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1.
Proc Natl Acad Sci U S A ; 119(3)2022 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-35022241

RESUMO

Decades of culture-independent analyses have resulted in proposals of many tentative archaeal phyla with no cultivable representative. Members of DPANN (an acronym of the names of the first included phyla Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanohaloarchaeota, and Nanoarchaeota), an archaeal superphylum composed of at least 10 of these tentative phyla, are generally considered obligate symbionts dependent on other microorganisms. While many draft/complete genome sequences of DPANN archaea are available and their biological functions have been considerably predicted, only a few examples of their successful laboratory cultivation have been reported, limiting our knowledge of their symbiotic lifestyles. Here, we investigated physiology, morphology, and host specificity of an archaeon of the phylum "Candidatus Micrarchaeota" (ARM-1) belonging to the DPANN superphylum by cultivation. We constructed a stable coculture system composed of ARM-1 and its original host Metallosphaera sp. AS-7 belonging to the order Sulfolobales Further host-switching experiments confirmed that ARM-1 grew on five different archaeal species from three genera-Metallosphaera, Acidianus, and Saccharolobus-originating from geologically distinct hot, acidic environments. The results suggested the existence of DPANN archaea that can grow by relying on a range of hosts. Genomic analyses showed inferred metabolic capabilities, common/unique genetic contents of ARM-1 among cultivated micrarchaeal representatives, and the possibility of horizontal gene transfer between ARM-1 and members of the order Sulfolobales Our report sheds light on the symbiotic lifestyles of DPANN archaea and will contribute to the elucidation of their biological/ecological functions.


Assuntos
Archaea/genética , Archaea/fisiologia , Genoma Arqueal , Simbiose/genética , Simbiose/fisiologia , Archaea/classificação , Archaea/citologia , Técnicas de Cocultura , Evolução Molecular , Transferência Genética Horizontal , Genômica , Nanoarchaeota , Filogenia
2.
J Bacteriol ; 206(2): e0035123, 2024 02 22.
Artigo em Inglês | MEDLINE | ID: mdl-38289045

RESUMO

The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeon Nanobdella aerobiophila strain MJ1T and its host Metallosphaera sedula strain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy, quick-freeze deep-etch TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1T were different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1T gene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1T and MJ1HA were motile, but sole MJ1T cells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila.IMPORTANCEDPANN archaea are widely distributed in a variety of natural and artificial environments and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon, Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics, including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle of Nanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.


Assuntos
Archaea , Archaea/genética , Genoma Arqueal , Genômica , Filogenia
3.
J Biol Chem ; 299(10): 105191, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37625588

RESUMO

Both the biogenesis and functions of osteoclasts and macrophages involves dynamic membrane traffic. We screened transcript levels for Rab family small GTPases related to osteoclasts and identified Rab38. Rab38 expression is upregulated during osteoclast differentiation and maturation. In osteoclasts, both Rab38 and its paralog, Rab32, colocalize to lysosome-related organelles (LROs). In macrophages, Rab32 is also found in LROs. LROs are part of the endocytic pathway but are distinct from lysosomes. After receptor activator of NF-κB ligand stimulation, LROs contain cathepsin K and tartrate-resistant acid phosphatase inside and help both proteins to accumulate around bone resorption pits. After osteoclast maturation, these enzymes are hardly found within LROs. In macrophages derived from Rab32 and Rab38 double knockout mice, both acidification and V-ATPase a3 localization were severely compromised. Both the double knockout macrophage and bafilomycin-treated wildtype macrophage show an increase in Lamp1-positive organelles, implying that biogenesis of lysosomes and LROs are related. These results indicate that Rab32 and Rab38 both play a crucial role in LRO biogenesis in macrophages and in osteoclasts.

4.
Chemistry ; 30(7): e202303908, 2024 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-38036463

RESUMO

Ion-endohedral-fullerene has attracted growing interest due to the unique electronic and structural characteristics arising from its distinctive ionic nature. Although there has been only one reported ion-encapsulated fullerene, Li+ @C60 , a significant number of fundamental and applied studies have been conducted, making a substantial impact not only in chemistry and physics but also across various interdisciplinary research fields. Nevertheless, studies on ion-endohedral fullerenes are still in their infancy due to the limitations in variety, and hence, it remains an open question how the size and symmetry of fullerene, as well as the motion and position of the encapsulated ion, affect their physical/chemical properties. Herein, we report the synthesis of lithium-ion-endohedral [70]fullerene (Li+ @C70 X- , X=PF6 - and TFSI- ), a novel ionic endohedral fullerene. X-ray crystallography confirmed the encapsulation of Li+ by C70 cage as well as its ion-pair structure stabilized by external TFSI- counter anion. The encapsulated Li+ drastically lowered the orbital energy of the C70 cage by Coulomb interactions but did not affect the orbital energy gap and degeneracy. DFT studies were also performed, which supported the experimentally observed electronic effects caused by the encapsulated Li+ .

5.
Artigo em Inglês | MEDLINE | ID: mdl-38922322

RESUMO

A neutrophilic iron-oxidizing and -reducing bacterium, strain MIZ03T, was previously isolated from a wetland in Ibaraki, Japan. Here, we report the detailed characteristics of this strain. It was motile with a single polar flagellum, and Gram-stain-negative. It could grow not only chemolithoautotrophically but also chemoorganotrophically by aerobic respiration and fermentation. Major cellular fatty acids were C16 : 1 ω7c/C16 : 1 ω6c, and C16 : 0. Phylogenetic analyses indicated that strain MIZ03T belonged to the genus Rhodoferax. This strain was closely related to Rhodoferax ferrireducens with 98.5 % of 16S rRNA gene sequence similarity. Based on its phenotypic and genomic based characteristics, we conclude that strain MIZ03T represents a new species in the genus Rhodoferax. We propose the name Rhodoferax lithotrophicus sp. nov. to accommodate this strain. The type strain is MIZ03T (=JCM 34246T=DSM 113266T). We also propose the name Rhodoferax koreensis sp. nov., of which the type strain is DCY110T (=KCTC 52288T=JCM 31441T), for the effectively, but not yet validly, published name 'Rhodoferax koreense'.


Assuntos
Técnicas de Tipagem Bacteriana , DNA Bacteriano , Ácidos Graxos , Sedimentos Geológicos , Ferro , Oxirredução , Filogenia , RNA Ribossômico 16S , Análise de Sequência de DNA , RNA Ribossômico 16S/genética , Ferro/metabolismo , Sedimentos Geológicos/microbiologia , DNA Bacteriano/genética , Japão , Água Doce/microbiologia , Composição de Bases , Áreas Alagadas , Crescimento Quimioautotrófico
6.
Diabetes Obes Metab ; 26(7): 2761-2773, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38646845

RESUMO

AIMS: To evaluate the correlation between C-peptide index (CPI) at 2 h post-meal and endogenous insulin secretory capacity and to develop clinical models to predict the possibility of withdrawal from insulin therapy in patients with type 2 diabetes. METHOD: This was a single-centre retrospective study of patients with type 2 diabetes admitted to our hospital. Patients were divided into a withdrawal group (n = 72) and a non-withdrawal group (n = 75) based on whether they were able to withdraw from insulin therapy at discharge, and the correlation between CPI at 2 h after meal and diabetes-related parameters was evaluated. In addition, we created two clinical models to predict the possibility of withdrawal from insulin therapy using machine learning. RESULTS: The glycated haemoglobin values of the study participants were 87.8 ± 22.6 mmol/mo. The CPI at 2 h post-meal was 1.93 ± 1.28 in the non-withdrawal group and 2.97 ± 2.07 in the withdrawal group (p < 0.001). CPI at 2 h post-meal was an independent predictor of withdrawal from insulin therapy. In addition, CPI at 2 h post-meal was a better predictor than fasting CPI. Six factors associated with insulin therapy withdrawal (age, duration of diabetes, creatinine, alanine aminotransferase, insulin therapy until hospitalization, and CPI at 2 h post-meal) were used to generate two clinical models by machine learning. The accuracy of the generated clinical models ranged from 78.3% to 82.6%. CONCLUSION: The CPI at 2 h post-meal is a clinically useful measure of endogenous insulin secretory capacity under non-fasting conditions.


Assuntos
Peptídeo C , Diabetes Mellitus Tipo 2 , Hipoglicemiantes , Secreção de Insulina , Insulina , Período Pós-Prandial , Humanos , Diabetes Mellitus Tipo 2/tratamento farmacológico , Diabetes Mellitus Tipo 2/sangue , Masculino , Feminino , Pessoa de Meia-Idade , Estudos Retrospectivos , Peptídeo C/sangue , Insulina/uso terapêutico , Insulina/administração & dosagem , Idoso , Hipoglicemiantes/uso terapêutico , Hemoglobinas Glicadas/análise , Hemoglobinas Glicadas/metabolismo , Suspensão de Tratamento/estatística & dados numéricos , Aprendizado de Máquina , Refeições
7.
Endocr J ; 71(5): 481-488, 2024 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-38447977

RESUMO

Acute necrotizing esophagitis (ANE) is a rare and potentially life-threatening complication of diabetic ketoacidosis (DKA). While its association with DKA is established, specific clinical characteristics that predict ANE in DKA patients remain less understood. This study aimed to identify these characteristics by analyzing data from 30 DKA patients admitted from January 2018 to September 2022. Seven patients in this study presented with ANE, forming the ANE group. The remaining 23 constituted the non-ANE group. We compared the clinical parameters and computed tomography (CT) between the groups. The mean age of participants was 57.7 ± 20.4 years, and their mean HbA1c was 11.1 ± 3.3%. Notably, ethanol intake was significantly higher in the ANE group (44.4 ± 25.4 g/day) compared to the non-ANE group (6.8 ± 14.0 g/day; p = 0.013). Additionally, sodium-glucose transport protein 2 inhibitor use was significantly more prevalent in the ANE group (p = 0.013). Gastrointestinal symptoms were also significantly more pronounced in the ANE group, with vomiting occurring in 85.7% of patients compared to only 13.0% in the non-ANE group. Admission CT scans revealed further distinguishing features, with the ANE group showing significantly higher rates of esophageal wall thickening, intra-esophageal effusion, and calcification of the celiac artery origin (p < 0.0001, 0.0038, 0.0038, respectively). In conclusion, our study suggests that heavy alcohol consumption and strong gastrointestinal symptoms in DKA patients warrant a heightened suspicion of ANE. Early consideration of CT or upper gastrointestinal endoscopy is recommended in such cases.


Assuntos
Cetoacidose Diabética , Esofagite , Humanos , Cetoacidose Diabética/complicações , Pessoa de Meia-Idade , Feminino , Masculino , Esofagite/complicações , Esofagite/patologia , Adulto , Idoso , Tomografia Computadorizada por Raios X , Necrose , Estudos Retrospectivos , Doença Aguda
8.
Nucleic Acids Res ; 49(D1): D694-D705, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33119759

RESUMO

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.


Assuntos
Bases de Dados Genéticas , Genoma , Filogenia , Células Procarióticas/metabolismo , Pesquisa , Sequência de Bases , Análise de Dados , RNA Ribossômico 16S/genética
9.
Artigo em Inglês | MEDLINE | ID: mdl-35476601

RESUMO

A neutrophilic iron-oxidizing bacterium, strain MIZ01T, which was previously isolated from a wetland in Ibaraki, Japan, was taxonomically characterized in detail. Strain MIZ01T was a motile, curved-rod shaped, Gram-stain-negative bacterium. It was able to grow at 10-40 °C (optimally at 30-35 °C) and at pH 5.5-7.0 (optimally at pH 6.0). It grew microaerobically and chemolithoautotrophically using thiosulfate, in addition to ferrous iron, as the sole electron donor. Major cellular fatty acids of strain MIZ01T were C16 : 1 ω7c/C16 : 1 ω6c and C16 : 0. The complete genome sequence (2.74 Mbp) was determined, showing that its DNA G+C content was 60.0 mol%. Phylogenetic analyses indicated that strain MIZ01T belonged to the family Gallionellaceae, class Betaproteobacteria, and was closely related to an isolate tentatively named 'Sideroxydans lithotrophicus' ES-1 (98.2 % of 16S rRNA gene sequence similarity). Based on its phenotypic and phylogenetic characteristics, we conclude that strain MIZ01T represents a new genus and species in the family Gallionellaceae for which we propose the name Sideroxyarcus emersonii gen. nov., sp. nov. The type strain is strain MIZ01T (=JCM 39089T=DSM 111897T).


Assuntos
Tiossulfatos , Áreas Alagadas , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Ferro , Oxirredução , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
10.
Artigo em Inglês | MEDLINE | ID: mdl-35993221

RESUMO

A co-culture of a novel thermoacidophilic, obligate symbiotic archaeon, designated as strain MJ1T, with its specific host archaeon Metallosphaera sedula strain MJ1HA was obtained from a terrestrial hot spring in Japan. Strain MJ1T grew in the co-culture under aerobic conditions. Coccoid cells of strain MJ1T were 200-500 nm in diameter, and attached to the MJ1HA cells in the co-culture. The ranges and optima of the growth temperature and pH of strain MJ1T in the co-culture were 60-75 °C (optimum, 65-70 °C) and pH 1.0-4.0 (optimum, pH 2.5), respectively. Core lipids of dialkyl glycerol tetraethers (GDGT)-3 and GDGT-4 were highly abundant in MJ1T cells concentrated from the co-culture. Strain MJ1T has a small genome (0.67 Mbp) lacking genes for biosynthesis of essential biomolecules, such as nucleotides, lipids and ATP. The genomic DNA G+C content was 24.9 mol%. The 16S rRNA gene sequence of strain MJ1T was most closely related to that of the cultivated species, 'Nanopusillus acidilobi' strain N7A (85.8 % similarity). Based on phylogenetic and physiological characteristics, we propose the name Nanobdella aerobiophila gen. nov., sp. nov. to accommodate the strain MJ1T (=JCM 33616T=DSM 111728T). In addition, we propose the names Nanobdellaceae fam. nov., Nanobdellales ord. nov., and Nanobdellia class. nov. to accommodate the novel genus.


Assuntos
Archaea , Ácidos Graxos , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Artigo em Inglês | MEDLINE | ID: mdl-33295866

RESUMO

A thermoacidophilic, anaerobic, and iron- and sulfur-reducing archaeon, strain NAS-02T, was isolated from a terrestrial hot spring in Japan, as previously reported. This organism is the first non-ammonia-oxidizing isolate in the phylum Thaumarchaeota. Here, we propose Conexivisphaera calida gen. nov., sp. nov. to accommodate this strain. The type strain of the type species is NAS-02T (=JCM 31663T=DSM 105898T). The values of 16S rRNA gene similarity and average amino acid identity between NAS-02T and its closest relatives are <86 and <42 %, respectively. Based on the phylogeny and physiology, we propose the family Conexivisphaeraceae fam. nov., the order Conexivisphaerales ord. nov. and the class Conexivisphaeria class. nov. to accommodate the novel genus.


Assuntos
Archaea/classificação , Fontes Termais/microbiologia , Filogenia , Archaea/isolamento & purificação , Composição de Bases , DNA Arqueal/genética , Ferro/metabolismo , Japão , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Enxofre/metabolismo
12.
Philos Trans A Math Phys Eng Sci ; 379(2209): 20200348, 2021 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-34510926

RESUMO

There is an urgent need to develop renewable sources of energy and use existing resources in an efficient manner. In this study, in order to improve the utilization of unused biomass and develop green processes and sustainable technologies for energy production and storage, unused Douglas fir sawdust (SD) was transformed into catalysts for the oxygen reduction reaction. Fe and N were doped into SD during hydrothermal carbonization, and the N- and Fe-doped wood-derived carbon (Fe/N/SD) was carbonized in a nitrogen atmosphere. After the catalyst had been calcined at 800°C, its showed the highest current density (-5.86 mAcm-2 at 0.5 V versus reversible hydrogen electrode or RHE) and Eonset value (0.913 V versus RHE). Furthermore, its current density was higher than that of Pt/C (20 wt% Pt) (-5.66 mA cm-2 @0.5 V versus RHE). Finally, after 50 000 s, the current density of sample Fe/N/SD (2 : 10 : 10) remained at 79.3% of the initial value. Thus, the synthesized catalysts, which can be produced readily at a low cost, are suitable for use in various types of energy generation and storage devices, such as fuel cells and air batteries. This article is part of the theme issue 'Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 2)'.

13.
J Cell Sci ; 131(3)2018 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-29222112

RESUMO

In response to amino acid supply, mTORC1, a master regulator of cell growth, is recruited to the lysosome and activated by the small GTPase Rheb. However, the intracellular localization of Rheb is controversial. In this study, we showed that a significant portion of Rheb is localized on the Golgi but not on the lysosome. GFP-Rheb could activate mTORC1, even when forced to exclusively localize to the Golgi. Likewise, artificial recruitment of mTORC1 to the Golgi allowed its activation. Accordingly, the Golgi was in contact with the lysosome at an newly discovered area of the cell that we term the Golgi-lysosome contact site (GLCS). The number of GLCSs increased in response to amino acid supply, whereas GLCS perturbation suppressed mTORC1 activation. These results suggest that inter-organelle communication between the Golgi and lysosome is important for mTORC1 regulation and the Golgi-localized Rheb may activate mTORC1 at GLCSs.


Assuntos
Complexo de Golgi/metabolismo , Membranas Intracelulares/metabolismo , Lisossomos/metabolismo , Alvo Mecanístico do Complexo 1 de Rapamicina/metabolismo , Proteína Enriquecida em Homólogo de Ras do Encéfalo/metabolismo , Aminoácidos/farmacologia , Complexo de Golgi/efeitos dos fármacos , Proteínas de Fluorescência Verde/metabolismo , Células HEK293 , Células HeLa , Humanos , Membranas Intracelulares/efeitos dos fármacos , Lisossomos/efeitos dos fármacos , Transporte Proteico/efeitos dos fármacos
14.
Int J Syst Evol Microbiol ; 70(3): 1837-1842, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31958046

RESUMO

Two novel, strictly aerobic, sulfur-dependent, thermoacidophilic strains, IC-006T and IC-007, were isolated from a solfataric field at Hakone Ohwaku-dani, Kanagawa, Japan. Cells of the two strains were irregular cocci with a diameter of 1.0-1.8 µm. They were strict aerobes and grew in a temperature range between 45 and 69 °C (optimally at 65 °C) and a pH range between 0.4 and 5.5 (optimally at pH 3.5). They required sulfur or a reduced sulfur compound, and sulfur was oxidized to sulfate. They grew autotrophically or mixotrophically utilizing several sugars and complex organic substances as carbon sources. The DNA G+C content was 42.4 mol%. A comparison of the 16S rRNA gene sequences among members of the order Sulfolobales indicated that they were closely related to Sulfolobus metallicus, forming an independent lineage within this order. The two isolates and Sulfolobus metallicus were also diffentiated based on their phenotypic properties from the other members of the order Sulfolobales. Detailed comparisons of the phenotypic properties and DNA-DNA hybridization study illustrated that the two isolates belong to a species different from Sulfolobus metallicus. On the basis of the phylogenetic and phenotypic comparisons, we propose a new genus and species, Sulfuracidifex tepidarius gen. nov., sp. nov. to accommodate strains IC-006T and IC-007. The type strain of Sulfuracidifex tepidarius is IC-006T (=JCM 16833T=DSM 104736T). In addition, Sulfolobus metallicus should be transferred to the new genus as Sulfuracidifex metallicus comb. nov.: the type strain is Kra23T (=DSM 6482T=JCM 9184T=NBRC 15436T).


Assuntos
Filogenia , Microbiologia do Solo , Sulfolobaceae/classificação , Sulfolobus/classificação , Processos Autotróficos , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Japão , Hibridização de Ácido Nucleico , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Sulfolobaceae/isolamento & purificação
15.
Int J Syst Evol Microbiol ; 70(5): 3399-3405, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32374250

RESUMO

The genus Natronolimnobius, currently including four species, is a member of the order Natrialbales, class Halobacteria, and consists of obligately alkaliphilic and extremely halophilic members found exclusively in highly alkaline hypersaline soda lakes. The species were classified into this genus mostly based on phylogenetic analysis of the 16S rRNA gene. However, a more advanced phylogenomic reconstruction based on 122 conserved single-copy archaeal protein markers clearly indicates a polyphyletic origin of the species included into this genus, thus warranting its reclassification into three separate genera. We therefore propose to transfer Nlb. innermongolicus (type strain N-1311) to a new genus Natronolimnohabitans as Nlh. innermongolicus comb. nov. and to transfer Nlb. aegyptiacus (type strain JW/NM-HA 15) and Nlb. sulfurireducens (type strain AArc1) to a new genus Natrarchaeobaculum as Nbl. aegyptiacum comb. nov. and Nbl. sulfurireducens comb. nov. The phylogenomic differentiation of these four species is also supported by the ANI/AAI distances and unique phenotypes. The most important physiological differences includes a previously unreported ability for cellulose and xylan utilization in Nlb. baerhuensis, thermophily in Nbl. aegyptiacus and anaerobic sulfur respiration in Nbl. sulfurireducens. We further present an emended description of Natronolimnobius baerhuensis.


Assuntos
Halobacteriaceae/classificação , Halobacteriales/classificação , Filogenia , Composição de Bases , DNA Arqueal/genética , Lagos/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
16.
Int J Syst Evol Microbiol ; 70(12): 6331-6337, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33095133

RESUMO

A mannan-degrading halophilic archaeal strain, MD130-1T, was isolated from a commercial salt sample. Cells were motile, rod-shaped, and stained Gram-negative. Colonies were pink pigmented. Strain MD130-1T was able to grow at 1.5-4.6 M NaCl (optimum, 3.6 M) at pH 6.0-8.0 (optimum, pH 7.0) and at 25-50 °C (optimum, 40 °C). The DNA G+C content was 62.1 mol% (genome). The orthologous 16S rRNA gene sequence showed the highest similarity (99.4 %) to those of Haloarcula japonica JCM 7785T and Haloarcula hispanica JCM 8911T. The values of genome relatedness between strain MD130-1T and Haloarcula species were 84.33-85.96 % in ANIb and 30.4-32.9 % using GGDC formula 2. The polar lipids of strain MD130-1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and triglycosyl diether-2. Based on the results of phenotypic and phylogenetic analyses, the strain represents a new species of the genus Haloarcula, for which the name Haloarcula mannanilytica sp. nov. is proposed. The type strain is MD130-1T (=JCM 33835T=KCTC 4287T) isolated from commercial salt made in Ishikawa prefecture, Japan.


Assuntos
Haloarcula/classificação , Filogenia , Cloreto de Sódio/análise , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Arqueal/genética , DNA Bacteriano/genética , Ácidos Graxos/química , Galactose/análogos & derivados , Haloarcula/isolamento & purificação , Japão , Mananas/metabolismo , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
17.
Extremophiles ; 24(3): 339-353, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32112303

RESUMO

In this study, a transformation system enabling large-scale gene recombination was developed for the hyperthermophilic archaeon Thermococcus kodakarensis. Using the uracil auxotroph T. kodakarensis KU216 (∆pyrF) as a parent strain, we constructed multiple host strains harboring two 1-kbp DNA regions from the genomes of either the hyperthermophilic archaeon Pyrococcus furiosus or Methanocaldococcus jannaschii. The two regions were selected so that the regions between them on the respective genomes would include pyrF genes, which can potentially be used for selection. Transformation using these host strains and genomic DNA from P. furiosus or M. jannaschii were carried out. Transformants with exogenous pyrF were obtained only using host strains with regions from P. furiosus, and only when the distances between the two regions were relatively short (2-5 kbp) on the P. furiosus genome. To insert longer DNA fragments, we examined the possibilities of using P. furiosus cells to provide intact genomic DNA. A cell pellet of P. furiosus was overlaid with that of T. kodakarensis so that cells were in direct contact. As a result, we were able to isolate T. kodakarensis strains harboring DNA fragments from P. furiosus with lengths of up to 75 kbp in a single transformation step.


Assuntos
Thermococcus , DNA , Pyrococcus furiosus
18.
Phys Chem Chem Phys ; 20(4): 2188-2195, 2018 Jan 24.
Artigo em Inglês | MEDLINE | ID: mdl-29230455

RESUMO

Energy storage devices using sodium ions have great potential in terms of their low cost, high power, and long life. In particular, there could be a significant cost reduction, because of the abundant resource of sodium. Recently, electro-chemical sodium storage performance has been demonstrated in graphite anodes using ether-based solvents. However, the high power and long life were not compatible in the same ether solution. Here, we demonstrated using mixed ether-based solvents that a long cycle life and high rate capability can coexist in the graphite anodes for sodium-ion batteries. The cycle performance indicated that the discharge capacity retention ratio after 10 000 cycles was more than 90% and the capability of 4 A g-1/0.2 A g-1 (40C/2C) was more than 75%. These results could advance the development of sodium storage devices for practical use.

19.
Int J Syst Evol Microbiol ; 67(7): 2274-2278, 2017 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-28671534

RESUMO

Two chitin-degrading halophilic archaeal strains, MC-74T and MC-23, were isolated from commercial salt samples. Cells were motile, rod-shaped and stained Gram-negative. Colonies were vermillion-pigmented. Strains MC-74T and MC-23 were able to grow with 1.5-5.1 M NaCl (optimum, 2.6-3.1 M) at pH 6.0-10.0 (optimum, pH 7.0) and at 20-50 °C (optimum, 40 °C). The orthologous 16S rRNA gene sequence similarity between the two strains was 99.8 %, and the closest phylogenetic relative was Salinarchaeum laminariae JCM 17267T with 99.3-99.5 % similarity. The level of DNA-DNA relatedness between the two strains was 93 and 94 % (reciprocally), and those between the two strains and Salinarchaeumlaminariae JCM 17267T were 35-36 % and 38-39 % (reciprocally). The polar lipids of both strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and phosphatidylglycerol sulfate. Glycolipids were not detected. Based on the phenotypic and phylogenetic analyses, the strains represent a novel species of the genus Salinarchaeum, for which the name Salinarchaeum chitinilyticum sp. nov. is proposed. The type strain is MC-74T (=JCM 19597T=KCTC 4262T), isolated from solar salt produced in France. Strain MC-23, isolated from a commercial solar salt sample produced in China, is an additional strain of the species.


Assuntos
Halobacteriaceae/classificação , Filogenia , Cloreto de Sódio/análise , China , Quitina/metabolismo , DNA Arqueal/genética , França , Glicolipídeos/química , Halobacteriaceae/genética , Halobacteriaceae/isolamento & purificação , Neisseriaceae/genética , Hibridização de Ácido Nucleico , Fosfatidilgliceróis/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
20.
Phys Chem Chem Phys ; 19(2): 1003-1009, 2017 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-27790663

RESUMO

We have previously synthesized highly amorphous GeOx powder by a soft chemical method and demonstrated its performance in electrochemical Na insertion-extraction reactions. However, electrolyte decomposition caused large irreversible capacity decay in the first charge-discharge, leading to poor cycling ability. Electrolyte decomposition was accelerated by the large volume change of amorphous GeOx during charge-discharge. Herein, we report the use of ether-based solvents in Na-ion batteries with amorphous GeOx anodes. XPS measurements were used to evaluate the surface state of the electrode after cycling. The surface layer of the electrolyte decomposition products was thin and mainly composed of Na alkoxide. Thus, the electrochemical performance of this system was greatly improved owing to the significant suppression of electrolyte decomposition. Consequently, electrolytes using ether-based solvents are strong candidates for practical use in Na-ion batteries.

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