Clustering Time-Series Gene Expression Data Using Smoothing Spline Derivatives

Microarray data acquired during time-course experiments allow the temporal variations in gene expression to be monitored. An original postprandial fasting experiment was conducted in the mouse and the expression of 200 genes was monitored with a dedicated macroarray at 11 time points between 0 and 72 hours of fasting. The aim of this study was to provide a relevant clustering of gene expression temporal profiles. This was achieved by focusing on the shapes of the curves rather than on the absolute level of expression. Actually, we combined spline smoothing and first derivative computation with hierarchical and partitioning clustering. A heuristic approach was proposed to tune the spline smoothing parameter using both statistical and biological considerations. Clusters are illustrated a posteriori through principal component analysis and heatmap visualization. Most results were found to be in agreement with the literature on the effects of fasting on the mouse liver and provide promising directions for future biological investigations

Encouraging Investors to Enable Corporate Sustainability Transitions: The Case of Responsible Investment in France

This paper studies the case of the socially responsible investment (SRI) industry in France. This case accounts for how the SRI category and practices have successfully moved from the margins of the industry in the late 1990s to become mainstream over two decades. We bring to the forefront the importance of three complementary factors in the process of causing corporations to transition toward more sustainable businesses: the role of investors and, in particular, institutional investors; the importance of the presence of a clear category definition and of intermediary organizations, providing ratings, scores, and other calculative devices; and the role of governments and regulators. With other studies, this case stresses the fundamental influence of investors in how corporations manage sustainability transitions

Muscle atrophy phenotype gene expression during spaceflight is linked to a metabolic crosstalk in both the liver and the muscle in mice

Human expansion in space is hampered by the physiological risks of spaceflight. The muscle and the liver are among the most affected tissues during spaceflight and their relationships in response to space exposure have never been studied. We compared the transcriptome response of liver and quadriceps from mice on NASA RR1 mission, after 37 days of exposure to spaceflight using GSEA, ORA, and sparse partial least square-differential analysis. We found that lipid metabolism is the most affected biological process between the two organs. A specific gene cluster expression pattern in the liver strongly correlated with glucose sparing and an energy-saving response affecting high energy demand process gene expression such as DNA repair, autophagy, and translation in the muscle. Our results show that impaired lipid metabolism gene expression in the liver and muscle atrophy gene expression are two paired events during spaceflight, for which dietary changes represent a possible countermeasure

Calculability as politics in the construction of markets: the case of socially responsible investment in France

This paper examines some of the processes by which power constitutes calculability and, in so doing, shapes the construction of markets. We combine insights from performativity studies about calculability with Lukes’ ‘radical view of power’ to investigate how multiple facets of power are mobilized to influence the creation and activities of calculative agencies in the process of market construction. An in-depth longitudinal study of the French socially responsible investment market shows how organizations acting as calculative agencies become sites of power through calculability. We identify how power is exercised over, through and against these calculative agencies by a variety of actors in order to build their position in the socially responsible investment market. Our results complement the broader question of the ‘government of economic life’ by showing how micro-level power games interact with the macro-politics of market building through calculative agencies. In so doing, our paper sheds light on neglected aspects of the changing geopolitics of calculative power in market construction and suggests approaching ‘calculability as politics’ when studying the construction of markets

The xylan utilization system of the plant pathogen Xanthomonas campestris pv campestris controls epiphytic life and reveals common features with oligotrophic bacteria and animal gut symbionts

Xylan is a major structural component of plant cell wall and the second most abundant plant polysaccharide in nature.Here, by combining genomic and functional analyses, we provide a comprehensive picture of xylan utilization by Xanthomonas campestris pv campestris (Xcc) and highlight its role in the adaptation of this epiphytic phytopathogen to the phyllosphere. The xylanolytic activity of Xcc depends on xylan-deconstruction enzymes but also on transporters, including two TonB-dependent outer membrane transporters (TBDTs) which belong to operons necessary for efficient growth in the presence of xylo-oligosaccharides and for optimal survival on plant leaves. Genes of this xylan utilization system are specifically induced by xylo-oligosaccharides and repressed by a LacI-family regulator named XylR. Part of the xylanolytic machinery of Xcc, including TBDT genes, displays a high degree of conservation with the xylose-regulon of the oligotrophic aquatic bacterium Caulobacter crescentus. Moreover, it shares common features, including the presence of TBDTs, with the xylan utilization systems of Bacteroides ovatus and Prevotella bryantii, two gut symbionts. These similarities and our results support an important role for TBDTs and xylan utilization systems for bacterial adaptation in the phyllosphere, oligotrophic environments and animal guts

Spiders in caves: the CAWEB project

World experts of different disciplines, from molecular biology to macroecology, recognize the value of cave ecosystems as ideal ecological and evolutionary laboratories. Among other subterranean taxa, spiders stand out as intriguing model organisms for their ecological role of top-predators, their unique adaptations to the hypogean medium and their sensitivity to anthropogenic disturbance. Here, we provide a general overview of the spider families recorded in hypogean habitats in Europe–20 families including nearly 500 species, most of them with restricted distributions. We also review the different adaptations of hypogean spiders to subterranean life and summarize the information gathered so far about their origin, population structure, ecology and conservation status. Taxonomic knowledge on subterranean spiders in Europe appears to be well, but not exhaustively documented. The origin of the European assemblages is mostly explained by past climate dynamics, although other factors are likely to be involved. Most of the macroecological issues related to spiders in European caves are based on qualitative assessments or have been quantified only at a sub-regional scale. In order to shed light on cave spiders’ biogeography and the macroecological patterns driving the diversity of European subterranean spiders we created the CAWEB network, a spontaneous collaboration between subterranean arachnologists from 30 different European countries. We here present the team and provide some preliminary results, which highlight Southern Europe as an important hot-spot for the European subterranean spider diversity

Modèle non linéaire à paramètres aléatoires de la dynamique de cultures observées par télédétection : comparaison de deux procédures d'estimation

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