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Surveillance Écologique et Halieutique Site de Gravelines. Novembre 2014 - Octobre 2015 ArchiMer
Antajan, Elvire; Lefebvre, Alain; Loots, Christophe; Rocroy, Mélanie; Ruellet, Thierry.
This is the 38th annual surveillance report concerning the nuclear power plant of Gravelines. Its very high power level results from six plant units located on the shore and is characterised by a cooling system with a coastal surface input and output. The production of electricity began in 1980 and reached maximum in 1986. Surveys concern monitoring of pelagic system (hydrology, microbiology, phytoplankton, and zooplankton), fish populations (larvae and eggs of Sole and Sprat) or crustaceans (shrimps), and benthic macrofauna (intertidal and subtidal). This survey deals with spatial and temporal approaches (i) study of the direct impact by comparison of the input and output seawater stations, (ii) study of medium and long term evolution of the area by...
Tipo: Text Palavras-chave: Centrale nucléaire; Gravelines; Surveillance; Hydrologie; Halieutique; Plancton; Benthos; Microbiologie; Nuclear power plant; Gravelines; Network survey; Hydrology; Fisheries; Plankton; Microbiology; Benthos.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00332/44313/43879.pdf
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Marinilactibacillus piezotolerans sp nov., a novel marine lactic acid bacterium isolated from deep sub-seafloor sediment of the Nankai Trough ArchiMer
Toffin, Laurent; Zink, Klaus; Kato, Chiaki; Pignet, Patricia; Bidault, Adeline; Bienvenu, Nadège; Birrien, Jean-louis; Prieur, Daniel.
A piezotolerant, mesophilic, marine lactic acid bacterium (strain LT20(T)) was isolated from a deep sub-seafloor sediment core collected at Nankai Trough, off the coast of Japan. Cells were Gram-positive, rod-shaped, non-sporulating and non-motile. The NaGl concentration range for growth was 0-120 gl(-1), with the optimum at 10-20 g l(-1). The temperature range for growth at PH 7.0 was 4-50 degreesC, with the optimum at 37-40 degreesC. The optimum pH for growth was 7.0-8.0. The optimum pressure for growth was 0.1 MPa with tolerance up to 30 MPa. The main cellular phospholipids were phosphatidylglycerols (25 %), diphosphatidylglycerols (34 %) and a group of compounds tentatively identified as ammonium-containing phosphatidylserines (32 %);...
Tipo: Text Palavras-chave: Phylogeny; Biochemistry; Microbiology; Thermophilic bacteria; Deep sub seafloor sediment.
Ano: 2005 URL: http://archimer.ifremer.fr/doc/2005/publication-592.pdf
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Quality assessment of ice-stored tropical yellowfin tuna (Thunnus albacares) and influence of vacuum and modified atmosphere packaging ArchiMer
Dauchy Silbande, Adele; Adenet, Sandra; Smith-ravin, Juliette; Joffraud, Jean-jacques; Rochefort, Katia; Leroi, Francoise.
Metagenomic, microbial, chemical and sensory analyses of Thunnus albacares from Martinique and stored in ice (AIR – 0 °C), vacuum (VP – 4/8 °C) and modified atmosphere packaging (MAP – 4/8 °C) (70% CO2 – 30% O2) were carried out. The organoleptic rejection of AIR tuna was observed at day 13 when total bacterial counts equaled 106–107 CFU g−1. No extension of shelf-life was provided by VP and MAP. According to 16S rRNA gene sequence analyzed by Illumina MiSeq and PCR-TTGE, Rhodanobacter terrae was the main species of the freshly caught tuna. At the sensory rejection time, Brochothrix thermosphacta and Pseudomonas dominated the AIR products while B. thermosphacta alone or a mix of B. thermosphacta, Enterobacteriaceae and lactic acid bacteria (LAB) dominated...
Tipo: Text Palavras-chave: Seafood; Fish; Microbiology; Sensory; NGS; 16S rRNA gene.
Ano: 2016 URL: https://archimer.ifremer.fr/doc/00344/45504/45056.pdf
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Surveillance Ecologique du site du Blayais - Année 2014 ArchiMer
Quintin, Jean-yves; Sottolichio, Aldo; Derriennic, Herve; Schmidt, Sabine; Doremus, Sandrine; Agion, Tony; Hervio Heath, Dominique; Sautour, Benoît; Parra, René; Dindinaud, François; Bachelet, Guy; Leconte, Michel.
Monitoring n° 37 of the BLAYAIS nuclear power plant takes into account studies conducted between April and November 2014. Physicochemistry, Bathymetry, Contaminants, Bacteriology, Zooplankton, Benthic macrofauna, are reported.
Tipo: Text Palavras-chave: Centrale nucléaire; Pelagos; Physico chimie; Hydrologie; Microbiologie; Zooplancton; Macrofaune benthique.; Bathymétrie; Estuaire de la Gironde; Surveillance; Nuclear power plant; Pelagos; Physico chemistry; Hydrology; Zooplankton; Benthic macrofauna.; Bathymetry; Microbiology; Gironde estuary; Monitoring.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00333/44424/44088.pdf
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Evaluation de la qualité des zones de production conchylicole : Département : Gironde - Edition 2006 ArchiMer
Cantin, Christian; Neaud-masson, Nadine; Mayeur, Didier.
After a reminder of the objectives, operation and method of interpreting the results of the REMI microbiological monitoring network, this report establishes a national assessment and describes the annual programme of the Gironde region. It presents all of the results obtained, in particular the assessment of the quality of listed shellfish production areas and the evolution of their quality.
Tipo: Text Palavras-chave: Escherichia coli; Contamination; Microbiology; Environment quality; Shellfish culture; Département de la Gironde; Classement sanitaire des zones de production; Contamination bactériologique des coquillages; Escherichia coli; REMI.
Ano: 2006 URL: http://archimer.ifremer.fr/doc/2006/rapport-2102.pdf
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Surveillance écologique et halieutique du site de production électronucléaire de Gravelines Novembre 2007 – Octobre 2008 ArchiMer
Antajan, Elvire; Delesmont, Régis; Dewarumez, Jean-marie; Lefebvre, Alain; Luczak, Christophe; Warembourg, Caroline.
This is the 31th annual surveillance report concerning the nuclear power plant of Gravelines. Its very high power level results from six plant units located on the shore and is characterised by a cooling system with a coastal surface input and output. The production of electricity began in 1980 and reached maximum in 1986. Surveillance studies concern monitoring of fish populations (larvae and eggs of Sole and Sprat) or crustaceans (shrimps), benthic system (intertidal and subtidal) and pelagic system (hydrology, microbiology, phytoplankton, zooplankton). This survey deals with spatial and temporal approaches (i) study of the direct impact by comparison of the input and output seawater stations, (ii) study of medium and long term evolution of the area by...
Tipo: Text Palavras-chave: Centrale nucléaire; Gravelines; Surveillance; Hydrologie; Halieutique; Plancton; Benthos; Microbiologie; Nuclear power plant; Gravelines; Network survey; Hydrology; Fisheries; Plankton; Microbiology; Benthos.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/00055/16591/14098.pdf
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Shewanella profunda sp nov., isolated from deep marine sediment of the Nankai Trough ArchiMer
Toffin, Laurent; Bidault, Adeline; Pignet, Patricia; Tindall, Brian; Slobodkin, Alexander; Kato, Chiaki; Prieur, Daniel.
A novel piezotolerant, mesophilic, facultatively anaerobic, organotrophic, polarly flagellated bacterium (strain LT13a(T)) was isolated from a deep sediment layer in the Nankai Trough (Leg 190, Ocean Drilling Program) off the coast of Japan. This organism used a wide range of organic substrates as sole carbon and energy sources: pyruvate, glutamate, succinate, fumarate, lactate, citrate, peptone and tryptone. Oxygen, nitrate, fumarate, ferric iron and cystine were used as electron acceptors. Maximal growth rates were observed at a hydrostatic pressure of 10 MPa. Hydrostatic pressure for growth was in the range 0.1-50 MPa. Predominant cellular fatty acids were 16:1 omega7c, 15: 0 iso, 16: 0 and 13: 0 iso. The G + C content of the DNA was 44.9 mol%. On the...
Tipo: Text Palavras-chave: Phylogeny; Bacteria; Microbiology; Deep sediment layer.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/2004/publication-590.pdf
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DNA Checkerboard Method for Bacterial Pathogen Identification in Oral Diseases International Journal of Morphology
Nascimento,Cássio do; Issa,João Paulo Mardegan; Watanabe,Evandro; Ito,Izabel Yoko.
This work aim to show by literature review the principal characteristics of the DNA checkerboard method for bacterial pathogens identification in oral diseases, showing the most varieties uses and applications of this technique
Tipo: Journal article Palavras-chave: DNA Checkerboard; DNA probes; Microbiology; Bacteria.
Ano: 2006 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-95022006000500017
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Bacterial biofilms with emphasis on coagulase-negative staphylococci J. Venom. Anim. Toxins incl. Trop. Dis.
Oliveira,A; Cunha,MLRS.
In addition to their capacity to attach to surfaces, various groups of microorganisms also produce an extracellular polymeric substance known as "slime". This slime forms a thin layer around cells known as biofilm. Thus, biofilm structure comprises bacterial cells and an extracellular polymeric substance. It also presents a defined architecture, providing the microorganisms with an excellent protective environment and favoring the exchange of genetic material between cells as well as intercellular communication. The ability to produce biofilm is observed in a large group of bacteria, including coagulase-negative staphylococci (CNS) which are the predominant microorganisms of normal skin flora and have been implicated as the causative agents of hospital...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Coagulase-negative staphylococci; Biofilm; Slime; Infection; Microbiology.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1678-91992008000400003
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Genome Replikin Count Predicts Increased Lethality of Resistant Tuberculosis Nature Precedings
Samuel Bogoch; Elenore S. Bogoch.
The genomic Replikin Count of all the sequences on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7141/version/1
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2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/2
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How gut sampling and microbial invasiveness/noninvasiveness provides mucosal immunity with a nonmolecular pattern means to distinguish commensals from pathogens: A review Nature Precedings
John R. Skoyles.
Mucosal immunity distinguishes not only different microbial antigens but also separates those of pathogens from those of commensals. How this is done is unknown. The present view is that the pathogen/commensal determination of antigens depends upon as yet to be discovered molecular patterns. Here I review the biological feasibility that it also involves the detection of the invasive differences in their motility towards the gut wall when they are sampled by differently biased methods. 

By their nature, pathogens and commensals have different motility – invasive and noninvasive – in regard to the epithelium. The immune system is in a position to detect such motility differences. This biological...
Tipo: Manuscript Palavras-chave: Immunology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/1895/version/1
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HP-23: Co-ordinated Regulation of Gene Expression in H. Pylori in Response to Low pH and Iron Limiting Growth Conditions Nature Precedings
Ananya Gupta; Sergey Ustinov; Kaveh Mashayekhi; Anthony P. Moran.
Establishing a successful infection within the gastric environment and its varied and changing niches requires adaptation achieved through regulation of bacterial gene expression. In the gastric environment in addition to the low pH Helicobacter pylori is required to adapt to conditions of iron limitation. In this study, we used cDNA microarrays to identify genes whose expression was altered when the bacterium was grown under differing conditions of pH (5 versus 7) and iron limitation. cDNA microarray analyses following exposure to different growth conditions were carried out for three H. pylori strains 26695 (gastritis-associated), J99 (ulcer-associated) and AG-1 (atrophic gastritis-associated). Genes were identified whose expression was acid pH-dependent...
Tipo: Poster Palavras-chave: Microbiology.
Ano: 2011 URL: http://precedings.nature.com/documents/5842/version/1
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The Human Virome in Children and its Relationship to Febrile Illness Nature Precedings
Gregory A. Storch; George M. Weinstock; Erica J. Sodergren; Kristine M. Wylie; Max Q. Arens; Richard S. Buller; David M. Jaffe; Jared T. Muenzer.
This study investigates the relationship of viruses to febrile illness in children. Subjects are normal children 2-36 months of age with fever along with normal children of the same age without fever, plus immunocompromised children with fever along with immunocompromised children without fever. Specimens obtained include blood, nasopharyngeal secretions, and feces. Specimens are analyzed using a panel of virus-specific PCR assays and also by high throughput sequencing using 454 and Illumina platforms.
Tipo: Marker Paper / Data Plan Palavras-chave: Biotechnology; Microbiology; Data Standards.
Ano: 2010 URL: http://precedings.nature.com/documents/5319/version/1
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Keratinocytes from human skin respond as typical immune cells after the stimulation with _Trichophyton rubrum_ Nature Precedings
Alfonso E. Islas-Rodríguez; Luz A. García-Madrid.
_Trichophyton rubrum_ is the main agent causing dermatophytosis (1). Keratinocytes are
considered to be the first physical barrier of defense against pathogens (2). But not
only a physical barrier. They recognize antigens through Toll like receptors (TLR) (3).
The activation of this TLR, present on the surface of the keratinocytes, induce the
expression of different pro-inflammatory cytokines, co-stimulatory molecules and
antimicrobial peptides such as [beta]-defensins (4).
The main objective of this work is to determine if lipopolysaccharides of G – bacteria
(LPS), lipotheichoic acid from G+ bacteria (LTA), and conidias,...
Tipo: Manuscript Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/930/version/1
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Is the innate bio-protection power against human virus the same between males and females? A conclusion based on blood donor data of HTLV-I infection and case data of infectious diseases Nature Precedings
Nobuoki Eshima; Minoru Tabata; Yasunori Higuchi; Shigeru Karukaya.
Human T-cell leukemia virus type I (HTLV-I) is a retrovirus that causes adult T-cell leukemia. The male-to-female transmission is stronger than the reverse, so the carrier proportion of women is greater than that of men. On the other hand, since the mother-to-child transmission route via the breast-feeding is common for baby boys and girls, it has been thought the HTLV-I proportions of boys and girls are the same until now. A question arises as to whether the ‘innate protection powers against human virus’ are the same between males and females. We utilize HTLV-I infection blood donor data in 1995-1998 and case data of main infectious diseases such as influenza, mumps, herpangina, hand-hoot-and-mouse disease, chicken pox, etc. Blood...
Tipo: Manuscript Palavras-chave: Cancer; Immunology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/1987/version/2
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DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences Nature Precedings
Xiaolong Wang; Shuang-yong Xu; Deming Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4898/version/1
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Expression profile of genes involved in hydrogen sulphide liberation by _Saccharomyces cerevisiae_ grown under different nitrogen concentrations Nature Precedings
Ana Mendes-Ferreira; Catarina Barbosa; Marcel.lí del Olmo; Arlete Mendes-Faia; Cecília Leão.
The present work aims to elucidate molecular mechanisms underlying hydrogen sulphide production in _S. cerevisiae_ associated to nitrogen deficiency. To assess, at a genome-wide level, how the yeast strain adapted to the progressive nitrogen depletion and to nitrogen re-feeding, gene expression profiles were evaluated during fermentation at different nitrogen concentrations, using the DNA array technology. The results showed that most MET genes displayed higher expression values at the beginning of both control and N-limiting fermentation, just before the time at which the release of sulphide was observed. MET genes were downregulated when yeast stopped growing which could associate MET gene expression levels with cell growth. The over expression of MET...
Tipo: Poster Palavras-chave: Biotechnology; Microbiology.
Ano: 2008 URL: http://precedings.nature.com/documents/2736/version/1
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Ecological, phenological and biochemical significance of bimodal fruiting of Boletus alutaceus morgan Nature Precedings
Nandkumar Kamat.
Boletus alutaceus Morgan an ectomycorrhizal species was extensively studied from an ecologically fragmented microhabitt colonized by its' host plant Ficus benghalensis L. in the Goa University campus, Taleigao, Goa, India. Qualitatively the fruiting cycles were monitored for three years and thereafter detail ecological and morphological investigations were carried out in May and November 2004. A bimodal temporal fruting pattern emerged which may have significant ecological, phenological and biochemical role in EM dynamics.
Tipo: Presentation Palavras-chave: Biotechnology; Developmental Biology; Ecology; Genetics & Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2009 URL: http://precedings.nature.com/documents/2835/version/1
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Stomatin-like Protein 2 Links Mitochondria to T-Cell Receptor Signalosomes at the Immunological Synapse and Enhances T-Cell Activation Nature Precedings
Mark G. Kirchhof; Luan A. Chau; Caitlin D. Lemke; Santosh Vardhana; Peter J. Darlington; Maria E. Marquez; Roy Taylor; Kamilia Rizkalla; Isaac Blaca; Michael L. Dustin; Joaquin Madrenas.
T cell activation through the antigen receptor (TCR) requires sustained signalling from microclusters in the peripheral region of the immunological synapse (IS). The bioenergetics of such prolonged signaling have been linked to the redistribution of mitochondria to the IS. Here, we report that stomatin-like protein-2 (SLP-2) plays an important role in this process by bridging polarized mitochondria to these signaling TCR microclusters or signalosomes in the IS in a polymerized actin-dependent manner. In this way, SLP-2 helps to sustain TCR-dependent signalling and enhances T cell activation.
Tipo: Manuscript Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/1068/version/1
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