La digestion ruminale : mise en place d’un modèle d’étude in vitro à long terme en cultures Batch

L’objectif de cette étude est de mettre au point une culture de contenu ruminal sur une durée de plus de 24h (i.e. 96h), avec renouvellement du milieu toutes les 12h. Les activités microbiennes et enzymatiques des inoculums prélevés sur 2 vaches et utilisés à J1 ont été comparées à celles obtenues avec les cultures de 96h. Les activités fermentaires se sont maintenues, cependant une diminution de l’activité fibrolytique et une augmentation de l’activité amylolytique ont été observées. La biohydrogénation a également augmentée. La concentration en acides gras volatils est restée constante avec une diminution de la proportion en acide acétique et une augmentation de celle en acide propionique. La concentration en ammoniac a été divisée par deux puis s’est stabilisée au bout de 48 h. Le pH est resté constant. Avec quelques adaptations, ce modèle pourrait ainsi être utilisé afin d’étudier les effets à long terme, en culture batch, de certains traitements sur la digestion microbienne dans le rumen

Ruminal digestion: development of medium-term cultures of ruminal content

Introduction: Batch cultures are commonly used to study ruminal digestion because they are easy to implement. Nevertheless, most are short term studies (a few hours) that are unable to evaluate effects of dietary changes that affect the microbiota, which needs more than 24h to become apparent. So, this study aimed at evaluating persistency of microbial activities during medium-term (96h) cultures of ruminal contents. Animals, material and methods: Ruminal contents were taken from two rumen-fistulated dairy cows receiving a meadow hay based diet (58% NDF and 3% starch). One portion of the contents was used for an immediate measurement of microbial activities (disappearance of fibre, starch and nitrogen, and biohydrogenation of unsaturated fatty acids) and the second portion was incubated during 96h, with a renewal of half of the 200mL media every 12 hours with substrate and 7-pH bicarbonate buffer. This incubation simulated the rumen of a cow receiving 2 equal meals per day, containing 50% wheat bran + 10% soybeans + 40% meadow hay (51% NDF and 5% starch), and having a 6% per hour ruminal emptying, on average. Fermentation parameters (volatile fatty acids, VFA; ammonia, NH3; pH) were recorded every 12h. After 96h, microbial activities of the cultures were assayed as in the fresh rumen content during the first day. The results obtained with fresh ruminal contents on day 1 were compared to those obtained with cultures, using GLM of SYSTAT. Results and discussion: Fermentative activities were maintained during cultures: pH and total VFA concentrations remained constant. Nevertheless a decrease of acetic acid proportion (C2) and an increase of propionic acid proportion (C3) were observed, with a reduction from 3.9 to 2.7 of the C2/C3 ratio, associated with a 22% increase of butyric acid (C4) proportion. NH3 concentration decreased by about half during the first 48h and remained stable thereafter. Compared to fresh ruminal contents, 96h cultures possessed a twice lower fibre disappearance, a similar nitrogen disappearance, a twice higher starch disappearance and a 24% higher biohydrogenation extent of linoleic acid with an increase by 61% of trans-11 isomers. Nitrogen degradation was not modified by medium-term cultures, and the lower NH3 concentration could have resulted from volatilization of aqueous ammonium solution (boiling temperature: 38°C) during our 39°C incubations. Fibrolytic activity and consequently C2 concentration were not favoured by the mid-term cultures, contrary to amylolytic activity and its associated C3 concentration, most probably because of particle size of culture substrates which had been finely ground. The increase of C4 concentration was in agreement with the increase of linoleic acid biohydrogenation by trans-11 pathway, since this pathway would be mainly due to Butyrivibrio fibrisolvens (Maia et al., 2007), a fibrolytic bacteria producing C4 and preferring hemicelluloses (Dehority, 2003), which was provided by the wheat bran in our experiment Conclusion: This incubation procedure can be used to compare medium-term effects of dietary treatments on rumen microbial digestion in cultures. Such cultures do not allow a quantitative measurement of the effects but allow screening procedures and description of the nature of the effects. Further studies will investigate changes of microbiota using pyrosequencing

Reasoning on Feature Models: Compilation-Based vs. Direct Approaches

Analyzing a Feature Model (FM) and reasoning on the corresponding configuration space is a central task in Software Product Line (SPL) engineering. Problems such as deciding the satisfiability of the FM and eliminating inconsistent parts of the FM have been well resolved by translating the FM into a conjunctive normal form (CNF) formula, and then feeding the CNF to a SAT solver. However, this approach has some limits for other important reasoning issues about the FM, such as counting or enumerating configurations. Two mainstream approaches have been investigated in this direction: (i) direct approaches, using tools based on the CNF representation of the FM at hand, or (ii) compilation-based approaches, where the CNF representation of the FM has first been translated into another representation for which the reasoning queries are easier to address. Our contribution is twofold. First, we evaluate how both approaches compare when dealing with common reasoning operations on FM, namely counting configurations, pointing out one or several configurations, sampling configurations, and finding optimal configurations regarding a utility function. Our experimental results show that the compilation-based is efficient enough to possibly compete with the direct approaches and that the cost of translation (i.e., the compilation time) can be balanced when addressing sufficiently many complex reasoning operations on large configuration spaces. Second, we provide a Java-based automated reasoner that supports these operations for both approaches, thus eliminating the burden of selecting the appropriate tool and approach depending on the operation one wants to perform

Identification des facteurs de transcription dont l'expression est régulée au cours de la maturation des cellules de Purkinje (rôle de Klf9 dans la survie cellulaire et le développement dendritique)

Au cours des 10 premiers jours de vie postnatale (P0-P10), les cellules de Purkinje de souris passent par une période de mort développpementale et subissent une régression puis une croissance dendritique. Afin de sélectionner des candidats susceptibles de contrôler l arrêt de la mort développementale ou la maturation dendritique, nous avons cherché les facteurs de transcription dont l expression varie entre P0 et P10. L analyse de transcriptomes de cortex cérébelleux à différents a ges, puis la validation de l expression des gènes candidats par différentes techniques, nous a permis de sélectionner 1 facteur de transcription dont l expression augmente : Klf9 (Krüppel like facteur). En culture organotypique de cervelet, l expression précoce de Klf9 par transduction lentivirale augmente la survie des cellules de Purkinje transduites, tandis que son inhibition par expression lentivirale de shARN la diminue. La diminution de cette survie peut être supprimée par ajout d IGF1, un facteur trophique des cellules de Purkinje. Le nombre de cellules de Purkinje diminue également dans le cervelet de souris Klf9-/- mis en culture organotypique. Ainsi, l expression de Klf9 est nécessaire et suffisante à la survie des cellules de Purkinje en culture organotypique, suggérant un rôle de ce facteur dans l arrêt de la mort développementale de ces neurones. Notre étude a permis également de montrer l induction de la rétraction des dendrites primaires et de la formation des épines des cellules de Purkinje suite à l expression précoce de Klf9. Ainsi, ce facteur intervient également dans le développement dendritique et la formation des épines des cellules de PurkinjePARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

La digestion ruminale (mise en place d un modèle d étude in vitro à long terme en cultures Batch)

L objectif de cette étude est de mettre au point une culture de contenu ruminal sur une durée de plus de 24h (i.e. 96h), avec renouvellement du milieu toutes les 12h. Les activités microbiennes et enzymatiques des inoculums prélevés sur 2 vaches et utilisés à J1 ont été comparées à celles obtenues avec les cultures de 96h. Les activités fermentaires se sont maintenues, cependant une diminution de l activité fibrolytique et une augmentation de l activité amylolytique ont été observées. La biohydrogénation a également augmentée. La concentration en acides gras volatils est restée constante avec une diminution de la proportion en acide acétique et une augmentation de celle en acide propionique. La concentration en ammoniac a été divisée par deux puis s est stabilisée au bout de 48 h. Le pH est resté constant. Avec quelques adaptations, ce modèle pourrait ainsi être utilisé afin d étudier les effets à long terme, en culture batch, de certains traitements sur la digestion microbienne dans le rumen.TOULOUSE-EN Vétérinaire (315552301) / SudocTOULOUSE3-BU Santé-Centrale (315552105) / SudocSudocFranceF

Pseudo Polynomial-Time Top-k Algorithms for d-DNNF Circuits

We are interested in computing $k$ most preferred models of a given d-DNNF circuit $C$, where the preference relation is based on an algebraic structure called a monotone, totally ordered, semigroup $(K, \otimes, <)$. In our setting, every literal in $C$ has a value in $K$ and the value of an assignment is an element of $K$ obtained by aggregating using $\otimes$ the values of the corresponding literals. We present an algorithm that computes $k$ models of $C$ among those having the largest values w.r.t. $<$, and show that this algorithm runs in time polynomial in $k$ and in the size of $C$. We also present a pseudo polynomial-time algorithm for deriving the top-$k$ values that can be reached, provided that an additional (but not very demanding) requirement on the semigroup is satisfied. Under the same assumption, we present a pseudo polynomial-time algorithm that transforms $C$ into a d-DNNF circuit $C'$ satisfied exactly by the models of $C$ having a value among the top-$k$ ones. Finally, focusing on the semigroup $(\mathbb{N}, +, <)$, we compare on a large number of instances the performances of our compilation-based algorithm for computing $k$ top solutions with those of an algorithm tackling the same problem, but based on a partial weighted MaxSAT solver

Pseudo Polynomial-Time Top-k Algorithms for d-DNNF Circuits

We are interested in computing $k$ most preferred models of a given d-DNNF circuit $C$, where the preference relation is based on an algebraic structure called a monotone, totally ordered, semigroup $(K, \otimes, <)$. In our setting, every literal in $C$ has a value in $K$ and the value of an assignment is an element of $K$ obtained by aggregating using $\otimes$ the values of the corresponding literals. We present an algorithm that computes $k$ models of $C$ among those having the largest values w.r.t. $<$, and show that this algorithm runs in time polynomial in $k$ and in the size of $C$. We also present a pseudo polynomial-time algorithm for deriving the top-$k$ values that can be reached, provided that an additional (but not very demanding) requirement on the semigroup is satisfied. Under the same assumption, we present a pseudo polynomial-time algorithm that transforms $C$ into a d-DNNF circuit $C'$ satisfied exactly by the models of $C$ having a value among the top-$k$ ones. Finally, focusing on the semigroup $(\mathbb{N}, +, <)$, we compare on a large number of instances the performances of our compilation-based algorithm for computing $k$ top solutions with those of an algorithm tackling the same problem, but based on a partial weighted MaxSAT solver

Pseudo Polynomial-Time Top-k Algorithms for d-DNNF Circuits

We are interested in computing $k$ most preferred models of a given d-DNNF circuit $C$, where the preference relation is based on an algebraic structure called a monotone, totally ordered, semigroup $(K, \otimes, <)$. In our setting, every literal in $C$ has a value in $K$ and the value of an assignment is an element of $K$ obtained by aggregating using $\otimes$ the values of the corresponding literals. We present an algorithm that computes $k$ models of $C$ among those having the largest values w.r.t. $<$, and show that this algorithm runs in time polynomial in $k$ and in the size of $C$. We also present a pseudo polynomial-time algorithm for deriving the top-$k$ values that can be reached, provided that an additional (but not very demanding) requirement on the semigroup is satisfied. Under the same assumption, we present a pseudo polynomial-time algorithm that transforms $C$ into a d-DNNF circuit $C'$ satisfied exactly by the models of $C$ having a value among the top-$k$ ones. Finally, focusing on the semigroup $(\mathbb{N}, +, <)$, we compare on a large number of instances the performances of our compilation-based algorithm for computing $k$ top solutions with those of an algorithm tackling the same problem, but based on a partial weighted MaxSAT solver

Pseudo Polynomial-Time Top-k Algorithms for d-DNNF Circuits

We are interested in computing $k$ most preferred models of a given d-DNNF circuit $C$, where the preference relation is based on an algebraic structure called a monotone, totally ordered, semigroup $(K, \otimes, <)$. In our setting, every literal in $C$ has a value in $K$ and the value of an assignment is an element of $K$ obtained by aggregating using $\otimes$ the values of the corresponding literals. We present an algorithm that computes $k$ models of $C$ among those having the largest values w.r.t. $<$, and show that this algorithm runs in time polynomial in $k$ and in the size of $C$. We also present a pseudo polynomial-time algorithm for deriving the top-$k$ values that can be reached, provided that an additional (but not very demanding) requirement on the semigroup is satisfied. Under the same assumption, we present a pseudo polynomial-time algorithm that transforms $C$ into a d-DNNF circuit $C'$ satisfied exactly by the models of $C$ having a value among the top-$k$ ones. Finally, focusing on the semigroup $(\mathbb{N}, +, <)$, we compare on a large number of instances the performances of our compilation-based algorithm for computing $k$ top solutions with those of an algorithm tackling the same problem, but based on a partial weighted MaxSAT solver

Elevated plasma complement factor H related 5 protein is associated with venous thromboembolism.

Venous thromboembolism (VTE) is a common, multi-causal disease with potentially serious short- and long-term complications. In clinical practice, there is a need for improved plasma biomarker-based tools for VTE diagnosis and risk prediction. Here we show, using proteomics profiling to screen plasma from patients with suspected acute VTE, and several case-control studies for VTE, how Complement Factor H Related 5 protein (CFHR5), a regulator of the alternative pathway of complement activation, is a VTE-associated plasma biomarker. In plasma, higher CFHR5 levels are associated with increased thrombin generation potential and recombinant CFHR5 enhanced platelet activation in vitro. GWAS analysis of ~52,000 participants identifies six loci associated with CFHR5 plasma levels, but Mendelian randomization do not demonstrate causality between CFHR5 and VTE. Our results indicate an important role for the regulation of the alternative pathway of complement activation in VTE and that CFHR5 represents a potential diagnostic and/or risk predictive plasma biomarker