Strengthening insights into host responses to mastitis infection in ruminants by combining heterogeneous microarray data sources

<p>Abstract</p> <p>Background</p> <p>Gene expression profiling studies of mastitis in ruminants have provided key but fragmented knowledge for the understanding of the disease. A systematic combination of different expression profiling studies via meta-analysis techniques has the potential to test the extensibility of conclusions based on single studies. Using the program Pointillist, we performed meta-analysis of transcription-profiling data from six independent studies of infections with mammary gland pathogens, including samples from cattle challenged <it>in vivo </it>with <it>S. aureus</it>, <it>E. coli</it>, and <it>S. uberis</it>, samples from goats challenged <it>in vivo </it>with <it>S. aureus</it>, as well as cattle macrophages and ovine dendritic cells infected <it>in vitro </it>with <it>S. aureus</it>. We combined different time points from those studies, testing different responses to mastitis infection: overall (common signature), early stage, late stage, and cattle-specific.</p> <p>Results</p> <p>Ingenuity Pathway Analysis of affected genes showed that the four meta-analysis combinations share biological functions and pathways (e.g. protein ubiquitination and polyamine regulation) which are intrinsic to the general disease response. In the overall response, pathways related to immune response and inflammation, as well as biological functions related to lipid metabolism were altered. This latter observation is consistent with the milk fat content depression commonly observed during mastitis infection. Complementarities between early and late stage responses were found, with a prominence of metabolic and stress signals in the early stage and of the immune response related to the lipid metabolism in the late stage; both mechanisms apparently modulated by few genes, including <it>XBP1 </it>and <it>SREBF1</it>.</p> <p>The cattle-specific response was characterized by alteration of the immune response and by modification of lipid metabolism. Comparison of <it>E. coli </it>and <it>S. aureus </it>infections in cattle <it>in vivo </it>revealed that affected genes showing opposite regulation had the same altered biological functions and provided evidence that <it>E. coli </it>caused a stronger host response.</p> <p>Conclusions</p> <p>This meta-analysis approach reinforces previous findings but also reveals several novel themes, including the involvement of genes, biological functions, and pathways that were not identified in individual studies. As such, it provides an interesting proof of principle for future studies combining information from diverse heterogeneous sources.</p

The Mastigamoeba balamuthi genome and the nature of the free-living ancestor of Entamoeba

The transition of free-living organisms to parasitic organisms is a mysterious process that occurs in all major eukaryotic lineages. Parasites display seemingly unique features associated with their pathogenicity; however, it is important to distinguish ancestral preconditions to parasitism from truly new parasite-specific functions. Here, we sequenced the genome and transcriptome of anaerobic free-living Mastigamoeba balamuthi and performed phylogenomic analysis of four related members of the Archamoebae, including Entamoeba histolytica, an important intestinal pathogen of humans. We aimed to trace gene histories throughout the adaptation of the aerobic ancestor of Archamoebae to anaerobiosis and throughout the transition from a free-living to a parasitic lifestyle. These events were associated with massive gene losses that, in parasitic lineages, resulted in a reduction in structural features, complete losses of some metabolic pathways, and a reduction in metabolic complexity. By reconstructing the features of the common ancestor of Archamoebae, we estimated preconditions for the evolution of parasitism in this lineage. The ancestor could apparently form chitinous cysts, possessed proteolytic enzyme machinery, compartmentalized the sulfate activation pathway in mitochondrion-related organelles, and possessed the components for anaerobic energy metabolism. After the split of Entamoebidae, this lineage gained genes encoding surface membrane proteins that are involved in host–parasite interactions. In contrast, gene gains identified in the M. balamuthi lineage were predominantly associated with polysaccharide catabolic processes. A phylogenetic analysis of acquired genes suggested an essential role of lateral gene transfer in parasite evolution (Entamoeba) and in adaptation to anaerobic aquatic sediments (Mastigamoeba)

Biosedimentary and paleoenvironmental evolution of the Southern Marion Platform from the middle to late Miocene (northeast Australia, ODP Leg 194, Sites 1196 and 1199)

International audienceThe Southern Marion Plateau (SMP) represents a vertical stacking of Miocene carbonate platform deposits. Two sites (1196 and 1199) were drilled on top of this plateau, penetrating a 663-m carbonate succession of bioclastic and reefal sedimentary bodies. The study focuses on the least dolomitized 410-m-thick upper part of the succession, which is middle to late Miocene in age. Sedimentological and paleontological studies were conducted at both sites in order to propose a paleoenvironmental model and its evolution through the Miocene age. Six main microfacies of possible environmental significance were defined using statistical multivariate analyses, based on the recognition and point counting of 24 biogenic components. Depositional environment reconstructions are proposed as well as the biosedimentary and the environmental evolution regarding seismic architectures, stratigraphy, biosedimentology, and microfacies analysis. The SMP platform mainly results from a vertical stacking of lens-shaped bodies in homoclinal to distally steepened ramp settings

(Table T1) Coral taxa and their ecological significance in ODP Site 194-1196 and Hole 194-1199A sediments

The Southern Marion Plateau (SMP) represents a vertical stacking of Miocene carbonate platform deposits. Two sites (1196 and 1199) were drilled on top of this plateau, penetrating a 663-m carbonate succession of bioclastic and reefal sedimentary bodies. The study focuses on the least dolomitized 410-m-thick upper part of the succession, which is middle to late Miocene in age. Sedimentological and paleontological studies were conducted at both sites in order to propose a paleoenvironmental model and its evolution through the Miocene age. Six main microfacies of possible environmental significance were defined using statistical multivariate analyses, based on the recognition and point counting of 24 biogenic components. Depositional environment reconstructions are proposed as well as the biosedimentary and the environmental evolution regarding seismic architectures, stratigraphy, biosedimentology, and microfacies analysis. The SMP platform mainly results from a vertical stacking of lens-shaped bodies in homoclinal to distally steepened ramp settings

Apports des foraminifères planctoniques à la biostratigraphie du Miocène supérieur et du Pliocène de Djebel Diss (bassin du Chélif, Algérie)

Belhadji, Ahmed, Belkebir, Lahcene, Martin, Jean-Paul Saint, Mansour, Bouhameur, Bessedik, Mostefa, Conesa, Gilles (2008): Apports des foraminifères planctoniques à la biostratigraphie du Miocène supérieur et du Pliocène de Djebel Diss (bassin du Chélif, Algérie). Geodiversitas 30 (1): 79-96, DOI: http://doi.org/10.5281/zenodo.537418

Du nouveau sur la civilisation ibérique : les fouilles de Cabezo Lucero (Alicante)

Rouillard Pierre, Llobregat Enrique, Aranegui Carmen, Grévin Gilles, Jodin André, Uroz José. Du nouveau sur la civilisation ibérique : les fouilles de Cabezo Lucero (Alicante). In: Comptes rendus des séances de l'Académie des Inscriptions et Belles-Lettres, 134ᵉ année, N. 2, 1990. pp. 538-557

Modèles paléoenvironnementaux de dépôts littoraux mixtes de plates-formes du Messinien supérieur, au début de la crise de salinité (bassin de Melilla-Nador, Maroc)

Garcia Frédéric, Conesa Gilles, Münch Philippe, Cornée Jean-Jacques, Saint Martin Jean-Paul, André Jean-Pierre. Modèles paléoenvironnementaux de dépôts littoraux mixtes de plates-formes du Messinien supérieur, au début de la crise de salinité (bassin de Melilla-Nador, Maroc). In: Documents des Laboratoires de Géologie, Lyon, n°156, 2002. STRATI 2002. 3ème congrès français de stratigraphie. Lyon, 8-10 juillet 2002. pp. 112-113

Micritic crusts in carbonate platforms

Penin C., Conesa G., Esteban M., Gatt P., Jasionowski M., Ribaud-Laurenti Anne, Montaggioni Lucien François, Saint Martin Jean-Paul. Micritic crusts in carbonate platforms. In: Géologie Méditerranéenne. Tome 21, numéro 1-2, 1994. Récifs et plates-formes carbonatées miocènes de Méditerranée / Miocene reefs and carbonate platforms of the Mediterranean. Interim colloquium R.C.M.N.S. (Marseille 3-6 mai 1994) sous la direction de Jean-Paul Saint-Martin et Jean-Jacques Cornée. p. 169