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1.
Acta biol. colomb ; 27(1): 5-16, ene.-abr. 2022. tab, graf
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1360044

ABSTRACT

RESUMEN Con el objetivo de determinar las diferencias morfo-agronómicas y de calidad, y la diversidad genética entre 14 variedades de arroz de América Latina con sus respectivas líneas de origen, se estableció un estudio (Bloques completos al azar, con 28 genotipos, tres repeticiones y dos siembras en el tiempo), en el cual se midieron 25 variables morfo-agronómicas y de calidad de grano. El análisis molecular se hizo mediante un arreglo de 96 marcadores tipo SNP de alta capacidad de discriminación para arroces Indica. El análisis estadístico se hizo combinando los datos de las dos siembras porque no hubo diferencias estadísticas entre ellas. Además, se analizaron en conjunto los datos moleculares con los morfo-agronómicos y de calidad, usando el índice de Gower para generar una matriz de similitud. Mediante el programa SAS se analizaron los datos agronómicos y moleculares tanto en forma independiente como en conjunto. Los resultados mostraron que, de las 14 variedades, ocho se agruparon con su línea de origen y hubo una variedad que se agrupó con una línea hermana de su ancestro. Los resultados fueron consistentes cuando el análisis de datos se hizo independientemente o combinado. Dada la amplia diversidad encontrada dentro de las variedades y que ninguna fue homocigota al 100 % no se pudieron establecer los perfiles genéticos distintivos de ellas, por lo que se debe hacer la purificación de las variedades para establecer su huella genética.


ABSTRACT This research aimed to determine the morpho-agronomic, grain quality, and molecular differences between 14 rice varieties and their ancestors. These rice varieties from Latin America were tested for 25 variables in a randomized complete block design with 28 genotypes, two planting dates, and three replications. The molecular analysis was done using an array of 96 SNP markers with a high discrimination capacity for Indica rice. A combined statistical analysis was done because there were no statistical differences between the planting dates. Also, molecular, morpho-agronomic, and grain quality data were analyzed together, using the Gower index to generate a similarity matrix. Agronomic and molecular data were analyzed both, together and independently, through the SAS program. Results showed that eight varieties were grouped with their respective ancestor, and one variety was grouped with a sibling of their ancestor and was consistent in all the analyses. However, given the wide heterozygosity found within the varieties, distinctive genetic profiles could not be established; the varieties must be purified to establish their genetic footprint.

2.
Biomédica (Bogotá) ; 42(1): 18-30, ene.-mar. 2022. graf
Article in English | LILACS | ID: biblio-1374504

ABSTRACT

Introduction: Fusarium is a very heterogeneous group of fungi, difficult to classify, with a wide range of living styles, acting as saprophytes, parasites of plants, or pathogens for humans and animals. Prevalence of clinical fusariosis and lack of effective treatments have increased the interest in the precise diagnosis, which implies a molecular characterization of Fusarium populations. Objective: We compared different genotyping markers in their assessment of the genetic variability and molecular identification of clinical isolates of Fusarium. Materials and methods: We evaluated the performance of the fingerprinting produced by two random primers: M13, which amplifies a minisatellite sequence, and (GACA)4, which corresponds to a simple repetitive DNA sequence. Using the Hunter Gaston Discriminatory Index (HGDI), an analysis of molecular variance (AMOVA), and a Mantel test, the resolution of these markers was compared to the reference sequencing-based and PCR genotyping methods. Results: The highest HGDI value was associated with the M13 marker followed by (GACA)4. AMOVA and the Mantel tests supported a strong correlation between the M13 classification and the reference method given by the partial sequencing of the transcription elongation factor 1-alpha (TEF1-α) and rDNA 28S. Conclusion: The strong correlation between the M13 classification and the sequencing-based reference together with its higher resolution demonstrates its adequacy for the characterization of Fusarium populations.


Introducción. Fusarium es un grupo heterogéneo de hongos, difícil de clasificar y con una amplia gama de estilos de vida, que actúa como saprófito, parásito de plantas o patógeno de humanos y animales. La prevalencia de la fusariosis clínica y la falta de tratamientos han incrementado el interés en su diagnóstico preciso, lo que conlleva la caracterización molecular de las poblaciones. Objetivo. Comparar marcadores de genotipificación en la evaluación de la variabilidad genética e identificación de aislamientos clínicos de Fusarium. Materiales y métodos. Se evaluó la huella genética producida por dos cebadores aleatorios: M13, que amplifica una secuencia minisatélite, y (GACA)4, que corresponde a una secuencia repetitiva de ADN. Utilizando el índice discriminatorio de Hunter Gaston (HGDI), el análisis de varianza molecular (AMOVA) y una prueba de Mantel, se comparó la resolución de estos marcadores con métodos de genotipificación basados en secuenciación y PCR. Resultados. El mayor HGDI se asoció con el marcador M13, seguido de (GACA)4. Las pruebas AMOVA y Mantel mostraron correlación entre las clasificaciones obtenidas con M13 y la referencia basada en la secuenciación parcial del factor de elongación de transcripción 1-alfa (TEF1-α) y el ADNr 28S. Conclusión. La fuerte correlación entre la clasificación obtenida con M13 y el método de referencia, así como su alta resolución, demuestran su idoneidad para la caracterización de poblaciones de Fusarium.


Subject(s)
Fusarium , DNA Fingerprinting , Bacteriophage M13 , Fusariosis , Genotyping Techniques , Elongin , Genetics, Population
3.
S. Afr. med. j ; 112(2): 81-85, 2022.
Article in English | AIM | ID: biblio-1358373

ABSTRACT

We describe a case of prolonged SARS-CoV-2 RNA shedding in an HIV-negative 21-year-old man recovering from abdominal and thoracic trauma. Nasopharyngeal (NP) swabs collected at 12 time points over a 95-day span all tested positive for SARS-CoV-2 by reverse transcription polymerase chain reaction (RT-PCR). Genotyping revealed canonical beta-variant E484K and N501Y mutations at earlier time points. Human rhinovirus, coronavirus NL63 and respiratory syncytial virus B were detected at different time points by RT-PCR. Full blood analysis at time point 9 (day 82) showed leukopenia with lymphocytosis. The patient's NP swab tested negative for SARS-CoV-2 by RT-PCR 101 days after the first positive test. The prolonged duration of SARS-CoV-2 RNA shedding in the context of trauma presented here is unique and has important implications for COVID-19 diagnosis, management and policy guidelines


Subject(s)
Humans , Male , Adult , Pneumothorax , COVID-19 Nucleic Acid Testing , SARS-CoV-2 , COVID-19
4.
Article in Chinese | WPRIM | ID: wpr-936455

ABSTRACT

Objective To analyze the relationship between hepatitis B virus genotyping and primary liver cancer (PHC) in Wuhan, and to provide a theoretical basis for the early prevention and diagnosis of PHC. Methods Patients with chronic hepatitis B (CHB) from Wuhan Sub-heart General Hospital for treatment from February 2020 to February 2021 were selected and divided into PHC group (182 cases) and control group (189 cases) according to whether they were complicated with primary liver cancer. 5ml of fasting elbow venous blood was taken from all subjects at admission. HBV genotyping was determined by real-time fluorescence quantitative PCR. The DNA of CHB virus was determined by fluorescence probe hybridization and PCR amplification, and genotyping and drug-resistant mutation points were detected according to the product sequencing analysis. Spearman linear correlation analysis was used to analyze the correlation between genotyping and mutation rate of PHC patients. Results The proportion of C genotype in PHC group was significantly higher than that in non-PHC group (P0.05). The proportion of HEPATITIS B virus mutation in PHC group (114/182) was significantly higher than that in control group (84/189) (χ2=12.331, P0.05). The proportion of HBV C mutant in PHC group was significantly higher than that in control group (P1=0.349, r2=0.305, P<0.05). Conclusion The HBV genotype of PHC patients is mainly TYPE C, and has a high mutation rate of C genotype. It can be used for diagnosis of PHC by detecting the genotyping of CHB and mutation rate of C genotype in clinic.

5.
Article in Chinese | WPRIM | ID: wpr-936425

ABSTRACT

Objective To classify and identify the 53 strains of non-polio enterovirus (NPEV) isolated from acute flaccid paralysis (AFP) cases in Chongqing from 2013 to 2020, and to investigate the genotype distribution of the strains. Methods Commercial real-time fluorescence quantitative polymerase chain reaction (real-time PCR) reagents were used for rapid identification of the strains. The nucleotide sequences of VP1 and VP4 regions were used for genotyping. Results Fifty enteroviruses were identified, 33 (66%) in group A and 17 (34%) in group B. Group C and D enteroviruses were not found in these strains,and 3 strains could not be identified. In this study, EV-A71 was the dominant type, with 11 strains (22%), but EV-A71 strain was not isolated since 2016. The sequences of VP4 region and VP1 region were completely consistent in enterovirus grouping. Conclusion When using commercial real-time PCR reagents for enterovirus typing, the identification results of high CT values may be inaccurate. In the genotyping of enterovirus, the nucleotide sequence of VP4 region is first used for grouping, and then the nucleotide sequence of VP1 region is used for genotyping, which could simplify the experimental process. NPEV isolates from AFP cases in Chongqing showed poor genotype diversity. In order to enrich and improve the enterovirus gene database in Chongqing, it is necessary to carry out research on enterovirus transmitted by respiratory tract.

6.
Article in Chinese | WPRIM | ID: wpr-939701

ABSTRACT

OBJECTIVE@#To investigate the molecular mechanism of one patient with abnormal serological phenotype in RhD and discuss the transfusion strategy.@*METHODS@#The RhD variant sample was screened from a patient with IgM type anti-D antibody and further determined by three different sources of anti-D antibodies. Ten exons and the adjacent introns of the RHD gene were amplified, purified and sequenced. RhCE phenotypes and RHCE genotypes were detected.@*RESULTS@#The patient with Rh variant showed abnormal results of serological tests. The RHD gene sequence analysis showed that the RHD*01W.01 with a variation (c.809T>G, p.Val270Gly) in exon 6 of the RHD gene was found in the patient. The RhCE phenotype was CcEe. The genotyping results of RHCE were consistent with the serological typing results.@*CONCLUSION@#The Rh variant of the patient is RHD*01W.01, these findings indicate that RhD variants should be analyzed by molecular assays for the sake of safe transfusion.


Subject(s)
Alleles , Blood Transfusion , Exons , Genotype , Humans , Phenotype , Rh-Hr Blood-Group System/genetics
7.
Chinese Journal of Hematology ; (12): 305-310, 2022.
Article in Chinese | WPRIM | ID: wpr-935086

ABSTRACT

Objective: To investigate the distribution characteristics of LymphGen genotyping in a diffuse large B-cell lymphoma (DLBCL) population and verify its prognostic value. Methods: We collected the clinical data and paraffin-embedded tumor tissue samples of 155 patients with newly diagnosed DLBCL in the People's Hospital of Xinjiang Uygur Autonomous Region from June 2014 to December 2020. DNA was extracted from tumor tissue and 475 gene mutations were detected by next-generation sequencing technology. We investigated the distribution of LymphGen genotyping in the DLBCL population, patients with different COO genotypes in the Xinjiang region, and their effects on PFS and OS. Results: ①Among 155 patients, 105 patients (67.7%) could be genotyped, including 14 (9.0%) for MCD, 26 (16.8%) for BN2, 10 (6.5%) for N1, 8 (5.2%) for EZB, 27 (17.4%) for A53, and 20 (12.9%) for ST2. ②The distribution of each gene subtype was different in different cell origin (COO) types (P=0.021) . ST2 was dominant in the germinal center type (GCB) group (28.8%) , and A53 and MCD were dominant in the non-GCB group (35.8%, 17.0%) . The BN2 type was the most common in both groups (23.1%, 26.4%) . ③There were statistically significant differences in progression-free survival (PFS) and overall survival (OS) among different gene subtypes (P=0.031 and 0.005, respectively) . N1 and A53 had poor prognosis. The 2-year PFS and OS rates of N1 were both (21.3±18.4) %, and the 3-year PFS and OS rates of A53 were (60.9±11.3) %, (46.8±10.9) %, respectively. ④ The 3-year PFS and OS rates of MCD were the best, but the 5-year PFS and OS rates were worse. ⑤In the ROC curve of LymphGen genotyping for OS prediction, the AUC was 0.66, showing a certain degree of differentiation. Conclusion: LymphGen genotyping in the DLBCL population was different from previous reports and was of great significance for the prognosis of patients with DLBCL.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols , Disease-Free Survival , Genotype , Humans , Interleukin-1 Receptor-Like 1 Protein , Lymphoma, Large B-Cell, Diffuse/drug therapy , Prognosis , Retrospective Studies
8.
Article in Chinese | WPRIM | ID: wpr-928764

ABSTRACT

The ABO blood group system is the most important blood group system in clinical transfusion. Serological technology is a routine method for the identification of ABO blood groups, however, which have some limitations in the identification of complicated ABO samples with weakened antigens or antibodies, abnormal plasma proteins, polyagglutination, or cold agglutinin, etc. With the development of molecular biology technology, ABO blood group gene was cloned, and ABO blood group genotyping technology based on DNA was established. The genotyping technologies with different throughputs such as PCR-SSP, Droplet-AS-PCR, PCR-RFLP, PCR-SBT, SNaPshot, MALDI-TOF MS and NGS have emerged. Genotyping has overcome the limitations of serology, and has become an indispensable method to solve difficult blood type, providing strong support for the correct identification of ABO blood group, and providing guarantee for precision blood transfusion. This review summarizes the progress and application of ABO blood group genotyping methods.


Subject(s)
ABO Blood-Group System/genetics , Blood Grouping and Crossmatching , Genotype , Humans , Polymerase Chain Reaction/methods , Technology
9.
Rev. Soc. Bras. Med. Trop ; 55: e0041, 2022. tab
Article in English | LILACS-Express | LILACS | ID: biblio-1387520

ABSTRACT

ABSTRACT Background: Microscopy and enzyme-linked immunosorbent assay (ELISA) are routinely used for Cryptosporidium diagnosis, without differentiating the parasite species. Methods: Children's feces were analyzed by modified Ziehl-Neelsen (mZN) and ELISA for Cryptosporidium diagnosis and by polymerase chain reaction-restriction fragment length polymorphism for species identification. Results: Cryptosporidium frequency was 2.6%. The sensitivity and specificity of ELISA were 85.7% and 99.7%, respectively, with excellent concordance with mZN (kappa=0.854). Parasite species were characterized as Cryptosporidium hominis (78.3%), Cryptosporidium felis (17.4%), and Cryptosporidium parvum (4.3%). Conclusions: Coproantigen ELISA is as efficient as mZN for Cryptosporidium diagnosis. Cryptosporidium genotyping suggests anthroponotic and zoonotic transmission to children.

10.
Rev. Soc. Bras. Med. Trop ; 55: e0013, 2022. tab, graf
Article in English | LILACS-Express | LILACS | ID: biblio-1387540

ABSTRACT

Abstract Background: Surveillance of multidrug resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB) is essential to guide disease dissemination control measures. Brazil contributes to a significant fraction of tuberculosis (TB) cases worldwide, but only few reports addressed MDR/XDR-TB in the country. Methods: This cross-sectional, laboratory-based study describes the phenotypic resistance profiles of isolates obtained between January 2008 and December 2011 in Bahia, Brazil, and sociodemographic, epidemiological, and clinical characteristics (obtained from mandatory national registries) of the corresponding 204 MDR/XDR-TB patients. We analyzed the mycobacterial spoligotyping and variable number of tandem repeats of mycobacterial interspersed repetitive units in 12-loci profiles obtained from Salvador. Results: MDR/XDR-TB patients were predominantly male, had a median age of 43 years, belonged to black ethnicity, and failed treatment before MDR-TB diagnosis. Nearly one-third of the isolates had phenotypic resistance (evaluated by mycobacteria growth indicator tube assay) to second-line anti-TB drugs (64/204, 31%), of which 22% cases (14/64) were diagnosed as XDR-TB. Death was a frequent outcome among these individuals and was associated with resistance to second-line anti-TB drugs. Most isolates successfully genotyped belonged to the Latin-American Mediterranean (LAM) Family, with an unprecedented high proportion of LAM10-Cameroon subfamily bacilli. More than half of these isolates were assigned to a unique cluster by the genotyping methods performed. Large clusters of identical genotypes were also observed among LAM SIT42 and SIT376 strains. Conclusions: We highlight the need for strengthening local and national efforts to perform early detection of TB drug resistance and to prevent treatment discontinuation to limit the emergence of drug-resistant strains.

11.
Hematol., Transfus. Cell Ther. (Impr.) ; 43(4): 489-493, Oct.-Dec. 2021. tab
Article in English | LILACS | ID: biblio-1350813

ABSTRACT

ABSTRACT Objective: Low levels of neutrophils can be an intrinsic condition, with no clinical consequences or immunity impairment. This condition is the benign constitutional neutropenia (BCN), defined as an absolute neutrophils count (ANC) ≤2000 cells/mm. Diagnosis of BCN is of exclusion where patients are submitted to blood tests and possibly to invasive diagnostic search until secondary causes of neutropenia are ruled out. The natural history of the disease suggests benign evolution and Brazilian study showed an overall frequency of 2.59%. The main mechanisms include reduced neutrophil production, increased marginalization, extravasation to the tissues and immune destruction. Genetic studies showed strong association between the single nucleotide variant rs2814778 located on chromosome 1q23.2 in the promoter region of the atypical chemokine receptor 1 (Duffy blood group system) gene (ACKR1, also termed DARC) and BCN. The aim of this study is to evaluate FY phenotypes and genotypes including the analysis of the rs2814778 SNP in Brazilian patients with BCN in order to determine an effective diagnostic tool, allowing reassurance of the patient and cost reduction in their care. Methods: Case control study, with 94 individuals (18 patients and 76 controls). Phenotyping was performed by gel test and genotyping was performed by PCR-RFLP. Results: White blood cell (WBC) and absolute neutrophils (AN) counts showed lower levels in patients compared to controls. In the patient group 83.3% were genotyped as FY*B/FY*B. The SNP rs2814778 (-67T > C) was identified in 77.8% of the patients genotyped as FY*B-67C/FY*B-67C. In the control group, 72.7% were homozygous for the wild type and 23.3% were heterozygous. Conclusion: This study reinforces that FY phenotyping and genotyping can be used to detect most people with BCN, avoiding excessive diagnostic investigation. Besides, this procedure may reduce health costs and be reproductible in clinical practice.


Subject(s)
Humans , Male , Female , Child , Adolescent , Adult , Middle Aged , Aged , Duffy Blood-Group System , Genotyping Techniques , Neutropenia , Immunophenotyping , Diagnostic Tests, Routine , Neutrophils
12.
Rev. chil. infectol ; 38(5)oct. 2021.
Article in Spanish | LILACS-Express | LILACS | ID: biblio-1388297

ABSTRACT

Resumen Antecedentes: El estado de Veracruz se ubica en el sureste de México y presenta una alta prevalencia de tuberculosis (TBC) y drogo resistencia. Sin embargo, la composición de los genotipos circulantes es poco conocida. Objetivo: Caracterizar la diversidad genética de la TBC en la jurisdicción sanitaria V del estado de Veracruz. Métodos: Estudio transversal realizado en aislados clínicos de pacientes con TBC residentes de la jurisdicción V. Se determinó la sensibilidad a medicamentos de primera línea. La genotipificación se realizó mediante espoligotipificación y MIRU-VNTR 15 loci. Resultados: Entre los 74 aislados analizados se observó resistencia a un fármaco en 44 (59%) aislados. Linaje L4 (EuroAmericano) se presentó en 73 aislados. Se identificaron cinco sublinajes; H (40%), T (22%), LAM (16%), X (13%) y U (7%). El 32% de los aislados se agrupó mediante su espoligotipo y 40% en 10 complejos clonales. Conclusiones: Es la primera descripción sobre la estructura genética de TBC en la región central de Veracruz. La diversidad de genotipos podría contribuir a su dispersión en la región. Esta información será útil para el desarrollo de intervenciones y reducir el impacto de TBC en la población.


Abstract Background: The state of Veracruz is placed in southeastern Mexico and has a high prevalence of tuberculosis (TB) and drug resistance. Nevertheless, the composition of circulating genotypes in the central region of the state is partially known. Aim: To characterize the genetic diversity of TB in the sanitary jurisdiction V of the state of Veracruz. Methods: A cross-sectional study was conducted among clinical isolates from patients with TB living in the jurisdiction V, in Jalapa Ver., Mexico. Sensitivity to first-line drugs was determined, and genotyping was performed by spoligotyping and MIRU-VNTR 15 loci. Results: Among the 74 isolates analyzed, resistance to one drug was observed in 44 isolates. L4 (EuroAmerican) was the major lineage identified. Five sublineages were the most abundant; H (40%), T (22%), LAM (16%), X (13%) and U (7%). Only 32% of the isolates were clustered by spoligotype and 40% were placed in ten clonal complexes. Conclusions: This is the first description of the genetic structure of TB in the central region of Veracruz. The diversity of genotypes could contribute to its dispersion. This information will be useful for the development of interventions to reduce the impact of TB in the population.

13.
Braz. dent. j ; 32(1): 3-8, Jan.-Feb. 2021. tab, graf
Article in English | LILACS, BBO | ID: biblio-1180729

ABSTRACT

Abstract Saliva is widely used for clinical and laboratory analysis. This study proposed to use DNA extracted from saliva for genotyping and pharmacokinetics of piroxicam. A fast and efficient genotyping method was used to determine relevant allelic variants of CYP2C9 (*2 and *3), since genetic factors can influence in non-steroidal anti-inflammatory drugs (NSAIDs) metabolization. DNA Extract All Reagents Kit® was used for DNA extraction and genotyping was performed using TaqMan® GTXpress™ Master Mix, SNP genotyping assays and a Viia7 Real-Time PCR system. Volunteers performed sequential collections of saliva samples before and after taking a single dose of piroxicam (0.25 to 72 h) which were used for pharmacokinetics assays. Piroxicam concentrations were analyzed using LC-MS/MS. Sixty-six percent of volunteers were ancestral homozygous (CYP2C9*1/*1), and 34% showed one or both polymorphisms. Of these 34%, 22 individuals showed CYP2C9*2 polymorphism, 8 CYP2C9*3, and 4 CYP2C9*2/*3. Piroxicam pharmacokinetics were performed in 5 subjects. Areas under the curve (AUC0-t(h*ng/mL)) for CYP2C9*1/*1, *1/*2 and *1/*3 were, respectively, 194.33±70.93, 166 and 303. Maximum concentrations (Cmax(ng/mL)) for these genotypes were respectively 6.46±2.56, 4.3 and 10.2. Saliva sampling was a very effective matrix for both pharmacogenetic and pharmacokinetic tests, ensuring the speed of the procedure and the well-being and agreement of the participants. Once having the knowledge about the slow and fast metabolizers, it is possible to make an adequate prescription in order to avoid the adverse effects of the medication and to guarantee greater analgesic comfort to the patients respectively.


Resumo Saliva é amplamente utilizada para análises clínicas e laboratoriais. Este estudo propôs o uso de DNA extraído da saliva para genotipagem e farmacocinética do piroxicam. Um método de genotipagem rápido e eficiente foi usado para determinar as variantes alélicas clinicamente relevantes de CYP2C9 (* 2 e * 3), uma vez que fatores genéticos podem influenciar nas respostas metabólicas individuais a medicamentos como anti-inflamatórios não esteroides (AINEs). DNA Extract All Reagents Kit® foi usado para extração de DNA e a genotipagem foi realizada usando TaqMan® GTXpress ™ Master Mix, ensaios de genotipagem SNP e um sistema Viia7 Real-Time PCR. Os voluntários realizaram coletas sequenciais de amostras de saliva antes e após a ingestão de uma única dose de piroxicam (0,25 a 72 h) que foram utilizadas para ensaios farmacocinéticos. As concentrações de piroxicam foram analisadas usando LC - MS / MS. Sessenta e seis por cento dos voluntários eram homozigotos ancestrais (CYP2C9 * 1 / * 1) e 34% apresentaram um ou ambos os polimorfismos. Destes 34%, 22 indivíduos apresentaram polimorfismo CYP2C9 * 2, 8 CYP2C9 * 3 e 4 CYP2C9 * 2 / * 3. A farmacocinética do piroxicam foi realizada em 5 indivíduos. As áreas sob a curva (AUC0-t (h * ng / mL)) para CYP2C9 * 1 / * 1, * 1 / * 2 e * 1 / * 3 foram, respectivamente, 194,33±70,93, 166 e 303. Concentrações máximas (Cmax (ng / mL)) para esses genótipos foram, respectivamente, 6,46±2,56, 4,3 e 10,2. A amostra de saliva foi uma matriz muito eficaz tanto para os testes farmacogenéticos quanto para os farmacocinéticos, garantindo a agilidade do procedimento e o bem-estar e concordância dos participantes. Com o conhecimento dos metabolizadores lentos e rápidos, é possível fazer uma prescrição adequada para evitar os efeitos adversos da medicação e garantir maior conforto analgésico aos pacientes respectivamente.


Subject(s)
Humans , Pharmacogenetics , Saliva , Drug Prescriptions , Chromatography, Liquid , Tandem Mass Spectrometry , Cytochrome P-450 CYP2C9/genetics
14.
Electron J Biotechnol ; 49: 72-81, Jan. 2021. tab, graf
Article in English | LILACS | ID: biblio-1291929

ABSTRACT

BACKGROUND: Persimmon (Diospyros kaki Thunb.) is the most widely cultivated species of the genus Diospyros. In this study, genetic diversity and variations in persimmon genotypes were investigated using single nucleotide polymorphism (SNP) markers identified by genotyping-by-sequencing (GBS) analysis. RESULTS: Ninety-five persimmon accessions grown in the Pear Research Institute, National Institute Horticultural and Herbal Science, were sequenced using the Illumina Hiseq2500 platform and polymorphic SNPs were detected to develop molecular markers. These reliable SNPs were analyzed using the Kompetitive Allele Specific PCR (KASP) assay to discriminate among persimmon genotypes. GBS generated a total of 447,495,724 trimmed reads, of which 89.7% were raw reads. After demultiplexing and sequence quality trimming, 108,876,644 clean reads were mapped to the reference transcriptome. An average of 1,146,070 genotype reads were mapped. Filtering of raw SNPs in each sample led to selection of a total of 1,725,401 high-quality SNPs. The number of homozygous and heterozygous SNPs ranged from 1,933 to 6,834 and from 846 to 5,927, respectively. CONCLUSIONS: Of the 49 SNPs selected for development of an identification system for persimmons, 15 SNPs were used in the KASP assay to analyze 32 persimmon accessions. These KASP markers discriminated among all accessions.


Subject(s)
Polymerase Chain Reaction/methods , Diospyros/genetics , Genetic Variation , Genetic Markers , Chromosome Mapping , Polymorphism, Single Nucleotide/genetics , Alleles , Genotyping Techniques , Homozygote
15.
Pesqui. vet. bras ; 41: e06717, 2021. tab, ilus
Article in English | LILACS, VETINDEX | ID: biblio-1250488

ABSTRACT

The brown howler monkey (Alouatta guariba clamitans) is a primate species widely distributed in South America. Infections by protozoa are common in primates. However, studies on protozoa in primates in Brazil are scarce, so the goal of this study was to investigate DNA from the apicomplexan protozoa Neospora caninum, Sarcocystis spp. and Toxoplasma gondii in tissues of A. guariba clamitans. DNA extraction was performed on tissue samples from the heart, brain, liver, spleen, lung and intestine of six A. guariba clamitans from Santa Maria, Central Region of Rio Grande do Sul, Brazil. Conventional PCR was performed using 18S rRNA gene general primers for Apicomplexa and also specific primers to amplify Neosporaspp. and Toxoplasma gondii DNA. All animals were positive in the 18S PCR and the genetic sequencing confirmed the presence of Sarcocystis spp. DNA in the tissues of four animals belonging to at least two species (S. neurona and S. gigantea) and T. gondii DNA in the other two animals. One positive sample for T. gondii was genotypically characterized as atypical by the restriction fragment length polymorphism technique. N. caninum DNA was not detected in the tested samples. The presence of Apicomplexa protozoan DNA in the tissues of the six animals tested in this study highlights the importance of howler monkeys as maintainers of these pathogens in nature.(AU)


O bugio ruivo (Alouatta guariba clamitans) é uma espécie de primata amplamente distribuída na América do Sul. As infecções por protozoários são comuns em primatas. Entretanto, estudos sobre protozoários em primatas no Brasil são escassos, portanto o objetivo deste estudo foi pesquisar DNA dos protozoários Apicomplexa Neospora caninum, Sarcocystisspp. e Toxoplasma gondii em tecidos de A. guariba clamitans. A extração de DNA foi realizada em amostras de tecido do coração, cérebro, fígado, baço, pulmão e intestino de seis A. guariba clamitans oriundos de Santa Maria, Região Central do Rio Grande do Sul, Brasil. Foi realizada PCR convencional utilizando primers geral do gene 18S rRNA para Apicomplexa e também primers específicos para amplificação de DNA de Neospora spp.e Toxoplasma gondii. Todos os animais foram positivos no PCR geral para Apicomplexa e no sequenciamento genético confirmou-se a presença de DNA de Sarcocystis nos tecidos de quatro animais pertencentes a pelo menos duas espécies (S. neurona e S. gigantea), e DNA de T. gondii foi detectado nos outros dois animais. Uma amostra positiva para T. gondii foi caracterizada genotipicamente como atípico pela técnica de polimorfismo do comprimento do fragmento de restrição. Não foi detectado DNA de N. caninum nas amostras testadas. A presença de DNA de protozoários apicomplexa nos tecidos dos seis animais testados neste estudo destaca a importância dos bugios ruivos como mantenedores desses patógenos na natureza.(AU)


Subject(s)
Animals , Toxoplasma/pathogenicity , Polymerase Chain Reaction , Apicomplexa/pathogenicity , Alouatta/microbiology , Genotyping Techniques/veterinary , Animals, Wild/microbiology , Protozoan Infections/diagnosis , DNA, Protozoan , Molecular Diagnostic Techniques , Infections
16.
Pesqui. vet. bras ; 41: e06729, 2021. tab, mapas
Article in English | LILACS, VETINDEX | ID: biblio-1250493

ABSTRACT

Mycobacterium bovis is responsible for bovine and buffalo tuberculosis, an important zoonotic disease with global distribution. The knowledge of the distribution and the precise identification of this disease, including advanced diagnoses such as spoligotyping, allows choosing the best strategies to fight the disease's progress. The present work aimed to investigate mycobacteria's presence, genotype their strains, and evaluate tuberculosis cases' spatial distribution from suggestive lesions in carcasses of bovine and buffalo inspected in slaughterhouses under an official inspection regime in the state of Bahia, Brazil. The study investigated 453,417 animals. Among these, 31 (0.007%) from 17 municipalities were suspected of tuberculosis. Among the culture medium growth, 95% of these were categorized as alcohol-acid resistant bacilli (BAAR). All isolates were subjected to spoligotyping and 95% were confirmed as M. bovis (SB0120, SB0121, SB0852, SB0828, SB0295, SB0881, SB1648, SB6119, SB0140, SB1055). The strain SB0120 was the most prevalent, and this profile has been described in cases of human tuberculosis by M. bovis, highlighting the zoonotic potential of this profile. This study also identified strains never reported in Bahia, highlighting a distinctive pattern from other parts of Brazil, besides mixed infections. Besides, to identify strains never before described in the state, highlighting a distinctive pattern in Brazil (SB6119 and SB0852, respectively). An unpublished profile was identified and inserted in the international database (Mbovis.org), named SB2715.(AU)


O Mycobacterium bovis é o responsável pela tuberculose bovina e bubalina, doença zoonótica importante e com distribuição global. O conhecimento da distribuição e a identificação precisa dessa enfermidade, incluindo diagnósticos mais avançados como o spoligotyping, permite escolher as melhores estratégias de combate ao avanço da doença. O presente trabalho objetivou investigar a presença de micobactérias, genotipar suas estirpes e avaliar a distribuição espacial dos casos de tuberculose a partir de lesões sugestivas nas carcaças de bovinos e bubalinos inspecionadas em frigoríficos sob regime de inspeção oficial no estado da Bahia. Foram investigados 453.417 animais dentre os quais 31 (0,007%) foram suspeitos de doença e provenientes de 17 municípios. Após o crescimento em meio de cultura, 95% foram categorizados como bacilos álcool-ácido resistentes (BAAR). Todos os isolados foram submetidos à spoligotyping e 95% foram confirmados M. bovis (SB0120, SB0121, SB0852, SB0828, SB0295, SB0881, SB1648, SB6119, SB0140, SB1055). A cepa SB0120 foi a mais prevalente e este perfil vem sendo descrito na literatura com casos de tuberculose humana por M. bovis ressaltando o potencial zoonótico deste perfil. Este estudo também identificou cepas nunca relatadas no estado da Bahia, destacando um padrão distinto de outras partes do Brasil, além da existência de infecções mistas. Permitiu ainda relatar linhagens nunca antes descritas no estado com destaque para um padrão novo no Brasil (SB6119 e SB0852 respectivamente). Um perfil inédito identificado foi identificado e inserido no banco de dados internacional (Mbovis.org), nomeado SB2715.(AU)


Subject(s)
Animals , Cattle , Buffaloes/genetics , Mycobacterium bovis , Cattle/genetics , Zoonoses , Genotyping Techniques
17.
Article in Chinese | WPRIM | ID: wpr-906636

ABSTRACT

Objective Though HCV genotyping , liver ultrasound and liver function indicators were used to assess the relationship between HCV genotyping, viral RNA copy number and liver damage related indicators in patients with chronic hepatitis C. Methods A total of 105 Uyghur hepatitis C patients in Aksu, Xinjiang were recruited in our hospital. All patients were carried out a test of HCV RNA copy number. HCV genotyping was performed by fluorescence quantitative PCR method. Fully automatic biochemical analyzer was used for alanine aminotransferase (ALT), aspartate aminotransferase (AST), direct bilirubin (DIBL) and total bilirubin (TIBL) by commercial kits. Color doppler ultrasound system was used for liver ultrasound. Results The genotyping results of 105 Uyghur hepatitis C patients showed that type 1b, 2a, 3a, 3b and 6a were 46, 41, 8, 8 and 2, respectively. Type 1b was the main type of HCV virus. The proportion of RNA copy number, AST and ALT levels, and liver cirrhosis were higher in patients with type 1b. Statistical analysis showed that there was a significant correlation between different HCV virus types and HCV RNA copy number (P = 0.032). In terms of AST and ALT levels, there were significant differences between type 1b, type 2a and other genotypes (type 3b and type 3a and type 6a) (P < 0.01). In addition, patients with normal liver, enlarged liver spots, fatty liver and cirrhosis have significant differences among type 1b, type 2a and other genotypes (P < 0.01). Conclusion There are regional differences in HCV genotyping among Uygur people in Aksu, Xinjiang. HCV RNA copy number and degree of liver damage are correlated with different HCV genotypes, which is of great significance to guide the clinical diagnosis and treatment of HCV in local populations.

18.
Article in Chinese | WPRIM | ID: wpr-911951

ABSTRACT

We describe a case of spontaneous conception following ovarian stimulation, in which a singleton pregnancy was revealed by ultrasound at 17 gestational weeks, with a multi-cystic "honeycomb" pattern in part of the placenta. With close monitoring, the patient delivered a healthy male neonate through cesarean section at 38 gestational weeks. The clinical findings, combined with ultrasound, laboratory, pathological, and immunohistochemistry examination, and short tandem repeat genotyping, confirmed a twin pregnancy consisting of a complete mole and coexisting fetus. No obvious abnormalities were found in the mother or the boy during a four-and-a-half-year's follow-up.

19.
Article in English | WPRIM | ID: wpr-876437

ABSTRACT

@#Candida albicans is an important opportunistic fungal pathogen capable of causing fatal systemic infections in humans. Presently in Malaysia, there is little information available on the genetic diversity of this organism and trends in behavioural characteristics. In this project, three genotyping methods: 25S rDNA genotyping, Alternative Lengthening of Telomerase (ALT) sequence typing and Multi-Locus Sequence Typing (MLST) were applied to study the genetic diversity of strains from infected hospital in-patients and asymptomatic individuals in the community. The results showed that, with the 25S rDNA genotyping, as in other parts of the world, the most common genotype was type A which accounted for approximately 70% of the 111 isolates tested. Further typing with the ALT sequence showed type 3 to be the most common in the isolates tested. MLST analysis revealed many possibly novel sequence types, as well as a statistically significant association between pathogenicity and a group of closely related isolates, most of which were from hospital samples. Further work on genotypes associated with enhanced virulence will help to clarify the value of genotyping for clinical and epidemiological investigations. Keywords:

20.
Braz. j. med. biol. res ; 54(2): e9549, 2021. tab, graf
Article in English | LILACS, ColecionaSUS | ID: biblio-1142579

ABSTRACT

Single nucleotide polymorphisms (SNPs) have important application value in the research of population genetics, hereditary diseases, tumors, and drug development. Conventional methods for detecting SNPs are typically based on PCR or DNA sequencing, which is time-consuming, costly, and requires complex instrumentation. In this study, we present a duplex probe-directed recombinase amplification (duplex-PDRA) assay that can perform real-time detection of two SNPs (rs6983267 and rs1447295) in four reactions in two tubes at 39°C within 30 min. The sensitivity of duplex-PDRA was 2×103-104 copies per reaction and no cross-reactivity was observed. A total of 382 clinical samples (179 prostate cancer patients and 203 controls) from northern China were collected and tested by duplex-PDRA assay and direct sequencing. The genotyping results were completely identical. In addition, the association analysis of two SNPs with prostate cancer risk and bone metastasis was conducted. We found that the TT genotype of rs6983267 (OR: 0.42; 95%CI: 0.23-0.78; P=0.005) decreased the risk of prostate cancer, while the CA genotype of rs1447295 (OR: 1.89; 95%CI: 1.20-2.96; P=0.005) increased the risk of prostate cancer. However, no association between the two SNPs (rs6983267 and rs1447295) and bone metastasis in prostate cancer was found in this study (P>0.05). In conclusion, the duplex-PDRA assay is an effective method for the simultaneous detection of two SNPs and shows great potential for widespread use in research and clinical settings.


Subject(s)
Humans , Male , Prostatic Neoplasms/genetics , Chromosomes, Human, Pair 8/genetics , DNA Mutational Analysis/methods , Polymorphism, Single Nucleotide , Case-Control Studies , China , Genetic Predisposition to Disease , Recombinases , Genotype
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