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1.
Ann Hematol ; 99(10): 2279-2288, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32772141

RESUMO

Sickle cell disease (SCD) is a monogenic disease characterized by multisystem morbidity and highly variable clinical course. Inter-individual variability in hemoglobin F (HbF) levels is one of the main modifiers that account for the clinical heterogeneity in SCD. HbF levels are affected by, among other factors, single nucleotide polymorphisms (SNPs) at the BCL11A gene and the HBS1L-MYB intergenic region and Xmn1 gene. Our aim was to investigate HbF-enhancer haplotypes at these loci to obtain a first overview of the genetic situation of SCD patients in Egypt and its impact on the severity of the disease. The study included 100 SCD patients and 100 matched controls. Genotyping of BCL11A (rs1886868 C/T), HBS1L-MYB (rs9389268 A/G) and Xmn1 γG158 (rs7842144 C/T) SNPs showed no statistically significant difference between SCD patients and controls except for the hetero-mutant genotypes of BCL11A which was significantly higher in SCD patients compared with controls. Baseline HbF levels were significantly higher in those with co-inheritance of polymorphic genotypes of BCL11A + HSB1L-MYB and BCL11A + Xmn1. Steady-state HbF levels, used as an indicator of disease severity, were significantly higher in SCD-Sß patients having the polymorphic genotypes of HSB1L-MYB. Fold change of HbF in both patient groups did not differ between those harboring the wild and the polymorphic genotypes of the studied SNPs. In conclusion, BCL11A, HSB1L, and Xmn1 genetic polymorphisms had no positive impact on baseline HbF levels solely but had if coexisted. Discovery of the molecular mechanisms controlling HbF production could provide a more effective strategy for HbF induction.


Assuntos
Anemia Falciforme/genética , DNA Intergênico/genética , Hemoglobina Fetal/análise , Proteínas de Ligação ao GTP/genética , Genes myb , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , Proteínas Repressoras/genética , gama-Globinas/genética , Adolescente , Alelos , Anemia Falciforme/sangue , Anemia Falciforme/etnologia , Estudos de Casos e Controles , Criança , Pré-Escolar , Estudos Transversais , Desoxirribonucleases de Sítio Específico do Tipo II , Egito , Feminino , Genótipo , Humanos , Desequilíbrio de Ligação , Masculino , Polimorfismo de Fragmento de Restrição , Adulto Jovem
2.
Nature ; 585(7824): 298-302, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32669707

RESUMO

Proteins are manufactured by ribosomes-macromolecular complexes of protein and RNA molecules that are assembled within major nuclear compartments called nucleoli1,2. Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. Here we show, however, that RNA polymerase II (Pol II) inside human nucleoli operates near genes encoding rRNAs to drive their expression. Pol II, assisted by the neurodegeneration-associated enzyme senataxin, generates a shield comprising triplex nucleic acid structures known as R-loops at intergenic spacers flanking nucleolar rRNA genes. The shield prevents Pol I from producing sense intergenic noncoding RNAs (sincRNAs) that can disrupt nucleolar organization and rRNA expression. These disruptive sincRNAs can be unleashed by Pol II inhibition, senataxin loss, Ewing sarcoma or locus-associated R-loop repression through an experimental system involving the proteins RNaseH1, eGFP and dCas9 (which we refer to as 'red laser'). We reveal a nucleolar Pol-II-dependent mechanism that drives ribosome biogenesis, identify disease-associated disruption of nucleoli by noncoding RNAs, and establish locus-targeted R-loop modulation. Our findings revise theories of labour division between the major RNA polymerases, and identify nucleolar Pol II as a major factor in protein synthesis and nuclear organization, with potential implications for health and disease.


Assuntos
Nucléolo Celular/enzimologia , Nucléolo Celular/genética , DNA Ribossômico/genética , RNA Polimerase II/metabolismo , RNA não Traduzido/biossíntese , RNA não Traduzido/genética , Ribossomos/metabolismo , Proteína 9 Associada à CRISPR/genética , Proteína 9 Associada à CRISPR/metabolismo , Linhagem Celular Tumoral , Nucléolo Celular/fisiologia , DNA Helicases/metabolismo , DNA Intergênico/genética , Humanos , Enzimas Multifuncionais/metabolismo , Biossíntese de Proteínas , Estruturas R-Loop , RNA Helicases/metabolismo , RNA Polimerase I/antagonistas & inibidores , RNA Polimerase I/metabolismo , Ribonuclease H/metabolismo , Ribossomos/química , Ribossomos/genética , Sarcoma de Ewing/genética , Sarcoma de Ewing/patologia
3.
PLoS One ; 15(6): e0234350, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32530926

RESUMO

Jackfruit-bronzing is caused by bacteria Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii), showing symptoms of yellowish-orange to reddish discolouration and rusty specks on pulps and rags of jackfruit. Twenty-eight pure bacterial strains were collected from four different jackfruit outbreak collection areas in Peninsular Malaysia (Jenderam, Maran, Muadzam Shah and Ipoh). Positive P. stewartii subsp. stewartii verification obtained in the study was based on the phenotypic, hypersensitivity, pathogenicity and molecular tests. Multilocus sequence analysis (MLSA) was performed using four housekeeping genes (gyrB, rpoB, atpD and infB) on all 28 bacterial strains. Single gyrB, rpoB, atpD and infB phylogenetic trees analyses revealed the bootstrap value of 99-100% between our bacterial strains with P. stewartii subsp. stewartii reference strains and P. stewartii subsp. indologenes reference strains. On the other hand, phylogenetic tree of the concatenated sequences of the four housekeeping genes revealed that our 28 bacterial strains were more closely related to P. stewartii subsp. stewartii (99% similarities) compared to its close relative P. stewartii subsp. indologenes, although sequence similarity between these two subspecies were up to 100%. All the strains collected from the four collection areas clustered together, pointing to no variation among the bacterial strains. This study improves our understanding and provided new insight on the genetic diversity of P. stewartii subsp. stewartii associated with jackfruit-bronzing in Malaysia.


Assuntos
Artocarpus/microbiologia , Pantoea/genética , Pantoea/patogenicidade , Doenças das Plantas/microbiologia , Técnicas de Tipagem Bacteriana , DNA Bacteriano/genética , DNA Intergênico/genética , Genes Bacterianos , Variação Genética , Malásia , Tipagem de Sequências Multilocus , Pantoea/classificação , Filogenia , Virulência/genética
4.
Int J Syst Evol Microbiol ; 70(5): 3433-3439, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32375982

RESUMO

During a survey of endophytic fungi in aquatic plants collected from Tibet, PR China, a novel species, Ramichloridium endophyticum, was isolated from Potamogeton pectinatus. This novel species differs from other species of the genus Ramichloridium by its finely verrucose, obovoid, ellipsoidal-obovoid and occasionally subglobose conidia. Phylogenetic analysis of the combined sequences of the internal transcribed spacers (ITS) and the translation elongation factor 1-alpha gene (tef1-α) confirmed that the isolated strain represents a member of the genus Ramichloridium. A full description, illustrations and a phylogenetic tree showing the position of R. endophyticum are provided.


Assuntos
Ascomicetos/classificação , Filogenia , Potamogetonaceae/microbiologia , Ascomicetos/isolamento & purificação , DNA Fúngico/genética , DNA Intergênico/genética , Genes Fúngicos , Técnicas de Tipagem Micológica , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Esporos Fúngicos , Tibet
5.
Nat Commun ; 11(1): 1528, 2020 03 23.
Artigo em Inglês | MEDLINE | ID: mdl-32251294

RESUMO

The occurrence of repetitive genomic changes that provide a selective growth advantage in pluripotent stem cells is of concern for their clinical application. However, the effect of different culture conditions on the underlying mutation rate is unknown. Here we show that the mutation rate in two human embryonic stem cell lines derived and banked for clinical application is low and not substantially affected by culture with Rho Kinase inhibitor, commonly used in their routine maintenance. However, the mutation rate is reduced by >50% in cells cultured under 5% oxygen, when we also found alterations in imprint methylation and reversible DNA hypomethylation. Mutations are evenly distributed across the chromosomes, except for a slight increase on the X-chromosome, and an elevation in intergenic regions suggesting that chromatin structure may affect mutation rate. Overall the results suggest that pluripotent stem cells are not subject to unusually high rates of genetic or epigenetic alterations.


Assuntos
Técnicas de Cultura de Células/métodos , Cromossomos Humanos X/genética , DNA Intergênico/genética , Taxa de Mutação , Células-Tronco Pluripotentes/fisiologia , Linhagem Celular , Meios de Cultura/farmacologia , Metilação de DNA , Análise Mutacional de DNA , Epigênese Genética , Humanos , Estresse Oxidativo/efeitos dos fármacos , Estresse Oxidativo/genética , Oxigênio/química , Oxigênio/farmacologia , Análise de Sequência de RNA , Sequenciamento Completo do Genoma
6.
PLoS One ; 15(4): e0231436, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298321

RESUMO

Molecular-based taxonomy, specifically DNA barcoding, has streamlined organism identification. For land plants, the recommended 2-locus barcode of rbcL and matK is not suitable for all groups, thus the second subunit of the nuclear internal transcribed spacer (ITS2) has received attention as a possible alternative. To date, evaluations of ITS2 have mostly been limited in scope to specific plant orders/families and single source material. Prior to using ITS2 to routinely characterize land plants present in environmental samples (i.e., DNA metabarcoding), a wet lab protocol optimized for bulk sample types is needed. To address this gap, in this study we determined the broad recoverability across land plants when using published ITS2 primer pairs, and subsequently optimized the PCR reaction constituents and cycling conditions for the best two performing primer pairs (ITS2F/ITSp4 and ITSp3/ITSu4). Using these conditions, both primer pairs were used to characterize land plants present in 17 diverse soils collected from across the US. The resulting PCR amplicons were prepared into libraries and pooled for sequencing on an Illumina® MiniSeq. Our existing bioinformatics workflow was used to process raw sequencing data and taxonomically assign unique ITS2 plant sequences by comparison to GenBank. Given strict quality criteria were imposed on sequences for inclusion in data analysis, only 43.6% and 7.5% of sequences from ITS2F/ITSp4 and ITSp3/ITSu4 respectively remained for taxonomic comparisons; ~7-11% of sequences originated from fungal co-amplification. The number of orders and families recovered did differ between primer pairs, with ITS2F/ITSp4 consistently outperforming ITSp3/ITSu4 by >15%. Primer pair bias was observed in the recovery of certain taxonomic groups; ITS2F/ITSp4 preferentially recovered flowering plants and grasses, whereas ITSp3/ITSu4 recovered more moss taxa. To maximize data recovery and reduce potential bias, we advocate that studies using ITS2 to characterize land plants from environmental samples such as soil use a multiple primer pair approach.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Intergênico/genética , DNA de Plantas/genética , Metagenômica/métodos , Briófitas/classificação , Briófitas/genética , Código de Barras de DNA Taxonômico/normas , DNA Intergênico/química , DNA de Plantas/química , Gleiquênias/classificação , Gleiquênias/genética , Magnoliopsida/classificação , Magnoliopsida/genética , Metagenômica/normas , Reação em Cadeia da Polimerase/métodos , Reação em Cadeia da Polimerase/normas , Solo/química
7.
Parasit Vectors ; 13(1): 62, 2020 Feb 12.
Artigo em Inglês | MEDLINE | ID: mdl-32051019

RESUMO

BACKGROUND: Red Vent Syndrome (RVS), a haemorrhagic inflammation of the vent region in Atlantic salmon, is associated with high abundance of Anisakis simplex (s.s.) third-stage larvae (L3) in the vent region. Despite evidence suggesting that increasing A. simplex (s.s.) intensity is a causative factor in RVS aetiology, the definitive cause remains unclear. METHODS: A total of 117 Atlantic salmon were sampled from commercial fisheries on the East, West, and North coasts of Scotland and examined for ascaridoid parasites. Genetic identification of a subsample of Anisakis larvae was performed using the internal transcribed spacer (ITS) region of ribosomal DNA. To assess the extent of differentiation of feeding grounds and dietary composition, stable isotope analysis of carbon and nitrogen was carried out on Atlantic salmon muscle tissue. RESULTS: In the present study, the obtained ITS rDNA sequences matched A. simplex (s.s.) sequences deposited in GenBank at 99-100%. Not all isolated larvae (n = 30,406) were genetically identified. Therefore, the morphotype found in this study is referred to as A. simplex (sensu lato). Anisakis simplex (s.l.) was the most prevalent (100%) nematode with the highest mean intensity (259.9 ± 197.3), in comparison to Hysterothylacium aduncum (66.7%, 6.4 ± 10.2) and Pseudoterranova decipiens (s.l.) (14.5%, 1.4 ± 0.6). The mean intensity of A. simplex (s.l.) represents a four-fold increase compared to published data (63.6 ± 31.9) from salmon captured in Scotland in 2009. Significant positive correlations between A. simplex (s.l.) larvae intensities from the body and the vent suggest that they play a role in the emergence of RVS. The lack of a significant variation in stable isotope ratios of Atlantic salmon indicates that diet or feeding ground are not driving regional differences in A. simplex (s.l.) intensities. CONCLUSIONS: This paper presents the most recent survey for ascaridoid parasites of wild Atlantic salmon from three coastal regions in Scotland. A significant rise in A. simplex (s.l.) intensity could potentially increase both natural mortality rates of Atlantic salmon and possible risks for salmon consumers due to the known zoonotic role of A. simplex (s.s.) and A. pegreffii within the A. simplex (s.l.) species complex.


Assuntos
Anisaquíase/veterinária , Salmo salar/parasitologia , Alimentos Marinhos/parasitologia , Animais , Anisaquíase/diagnóstico , Anisakis/genética , Anisakis/patogenicidade , DNA Intergênico/genética , DNA Ribossômico/genética , Doenças dos Peixes/parasitologia , Larva/genética , Escócia
8.
PLoS Genet ; 16(1): e1008544, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31978080

RESUMO

The genetic architecture of the small and isolated Greenlandic population is advantageous for identification of novel genetic variants associated with cardio-metabolic traits. We aimed to identify genetic loci associated with body mass index (BMI), to expand the knowledge of the genetic and biological mechanisms underlying obesity. Stage 1 BMI-association analyses were performed in 4,626 Greenlanders. Stage 2 replication and meta-analysis were performed in additional cohorts comprising 1,058 Yup'ik Alaska Native people, and 1,529 Greenlanders. Obesity-related traits were assessed in the stage 1 study population. We identified a common variant on chromosome 11, rs4936356, where the derived G-allele had a frequency of 24% in the stage 1 study population. The derived allele was genome-wide significantly associated with lower BMI (beta (SE), -0.14 SD (0.03), p = 3.2x10-8), corresponding to 0.64 kg/m2 lower BMI per G allele in the stage 1 study population. We observed a similar effect in the Yup'ik cohort (-0.09 SD, p = 0.038), and a non-significant effect in the same direction in the independent Greenlandic stage 2 cohort (-0.03 SD, p = 0.514). The association remained genome-wide significant in meta-analysis of the Arctic cohorts (-0.10 SD (0.02), p = 4.7x10-8). Moreover, the variant was associated with a leaner body type (weight, -1.68 (0.37) kg; waist circumference, -1.52 (0.33) cm; hip circumference, -0.85 (0.24) cm; lean mass, -0.84 (0.19) kg; fat mass and percent, -1.66 (0.33) kg and -1.39 (0.27) %; visceral adipose tissue, -0.30 (0.07) cm; subcutaneous adipose tissue, -0.16 (0.05) cm, all p<0.0002), lower insulin resistance (HOMA-IR, -0.12 (0.04), p = 0.00021), and favorable lipid levels (triglyceride, -0.05 (0.02) mmol/l, p = 0.025; HDL-cholesterol, 0.04 (0.01) mmol/l, p = 0.0015). In conclusion, we identified a novel variant, where the derived G-allele possibly associated with lower BMI in Arctic populations, and as a consequence also leaner body type, lower insulin resistance, and a favorable lipid profile.


Assuntos
Índice de Massa Corporal , Cromossomos Humanos Par 11/genética , Inuítes/genética , Polimorfismo de Nucleotídeo Único , Adiposidade , Colesterol/sangue , DNA Intergênico/genética , Feminino , Groenlândia , Humanos , Resistência à Insulina , Masculino , Metaboloma , Circunferência da Cintura
9.
Parasitol Res ; 119(2): 473-481, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31897790

RESUMO

Equine ocular setariasis arising mainly from ectopic infestation of Setaria digitata is a common vision impairing ophthalmic disease in India, and the identification of this filarial nematode is based solely on morphology. However, morphological characters alone are inadequate to detect and differentiate S. digitata from its congeners. The present communication reports the first phylogenetic characterization of equine S. digitata from India based on sequences derived from the mitochondrial cytochrome c oxidase subunit 1 (COI), the mitochondrial small subunit ribosomal DNA (12S rDNA), and the nuclear internal transcribed spacer 2 (ITS2). Three isolates were characterized for each gene, and respective sequences were submitted to NCBI database (MN078131, MN078132, and MN095798). The sequences were also compared with the other related sequences available from PubMed around the globe, and phylogenetic analysis was carried out in conjunction with nucleotide homologies. There was no intraspecific variation among the Indian isolates. The phylogenetic analysis of S. digitata, inferred from these genes, showed that the isolate sequences obtained from different host species created a separate monophyletic clade within the genus Setaria with minor sequence variations revealing similar molecular characteristics of S. digitata isolates throughout the globe. In addition, the studied Indian isolates were found closer to Sri Lankan isolates. The S. digitata and S. labiatopapillosa appeared as sister species.


Assuntos
Oftalmopatias/veterinária , Filarioidea/isolamento & purificação , Doenças dos Cavalos/parasitologia , Cavalos/parasitologia , Setaria (Nematoide)/isolamento & purificação , Setaríase/parasitologia , Animais , DNA Intergênico/genética , DNA Ribossômico/genética , Complexo IV da Cadeia de Transporte de Elétrons/genética , Oftalmopatias/parasitologia , Filarioidea/genética , Índia , Filogenia , Reação em Cadeia da Polimerase/veterinária , RNA Ribossômico/genética , Análise de Sequência de DNA , Setaria (Nematoide)/genética
10.
Int J Food Microbiol ; 319: 108496, 2020 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-31911209

RESUMO

Cassiae Semen (CS) has been widely used as roasted tea and traditional Chinese medicine for decades. However, CS is easily contaminated by fungi and mycotoxins during pre-harvest and post-harvest process, thus posing a potential threat to consumer health. In this study, we used the Illumina MiSeq PE300 platform and targeted the internal transcribed spacer 2 sequences to survey the occurrence of fungi in raw and roasted CS samples. Results showed the fungal contamination in all 12 test samples. Ascomycota was the prevailing fungus at the phylum level, with the relative abundance of 66.50%-99.42%. At the genus level, Aspergillus, Cladosporium, and Penicillium were the most dominant genera, accounting for 0.66%-85.51%, 0.20%-29.11%, and 0.11%-32.92% of the fungal reads, respectively. A total of 68 species were identified, among which six potential toxigenic fungi belonging to Aspergillus, Penicillium, Candida, and Schizophyllum genera were detected. Moreover, differences in fungal communities were observed in raw and roasted CS samples. In conclusion, amplicon sequencing is feasible for analyzing fungal communities in CS samples, which provides a new approach to investigate the fungal contamination in edible-medicinal herb, thereby ensuring food safety and drug efficacy.


Assuntos
Cinnamomum aromaticum/microbiologia , Fungos/classificação , Fungos/genética , Pólen/microbiologia , Aspergillus/genética , Candida/genética , Cladosporium/genética , DNA Intergênico/genética , Contaminação de Alimentos/análise , Inocuidade dos Alimentos/métodos , Fungos/isolamento & purificação , Sequenciamento de Nucleotídeos em Larga Escala , Medicina Tradicional Chinesa , Micobioma , Micotoxinas/análise , Penicillium/genética , Chá/microbiologia
11.
BMC Res Notes ; 13(1): 35, 2020 Jan 17.
Artigo em Inglês | MEDLINE | ID: mdl-31952556

RESUMO

OBJECTIVE: Grasslands are widespread ecosystems that fulfil many functions. Plant species richness (PSR) is known to have beneficial effects on such functions and monitoring PSR is crucial for tracking the effects of land use and agricultural management on these ecosystems. Unfortunately, traditional morphology-based methods are labor-intensive and cannot be adapted for high-throughput assessments. DNA barcoding could aid increasing the throughput of PSR assessments in grasslands. In this proof-of-concept work, we aimed at determining which of three plant DNA barcodes (rbcLa, matK and trnH-psbA) best discriminates 16 key grass and legume species common in temperate sub-alpine grasslands. RESULTS: Barcode trnH-psbA had a 100% correct assignment rate (CAR) in the five analyzed legumes, followed by rbcLa (93.3%) and matK (55.6%). Barcode trnH-psbA had a 100% CAR in the grasses Cynosurus cristatus, Dactylis glomerata and Trisetum flavescens. However, the closely related Festuca, Lolium and Poa species were not always correctly identified, which led to an overall CAR in grasses of 66.7%, 50.0% and 46.4% for trnH-psbA, matK and rbcLa, respectively. Barcode trnH-psbA is thus the most promising candidate for PSR assessments in permanent grasslands and could greatly support plant biodiversity monitoring on a larger scale.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Intergênico/genética , Fabaceae/genética , Poaceae/genética , Biodiversidade , DNA de Plantas , Ecossistema , Filogenia , Análise de Sequência de DNA , Especificidade da Espécie
12.
Int J Med Sci ; 17(1): 45-52, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31929737

RESUMO

Background: The Trichophyton mentagrophytes complex is the second most common causal agent of dermatophytosis. It comprises five species-T. mentagrophytes, T. interdigitale, T. erinacei, T quinckeanum, and T. benhamie, as well as nine different genotypes of T. mentagrophytes / T. interdigitale-which are morphologically similar; however, their susceptibility to antifungal agents may differ. For targeted therapy and better prognosis, it is important to identify these species at a molecular level. However, since many hospitals lack molecular methods, the actual aetiology of dermatophytosis caused by this complex remains unknown. Objective: To characterize 55 anthropophilic isolates of the T. mentagrophytes complex recovered from a dermatological centre in Yucatán, Mexico. Material and methods: Fifty-five isolates of the T. mentagrophytes complex were obtained from patients with tinea capitis, tinea pedis, tinea corporis, tinea barbae, and tinea unguium. They were characterized by their colonial and microscopic morphology on Sabouraud dextrose agar (SDA) and through the sequencing of a fragment from the region ITS1-5.8S-ITS2. Results: All colonies grown on SDA were white. Forty-six isolates formed colonies with a powdery texture, while nine isolates formed colonies with a velvety texture. The micromorphological features were typical of the T. mentagrophytes complex. The molecular analysis revealed that 55 isolates were microorganisms that belonged to the T. mentagrophytes complex, that 46 formed powdery colonies representing T. mentagrophytes, and that the other nine isolates that formed velvety colonies represented T. interdigitale. The latter nine isolates were obtained from patients with tinea pedis, tinea corporis, and tinea unguium. Conclusions: The colony morphology on SDA led to the identification of 46 isolates as T. mentagrophytes and nine isolates as T. interdigitale. At a molecular level, the species identified by their morphology were identified only as T. mentagrophytes complex.


Assuntos
Antifúngicos/farmacologia , DNA Intergênico/genética , Tinha/genética , Trichophyton/genética , Dermatoses Faciais/genética , Dermatoses Faciais/microbiologia , Genótipo , Humanos , Onicomicose/genética , Onicomicose/microbiologia , Análise de Sequência de DNA , Tinha/microbiologia , Tinha/patologia , Tinha do Couro Cabeludo/genética , Tinha do Couro Cabeludo/microbiologia , Tinha dos Pés/genética , Tinha dos Pés/microbiologia , Trichophyton/classificação , Trichophyton/efeitos dos fármacos , Trichophyton/patogenicidade
13.
Clin Exp Rheumatol ; 38(5): 993-1000, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31994481

RESUMO

OBJECTIVES: 2p15 polymorphisms have been reported to increase ankylosing spondylitis (AS) susceptibility in several studies; however, when it comes to whether and how much of this risk exists, the results are inconclusive. The aim of this study is to investigate the correlation between rs10865331 in 2p15 and the risk of AS. METHODS: We conducted a HuGE review and meta-analysis of studies published through September 2019. Studies were identified in PubMed, Scopus, HuGE Navigator, Embase, and Web of Science databases. Odds ratios (ORs) and 95% confidence intervals (CIs) for risk estimations were calculated. Sensitivity analysis, subgroup analysis and analysis for potential publication bias were also estimated. RESULTS: Eleven studies with 18555 AS patients and 43777 unrelated healthy individuals, each with a score greater than 6 on the Newcastle-Ottawa Scale (NOS), that investigated the association between rs10865331 in 2p15 and AS were included in our meta-analysis. Data were classified into the genotype analysis cohort, the OR-value cohort, and the pooled analysis cohort, and then a meta-analysis was performed. The OR value of the recessive model in the genotype analysis cohort was 1.376 (95% CI=1.204-1.572, p<0.001, I²=56.30%), and the OR value of the pooled analysis cohort was 1.295 (95% CI=1.228-1.365, p<0.001, I²=73.70%). These findings suggest that individual who carries this single nucleotide polymorphism (SNP) are about 30% more susceptible to developing AS. CONCLUSIONS: Our results suggest that rs10865331 is associated with a significantly higher risk of AS in all race and country subgroups that we have evaluated. Therefore, rs10865331 may be a useful genetic marker for predicting AS susceptibility. However, further studies are needed to confirm our findings.


Assuntos
Espondilite Anquilosante , Alelos , DNA Intergênico/genética , Predisposição Genética para Doença , Genótipo , Humanos , Polimorfismo de Nucleotídeo Único , Espondilite Anquilosante/diagnóstico , Espondilite Anquilosante/genética
14.
J Nat Med ; 74(1): 106-118, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31377923

RESUMO

The tuberous roots of Pueraria candollei Grah. ex Benth. (Fabaceae), commonly known as white Kwao Krua, are used to relieve menopausal symptoms in Thai traditional medicine because they contain phytoestrogens. Black and red Kwao Krua crude drugs exist as well, but they have different botanical origins and pharmacological activities. There is a high demand for white Kwao Krua products, but because of the limited availability of the plant material, it is suspected that the adulteration and misidentification of white Kwao Krua crude drugs and products occur. In this study, we authenticated white Kwao Krua products collected from Thai herbal markets by molecular, chemical, and microscopic analyses. The nucleotide sequences in the internal transcribed spacer (ITS) and trnH-psbA regions of 23 samples of authentic P. candollei were analyzed, and both regions were found to have intraspecific DNA polymorphisms. Based on the single nucleotide polymorphisms in the ITS1 region, species-specific primer sets of P. candollei were designed to authenticate white Kwao Krua and differentiate it from red and black Kwao Krua. Only the PCR products of KWP02 were not amplified by the primer sets. Isoflavonoid contents and microscopic features were used to support the results of molecular analysis to clarify the botanical origin of white Kwao Krua. Molecular, chemical and microscopic methods confirmed that all the Thai Kwao Krua products examined in this study contained authentic "white Kwao Krua" as claimed on their labels.


Assuntos
Preparações de Plantas/farmacologia , Raízes de Plantas/química , Pueraria/química , Pueraria/classificação , DNA Intergênico/genética , Fitoestrógenos/análise , Preparações de Plantas/análise , Reação em Cadeia da Polimerase , Polimorfismo de Nucleotídeo Único/genética , Pueraria/genética , Tailândia
15.
J Nat Med ; 74(1): 282-293, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31587135

RESUMO

The dried fruits of Terminalia plant (Combretaceae) called "Samo" have been used as herbal medicine in Thai traditional medicine. Four "Samo" crude drugs, namely, Samo thai, Samo thed, Samo dee-ngu, and Samo phiphek, are used as the main ingredients in Triphala and Trisamo recipes. Their commercial products are available in processed and powdered form, but are difficult to authenticate by conventional methods. In this study, we aimed to discriminate species of genus Terminalia for the identification of their crude drugs by a DNA barcoding technique. A total of 208 closely related nucleotide sequences were obtained from nine Terminalia species collected from Thailand and the DDBJ/EMBL/GenBank database. An effective DNA barcode marker was selected from six DNA loci (matK, rbcL, psbA-trnH, ITS, ITS1, and ITS2) and their two-locus combination. All sequences were analyzed by three major methods: (1) BLAST search; (2) the genetic divergence method using Kimura 2-parameter (K2P) distance matrices; and (3) tree topology analysis based on the neighbor-joining method. Comparison of the six candidate DNA loci indicated that ITS identified Terminalia with 100% accuracy at the species and genus levels in the BLAST1 method. ITS2 showed the highest K2P variability. The data from the single markers and the two-locus combinations revealed that only the two-locus combinations, namely, the combinations of rbcL, ITS, ITS1, and ITS2 with psbA-trnH, clearly discriminated all the species. From the results of DNA sequence analysis and the three methods, ITS2 is recommended for the identification of Terminalia species to supplement psbA-trnH.


Assuntos
Código de Barras de DNA Taxonômico/métodos , DNA Intergênico/genética , Complexo de Proteína do Fotossistema II/genética , Terminalia/classificação , Terminalia/genética , Sequência de Bases , DNA de Plantas/genética , Marcadores Genéticos/genética , Fitoterapia , Extratos Vegetais/química , Plantas Medicinais/genética , Análise de Sequência de DNA , Tailândia
16.
Int J Food Microbiol ; 312: 108373, 2020 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-31654841

RESUMO

The use of non-Saccharomyces yeast in conjunction with Saccharomyces cerevisiae in wine fermentation is a growing trend in the wine industry. Non-Saccharomyces, through their distinctive production of secondary metabolites, have the potential to positively contribute to wine sensory profile. To discover new candidate strains for development as starter cultures, indigenous non-Saccharomyces were isolated from un-inoculated fermenting Shiraz musts from a South Australian vineyard (McLaren Vale wine region) and characterised. Among the 77 isolates, 7 species belonging to 5 genera (Kazachstania, Aureobasidium, Meyerozyma, Wickerhamomyces and Torulaspora) were identified by sequencing the internal transcribed spacer regions of the 5.8S rRNA gene (ITS1-5.8S-ITS2 region). The indigenous isolates were evaluated for oenological properties, namely, ethanol tolerance, enzyme activity, and H2S production. To determine their potential industrial use as starter cultures, representative isolates of each species were assessed in a sterile chemically defined grape juice and Viognier grape juice to evaluate their contribution to fermentation kinetics and production of key metabolites, including volatile compounds.


Assuntos
Saccharomycetales/genética , Saccharomycetales/metabolismo , Vitis/metabolismo , Vinho/microbiologia , Leveduras/metabolismo , Austrália , DNA Intergênico/genética , Fazendas , Fermentação , RNA Ribossômico 5,8S/genética , Saccharomycetales/classificação , Saccharomycetales/isolamento & purificação , Austrália do Sul , Vinho/análise
17.
Parasitol Int ; 74: 101976, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31513918

RESUMO

Species in the genus Notocotylus (Trematoda, Notocotylidae) are cosmopolitan parasites of mainly aquatic birds and, to a lesser extent, mammals. In this paper we describe Notocotylus primulus n. sp. parasitizing the Crested Duck, Lophonetta specularioides, from the Patagonian coast, southwestern Atlantic Ocean, based on morphological and molecular data. The new species could be distinguished from its congeners by the combination of several features; among them, the position of the genital pore that is prebifurcal and located close to the posterior margin of the oral sucker, a greater number of both ventral papillae and uterine loops, and a large cirrus sac. Molecular results of the ITS2 sequence support the location of this new species in the genus Notocotylus due to a close relationship with Notocotylus malhamensis (the lower genetic distance of the ITS2 sequences).


Assuntos
Patos/parasitologia , Filogenia , Trematódeos/anatomia & histologia , Trematódeos/classificação , Animais , Oceano Atlântico , DNA Intergênico/genética , Feminino , Genitália/anatomia & histologia , Masculino , RNA Ribossômico 28S/genética
18.
J Basic Microbiol ; 60(2): 126-135, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-31840846

RESUMO

Trichoderma species are recognized as biocontrol agents with great potential in inhibiting fungal pathogens that cause significant crop losses. In this study, 15 Trichoderma isolates were collected from various Egyptian locations. Internal transcribed spacer sequencing revealed four different Trichoderma species; Trichoderma harzianum, Trichoderma asperellum, Trichoderma longibrachiatum, and Trichoderma viride. The antagonistic activity of Trichoderma isolates against Fusarium oxysporum f. sp. capsici was evaluated in vitro. The effect of Trichoderma isolates on pepper growth plants in the presence of F. oxysporum was studied in planta. The inhibition of pathogen mycelial growth in vitro ranged between 35.71% and 85.75%. The isolates Ta3 and Tl had the highest antagonistic ability in vitro against F. oxysporum f. sp. capsici. However, Th7 and Th6 of T. harzianum isolates showed the highest values of disease severity reduction under greenhouse conditions. The genetic diversity of the Trichoderma isolates (Ta1, Ta2, Th1, Th2, Th3, Th4, Th5, and Tv) was investigated on the basis of ISSR and SCoT markers. SCoT primers generated a total of 28 bands, out of which 14 (50%) were polymorphic. ISSR primers gave 32 bands, and 11 of these bands (34.37%) were polymorphic.


Assuntos
Antibiose , Fusarium/patogenicidade , Variação Genética , Controle Biológico de Vetores , Piper nigrum/microbiologia , Doenças das Plantas/prevenção & controle , Trichoderma/genética , DNA Intergênico/genética , Egito , Filogenia , Piper nigrum/crescimento & desenvolvimento , Doenças das Plantas/microbiologia , Microbiologia do Solo , Trichoderma/fisiologia
19.
Molecules ; 25(1)2019 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-31877894

RESUMO

In CRISPR genome editing, CRISPR proteins form ribonucleoprotein complexes with guide RNAs to bind and cleave the target DNAs with complete sequence complementarity. CRISPR genome editing has a high potential for use in precision gene therapy for various diseases, including cancer and genetic disorders, which are caused by DNA mutations within the genome. However, several studies have shown that targeting the DNA via sequence complementarity is imperfect and subject to unintended genome editing of other genomic loci with similar sequences. These off-target problems pose critical safety issues in the therapeutic applications of CRISPR technology, with particular concerns in terms of the genome editing of pathogenic point mutations, where non-mutant alleles can become an off-target with only a one-base difference. In this study, we sought to assess a novel CRISPR genome editing technique that has been proposed to achieve a high specificity by positioning the mismatches within the protospacer adjacent motif (PAM) sequence. To this end, we compared the genome editing specificities of the PAM-based and conventional methods on an oncogenic single-base mutation in the endothelial growth factor receptor (EGFR). The results indicated that the PAM-based method provided a significantly increased genome editing specificity for pathogenic mutant alleles with single-base precision.


Assuntos
Edição de Genes/métodos , Mutação Puntual , Sistemas CRISPR-Cas , DNA Complementar/genética , DNA Intergênico/genética , Receptores ErbB/genética , Humanos
20.
J Helminthol ; 94: e105, 2019 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-31735179

RESUMO

The superfamily Pronocephaloidea Looss, 1899 comprises digeneans occurring in the gut and respiratory organs of fishes, turtles, marine iguanas, birds and mammals. Although many life cycles are known for species of the Notocotylidae Lühe, 1909 maturing in birds and mammals, relatively few are known for the remaining pronocephaloid lineages. We report the cercariae of five pronocephaloid species from marine gastropods of the Queensland coast, Australia. From Lizard Island, northern Great Barrier Reef, we report three cercariae, two from Rhinoclavis vertagus (Cerithiidae) and one from Nassarius coronatus (Nassariidae). From Moreton Bay, southern Queensland, an additional two cercariae are reported from two genotypes of the gastropod worm shell Thylacodes sp. (Vermetidae). Phylogenetic analysis using 28S rRNA gene sequences shows all five species are nested within the Pronocephaloidea, but not matching or particularly close to any previously sequenced taxon. In combination, phylogenetic and ecological evidence suggests that most of these species will prove to be pronocephalids parasitic in marine turtles. The Vermetidae is a new host family for the Pronocephaloidea.


Assuntos
Gastrópodes/parasitologia , Filogenia , Trematódeos/anatomia & histologia , Trematódeos/classificação , Animais , Organismos Aquáticos/classificação , Organismos Aquáticos/parasitologia , Cercárias/anatomia & histologia , Cercárias/classificação , Cercárias/isolamento & purificação , DNA Intergênico/genética , Gastrópodes/classificação , Genótipo , Estágios do Ciclo de Vida , Queensland , RNA Ribossômico 28S/genética , Trematódeos/isolamento & purificação
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