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1.
Int Heart J ; 60(5): 1176-1183, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31564708

RESUMO

Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.


Assuntos
Bactérias/classificação , Microbioma Gastrointestinal/efeitos dos fármacos , Insuficiência Cardíaca/microbiologia , Isoproterenol/efeitos adversos , Metagenômica/métodos , Animais , Bactérias/genética , Modelos Animais de Doenças , Ecocardiografia , Insuficiência Cardíaca/induzido quimicamente , Insuficiência Cardíaca/diagnóstico por imagem , Sequenciamento de Nucleotídeos em Larga Escala , Injeções Intraperitoneais , Isoproterenol/farmacologia , Masculino , Filogenia , Ratos , Análise de Sequência de DNA
2.
Int J Syst Evol Microbiol ; 69(9): 2735-2738, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31483242

RESUMO

Early characterization of strains designated into the genera Entomoplasma and Mesoplasma was based upon biological and chemical characteristics. With the advent of 16S rRNA gene sequence analysis as an added taxonomic character, it became clear that the two genera did not form distinct and separate monophyletic clusters. A genome-level analysis of all 17 validly published species within the family Entomoplasmataceae has recently been performed. Phylogenetic analyses, comparisons of gene content, and the lack of genus-specific genes supported that species from the two genera are intermixed and should not be taxonomically separated. This level of analysis clearly reveals the necessity to revise the taxonomy of this family by merging the two genera into one, Entomoplasma. Additionally, it was definitively determined that the strain originally designated as Acholeplasma multilocale resides in this cluster and should be formally renamed as Entomoplasma multilocale. Merging Mesoplasma and Entomoplasma yields a paraphyletic genus, but is supported by cell morphology and ecology to be distinguished from the genera Spiroplasma and Mycoplasma.


Assuntos
Entomoplasmataceae/classificação , Genoma Bacteriano , Filogenia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
3.
Arch Virol ; 164(11): 2843-2848, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31494777

RESUMO

The Cooper and Los Angeles (LA) strains were the two original respiratory strains of bovine herpesvirus type 1.1 (BoHV-1.1) isolated in the 1950s from cattle with infectious bovine rhinotracheitis. We report the complete genome sequence for the BoHV-1.1 LA strain and compare it to the prototype Cooper strain and six wild-type BoHV-1.1 isolates. A nucleotide sequence divergence of 0.74% was noted across the two complete genomes, caused by 19 single-nucleotide polymorphisms (SNPs) involving 12 genes and insertions/deletions that primarily affected the number of repeats within reiterated repeat regions of the genome. Phylogenetic analysis revealed that Cooper and LA strains are genetically the most ancient strains from which all of the more-recently isolated field strains of BoHV-1.1 evolved.


Assuntos
Genoma Viral/genética , Infecções por Herpesviridae/veterinária , Herpesvirus Bovino 1/genética , Rinotraqueíte Infecciosa Bovina/virologia , Animais , Sequência de Bases , Bovinos , Doenças dos Bovinos/virologia , Genótipo , Herpesvirus Bovino 1/classificação , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA , Sequenciamento Completo do Genoma
4.
Arch Virol ; 164(11): 2761-2768, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31506786

RESUMO

A multiplex polymerase chain reaction (mPCR) assay was developed to detect and distinguish feline panleukopenia virus (FPV), feline bocavirus (FBoV) and feline astrovirus (FeAstV). Three pairs of primers were designed based on conserved regions in the genomic sequences of the three viruses and were used to specifically amplify targeted fragments of 237 bp from the VP2 gene of FPV, 465 bp from the NP1 gene of FBoV and 645 bp from the RdRp gene of FeAstV. The results showed that this mPCR assay was effective, because it could detect at least 2.25-4.04 × 104 copies of genomic DNA of the three viruses per µl, was highly specific, and had a good broad-spectrum ability to detect different genotypes of the targeted viruses. A total of 197 faecal samples that had been screened previously for FeAstV and FBoV were collected from domestic cats in northeast China and were tested for the three viruses using the newly developed mPCR assay. The total positive rate for these three viruses was 59.89% (118/197). From these samples, DNA from FPV, FBoV and FeAstV was detected in 73, 51 and 46 faecal samples, respectively. The mPCR testing results agreed with the routine PCR results with a coincidence rate of 100%. The results of this study show that this mPCR assay can simultaneously detect and differentiate FPV, FBoV and FeAstV and can be used as an easy, specific and efficient detection tool for clinical diagnosis and epidemiological investigation of these three viruses.


Assuntos
Bocavirus/genética , Proteínas do Capsídeo/genética , Vírus da Panleucopenia Felina/genética , Mamastrovirus/genética , Reação em Cadeia da Polimerase Multiplex/métodos , Animais , Bocavirus/isolamento & purificação , Doenças do Gato/diagnóstico , Doenças do Gato/virologia , Gatos , China , Primers do DNA/genética , Fezes/virologia , Vírus da Panleucopenia Felina/isolamento & purificação , Mamastrovirus/isolamento & purificação , Filogenia , Análise de Sequência de DNA
5.
Hum Genet ; 138(10): 1183-1200, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31471722

RESUMO

The glutamate pyruvate transaminase 2 (GPT2) gene produces a nuclear-encoded mitochondrial enzyme that catalyzes the reversible transfer of an amino group from glutamate to pyruvate, generating alanine and alpha-ketoglutarate. Recessive mutations in GPT2 have been recently identified in a new syndrome involving intellectual and developmental disability (IDD), postnatal microcephaly, and spastic paraplegia. We have identified additional families with recessive GPT2 mutations and expanded the phenotype to include small stature. GPT2 loss-of-function mutations were identified in four families, nine patients total, including: a homozygous mutation in one child [c.775T>C (p.C259R)]; compound heterozygous mutations in two siblings [c.812A>C (p.N271T)/c.1432_1433delGT (p.V478Rfs*73)]; a novel homozygous, putative splicing mutation [c.1035C>T (p.G345=)]; and finally, a recurrent mutation, previously identified in a distinct family [c.1210C>T (p.R404*)]. All patients were diagnosed with IDD. A majority of patients had remarkably small stature throughout development, many < 1st percentile for height and weight. Given the potential biological function of GPT2 in cellular growth, this phenotype is strongly suggestive of a newly identified clinical susceptibility. Further, homozygous GPT2 mutations manifested in at least 2 of 176 families with IDD (approximately 1.1%) in a Pakistani cohort, thereby representing a relatively common cause of recessive IDD in this population, with recurrence of the p.R404* mutation in this population. Based on variants in the ExAC database, we estimated that approximately 1 in 248 individuals are carriers of moderately or severely deleterious variants in GPT2.


Assuntos
Deficiências do Desenvolvimento/diagnóstico , Deficiências do Desenvolvimento/genética , Genes Recessivos , Predisposição Genética para Doença , Mutação , Fenótipo , Transaminases/genética , Adolescente , Alelos , Substituição de Aminoácidos , Deficiências do Desenvolvimento/metabolismo , Ativação Enzimática , Éxons , Feminino , Frequência do Gene , Estudos de Associação Genética , Genética Populacional , Genótipo , Humanos , Deficiência Intelectual/diagnóstico , Deficiência Intelectual/genética , Imagem por Ressonância Magnética , Masculino , Mitocôndrias/genética , Mitocôndrias/metabolismo , Modelos Moleculares , Linhagem , Conformação Proteica , Sítios de Splice de RNA , Análise de Sequência de DNA , Relação Estrutura-Atividade , Transaminases/química , Transaminases/metabolismo
6.
Rev Bras Parasitol Vet ; 28(3): 367-375, 2019 Aug 29.
Artigo em Inglês | MEDLINE | ID: mdl-31483030

RESUMO

Renicolids are parasites that inhabit the renal tubules and ureters of molluscivorous and piscivorous birds. Puffinus puffinus is a migratory seabird that was identified as the definitive host of Renicola spp. Studies focusing on the renicolid species and the resulting renal lesions are valuable for their association with causes of stranding in seabirds. The aim of this study was to identify the renicolid trematodes and evaluate the histological findings in two P. puffinus stranded on the coast of Paraná state, Brazil. The parasites were evaluated by histologic, ultrastructural and molecular assays, while tissue changes were analyzed by histologic methods. The morphological and morphometrical characteristics of the parasites, along with polymerase chain reaction and sequencing assays (ribosomal and mitochondrial regions), identified the species as Renicola sloanei. The results also suggest that this helminth can be the adult form of Cercaria pythionike. The dilation of collecting ducts was the main histological finding in the kidneys. In conclusion, R. sloanei was identified, and for the first time, P. puffinus was described as a host of this digenean inducing mild renal changes.


Assuntos
Doenças das Aves/parasitologia , Aves/parasitologia , Rim/parasitologia , Trematódeos/isolamento & purificação , Animais , DNA de Helmintos/genética , DNA Mitocondrial/genética , DNA Ribossômico/genética , Filogenia , Análise de Sequência de DNA , Trematódeos/classificação , Trematódeos/genética , Trematódeos/ultraestrutura
7.
World J Microbiol Biotechnol ; 35(8): 128, 2019 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-31375920

RESUMO

Large patch disease, caused by Rhizoctonia solani AG2-2, is the most devastating disease in Zoysiagrass (Zoysia japonica). Current large patch disease control strategies rely primarily upon the use of chemical pesticides. Streptomyces sp. S8 is known to possess exceptional antagonistic properties that could potentially suppress the large patch pathogen found at turfgrass plantations. This study aims to demonstrate the feasibility of using the strain as a biological control mechanism. Sequencing of the S8 strain genome revealed a valinomycin biosynthesis gene cluster. This cluster is composed of the vlm1 and vlm2 genes, which are known to produce antifungal compounds. In order to verify this finding for the large patch pathogen, a valinomycin biosynthesis knockout mutant was created via the CRISPR/Cas9 system. The mutant lost antifungal activity against the large patch pathogen. Consequently, it is anticipated that eco-friendly microbial preparations derived from the S8 strain can be utilized to biologically control large patch disease.


Assuntos
Antifúngicos/metabolismo , Antifúngicos/farmacologia , Rhizoctonia/efeitos dos fármacos , Streptomyces/metabolismo , Valinomicina/metabolismo , Valinomicina/farmacologia , Vias Biossintéticas/genética , Técnicas de Inativação de Genes , Genoma Bacteriano , Família Multigênica , Controle Biológico de Vetores/métodos , Doenças das Plantas/microbiologia , Doenças das Plantas/prevenção & controle , Poaceae/microbiologia , Rhizoctonia/crescimento & desenvolvimento , Análise de Sequência de DNA , Streptomyces/genética
8.
BMC Plant Biol ; 19(1): 339, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31382883

RESUMO

BACKGROUND: Tartary buckwheat (Fagopyrum tataricum) is an edible cereal crop whose sprouts have been marketed and commercialized for their higher levels of anti-oxidants, including rutin and anthocyanin. UDP-glucose flavonoid glycosyltransferases (UFGTs) play an important role in the biosynthesis of flavonoids in plants. So far, few studies are available on UFGT genes that may play a role in tartary buckwheat flavonoids biosynthesis. Here, we report on the identification and functional characterization of seven UFGTs from tartary buckwheat that are potentially involved in flavonoid biosynthesis (and have varying effects on plant growth and development when overexpressed in Arabidopsis thaliana.) RESULTS: Phylogenetic analysis indicated that the potential function of the seven FtUFGT proteins, FtUFGT6, FtUFGT7, FtUFGT8, FtUFGT9, FtUFGT15, FtUFGT40, and FtUFGT41, could be divided into three Arabidopsis thaliana functional subgroups that are involved in flavonoid biosynthesis of and anthocyanin accumulation. A significant positive correlation between FtUFGT8 and FtUFGT15 expression and anthocyanin accumulation capacity was observed in the tartary buckwheat seedlings after cold stress. Overexpression in Arabidopsis thaliana showed that FtUFGT8, FtUFGT15, and FtUFGT41 significantly increased the anthocyanin content in transgenic plants. Unexpectedly, overexpression of FtUFGT6, while not leading to enhanced anthocyanin accumulation, significantly enhanced the growth yield of transgenic plants. When wild-type plants have only cotyledons, most of the transgenic plants of FtUFGT6 had grown true leaves. Moreover, the growth speed of the oxFtUFGT6 transgenic plant root was also significantly faster than that of the wild type. At later growth, FtUFGT6 transgenic plants showed larger leaves, earlier twitching times and more tillers than wild type, whereas FtUFGT15 showed opposite results. CONCLUSIONS: Seven FtUFGTs were isolated from tartary buckwheat. FtUFGT8, FtUFGT15, and FtUFGT41 can significantly increase the accumulation of total anthocyanins in transgenic plants. Furthermore, overexpression of FtUFGT6 increased the overall yield of Arabidopsis transgenic plants at all growth stages. However, FtUFGT15 shows the opposite trend at later growth stage and delays the growth speed of plants. These results suggested that the biological function of FtUFGT genes in tartary buckwheat is diverse.


Assuntos
Fagopyrum/genética , Genes de Plantas/genética , Glicosiltransferases/genética , Proteínas de Plantas/genética , Antocianinas/metabolismo , Arabidopsis/genética , Sequência Conservada , Fagopyrum/enzimologia , Flavonoides/metabolismo , Genes de Plantas/fisiologia , Glicosiltransferases/fisiologia , Filogenia , Proteínas de Plantas/fisiologia , Plantas Geneticamente Modificadas , Análise de Sequência de DNA
9.
World J Microbiol Biotechnol ; 35(9): 133, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31432254

RESUMO

There is a significant increase in the discovery of new antimicrobial compounds in recent past to combat drug resistant pathogens. Members of the genus Bacillus and related genera have been screened extensively due to their ability to produce wide range of antimicrobial compounds. In this study, we have isolated and characterized a new antimicrobial peptide from a marine bacterium identified as Virgibacillus species. The low molecular mass and stability of the antimicrobial substance pointed towards the bacteriocinogenic nature of the compound. The RAST analysis of genome sequence showed presence of a putative bacteriocin biosynthetic cluster containing genes necessary for synthesis of a lanthipeptide. Translated amino acid sequence of mature C-terminal propeptide showed identity with salivaricin A (52.2%) and lacticin A (33.3%). Accordingly, the mass (2417 Da) obtained by MALDI analysis was in agreement with posttranslational modifications of the leader peptide to yield three methyl lanthionine rings and a disulfide bond between two free cysteine residues. The lanthipeptide was named as virgicin, which selectively inhibited the growth of Gram-positive bacteria and biofilm formation by Enterococcus faecalis. Inhibition of biofilm formation by E. faecalis was also observed in in vitro model experiments using hydroxyapatite discs. Thus, virgicin appears to be a promising new bacteriocin to control oral biofilm formation by selective pathogens.


Assuntos
Bacteriocinas/isolamento & purificação , Bacteriocinas/farmacologia , Enterococcus faecalis/efeitos dos fármacos , Enterococcus faecalis/crescimento & desenvolvimento , Peptídeos/isolamento & purificação , Peptídeos/farmacologia , Virgibacillus/metabolismo , Bacteriocinas/química , Bacteriocinas/genética , Biofilmes/efeitos dos fármacos , Biofilmes/crescimento & desenvolvimento , Vias Biossintéticas/genética , Genoma Bacteriano , Peso Molecular , Família Multigênica , Peptídeos/química , Peptídeos/genética , Água do Mar/microbiologia , Análise de Sequência de DNA , Homologia de Sequência de Aminoácidos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Virgibacillus/classificação , Virgibacillus/isolamento & purificação
10.
World J Microbiol Biotechnol ; 35(9): 132, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31432260

RESUMO

This paper aims to characterize halophilic bacteria inhabiting Algerian Saline Ecosystems (Sebkha and Chott) located in arid and semi-arid ecoclimate zones (Northeastern Algeria). In addition, screening of enzymatic activities, heavy metal tolerance and antagonistic potential against phytopathogenic fungi were tested. A total of 74 bacterial isolates were screened and phylogenetically characterized using 16S rRNA gene sequencing. The results showed a heterogeneous group of microorganisms falling within two major phyla, 52 strains belonging to Firmicutes (70.2%) and 22 strains (30.8%) of γ-Proteobacteria. In terms of main genera present, the isolates were belonging to Bacillus, Halobacillus, Lentibacillus, Oceanobacillus, Paraliobacillus, Planomicrobium, Salicola, Terribacillus, Thalassobacillus, Salibacterium, Salinicoccus, Virgibacillus, Halomonas, Halovibrio, and Idiomarina. Most of the enzymes producers were related to Bacillus, Halobacillus, and Virgibacillus genera and mainly active at 10% of growing salt concentrations. Furthermore, amylase, esterase, gelatinase, and nuclease activities ranked in the first place within the common hydrolytic enzymes. Overall, the isolates showed high minimal inhibitory concentration values (MIC) for Ni2+ and Cu2+ (0.625 to 5 mM) compared to Cd2+ (0.1 to 2 mM) and Zn2+ (0.156 to 2 mM). Moreover, ten isolated strains belonging to Bacillus, Virgibacillus and Halomonas genera, displayed high activity against the pathogenic fungi (Botrytis cinerea, Fusarium oxyporum, F. verticillioides and Phytophthora capsici). This study on halophilic bacteria of unexplored saline niches provides potential sources of biocatalysts and novel bioactive metabolites as well as promising candidates of biocontrol agents and eco-friendly tools for heavy metal bioremediation.


Assuntos
Antibiose , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biota , Microbiologia Ambiental , Salinidade , Argélia , Bactérias/classificação , Bactérias/genética , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Fungos/crescimento & desenvolvimento , Hidrolases/análise , Metais Pesados/metabolismo , Metais Pesados/toxicidade , Testes de Sensibilidade Microbiana , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
11.
Rev Soc Bras Med Trop ; 52: e20190234, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31390444

RESUMO

INTRODUCTION: We investigated the occurrence of relapsing fever (RF) causing Borrelia genus spirochetes in synanthropic bats from the municipality of Maringá, Paraná, South of Brazil. METHODS: Tissue samples from the wings of bats were collected monthly from April 2013 to February 2014 and extracted DNA was used to evaluate the presence of RF causing Borrelia spp. RESULTS: All bat tissues tested negative for RF causing Borrelia spp. CONCLUSIONS: Borrelia spp. do not occur in chiropterans from Maringá.


Assuntos
Borrelia/isolamento & purificação , Quirópteros/microbiologia , Animais , Brasil , DNA Bacteriano , Eletroforese em Gel de Ágar , Florestas , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Fatores de Tempo
12.
Rev Inst Med Trop Sao Paulo ; 61: e37, 2019 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-31411267

RESUMO

Candida glabrata complex includes three species identified through molecular biology methods: C. glabrata sensu stricto , C. nivariensis and C. bracarensis . In Mexico, the phenotypic methods are still used in the diagnosis; therefore, the presence of C. nivariensis and C. bracarensis among clinical isolates is still unknown. The aim of this study was to evaluate the utility of a multiplex PCR for the identification of the C. glabrata species complex. DNA samples from 92 clinical isolates that were previously identified through phenotypic characteristics as C. glabrata were amplified by four oligonucleotides (UNI-5.8S, GLA-f, BRA-f, and NIV-f) that generate amplicons of 397, 293 and 223-bp corresponding to C. glabrata sensu stricto , C. nivariensis , and C. bracarensis , respectively. The amplicon sequences were used to perform a phylogenetic analysis through the Maximum Likelihood method (MEGA6), including strains and reference sequences of species belonging to C. glabrata complex. In addition, recombination and linkage disequilibrium were estimated (DnaSP version 5.0) for C. glabrata sensu stricto isolate s . Eighty-eight isolates generated a 397-bp fragment and only in one isolate a 223-bp amplicon was observed. In the phylogenetic tree, the sequences of 397-bp were grouped with C. glabrata reference sequences , and the sequence of 223-bp was grouped with C. bracarensis reference sequences, corroborating the PCR identification. The number of recombination events for the isolates of C. glabrata sensu stricto was zero, suggesting a clonal population structure. Three isolates that did not amplify any of the expected fragments were identified as Saccharomyces cerevisiae through the sequencing of the D1/D2 domain region within the 28S rDNA gene. The multiplex PCR is a fast, cost-effective and reliable tool that can be used in clinical laboratories to identify C. glabrata complex species.


Assuntos
Candida glabrata/genética , Candidíase/microbiologia , DNA Fúngico/genética , Técnicas de Tipagem Micológica/métodos , Candida glabrata/isolamento & purificação , DNA Ribossômico/genética , DNA Espaçador Ribossômico/genética , Feminino , Humanos , Masculino , México , Reação em Cadeia da Polimerase Multiplex , Filogenia , Análise de Sequência de DNA
13.
Medicine (Baltimore) ; 98(33): e16899, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31415434

RESUMO

Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive multisystem disorder characterized by oculocutaneous albinism (OCA) and bleeding diathesis, although it displays both genetic and phenotypic heterogeneity. Several genetic subtypes of HPS have been identified in human; however, the characterizations of HPS type 4 (HPS-4) genotype and phenotype remain unclear. This study was aimed to identify gene mutation responsible for HPS-4 with pulmonary fibrosis (PF).Two Chinese siblings in their 50 s afflicted with OCA and progressive dyspnea were recruited and underwent clinical and genetic examinations. In both patients, chest high-resolution computerized tomography showed severe interstitial PF in bilateral lung fields, and the pulmonary function test indicated restrictive lung disease. A novel homozygous frameshift mutation (NM_022081: c.630dupC; p.A211fs) in the HPS4 gene was identified by whole-exome sequencing analysis followed by Sanger DNA sequencing, and it segregated with the phenotypes. The c.630dupC mutation was not found in unaffected healthy controls. The patients were considered as HPS-4 with interstitial PF and eventually died of respiratory failure.This is the first report on the genotype and clinical phenotype of HPS-4 in China. Our results demonstrate the association between a novel frameshift mutation in HPS4 and severe PF with poor prognosis in HPS is presented.


Assuntos
Mutação da Fase de Leitura , Síndrome de Hermanski-Pudlak/genética , Fibrose Pulmonar Idiopática/genética , Proteínas/genética , Adulto , China , Testes Genéticos , Humanos , Fibrose Pulmonar Idiopática/diagnóstico por imagem , Masculino , Pessoa de Meia-Idade , Análise de Sequência de DNA , Irmãos
14.
Int J Syst Evol Microbiol ; 69(10): 3128-3134, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31364963

RESUMO

A novel Gram-stain-positive actinobacterial strain, designated C9-28T, was isolated from soil sampled in a natural cave on Jeju Island, Republic of Korea. Strain C9-28T morphologically exhibited a rod-coccus life cycle and grew at 10-37 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and 0-3 % (optimum, absence of NaCl). In the maximum-likelihood tree based on 16S rRNA gene sequences, strain C9-28T formed a sublineage between a Rhodococcus equi-Rhodococcus soli-Rhodococcus agglutinans clade and the type strain of Rhodococcus defluvii. The closest relatives of strain C9-28T were the type strains of R. defluvii (98.88 % 16S rRNA gene sequence similarity), R. equi (98.88 %) and R. soli (98.60 %). The phylogenomic tree based on whole genome sequences supported the distinct position of the novel strain within the genus Rhodococcus. The following chemotaxonomic characteristics also supported the assignment to the genus: meso-diaminopimelic acid; arabinose and galactose in whole-cell hydrolysates; the predominant menaquinone of MK-8(H2); and polar lipids including diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified glycolipids and two unidentified lipids. The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω9c and C14 : 0. Based on the values of average nucleotide identity and digital DNA-DNA hybridization from whole genome sequences, and in vitro DNA-DNA hybridization between the isolate and the closest relatives, strain C9-28T (=KACC 19823T=DSM 107559T) represents a novel species of the genus Rhodococcus, for which the name Rhodococcussubtropicus sp. nov. is proposed.


Assuntos
Cavernas/microbiologia , Filogenia , Rhodococcus/classificação , Microbiologia do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Fosfolipídeos/química , RNA Ribossômico 16S/genética , República da Coreia , Rhodococcus/isolamento & purificação , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
15.
Int J Syst Evol Microbiol ; 69(10): 3161-3169, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31390326

RESUMO

During a survey of fungal diversity in a deserted rocky area in Yunnan, PR China, a new species, Memnoniella sinensis, was identified. This new species is characterized by having phialidic conidiogenous cells with conspicuous collarettes, and aseptate, verrucose, ellipsoidal to sometimes ovoid, olivaceous brown to dark brown conidia. Morphologically, M. sinensis is similar to M. dichroa, but can be easily distinguished due to its hyaline conidiophores and smaller conidia. Phylogenetic analysis based on DNA sequences at five loci showed that our strain grouped together with M. dichroa and M. oenanthes. Here, the new species is described and illustrated, and a key to the species of the genus Memnoniella is provided.


Assuntos
Hypocreales/classificação , Filogenia , China , DNA Fúngico/genética , Hypocreales/isolamento & purificação , Técnicas de Tipagem Micológica , Análise de Sequência de DNA , Esporos Fúngicos
16.
Int J Syst Evol Microbiol ; 69(10): 3041-3048, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31395120

RESUMO

A novel irregularly shaped and slightly curved rod bacterial strain, GLDI4/2T, showing activity of fructose 6-phosphate phosphoketolase was isolated from a faecal sample of an adult gelada baboon (Theropithecus gelada). Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing fusA, gyrB and xfp genes) and the core genome revealed that GLDI4/2T exhibited phylogenetic relatedness to Alloscardovia omnicolens DSM 21503T and to Alloscardovia macacae DSM 24762T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain A. omnicolens DSM 21503T (96.0 %). Activities of α- and ß-gluco(galacto)sidases were detected in strain GLDI4/2T, which is characteristic for almost all members of the family Bifidobacteriaceae. Compared to other Alloscardovia species its DNA G+C content (43.8 mol%) was very low. Phylogenetic studies and the evaluation of phenotypic characteristics, including the results of biochemical, physiological and chemotaxonomic analyses, confirmed the novel species status for strain GLDI4/2T, for which the name Alloscardoviatheropitheci sp. nov. is proposed. The type strain is GLDI4/2T (=DSM 106019T=JCM 32430T).


Assuntos
Actinobacteria/classificação , Filogenia , Theropithecus/microbiologia , Actinobacteria/isolamento & purificação , Aldeído Liases , Animais , Animais de Zoológico/microbiologia , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Fezes/microbiologia , Itália , RNA Ribossômico 16S/genética , Análise de Sequência de DNA
17.
Int J Syst Evol Microbiol ; 69(10): 2966-2971, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31418670

RESUMO

A novel actinobacterium, designated LHW52908T, was isolated from a marine sponge, Leucettachagosensis, collected in the South China Sea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain LHW52908T was member of the family Geodermatophilaceae, with highest similarities to Geodermatophilus obscurus DSM 43160T (97.7 %), Geodermatophilus siccatus CF6T (97.6 %) and Geodermatophiluschilensis B12T (97.5 %). Multilocus sequence analysis confirmed that the strain should be a member of genus Geodermatophilus. Chemotaxonomic characteristics confirmed the genus-level affiliation of strain LHW52908T. Based on phylogenetic data, average nucleotide identity and digital DNA-DNA hybridization results, strain LHW52908T could be distinguished from its closest neighbours, representing a novel species of the genus Geodermatophilus, for which the name Geodermatophilusmarinus sp. nov. is proposed, with the type strain LHW52908T (=DSM 106570T=CCTCC AA 2018014T).


Assuntos
Actinobacteria/classificação , Filogenia , Poríferos/microbiologia , Actinobacteria/isolamento & purificação , Animais , Técnicas de Tipagem Bacteriana , Composição de Bases , China , DNA Bacteriano/genética , Ácidos Graxos/química , Tipagem de Sequências Multilocus , Hibridização de Ácido Nucleico , Oceanos e Mares , Fosfolipídeos/química , Pigmentação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
18.
Plant Dis ; 103(10): 2494-2497, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31453748

RESUMO

Phytoplasmas are plant-pathogenic bacteria that are associated with yield losses in many crop plants worldwide. Phytoplasma strain differentiation is accomplished using in silico restriction fragment length polymorphism (RFLP) analysis of 16S ribosomal RNA-encoding gene sequences, which has resulted in the definition of ribosomal groups and subgroups of phytoplasmas. Due to limitations associated with this approach, a complementary classification scheme was recently developed based on RFLP analysis of the single-copy, protein-encoding gene chaperonin-60 (cpn60). We present the CpnClassiPhyR, software that facilitates phytoplasma strain classification using both RFLP and automated phylogenetic analysis of cpn60 sequences. This software is available through a web interface at http://cpnclassiphyr.ca.


Assuntos
Chaperonina 60 , Phytoplasma , Análise de Sequência de DNA , Software , Chaperonina 60/genética , DNA Bacteriano/genética , Filogenia , Phytoplasma/classificação , Phytoplasma/genética , Doenças das Plantas/microbiologia , Software/normas
19.
Mol Biol (Mosk) ; 53(4): 648-653, 2019.
Artigo em Russo | MEDLINE | ID: mdl-31397438

RESUMO

Acral melanoma is one of the most aggressive and fast-growing forms of cutaneous melanoma and is characterized by a predominant location on the palms and feet. Primary tumors, metastases, and normal tissue samples from five acral melanoma patients were examined by massive parallel sequencing, focusing on the coding regions of 4100 genes involved in the origin and progression of hereditary and oncology diseases. Somatic mutations were found in genes related to cell division, proliferation, and apoptosis (BRAF, NRAS, VAV1, GATA1, and GCM2); cell adhesion (CTNND2 and ITGB4); angiogenesis (VEGFA); and the regulation of energy metabolism (BCS1L). Comparisons of target DNA sequences between morphologically normal and primary tumor tissues and between normal and metastatic tissues identified the candidate genes responsible for rapid metastasis in acral melanoma.


Assuntos
Melanoma/genética , Melanoma/patologia , Mutação , Metástase Neoplásica/genética , Neoplasias Cutâneas/genética , Neoplasias Cutâneas/patologia , Humanos , Análise de Sequência de DNA
20.
Int J Syst Evol Microbiol ; 69(10): 3022-3030, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31364965

RESUMO

Two novel strains, designated YLB-02T and YLB-04T, were isolated from the deep-sea sediments of Yap Trench located in the Pacific Ocean. Cells of the strains were Gram-stain-positive, oxidase- and catalase-positive and rod-shaped. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain YLB-02T belonged to the genus Oceanobacillus and strain YLB-04T belonged to the genus Bacillus. Strain YLB-02T showed similarities of 96.9 % with Ornithinibacillus contaminans CCUG 53201T, 96.3 % with Oceanobacillus profundus CL-MP28T, 96.1 % with Oceanobacillus halophilus J8BT and 95.7 % with Oceanobacillus bengalensis Ma-21T. Strain YLB-04T showed the highest sequence similarity of 97.4 % with Bacillus notoginsengisoli SYP-B691T. The average nucleotide identity (ANI) and the DNA-DNA hybridisation (DDH) estimate values for strain YLB-02T and YLB-04T with their related type strains were below the respective threshold for species differentiation. The G+C contents of strains YLB-02T and YLB-04T were 37.3 and 45.4 mol%. The predominant (>10 %) cellular fatty acids of strain YLB-02T were iso-C14 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 1ω7c alcohol, and those of strain YLB-04T were C16 : 0, iso-C15 : 0, anteiso-C15 : 0 and C18 : 0. Their predominant ubiquinone was MK-7. The cell-wall peptidoglycan of strain YLB-02T contained glutamic acid, alanine, aspartic acid, lysine and ornithine, but no meso-diaminopimelic acid, while strain YLB-04T contained meso-diaminopimelic acid, glutamic acid, alanine, aspartic acid, lysine and ornithine. In addition to diphosphatidylglycerol (DPG) and phosphatidylglycerol (PG), the polar lipids of strain YLB-02T also consisted of an unidentified glycolipid (GL), two unidentified polar lipids (L1 and L2) and two unidentified phospholipids (PL1 and PL2), and those of strain YLB-04T also consisted of phosphatidylethanolamine (PE) and an unidentified phospholipid (PL). Based on phenotypic, genotypic and chemotaxonomic characteristics, two novel species are proposed, Oceanobacillus piezotolerans sp. nov. with YLB-02T (=MCCC 1A12699T=JCM 32870T) and Bacillus piezotolerans sp. nov. with YLB-04T (=MCCC 1A12711T=JCM 32872T) as the type strains.


Assuntos
Bacillaceae/classificação , Bacillus/classificação , Sedimentos Geológicos/microbiologia , Filogenia , Água do Mar/microbiologia , Bacillaceae/isolamento & purificação , Bacillus/isolamento & purificação , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácido Diaminopimélico/química , Ácidos Graxos/química , Hibridização de Ácido Nucleico , Oceano Pacífico , Peptidoglicano/química , Fosfolipídeos/química , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/análogos & derivados , Vitamina K 2/química
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