A Holistic Approach to Marine Eco-Systems Biology

With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosystems are crucial in the regulation of Earth's biogeochemical cycles and climate [6],[7]. Yet their organization, evolution, and dynamics remain poorly understood [8],[9]. The Tara Oceans project was launched in September 2009 for a 3-year study of the global ocean ecosystem aboard the ship Tara. A unique sampling programme encompassing optical and genomic methods to describe viruses, bacteria, archaea, protists, and metazoans in their physico-chemical environment has been implemented. Starting as a grassroots initiative of a few scientists, the project has grown into a global consortium of over 100 specialists from diverse disciplines, including oceanography, microbial ecology, genomics, molecular, cellular, and systems biology, taxonomy, bioinformatics, data management, and ecosystem modeling. This multidisciplinary community aims to generate systematic, open access datasets usable for probing the morphological and molecular makeup, diversity, evolution, ecology, and global impacts of plankton on the Earth system

Open science resources for the discovery and analysis of Tara Oceans data

Le " Tara Expéditions" organise des expéditions pour étudier et comprendre l'impact des changements climatiques sur nos océans.International audienceThe Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events

Control of Gene Expression by the Retinoic Acid-Related Orphan Receptor Alpha in HepG2 Human Hepatoma Cells

Retinoic acid-related Orphan Receptor alpha (RORα; NR1F1) is a widely distributed nuclear receptor involved in several (patho)physiological functions including lipid metabolism, inflammation, angiogenesis, and circadian rhythm. To better understand the role of this nuclear receptor in liver, we aimed at displaying genes controlled by RORα in liver cells by generating HepG2 human hepatoma cells stably over-expressing RORα. Genes whose expression was altered in these cells versus control cells were displayed using micro-arrays followed by qRT-PCR analysis. Expression of these genes was also altered in cells in which RORα was transiently over-expressed after adenoviral infection. A number of the genes found were involved in known pathways controlled by RORα, for instance LPA, NR1D2 and ADIPOQ in lipid metabolism, ADIPOQ and PLG in inflammation, PLG in fibrinolysis and NR1D2 and NR1D1 in circadian rhythm. This study also revealed that genes such as G6PC, involved in glucose homeostasis, and AGRP, involved in the control of body weight, are also controlled by RORα. Lastly, SPARC, involved in cell growth and adhesion, and associated with liver carcinogenesis, was up-regulated by RORα. SPARC was found to be a new putative RORα target gene since it possesses, in its promoter, a functional RORE as evidenced by EMSAs and transfection experiments. Most of the other genes that we found regulated by RORα also contained putative ROREs in their regulatory regions. Chromatin immunoprecipitation (ChIP) confirmed that the ROREs present in the SPARC, PLG, G6PC, NR1D2 and AGRP genes were occupied by RORα in HepG2 cells. Therefore these genes must now be considered as direct RORα targets. Our results open new routes on the roles of RORα in glucose metabolism and carcinogenesis within cells of hepatic origin

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009-2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge collection of samples. A strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics and metatranscriptomics, has been chosen for analysis of size-fractionated plankton communities. Here, we provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA, www.ebi.ac.uk/ena). The association of these metadata to the experimental procedures applied for their generation will help the scientific community to access these data and facilitate their analysis. This paper complements other efforts to provide a full description of experiments and open science resources generated from the Tara Oceans project, further extending their value for the study of the world's planktonic ecosystems

Community-Level Responses to Iron Availability in Open Ocean Plankton Ecosystems

Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron availability on plankton communities, we explored the comprehensive bio-oceanographic and bio-omics data sets from Tara Oceans in the context of the iron products from two state-of-the-art global scale biogeochemical models. We obtained novel information about adaptation and acclimation toward iron in a range of phytoplankton, including picocyanobacteria and diatoms, and identified whole subcommunities covarying with iron. Many of the observed global patterns were recapitulated in the Marquesas archipelago, where frequent plankton blooms are believed to be caused by natural iron fertilization, although they are not captured in large-scale biogeochemical models. This work provides a proof of concept that integrative analyses, spanning from genes to ecosystems and viruses to zooplankton, can disentangle the complexity of plankton communities and can lead to more accurate formulations of resource bioavailability in biogeochemical models, thus improving our understanding of plankton resilience in a changing environment

MECANISMES DE LA DIVISION CELLULAIRE CHEZ L'EMBRYON D'OURSIN (ROLE DE LA KINESINE BOURSIN)

LA CYTOCINESE EST L'ETAPE ULTIME DE LA DIVISION CELLULAIRE. AFIN D'EVITER TOUT PROBLEME D'ANEUPLOIDIE OU DE POLYPLOIDIE QUI DECOULERAIT D'UNE MAUVAISE SEGREGATION DES CHROMOSOMES, LA CYTOCINESE SE DOIT D'ETRE EN RELATION ETROITE AVEC LA MITOSE AU NIVEAU TEMPOREL ET SPATIAL. PAR UNE APPROCHE BIOCHIMIQUE SYSTEMATIQUE REPOSANT SUR UN SYSTEME DE CHROMATOGRAPHIE D'AFFINITE SUR COLONNE D'ACTINE POLYMERIQUE ET SUR COLONNE DE DOUBLETS DE MICROTUBULES AXONEMAUX ISOLES A PARTIR DE FLAGELLES DE SPERMATOZOIDES D'OURSINS, NOUS AVONS ISOLE DES PROTEINES D'EMBRYONS D'OURSIN CAPABLES D'INTERAGIR A LA FOIS AVEC LES FILAMENTS D'ACTINE ET LES MICROTUBULES ET QUI SERAIENT SUSCEPTIBLES DE CONSTITUER UN ELEMENT DU SIGNAL DE LA REGULATION DU CLIVAGE. PARMI, CES PROTEINES, BOURSIN, UNE KINESINE DE LA FAMILLE BIMC, A ETE CARACTERISEE. L'UTILISATION D'ANTICORPS SPECIFIQUES A PERMIS DE MONTRER QUE BOURSIN EST FORTEMENT EXPRIMEE DEPUIS LE STADE UF JUSQU'AUX STADES DE SEGMENTATION, QU'ELLE EST ASSOCIEE SPECIFIQUEMENT AU FUSEAU TOUT AU LONG DE LA MITOSE PUIS AU MIDBODY EN FIN DE TELOPHASE. L'EXPRESSION D'UNE BOURSIN MUTEE DANS SON SITE D'HYDROLYSE DE L'ATP SUITE A L'INJECTION DES L'ARNM CORRESPONDANTS DANS DES UFS NON FECONDES EST A L'ORIGINE DE DEFAUTS SEVERES DANS LA DIVISION CELLULAIRE ET RESULTE EN LA FORMATION D'EMBRYONS COMPORTANT DES BLASTOMERES POLYPLOIDES ET MULTIASTRAUX. L'OBSERVATION EN TEMPS REEL DES CYCLES CELLULAIRES DE TELS EMBRYONS MONTRE QUE LES PHENOTYPES OBSERVES PROVIENNENT DE PERTURBATIONS DE L'ANAPHASE ET DE L'INCAPACITE DES BLASTOMERES A REALISER LA FINITION DE LA CYTOCINESE. LA FORMATION DE L'ANNEAU DE CLIVAGE ET L'INITIATION DE LA CONTRACTION DE CELUI-CI NE SONT PAS AFFECTEES MAIS LES CELLULES FILLES NE SE FORMENT QUE TRES RAREMENT SUITE A UNE RESORPTION DU SILLON DE CLIVAGE. CES PHENOTYPES DIFFERENT DE CEUX PRECEDEMMENT OBSERVES CHEZ D'AUTRES ORGANISMES SUITE A LA PERTURBATION DES PROTEINES DE LA FAMILLE BIMC.PARIS-BIUSJ-Thèses (751052125) / SudocCentre Technique Livre Ens. Sup. (774682301) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Polarisation des ARNm maternels et des régulateurs de l'initiation de la traduction dans le cortex des oeufs et embryons précoces d'ascidie

Ascidians (urochodates: Ciona intestinalis and Phallusia mammillata ) are considered the closest invertebrate ancestors of vertebrates. They develop into simple tadpoles made of 2600 cells harboring a notochord and a dorsal nerve chord. At the turn of the 20th century, the ascidians model contributed much to the idea that oocytes contained localized determinants of development. This led to the concept of mosaic development. Today we know that some of these determinants are maternal RNAs localized in the egg cortex. Ascidian determinant RNAs are part of a large family of maternal RNAs called postplasmic/PEM RNAs. They include about 40 transcrips classified as Type I (localized before fertilization) and Type II (localized after fertilization). Type I postplasmic/PEM RNAs are relocalized after fertilization in a stereotyped fashion such that they concentrate in the posterior region of the zygote and form a compact cortical zone in the 2 posterior vegetal blastomeres at the 8 cell stage called the CAB (Centrosome Attracting Body). The large numbers of postplasmic/PEM RNAs identified, the synchronicity and abundance of embryos, and the ability to isolate cortical fragments retaining the RNAs make the ascidian model particularly attractive for studying localization and cortical anchorage of polarized RNAs. It is possible to operate a first classification of postplasmic/PEM RNAs based on their localization in cells in the tail of the tadpole. The determinant Macho1 and PEM1 segregate in 2 B8.11 cells with somatic destinies while RNAs such as the germ plasm marker Vasa is in addition localized in 2 B.12 cells precursors of the germ line. The 3 UTR regions of postplasmic/PEM RNA are considered to contain part of the code for localization and anchorage. In Ascidians as in the amphibian Xenopus these regions are characterized by frequent xCACx repeats. Using this criteria to screen 3 UTRs of all Ciona intestinalis genes, we confirmed that frequent xCACx repeats constituted a predictive signature for postplasmic/PEM RNAs and found 2 new members (MnK et PSD). We have also identified subcellular anchorage sites of postplasmic/PEM RNAs using high resolution immuno-in situ localization techniques in oocytes and embryos as well as in cortical fragments isolated from them. The RNA determinants Macho1 and PEM1 are associated with a sub-domain of cortical Endoplasmic Reticulum (cER) while Vasa, PEM3, POPK RNAs are localized in granules (putative germ granules). This demonstrates that although at low resolution these RNAs appear co-localized in the cortex they have in fact different structures of anchorage. This allows to propose that postplasmic/PEM RNAs belong to 2 categories: a category ( Vasa-Type ) associated with granules and segregating in both 8.11 and 8.12 cells and a category ( Macho1-Type ) associated to cER which segregates only into B8.11 cells. We also investigated whether, as in nerve terminals, the translation machinery was also polarized in oocytes and embryos. Indeed we found that some factors (PAPB) and regulators (phosporylated forms of MnK, 4EBP et S6Kinase ) of translation initiation were co-localized with postplasmic/PEM RNAs associated with the cER (Macho1 and PEM1 RNAs). The fact that regulators such as MnK and S6Kinase change phosphorylation status after fertilization suggests that they control translation initiation of determinants RNAs in the cortex following egg activation.NICE-BU Sciences (060882101) / SudocSudocFranceF

Polarisation corticale des oeufs et embryons d'ascidie de la maturation à la 1ère division inégale

Le cortex des œufs d ascidies est hautement polarisé suivant l axe animal-végétatif (a-v) à l issue de l ovogenèse, puis suivant les axes Dorso-Ventral (D-V) et Antero-Posterieur (A-P) à partir de la fécondation jusqu au 1er clivage. Les ovocytes matures d ascidie sont caractérisés par la distribution en gradient (a-v) de - 1) un domaine sous-cortical riche en mitochondries (appelé myoplasme) ; - 2) d un domaine riche en Reticulum Endoplasmique cortical (REc) et d une classe d ARN messagers corticaux d origine maternelle (appelée ARNm postplasmiques/PEM). Nous avons montré que la polarisation (a-v) de ces domaines s effectue au cours de la maturation des ovocytes. Le cortex des œufs subit à l issue de la fécondation 2 phases majeures de réorganisations. Le myoplasme, le REc ainsi que les ARNm postplasmiques/PEM se concentrent dans le pôle de contraction végétatif (futur pôle Dorsal) au cours d une première phase majeure de réorganisation acto-myosine dépendante. Le myoplasme, le REc/ARNm corticaux sont ensuite déplacés au niveau du pôle postérieur lors d une seconde phase majeure de réorganisation dépendante des microtubules. Ces domaines sont répartis de façon équivalente entre les blastomères au cours du premier clivage. Aux stades 2-4 cellules, le myoplasme, le REc et les ARNm postplasmiques/PEM s accumulent dans les blastomères postérieurs. Au stade 8 cellules, le REc et les ARNm postplasmiques/PEM se concentrent au niveau d une structure macroscopique corticale appelée CAB (pour Centrosome Attracting Body) localisée dans les blastomères végétatifs les plus postérieurs (B4.1). Le CAB est impliqué dans la genèse de 3 divisions inégales successives et la ségrégation des ARNm postplasmiques/PEM. Nous avons caractérisé pour la première fois l évolution et la dynamique de cette polarité corticale en utilisant des cortex isolés à partir d ovocytes, de zygotes et d embryons au stade 8 cellules. Nous avons montré que deux ARNm postplasmiques/PEM, PEM1 et macho1, respectivement impliqués dans la formation des axes et la différenciation des cellules musculaires primaires, sont ancrés à la surface d un réseau polarisé de RE corticale rugueux déjà présent dans les ovocytes matures. Après fécondation, ces ARNm corticaux se concentrent dans le cortex végétatif avec le REc (formant un domaine REc/ ARNm). Ce domaine REc/ARNm se relocalise ensuite en position postérieure avant le 1er clivage et s accumulent avec celui-ci dans le CAB au stade 8 cellules. Nous discutons 1) le rôle du cytosquelette dans la relocalisation du domaine polarisé riche en REc/ARNm après fécondation, et dans la formation du CAB ; 2) les mécanismes de ségrégation des ARNm postplasmiques/PEM dans les blastomères postérieurs de l embryon ; 3) les conséquences de ces remaniements dans la différenciation de l embryon d ascidie et en particulier celle des cellules musculaires primaires.The ascidian egg cortex is highly polarized along the animal-vegetal (a-v) axis at the end of oogenesis, and along the Dorso-Ventral (D-V) axis and Antero-Posterior (A-P) axis between fertilization and first cleavage. Mature ascidian oocytes display (a-v) gradients of 1) a mitochondria-rich subcortical domain (called myoplasm), 2) a network of cortical Endoplasmic Reticulum (cER), and several cortical maternal mRNAs called postplasmic/PEM RNAs. We show that these domains and mRNAs acquire their polarized distribution during oocyte maturation. After fertilization the oocyte cortex undergoes 2 major phases of reorganization. The cortical (cER) and subcortical (myoplasm) domains are first concentrated in the vegetal contraction pole (future dorsal pole) during an acto-myosin dependant cortical contraction(first major phase of reorganization). The myoplasm, cER/mRNA domains are then translocated posteriorly by a microtubule-dependant movement of the sperm aster with respect to the cortex (second major phase of reorganization). The domains are distributed equally between blastomeres during the first cleavage. At the 2-4 cell stage, the myoplasm, cER and postplasmic/PEM RNAs accumulate in posterior blastomeres. At the 8 cell stage, cER and postplasmic/PEM RNAs are concentrated in a cortical macroscopic structure called Centrosome Attracting Body (CAB) located in the vegetal posterior-most blastomeres (B4.1). The CAB is involved in the formation of three successive unequal cleavages and in mRNA segregation in small posterior blastomeres. We have characterized for the first time the evolution and dynamics of this cortical polarity using cortex isolation and characterization in oocytes, zygotes and early embryos (8 cell stage). We observe that two postplasmic/PEM RNAs, PEM1 and macho1 respectively involved in axes formation and primary muscle cell formation, are anchored to the surface of the polarized network of cortical rough ER. After fertilization these cortical RNAs are concentrated in the vegetal cortex with the cER (forming a cER/mRNA domain). The cER/mRNA domain moves posteriorly before the first cleavage and compacts into the CAB at the 8 cell stage. We discuss how the cytoskeleton relocates the cER/mRNA domain and how the CAB may form from the translocation and compaction of polarized cER/mRNA domain already present in the oocyte. We also discuss how the segregation of postplasmic/PEM RNAs into specific blastomeres directs development and differentiation of the posterior region of the embryo and particular primary muscle cell formation.NICE-BU Sciences (060882101) / SudocSudocFranceF

Demonstration of calcium uptake and release by sea urchin egg cortical endoplasmic reticulum

Abstract. The calcium indicator dye fluo-3/AM was loaded into the ER of isolated cortices of unfertilized eggs of the sea urchin Arbacia punctulata. Development of the fluorescent signal took from 8 to 40 min and usually required 1 mM ATP The signal decreased to a minimum level within 30 s after perfusion with 1 FAM InsP3 and increased within 5 min when InsP3 was replaced with 1 mM ATP. Also, the fluorescence signal was lowered rapidly by perfusion with 10 p,M A23187 or 10 pM ionomycin. These findings demonstrate that the cortical ER is a site of ATP-dependent calcium sequestration and InSP3-induced calcium release. A light-induced wave of calcium release, traveling between 0.7 and 2.8 pm/s (average speed 1.4 jam/s, N = 8), was sometimes observed during time lapse recordings; it may therefore be possible to use the isolate