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1.
Nucleic Acids Res ; 2020 Oct 29.
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/.

2.
Microbiol Resour Announc ; 9(16)2020 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-32299873

RESUMO

We report a complete genome sequence of Collinsella aerofaciens JCM 10188T (=VPI 1003T). The genome consists of a circular chromosome (2,428,218 bp with 60.6% G+C content) and two extrachromosomal elements. The genome was predicted to contain 5 sets of rRNA genes, 58 tRNA genes, and 2,079 protein-encoding sequences.

3.
Microbiol Resour Announc ; 9(16)2020 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-32299874

RESUMO

We announce the complete genome sequence of Megamonas funiformis JCM 14723T (YIT 11815T). The genome consists of a circular chromosome (2,522,577 bp, 31.5% G+C content) and a plasmid of 46,189 bp (29.4% G+C content). The genome was predicted to contain 6 rRNA operons, 53 tRNA genes, and 2,440 protein-coding sequences.

4.
Microbiol Resour Announc ; 9(17)2020 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327522

RESUMO

We report the complete genome sequence of Flavonifractor plautii JCM 32125T (=VPI 0310T). The genome consists of a single circular chromosome of 3,985,392 bp (G+C content, 60.9%) and was predicted to contain 3 complete sets of rRNA genes, 63 tRNA genes, and 3,764 protein-coding sequences.

5.
Microbiol Resour Announc ; 9(17)2020 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-32327523

RESUMO

We report a complete genome sequence of Blautia producta JCM 1471T The genome consists of a single circular chromosome of 6,197,116 bp with a G+C content of 45.7%. The genome was annotated as containing 5 complete sets of rRNA genes, 70 tRNA genes, and 5,516 protein-coding sequences.

6.
Int J Syst Evol Microbiol ; 70(2): 1372-1397, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32122458

RESUMO

Fourteen novel lipomycetaceous yeasts species were isolated from soil samples collected from the Hokkaido, Chiba and Okinawa prefectures of Japan. Phylogenetic analyses of the D1/D2 domains of the large subunit rRNAs and translation elongation factor 1 alpha genes (TEF1-α) revealed that five strains of two species from the soil in Furano-shi, Hokkaido were related to Dipodascopsis anomala and 29 strains representing 12 species from soils in Kamogawa-shi, Chiba and Iriomote Island, Okinawa were in the Myxozyma clade. The two species of Dipodascopsis form globose or ellipsoid ascospores in their sac-like ascus and pseudohyphae. Furthermore, these species produce ascospores in their pseudohyphae and do not produce an acicular ascus, which is common among the three species including D. anomala. Therefore, we propose transferring D. anomala to the genus Babjevia and amending Babjevia. Two novel species were described and included in the genus Babjevia: Babjevia hyphoforaminiformans sp. nov. (holotype NBRC 111233; MycoBank no. MB 829051) and Babjevia hyphasca sp. nov. (holotype NBRC 112965; MycoBank no. MB 829053). The 12 species in the Myxozyma clade produce neither ascospores nor pseudohyphae and have different characteristics in assimilating several carbon sources from each other. Thus, we propose that the novel species of Lipomyces be classified as forma asexualis (f.a.). From Kamogawa-shi, Chiba (19 strains representing five species): Lipomyces melibiosiraffinosiphilus f.a., sp. nov. (holotype NBRC 111411; MycoBank no. MB 829034), Lipomyces kiyosumicus f.a., sp. nov. (holotype NBRC 111424; MycoBank no. MB 829035), Lipomyces chibensis f.a., sp. nov. (holotype NBRC 111413; MycoBank no. MB 829036), Lipomyces kamogawensis f.a., sp. nov. (holotype NBRC 112967; MycoBank no. MB 829037), Lipomyces amatsuensis f.a., sp. nov. (holotype NBRC 111420; MycoBank no. MB 829041). From Iriomote island, Okinawa (10 strains representing seven species): Lipomyces taketomicus f.a., sp. nov. (holotype NBRC 112966; MycoBank no. MB 829042), Lipomyces yaeyamensis f.a., sp. nov. (holotype NBRC 110433; MycoBank no. MB 829050), Lipomyces iriomotensis f.a., sp. nov. (holotype NBRC 110436; MycoBank no. MB 829045), Lipomyces haiminakanus f.a., sp. nov. (holotype NBRC 110435; MycoBank no. MB 829046), Lipomyces komiensis f.a., sp. nov. (holotype NBRC 110440; MycoBank no. MB 829047), Lipomyces nakamensis f.a., sp. nov. (holotype NBRC 110434; MycoBank no. MB 829048), Lipomyces sakishimensis f.a., sp. nov. (holotype NBRC 110439; MycoBank no. MB 829049).


Assuntos
Lipomyces/classificação , Filogenia , Microbiologia do Solo , DNA Fúngico/genética , Genes Fúngicos , Japão , Lipomyces/isolamento & purificação , Técnicas de Tipagem Micológica , Fator 1 de Elongação de Peptídeos/genética , Fenótipo , Saccharomycetales/classificação , Análise de Sequência de DNA , Esporos Fúngicos
7.
Biopreserv Biobank ; 17(5): 395-400, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-30938541

RESUMO

Subculturing is frequently used for the preservation of basidiomycetes. In this study, to assess and verify the risks of repeated subculturing on the long-term preservation of strains of culture collections, we performed single nucleotide polymorphism (SNP) analysis in genes encoding enzymes of the mevalonate pathway, 1,3-ß-glucan synthesis, lignin degradation, and the tricarboxylic acid (TCA) cycle of mycelia before and after preserving for a 4-year period by the subculturing 30 times every 45 days of Ganoderma lucidum NBRC 8346. As a result of analyzing 60 genes of the strain, SNPs were found in 18 genes, and 14 of them were found in the exon region. Nonsynonymous coding SNPs were found in two genes (atoB_2, hmgr) encoding enzymes of mevalonate pathway and five genes (lcc1_9, lcc1_11, lcc1_13, dslcc6, aa5_1_9) encoding enzymes of lignin degradation after subculturing of G. lucidum NBRC 8346.


Assuntos
Proteínas Fúngicas/genética , Micologia/métodos , Polimorfismo de Nucleotídeo Único , Reishi/crescimento & desenvolvimento , Éxons , Sequenciamento de Nucleotídeos em Larga Escala , Preservação Biológica , Reishi/genética , Análise de Sequência de DNA
8.
Mod Pathol ; 32(7): 997-1007, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-30809000

RESUMO

Nonalcoholic fatty liver disease is a major liver disease that leads to cirrhosis and/or hepatocellular carcinoma in a subset of patients. The mechanism underlying disease progression is largely unknown. p53-binding protein 1 (53BP1) is a DNA damage response protein that rapidly localizes at the site of DNA double-strand breaks. In this study, we investigated nuclear 53BP1-positive foci formation as an indicator of DNA double-strand breaks in human nonalcoholic fatty liver disease liver tissues by immunofluorescence microscopy. A total of 52 liver tissue samples, including 43 nonalcoholic fatty liver disease samples and 9 controls, were studied. Our results show that the number of abnormal 53BP1-positive foci in hepatocytes (defined as three or more discrete nuclear foci and/or large foci greater than 1 µM) was significantly increased in nonalcoholic fatty liver disease patients compared to that in controls, both in nonalcoholic fatty liver (p < 0.01) and nonalcoholic steatohepatitis patients (p < 0.01). The number of large foci was significantly increased in the nonalcoholic steatohepatitis cases compared to that in the nonalcoholic fatty liver cases (p < 0.05) and correlated with increased stage of fibrosis. The number of large-foci-expressing hepatocytes was positively correlated with increased age (p < 0.01) and negatively correlated with serum platelet count (p < 0.05). In addition, we performed an in vitro assay using rat hepatocytes treated with the saturated free fatty acid palmitate. Treatment appeared to augment the number of abnormal foci, indicating an induction of double-strand breaks in the hepatocytes through free fatty acid treatment in a caspase-dependent manner. This study demonstrates that 53BP1-positive nuclear foci formation is associated with disease progression in nonalcoholic fatty liver disease patients. Analysis of 53BP1 expression might be a feasible technique to estimate genomic instability in nonalcoholic fatty liver disease.


Assuntos
Núcleo Celular/metabolismo , Dano ao DNA/fisiologia , Hepatócitos/metabolismo , Hepatopatia Gordurosa não Alcoólica/metabolismo , Proteína 1 de Ligação à Proteína Supressora de Tumor p53/metabolismo , Adulto , Idoso , Animais , Apoptose/fisiologia , Linhagem Celular , Progressão da Doença , Feminino , Instabilidade Genômica , Hepatócitos/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Hepatopatia Gordurosa não Alcoólica/patologia , Ratos
9.
Intern Med ; 58(2): 195-199, 2019 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-30146582

RESUMO

A 57-year-old woman was admitted with lower abdominal pain and bloody bowel discharge. She was diagnosed with rectal tumor by colonoscopy, and a biopsy was performed. Surgery was performed, resulting in a diagnosis of rectal paraganglioma. Since recurrence was confirmed three years later, reoperation was done, and chemotherapy with cyclophosphamide, vincristine and dacarbazine (CVD) was subsequently carried out for further recurrence. After the administration of up to 15 courses of CVD, we delivered best supportive care due to disease progression. She died a year and a half after starting chemotherapy. We herein report this rare disease with a review of the relevant literature.


Assuntos
Paraganglioma/diagnóstico , Paraganglioma/terapia , Neoplasias Retais/diagnóstico , Neoplasias Retais/terapia , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Biópsia , Colonoscopia , Terapia Combinada , Ciclofosfamida/uso terapêutico , Dacarbazina/uso terapêutico , Progressão da Doença , Evolução Fatal , Feminino , Humanos , Pessoa de Meia-Idade , Recidiva Local de Neoplasia/terapia , Paraganglioma/patologia , Neoplasias Retais/patologia , Reoperação , Vincristina/uso terapêutico
10.
J Gen Appl Microbiol ; 65(2): 53-63, 2019 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-30305477

RESUMO

Pseudozyma antarctica and Malassezia furfur are basidiomycetous yeasts under the subphylum Ustilaginomycotina. P. antarctica is a commensal organism found in certain plant species, while M. furfur is associated with several skin diseases of animals including humans. N-linked glycans of P. antarctica and M. furfur were prepared, digested with glycosidases, and structurally analyzed using high performance liquid chromatography (HPLC) and mass spectrometry (MS). Analyses revealed the presence of neutral N-linked glycans ranging in length from Man3GlcNAc2-PA to Man9GlcNAc2-PA. The two species shared the most abundant neutral N-linked glycan: Manα1-2Manα1-6(Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M8A). The second and third most abundant neutral N-linked glycans for P. antarctica were Manα1-2Manα1-6(Manα1-2Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M9A) and Manα1-6(Manα1-3)Manα1-6(Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M5A), respectively. In the case of M. furfur, Manα1-2Manα1-6(Manα1-3)Manα1-6(Manα1-2Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M7A) was the second most abundant, while both M8A and M9A were tied for the third most abundant. The presence of putative galactose residues in the hypermannosylated neutral N-linked glycans is also discussed. This report is the first to analyze the neutral N-linked glycans of P. antarctica and M. furfur.


Assuntos
Polissacarídeos Fúngicos/química , Malassezia/química , Ustilaginales/química , Basidiomycota/química , Cromatografia Líquida de Alta Pressão , Polissacarídeos Fúngicos/metabolismo , Glicosídeo Hidrolases/metabolismo , Isomerismo , Espectrometria de Massas , Monossacarídeos/química
11.
Gigascience ; 7(5)2018 05 01.
Artigo em Inglês | MEDLINE | ID: mdl-29718202

RESUMO

Genomic information is essential for taxonomic, phylogenetic, and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microorganisms. Hence, the GCM aims to promote research by deep-mining genomic data.


Assuntos
Bactérias/genética , Fungos/genética , Genômica/métodos , Células Procarióticas/metabolismo , Análise de Sequência de DNA/métodos , Reprodutibilidade dos Testes
12.
Int J Syst Evol Microbiol ; 68(5): 1815-1821, 2018 May.
Artigo em Inglês | MEDLINE | ID: mdl-29557768

RESUMO

Phenotypic and genetic changes during long-term preservation have been observed in microbial strains at culture collections (CCs). It is imperative to verify the effects of these changes on quality of the strains preserved at CCs. In this study, we performed genome-wide single-nucleotide polymorphism (SNP) analysis of different production lots, which had been derived from the same origin and preserved at the NITE Biological Resource Center (NBRC) for a 4-38-year period by the vacuum liquid drying method at 4 °C. The analysis was conducted for three sets of lots derived from Cellulomonas fimi NBRC 15513T, Corynebacterium glutamicum NBRC 12168T, and Saccharomonospora viridis NBRC 12207T. SNPs were found in all sets studied for comparison purposes. In sets of two or three lots, genomic SNPs were found in both non-coding sequences (non-CDSs) and in coding sequences (CDSs), and the SNPs in the CDSs resulted in non-synonymous mutations. These data indicated that genomic variation occurred during long-term preservation.


Assuntos
Bactérias/genética , Bancos de Espécimes Biológicos , Polimorfismo de Nucleotídeo Único , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , Éxons , Íntrons , Fenótipo , Análise de Sequência de DNA
13.
Nihon Shokakibyo Gakkai Zasshi ; 114(10): 1836-1844, 2017.
Artigo em Japonês | MEDLINE | ID: mdl-28978883

RESUMO

An 87-year-old woman with a 4-month history of postprandial gastrointestinal obstruction was admitted to our facility after suddenly vomiting black matter. Computed tomography and esophagogastroduodenoscopy revealed gastric prolapse and prolapse of the duodenum and transverse colon. Morgagni hernia combined with esophageal hiatal hernia was diagnosed. Gastric and duodenal obstructions were successfully repaired by endoscopy, followed by laparoscopic repair. Endoscopic repair helped the patient avoid fasting before surgery. The patient had a history of several chest bruises, which were detected by chest X-rays and suspected to be the cause of the hernias over time.


Assuntos
Doenças do Esôfago/cirurgia , Hérnia Hiatal/cirurgia , Hérnias Diafragmáticas Congênitas/cirurgia , Idoso de 80 Anos ou mais , Endoscopia do Sistema Digestório , Doenças do Esôfago/diagnóstico por imagem , Hérnia Hiatal/diagnóstico por imagem , Hérnias Diafragmáticas Congênitas/diagnóstico por imagem , Humanos , Laparoscopia , Masculino , Tomografia Computadorizada por Raios X
14.
Int J Syst Evol Microbiol ; 67(10): 3971-3976, 2017 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-28895520

RESUMO

This study describes three novel xylose-assimilating yeasts, which were isolated from decayed wood collected from Bung Hatta Botanical Garden in West Sumatra and Cibodas Botanic Garden in West Java, or from litter from Eka Karya Bali Botanic Garden in Bali, Indonesia. Phylogenetic analysis was performed based on the sequences of the D1/D2 domains of the large ribosomal subunit (LSU), the small ribosomal subunit (SSU), the internal transcribed spacer (ITS) and elongation factor-1α (EF-1α), and the three strains were found to represent three novel species belonging to genera Barnettozyma or Wickerhamomyces. The morphological, biochemical and physiological characteristics indicated that the strains were distinct from other closely related species. Strains 13Y206T and 14Y196T belonging to the Barnettozyma clade are described as the type strains of Barnettozyma xylosiphila sp. nov. (type strain 13Y206T=NBRC 110202T=InaCC Y726T; MycoBank MB808598) and Barnettozyma xylosica sp. nov. (type strain 14Y196T=NBRC 111558T=InaCC Y1030T; MycoBank MB819485). Strain 14Y125T belonging to the Wickerhamomyces clade is described as the type strain of Wickerhamomyces xylosivorus f.a., sp. nov. (type strain 14Y125T=NBRC 111553T=InaCC Y1026T; MycoBank MB819484).


Assuntos
Filogenia , Saccharomycetales/classificação , Madeira/microbiologia , Xilose/metabolismo , DNA Fúngico/química , DNA Espaçador Ribossômico/genética , Indonésia , Técnicas de Tipagem Micológica , Fator 1 de Elongação de Peptídeos/genética , Saccharomycetales/genética , Saccharomycetales/isolamento & purificação , Análise de Sequência de DNA
15.
Yeast ; 34(7): 305-317, 2017 07.
Artigo em Inglês | MEDLINE | ID: mdl-28384382

RESUMO

Sympodiomycopsis paphiopedili is a basidiomycetous yeast under the subphylum Ustilaginomycotina and is a commensal organism originally isolated from the nectar of a plant species in Japan. In this study, the neutral N-linked glycans of S. paphiopedili were prepared and structurally analysed using high-performance liquid chromatography (HPLC) and mass spectrometry (MS). Glycosidase digestion analyses were also performed to verify certain glycan linkages. HPLC and MS analyses revealed the presence of neutral N-linked glycans ranging from Man3 GlcNAc2 -PA to Man9 GlcNAc2 -PA in length. The most abundant neutral N-linked glycan structure in this species was found to be the Manα1-2Manα1-6(Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M8A). Moreover, the second and third most abundant neutral N-linked glycan in S. paphiopedili were the Manα1-2Manα1-6(Manα1-2Manα1-3)Manα1-6(Manα1-2Manα1-2Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M9A) and the Manα1-6(Manα1-3)Manß1-4GlcNAcß1-4GlcNAc (M3B). On the other hand, the effect of the combination of glycoprotein extraction methods (citrate buffer extraction or bead extraction) and the subsequent glycan release methods (hydrazinolysis or PNGase F digestion) on the detection of N-linked glycan peaks was also examined for S. paphiopedili and Saccharomyces cerevisiae in order to avoid under-representation of N-linked glycan structures. High mannose and possible hypermannosylated glycan peaks were detected in all method combinations in S. cerevisiae with the citrate buffer extraction-hydrazinolysis method giving the highest peak yields as compared with the other methods. Here we report the first account of the structural analysis of the neutral N-linked glycan of S. paphiopedili and the comparison of the effect of combinations of glycoprotein extraction methods and glycan release methods with that of the glycan analysis in S. paphiopedili and S. cerevisiae. Copyright © 2017 John Wiley & Sons, Ltd.


Assuntos
Basidiomycota/química , Polissacarídeos/análise , Cromatografia Líquida de Alta Pressão , Espectrometria de Massas , Polissacarídeos/química , Saccharomyces cerevisiae/química
16.
Int J Syst Evol Microbiol ; 67(4): 1024-1027, 2017 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-27974086

RESUMO

Three strains (14Y260T, 14Y268 and 14Y276) of xylose-assimilating yeasts were isolated from decayed wood and soil collected in West Java in Indonesia. A phylogenetic analysis was performed based on the sequences of the D1/D2 domains of LSU, SSU and EF-1α, and the three strains were found to belong to the genus Pichia. The morphological, biochemical, physiological and chemotaxonomic characteristics indicated that these strains were distinct from other closely related species. Strains 14Y260T, 14Y268 and 14Y276 belonged to the Pichia clade and represent a novel species, named Pichia chibodasensis sp. nov. ; The type strain is 14Y260T (=NBRC 111569T=InaCC Y1042T).


Assuntos
Filogenia , Pichia/classificação , Madeira/microbiologia , DNA Fúngico/genética , Indonésia , Técnicas de Tipagem Micológica , Fator 1 de Elongação de Peptídeos , Pichia/genética , Pichia/isolamento & purificação , Saccharomycetales/classificação , Análise de Sequência de DNA , Xilose/metabolismo
17.
Int J Syst Evol Microbiol ; 66(10): 3799-3804, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-27374928

RESUMO

A novel and extremely halophilic archaeon, designated strain 2a_47_2T, was isolated from a solar saltern sample collected in Indonesia. Cells of the strain were Gram-stain-negative, non-motile and pleomorphic and formed orange-red pigmented colonies. Strain 2a_47_2T grew at 20-48 °C (optimum 38-41 °C), pH 6.0-8.5 (optimum pH 7.5), >1.7 M NaCl (optimum 2.6 M) and <0.5 M MgCl2 (optimum 0.3 M). The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two phospholipids and sulfated diglycosyl diether. The cells mainly contained menaquinone-8. The G+C content in the genomic DNA of the strain was 67.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2a_47_2T represents a member of the family Halorubraceae and is different from any other known halophilic archaea. This finding was also demonstrated by phylogenetic analyses based on deduced RpoB' amino acid sequences. Collectively, these results show that strain 2a_47_2T represents a novel genus and species in the family Halorubraceae, and the name Halobium palmae gen. nov., sp. nov. is proposed. The type strain is 2a_47_2T (=NBRC 111368T=InaCC Ar34T).


Assuntos
Halobacteriaceae/classificação , Filogenia , Salinidade , Composição de Bases , DNA Arqueal/genética , Halobacteriaceae/genética , Halobacteriaceae/isolamento & purificação , Indonésia , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
18.
Biochem Biophys Res Commun ; 478(1): 343-348, 2016 09 09.
Artigo em Inglês | MEDLINE | ID: mdl-27416753

RESUMO

Transglutaminase (TGase) catalyzes protein cross-linking reactions essential for several biological processes. In differentiating keratinocytes, TG1 (keratinocyte-type) is crucial for the cross-linking of substrate proteins required for the complete formation of the cornified envelop, a proteinaceous supermolecule located in the outermost layer of the epidermis. TG1 expressions and its substrate were induced in cultured keratinocytes at differentiation-stage specific manner. In the cultured keratinocytes, we used the TG1-specific substrate peptide, which enables the specific detection of enzymatic activity to investigate its induction patterns. As a further application of the substrate peptide, several substrate candidates of TG1 that may be essential for cornified envelope formation were identified and characterized.


Assuntos
Regulação Enzimológica da Expressão Gênica/fisiologia , Queratinócitos/enzimologia , Peptídeos/metabolismo , Transglutaminases/metabolismo , Células Cultivadas , Ativação Enzimática , Humanos , Ligação Proteica , Especificidade por Substrato
19.
Int J Syst Evol Microbiol ; 66(1): 38-43, 2016 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-26449644

RESUMO

A novel halophilic archaeon, designated strain 2b_61_3T, was isolated from a solar saltern in Indonesia. Cells of the strain were Gram-stain-negative, motile, pleomorphic rods that formed orange-red-pigmented colonies on solid medium. The isolate grew optimally at 42-44 °C, pH 6.5-7.0, and with 2.6 M NaCl, and MgCl2 was required for growth. Strain 2b_61_3T had two differential 16S rRNA genes (rrnA and rrnB), and phylogenetic analysis revealed that the strain belonged to the genus Haloarchaeobius. The rrnA and rrnB sequence similarities between strain 2b_61_3T and species of the genus Haloarchaeobius were 98.4-99.2 % and 98.5-98.8 %, respectively. The findings from the 16S rRNA gene analysis were supported by sequence analysis of rpoB', the B' subunit of RNA polymerase. On the basis of the phenotypic characteristics and phylogenetic analyses, as well as DNA-DNA hybridization experiments with Haloarchaeobius iranensis NBRC 110930T, strain 2b_61_3T represents a novel species of the genus Haloarchaeobius, for which the name Haloarchaeobius baliensis sp. nov. is proposed. The type strain is 2b_61_3T ( = NBRC 110517T = InaCC Ar2T).


Assuntos
Halobacteriaceae/classificação , Filogenia , Águas Salinas , Microbiologia da Água , Composição de Bases , DNA Arqueal/genética , RNA Polimerases Dirigidas por DNA/genética , Ácidos Graxos/química , Genes Arqueais , Halobacteriaceae/genética , Halobacteriaceae/isolamento & purificação , Indonésia , Dados de Sequência Molecular , Hibridização de Ácido Nucleico , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
20.
Int J Syst Evol Microbiol ; 64(Pt 8): 2566-2572, 2014 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-24812367

RESUMO

We isolated two strains of a novel Lipomyces species from soil collected in Chichibu forest, Saitama prefecture, Japan. Based on their morphological and biochemical characteristics, along with multilocus sequence typing using the D1/D2 domain of the large-subunit (LSU) rRNA gene, the internal transcribed spacer (ITS) region and the translation elongation factor 1 alpha gene (EF-1α), the two strains were shown to represent a novel species of the genus Lipomyces, described as Lipomyces chichibuensis sp. nov. (type strain CB08-2(T) = NBRC 109582(T) = CBS 12929(T); Mycobank no. MB808164). In addition, we reidentified the type strains of Lipomyces kononenkoae and Lipomyces spencermartinsiae maintained in culture collections based on phenotypic characters and/or DNA-DNA hybridization to ensure correct future identification of species of the genus Lipomyces. The correct type strains of L. kononenkoae and L. spencermartinsiae are NBRC 107661(T) ( = CBS 2514(T)) and NBRC 10376(T) ( = CBS 5608(T)), respectively.


Assuntos
Lipomyces/classificação , Filogenia , Microbiologia do Solo , DNA Fúngico/genética , DNA Espaçador Ribossômico/genética , Japão , Lipomyces/genética , Lipomyces/isolamento & purificação , Dados de Sequência Molecular , Técnicas de Tipagem Micológica , Hibridização de Ácido Nucleico , Fator 1 de Elongação de Peptídeos/genética , Análise de Sequência de DNA
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