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1.
Biomédica (Bogotá) ; 40(4): 604-608, oct.-dic. 2020. tab
Article in English | LILACS | ID: biblio-1142426

ABSTRACT

Abstract: Heteropaternal superfecundation is an extremely rare phenomenon that occurs when a second ova released during the same menstrual cycle is additionally fertilized by the sperm cells of a different man in separate sexual intercourse. In August, 2018, the Grupo de Genética de Poblaciones e Identificación at Universidad Nacional de Colombia received a request to establish the paternity of a pair of male twins with genetic markers. The following analyses were performed: amelogenin gene, autosomal short tandem repeat (STR), and Y-STR analyses by means of human identification commercial kits, paternity index, and the probability of paternity calculation and interpretation. A paternity index of 2.5134E+7 and a probability of paternity of 99.9999% for twin 2 were obtained while 14 out of 17 Y-chromosome markers and 14 out of 21 autosomal short tandem repeats were excluded for twin 1. The results indicated that the twins have different biological fathers. Although heteropaternal superfecundation is rarely observed among humans given its low frequency, in paternity disputes for dizygotic twins it is mandatory to demand the presence of the two twins in the testing to avoid wrong conclusions.


Resumen: La superfecundación heteropaternal es un fenómeno extremadamente raro que se produce cuando un segundo óvulo, liberado durante el mismo ciclo menstrual, es fertilizado por un espermatozoide de un hombre diferente en relaciones sexuales separadas. En agosto de 2018, el Grupo de Genética de Poblaciones e Identificación de la Universidad Nacional de Colombia recibió una solicitud para establecer la paternidad mediante marcadores genéticos de un par de mellizos varones, en quienes se hizo el análisis del gen de amelogenina, el análisis de repeticiones cortas en tándem (Short Tandem Repeats, STR) autosómicas y del cromosoma Y (Y-STR) mediante kits comerciales de identificación humana y cálculos e interpretación del índice de paternidad y probabilidad de paternidad. Se obtuvo un índice de paternidad de 2,5134E+7 y una probabilidad de paternidad de 99,9999 % para el gemelo 2, en tanto que en el gemelo 1 se excluyeron 14 de los 17 marcadores del cromosoma Y y 14 de los 21 sistemas STR autosómicos evaluados. Los resultados indicaron que los gemelos tienen diferentes padres biológicos. A pesar de que la superfecundación heteropaternal rara vez se observa en humanos debido a su baja frecuencia, en las disputas de paternidad para los gemelos dicigóticos, es obligatorio exigir en la prueba la presencia de los dos gemelos para evitar conclusiones incorrectas.


Subject(s)
Twins, Dizygotic , Paternity , DNA Fingerprinting , Microsatellite Repeats , Fertilization
2.
Biosci. j. (Online) ; 36(4): 1137-1145, 01-06-2020. ilus, tab, graf
Article in English | LILACS | ID: biblio-1147212

ABSTRACT

Morphological and agronomical describers are traditionally used in plant characterization. However, the usage of these describers have some limitations such as susceptibility to abiotic and biotic stress and environmental factors. Furthermore, the describers are not stable over time and many can only be evaluated during the adult phase of the plants, which requires time and physical space. Molecular markers offer numerous advantages compared to the conventional alternatives based on phenotype: they are stable and detectable in all vegetable tissues, and are independent of the environment and development phase. One of the main advantages of the use of molecular markers is the time reduction in the identification of genetic diversity among the studied subjects, as the genotypes may even be described for the seed or seedling phase. Many countries have already adopted molecular markers to identify olive cultivars more accurately. The aim of this study was to evaluate the genetic identity of eight olive accessions supposedly belonging to cultivar Arbequina by using microsatellite (SSR) and Sequence Characterized Amplified Region (SCAR) markers. One accession corresponding to the cultivar was also incorporated into the analysis as a reference genotype. The molecular marker data were analyzed on the software GENALEX6.The markers generated an accumulated PI and PE of 1.26 x 10-6 and 0.949, respectively.The results supported the hypothesis that all accessions belong to the cultivar Arbequina, and the markers can therefore be applied to other varieties of olive species.


Descritores morfológicos e agronômicos são tradicionalmente utilizados na caracterização de plantas. Apesar de recomendado, o emprego destes descritores apresenta algumas limitações como a influência a estresses abióticos e bióticos e aos efeitos do ambiente. Além disso, não são estáveis ao longo do tempo e muitos só podem ser avaliados durante a fase adulta das plantas, o que requer tempo e espaço físico para as avaliações. Os marcadores moleculares oferecem numerosas vantagens relativamente às alternativas convencionais baseadas no fenótipo, pois são estáveis e detectáveis em todos os tecidos vegetais, independente do ambiente e fase de desenvolvimento e uma das principais vantagens da utilização destes é proporcionar a redução do tempo na identificação da diversidade genética entre os indivíduos trabalhados, podendo ser avaliadas genótipos ainda na fase de semente ou de plântula. O objetivo deste estudo foi avaliar a identidade genética de oito acessos de oliveira supostamente pertencentes a cultivar Arbequina usando microssatélites (SSR) e Sequence Characterized Amplified Region (SCAR) marcadores. Um acesso correspondente a cultivar também foi incorporado na análise como o genótipo de referência. Os dados de marcadores moleculares foram analisados com o software GENALEX 6. Como resultado, os marcadores SSR geraram um PI acumulada e PE de 1,26 x 10- 6 e 0,949, respectivamente. Os resultados suportam a hipótese de que todos os acessos pertencem a cultivar Arbequina, e, por conseguinte, esses marcadores podem ser aplicados em situações semelhantes em outras variedades de espécies de oliveira.


Subject(s)
DNA Fingerprinting , Olea
3.
Article in Chinese | WPRIM | ID: wpr-828401

ABSTRACT

As a traditional Chinese medicinal material, Chrysosplenium is urgently needed for genetic resource investigation and protection research due to the decrease of its wild resources in recent years. After investigating the wild resources, we conducted genetic polymorphism and clustering studies of 24 species(a total of 36 samples) of Chrysosplenium using SRAP technique. The results showed that a total of 374 polymorphic bands were obtained using 18 pairs of SRAP primers to amplify these samples, on average of 20.7 bands for each primer pair. We used the biological software to analyze the population's genetic parameter and got the N_a value as 2.000 0, N_(e )value as 1.408 4, the average Nei's index as 0.263 5, and the average Shannon information index as 0.419 1. UPGMA cluster analysis showed that all the samples can be divided into three major groups at the genetic similarity coefficient of 0.70: there are 18 species(24 samples) gathered for the Ⅰ groups, 3 species or variation(7 samples) for Ⅱ groups, and 3 species(5 samples) for Ⅲ groups. The differences of these Chrysosplenium species at the molecular level are consistent with that of their geographical and ecological distribution. At the same time, we used SRAP technology to construct 36 DNA digital fingerprints of Chrysosplenium and obtained the unique molecular identification band type of each material. These results will provide effective methods and reliable basis for the identification, protection and genetic diversity analysis of the germplasm resources of Chrysosplenium, and lay a foundation for the further development and utilization of them.


Subject(s)
Cluster Analysis , DNA Fingerprinting , Genetic Markers , Genetic Variation , Phylogeny , Polymorphism, Genetic
4.
Biol. Res ; 53: 13, 2020. tab, graf
Article in English | LILACS | ID: biblio-1100919

ABSTRACT

BACKGROUND: Gallbladder cancer (GBC) is the most common tumor of the biliary tract. The incidence of GBC shows a large geographic variability, being particularly frequent in Native American populations. In Chile, GBC represents the second cause of cancer-related death among women. We describe here the establishment of three novel cell lines derived from the ascitic fluid of a Chilean GBC patient, who presented 46% European, 36% Mapuche, 12% Aymara and 6% African ancestry. RESULTS: After immunocytochemical staining of the primary cell culture, we isolated and comprehensively characterized three independent clones (PUC-GBC1, PUC-GBC2 and PUC-GBC3) by short tandem repeat DNA profiling and RNA sequencing as well as karyotype, doubling time, chemosensitivity, in vitro migration capability and in vivo tumorigenicity assay. Primary culture cells showed high expression of CK7, CK19, CA 19-9, MUC1 and MUC16, and negative expression of mesothelial markers. The three isolated clones displayed an epithelial phenotype and an abnormal structure and number of chromosomes. RNA sequencing confirmed the increased expression of cytokeratin and mucin genes, and also of TP53 and ERBB2 with some differences among the three cells lines, and revealed a novel exonic mutation in NF1. The PUC-GBC3 clone was the most aggressive according to histopathological features and the tumorigenic capacity in NSG mice. CONCLUSIONS: The first cell lines established from a Chilean GBC patient represent a new model for studying GBC in patients of Native American descent.


Subject(s)
Humans , Animals , Male , Middle Aged , Antigens, Tumor-Associated, Carbohydrate/genetics , Indians, South American/genetics , Gallbladder Neoplasms/genetics , Ascitic Fluid/metabolism , Tumor Cells, Cultured , Carcinogenicity Tests , Chile , DNA Fingerprinting , Tumor Suppressor Protein p53/genetics , Cisplatin/pharmacology , Mice, Inbred NOD , Clone Cells/drug effects , Clone Cells/metabolism , Sequence Analysis, RNA , Receptor, ErbB-2/genetics , Genes, erbB-2/genetics , Gene Expression Profiling , Cell Line, Tumor/drug effects , Cell Line, Tumor/metabolism , Deoxycytidine/analogs & derivatives , Deoxycytidine/pharmacology , Epithelial Cells/metabolism , Keratin-19/genetics , Keratin-7/genetics , Carcinogenesis/genetics , Gallbladder Neoplasms/metabolism , Antineoplastic Agents/pharmacology
5.
Electron. j. biotechnol ; 37: 25-33, Jan. 2019. tab, graf, ilus
Article in English | LILACS | ID: biblio-1051225

ABSTRACT

Background: Ammonium stress is a prime limiting phenomenon that occurs during methane formation from poultry manure. It is caused by elevated ammonium nitrogen concentrations that result from substrate decomposition. The amounts of methane formed depend on the activity of methanogenic microbes. Results: During the research reported in this paper, the response of a mesophilic consortium inhabiting a biogas reactor to rising load of poultry manure was investigated. The taxonomic composition of bacterial population was mostly typical, however syntrophic bacteria were not detected. This absence resulted in limitation of succession of some methanogenic microorganisms, especially obligate hydrogenotrophs. The methanogenic activity of the consortium was totally dependent on the activity of Methanosaeta. Inhibition of methanoganesis was noticed at ammonium nitrogen concentration of 3.68 g/L, total cessation occurred at 5.45 g/L. Significant amounts of acetic acid in the fermentation pulp accompanied the inhibition. Conclusions: The effectiveness of the consortium was totally dependent on the metabolic activity of the acetoclastic Methanoseata genus and lack of SAOB did not allow hydrogenotrophic methanogens to propagate and lead to cessation of biogas production at an elevated ammonium concentration at which acetoclastic methanogens were inhibited.


Subject(s)
Methanosarcinaceae/metabolism , Biofuels , Microbiota , Anaerobiosis , Poultry , Stress, Physiological , Polymerase Chain Reaction , DNA Fingerprinting , Chromatography, High Pressure Liquid , Archaea/metabolism , Biodiversity , Fermentation , Microbial Consortia , Ammonium Compounds , Manure , Methane , Nitrogen
6.
Article in English | WPRIM | ID: wpr-764413

ABSTRACT

The modern era of microbial genome analysis began in earnest in the 2000s with the generalization of metagenomics and gene sequencing techniques. Studying complex microbial community such as oral cavity and colon by a pure culture is considerably ineffective in terms of cost and time. Therefore, various techniques for genomic analysis have been developed to overcome the limitation of the culture method and to explore microbial communities existing in the natural environment at the gene level. Among these, DNA fingerprinting analysis and microarray chip have been used extensively; however, the most recent method of analysis is metagenomics. The study summarily examined the overview of metagenomics analysis techniques, as well as domestic and foreign studies on disease genomics and cluster analysis related to oral metagenome. The composition of oral bacteria also varies across different individuals, and it would become possible to analyze what change occurs in the human body depending on the activity of bacteria living in the oral cavity and what causality it has with diseases. Identification, isolation, metabolism, and presence of functional genes of microorganisms are being identified for correlation analysis based on oral microbial genome sequencing. For precise diagnosis and treatment of diseases based on microbiome, greater effort is needed for finding not only the causative microorganisms, but also indicators at gene level. Up to now, oral microbial studies have mostly involved metagenomics, but if metatranscriptomic, metaproteomic, and metabolomic approaches can be taken together for assessment of microbial genes and proteins that are expressed under specific conditions, then doing so can be more helpful for gaining comprehensive understanding.


Subject(s)
Bacteria , Colon , Dental Caries , Diagnosis , DNA Fingerprinting , Generalization, Psychological , Genes, Microbial , Genome, Microbial , Genomics , Human Body , Metabolism , Metabolomics , Metagenome , Metagenomics , Methods , Microbiota , Mouth
7.
Mem. Inst. Oswaldo Cruz ; 114: e190260, 2019. tab, graf
Article in English | LILACS | ID: biblio-1040612

ABSTRACT

BACKGROUND Sporotrichosis is a subcutaneous mycosis caused by dimorphic pathogenic fungi belonging to the Sporothrix genus. Pathogenic Sporothrix species typically produce melanin, which is known to be a virulence factor. OBJECTIVES The aim of this study was to perform phenotypic, genotypic, and virulence analyses of two distinct Sporothrix brasiliensis strains isolated from the same lesion on a patient from Rio de Janeiro. METHODS AND FINDINGS Genotypic analyses by partial sequencing of the calmodulin, β-tubulin, and chitin synthase genes, as well as polymerase chain reaction (PCR)-fingerprinting by T3B, M13, and GACA, showed that the isolates were very similar but not identical. Both isolates had similar phenotypic characteristics and effectively produced melanin in their yeast forms, accounting for their ability of causing disease in a murine sporotrichosis model. Remarkably, isolate B was albino in its environmental form but caused more severe disease than the pigmented A isolate. CONCLUSIONS These findings indicate that the patient was infected by two genetically and biologically distinct S. brasiliensis that vary in their production of melanin in their environmental forms. The results underscore the importance of characterizing phenotypically different isolates found in the same clinical specimen or patient.


Subject(s)
Humans , Animals , Mice , Sporotrichosis/pathology , Sporotrichosis/virology , Sporothrix/pathogenicity , Antifungal Agents/pharmacology , Phenotype , Sporothrix/drug effects , Sporothrix/genetics , Virulence , Microbial Sensitivity Tests , Polymerase Chain Reaction , DNA Fingerprinting , Disease Models, Animal , Genotype , Mice, Inbred BALB C
8.
Rev. Fac. Odontol. (B.Aires) ; 34(76): 43-51, 2019. ilus, tab
Article in Spanish | LILACS | ID: biblio-1102564

ABSTRACT

Una catástrofe es un acontecimiento súbito y violento que genera múltiples víctimas requiriendo del abordaje de expertos en diferentes áreas del conocimiento técnico científico para lograr una identificación inequívoca. El rol del odontólogo legista como integrante de los equipos interdisciplinarios conformados para la investigación en este tipo de hechos aparece definido en el Protocolo de Interpol, guía de operaciones estandarizada, diseñada para optimizar la comunicación, planificación, organización y estrategias entre peritos de diferentes latitudes ante incidentes naturales, accidentales o intencionales. El presente trabajo tiene por objetivo analizar las directrices de la citada norma en lo atinente a la coordinación de la actuación de los equipos de odontólogos legistas para contribuir en tales contextos, apuntada fundamentalmente a auxiliar a la justicia, aportando mayor celeridad en la identificación humana y acotando la angustia e incertidumbre de los familiares de la víctimas (AU)


Subject(s)
Humans , Male , Female , Forensic Anthropology/methods , Victims Identification , Protocols , Disasters , Forensic Dentistry , Dental Records , DNA Fingerprinting , Denture Identification Marking
9.
Mem. Inst. Oswaldo Cruz ; 113(3): 185-196, Mar. 2018. tab, graf
Article in English | LILACS | ID: biblio-894908

ABSTRACT

BACKGROUND Sporotrichosis is caused by species of the genus Sporothrix. From 1998 to 2015, 4,703 cats were diagnosed at the Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil. Even after the description of the Sporothrix species, the characterisation of feline isolates is not performed routinely. OBJECTIVES To characterise the clinical isolates from cats at the species level and correlate them with the clinical and epidemiological characteristics of the cats. METHODS Forty seven Sporothrix spp. isolates from cats assisted at Fiocruz from 2010 to 2011 were included. Medical records were consulted to obtain the clinical and epidemiological data. The isolates were identified through their morphological and physiological characteristics. T3B polymerase chain reaction (PCR) fingerprinting was used for molecular identification of the species. FINDINGS In phenotypic tests, 34 isolates were characterised as S. brasiliensis, one as S. schenckii and 12 as Sporothrix spp. PCR identified all isolates as S. brasiliensis. MAIN CONCLUSIONS S. brasiliensis is the only etiological agent of feline sporotrichosis in Rio de Janeiro to date. None association was found between the isolates and the clinical and epidemiological data. In addition, we strongly recommend the use of molecular techniques for the identification of isolates of Sporothrix spp.


Subject(s)
Sporothrix/classification , Cat Diseases/microbiology , Cat Diseases/epidemiology , Sporothrix/genetics , Brazil/epidemiology , DNA Fingerprinting
10.
Article in English | WPRIM | ID: wpr-812034

ABSTRACT

"Wu zhu yu", which is obtained from the dried unripe fruits of Tetradium ruticarpum (A. Jussieu) T. G. Hartley, has been used as a traditional Chinese medicine for treatment of headaches, abdominal colic, and hypertension for thousands of years. The present study was designed to assess the molecular genetic diversity among 25 collected accessions of T. ruticarpum (Wu zhu yu in Chinese) from different areas of China, based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers generated 151 amplification bands, of which 130 were polymorphic. Out of 165 bands that were amplified using 10 iPBS primers, 152 were polymorphic. The iPBS markers displayed a higher proportion of polymorphic loci (PPL = 92.5%) than the ISSR markers (PPL = 84.9%). The results showed that T. ruticarpum possessed high loci polymorphism and genetic differentiation occurred in this plant. The combined data of iPBS and ISSR markers scored on 25 accessions produced five clusters that approximately matched the geographic distribution of the species. The results indicated that both iPBS and ISSR markers were reliable and effective tools for analyzing the genetic diversity in T. ruticarpum.


Subject(s)
Base Sequence , Binding Sites , DNA Fingerprinting , DNA Primers , Metabolism , DNA, Plant , Genetics , Evodia , Classification , Genetics , Genetic Markers , Genetics , Genetic Variation , Interspersed Repetitive Sequences , Genetics , Phylogeny , Polymorphism, Genetic , Random Amplified Polymorphic DNA Technique , Terminal Repeat Sequences , Genetics
11.
Article in English | WPRIM | ID: wpr-773644

ABSTRACT

"Wu zhu yu", which is obtained from the dried unripe fruits of Tetradium ruticarpum (A. Jussieu) T. G. Hartley, has been used as a traditional Chinese medicine for treatment of headaches, abdominal colic, and hypertension for thousands of years. The present study was designed to assess the molecular genetic diversity among 25 collected accessions of T. ruticarpum (Wu zhu yu in Chinese) from different areas of China, based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers generated 151 amplification bands, of which 130 were polymorphic. Out of 165 bands that were amplified using 10 iPBS primers, 152 were polymorphic. The iPBS markers displayed a higher proportion of polymorphic loci (PPL = 92.5%) than the ISSR markers (PPL = 84.9%). The results showed that T. ruticarpum possessed high loci polymorphism and genetic differentiation occurred in this plant. The combined data of iPBS and ISSR markers scored on 25 accessions produced five clusters that approximately matched the geographic distribution of the species. The results indicated that both iPBS and ISSR markers were reliable and effective tools for analyzing the genetic diversity in T. ruticarpum.


Subject(s)
Base Sequence , Binding Sites , DNA Fingerprinting , DNA Primers , Metabolism , DNA, Plant , Genetics , Evodia , Classification , Genetics , Genetic Markers , Genetics , Genetic Variation , Interspersed Repetitive Sequences , Genetics , Phylogeny , Polymorphism, Genetic , Random Amplified Polymorphic DNA Technique , Terminal Repeat Sequences , Genetics
12.
Electron. j. biotechnol ; 30: 48-57, nov. 2017. ilus, tab, graf
Article in English | LILACS | ID: biblio-1021453

ABSTRACT

Background: Availability of related rice species is critical for rice breeding and improvement. Two distinct species of domesticated rice exist in the genus Oryza: Oryza sativa (Asian rice) and Oryza glaberrima (African rice). New rice for Africa (NERICA) is derived from interspecific crosses between these two species. Molecular profiling of these germplasms is important for both genetics and breeding studies. We used 30 polymorphic SSR markers to assess the genetic diversity and molecular fingerprints of 53 rice genotypes of O. sativa, O. glaberrima, and NERICA. Results: In total, 180 alleles were detected. Average polymorphism information content and Shannon's information index were 0.638 and 1.390, respectively. Population structure and neighbor-joining phylogenetic tree revealed that 53 genotypes grouped into three distinct subpopulations conforming to the original three groups, except three varieties (IR66417, WAB450-4, MZCD74), and that NERICA showed a smaller genetic distance from O. sativa genotypes (0.774) than from O. glaberrima genotypes (0.889). A molecular fingerprint map of the 53 accessions was constructed with a novel encoding method based on the SSR polymorphic alleles. Ten specific SSR markers displayed different allelic profiles between the O. glaberrima and O. sativa genotypes. Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms.


Subject(s)
Oryza/genetics , Genetic Variation , Polymorphism, Genetic , Breeding , DNA Fingerprinting , Microsatellite Repeats , Genotype
13.
Int. j. odontostomatol. (Print) ; 11(2): 173-177, June 2017. ilus
Article in English | LILACS | ID: biblio-893247

ABSTRACT

The aim of this study was to evaluate the extraction of dental DNA exposed to different chemical solutions. The sample was composed by 15 subjects, from which 5 samples of oral mucosal cells (reference population) and 15 teeth (experimental population) were collected. The experimental population was divided in three equal parts, which were exposed to different chemical solutions, namely hydrochloric acid (HCl) at 37 %, formaldehyde (CH2O) at 10 % and sodium hypochlorite (NaOCl) at 2.5 %. The DNA from the oral mucosa was extracted using organic method, while the dental DNA was extracted using the AFDIL method, including amplification by PCR and sequencing through capillary electrophoresis. The DNA exposed to hydrochloric acid dissolved, lacking extraction. The exposure of teeth to formaldehyde and sodium hypochlorite did not interfere in the extraction of DNA, once the amplification was visible in both experimental populations. The present outcomes demonstrated that DNA extraction may be limited under exposure to chemical solutions.


El objetivo de este estudio fue evaluar la extracción de ADN dental expuesto a diferentes soluciones químicas. La muestra estuvo compuesta por 15 sujetos, de los cuales se recogieron 5 muestras de células de la mucosa oral (población de referencia) y 15 dientes (población experimental). La población experimental se dividió en tres partes iguales, que fueron expuestas a diferentes soluciones químicas, a saber, ácido clorhídrico (HCl) al 37 %, formaldehído (CH2O) al 10 % e hipoclorito de sodio (NaOCl) al 2,5 %. El ADN de la mucosa oral se extrajo utilizando el método orgánico, mientras que el ADN dental se extrajo utilizando el método AFDIL, incluyendo la amplificación por PCR y la secuenciación a través de electroforesis capilar. El ADN expuesto al ácido clorhídrico se disolvió, careciendo de extracción. La exposición de los dientes al formaldehído e hipoclorito de sodio no interfirió en la extracción de ADN, una vez que la amplificación era visible en ambas poblaciones experimentales. Los resultados actuales demostraron que la extracción de ADN puede ser limitada bajo la exposición a soluciones químicas.


Subject(s)
Humans , DNA Fingerprinting/methods , Forensic Dentistry/methods , Solutions , Tooth , DNA/analysis , Forensic Genetics
14.
Mem. Inst. Oswaldo Cruz ; 112(3): 214-219, Mar. 2017. tab, graf
Article in English | LILACS | ID: biblio-1040568

ABSTRACT

Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis.


Subject(s)
Humans , Candida/isolation & purification , Mycological Typing Techniques/methods , Polymorphism, Restriction Fragment Length , Candida/classification , Candida/genetics , DNA, Fungal/analysis , Polymerase Chain Reaction , DNA Fingerprinting , Sequence Analysis, DNA , DNA, Ribosomal Spacer/genetics , Genotype
15.
Rev. Inst. Med. Trop. Säo Paulo ; 59: e40, 2017. tab, graf
Article in English | LILACS | ID: biblio-842765

ABSTRACT

ABSTRACT Tuberculosis remains as the world’s biggest threat. In 2014, human tuberculosis ranked as a major infectious disease by the first time, overcoming HIV death rates. Bovine tuberculosis is a chronic disease of global distribution that affects animals and can be transmitted to humans by the consumption of raw milk, representing a serious public health concern. Despite the efforts of different countries to control and eradicate bovine tuberculosis, the high negative economic impact on meat and milk production chains remains, given the decreased production efficiency (approximately 25%), the high number of condemned carcasses, and increased animal culling rates. This scenario has motivated the establishment of official programs based on regulations and diagnostic procedures. Although Mycobacterium tuberculosis and Mycobacterium bovis are the major pathogenic species to humans and bovines, respectively, nontuberculous mycobacteria within the Mycobacterium genus have become increasingly important in recent decades due to human infections, including the ones that occur in immunocompetent people. Diagnosis of mycobacteria can be performed by microbiological culture from tissue samples (lymph nodes, lungs) and secretions (sputum, milk). In general, these pathogens demand special nutrient requirements for isolation/growth, and the use of selective and rich culture media. Indeed, within these genera, mycobacteria are classified as either fast- or slow-growth microorganisms. Regarding the latter ones, incubation times can vary from 45 to 90 days. Although microbiological culture is still considered the gold standard method for diagnosis, molecular approaches have been increasingly used. We describe here an overview of the diagnosis of Mycobacterium species in bovine milk.


Subject(s)
Humans , Animals , Cattle/microbiology , Milk/microbiology , Mycobacterium/isolation & purification , DNA Fingerprinting/methods , Mycobacterium/genetics , Polymerase Chain Reaction/methods , Tuberculosis, Bovine/epidemiology , Tuberculosis, Bovine/microbiology
16.
Mem. Inst. Oswaldo Cruz ; 111(10): 642-648, Oct. 2016. tab, graf
Article in English | LILACS | ID: lil-796905

ABSTRACT

The propagules of the fungal species Cryptococcus neoformans and C. gattii, whose varieties are distributed world wide, are the primary cause of cryptococcosis, a life threatening disease. The study of environmental and clinical isolates of Cryptococcosis is an important contribution to the epidemiology and ecology of the fungus. The aim of this work was to determine the presence of C. neoformans and C. gattii in the environment in Bogotá, Colombia’s capital city and to establish the relation between clinical and environmental isolates in the period 2012-2015. From a total of 4.116 environmental samples collected between October 2012 - March 2014, 35 were positive for C. neoformans var. grubii. From 55 cryptococcosis cases reported in Bogotá during 2012-2015, 49 isolates were recovered. From those, 94% were identified as C. neoformans var. grubii molecular type VNI; 4% as VNII and 1,2% as C. neoformans var neoformans VNIV. The 84 detected clinical and environmental isolates studied had a similarity between 49-100% according with molecular typing. The correlation between environmental and clinical samples confirms the hypothesis that patients acquire the disease from environmental exposure to the fungal propagules.


Subject(s)
Humans , Male , Female , Cryptococcosis/microbiology , Cryptococcus gattii/isolation & purification , Cryptococcus neoformans/isolation & purification , Environmental Microbiology , Cities , Colombia , Cryptococcus gattii/genetics , Cryptococcus neoformans/genetics , DNA Fingerprinting , DNA, Fungal , Genotype , Molecular Typing , Mycological Typing Techniques
18.
Electron. j. biotechnol ; 19(3): 65-71, May 2016. ilus
Article in English | LILACS | ID: lil-787010

ABSTRACT

Background: Pigeonpea (Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family and the only cultivated species in the genus Cajanus. It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, it is grown as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant quality reduction and yield losses. In this study, 48 polymorphic SSR markers were used to assess the diversity among all pigeonpea varieties cultivated in Malawi to determine if a genetic fingerprint could be identified to distinguish the popular varieties. Results: A total of 212 alleles were observed with an average of 5.58 alleles per marker and a maximum of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC), ranged from 0.03 to 0.89 with an average of 0.30. A neighbor-joining tree produced 4 clusters. The most commonly cultivated varieties, which include released varieties and cultivated land races, were well-spread across all the clusters observed, indicating that they generally represented the genetic diversity available in Malawi, although substantial variation was evident that can still be exploited through further breeding. Conclusion: Screening of the allelic data associated with the five most popular cultivated varieties, revealed 6 markers - CCB1, CCB7, Ccac035, CCttc003, Ccac026 and CCttc019 - which displayed unique allelic profiles for each of the five varieties. This genetic fingerprint can potentially be applied for seed certification to confirm the genetic purity of seeds that are delivered to Malawi farmers.


Subject(s)
Genetic Variation , Microsatellite Repeats , Cajanus/genetics , Fabaceae/genetics , Seeds , Polymerase Chain Reaction , DNA Fingerprinting , Alleles , Genotype , Malawi
19.
Rev. Soc. Bras. Med. Trop ; 49(2): 204-210, Mar.-Apr. 2016. tab, graf
Article in English | LILACS | ID: lil-782105

ABSTRACT

Abstract: INTRODUCTION Characterization of Mycobacterium tuberculosis (MTB) isolates by DNA fingerprinting has contributed to tuberculosis (TB) control. The aim of this study was to determine the genetic diversity of MTB isolates from Tehran province in Iran. METHODS MTB isolates from 60 Iranian and 10 Afghan TB patients were fingerprinted by standard IS6110-restriction fragment length polymorphism (RFLP) analysis and spoligotyping. RESULTS The copy number of IS6110 ranged from 10-24 per isolate. The isolates were classified into 22 clusters showing ≥ 80% similarity by RFLP analysis. Fourteen multidrug-resistant (MDR) isolates were grouped into 4 IS6110-RFLP clusters, with 10 isolates [71% (95% CI: 45-89%)] in 1 cluster, suggesting a possible epidemiological linkage. Eighteen Iranian isolates showed ≥ 80% similarity with Afghan isolates. There were no strains with identical fingerprints. Spoligotyping of 70 isolates produced 23 distinct patterns. Sixty (85.7%) isolates were grouped into 13 clusters, while the remaining 10 isolates (14.2%) were not clustered. Ural (formerly Haarlem4) (n = 22, 31.4%) was the most common family followed by Central Asian strain (CAS) (n = 18, 25.7%) and T (n = 9, 12.8%) families. Only 1strain was characterized as having the Beijing genotype. Among 60 Iranian and 10 Afghan MTB isolates, 25% (95% CI: 16-37) and 70% (95% CI: 39-89) were categorized as Ural lineage, respectively. CONCLUSIONS A higher prevalence of Ural family MTB isolates among Afghan patients than among Iranian patients suggests the possible transmission of this lineage following the immigration of Afghans to Iran.


Subject(s)
Humans , Tuberculosis/microbiology , Genetic Variation/genetics , DNA, Bacterial/genetics , Bacterial Typing Techniques/methods , Mycobacterium tuberculosis/genetics , Polymorphism, Restriction Fragment Length , Cluster Analysis , DNA Fingerprinting , Molecular Epidemiology , Genotype , Iran , Mycobacterium tuberculosis/isolation & purification
20.
Braz. j. microbiol ; 47(1): 181-190, Jan.-Mar. 2016. tab, graf
Article in English | LILACS | ID: lil-775120

ABSTRACT

Abstract In the present work we isolated and identified various indigenous Saccharomyces cerevisiae strains and screened them for the selected oenological properties. These S. cerevisiae strains were isolated from berries and spontaneously fermented musts. The grape berries (Sauvignon blanc and Pinot noir) were grown under the integrated and organic mode of farming in the South Moravia (Czech Republic) wine region. Modern genotyping techniques such as PCR-fingerprinting and interdelta PCR typing were employed to differentiate among indigenous S. cerevisiae strains. This combination of the methods provides a rapid and relatively simple approach for identification of yeast of S. cerevisiae at strain level. In total, 120 isolates were identified and grouped by molecular approaches and 45 of the representative strains were tested for selected important oenological properties including ethanol, sulfur dioxide and osmotic stress tolerance, intensity of flocculation and desirable enzymatic activities. Their ability to produce and utilize acetic/malic acid was examined as well; in addition, H2S production as an undesirable property was screened. The oenological characteristics of indigenous isolates were compared to a commercially available S. cerevisiae BS6 strain, which is commonly used as the starter culture. Finally, some indigenous strains coming from organically treated grape berries were chosen for their promising oenological properties and these strains will be used as the starter culture, because application of a selected indigenous S. cerevisiae strain can enhance the regional character of the wines.


Subject(s)
Saccharomyces cerevisiae/classification , Saccharomyces cerevisiae/isolation & purification , Vitis/microbiology , Acetic Acid/metabolism , Bacterial Adhesion , Czech Republic , DNA Fingerprinting , Drug Tolerance , Ethanol/toxicity , Hydrogen Sulfide/metabolism , Molecular Typing , Mycological Typing Techniques , Malates/metabolism , Osmotic Pressure , Polymerase Chain Reaction , Stress, Physiological , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/physiology , Sulfur Dioxide/toxicity
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