Applying FAIR Principles to plant phenotypic data management in GnpIS

GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems

Denitrification likely catalyzed by endobionts in an allogromiid foraminifer

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 6 (2012): 951–960, doi:10.1038/ismej.2011.171.Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N2) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear and it is possible that the ability to perform complete denitrification is due to symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. These associations may have been a driving force for early foraminiferal diversification, which is thought to have occurred in the Neoproterozoic when anoxia was widespread.This research was supported by NSF grant EF-0702491 to JMB, KLC and VPE; some ship support was provided by NSF MCB-0604084 to VPE and JMB.2012-06-0

Characterisation of the mcpA and mcpB genes capable of encoding methyl-accepting type chemoreceptors in Rhodobacter capsulatus

Two contiguous mcp genes, mcpA and mcpB, transcribed from the same DNA strand and capable of encoding methyl-accepting chemotaxis proteins (Mcp) have been isolated from Rhodobacter capsulatus (Re), sequenced and overexpressed in Escherichia coli (Ec). The deduced proteins (McpA, 69171 Da; McpB, 81629 Da) show a structure similar to that of Ec Mcp. The products of mcpA and mcpB, overproduced in Ec, were recognized by anti-Ec Mcp (Trg) antibodies

Bacterial biogas production in coastal systems affected by freshwater inputs

International audienc

Denitrification activity is closely linked to the total ambient Fe concentration in mangrove sediments of Goa, India

International audienceDenitrification activity (DNT) and associated environmental parameters were examined in two mangrove ecosystems of Goa, India e the relatively unimpacted Tuvem and the anthropogenically-influenced Divar. Sampling was carried out at every 2 cm interval within the 0-10 cm depth range to determine (1) seasonal (pre-monsoon, monsoon and post-monsoon) down-core variation in DNT (2) assess the environmental factors influencing the DNT and (3) to build predictive models for benthic DNT. Denitrification generally decreased with depth and showed marked seasonal variation at both the locations. Denitrification peaked during the pre-monsoon occurring at a rate of up to 21.00- 12.84 nmol N2O /g h within 0-4 cm at both the locations. Further, DNT at pre-monsoon was significantly influenced by Fe content at Tuvem and Divar suggesting Fe-mediated nitrate respiration. The influence of other limiting substrates such as NO3 and NO2 was most important during the monsoon and post-monsoon especially at Divar. The multiple regression models developed could predict 67-98% of the observed variability inDNT through the seasons. About 6-9 environmental variables were required to relatively well-predict DNT in these sediments with the complexity governing DNT decreasing from pre-monsoon to postmonsoon. Our results reveal that seasonal dynamics of DNT in tropical mangrove sediments are closely linked to the total Fe at the prevailing ambient concentration in both the system

Denitrification prevails over anammox in tropical mangrove sediments (Goa, India)

Denitrification, anammox (Anx) and di-nitrogen fixation were examined in two mangrove ecosystemsthe anthropogenically influenced Divar and the relatively pristine Tuvem. Stratified sampling at 2 cm increments from 0 to 10 cm depth revealed denitrification as the main process of N-2 production in mangrove sediments. At Divar, denitrification was similar to 3 times higher than at Tuvem with maximum activity of 224.51 +/- 6.63 nmol N-2 g(-1) h(-1) at 0-2 cm. Denitrifying genes (nosZ) numbered up to 2 x 10(7) copies g(-1) sediment and belonged to uncultured microorganisms clustering within Proteobacteria. Anammox was more prominent at deeper depths (8-10 cm) mainly in Divar with highest activity of 101.15 +/- 87.73 nmol N-2 g(-1) h(-1) which was 5 times higher than at Tuvem. Di-nitrogen fixation was detected only at Tuvem with a maximum of 12.47 +/- 8.36 nmol N-2 g(-1) h(-1). Thus, in these estuarine habitats prone to high nutrient input, N-2-fixation is minimal and denitrification rather than Anx serves as an important mechanism for counteracting N loading. (C) 2011 Elsevier Ltd. All rights reserved

Proton magnetic resonance neurospectroscopy and EEG cartography in corticobasal degeneration: correlations with neuropsychological signs

Methods: Eight patients with probable CBD were included in the study after full neurological examination and extensive neuropsychological testing, single photon emission computed tomography, anatomical x ray tomodensitometry (TDM), magnetic resonance imaging, and MRS examination. Results: MR spectra were abnormal in all seven patients in whom the examination could be completed. The EEG was also always modified in the CBD patients, and the abnormalities were enhanced by activation procedures. There was a good correlation between MRS anomalies and clinical presentation, between EEG modifications and neuropsychological patterns, and between metabolic (MRS) impairment and electrophysiological (EEG) slowing. Conclusions: These results confirm the asymmetrical features of CBD. Combined EEGq/MRS examinations at disease onset and during its subsequent course could provide strong diagnostic evidence of CBD

Caldinitratiruptor microaerophilus, gen. nov., sp. nov. isolated from a French hot spring (Chaudes-Aigues, Massif Central) : a novel cultivated facultative microaerophilic anaerobic thermophile pertaining to the Symbiobacterium branch within the Firmicutes

A novel facultative microaerophilic nitrate-reducing bacterium designated CA62N(T) was isolated from a thermal spring in France. Cells were non-motile rods (2-3 x 0.2 mu m) and showed low cytoplasmic density when observed under a phase-contrast microscope. Strain CA62N(T) grew at temperatures between 50 and 75A degrees C (optimum 65A degrees C) and at a pH between 6.3 and 7.9 (optimum 7.0). NaCl was not required for growth but was tolerated up to 10 gl(-1). Sulfate, thiosulfate, elemental sulfur, sulfite, and nitrite were not used as electron acceptors. Nitrate was reduced to nitrite. Strain CA62N(T) used lactate, pyruvate, glucose, mannose, fructose, and casamino acids and some amino acids as electron donors only in the presence of nitrate as electron acceptor. None of these substrates was fermented. The main end-products of glucose oxidation were acetate, CO2, and traces of H-2. The G + C content of the genomic DNA was 70.3 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit (SSU) ribosomal RNA (rRNA) gene sequence indicated that strain CA62N(T) was affiliated to the Symbiobacterium branch within the Firmicutes and had Symbiobacterium thermophilum and "S. toebii" as its closest phylogenetic relatives. On the basis of phylogenetical and physiological characteristics, strain CA62N(T) is proposed to be the type strain for the novel species in the novel genus, Caldinitratiruptor microaerophilus gen. nov., sp. nov. (DSM 22660, JCM 16183)