Showing papers by "Agrocampus Ouest published in 2016"

Liver PPARα is crucial for whole-body fatty acid homeostasis and is protective against NAFLD

Abstract: Objective Peroxisome proliferator-activated receptor α (PPARα) is a nuclear receptor expressed in tissues with high oxidative activity that plays a central role in metabolism. In this work, we investigated the effect of hepatocyte PPARα on non-alcoholic fatty liver disease (NAFLD). Design We constructed a novel hepatocyte-specific PPARα knockout ( Pparα hep−/−) mouse model. Using this novel model, we performed transcriptomic analysis following fenofibrate treatment. Next, we investigated which physiological challenges impact on PPARα. Moreover, we measured the contribution of hepatocytic PPARα activity to whole-body metabolism and fibroblast growth factor 21 production during fasting. Finally, we determined the influence of hepatocyte-specific PPARα deficiency in different models of steatosis and during ageing. Results Hepatocyte PPARα deletion impaired fatty acid catabolism, resulting in hepatic lipid accumulation during fasting and in two preclinical models of steatosis. Fasting mice showed acute PPARα-dependent hepatocyte activity during early night, with correspondingly increased circulating free fatty acids, which could be further stimulated by adipocyte lipolysis. Fasting led to mild hypoglycaemia and hypothermia in Pparα hep−/− mice when compared with Ppar α−/− mice implying a role of PPARα activity in non-hepatic tissues. In agreement with this observation, Pparα −/− mice became overweight during ageing while Ppar αhep−/− remained lean. However, like Ppar α−/− mice, Ppar αhep−/− fed a standard diet developed hepatic steatosis in ageing. Conclusions Altogether, these findings underscore the potential of hepatocyte PPARα as a drug target for NAFLD.

How Muscle Structure and Composition Influence Meat and Flesh Quality

Abstract: Skeletal muscle consists of several tissues, such as muscle fibers and connective and adipose tissues. This review aims to describe the features of these various muscle components and their relationships with the technological, nutritional, and sensory properties of meat/flesh from different livestock and fish species. Thus, the contractile and metabolic types, size and number of muscle fibers, the content, composition and distribution of the connective tissue, and the content and lipid composition of intramuscular fat play a role in the determination of meat/flesh appearance, color, tenderness, juiciness, flavor, and technological value. Interestingly, the biochemical and structural characteristics of muscle fibers, intramuscular connective tissue, and intramuscular fat appear to play independent role, which suggests that the properties of these various muscle components can be independently modulated by genetics or environmental factors to achieve production efficiency and improve meat/flesh quality.

Plausible and desirable futures in the Anthropocene: A new research agenda

Abstract: While the concept of the Anthropocene reflects the past and present nature, scale and magnitude of human impacts on the Earth System, its true significance lies in how it can be used to guide attitudes, choices, policies and actions that influence the future. Yet, to date much of the research on the Anthropocene has focused on interpreting past and present changes, while saying little about the future. Likewise, many futures studies have been insufficiently rooted in an understanding of past changes, in particular the long-term co-evolution of bio-physical and human systems. The Anthropocene perspective is one that encapsulates a world of intertwined drivers, complex dynamic structures, emergent phenomena and unintended consequences, manifest across different scales and within interlinked biophysical constraints and social conditions. In this paper we discuss the changing role of science and the theoretical, methodological and analytical challenges in considering futures of the Anthropocene. We present three broad groups of research questions on: (1) societal goals for the future; (2) major trends and dynamics that might favor or hinder them; (3) and factors that might propel or impede transformations towards desirable futures. Tackling these questions requires the development of novel approaches integrating natural and social sciences as well as the humanities beyond what is current today. We present three examples, one from each group of questions, illustrating how science might contribute to the identification of desirable and plausible futures and pave the way for transformations towards them. We argue that it is time for debates on the sustainability of the Anthropocene to focus on opportunities for realizing desirable and plausible futures.

Transit times – the link between hydrology and water quality at the catchment scale

Abstract: In spite of trying to understand processes in the same spatial domain, the catchment hydrology and water quality scientific communities are relatively disconnected and so are their respective models. This is emphasized by an inadequate representation of transport processes, in both catchment-scale hydrological and water quality models. While many hydrological models at the catchment scale only account for pressure propagation and not for mass transfer, catchment scale water quality models are typically limited by overly simplistic representations of flow processes. With the objective of raising awareness for this issue and outlining potential ways forward we provide a nontechnical overview of (1) the importance of hydrology-controlled transport through catchment systems as the link between hydrology and water quality; (2) the limitations of current generation catchment-scale hydrological and water quality models; (3) the concept of transit times as tools to quantify transport; and (4) the benefits of transit time based formulations of solute transport for catchment-scale hydrological and water quality models. There is emerging evidence that an explicit formulation of transport processes, based on the concept of transit times has the potential to improve the understanding of the integrated system dynamics of catchments and to provide a stronger link between catchment-scale hydrological and water quality models. WIREs Water 2016, 3:629-657. doi: 10.1002/wat2.1155 For further resources related to this article, please visit the .

Re-conceptualizing the Anthropocene: A call for collaboration

Abstract: Since it was first proposed in 2000, the concept of the Anthropocene has evolved in breadth and diversely. The concept encapsulates the new and unprecedented planetary-scale changes resulting from societal transformations and has brought to the fore the social drivers of global change. The concept has revealed tensions between generalized interpretations of humanity’s contribution to global change, and interpretations that are historically, politically and culturally situated. It motivates deep ethical questions about the politics and economics of global change, including diverse interpretations of past causes and future possibilities. As such, more than other concepts, the Anthropocene concept has brought front-and-center epistemological divides between and within the natural and social sciences, and the humanities. It has also brought new opportunities for collaboration. Here we explore the potential and challenges of the concept to encourage integrative understandings of global change and sustainability. Based on bibliometric analysis and literature review, we discuss the now wide acceptance of the term, its interpretive flexibility, the emerging narratives as well as the debates the concept has inspired. We argue that without truly collaborative and integrative research, many of the critical exchanges around the concept are likely to perpetuate fragmented research agendas and to reinforce disciplinary boundaries. This means appreciating the strengths and limitations of different knowledge domains, approaches and perspectives, with the concept of the Anthropocene serving as a bridge, which we encourage researchers and others to cross. This calls for institutional arrangements that facilitate collaborative research, training, and action, yet also depends on more robust and sustained funding for such activities. To illustrate, we briefly discuss three overarching global change problems where novel types of collaborative research could make a difference: (1) Emergent properties of socioecological systems; (2) Urbanization and resource nexus; and (3) Systemic risks and tipping points. Creative tensions around the Anthropocene concept can help the research community to move toward new conceptual syntheses and integrative action-oriented approaches that are needed to producing useful knowledge commensurable with the challenges of global change and sustainability.

Re-conceptualizing the Anthropocene: A call for collaboration

Abstract: Since it was first proposed in 2000, the concept of the Anthropocene has evolved in breadth and diversely. The concept encapsulates the new and unprecedented planetary-scale changes resulting from societal transformations and has brought to the fore the social drivers of global change. The concept has revealed tensions between generalized interpretations of humanity’s contribution to global change, and interpretations that are historically, politically and culturally situated. It motivates deep ethical questions about the politics and economics of global change, including diverse interpretations of past causes and future possibilities. As such, more than other concepts, the Anthropocene concept has brought front-and-center epistemological divides between and within the natural and social sciences, and the humanities. It has also brought new opportunities for collaboration. Here we explore the potential and challenges of the concept to encourage integrative understandings of global change and sustainability. Based on bibliometric analysis and literature review, we discuss the now wide acceptance of the term, its interpretive flexibility, the emerging narratives as well as the debates the concept has inspired. We argue that without truly collaborative and integrative research, many of the critical exchanges around the concept are likely to perpetuate fragmented research agendas and to reinforce disciplinary boundaries. This means appreciating the strengths and limitations of different knowledge domains, approaches and perspectives, with the concept of the Anthropocene serving as a bridge, which we encourage researchers and others to cross. This calls for institutional arrangements that facilitate collaborative research, training, and action, yet also depends on more robust and sustained funding for such activities. To illustrate, we briefly discuss three overarching global change problems where novel types of collaborative research could make a difference: (1) Emergent properties of socioecological systems; (2) Urbanization and resource nexus; and (3) Systemic risks and tipping points. Creative tensions around the Anthropocene concept can help the research community to move toward new conceptual syntheses and integrative action-oriented approaches that are needed to producing useful knowledge commensurable with the challenges of global change and sustainability.

Nitrogen use efficiency in rapeseed. A review

Abstract: Mineral nitrogen fertilization has improved crop yield over the last century but has also caused air and water pollution. Reduction of nitrogen inputs and maintaining high yields are therefore essential to ensure a more sustainable agriculture. Improving the nitrogen use efficiency (NUE) of crops is therefore needed. Rapeseed, Brassica napus, depends on nitrogen fertilization due to its low NUE, with the ratio of plant nitrogen content to nitrogen supplied often not exceeding 60 %. Here, we review the major phenotypic traits associated with NUE in B. napus, with special emphasis on winter oilseed rape. We discuss the genetic diversity available and potential breeding strategies. The major points are the following: (1) rapeseed seed yield elaboration is complex, with overlapping phases of nitrogen uptake and remobilization during the crop cycle; (2) traits related to nitrogen uptake, such as root length and the amount of nitrogen absorbed after flowering, and traits related to nitrogen remobilization, such as the “stay-green” phenotype, have been identified as possible levers to improve NUE in rapeseed; (3) a substantial body of studies investigating the genetic control of NUE traits have already published and potential candidate genes identified; and (4) rapeseed genetic diversity may be enriched by exploiting interpopulation genetic variation and the closely related gene pools of Brassica rapa and Brassica oleracea.

Using ecology, physiology, and genomics to understand host specificity in Xanthomonas

Abstract: How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.

Bovine Teat Microbiome Analysis Revealed Reduced Alpha Diversity and Significant Changes in Taxonomic Profiles in Quarters with a History of Mastitis

Abstract: Mastitis is a mammary gland inflammatory disease often due to bacterial infections. Like many other infections, it used to be considered as a host-pathogen interaction driven by host and bacterial determinants. Until now, the involvement of the bovine mammary gland microbiota in the host-pathogen interaction has been poorly investigated, and mainly during the infectious episode. In this study, the bovine teat microbiome was investigated in 31 quarters corresponding to 27 animals, which were all free of inflammation at sampling time but which had different histories regarding mastitis: from no episode of mastitis on all the previous lactations (Healthy quarter, Hq) to one or several clinical mastitis events (Mastitic quarter, Mq). Several quarters whose status was unclear (possible history of subclinical mastitis) were classified as NDq. Total bacterial DNA was extracted from foremilk samples and swab samples of the teat canal. Taxonomic profiles were determined by pyrosequencing on 16s amplicons of the V3-4 region. Hq quarters showed a higher diversity compared to Mq ones (Shannon index: ~8 and 6, respectively). Clustering of the quarters based on their bacterial composition made it possible to separate Mq and Hq quarters into two separate clusters (C1 and C2, respectively). Discriminant analysis of taxonomic profiles between these clusters revealed several differences and allowed the identification of taxonomic markers in relation to mastitis history. C2 quarters were associated with a higher proportion of the Clostridia class (including genera such as Ruminococcus, Oscillospira, Roseburia, Dorea, etc.), the Bacteroidetes phylum (Prevotella, Bacteroides, Paludibacter, etc.), and the Bifidobacteriales order (Bifidobacterium), whereas C1 quarters showed a higher proportion of the Bacilli class (Staphylococcus) and Chlamydiia class. These results indicate that microbiota is altered in udders which have already developed mastitis, even far from the infectious episode. Microbiome alteration may have resulted from the infection itself and or the associated antibiotic treatment. Alternatively, differences in microbiome composition in udders with a history of mastitis may have occurred prior to the infection and even contributed to infection development. Further investigations on the dynamics of mammary gland microbiota will help to elucidate the contribution of this endogenous microbiota to the mammary gland health.

A principal component method to impute missing values for mixed data

Abstract: We propose a new method to impute missing values in mixed data sets. It is based on a principal component method, the factorial analysis for mixed data, which balances the influence of all the variables that are continuous and categorical in the construction of the principal components. Because the imputation uses the principal axes and components, the prediction of the missing values is based on the similarity between individuals and on the relationships between variables. The properties of the method are illustrated via simulations and the quality of the imputation is assessed using real data sets. The method is compared to a recent method (Stekhoven and Buhlmann Bioinformatics 28:113---118, 2011) based on random forest and shows better performance especially for the imputation of categorical variables and situations with highly linear relationships between continuous variables.

Heat-Induced Denaturation, Aggregation and Gelation of Whey Proteins

Abstract: Whey proteins, a group of acid-soluble proteins, represent approximately 20 % of the total protein in bovine milk. The two main proteins, β-lactoglobulin (18.3 kDa) and α-lactalbumin (14.2 kDa) have been the subject of numerous studies. The purpose has mostly been to elucidate and exploit potential structure/function relationships. Both proteins provide high nutritional value and are utilised in the production of nutritional beverages such as infant formula and energy drinks. In addition, β-lactoglobulin offers a range of useful techno-functional properties, such as thickening, emulsification, gelation or foaming. Exposure of whey proteins to heat is a common industrial processing step that causes structural changes in proteins and that can lead to increases in viscosity and/or formation of potentially extensive gel networks above a critical protein concentration. This chapter describes such heat-induced unfolding, denaturation and aggregation processes, and their kinetics, as well as cases of ordered protein structures such as fibrils or nanoparticles. Heat-induced and cold gelation of whey proteins is also described. Gel formation is brought about by the assembly of soluble aggregates formed during the initial stages of heating. Such gel networks develop through electrostatic, hydrophobic and covalent interactions between denatured whey proteins. The micro- and macro-structure of whey protein gels vary widely and are dependent on the nature of the aggregation processes involved. The influence of protein type and concentration, salt type and ionic strength, pH and heating conditions on the above processes are reviewed.

Panta Rhei 2013-2015: Global perspectives on hydrology, society and change

Abstract: In 2013, the International Association of Hydrological Sciences (IAHS) launched the hydrological decade 2013–2022 with the theme “Panta Rhei: Change in Hydrology and Society”. The decade recognizes the urgency of hydrological research to understand and predict the interactions of society and water, to support sustainable water resource use under changing climatic and environmental conditions. This paper reports on the first Panta Rhei biennium 2013–2015, providing a comprehensive resource that describes the scope and direction of Panta Rhei. We bring together the knowledge of all the Panta Rhei working groups, to summarize the most pressing research questions and how the hydrological community is progressing towards those goals. We draw out interconnections between different strands of research, and reflect on the need to take a global view on hydrology in the current era of human impacts and environmental change. Finally, we look back to the six driving science questions identified at the outset of Panta Rhei, to quantify progress towards those aims.

Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals.

Abstract: The liver is a key organ of metabolic homeostasis with functions that oscillate in response to food intake. Although liver and gut microbiome crosstalk has been reported, microbiome-mediated effects on peripheral circadian clocks and their output genes are less well known. Here, we report that germ-free (GF) mice display altered daily oscillation of clock gene expression with a concomitant change in the expression of clock output regulators. Mice exposed to microbes typically exhibit characterized activities of nuclear receptors, some of which (PPARα, LXRβ) regulate specific liver gene expression networks, but these activities are profoundly changed in GF mice. These alterations in microbiome-sensitive gene expression patterns are associated with daily alterations in lipid, glucose, and xenobiotic metabolism, protein turnover, and redox balance, as revealed by hepatic metabolome analyses. Moreover, at the systemic level, daily changes in the abundance of biomarkers such as HDL cholesterol, free fatty acids, FGF21, bilirubin, and lactate depend on the microbiome. Altogether, our results indicate that the microbiome is required for integration of liver clock oscillations that tune output activators and their effectors, thereby regulating metabolic gene expression for optimal liver function.

Projecting changes in the distribution and productivity of living marine resources: A critical review of the suite of modelling approaches used in the large European project VECTORS

Abstract: We review and compare four broad categories of spatially-explicit modelling approaches currently used to understand and project changes in the distribution and productivity of living marine resources including: 1) statistical species distribution models, 2) physiology-based, biophysical models of single life stages or the whole life cycle of species, 3) food web models, and 4) end-to-end models Single pressures are rare and, in the future, models must be able to examine multiple factors affecting living marine resources such as interactions between: i) climate-driven changes in temperature regimes and acidification, ii) reductions in water quality due to eutrophication, iii) the introduction of alien invasive species, and/or iv) (over-)exploitation by fisheries Statistical (correlative) approaches can be used to detect historical patterns which may not be relevant in the future Advancing predictive capacity of changes in distribution and productivity of living marine resources requires explicit modelling of biological and physical mechanisms New formulations are needed which (depending on the question) will need to strive for more realism in ecophysiology and behaviour of individuals, life history strategies of species, as well as trophodynamic interactions occurring at different spatial scales Coupling existing models (eg physical, biological, economic) is one avenue that has proven successful However, fundamental advancements are needed to address key issues such as the adaptive capacity of species/groups and ecosystems The continued development of end-to-end models (eg, physics to fish to human sectors) will be critical if we hope to assess how multiple pressures may interact to cause changes in living marine resources including the ecological and economic costs and trade-offs of different spatial management strategies Given the strengths and weaknesses of the various types of models reviewed here, confidence in projections of changes in the distribution and productivity of living marine resources will be increased by assessing model structural uncertainty through biological ensemble modelling

sHSPdb: a database for the analysis of small Heat Shock Proteins

Abstract: small Heat Shock Proteins (sHSP) is a wide proteins family. SHSP are found in all kingdoms and they play critical roles in plant stress tolerance mechanisms (as well as in pathogenic microorganisms and are implicated in human diseases). sHSPdb (small Heat Shock Proteins database) is an integrated resource containing non-redundant, full-length and curated sequences of sHSP, classified on the basis of amino acids motifs and physico-chemical properties. sHSPdb gathers data about sHSP defined by various databases (Uniprot, PFAM, CDD, InterPro). It provides a browser interface for retrieving information from the whole database and a search interface using various criteria for retrieving a refined subset of entries. Physicochemical properties, amino acid composition and combinations are calculated for each entry. sHSPdb provides automatic statistical analysis of all sHSP properties. Among various possibilities, sHSPdb allows BLAST searches, alignment of selected sequences and submission of sequences. sHSPdb is a new database containing information about sHSP from all kingdoms. sHSPdb provides a classification of sHSP, as well as tools and data for the analysis of the structure - function relationships of sHSP. Data are mainly related to various physico-chemical properties of the amino acids sequences of sHSP. sHSPdb is accessible at http://forge.info.univ-angers.fr/~gh/Shspdb/index.php .

Caking of lactose: A critical review

Abstract: Background Caking is a recurrent problem in various industries, whether it occurs during the production, storage or transport of powders. Caked powder results in longer processing times and decreased product quality, leading to significant economic loss. Several caking mechanisms have been described in the literature. However, they are often difficult to take into account in an industrial context, given the many parameters which influence the overall caking phenomenon. Scope and approach This review describes the three relevant caking mechanisms for food powders in general. Focussing on predominantly crystalline lactose powder, we discuss how each of these mechanisms can explain caking and be prevented in the industrial context. The second part of this paper presents a critical review of the methods used to characterise caking to date. Key findings and conclusions The presence of amorphous material and other impurities must be assessed in crystalline lactose powders, as they can trigger amorphous and humidity caking. Particle size distribution is another key parameter requiring control as it can encourage caking through enhancement of particle interactions. In general, preventing caking in food powders can only be achieved by a thorough understanding of the production process and storage conditions. Moreover, the characterisation of caking remains a challenge as most methods published in the literature do not fit the needs of the food industry. The real demand is for a reliable method to predict caking which would be rapid and easy enough to be applied to each batch for quality control.