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1.
Lancet ; 394(10197): 533-540, 2019 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-31395441

RESUMO

One of the primary goals of genomic medicine is to improve diagnosis through identification of genomic conditions, which could improve clinical management, prevent complications, and promote health. We explore how genomic medicine is being used to obtain molecular diagnoses for patients with previously undiagnosed diseases in prenatal, paediatric, and adult clinical settings. We focus on the role of clinical genomic sequencing (exome and genome) in aiding patients with conditions that are undiagnosed even after extensive clinical evaluation and testing. In particular, we explore the impact of combining genomic and phenotypic data and integrating multiple data types to improve diagnoses for patients with undiagnosed diseases, and we discuss how these genomic sequencing diagnoses could change clinical management.


Assuntos
Doenças Raras/diagnóstico , Análise de Sequência de DNA/métodos , Adulto , Criança , Diagnóstico Precoce , Genômica , Humanos , Fenótipo , Diagnóstico Pré-Natal/métodos , Doenças Raras/genética , Sequenciamento Completo do Exoma , Sequenciamento Completo do Genoma
2.
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
3.
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
4.
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
5.
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
6.
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
7.
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
8.
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
9.
Am J Orthod Dentofacial Orthop ; 156(1): 104-112.e3, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31256822

RESUMO

INTRODUCTION: Mandibular prognathism (MP) is subject to major polygenic influence and segregates within families in autosomal dominance with variable expressivity and incomplete penetrance. We aimed to identify the inheritance pattern and genes and loci involved in the development of MP in Mediterranean families and to evaluate the dentoskeletal characteristics of affected individuals. METHODS: Fifty-one eastern Mediterranean families with individuals affected by MP were identified. Data and biospecimens were collected from 14 of the families, including clinical examination, lateral cephalography (on subjects with Class III malocclusion), and 5 mL blood drawn from consenting affected and nonaffected relatives. Next-generation sequencing (NGS) was performed on 8 families (7 Lebanese, 1 Lebanese/Syrian), including large numbers of affected individuals over many generations and severe conditions, with the use of whole-exome sequencing. RESULTS: Most pedigrees suggested autosomal-dominant inheritance with an equal number of affected male and female individuals. Affected individuals had macrognathic and prognathic mandibles with dentoalveolar compensation. Genetic screening did not correspond with previously reported MP-linked genes, but yielded 3 novel genes (C1orf167, NBPF8, NBPF9) on chromosome 1 potentially responsible for mandibular development and macrognathism. CONCLUSIONS: In this first genetic study with the use of NGS on the largest reported number of families with MP, novel genes (C1orf167, NBPF8, NBPF9) were associated with familial MP in the eastern Mediterranean population.


Assuntos
Estudos de Associação Genética , Predisposição Genética para Doença/genética , Má Oclusão de Angle Classe III/genética , Prognatismo/genética , Adulto , Grupo com Ancestrais do Continente Asiático , Cefalometria , Cromossomos Humanos Par 1/genética , Feminino , Genoma Humano , Humanos , Líbano , Masculino , Má Oclusão de Angle Classe III/sangue , Má Oclusão de Angle Classe III/diagnóstico por imagem , Má Oclusão de Angle Classe III/patologia , Pessoa de Meia-Idade , Linhagem , Prognatismo/sangue , Prognatismo/diagnóstico por imagem , Prognatismo/patologia , Análise de Sequência de DNA , Síria , Adulto Jovem
10.
Onderstepoort J Vet Res ; 86(1): e1-e6, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31291734

RESUMO

Between July and September 2017, samples collected from six unvaccinated chickens in Namibia were shown to be positive for infectious bursal disease virus (IBDV) by RT-PCR. Partial sequence and phylogenetic analysis of the VP1 and VP2 genes from six viruses revealed that they all belong to the very virulent pathotype (Genogroup 3) and are genetically very similar to IBDVs identified in neighbouring Zambia. This is the first molecular characterisation of IBDV in Namibia and has implications on the control and management of the disease in the country.


Assuntos
Infecções por Birnaviridae/veterinária , Galinhas , Vírus da Doença Infecciosa da Bursa/isolamento & purificação , Doenças das Aves Domésticas/epidemiologia , Animais , Infecções por Birnaviridae/epidemiologia , Vírus da Doença Infecciosa da Bursa/genética , Namíbia/epidemiologia , Filogenia , Doenças das Aves Domésticas/virologia , Análise de Sequência de DNA/veterinária
11.
BMC Plant Biol ; 19(1): 321, 2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31319815

RESUMO

BACKGROUND: Magnolia wufengensis is a new species of Magnolia L. and has considerable ornamental and economic value due to its unique characteristics. However, because of its characteristic of poor low temperature resistance, M. wufengensis is hardly popularization and application in the north of China. Furthermore, the mechanisms of gene regulation and signaling pathways involved in the cold-stress response remained unclear in this species. In order to solve the above-mentioned problems, we performed de novo transcriptome assembly and compared the gene expression under the natural (25 °C) and cold (4 °C) conditions for M. wufengensis seedlings. RESULTS: More than 46 million high-quality clean reads were produced from six samples (RNA was extracted from the leaves) and were used for performing de novo transcriptome assembly. A total of 59,764 non-redundant unigenes with an average length of 899 bp (N50 = 1,110) were generated. Among these unigenes, 31,038 unigenes exhibited significant sequence similarity to known genes, as determined by BLASTx searches (E-value ≤1.0E-05) against the Nr, SwissProt, String, GO, KEGG, and Cluster of COG databases. Based on a comparative transcriptome analysis, 3,910 unigenes were significantly differentially expressed (false discovery rate [FDR] < 0.05 and |log2FC (CT/CK)| ≥ 1) in the cold-treated samples, and 2,616 and 1,294 unigenes were up- and down-regulated by cold stress, respectively. Analysis of the expression patterns of 16 differentially expressed genes (DEGs) by quantitative real-time RT-PCR (qRT-PCR) confirmed the accuracy of the RNA-Seq results. Gene Ontology and KEGG pathway functional enrichment analyses allowed us to better understand these differentially expressed unigenes. The most significant transcriptomic changes observed under cold stress were related to plant hormone and signal transduction pathways, primary and secondary metabolism, and photosynthesis. In addition, 113 transcription factors, including members of the AP2-EREBP, bHLH, WRKY, MYB, NAC, HSF, and bZIP families, were identified as cold responsive. CONCLUSION: We generated a genome-wide transcript profile of M. wufengensis and a de novo-assembled transcriptome that can be used to analyze genes involved in biological processes. In this study, we provide the first report of transcriptome sequencing of cold-stressed M. wufengensis. Our findings provide important clues not only for understanding the molecular mechanisms of cold stress in plants but also for introducing cold hardiness into M. wufengensis.


Assuntos
Regulação da Expressão Gênica de Plantas/genética , Magnolia/genética , Resposta ao Choque Frio , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/fisiologia , Genes de Plantas/genética , Genes de Plantas/fisiologia , Magnolia/fisiologia , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA , Transdução de Sinais , Transcriptoma
12.
Gene ; 715: 143970, 2019 Oct 05.
Artigo em Inglês | MEDLINE | ID: mdl-31330235

RESUMO

BACKGROUND: Bicuspid aortic valve (BAV) formation is genetically determined, with reduced penetrance and variable expressivity. NOTCH1 is a proven candidate gene and its mutations have been found in familial and sporadic cases of BAV. METHODS: 66 BAV patients from the GISSI VAR study were genotyped for the NOTCH1 gene. RESULTS: We identified 63 variants, in heterozygous and homozygous states. Fifty-two are common polymorphisms present in almost all patients. Eleven variants are new and never yet reported: two are non-synonymous substitutions, Gly540Asp in exon 10 and Glu851Gln in exon 16; one is in the 3'UTR region and seven in introns, one corresponds to a T allele insertion in intron 27. We selected four statistically noteworthy and seven new variants identified in six BAV patients and correlated them with clinical and demographic variables and with imaging and histological parameters. Preliminary data show that four were BAV patients with isolated stenosis in patients over 60 aged. These variants may correlate with a later need for surgery for the presence of stenosis and not aortic valve regurgitation or ascending aortic aneurysm. CONCLUSIONS: Completing the genotyping of 62 BAV patients we found 11 new variants in the NOTCH1 gene never yet reported. These findings confirm that the identification of new, clinically remarkable biomarkers for BAV requires a deeper genetic understanding of the NOTCH1 gene variants, which could be targeted by future diagnostic and therapeutic strategies.


Assuntos
Estenose da Valva Aórtica/genética , Valva Aórtica/anormalidades , Doenças das Valvas Cardíacas , Mutação de Sentido Incorreto , Penetrância , Receptor Notch1/genética , Adulto , Alelos , Substituição de Aminoácidos , Éxons , Feminino , Heterozigoto , Homozigoto , Humanos , Íntrons , Itália , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Estudos Prospectivos , Análise de Sequência de DNA
13.
J Agric Food Chem ; 67(31): 8626-8631, 2019 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-31287307

RESUMO

An almond allergen with two known short peptide sequences was reported as the almond 2S albumin but was later suspected to be almond vicilin. However, this allergen was not designated by the World Health Organization/International Union of Immunological Societies. This study aimed to determine the true identity of this elusive almond allergen. cDNAs were synthesized from total RNA of the Nonpareil almond. The complete sequence of the previously reported almond allergen was determined from its coding sequence. The deduced protein was produced recombinantly and was confirmed to be a food allergen by testing with 18 almond-allergic sera. The allergen is a potential cysteine-rich antimicrobial protein with characteristic C[X]3C-[X]10-12-C[X]3C motifs of the hairpinin antimicrobial protein. This first member of a novel family of food allergens was named Pru du 8. The signature motif of the hairpinin antimicrobial protein can be found in the N-terminal region of some vicilin allergens (e.g., Ara h 1). It can also be found in the signal peptide of other vicilin allergens (e.g., Car i 2). In many species, however, vicilins do not contain such a motif, indicating that the presence of the signature motifs of the hairpinin antimicrobial protein in vicilins might be a result of translocation during evolution.


Assuntos
Alérgenos/imunologia , Antígenos de Plantas/imunologia , Prunus dulcis/imunologia , Alérgenos/química , Alérgenos/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Antígenos de Plantas/química , Antígenos de Plantas/genética , DNA Complementar/genética , Hipersensibilidade Alimentar/imunologia , Humanos , Prunus dulcis/química , Prunus dulcis/genética , Proteínas de Armazenamento de Sementes/química , Proteínas de Armazenamento de Sementes/genética , Proteínas de Armazenamento de Sementes/imunologia , Alinhamento de Sequência , Análise de Sequência de DNA
14.
Int J Syst Evol Microbiol ; 69(8): 2555-2564, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31287396

RESUMO

A pink-pigmented, Gram-stain-positive, aerobic, coccoid-shaped bacterial strain, designated as S5-TSA-19T, was isolated from an explosives contaminated site in Panchkula, Haryana, India. The 16S rRNA gene sequencing blast analysis indicated that the strain is a member of the family Planococcaceae with the highest sequence similarity to Planomicrobium soli XN13T (96.1 %), followed by Planococcus maitriensis S1T (95.6 %), Planococcus plakortidis DSM 23997T (95.6 %), Planomicrobium flavidum ISL-41T (95.6 %), Planococcus rifietoensis M8T (95.5 %), Planococcus salinus LCB217T (95.5 %) and Planococcus maritimus DSM 17275T (95.5 %). Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences (based on a conserved set of 400 proteins) retrieved the strain in a distinct branch indicating a separate lineage within the family Planococcaceae. Strain S5-TSA-19T had a distinctive chemotaxonomic pattern comprising A4α type peptidoglycan based on l-Lys-d-Asp, iso-C15 : 0 as the major fatty acid, absence of phosphatidylethanolamine as a major lipid and MK-7 and MK-6 as the major menaquinones, differentiating it from the genera Planococcus and Planomicrobium, thus supporting the findings of molecular phylogeny. Further, strain S5-TSA-19T was able to biotransform hexahydro-1,3,5,-trinitro-1,2,5-triazine (RDX) into nitrite derivatives under aerobic conditions in 2-4 days, whereas the closest reference strains did not possess this property. On the basis of polyphasic taxonomic characterization and a phylogenomics approach, strain S5-TSA-19T is proposed as the type strain of a novel species in a novel genus for which the name Indiicoccus explosivorum gen. nov., sp. nov. is proposed (=JCM 31737T=KCTC 33871T=MTCC 12608T).


Assuntos
Substâncias Explosivas , Filogenia , Planococáceas/classificação , Poluentes do Solo , Técnicas de Tipagem Bacteriana , Composição de Bases , DNA Bacteriano/genética , Ácidos Graxos/química , Índia , Peptidoglicano/química , Fosfatidiletanolaminas , Pigmentação , Planococáceas/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Vitamina K 2/química
15.
Zhonghua Er Ke Za Zhi ; 57(7): 520-525, 2019 Jul 02.
Artigo em Chinês | MEDLINE | ID: mdl-31269551

RESUMO

Objective: To analyze the clinical and genotypic characteristics of infantile inflammatory bowel disease (IBD). Methods: The age of onset, family history, clinical manifestations, and treatment effect were retrospectively analyzed in 39 infants (male 23 cases, female 16 cases) with IBD who were admitted to the Department of Gastroenterology in Children's Hospital, Capital Institute of Pediatrics from January 2007 to December 2017. Next generation sequencing (NGS) based on target gene panel was used for gene analysis in 17 patients. Results: The median age of onset was 0.5 (0.5, 1.0) month. The most common clinical symptoms included diarrhea (39, 100%), malnutrition (38, 97%), hematochezia (34, 87%), fever (25, 64%), and perianal diseases (24, 61%). Four children had associated family history. Among the 17 patients whose gene was analyzed, 10 were found to have the pathogenic gene variation, within whom 7 had interleukin-10 receptor α subunit (IL-10RA) mutation, 2 had CYBB heterozygous mutation, 1 had interleukin-10 receptor ß subunit (IL-10RB) mutation. The therapeutic medicine included mesalazine, steroids, and thalidomide. Eighteen children (46%) reached clinical remission (10 cases) or partial remission (8 cases). Conclusions: The incidence of single gene mutation in infants with IBD is high, with IL-10RA mutation as the most common. Refractory diarrhea and malnutrition may indicate infantile IBD.


Assuntos
Doenças Inflamatórias Intestinais/diagnóstico , Subunidade alfa de Receptor de Interleucina-10/genética , Subunidade beta de Receptor de Interleucina-10/genética , NADPH Oxidase 2/genética , Criança , Feminino , Marcadores Genéticos , Genótipo , Humanos , Lactente , Doenças Inflamatórias Intestinais/genética , Interleucina-10 , Masculino , Mutação , Estudos Retrospectivos , Análise de Sequência de DNA
16.
J Med Microbiol ; 68(8): 1173-1188, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31268417

RESUMO

PURPOSE: Correct serotype identification of Streptococcus pneumoniae (pneumococcus) is important for monitoring disease epidemiology and assessing the impacts of pneumococcal vaccines. Furthermore, correct identification and differentiation of the pathogenic S. pneumoniae from closely related commensal species of the mitis group of the genus Streptococcus are essential for correct serotype identification. METHODOLOGY: A new protocol for determining the existing 98 serotypes of pneumococcus was developed, applying two PCR amplifications and amplicon sequencing, using newly designed internal primers. The new protocol was validated using S. pneumoniae genome sequences, reference strains with confirmed serotypes and clinical isolates, and comparing the results with those from the traditional Quellung reaction or antiserum panel gel precipitation, in addition to real-time PCR analysis. The taxonomic identifications of 422 publicly available (GenBank) genome sequences of S. pneumoniae, Streptococcus pseudopneumoniae and Streptococcus mitis were assessed by whole-genome sequence average nucleotide identity based on blast (ANIb) analysis. RESULTS: The proposed sequetyping protocol generates a 1017 bp whole cpsB region sequence, increasing resolution for serotype identification in pneumococcus isolates. The identifications of all GenBank genome sequences of S. pneumoniae were confirmed, whereas most of the S. pseudopneumoniae and almost all of the S. mitis genome sequences did not fulfil the ANIb thresholds for species-level identification. The housekeeping biomarker gene, groEL, correctly identified S. pneumoniae but often misclassified S. pseudopneumoniae and S. mitis as S. pneumoniae. CONCLUSIONS: These studies affirm the importance of applying reliable identification protocols for S. pneumoniae before serotyping; our protocols provide reliable diagnostic tools, as well as an improved workflow, for serotype identification of pneumococcus and differentiation of serogroup 6 types.


Assuntos
Cápsulas Bacterianas/genética , Tipagem Molecular/métodos , Streptococcus pneumoniae/classificação , Streptococcus pneumoniae/genética , Proteínas de Bactérias/genética , DNA Bacteriano/genética , Genoma Bacteriano/genética , Humanos , Infecções Pneumocócicas/microbiologia , Proteínas Tirosina Fosfatases/genética , Reação em Cadeia da Polimerase em Tempo Real , Análise de Sequência de DNA , Sorogrupo , Sorotipagem/normas , Streptococcus/classificação , Streptococcus/genética , Streptococcus/isolamento & purificação , Streptococcus pneumoniae/isolamento & purificação , Fluxo de Trabalho
17.
Parasite ; 26: 44, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31335315

RESUMO

Anacanthorus (Anacanthorinae) is one of the most speciose and common genera of neotropical monogeneans, yet there are still many gaps in our knowledge concerning their diversity and phylogeny. We performed phylogenetic analyses of molecular sequences in order to investigate the phylogenetic position within the Dactylogyridae of Anacanthorus spp. infesting serrasalmids from two Brazilian river basins. Sequences of partial 28S rDNA obtained for nine species of Anacanthorus and Mymarothecium viatorum parasitizing serrasalmids and the published sequences of other members of the Dactylogyridae were included in the phylogenetic reconstruction. Phylogenetic analyses supported the monophyly of anacanthorine monogeneans. The Anacanthorinae (represented in this study by Anacanthorus spp.) formed a monophyletic group included in a large clade together with a group of solely freshwater Ancyrocephalinae and species of the Ancylodiscoidinae. Mymarothecium viatorum (Ancyrocephalinae) was placed within the clade of freshwater Ancyrocephalinae. The phylogenetic analyses indicated that the relationships among species of Anacanthorus reflect those of their serrasalmid hosts: the first subgroup includes a species specific to hosts assigned to Piaractus, a member of the "pacus" lineage; the second subgroup includes a species parasitizing the "Myleus-like pacus" lineage; and the third subgroup includes species parasitizing the lineage of the "true piranhas". We suggest that Anacanthorus and their serrasalmid hosts can be considered a useful model to assess host-parasite biogeography and coevolution in the neotropics. However, future studies focusing on a wider spectrum of host species and their specific Anacanthorus spp. are needed in order to investigate coevolution in this highly diversified system.


Assuntos
Caraciformes/parasitologia , Doenças dos Peixes/parasitologia , Filogenia , Trematódeos/classificação , Animais , Brasil , DNA de Helmintos/genética , DNA Ribossômico/genética , Análise de Sequência de DNA , Especificidade da Espécie
18.
Arch Insect Biochem Physiol ; 102(1): e21599, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31328816

RESUMO

A complementary DNA that encodes an omega-class glutathione S-transferase (GST) of the brown planthopper, Nilaparvata lugens (nlGSTO), was isolated by reverse transcriptase polymerase chain reaction. A recombinant protein (nlGSTO) was obtained via overexpression in the Escherichia coli cells and purified. nlGSTO catalyzes the biotransformation of glutathione with 1-chloro-2,4-dinitrobenzene, a general substrate for GST, as well as with dehydroascorbate to synthesize ascorbate. Mutation experiments revealed that putative substrate-binding sites, including Phe28, Cys29, Phe30, Arg176, and Lue225, were important for glutathione transferase and dehydroascorbate reductase activities. As ascorbate is a reducing agent, nlGSTO may participate in antioxidant resistance.


Assuntos
Glutationa Transferase/metabolismo , Hemípteros/enzimologia , Oxirredutases/metabolismo , Sequência de Aminoácidos , Animais , Proteínas de Insetos/metabolismo , Análise de Sequência de DNA
19.
Medicine (Baltimore) ; 98(30): e16485, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31348255

RESUMO

RATIONALE: Spondylometaphyseal dysplasia (SMD) is an extremely rare disorder of irregular development of spine and metaphyses of long tubular bones. Mutations in the collagen type X alpha 1 gene were found to underlie this condition. Previously reported mutations in the N-terminal non-collagenous NC2 domain and C-terminal non-collagenous NC1 domain failed to be identified in some specific patients. PATIENT CONCERNS: A 23-year-old male was referred to us for fixed, angular thoracolumbar kyphosis with semi-paralysis, numbness, and tremor on his left lower limb. Marked hypoplasia of thoracolumbar vertebra and spinal canal stenosis were observed on radiology. DIAGNOSES: He was diagnosed with spondylometaphyseal dysplasia (Type A4). Gene sequencing was performed using normalized targeted regions sequencing (TRS). A novel heterozygous missense variant p.Gly139Cys in the triple-helical region. Multiple lines of evidence imply this mutation to be pathogenic. INTERVENTIONS: Posterior instrumentation and vertebral column resection were given to correct his fixed, angular thoracolumbar kyphosis. OUTCOMES: The correction was satisfying and the functional outcomes were good. LESSONS SUBSECTIONS AS PER STYLE: The findings corroborated that type X collagen plays a critical role in the formation of the human spine as well as the long bones, and further expanded the range of type X collagenopathy. Surgical procedure could be considered for patients with severe malformation and neurological impairments.


Assuntos
Colágeno Tipo X/genética , Coxa Valga/complicações , Osteocondrodisplasias/complicações , Osteocondrodisplasias/genética , Coxa Valga/cirurgia , Humanos , Cifose/etiologia , Cifose/cirurgia , Masculino , Osteocondrodisplasias/cirurgia , Análise de Sequência de DNA , Adulto Jovem
20.
Anticancer Res ; 39(7): 3565-3570, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31262880

RESUMO

BACKGROUND/AIM: Trifluridine (FTD) is a key component of the novel oral antitumor drug trifluridine/tipiracil that has been approved for the treatment of metastatic colorectal cancer. In this study, a comprehensive analysis of DNA replication profile in FTD-treated colon cancer cells was performed. MATERIALS AND METHODS: HCT-116 cells were exposed to BrdU or FTD and subjected to DNA immunoprecipitation. Immunoprecipitated DNA was sequenced; the density of aligned reads along the genome was calculated. Peak finding, gene ontology, and motif analysis were performed using MACS, GREAT, and MEME, respectively. RESULTS: We identified 6,043 and 5,080 high-confidence FTD and BrdU peaks in HCT-116 cells, respectively. Of 6,043 FTD peaks, 2,911 peaks were uncommon to BrdU. We observed that FTD was preferentially incorporated into genomic regions containing simple repeats, CpG islands, and gene bodies. Conserved motifs in FTD peaks contained dinucleotide repeats such as (GT)n. CONCLUSION: Global FTD incorporation patterns delineated FTD, preferentially incorporating loci in cancer cells.


Assuntos
Antimetabólitos Antineoplásicos/farmacologia , Bromodesoxiuridina/farmacologia , Neoplasias Colorretais/genética , Replicação do DNA/efeitos dos fármacos , Trifluridina/farmacologia , Células HCT116 , Humanos , Análise de Sequência de DNA
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