation over time and synoptic consideration of the main institutional sectors, as proposed in this issue of In Situ. Revue des patrimoines, give coherence to this approach to the field of gastronomy through tangible and intangible heritage, i.e., at the national, regional or local level, through inventories, legal protection, collection of archives and works of art or scientific, didactic and educational projects

Le numéro en bref – Patrimoines gastronomiques : définitions, typologies et enjeux de conservation

Les contours du patrimoine gastronomique sont difficiles à cerner, d’où l’usage fréquent de l’expression au pluriel. À la fois matériel, immatériel et mémoriel, aux confins des champs de recherche de l’alimentation, de la botanique, de l’architecture, des arts décoratifs ou encore de la sociabilité, ce patrimoine protéiforme exige pour son étude la mobilisation de nombreuses disciplines scientifiques ; il a renouvelé, au plan national et international, le regard des professionnels du patrimoi..

A dietary supplementation with leucine and antioxidants is capable to accelerate muscle mass recovery after immobilization in adult rats

Prolonged inactivity induces muscle loss due to an activation of proteolysis and decreased protein synthesis; the latter is also involved in the recovery of muscle mass. The aim of the present work was to explore the evolution of muscle mass and protein metabolism during immobilization and recovery and assess the effect of a nutritional strategy for counteracting muscle loss and facilitating recovery. Adult rats (6-8 months) were subjected to unilateral hindlimb casting for 8 days (10-18) and then permitted to recover for 10 to 40 days (R10-R40). They were fed a Control or Experimental diet supplemented with antioxidants/polyphenols (AOX) (10 to 18), AOX and leucine (AOX + LEU) (18 to R15) and LEU alone (R15 to R40). Muscle mass, absolute protein synthesis rate and proteasome activities were measured in gastrocnemius muscle in casted and non-casted legs in post prandial (PP) and post absorptive (PA) states at each time point. Immobilized gastrocnemius protein content was similarly reduced (-37%) in both diets compared to the non-casted leg. Muscle mass recovery was accelerated by the AOX and LEU supplementation (+6% AOX+LEU vs. Control, P<0.05 at R40) due to a higher protein synthesis both in PA and PP states (+23% and 31% respectively, Experimental vs. Control diets, P<0.05, R40) without difference in trypsin-and chymotrypsin-like activities between diets. Thus, this nutritional supplementation accelerated the recovery of muscle mass via a stimulation of protein synthesis throughout the entire day (in the PP and PA states) and could be a promising strategy to be tested during recovery from bed rest in humans