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1.
An Acad Bras Cienc ; 91(3): e20180568, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31596388

RESUMO

Cyclodextrin glycosyltransferases (CGTases) are important enzymes in the biotechnology field because they catalyze starch conversion into cyclodextrins and linear oligosaccharides, which are used in food, pharmaceutical and cosmetic industries. The CGTases are classified according to their product specificity in α-, ß-, α/ß- and γ-CGTases. As molecular markers are the preferred tool for bacterial identification, we employed six molecular markers (16S rRNA, dnaK, gyrB, recA, rpoB and tufA) to test the identification of a CGTase-producing bacterial strain (DF 9R) in a phylogenetic context. In addition, we assessed the phylogenetic relationship of CGTases along bacterial evolution. The results obtained here allowed us to identify the strain DF 9R as Paenibacillus barengoltzii, and to unveil a complex origin for CGTase types during archaeal and bacterial evolution. We postulate that the α-CGTase activity represents the ancestral type, and that the γ-activity may have derived from ß-CGTases.


Assuntos
Bacillus/genética , Bacillus/isolamento & purificação , Glucosiltransferases/genética , Filogenia , Bacillus/classificação , Genes Essenciais , Marcadores Genéticos , Genoma Bacteriano , Glucosiltransferases/classificação , Glucosiltransferases/isolamento & purificação , RNA Ribossômico 16S/genética , Análise de Sequência
2.
BMC Bioinformatics ; 20(1): 455, 2019 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-31492097

RESUMO

BACKGROUND: Evolutionary information contained in the amino acid sequences of proteins specifies the biological function and fold, but exactly what information contained in the protein sequence drives both of these processes? Considerable progress has been made to answer this fundamental question, but it remains challenging to explore the potential space of cooperative interactions between amino acids. Statistical analysis plays a significant role in studying such interactions and its use has expanded in recent years to studies ranging from coevolution-guided rational protein design to protein folding in silico. RESULTS: Here we describe a computational tool named Sibe for use in studies of protein sequence, folding, and design using evolutionary coupling between amino acids as a driving factor. In this study, Sibe is used to identify positionally conserved couplings between pairwise amino acids and aid rational protein design. In this process, pairwise couplings are filtered according to the relative entropy computed from the positional conservations and grouped into several 'blocks', which could contribute to driving protein folding and design. A human ß2-adrenergic receptor (ß2AR) was used to demonstrate that those 'blocks' contribute the rational design for specifying functional residues. Sibe also provides folding modules based on both the positionally conserved couplings and well-established statistical potentials for simulating protein folding in silico and predicting tertiary structure. Our results show that statistically inferences of basic evolutionary principles, such as conservations and coupled-mutations, can be used to rapidly design a diverse set of proteins and study protein folding. CONCLUSIONS: The developed software Sibe provides a computational tool for systematical analysis from protein primary to its tertiary structure using the evolutionary couplings as a driving factor. Sibe, written in C++, accounts for compatibility with the 'big data' era in biological science, and it primarily focuses on protein sequence analysis, but it is also applicable to extend to other modeling and predictions of experimental measurements.


Assuntos
Biologia Computacional/métodos , Simulação por Computador , Engenharia de Proteínas , Dobramento de Proteína , Proteínas/química , Proteínas/genética , Sequência de Aminoácidos , Entropia , Humanos , Mutação , Receptores Adrenérgicos beta 2/química , Receptores Adrenérgicos beta 2/genética , Análise de Sequência , Software
3.
Microbiol Res ; 228: 126302, 2019 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-31442862

RESUMO

Endophytic bacteria isolated from cactus were characterized and assessed for their capability to induce drought tolerance and growth promotion in tomato. A total of 191-bacteria representing 13-genera and 18-species were isolated from wild cactus, Euphorbia trigonas. Bacillus (58), Lysinibacillus (36), Enterobacter (29), Stenotrophomonas (18), Lelliottia (12) and Pseudomonas (12) were the most represented genera. 16S rDNA sequence (>1400-bp) comparison placed the bacterial isolates with Bacillus xiamenensis; Bacillus megaterium; Bacillus cereus; Bacillus amyloliquefaciens; Bacillus velezensis; Brevibacillus brevis; Lysinibacillus fusiformis; Enterobacter cloacae; Lelliottia nimipressuralis; Proteus penneri; Sphingobacterium multivorum; Klebsiella pneumoniae; Pseudomonas putida; Pseudomonas aeruginosa; Stenotrophomonas maltophilia; Citrobacter freundii; Chryseobacterium indologenes and Paracoccus sp. Bacillus xiamenensis was identified for the first time as plant endophyte. Upon bacterization, the endophytes triggered germination and growth promotion in tomato as indicated by 118 % and 52 % more root-biomass under drought-free and drought-induced conditions, respectively. Bacillus amyloliquefaciens CBa_RA37 and B. megaterium RR10 displayed broad spectrum endophytism in tomato. Bacterization of tomato with cactus endophyte showed altered oxidative status, stomatal and photosystem II functioning, internal leaf temperature and relative water content suggestive of physiological de-stressing from moisture stress. Activity of oxidative stress enzymes such as guaiacol peroxidase and catalase was also indicative of endophyte assisted de-stressing of tomato. Re-irrigation on 20-days of drought infliction showed 86.9% recovery of B. amyloliquefaciens CBa_RA37 primed tomato when non-primed plantlets succumbed. The cactus endophytic bacterial strain B. amyloliquefaciens CBa_RA37 showed promise for low-cost, efficient and environmentally friendly bio-inoculant technology to mitigate drought in arid zones of Asian and African continents.


Assuntos
Cactaceae/microbiologia , Secas , Endófitos/classificação , Endófitos/isolamento & purificação , Endófitos/fisiologia , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/microbiologia , Desenvolvimento Vegetal , Aclimatação , Bacillus/classificação , Bacillus/genética , Bacillus/isolamento & purificação , Bacillus/fisiologia , Biomassa , Camarões , DNA Ribossômico/genética , Clima Desértico , Endófitos/genética , Filogenia , Folhas de Planta , Raízes de Plantas , RNA Ribossômico 16S/genética , Rifamicinas/farmacologia , Análise de Sequência , Microbiologia do Solo , Estresse Fisiológico
4.
Gene ; 716: 144024, 2019 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-31390541

RESUMO

The young leaves generally accumulate a certain concentration anthocyanins in the dominant species of the subtropical forest, and the changes of anthocyanin synthesis-related enzyme genes expression levels had an important effect on the study photoprotection of anthocyanins in the young leaves of subtropical forests. The determination of anthocyanin synthesis-related enzyme gene sequences and the selection of appropriate reference genes provide a basis for analyzing the functional properties of anthocyanins. In this study, four dominant subtropical forest species (i.e., Schima superba, Castanopsis fissa, Acmena acuminatissima, Cryptocarya concinna) were taken as materials. To obtain the correct nucleotide sequences of anthocyanin-related enzymes, the nucleotide sequences of CHS, DFR and ANS in each dominant species were obtained by sequencing and comparison. Then, to select the most stable reference genes for leaves at different developmental stages and different light conditions, the expression levels of six reference genes, including 18S, Actin, GAPDH, TUB, EF1 and UBQ, were studied by real-time fluorescent quantitative PCR (qRT-PCR), and reference gene stability was analyzed by GeNorm and NormFinder software. The results showed that the expression level of Actin was the most stable in S. superba, A. acuminatissima and C. concinna, and the expression level of GAPDH was the most stable in C. fissa. Finally, the expression levels of the anthocyanin synthesis genes CHS, DFR and ANS were analyzed and found to be consistent with the accumulation trend of anthocyanins in leaves. This study has important theoretical and practical significance for future research into the expression of anthocyanin synthesis-related enzyme genes in the dominant tree species in subtropical forests and reveals that anthocyanin has a photoprotective effect for young leaves in high-light environments.


Assuntos
Antocianinas/biossíntese , Árvores/genética , Aciltransferases/genética , Aciltransferases/metabolismo , Oxirredutases do Álcool/genética , Oxirredutases do Álcool/metabolismo , Antocianinas/metabolismo , Florestas , Genes de Plantas , Folhas de Planta/genética , Folhas de Planta/metabolismo , RNA de Plantas/isolamento & purificação , Reação em Cadeia da Polimerase em Tempo Real/normas , Padrões de Referência , Alinhamento de Sequência , Análise de Sequência , Árvores/enzimologia , Árvores/metabolismo
5.
Genome Biol ; 20(1): 144, 2019 07 25.
Artigo em Inglês | MEDLINE | ID: mdl-31345254

RESUMO

BACKGROUND: Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. RESULTS: Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference, and reconstruction of species trees under horizontal gene transfer and recombination events. CONCLUSION: The interactive web service allows researchers to explore the performance of alignment-free tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-the-art tools, accelerating the development of new, more accurate AF solutions.


Assuntos
Análise de Sequência , Benchmarking , Transferência Genética Horizontal , Internet , Filogenia , Sequências Reguladoras de Ácido Nucleico , Alinhamento de Sequência , Análise de Sequência de Proteína , Software
6.
Vet Clin North Am Small Anim Pract ; 49(5): 809-818, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31256903

RESUMO

We introduce a next phase in the evolution of medicine affecting human and veterinary patients. This evolution, genomic cancer medicine (Pmed), involves expansion of genomic and molecular biology into clinical medicine. The implementation of these new technologies has already begun and is a commercial reality. We introduce the underpinnings for this evolution, and focus on application in complex disease states. Pet owners have begun requesting Pmed technologies. To meet this demand, it is important to be aware of the opportunities and obstacles associated with available Pmed offerings as well as the current state of the field.


Assuntos
Doenças do Gato/genética , Doenças do Gato/terapia , Doenças do Cão/genética , Doenças do Cão/terapia , Neoplasias/veterinária , Medicina de Precisão/veterinária , Animais , Gatos , Cães , Predisposição Genética para Doença , Genômica/métodos , Hemangiossarcoma/genética , Hemangiossarcoma/terapia , Hemangiossarcoma/veterinária , Humanos , Neoplasias/genética , Neoplasias/terapia , Medicina de Precisão/métodos , Análise de Sequência , Medicina Veterinária/métodos
7.
World J Microbiol Biotechnol ; 35(7): 108, 2019 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-31267227

RESUMO

A total of 191 yeasts were isolated from 197 samples collected from eight estuarine mangrove forests along four different coastlines of Thailand (Andaman Sea and the East, North and West coasts of the Gulf of Thailand). Of these, 178 isolates were identified as 32 species in 16 genera of Ascomycota, 12 species in nine genera of Basidiomycota, and 13 isolates as potential new species, respectively. Mangroves located along the Andaman Sea coastline had a higher yeast diversity at the species and genera levels than those along the Gulf of Thailand. Kluyveromyces siamensis was the most frequently isolated species, whilst Candida tropicalis was the only species isolated at all eight sites. Screening isolated yeast strains belonging to genera previously reported as oleaginous yeast plus the 13 potential new species, revealed two oleaginous strains, Rhodotorula sphaerocarpa 11-14.4 and Saitozyma podzolica 11-11.3.1. Both of these strains were isolated from the same mangrove forest on the Andaman Sea coastline. They could accumulate lipid when suspended in glucose solution without any supplementation, while the fatty acid composition and oil profile of Rh. sphaerocarpa 11-14.4 and Sait. podzolica 11-11.3.1 were similar to vegetable oil and cocoa butter, respectively.


Assuntos
Filogenia , Áreas Alagadas , Leveduras/classificação , Leveduras/isolamento & purificação , Ascomicetos/química , Ascomicetos/classificação , Ascomicetos/isolamento & purificação , Basidiomycota/química , Basidiomycota/classificação , Basidiomycota/isolamento & purificação , Biodiversidade , Biocombustíveis , DNA Fúngico/análise , DNA Fúngico/isolamento & purificação , Gorduras na Dieta , Ácidos Graxos/análise , Glucose/metabolismo , Metabolismo dos Lipídeos , Lipídeos/análise , Tipagem Molecular , Óleos Vegetais , RNA Ribossômico/genética , Análise de Sequência , Tailândia , Leveduras/química , Leveduras/genética
8.
World J Microbiol Biotechnol ; 35(7): 113, 2019 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-31289918

RESUMO

Camellia taliensis (W. W. Smith) Melchior is a wild tea plant endemic from the west and southwest of Yunnan province of China to the north of Myanmar and is used commonly to produce tea by the local people of its growing areas. Its chemical constituents are closely related to those of C. sinensis var. assamica, a widely cultivated tea plant. In this study, the α diversity and phylogeny of endophytic fungi in the branches of C. taliensis were explored for the first time. A total of 160 fungal strains were obtained and grouped into 42 species from 29 genera, which were identified based on rDNA internal transcribed spacer sequence analysis. Diversity analysis showed that the endophytic fungal community of the branches of C. taliensis had high species richness S (42), Margalef index D' (8.0785), Shannon-Wiener index H' (2.8494), Simpson diversity index DS (0.8891), PIE index (0.8947) and evenness Pielou index J (0.7623) but a low dominant index λ (0.1109). By contrast, that in the branches of C. taliensis had abundant species and high species evenness. Diaporthe tectonigena, Acrocalymma sp. and Colletotrichum magnisporum were the dominant endophytic fungi. The phylogenetic tree was established by maximum parsimony analysis, and the 11 orders observed for endophytic fungi belonging to Ascomycota and Basidiomycota were grouped into 4 classes.


Assuntos
Camellia/microbiologia , Endófitos/classificação , Endófitos/isolamento & purificação , Fungos/classificação , Fungos/isolamento & purificação , Filogenia , Chá , Ascomicetos/classificação , Ascomicetos/genética , Ascomicetos/isolamento & purificação , Basidiomycota/classificação , Basidiomycota/genética , Basidiomycota/isolamento & purificação , Biodiversidade , China , Análise por Conglomerados , DNA Ribossômico/genética , Endófitos/genética , Fungos/genética , Mianmar , Análise de Sequência
9.
Plant Dis ; 103(9): 2199-2203, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31322493

RESUMO

Viral diseases are a limiting factor to wheat production. Viruses are difficult to diagnose in the early stages of disease development and are often confused with nutrient deficiencies or other abiotic problems. Immunological methods are useful to identify viruses, but specific antibodies may not be available or require high virus titer for detection. In 2015 and 2017, wheat plants containing Wheat streak mosaic virus (WSMV) resistance gene, Wsm2, were found to have symptoms characteristic of WSMV. Serologically, WSMV was detected in all four samples. Additionally, High Plains wheat mosaic virus (HPWMoV) was also detected in one of the samples. Barley yellow dwarf virus (BYDV) was not detected, and a detection kit was not readily available for Triticum mosaic virus (TriMV). Initially, cDNA cloning and Sanger sequencing were used to determine the presence of WSMV; however, the process was time-consuming and expensive. Subsequently, cDNA from infected wheat tissue was sequenced with single-strand, Oxford Nanopore sequencing technology (ONT). ONT was able to confirm the presence of WSMV. Additionally, TriMV was found in all of the samples and BYDV in three of the samples. Deep coverage sequencing of full-length, single-strand WSMV revealed variation compared with the WSMV Sidney-81 reference strain and may represent new variants which overcome Wsm2. These results demonstrate that ONT can more accurately identify causal virus agents and has sufficient resolution to provide evidence of causal variants.


Assuntos
Doenças das Plantas , Vírus de Plantas , Análise de Sequência , Triticum , Bunyaviridae/classificação , Bunyaviridae/genética , Luteovirus/classificação , Luteovirus/genética , Nanoporos , Doenças das Plantas/virologia , Vírus de Plantas/classificação , Vírus de Plantas/genética , Potyviridae/classificação , Potyviridae/genética , Análise de Sequência/normas , Triticum/virologia
10.
Microbiol Res ; 226: 55-64, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284945

RESUMO

Functional association between genomic loci and specific biological traits remains lacking in many fungi, including the African tree pathogen Ceratocystis albifundus. This is mainly because of the absence of suitable transformation systems for allowing genetic manipulation of this and other fungi. Here, we present an optimized protocol for Agrobacterium tumefaciens-mediated transformation of C. albifundus. Strain AGL-1 of A. tumefaciens and four binary T-DNA vectors (conferring hygromycin B or geneticin resistance and/or expressing the green fluorescent protein [GFP]) were used for transforming germinated conidia of three isolates of C. albifundus. Stable expression of these T-DNA-encoded traits was confirmed through sequential sub-culturing of fungal transformants on selective and non-selective media and by using PCR and sequence analysis. Single-copy integration of the respective T-DNAs into the genomes of these fungi was confirmed using Southern hybridization analysis. The range of experimental parameters determined and optimised included: (i) concentrations of hygromycin B and geneticin required for inhibiting growth of the wild type fungus and (ii) the dependence of transformation on acetosyringone for inducing the bacterium's virulence genes, as well as (iii) the duration of fungus-bacterium co-cultivation periods and (iv) the concentrations of fungal conidia and bacterial cells used for the latter. The system developed in this study is stable with a high-efficiency, yielding up to 400 transformants per 106 conidia. This is the first report of a transformation protocol for C. albifundus and its availability will be invaluable for functional studies in this important fungus.


Assuntos
Agrobacterium tumefaciens/genética , Ascomicetos/genética , Transformação Genética , Ascomicetos/citologia , Ascomicetos/efeitos dos fármacos , Ascomicetos/crescimento & desenvolvimento , Southern Blotting , Carbenicilina/farmacologia , Técnicas de Cocultura , DNA Bacteriano , Regulação Fúngica da Expressão Gênica , Gentamicinas/farmacologia , Proteínas de Fluorescência Verde/genética , Higromicina B/farmacologia , Canamicina/farmacologia , Reação em Cadeia da Polimerase , Análise de Sequência , Virulência/genética
11.
Microbiol Res ; 226: 65-73, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31284946

RESUMO

Bacterial communities are resilient to the environmental changes, yet the effect of long term ecological changes on bacterial communities remain poorly explored. To study the effect of prolonged environmental changes, a 25 m long sediment core was excavated from a paleo beach ridge located on the Cauvery delta, south east coast of India. Geological evidences suggested that the site has experienced multiple marine transgressions and regressions. The three paleosols from Vettaikaraniruppu (VKI) beach ridge, VKI-2 (2.8 m bgl; 3 kybp), VKI-5 (7.2 m bgl; 6 kybp) and VKI-14 (24.5 m bgl; 146 kybp) was chosen for bacterial community analysis based on their formation period. Bacterial community structure of paleosols was reconstructed using V3 hypervariable region of bacterial 16S rDNA targeted Illumina sequencing. The VKI-5 sediment layer which formed under marine environment contained highest bacterial diversity, and the community was a mix up of terrestrial and marine bacterial population. The final community VKI-2 exhibited an approximate structural pattern witnessed in the native bacterial community VKI-14 which formed during marine regression. Furthermore, marine transgression and regression experienced in VKI resulted in the formation of distinct biogeographic patterns.


Assuntos
Bactérias/classificação , Biodiversidade , Ecossistema , Microbiota , Água do Mar/microbiologia , Bactérias/genética , DNA Bacteriano/genética , DNA Ribossômico/genética , Ecologia , Sedimentos Geológicos/microbiologia , Índia , Biologia Marinha , Microbiota/genética , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência
12.
Int J Food Microbiol ; 304: 68-74, 2019 Sep 02.
Artigo em Inglês | MEDLINE | ID: mdl-31174037

RESUMO

Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried blaTEM-1B, 78.95% carried sul3, and 78.95% carried dfrA12. The genotypic prediction of phenotypic resistance resulted in a mean sensitivity of 97.45% and specificity of 75.48%. Analysis by core genome multilocus sequence typing (cgMLST) demonstrated that the Salmonella isolates from various sources and different locations shared many of the same core genome loci. This implies that serovar Rissen has infected every stage of the pork production process and that contamination can occur in every part of the production chain.


Assuntos
Antibacterianos/farmacologia , Farmacorresistência Bacteriana Múltipla/genética , Contaminação de Alimentos/análise , Carne Vermelha/microbiologia , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/genética , Animais , Doenças Transmitidas por Alimentos/microbiologia , Genótipo , Humanos , Testes de Sensibilidade Microbiana , Tipagem de Sequências Multilocus , Fenótipo , Salmonelose Animal/microbiologia , Salmonella enterica/isolamento & purificação , Análise de Sequência , Suínos , Doenças dos Suínos/microbiologia , Tailândia
14.
Acta Virol ; 63(2): 223-228, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31230452

RESUMO

Continuous monitoring and surveillance of avian avulaviruses (AAvVs) in water/migratory fowl is imperative to ascertain the evolutionary dynamics of these viruses. Here, we report genomic and amino acid characteristics of two AAvVs strains isolated from asymptomatic waterfowl (Anas carolinensis). Sequence characteristics including the presence of virulent motif (112RRQKR↓F117) and biological assessment confirmed the virulent nature of study isolates. Phylogenetic analysis of complete fusion (F) and hemagglutinin-neuraminidase (HN), and hyper-variable region of F gene revealed clustering of both strains within genotype VII and sub-genotype VIIi. The inferred residue analysis of complete F and HN genes revealed a number of substitutions in functionally and structurally important motif/s compared to reference strains of each genotype (I-XI). This study concludes an evolutionary nature of avian avulavaris 1 (AAvV-1), ascertaining continuous surveillance of migratory fowl to better elucidate their infection, epidemiology and subsequent impacts on commercial and backyard poultry. Keywords: virulent AAvV-1; migratory fowl; genetic characterization; evolutionary analysis; Pakistan.


Assuntos
Avulavirus , Genoma Viral , Animais , Avulavirus/classificação , Avulavirus/genética , Avulavirus/patogenicidade , Avulavirus/fisiologia , Doenças das Aves/virologia , Aves/virologia , Genoma Viral/genética , Genótipo , Paquistão , Filogenia , Análise de Sequência
15.
Biomed Environ Sci ; 32(5): 363-370, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31217053

RESUMO

OBJECTIVE: People in Western Africa suffer greatly from febrile jaundice, which is caused by a variety of pathogens. However, yellow fever virus (YFV) is the only pathogen under surveillance in Sierra Leone owing to the undeveloped medical and public health system there. Most of the results of YFV identification are negative. Elucidation of the pathogen spectrum is required to reduce the prevalence of febrile jaundice. METHODS: In the present study, we used Ion Torrent semiconductor sequencing to profile the pathogen spectrum in archived YFV-negative sera from 96 patients in Sierra Leone who presented with unexplained febrile jaundice. RESULTS: The most frequently identified sequencing reads belonged to the following pathogens: cytomegalovirus (89.58%), Epstein-Barr virus (55.21%), hepatitis C virus (34.38%), rhinovirus (28.13%), hepatitis A virus (20.83%), coxsackievirus (10.42%), Ebola virus (8.33%), hepatitis E virus (8.33%), lyssavirus (4.17%), leptospirosis (4.17%), chikungunya virus (2.08%), Crimean-Congo hemorrhagic fever virus (1.04%), and hepatitis B virus (1.04%). CONCLUSION: The distribution of sequencing reads suggests a broader spectrum of pathogens for consideration in clinical diagnostics and epidemiological surveillance in Sierra Leone.


Assuntos
Febre/virologia , Icterícia/virologia , Adolescente , Adulto , Estudos de Casos e Controles , Feminino , Febre/epidemiologia , Humanos , Icterícia/epidemiologia , Masculino , Análise de Sequência , Serra Leoa/epidemiologia , Adulto Jovem
16.
Artigo em Inglês | MEDLINE | ID: mdl-31174695

RESUMO

Canine monocytic ehrlichiosis, an important tick-borne disease caused by Ehrlichia canis, is cosmopolitan but particularly prevalent in tropical and subtropical regions. In Turkey, the genetic diversity of E. canis remains undefined. The aim of this study was to characterize E. canis in naturally infected dogs from Turkey by sequencing and phylogenetic analysis of the Tandem Repeat Protein 36 (TRP36) encoded by the trp36 gene. A total of 167 archived blood samples randomly collected from municipal shelter dogs in three distinct geographic regions were analyzed for E. canis. Only ten samples (5.98%) were found positive by PCR assays target regions of the trp36 and 16S rRNA genes. Sequence analysis of Turkish E. canis TRP36 revealed five Tanden Repeat sequences (TRs) resulting to three TR genotypes: i) the previously reported US genotype composed exclusively from TRs of "TEDSVSAPA" sequence (14 or 8 TRs), ii) the previously Brazilian genotype composed exclusively from TRs of ASVVPEAE sequence (13 TRs), and iii) a novel genotype. In addition, phylogenetic analysis based on the entire sequences of TRP36 revealed that these genotypes correspond to four distinct genogroups (US genogroups I and II, Brazilian genogroup and Costa Rica-Turkey genogroup), all containing Turkish genotypes amongst other geographically distant E. canisgenotypes.


Assuntos
Ehrlichia canis/genética , Ehrlichiose/veterinária , Variação Genética , Filogenia , Sequências de Repetição em Tandem , Animais , Proteínas de Bactérias/genética , Doenças do Cão/microbiologia , Cães , Ehrlichia canis/isolamento & purificação , Genótipo , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/genética , Análise de Sequência , Doenças Transmitidas por Carrapatos/microbiologia , Doenças Transmitidas por Carrapatos/veterinária , Turquia
17.
Genome Biol ; 20(1): 93, 2019 05 30.
Artigo em Inglês | MEDLINE | ID: mdl-31142365

RESUMO

Herein we present a meeting report on the third edition of the 'Revolutionizing Next-Generation Sequencing' conference, organized by the Flemish life-science research institute VIB and held at Antwerp, Belgium, 25-26 March 2019.


Assuntos
Análise de Sequência/tendências , Metagenômica , Análise de Célula Única
18.
Anal Chim Acta ; 1071: 25-35, 2019 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-31128752

RESUMO

Mass spectrometry (MS) has become the primary method for high-sensitivity structural determination of oligosaccharides. Fragmentation in the negative-ion MS can provide a wealth of structural information and these can be used for sequence determination. However, although negative-ion MS of neutral oligosaccharide using the deprotonated molecule [M-H]- as the precursor has been very successful for electrospray ionization (ESI), it has only limited success for matrix-assisted laser desorption/ionization (MALDI). In the present study, the features of negative-ion MALDI primary spectra were investigated in detail and the product-ion spectra using [M-H]- and [M+Cl]- as the precursors were carefully compared. The formation of [M-H]- was the main difficulty for MALDI while [M+Cl]- was proved to be useful as alternative precursor anion for MALDI-MS/MS to produce similar fragmentation for sequencing of neutral oligosaccharides. N-(1-naphthyl)ethylenediamine dihydrochloride was then used as both the matrix and the Cl- dopant to evaluate the extent of structural information that can be obtained by negative-ion fragmentation from [M+Cl]- using laser-induced dissociation (LID)-MS/MS for linkage assignment of gluco-oligosaccharides and for typing of blood-group ABO(H) and Lewis antigens on either type 1 or type 2 backbone-chains.


Assuntos
Sistema do Grupo Sanguíneo ABO/análise , Glucanos/análise , Sistema do Grupo Sanguíneo de Lewis/análise , Oligossacarídeos/análise , Sistema do Grupo Sanguíneo ABO/química , Tipagem e Reações Cruzadas Sanguíneas/métodos , Sequência de Carboidratos , Glucanos/química , Sistema do Grupo Sanguíneo de Lewis/química , Oligossacarídeos/química , Análise de Sequência , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Espectrometria de Massas em Tandem/métodos
19.
Mol Med Rep ; 19(6): 4711-4718, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31059048

RESUMO

Autosomal recessive cornea plana is a very rare hereditary ocular disease, characterized by a flattened corneal curvature, marked hyperopia due to low refractive power and frequently consequent accommodative esotropia. Other features include various cornea anterior segment abnormalities, without systemic problems. The purpose of the present study was to investigate the clinical and molecular alterations in a Chinese family with cornea plana. Full ophthalmic examinations of the patients were performed, including slit­lamp examination, fundus examination and ocular ultrasound. Whole­exome sequencing data were screened for pathological variants in the proband, which were confirmed by Sanger sequencing. One novel missense mutation, c.242A>G (p.N81S) and another novel 7 base­pair deletion mutation, c.772­779del (p.G258Cfs*30), were detected in the keratocan (KERA) gene; two affected siblings inherited these variations in a compound heterozygous state, which were derived from the clinically unaffected heterozygous father (c.772_779del) and mother (c.242A>G), respectively. Neither mutation was observed in unrelated healthy controls (n=200). Multiple computer software predictions supported the pathogenicity of the two variants. Furthermore, protein modeling prediction was performed to better understand the molecular basis of cornea plana, particularly the importance of the leucine­rich repeat domain. This study presents the 14th pathogenic KERA mutations identified worldwide and the first in East Asia so far, to the best of our knowledge. These findings guided prenatal diagnosis for the family in question and expand on the variant spectrum of KERA, therefore facilitating genetic counseling.


Assuntos
Doenças da Córnea/genética , Genes Recessivos/genética , Proteoglicanas/genética , Grupo com Ancestrais do Continente Asiático , Sequência de Bases , China , Córnea/anormalidades , Córnea/patologia , Doenças da Córnea/diagnóstico , Doenças da Córnea/patologia , Distrofias Hereditárias da Córnea/diagnóstico , Distrofias Hereditárias da Córnea/genética , Análise Mutacional de DNA , Éxons/genética , Anormalidades do Olho/genética , Anormalidades do Olho/patologia , Feminino , Humanos , Mutação de Sentido Incorreto , Linhagem , Análise de Sequência , Deleção de Sequência , Sequenciamento Completo do Exoma
20.
Plant Mol Biol ; 100(3): 215-230, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31053988

RESUMO

KEY MESSAGE: Two homologs PsnSuSy1 and PsnSuSy2 from poplar played largely similar but little distinct roles in modulating sink strength, accelerating vegetative growth and modifying secondary growth of plant. Co-overexpression of them together resulted in small but perceptible additive effects. Sucrose synthase (SuSy) acts as a crucial determinant of sink strength by controlling the conversion of sucrose into UDP-glucose, which is not only the sole precursor for cellulose biosynthesis but also an extracellular signaling molecule for plants growth. Therefore, modification of SuSy activity in plants is of utmost importance. We have isolated two SuSy genes from poplar, PsnSuSy1 and PsnSuSy2, which were preferentially expressed in secondary xylem/phloem. To investigate their functions, T2 tobacco transgenic lines of PsnSuSy1 and PsnSuSy2 were generated and then crossed to generate PsnSuSy1/PsnSuSy2 dual overexpression transgenic lines. SuSy activities in all lines were significantly increased though PsnSuSy1/PsnSuSy2 lines only exhibited slightly higher SuSy activities than either PsnSuSy1 or PsnSuSy2 lines. The significantly increased fructose and glucose, engendered by augmented SuSy activities, caused the alternations of many physiological, biochemical measures and phenotypic traits that include accelerated vegetative growth, thickened secondary cell wall, and increased stem breaking force, accompanied with altered expression levels of related pathway genes. The correlation relationships between SuSy activities and many of these traits were statistically significant. However, differences of almost all traits among three types of transgenic lines were insignificant. These findings clearly demonstrated that PsnSuSy1 and PsnSuSy2 had similar but little distinct functions and insubstantial additive effects on modulating sink strength and affecting allocation of carbon elements among secondary cell wall components.


Assuntos
Parede Celular/metabolismo , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Glucosiltransferases/genética , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/genética , Tabaco/genética , Parede Celular/ultraestrutura , Celulose/biossíntese , Clorofila/análise , Clonagem Molecular , Perfilação da Expressão Gênica , Glucosiltransferases/metabolismo , Lignina/metabolismo , Floema/metabolismo , Fotossíntese , Polissacarídeos/metabolismo , Populus/genética , Análise de Sequência , Sacarose/metabolismo , Tabaco/citologia , Tabaco/crescimento & desenvolvimento , Xilema/metabolismo
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