Deferribacter autotrophicus sp. nov., an iron(III)-reducing bacterium from a deep-sea hydrothermal vent

En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2009/publication-6598.pdfInternational audienceA thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50(T)) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) at a depth of 4100 m. Cells of strain SL50(T) were motile, straight to bent rods with one polar flagellum, 0.5-0.6 mum in width and 3.0-3.5 mum in length. The temperature range for growth was 25-75 degrees C, with an optimum at 60 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.5. Growth of strain SL50(T) was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50(T) was 60 min. Strain SL50(T) used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50(T) was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50(T) was Deferribacter abyssi JR(T) (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50(T) (=DSM 21529(T)=VKPM B-10097(T)). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO(2) as the carbon source

Observation of time quasicrystal and its transition to superfluid time crystal

We report experimental realization of a quantum time quasicrystal, and its transformation to a quantum time crystal. We study Bose-Einstein condensation of magnons, associated with coherent spin precession, created in a flexible trap in superfluid $^3$He-B. Under a periodic drive with an oscillating magnetic field, the coherent spin precession is stabilized at a frequency smaller than that of the drive, demonstrating spontaneous breaking of discrete time translation symmetry. The induced precession frequency is incommensurate with the drive, and hence the obtained state is a time quasicrystal. When the drive is turned off, the self-sustained coherent precession lives a macroscopically-long time, now representing a time crystal with broken symmetry with respect to continuous time translations. Additionally, the magnon condensate manifests spin superfluidity, justifying calling the obtained state a time supersolid or a time super-crystal

Resistive and magnetoresistive properties of CrO2 pressed powders with different types of inter-granular dielectric layers

Resistive, magnetoresistive and magnetic properties of four kinds of pressed CrO2 powders, synthesized by hydrothermal method of chromic anhydride have been investigated. The particles in powders constituted of rounded particles (diameter 120 nm) or needle-shaped crystals with an average diameter of 22.9 nm and average length of 302 nm. All of the particles had a surface dielectric shell of varying thickness and different types (such as oxyhydroxide -CrOOH or chromium oxide Cr2O3). For all the samples at low temperatures we found non-metallic temperature dependence of resistivity and giant negative magnetoresistance (MR). The maximum value of MR at low temperatures (T \approx 5 K) is \approx 37% in relatively small fields (0.5 T). At higher temperatures there was a rapid decrease of MR (up to \approx 1% / T at T \approx 200 K). The main objective of this work was studying the influence of properties and thickness of the intergranular dielectric layers, as well as CrO2 particle shape, on the magnitude of the tunneling resistance and MR of the pressed powder. The new results obtained in this study include: (1) detection at low temperatures in powders with needle-like particles a new type of MR hysteresis, and nonmonotonic MR behaviour with increasing magnetic field (absolute value of the MR at first grows rather rapidly with the field, and then begins diminishing markedly, forming a maximum), and (2) detection of non-monotonic temperature dependence, where - a field in which the resistance in a magnetic field has a maximum, as well as finding discrepancies in values of and coercivity fields, (3) detection of the anisotropy of MR, depending on the relative orientation of the transport current and the magnetic field, (4) a new method of synthesis, to regulate the thickness of dielectric coating.Comment: 19 pages, 8 figure

YARN begins

В статье представлен проект создания большого открытого тезауруса русского языка YARN (Yet Another RussNet). Основная особенность проекта — использование wiki-подхода к наполнению и редактированию ресурса. В статье описаны лингвистические принципы создания тезауруса YARN, формат данных, а также ближайшие практические шаги, которые планируется предпринять в рамках проекта.YARN (Yet Another RussNet) is a work-in-progress on development of a large and open WordNet-like thesaurus for Russian. The paper reports on linguistic design, development and organizational principles, and interchange format of YARN.Исследование осуществляется при финансовой поддержке РГНФ (проект № 13-04-12020 «Новый открытый электронный тезаурус русского языка»). Мы благодарим участников группы yarn_org за активность, замечания и предложения. Работа Андрея Крижановского выполнена при частичной финансовой поддержке РФФИ (проект № 11-01-00251, № 12-01-00481, № 12-07-00070) и РГНФ (проект № 12-04-12062). Работа Ольги Ляшевской и Анастасии Бонч-Осмоловской отражает результаты исследований, проведенных при поддержке Программы фундаментальных исследований НИУ Высшая школа экономики (2013), проект «Корпусные технологии в лингвистических и междисциплинарных исследованиях». Павел Браславский благодарит группу разработчиков GermaNet под руководством проф. Эрхарда Хинрихса из университета Тюбингена за гостеприимство, плодотворное обсуждение проекта и обмен опытом, а также MUMIA Network30 за финансовую поддержку визита в Тюбинген в рамках программы Short Term Scientific Missions (STSM)

Optimization of intravascular volume determination in patients with acute decompensated heart failure

Acute decompensated heart failure (ADHF) is based on multilevel pathological pathways, which include hemodynamic overload and venous stasis. Determination of the volemic status is one of the most important tasks in managing such patients. Despite the availability of modern diagnostic markers (physical examination, chest x-ray, and brain natriuretic peptide (BNP) assessment), they do not accurately assess the degree of fluid overload, and therefore there remains a need to find a new, accurate and simple technology for assessing pulmonary congestion. The urgency of this problem has led to the development of a novel non-invasive remote dielectric sensing (ReDS) technology, which is a quantitative method for measuring the total volume of lung fluid by determining the tissue dielectric properties. The use of this technology makes it possible to quickly, non-invasively and quantitatively measure the fluid content in the lungs, makes it possible to optimize the treatment regimen and reduces the number of readmissions. This article presents the results of studies on the efficacy, safety and prospects for using a ReDS technology for the quantitative measurement of total lung fluid in patients with ADHF

Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism

Dissimilatory sulfate reduction (DSR)—an important reaction in the biogeochemical sulfur cycle—has been dated to the Palaeoarchaean using geological evidence, but its evolutionary history is poorly understood. Several lineages of bacteria carry out DSR, but in archaea only Archaeoglobus, which acquired DSR genes from bacteria, has been proven to catalyse this reaction. We investigated substantial rates of sulfate reduction in acidic hyperthermal terrestrial springs of the Kamchatka Peninsula and attributed DSR in this environment to Crenarchaeota in the Vulcanisaeta genus. Community profiling, coupled with radioisotope and growth experiments and proteomics, confirmed DSR by ‘Candidatus Vulcanisaeta moutnovskia’, which has all of the required genes. Other cultivated Thermoproteaceae were briefly reported to use sulfate for respiration but we were unable to detect DSR in these isolates. Phylogenetic studies suggest that DSR is rare in archaea and that it originated in Vulcanisaeta, independent of Archaeoglobus, by separate acquisition of qmoABC genes phylogenetically related to bacterial hdrA genes.This work was supported by the Russian Science Foundation (grant number 17-74-30025) and in part by the grant from the Russian Ministry of Science and Higher Education (to N.A.C., A.V.L., E.N.F., M.L.M., A.Y.M., N.V.P. and E.A.B.-O.). Sequencing of PCR amplicons was performed using the scientific equipment of the core research facility ‘Bioengineering’ by T. Kolganova. The proteomics analysis was performed at the Proteomics Facility of the Spanish National Center for Biotechnology (CNB-CSIC), which belongs to ProteoRed, PRB2-ISCIII, supported by grant PT13/0001 (to S.C., M.C.M. and M.F.). P.N.G. acknowledges funding from the UK Biotechnology and Biological Sciences Research Council (BBSRC) within the ERA NET-IB2 programme, grant number ERA-IB-14-030 and the European Union Horizon 2020 Research and Innovation programme (Blue Growth: Unlocking the Potential of Seas and Oceans) under grant agreement number 634486, as well as support from the Centre for Environmental Biotechnology project, part funded by the European Regional Development Fund (ERDF) through the Welsh Government, and support from the Centre of Environmental Biotechnology. D.Y.S. was supported by the SIAM/Gravitation Program (Dutch Ministry of Education, Culture and Science; grant 24002002) and RFBR grant 19-04-00401. F.L.S. and S.N. acknowledge support from the Wiener Wissenschafts, Forschungs- und Technologiefonds (Austria) through the grant VRG15-007. F.L.S. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation programme (grant agreement 803768). I.A.C.P. acknowledges support from the Fundação para a Ciência e Tecnologia (Portugal) through grant PTDC/BIA-BQM/29118/2017 and R&D unit MOSTMICRO-ITQB (UIDB/04612/2020 and UIDP/04612/2020)

Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota

The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231. OS and MSG were supported by the Russian Science Foundation (RSF, grant 14-24-00155). EB-O and SG were supported by the RSF grant 14-24-00165. IK, NC, AL, and MM were supported by the Russian Foundation for Basic Research grant 14-04-00503.http://www.frontiersin.orgam2017Biochemistr

Molecular Detection of Anaerobic Ammonium-Oxidizing (Anammox) Bacteria in High-Temperature Petroleum Reservoirs

Anaerobic ammonium-oxidizing (anammox) process plays an important role in the nitrogen cycle of the worldwide anoxic and mesophilic habitats. Recently, the existence and activity of anammox bacteria have been detected in some thermophilic environments, but their existence in the geothermal subterranean oil reservoirs is still not reported. This study investigated the abundance, distribution and functional diversity of anammox bacteria in nine out of 17 high-temperature oil reservoirs by molecular ecology analysis. High concentration (5.31–39.2 mg l−1) of ammonium was detected in the production water from these oilfields with temperatures between 55°C and 75°C. Both 16S rRNA and hzo molecular biomarkers indicated the occurrence of anammox bacteria in nine out of 17 samples. Most of 16S rRNA gene phylotypes are closely related to the known anammox bacterial genera Candidatus Brocadia, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia, while hzo gene phylotypes are closely related to the genera Candidatus Anammoxoglobus, Candidatus Kuenenia, Candidatus Scalindua, and Candidatus Jettenia. The total bacterial and anammox bacterial densities were 6.4 ± 0.5 × 103 to 2.0 ± 0.18 × 106 cells ml−1 and 6.6 ± 0.51 × 102 to 4.9 ± 0.36 × 104 cell ml−1, respectively. The cluster I of 16S rRNA gene sequences showed distant identity (<92%) to the known Candidatus Scalindua species, inferring this cluster of anammox bacteria to be a new species, and a tentative name Candidatus “Scalindua sinooilfield” was proposed. The results extended the existence of anammox bacteria to the high-temperature oil reservoirs

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)