53161 research outputs found
Sort by
Phytoel - Quels systèmes de polycultures élevages demain face aux enjeux de réduction d’usage de produits phytosanitaires ?
No full textLoin de se cantonner aux seules pratiques agronomiques, la réduction d’usage des produits
phytosanitaires dans les exploitations de polyculture-élevage nécessite de repenser globalement le
fonctionnement des systèmes. Les approches complexes que nous avons développées pour atteindre
le niveau de réduction de 50 % fixée par le plan Ecophyto, s’appuient sur la combinaison de
compétences agronomiques, zootechniques et économiques. Ces sommes de compétences ont été
mises à disposition du projet pour co-construire avec les chefs d’exploitations des systèmes économes,
durables et qui correspondent à l’attente des éleveurs. Ces nouveaux systèmes simulés sont
globalement moins productifs, plus complexes et nécessitent une réorganisation profonde du travail.
Leurs performances économiques, bien que construites sur de nouveaux équilibres restent globalement
les mêmes et leurs performances environnementales globales (GES, eutrophisation, …) s’améliorent.
Cependant, les objectifs des chefs d’exploitations, le contexte pédoclimatique, l’organisation structurelle
du système et le contexte social font de chaque exploitation un cas particulier. Les niveaux de réduction
d’usage des produits phytosanitaires peuvent donc être très variables, même si globalement les
objectifs du plan Ecophyto sont atteignables.Far from confining itself to agronomic issues, pesticides use reduction in mixed crop-animal farms
requires to rethink globally the way systems work. The complex approaches which we developed to
reach the level of 50 % reduction of pesticides use defined by the Ecophyto plan, lean on the
combination of agronomic, zootechnic and economic skills. These combinations of skills were used to
co-design new farming systems, which use less pesticides, are sustainable and correspond to farmers’
needs. These new simulation systems are globally less productive, more complex and require a deep
reorganization of the work. Their economic performances remain globally the same, although built on
new balances. Their global environmental performances (GES, eutrophication) improve.
However, every farm is a particular case, when considering farmers’ objectives, soil-climate context,
structural organization of the system and social context. Pesticides use reduction levels may thus be
quite variable from one farm to another, but the Ecophyto plan objectives appear to be reachabl
Statistical model choice including variable selection based on variable importance: A relevant way for biomarkers selection to predict meat tenderness
No full textIn this paper, we describe a new computational methodology to select the best regression model to predict a numerical variable of interest Y and to select simultaneously the most interesting numerical explanatory variables strongly linked to Y. Three regression models (parametric, semi-parametric and non-parametric) are considered and estimated by multiple linear regression, sliced inverse regression and random forests. Both the variables selection and the model choice are computational. A measure of importance based on random perturbations is calculated for each covariate. The variables above a threshold are selected. Then a learning/test samples approach is used to estimate the Mean Square Error and to determine which model (including variable selection) is the most accurate. The R package modvarsel (MODel and VARiable SELection) implements this computational approach and applies to any regression datasets. After checking the good behavior of the methodology on simulated data, the R package is used to select the proteins predictive of meat tenderness among a pool of 21 candidate proteins assayed in semitendinosus muscle from 71 young bulls. The biomarkers were selected by linear regression (the best regression model) to predict meat tenderness. These biomarkers, we confirm the predominant role of heat shock proteins and metabolic ones
Mitochondrial transcriptome control and intercompartment cross-talk during plant development.
No full textmitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a "buffering" mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus
What makes a bad egg? Egg transcriptome reveals dysregulation of translational machinery and novel fertility genes important for fertilization
No full textBackground: Egg quality can be defined as the egg ability to be fertilized and subsequently develop into a normal
embryo. Previous research has shed light on factors that can influence egg quality. Large gaps however remain
including a comprehensive view of what makes a bad egg. Initial development of the embryo relies on maternallyinherited molecules, such as transcripts, deposited in the egg during its formation. Bad egg quality is therefore
susceptible to be associated with alteration or dysregulation of maternally-inherited transcripts. We performed
transcriptome analysis on a large number (N = 136) of zebrafish egg clutches, each clutch being split to monitor
developmental success and perform transcriptome analysis in parallel. We aimed at drawing a molecular portrait of
the egg in order to characterize the relation between egg transcriptome and developmental success and to
subsequently identify new candidate genes involved in fertility.
Results: We identified 66 transcript that were differentially abundant in eggs of contrasted phenotype (low or high
developmental success). Statistical modeling using partial least squares regression and genetics algorithm
demonstrated that gene signatures from transcriptomic data can be used to predict developmental success. The
identity and function of differentially expressed genes indicate a major dysregulation of genes of the translational
machinery in poor quality eggs. Two genes, otulina and slc29a1a, predominantly expressed in the ovary and
dysregulated in poor quality eggs were further investigated using CRISPR/Cas9 mediated genome editing. Mutants
of each gene revealed remarkable subfertility whereby the majority of their eggs were unfertilizable. The Wnt
pathway appeared to be dysregulated in the otulina mutant-derived eggs.
Conclusions: Here we show that egg transcriptome contains molecular signatures, which can be used to predict
developmental success. Our results also indicate that poor egg quality in zebrafish is associated with a
dysregulation of (i) the translational machinery genes and (ii) novel fertility genes, otulina and slc29a1a, playing an
important role for fertilization. Together, our observations highlight the diversity of the possible causes of egg
quality defects and reveal mechanisms of maternal origin behind the lack of fertilization and early embryonic
failures that can occur under normal reproduction conditions
Meth@+.com - Modéliser le développement d’un système innovant de méthanisation collective et à hautes performances environnementales à l’échelle d’un micro-territoires.
No full textEn 2013, le plan Energie Méthanisation Autonomie Azote était publié, et un modèle « français de
méthanisation agricole collective » était appelé à devenir l’un des leviers de la transition énergétique et
écologique. Les travaux présentés ici ont été réalisés entre 2013 et 2016 et se sont appliqués à
explorer plusieurs composantes de ce modèle de méthanisation afin de cerner les stratégies à l’origine
des schémas de méthanisation, et leurs implications environnementales et agronomiques. Ainsi assortie
d’un état des lieux des pratiques agronomiques de 4 méthaniseurs, la connaissance des digestats a été
approfondie afin de permettre une meilleure prise en compte de leurs propriétés dans leur stratégie de
gestion des ressources. Les logiques associées aux flux de matières et d’éléments fertilisants en amont et en aval des installations de méthanisation ont ainsi été explorées afin d’établir un cadre d’analyse des stratégies de
gestion des ressources par les méthaniseurs. L’approche des implications agro-environnementale s’est
faite par l’étude de la valeur fertilisante et amendante de plusieurs sortes de digestats.
La valeur fertilisante azotée de 5 formes de digestats a donc été définie, mettant en évidence la forte
variabilité de l’intérêt des digestats au regard de ce critère, même si l’ammonium représente toujours la
grande majorité de l’azote total (>70%). Une biodisponibilité de 100% du phosphore des digestats a été
mise en évidence par traçage isotopique. La variabilité des propriétés amendantes des digestats a été
mise en évidence par application de fractionnement biochimique (ISMO 73±8%, n=19)), et par
minéralisation potentielle du carbone et de l’azote.
Ces travaux restent limités par le nombre d’unités de méthanisation suivies (n=3), et appellent
l’approfondissement des tendances soulevées.In 2013, in France, the « Energie Méthanisation Autonomie Azote » plan was published, and the
‘French agricultural and collective biogas model” should become a lever of the energetic and ecological
transition. The results presented in this paper were produced between 2013 and 2016 and planned to
explore several dimensions of this methane production plan. These works aimed at produce knowledges about biogas plant resources management and about digestate. Such knowledges and tools should be used to support biogas plant managers and territory stakeholders in order to analyze their own model from an agronomic and environmental point of view. Based on field experience cases, brakes and levers of such projects development have been gathered in a methodology guide. Upstream and downstream biomass and fertilizers flux have equally been explored in order to establish an analysis frame of resources management per biogas plant.
Additional works have been conducted about digestate. Several digestates features were studied.
Nitrogen fertilizing value of 5 digestate types were determined, and evidenced a great variability of
digestates quality regarding this topic. Ammonia remains the major part of total nitrogen (>70%).
Phosphorus bioavailability is 100%, as revealed by isotopic tracing. Biochemical fractioning and Carbon
and Nitrogen potential mineralization showed variability of amending digestates properties (ISMO
73±8%, n=19). Nevertheless, these works remain limited by the number of biogas plants under study
(n=3) and argue for going further into such analyses
Reducing MSH4 copy number prevents meiotic crossovers between non-homologous chromosomes in Brassica napus
No full textIn allopolyploids, correct chromosome segregation requires suppression of non-homologous crossovers while levels of homologous crossovers are ensured. To date, no mechanism able to specifically inhibit non-homologous crossovers has been described in allopolyploids other than in bread wheat. Here, we show that reducing the number of functional copies of MSH4, an essential gene for the main crossover pathway, prevents non-homologous crossovers in allotetraploid Brassica napus. We show that non-homologous crossovers originate almost exclusively from the MSH4-dependent recombination pathway and that their numbers decrease when MSH4 returns to single copy in B. napus; by contrast, homologous crossovers remain unaffected by MSH4 duplicate loss. We also demonstrate that MSH4 systematically returns to single copy following numerous independent polyploidy events, a pattern that is probably not by chance. These results suggest that stabilization of allopolyploid meiosis can be enhanced by loss of a key meiotic recombination gene
Exploiting vulnerabilities of cancer by targeting nuclear receptors of stromal cells in tumor microenvironment
No full textThe tumor microenvironment is a complex and dynamic cellular community comprising the tumor epithelium and various tumor-supporting cells such as immune cells, fibroblasts, immunosuppressive cells, adipose cells, endothelial cells, and pericytes. The interplay between the tumor microenvironment and tumor cells represents a key contributor to immune evasiveness, physiological hardiness and the local and systemic invasiveness of malignant cells. Nuclear receptors are master regulators of physiological processes and are known to play pro-/anti-oncogenic activities in tumor cells. However, the actions of nuclear receptors in tumor-supporting cells have not been widely studied. Given the excellent druggability and extensive regulatory effects of nuclear receptors, understanding their biological functionality in the tumor microenvironment is of utmost importance. Therefore, the present review aims to summarize recent evidence about the roles of nuclear receptors in tumor-supporting cells and their implications for malignant processes such as tumor proliferation, evasion of immune surveillance, angiogenesis, chemotherapeutic resistance, and metastasis. Based on findings derived mostly from cell culture studies and a few in vivo animal cancer models, the functions of VDR, PPARs, AR, ER and GR in tumor-supporting cells are relatively well-characterized. Evidence for other receptors, such as RAR, ROR, and FXR, is limited yet promising. Hence, the nuclear receptor signature in the tumor microenvironment may harbor prognostic value. The clinical prospects of a tumor microenvironment-oriented cancer therapy exploiting the nuclear receptors in different tumor-supporting cells are also encouraging. The major challenge, however, lies in the ability to develop a highly specific drug delivery system to facilitate precision medicine in cancer therapy
Thrombosis Risk Associated with Head and Neck Cancer: A Review
No full textVenous thromboembolism (VTE) is a common complication for cancer patients. VTE-associated risk varies according to the type of tumor disease. Head and neck cancer is a common cancer worldwide, and most tumors are squamous cell carcinomas due to tobacco and alcohol abuse. The risk of VTE associated with head and neck (H&N) cancer is considered empirically low, but despite the high incidence of H&N cancer, few data are available on this cancer; thus, it is difficult to state the risk of VTE. Our review aims to clarify this situation and tries to assess the real VTE risk associated with H&N cancer. We report that most clinical studies have concluded that there is a very low thrombosis risk associated with H&N cancer. Even with the biases that often exist, this clinical review seems to confirm that the risk of VTE was empirically hypothesized. Furthermore, we highlight that H&N cancer has all the biological features of a cancer associated with a high thrombosis risk, including a strong expression of procoagulant proteins, modified thrombosis/fibrinolysis mechanisms, and secretions of procoagulant microparticles and procoagulant cytokines. Thus, this is a paradoxical situation, and some undiscovered mechanisms that could explain this clinical biological ambivalence might exist
Qualité des eaux pluviales du réseau séparatif de la ville de Toulouse
No full textLa ville de Toulouse est dotée d’un réseau d’assainissement séparatif, où donc la présence de composés traces organiques ne pourra pas avoir pour origine des eaux usées. Des prélèvements ont été réalisés en sortie de deux collecteurs d’eaux pluviales situés dans des zones d’urbanisation forte et modérée. Soixante prélèvements ont eu lieu durant des évènements pluvieux et durant des évènements de temps sec de juin 2014 à juin 2016. Les paramètres globaux de pollution ont été analysés (DCO, DBO5, NT, NH4+, NO3-, PT, MES, MVS, pH, conductivité, turbidité). La caractérisation a été complétée par l’analyse de composés traces organiques. L’occurrence des hydrocarbures aromatiques polycycliques et des pesticides (lindane et dieldrine) est faible dans les échantillons analysés. En revanche les résidus pharmaceutiques (diclofénac, acide acétylsalicylique, ibuprofène), le bisphénol A
et les alkyklbenzènes sulfonates linéaires sont présents dans quasiment tous les échantillons.The city of Toulouse with its separate sewer system is ideal for studying stormwater, because trace organic compounds cannot come from waste water. Samples have been taken from the outlets of two storm drains located in heavily and moderately urbanized areas. Sixty samples have been taken during wet weather and during dry weather between June 2014 and June 2016. The overall pollution parameters have been analyzed (COD, BOD, Tot-N, NH4+, NO3-, Tot-P, SSM, VSM, pH, conductivity, turbidity). Characterization has been completed by analysis of trace organic compounds. Occurrence of polycyclic aromatic hydrocarbons and pesticides (lindane and dieldrin) is low in analyzed samples. However, pharmaceuticals (diclofenac, acetylsalicylic acid, ibuprofene), bisphenol A and linear alkylbenzene sulphonates have been quantified in almost all samples
Multiplexing polysome profiling experiments to study translation in Escherichia coli
No full textPolysome profiling is a widely used method to monitor the translation status of mRNAs. Although it is theoretically a simple technique, it is labor intensive. Repetitive polysome fractionation rapidly generates a large number of samples to be handled in the downstream processes of protein elimination, RNA extraction and quantification. Here, we propose a multiplex polysome profiling experiment in which distinct cellular extracts are pooled before loading on the sucrose gradient for fractionation. We used the multiplexing method to study translation in E. coli. Multiplexing polysome profiling experiments provided similar mRNA translation status to that obtained with the non-multiplex method with comparable distribution of mRNA copies between the polysome profiling fractions, similar ribosome occupancy and ribosome density. The multiplexing method was used for parallel characterization of
gene translational responses to changing mRNA levels. When the mRNA level of two native genes, cysZ and lacZ was increased by transcription induction, their global translational response was similar, with a higher ribosome load leading to increased ribosome occupancy and ribosome densities. However the pattern and the magnitude of the translational response were gene specific. By reducing the number of polysome profiling experiments, the multiplexing method saved time and effort and reduced cost and technical bias. This method would be useful to study the translational effect of mRNA sequence-dependent parameters that often require testing multiple samples and conditions in parallel