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Biomédica (Bogotá) ; 37(supl.2): 215-223, jul.-set. 2017. tab, graf
Article in Spanish | LILACS | ID: biblio-1038794


Resumen Introducción. Los departamentos de Chocó y Antioquia en Colombia presentan condiciones climáticas y de vegetación que favorecen el establecimiento de especies de vectores del género Lutzomyia y la transmisión de Leishmania spp. a poblaciones humanas que ingresan a ambientes selváticos conservados. Objetivo. Reportar las especies de flebotomíneos presentes en tres reservas naturales de las regiones del Darién y del Pacífico en Colombia. Materiales y métodos. Los flebotomíneos se recolectaron en las reservas naturales El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) y Tulenapa (Carepa, Antioquia). La recolección se hizo con trampas de luz CDC, mediante búsqueda activa en sitios de reposo y con trampas Shannon. La determinación taxonómica de especies se basó en las claves taxonómicas. En algunas especies de interés taxonómico, se evaluó el uso de secuencias parciales de la región 5' del gen COI. Resultados. Se recolectaron 611 flebotomíneos adultos: 531 en Acandí, 45 en Carepa y 35 en Bahía Solano. Se identificaron 17 especies del género Lutzomyia, tres del género Brumptomyia y una del género Warileya. Las distancias genéticas (K2P) y los soportes de agrupación (>99 %) en el dendrograma de neighbor joining correspondieron a la mayoría de unidades taxonómicas operacionales moleculares (Molecular Operational Taxonomic Units, MOTU) establecidas para el grupo Aragaoi y confirmaron claramente la identidad de Lu. coutinhoi. Conclusión. Se identificaron especies que tienen importancia en la transmisión de la leishmaniasis en Acandí, Bahía Solano y Carepa. Se confirmó la presencia de Lu. coutinhoi en Colombia.

Abstract Introduction: The departments of Chocó and Antioquia in Colombia show climatic and vegetation conditions favoring the establishment of vector species of the genus Lutzomyia and the transmission of Leishmania spp. to human populations entering conserved forest environments. Objective: To report the species of Phlebotomine sandflies present in three natural reserves in the Darien and Pacific regions of Colombia. Materials and methods: Sand flies were collected specifically in the natural reserves El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) and Tulenapa (Carepa, Antioquia). Sand flies were collected with CDC light traps, active search in resting places and Shannon traps. The taxonomic determination of species was based on taxonomic keys. For some species of taxonomic interest, we evaluated the partial sequences of the 5' region of COI gene. Results: A total of 611 adult sand flies were collected: 531 in Acandí, 45 in Carepa and 35 in Bahía Solano. Seventeen species of the genus Lutzomyia, three of the genus Brumptomyia and one of the genus Warileya were identified. The genetic distances (K2P) and grouping supported (>99%) in the neighbor joining dendrogram were consistent for most established molecular operational taxonomic units (MOTU) of the Aragaoi group and clearly confirmed the identity of Lu. coutinhoi. Conclusion: Species that have importance in the transmission of leishmaniasis in Acandí, Bahía Solano and Carepa were identified. The presence of Lu. coutinhoi was confirmed and consolidated in Colombia.

Animals , Psychodidae , Insect Vectors , Phylogeny , Psychodidae/classification , Psychodidae/genetics , Species Specificity , Base Sequence , Sequence Homology, Nucleic Acid , Forests , Sequence Alignment , Leishmaniasis, Cutaneous/transmission , Leishmaniasis, Cutaneous/epidemiology , Colombia/epidemiology , Electron Transport Complex IV/genetics , Insect Proteins/genetics , Ecology , Animal Distribution , Parks, Recreational , Insect Vectors/classification , Insect Vectors/genetics
Article in Chinese | WPRIM | ID: wpr-335173


<p><b>OBJECTIVE</b>To explore the genetic cause of a female case with intellectual development disorder.</p><p><b>METHODS</b>G banding karyotyping was performed for the patient. Following DNA extraction, the coding sequence of SRY gene was amplified with PCR and subjected to Sanger sequencing. qPCR was used to detect the copy numbers of the SRY gene.</p><p><b>RESULTS</b>The karyotype of the patient was 47,XXY. PCR and qPCR analyses of the SRY gene showed a large deletion with null copy number.</p><p><b>CONCLUSION</b>The female phenotype of the patient is probably due to deletion of the SRY gene on the Y chromosome. This is the first report of 47,XXY female case with deletion of the SRY gene in China.</p>

Base Sequence , Chromosome Banding , Chromosomes, Human, Y , Genetics , Female , Genes, sry , Genetics , Humans , Intellectual Disability , Genetics , Karyotype , Karyotyping , Klinefelter Syndrome , Genetics , Male , Polymerase Chain Reaction , Review Literature as Topic , Sequence Analysis, DNA , Methods , Sequence Deletion , Sequence Homology, Nucleic Acid
Article in Chinese | WPRIM | ID: wpr-345332


<p><b>OBJECTIVE</b>To detect potential mutation of NFU1 gene in a Chinese family affected with multiple mitochondrial dysfunction syndrome (MMDS).</p><p><b>METHODS</b>For a mother with two children died of MMDS, next-generation sequencing (NGS) was used to scan her exome. Suspected mutation was validated with PCR and Sanger sequencing. Potential mutation of exons 1 to 8 and flanking regions of the NFU1 gene was also detected in the father by PCR and Sanger sequencing.</p><p><b>RESULTS</b>A novel deletional mutation c.90delC(p.Tyr30Ter) of the NFU1 gene was found in the mother, while the father was found to have carried a heterozygous c.572A>T (p.Asp191Val) mutation. The same mutations were not found among 100 healthy controls.</p><p><b>CONCLUSION</b>The novel mutations c.90delC (p.Tyr30Ter) and c.572A>T (p.Asp191Val) of the NFU1 gene probably underlie the pathogenesis of MMDS in our case. Combined NGS and Sanger sequencing may provide efficient and accurate diagnosis for this disease.</p>

Asians , Genetics , Base Sequence , Carrier Proteins , Genetics , China , Exome , Genetics , Family Health , Fatal Outcome , Female , Genetic Predisposition to Disease , Ethnology , Genetics , Heterozygote , High-Throughput Nucleotide Sequencing , Methods , Humans , Infant , Male , Mitochondrial Diseases , Ethnology , Genetics , Mutation , Pedigree , Sequence Deletion , Sequence Homology, Nucleic Acid
Article in English | WPRIM | ID: wpr-36481


We report here a human case of Taenia asiatica infection which was confirmed by genetic analyses in Dali, China. A patient was found to have symptoms of taeniasis with discharge of tapeworm proglottids. By sequencing of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene, we observed nucleotide sequence identity of 99% with T. asiatica and 96% with T. saginata. Using the cytochrome b (cytb) gene, 99% identity with T. asiatica and 96% identity with T. saginata were found. Our findings suggest that taeniasis of people in Dali, China may be mainly caused by T. asiatica.

Adult , Animals , China , Cytochromes b/genetics , Electron Transport Complex IV/genetics , Humans , Male , Phylogeny , Sequence Homology, Nucleic Acid , Taenia/classification , Taeniasis/parasitology
Braz. j. microbiol ; 46(2): 565-570, Apr-Jun/2015. tab, graf
Article in English | LILACS | ID: lil-749724


Partial nucleotide sequences of ORF72 (glycoprotein D, gD), ORF64 (infected cell protein 4, ICP4) and ORF30 (DNA polymerase) genes were compared with corresponding sequences of EHV-1 reference strains to characterize the molecular variability of Brazilian strains. Virus isolation assays were applied to 74 samples including visceral tissue, total blood, cerebrospinal fluid (CSF) and nasal swabs of specimens from a total of 64 animals. Only one CSF sample (Iso07/05 strain) was positive by virus isolation in cell culture. EHV-1 Iso07/05 neurologic strain and two abortion visceral tissues samples (Iso11/06 and Iso33/06) were PCR-positive for ORF33 (glycoprotein B, gB) gene of EHV-1. A sequence analysis of the ORF72, ORF64 and ORF30 genes from three EHV-1 archival strains (A3/97, A4/72, A9/92) and three clinical samples (Iso07/05, Iso11/06 and Iso33/06) suggested that among Brazilian EHV-1 strains, the amplified region of the gD gene sequence is highly conserved. Additionally, the analysis of ICP4 gene showed high nucleotide and amino acid identities when compared with genotype P strains, suggesting that the EHV-1 Brazilian strains belonged to the same group. All the EHV-1 Brazilian strains were classified as non-neuropathogenic variants (N752) based on the ORF30 analysis. These findings indicate a high conservation of the gD-, ICP4- and ORF30-encoding sequences. Different pathotypes of the EHV-1 strain might share identical genes with no specific markers, and tissue tropism is not completely dependent on the gD envelope, immediate-early ICP4 and DNA polymerase proteins.

Animals , Genetic Variation , Herpesviridae Infections/veterinary , Herpesvirus 1, Equid/classification , Herpesvirus 1, Equid/genetics , Horse Diseases/virology , Brazil , Cluster Analysis , Conserved Sequence , DNA, Viral/chemistry , DNA, Viral/genetics , Genotype , Horses , Herpesviridae Infections/virology , Molecular Sequence Data , Open Reading Frames , Phylogeny , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid
Protein & Cell ; (12): 575-588, 2015.
Article in English | WPRIM | ID: wpr-757578


Human papillomaviruses (HPVs) including high-risk (HR) and low-risk (LR) subtypes have distinguishable variation on both genotypes and phenotypes. The co-infection of multiple HR-HPVs, headed by HPV16, is common in cervical cancer in female. Recently accumulating reports have focused on the interaction between virus and host, particularly the role of human microRNAs (miRNAs) in anti-viral defense by targeting viral genome. Here, we found a well-conserved target site of miRNAs in the genomes of most HR-HPVs, not LR-HPVs, by scanning all potential target sites of human miRNAs on 24 HPVs of unambiguous subtypes of risk. The site is targeted by two less common human miRNAs, miR-875 and miR-3144, and is located in E6 oncogene open reading frame (ORF) and overlap with the first alternative splice exon of viral early transcripts. In validation tests, miR-875 and miR-3144 were identified to suppress the target reporter activity markedly and inhibit the expression of both synthetically exogenous E6 and endogenous E6 oncogene. High level of two miRNAs can inhibit cell growth and promote apoptosis in HPV16-positive cervical cancer cells. This study provides a promising common target of miRNAs for most HR-HPVs and highlights the effects of two low expressed human miRNAs on tumour suppression.

Apoptosis , Genetics , Base Sequence , Binding Sites , Genetics , Cell Line, Tumor , Cell Proliferation , Genetics , Female , Gene Expression , Host-Pathogen Interactions , Genetics , Human papillomavirus 16 , Genetics , Physiology , Humans , MicroRNAs , Genetics , Microscopy, Fluorescence , Molecular Sequence Data , Oncogene Proteins, Viral , Genetics , Repressor Proteins , Genetics , Reverse Transcriptase Polymerase Chain Reaction , Sequence Homology, Nucleic Acid , Uterine Cervical Neoplasms , Genetics , Pathology , Virology
Recife; s.n; 2015. 74 p. ilus, graf, tab.
Thesis in Portuguese | LILACS | ID: lil-773006


Os tripanossomatídeos são organismos caracterizados pelo controle póstranscricional da expressão gênica, principalmente em nível de tradução. Na tradução em eucariotos, tem grande destaque o complexo eIF4F, sendo um de seus principais componentes o fator de iniciação da tradução eIF4E. Já foram descritos em tripanossomatídeos seis homólogos para o eIF4E, nomeados EIF4E1 a 6. Em um estudo com Leishmania amazonensis, focado no EIF4E3, percebeu-se que seu perfil de expressão se alterava rapidamente numa curva de crescimento, com este apresentando ao menos duas bandas. As mudanças observadas sugeriam modificações pós-traducionais do tipo fosforilação, algo posteriormente confirmado. Analisando-se a sequência do EIF4E3 de Leishmania, foi possível identificar a presença de possíveis sítios de fosforilação e de ligação a parceiros funcionais como homólogos do eIF4G, outro componente do complexo eIF4F, e da proteína de ligação á cauda poli-A (PABP). No presente estudo foi analisado o perfil de expressão e a capacidade de ligação a parceiros funcionais do EIF4E3 de Leishmania superexpresso em células transfectadas e no qual foram introduzidas mutações em motivos específicos. Os resultados mostraram um perfil de expressão de ao menos três bandas para o EIF4E3 de L. amazonensis e duas para L. infantum, com o sítio S75, presente apenas na primeira, sendo o responsável por esta diferença...

Humans , Animals , Gene Expression , Leishmania infantum/genetics , Leishmania infantum/metabolism , Leishmania mexicana/genetics , Leishmania mexicana/metabolism , Poly(A)-Binding Proteins , Protein Binding , Protein Biosynthesis , Protozoan Proteins , Sequence Homology, Nucleic Acid
Article in Chinese | WPRIM | ID: wpr-296634


<p><b>OBJECTIVE</b>To investigate the genetic characteristics of coxsackievirus A10(CV-A10) strains isolated from hand, foot and mouth disease (HFMD) cases in Ningxia province.</p><p><b>METHODS</b>Based on the HFMD laboratory network surveillance system, 2 470 patients clinical specimens including 450 faeces and 2 020 throat swaps were collected from various regions people's hospital in Ningxia Hui Autonomous Region during January, 2013 to December, 2014. All specimens were isolated using rhabdomyosarcoma cells. VP1 regional gene of isolated strains was amplified by RT-PCR using degenerate primers and sequenced. Sequences were compared with the database of GenBank by the Blast algorithm to identify the enterovirus genotypes. All the CV-A10 strains were performed the homology and phylogenetic evolution analysis.</p><p><b>RESULTS</b>450 specimens identified as non-EV-A71, non-CV-A16 enterovirus were collected and 36 CV-A10 strains were isolated, 6 strains were isolated in 2013 and 30 strains were isolated in 2014. The homology of nucleotides and amino acids among 36 CV-A10 strains were 90.6%-100.0% , and 90.2%-100.0%, respectively. Compared 36 strains with genotype A, B, C, D representative strains, it has the highest homology with the genotype C, the nucleotide and amino acids homogeneity were 90.2%-98.9% and 95.7%-99.7%. The phylogenetic tree showed 36 strains and genotype C representative strains located in the same evolutionary branch.</p><p><b>CONCLUSION</b>CV-A10 was one of the most common pathogen of HFMD in Ningxia Hui Autonomous Region. All CV-A10 strains belonged to genotype C and contained wide homology range.</p>

China , Enterovirus , Genetics , Genotype , Hand, Foot and Mouth Disease , Virology , Humans , Phylogeny , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid
Chinese Journal of Virology ; (6): 620-628, 2015.
Article in Chinese | WPRIM | ID: wpr-296238


The replicase genes of five isolates of Cucumber green mottle mosaic virus from Jiangsu, Zhejiang, Hunan and Beijing were amplificated, sequenced and analyzed. The similarities of nucleotide acid sequences indicated that 129 kD and 57 kD replicase genes of CGMMV-No. 1, CGMMV-No. 2, CGMMV-No. 3, CGMMV-No. 4 and CGMMV-No. 5 were 99.64% and 99.74%, respectively. The similarities of 129 kD and 57 kD replicase genes of CGMMV-No. 1, CGMMV-No. 3 and CGMMV-No. 4 were 99.95% and 99.94%, while they were lower between CGMMV-No. 2 and the rest of four reference sequences, just from 99.16% to 99.27% and from 99.04% to 99.18%. All reference sequences could be divided into six groups in neighbor-joining (NJ) phylogenetic trees based on the replicase gene sequences of 129 kD, 57 kD protein respectively. CGMMV-No. 1, CGMMV-No. 3 and CGMMV-No. 4 were clustered together with Shandong isolate (Accession No. KJ754195) in two NJ trees; CGMMV-No. 5 was clustered together with Liaoning isolate (Accession No. EF611826) in two NJ trees; CGMMV-No. 2 was clustered together with Korea watermelon isolate (Accession No. AF417242) in phylogenetic tree of 129 kD replicase gene of CGMMV; Interestingly, CGMMV-No. 2 was classified as a independent group in phylogenetic tree of 57 kD replicase gene of CGMMV. There were no significant hydrophobic and highly coiled coil regions on 129 kD and 57 kD proteins of tested CGMMV isolates. Except 129 kD protein of CGMMV-No. 4, the rest were unstable protein. The number of transmembrane helical segments (TMHs) of 129 kD protein of CGMMV-No. 1, CGMMV-No. 2, CGMMV-No. 3 and CGMMV-No. 5 were 6, 6, 2 and 4, respectively, which were 13, 13 and 5 on the 57 kD protein of CGMMV-No. 2, CGMMV-No. 4 and CGMMV-No. 5. The glycosylation site of 129 kD protein of tested CGMMV isolates were 2, 4, 4, 4 and 4, and that of 57 kD protein were 2, 5, 2, 5 and 2. There were difference between the disorders, globulins, phosphorylation sites and B cell antigen epitopes of 129 kD and 57 kD proteins of tested CGMMV isolates. The current results that there was no significant difference between the replicase gene sequences, it was stable and conservative for intra-species and clearly difference for inter-species. CGMMV-No. 1, CGMMV-No. 3, CGMMV-No. 4 and CGMMV-No. 5 had. a close genetic relationship with Shandong and Liangning isolates (Accession No. KJ754195 and EF611826), they are potentially originate from the same source. CGMMV-No. 2 was closer with Korea isolate. High sequence similarity of tested samples were gathered for a class in phylogenetic tree. It didn't show regularity of the bioinformatics analysis results of 129 kD and 57 kD proteins of tested CGMMV isolates. There was no corresponding relationship among the molecular phylogeny and the bioinformatics analysis of the tested CGMMV isolates.

Computational Biology , Cucumis sativus , Chemistry , Classification , Genetics , Molecular Sequence Data , Phylogeny , Plant Diseases , Virology , RNA-Dependent RNA Polymerase , Chemistry , Genetics , Metabolism , Sequence Homology, Nucleic Acid , Viral Proteins , Chemistry , Genetics , Metabolism
Article in English | WPRIM | ID: wpr-180023


Fascioliasis, a food-borne trematode zoonosis, is a disease primarily in cattle and sheep and occasionally in humans. Water dropwort (Oenanthe javanica), an aquatic perennial herb, is a common second intermediate host of Fasciola, and the fresh stems and leaves are widely used as a seasoning in the Korean diet. However, no information regarding Fasciola species contamination in water dropwort is available. Here, we collected 500 samples of water dropwort in 3 areas in Korea during February and March 2015, and the water dropwort contamination of Fasciola species was monitored by DNA sequencing analysis of the Fasciola hepatica and Fasciola gigantica specific mitochondrial cytochrome c oxidase subunit 1 (cox1) and nuclear ribosomal internal transcribed spacer 2 (ITS-2). Among the 500 samples assessed, the presence of F. hepatica cox1 and 1TS-2 markers were detected in 2 samples, and F. hepatica contamination was confirmed by sequencing analysis. The nucleotide sequences of cox1 PCR products from the 2 F. hepatica-contaminated samples were 96.5% identical to the F. hepatica cox1 sequences in GenBank, whereas F. gigantica cox1 sequences were 46.8% similar with the sequence detected from the cox1 positive samples. However, F. gigantica cox1 and ITS-2 markers were not detected by PCR in the 500 samples of water dropwort. Collectively, in this survey of the water dropwort contamination with Fasciola species, very low prevalence of F. hepatica contamination was detected in the samples.

Animals , Base Sequence , Cluster Analysis , DNA, Helminth/chemistry , DNA, Ribosomal Spacer/chemistry , Electron Transport Complex IV/genetics , Fasciola hepatica/genetics , Korea , Molecular Sequence Data , Oenanthe/parasitology , Phylogeny , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
Article in English | WPRIM | ID: wpr-331068


This study looked into a family involving a rare mother-child ABO blood type inconsistency and explored its genetic and molecular basis. In the family, the mother had type AB blood and the father was blood type B and they gave birth to a baby of blood type O. Their blood types were phenotypically identified by using different techniques, including micro-column gel test, immune inhibition test, absorption and elution tests. The sequences of all 7 exons of ABO allele from the core family members were determined by using PCR and clone-based sequencing. The loci of mutated gene were compared against normal human genes. The result showed that the mother's erythrocytes were agglutinable with monoclonal anti-A antibody (2+) and had agglutination reaction with anti-B antibody (4+). The mother's serum registered agglutination action with standard blood type A cells. The findings showed an ABO inconsistency. When domestic antibodies were used, the mother's erythrocytes yielded agglutination reaction with humanized anti-B serum (4+) and anti-B monoclonal antibody but were non-agglutinable with humanized anti-A serum and anti-A monoclonal antibody. Upon absorption and elution, the titer of anit-A antibody was 128 both before and after the absorption test, with no significant difference found between pre- and post-absorption values. Our results confirmed that the mother's allelic gene was type B and contained type A. The father's blood type was type B, and son's blood type was type O. Clone-based sequencing revealed that the mother carried a heterozygous gene of B101.01 (ntA640→G)/O01, which contained an M214→V mutation that could express a weak expression of antigen A, resulting in blood type AB. However, their son did not have the M214→V mutation, which yielded a false ABO-inconsistency between him and his mother. We were led to conclude that type B gene with a M214→V mutation can encode both antigen B and weak antigen B that can lead to false ABO-inconsistencies.

ABO Blood-Group System , Genetics , Allergy and Immunology , Adult , Base Sequence , DNA Primers , Female , Humans , Maternal-Fetal Exchange , Molecular Sequence Data , Mutation , Polymerase Chain Reaction , Pregnancy , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
Invest. clín ; 55(4): 332-351, dic. 2014. ilus, tab
Article in English | LILACS | ID: lil-783088


Sucre municipality is a large, densely populated marginal area in the eastern part of Caracas, Venezuela that consistently has more cases of tuberculosis than other municipalities in the country. To identify the neighborhoods in the municipality with the highest prevalence of tuberculosis, and determine whether the Mycobacterium tuberculosis strain distribution in this municipality is different from that previously found in the western part of Caracas and the rest of Venezuela, we collected data on all tuberculosis cases in the municipality diagnosed in 2005-6. We performed two separate molecular epidemiological studies, spoligotyping 44 strains in a first study, and spoligotyping 131 strains, followed by MIRU-VNTR 15 on 21 clustered isolates in the second. With spoligotyping, the most common patterns were Shared International Type SIT17 (21%); SIT42 (15%); SIT93 (11%); SIT20 (7%); SIT53 (6%), a distribution similar to other parts of Venezuela, except that SIT42 and SIT20 were more common. MIRU-VNTR 15 showed that six of seven SIT17 strains examined belonged to a large cluster previously found circulating in Venezuela, but all of the SIT42 strains were related to a cluster centered in the neighborhoods of Unión and Maca, with a MIRU-VNTR pattern not previously seen in Venezuela. It appears that a large percentage of the tuberculosis in the Sucre municipality is caused by the active transmission of two strain families centered within distinct neighborhoods, one reflecting communication with the rest of the country, and the other suggesting the insular, isolated nature of some sectors.

El municipio Sucre es un área densamente poblada del este de Caracas, Venezuela, con más casos de tuberculosis que otros municipios del país. Para establecer las áreas en el municipio Sucre con la mas alta prevalencia de tuberculosis y determinar sí la distribución de cepas de Mycobacterium tuberculosis es diferente de las encontradas previamente en el Oeste de Caracas y el resto de Venezuela, se recolectaron los datos de todos los casos diagnosticados de tuberculosis en el municipio en el 2005-6. Además, se aplicaron dos estudios de epidemiología molecular, el primero con 44 aislados en 2006 y el segundo con 131 aislados del 2006 al 2011, todos caracterizados por spoligotyping. Fue aplicada la técnica MIRU VNTR15 sobre 21 aislados agrupados. Con spoligotyping, los patrones encontrados fueron SIT17 (21%); SIT42 (15%); SIT93 (11%); SIT20 (7%); SIT53 (6%), presentando una distribución similar en otras partes de Venezuela, con la diferencia de que el SIT42 y el SIT20 fueron comunes en el municipio. MIRU VNTR15 mostró que seis de las siete cepas SIT17 pertenecían a un gran grupo encontrado previamente en Venezuela, mientras las cepas SIT42, estaban relacionados a un grupo concentrado en los Barrios Unión y Maca, con un patrón MIRU VNTR no visto previamente en Venezuela. Los resultados indicarían que un gran porcentaje de tuberculosis en el municipio Sucre es causada por transmisión activa de dos familias, una reflejando comunicación con el resto del país, y otra sugiriendo que es un aislado propio de algunos Barrios del municipio.

Humans , Mycobacterium tuberculosis/classification , Tuberculosis/microbiology , Bacterial Typing Techniques , Cluster Analysis , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/isolation & purification , Pilot Projects , Polymerase Chain Reaction/methods , Residence Characteristics , Retrospective Studies , Sequence Homology, Nucleic Acid , Species Specificity , Tuberculosis/epidemiology , Urban Population , Venezuela/epidemiology
Biomédica (Bogotá) ; 34(4): 556-566, oct.-dic. 2014. ilus, graf, tab
Article in Spanish | LILACS | ID: lil-730939


Introducción. No existen reportes sobre las variaciones en la secuencia de los genes blanco de los medicamentos anti- Toxoplasma en aislamientos provenientes de Suramérica. Objetivo. Clonar y secuenciar los genes de la dihidrofolato-reductasa ( dhfr ) y la dihidropteroato-sintetasa ( dhps ) de la cepa de referencia RH y de dos aislamientos colombianos de Toxoplasma gondii. Materiales y métodos. Se obtuvieron dos aislamientos de T. gondii en líquido céfalorraquídeo de pacientes colombianos positivos para HIV con toxoplasmosis cerebral. Se extrajo el ADN de los genes dhfr y dhps y se amplificaron mediante reacción en cadena de la polimerasa (PCR). Los productos fueron clonados en el vector pGEM-T y secuenciados. Resultados. Se encontró un cambio de adenina por guanina (A « G) en la posición 235 del exón 2 del gen dhps , dos cambios de guanina por citocina (G « C) en las posiciones 259 y 260 y un cambio de timina por guanina (T « G) en la posición 371 del exón 4 del gen dhps. Por análisis bioinformático, en este último exón se identificó un polimorfismo no sinónimo en la región codificante, que podría llevar al cambio de una Glu (CAA o CAG) por una His (codificada por los codones AAU o AAC). Se calculó el modelo estructural de la enzima dihidropteroato-sintetasa (DHPS) de T. gondii y se identificaron las modificaciones en la estructura secundaria ocasionadas por las mutaciones. Conclusiones. La metodología estandarizada puede servir como base para la búsqueda de polimorfismos en muestras de pacientes con diferentes manifestaciones clínicas de toxoplasmosis y para establecer su posible relación con los cambios en la sensibilidad a los antifolatos y la reacción al tratamiento.

Introduction: There are no reports describing polymorphisms in target genes of anti- Toxoplasma drugs in South American isolates. Objective: This study sought to perform cloning and sequencing of the dihydrofolate reductase ( dhfr ) and dihydropteroate-synthase ( dhps ) genes of the reference Rh strain and two Colombian isolates of Toxoplasma gondii . Materials and methods: Two isolates were obtained from the cerebrospinal fluid of HIV-infected patients with cerebral toxoplasmosis. A DNA extraction technique and PCR assay for the dhfr and dhps genes were standardized, and the products of amplification were cloned into Escherichia coli and sequenced. Results: One polymorphism (A « G) was found at position 235 of exon 2 in the dhps gene. In addition, two polymorphisms (G « C) at positions 259 and 260 and one polymorphism (T « G) at position 371 within exon 4 of the dhps gene were detected. In this last exon, a bioinformatic analysis revealed a non-synonymous polymorphism in the coding region that could lead to the substitution of Glu (CAA or CAG) for His (encoded by codons AAU or AAC). A structural model of the T. gondii DHPS protein was calculated, and the results revealed modifications in secondary structure due to mutations. Conclusions: The methods described in this study can be used as a tool to search for polymorphisms in samples from patients with different clinical manifestations of toxoplasmosis and to examine their relationship with the therapeutic response.

Animals , Humans , Male , Mice , Dihydropteroate Synthase/genetics , Polymorphism, Single Nucleotide , Protozoan Proteins/genetics , Tetrahydrofolate Dehydrogenase/genetics , Toxoplasma/enzymology , AIDS-Related Opportunistic Infections/cerebrospinal fluid , AIDS-Related Opportunistic Infections/parasitology , Amino Acid Substitution , Base Sequence , Cloning, Molecular , Colombia , Cerebrospinal Fluid/parasitology , DNA, Protozoan/genetics , DNA, Recombinant/genetics , Dihydropteroate Synthase/chemistry , Exons/genetics , Models, Molecular , Molecular Sequence Data , Protein Conformation , Protozoan Proteins/chemistry , Sequence Alignment , Sequence Homology, Nucleic Acid , Toxoplasma/genetics , Toxoplasma/isolation & purification , Toxoplasmosis, Animal/parasitology , Toxoplasmosis, Cerebral/cerebrospinal fluid , Toxoplasmosis, Cerebral/parasitology
Biomédica (Bogotá) ; 34(4): 598-604, oct.-dic. 2014. graf, tab
Article in Spanish | LILACS | ID: lil-730944


Institución donde se ejecutó el trabajo: Programa de Estudio y Control de Enfermedades Tropicales, PECET, Unidad de Malacología Médica y Trematodos (UMMT), Sede de Investigación Universitaria, Universidad de Antioquia, Medellín, Colombia Introducción. La fasciolosis es la enfermedad transmitida por vectores con mayor distribución latitudinal, longitudinal y altitudinal, debido a la capacidad colonizadora del parásito Fasciola hepatica y de sus huéspedes intermediarios, los moluscos limneidos. Estos caracoles se investigan por su importancia epidemiológica, pero su identificación taxonómica es difícil por la similitud fenotípica entre especies. En este sentido, con respecto a Lymnaea cousini , un huésped de F. hepatica en Colombia, existe incertidumbre en razón de su similitud morfológica con L. meridensis , descrita recientemente en Venezuela. Objetivo. Confirmar con el marcador del gen de la citocromo oxidasa I en el ADN mitocondrial COI (ADNmt), el estatus taxonómico de ejemplares morfológicamente caracterizados como L. cousini provenientes de Nariño, Norte de Santander y Santander (Colombia), depositados en la Colección de Moluscos Vectores de la Universidad de Antioquia, VHET N° 37. Materiales y métodos. Para la amplificación del COI mitocondrial, se extrajo ADN total del pie de cada ejemplar con el estuche DNeasy Blood and Tissue (Qiagen ® ). Los productos amplificados se enviaron a secuenciar a Macrogen Inc., Corea. Las 27 secuencias generadas en esta investigación se compararon con secuencias publicadas en el GenBank, incluidas las secuencias de la localidad tipo de L. cousini. Resultados. Se encontraron dos nuevos haplotipos de L. cousini para Colombia. Los especímenes de Nariño correspondían al haplotipo A, referenciado en Ecuador, y los especímenes de Santander y Norte de Santander, a un nuevo haplotipo al que se denominó D. Conclusión. Mediante el marcador mitocondrial del COI , se confirmó que los especímenes pertenecían a la especie L. cousini . Con el hallazgo se duplicó el número de haplotipos conocidos de la especie en Colombia y se amplió su distribución geográfica al suroeste y nordeste de la región altoandina colombiana.

Introduction: Fasciolosis is the disease transmitted by vectors with the highest latitudinal, longitudinal, and altitudinal distribution due to the colonizing capacity of the parasite Fasciola hepatica and its intermediate hosts, Lymnaeidae mollusks. These snails are under research due to their epidemiological importance, but their taxonomic identification is difficult given their interspecific phenotypical similarity. For this reason, there is uncertainty regarding Lymnaea cousini -a host of F. hepatica in Colombia- due to the morphological similarity it has with Lymnaea meridensis , recently described for Venezuela. Objective: To confirm with the COI marker (ADNmt) the taxonomic status of individuals morphologically identified as L. cousini from Nariño, Norte de Santander, and Santander (Colombia), deposited in the Vector Mollusks Collection VHET No. 37 of Universidad de Antioquia. Materials and methods: The amplification of the mitochondrial COI required total DNA extraction of each individual´s foot using the DNeasy Blood and Tissue Kit (Qiagen®). Products amplified were sent for sequencing to Macrogen Inc., Korea. Twenty seven sequences generated in this research were compared to sequences published in the GenBank, including sequences of the type locality of L. cousini . Results: Two new haplotypes of L. cousini were obtained for Colombia. Specimens from Nariño correspond to haplotype A, referenced for Ecuador, and specimens from Santander and Norte de Santander belong to a new haplotype we called haplotype D. Conclusion : By using the mitochondrial COI marker, we confirmed that the species under study did correspond to L. cousini . The number of known haplotypes of the species for Colombia has been duplicated and its geographical distribution has been extended to the southwest and northeast of the Colombian high Andean region.

Animals , Disease Vectors/classification , Electron Transport Complex IV/analysis , Fasciola hepatica , Lymnaea/classification , Base Sequence , Biomarkers , Colombia , DNA , DNA, Mitochondrial/genetics , Electron Transport Complex IV/genetics , Haplotypes/genetics , Lymnaea/enzymology , Lymnaea/genetics , Molecular Sequence Data , Phylogeny , Protein Subunits , Sequence Alignment , Sequence Homology, Nucleic Acid
Rev. argent. microbiol ; 46(3): 210-217, oct. 2014. tab
Article in English | LILACS | ID: lil-734582


La resistencia a la combinación de ß-lactámico/inhibidor de ß-lactamasa en enterobacterias es un problema creciente que no ha sido estudiado intensamente en Argentina. En el presente trabajo, 54/843 enterobacterias recolectadas en un hospital universitario de la ciudad de Buenos Aires fueron resistentes a ampicilina-sulbactama, pero se mantuvieron sensibles a las cefalosporinas de segunda y tercera generación. Se analizaron los mecanismos enzimáticos presentes en los aislamientos que también fueron resistentes a amoxicilina-ácido clavulánico (AMC) (18/54). La secuenciación reveló dos variantes diferentes de blaTEM-1, donde blaTEM-1b es el alelo más frecuentemente detectado (10 Escherichia coli, 3 Klebsiella pneumoniae, 2 Proteus mirabilis y 1 Raoultella terrigena), seguidos por blaTEM-1a(1 K. pneumoniae). La resistencia a AMC parece estar asociada principalmente con la hiperproducción de TEM-1 (sobre todo en E. coli) o con la coexpresión con ß-lactamasas tipo OXA-2 y/o SHV (K. pneumoniae y P. mirabilis). Se describió una nueva variante de blaTEM(TEM-163) en un aislamiento de E. coli que presentó una CIM frente a AMC de 16/8 µg/ml. La enzima TEM-163 contiene dos sustituciones de aminoácidos respecto de TEM-1, Arg275Gln y His289Leu. Teniendo en cuenta la alta actividad específica observada y la baja IC50 para el ácido clavulánico, el patrón de resistencia de este aislamiento parece obedecer a la hiperproducción de la nueva variante de la ß-lactamasa de amplio espectro, en lugar de vincularse con un comportamiento similar al de una TEM resistente a inhibidores (IRT).

Resistance to ß-lactam/ß-lactamase inhibitors in enterobacteria is a growing problem that has not been intensively studied in Argentina. In the present work, 54/843 enterobacteria collected in a teaching hospital of Buenos Aires city were ampicillin-sulbactam-resistant isolates remaining susceptible to second-and third-generation cephalosporins. The enzymatic mechanisms present in the isolates, which were also amoxicillin-clavulanic acid (AMC)-resistant (18/54) were herein analyzed. Sequencing revealed two different variants of blaTEM-1, being blaTEM-1b the most frequently detected allelle (10 Escherichia coli, 3 Klebsiella pneumoniae, 2 Proteus mirabilis and 1 Raoultella terrigena) followed by blaTEM-1a(1 K. pneumoniae). Amoxicillin-clavulanate resistance seems to be mainly associated with TEM-1 overproduction (mostly in E. coli) or co-expressed with OXA-2-like and/or SHV ß-lactamases (K. pneumoniae and P. mirabilis). A new blaTEMvariant (TEM-163) was described in an E. coli strain having an AMC MIC value of 16/8 µg/ml. TEM-163 contains Arg275Gln and His289Leu amino acid substitutions. On the basis of the high specific activity and low IC50 for clavulanic acid observed, the resistance pattern seems to be due to overproduction of the new variant of broad spectrumß-lactamase rather than to an inhibitor-resistant TEM (IRT)-like behavior.

Humans , Amoxicillin-Potassium Clavulanate Combination/pharmacology , Drug Resistance, Bacterial/genetics , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae/enzymology , beta-Lactamases/isolation & purification , Amino Acid Substitution , Argentina/epidemiology , Base Sequence , Cross Infection/epidemiology , Cross Infection/microbiology , Disk Diffusion Antimicrobial Tests , DNA, Bacterial/genetics , Enterobacteriaceae Infections/epidemiology , Enterobacteriaceae/drug effects , Enterobacteriaceae/genetics , Enterobacteriaceae/isolation & purification , Escherichia coli Proteins/genetics , Escherichia coli Proteins/isolation & purification , Escherichia coli Proteins/metabolism , Escherichia coli/drug effects , Escherichia coli/enzymology , Escherichia coli/genetics , Escherichia coli/isolation & purification , Genes, Bacterial , Hospitals, Teaching , Hospitals, Urban , Molecular Sequence Data , Sequence Homology, Nucleic Acid , Substrate Specificity , beta-Lactamases/genetics , beta-Lactamases/metabolism
Braz. j. microbiol ; 45(3): 1075-1082, July-Sept. 2014. ilus, tab
Article in English | LILACS | ID: lil-727040


Staphylococcus aureus antimicrobial resistance, especially to beta-lactams, favors treatment failures and its persistence in herd environment. This work aimed to develop a more specific primer for mecA gene detection based on the comparison of the conserved regions from distinct host origins and also investigated the presence of homologue mecA LGA251 in bovine strains. A total of 43 Staphylococcus spp. were included in this study, comprising 38 bovine S. aureus, two human and three equine coagulase-negative staphylococci (CNS). Phenotypical methicillin-resistance detection was performed through oxacillin agar-screening and cefoxitin disk-diffusion test. None isolate tested positive for mecA LGA251 gene. For mecA gene PCR, new primers were designed based on the sequences of human S. aureus (HE681097) and bovine S. sciuri (AY820253) mecA. The new primers based on the S. aureus mecA sequence amplified fragments of human and equine CNS and the ones based on S. sciuri mecA sequence only yielded fragments for S. aureus bovine strains. Multiples alignments of mecA gene sequences from bovine, human and equine revealed punctual but significant differences in bovine strains that can lead to the mecA gene detection impairment. The observed divergences of mecA gene sequences are not a matter of animal or human origin, it is a specificity of bovine samples.

Animals , Cattle , Humans , Bacterial Proteins/genetics , Staphylococcal Infections/microbiology , Staphylococcal Infections/veterinary , Staphylococcus aureus/genetics , Staphylococcus aureus/isolation & purification , DNA Primers/genetics , DNA, Bacterial/genetics , Genetic Variation , Horses , Methicillin Resistance , Microbial Sensitivity Tests , Polymerase Chain Reaction/methods , Sequence Alignment , Sequence Homology, Nucleic Acid
Braz. j. microbiol ; 45(2): 677-687, Apr.-June 2014. ilus, graf, tab
Article in English | LILACS | ID: lil-723134


A mesophilic Enterobacter sp. Bn12 producing an alkaline thermostable lipase was isolated from soil in Tehran, Iran. The lipase gene (ELBn12) was identified from a genomic library. Sequence analysis of the DNA fragment revealed an open reading frame of 879 bp encoding a lipase with a molecular mass of 31.3 kDa. The deduced amino acid sequence showed 96% identity with a lipase of Enterobacter sp. Ag1 and the identity of their DNA sequences was 88.9%. ELBn12 belongs to the lipase subfamily I.1 and its catalytic triad consists of Ser82, Asp237 and His259. The lipase was expressed in Escherichia coli (BL21) pLysS and partially purified by anion exchange chromatography. The maximum activity of ELBn12 was obtained at temperature of 60 °C and pH 8.0 towards tricaprylin (C8) and its specific activity was around 2900 U/mg. ELBn12 was stable within a broad pH range from 6.0 to 11.0. The enzyme showed high stability in both polar and nonpolar organic solvents at 50% (v/v). The lipase activity was enhanced in the presence of 10 mM of Ca2+, Mg2+ and K+, while heavy metals (Fe3+ and Zn2+) had strong inhibitory effect. ELBn12 showed high activity in the presence of 1% (w/v) nonionic surfactants, however ionic surfactants inhibited the lipolytic activity. ELBn12 characteristics show that it has a potential to be used in various industrial processes.

Enterobacter/enzymology , Lipase/isolation & purification , Lipase/metabolism , Amino Acid Sequence , Bacterial Typing Techniques , Base Sequence , Chromatography, Ion Exchange , Cloning, Molecular , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Enzyme Stability , Enterobacter/classification , Enterobacter/genetics , Enterobacter/isolation & purification , Enzyme Activators/analysis , Enzyme Inhibitors/analysis , Escherichia coli/genetics , Gene Expression , Hydrogen-Ion Concentration , Iran , Lipase/chemistry , Lipase/genetics , Molecular Sequence Data , Molecular Weight , Open Reading Frames , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Sequence Analysis, DNA , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid , Soil Microbiology , Temperature
Indian J Biochem Biophys ; 2014 Apr; 51(2): 100-114
Article in English | IMSEAR | ID: sea-154245


The pseudorabies virus (PRV) early protein EP0 is a homologue of the herpes simplex virus 1 (HSV-1) immediate-early protein ICP0, which is a multifunctional protein and important for HSV-1 infection. However, the exact function of EP0 is not clear. In this study, using polymerase chain reaction, a 1,104 base-pair sequence of the EP0 gene was amplified from the PRV Becker strain genome and identification of the EP0 gene was confirmed by further cloning and sequencing. Bioinformatics analysis indicated that the PRV EP0 gene encoded a putative polypeptide with 367 amino acids. The encoded protein, designated as EP0 contained a conserved RING-finger superfamily domain and was found to be closely related with the herpes virus RING-finger superfamily and was highly conserved among the counterparts encoded by RING-finger genes. Multiple nucleic acid sequence and amino-acid sequence alignments suggested that PRV EP0 showed a relatively higher similarity with EP0-like proteins of genus Varicellovirus than with those of other genera of Alphaherpesvirinae. In addition, phylogenetic analysis showed that PRV EP0 had a close evolutionary relationship with members of genus Varicellovirus, especially bovine herpesvirus 1 (BoHV-1) and BoHV-5. Antigen prediction indicated that several potential B-cell epitopes were located in EP0. Also, subcellular localization analysis demonstrated that EP0 was predominantly localized in the nucleus, suggesting that it might function as a nuclear-targeted protein.

Amino Acid Sequence , Animals , Base Sequence , Cattle , Cloning, Molecular , Computational Biology , DNA, Viral/genetics , Herpesvirus 1, Suid/genetics , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction , Protein Structure, Secondary , Sequence Homology, Amino Acid , Sequence Homology, Nucleic Acid , Viral Proteins/chemistry , Viral Proteins/genetics
Biomédica (Bogotá) ; 34(supl.1): 156-162, abr. 2014. graf, tab
Article in Spanish | LILACS | ID: lil-712432


Introducción. La terapia antibiótica combinada para la erradicación de Helicobacter pylori debería basarse en los patrones locales de resistencia. Objetivo. Determinar la resistencia de H. pylori a claritromicina en una población del departamento del Cauca mediante la identificación de mutaciones en el gen 23S r RNA en ADN obtenido de biopsias gástricas. Materiales y métodos. Se incluyeron en el estudio 162 pacientes con dispepsia funcional. El gen 23S rRNA se amplificó por PCR y el patrón de mutaciones se identificó por secuenciación directa. Resultados. La frecuencia de resistencia a claritromicina fue de 4 %. La mutación A2143G del gen se encontró en cuatro pacientes (2,46 %) y la mutación A2142G, en tres pacientes (1,85 %). Conclusiones. El estudio encontró que el genotipo más frecuente en los especímenes positivos para H. pylori fue 2143G, seguido por A2142G. La prevalencia observada de resistencia de H. pylori fue baja; por lo tanto, se considera que el tratamiento con claritromicina es una opción válida para la erradicación de H. pylori en la población objeto de estudio.

Introduction: Antibiotic combination therapy for the eradication of Helicobacter pylori should be based on local resistance patterns. Objective: To d etermine the resistance of H. pylori to clarithromycin in a population from Cauca province, through the identification of mutations in the 23S rRNA gene in DNA from gastric biopsies. Materials and methods: A total of 162 patients with functional dyspepsia were included in the study. The 23S rRNA gene and the DNA from 162 gastric specimens were amplified by PCR, and the mutation pattern was identified by direct sequencing. Results: The frequency of clarithromycin resistance was 4%. A2143G mutation was found in four patients (2.46%) and A2142G mutation was found in three patients (1.85%). Conclusions: Our study shows that the most frequent genotype in H. pylori -positive specimens was A2143G, followed by A2142G. The observed resistance prevalence of H. pylori was low; thus, we consider that clarithromycin treatment is a valid option for H. pylori eradication in the study population.

Adolescent , Adult , Aged , Female , Humans , Male , Middle Aged , Young Adult , Clarithromycin/pharmacology , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Drug Resistance, Bacterial/genetics , Gastritis/microbiology , Helicobacter Infections/microbiology , Helicobacter pylori/genetics , Polymorphism, Single Nucleotide , RNA, Bacterial/genetics , /genetics , Bacterial Typing Techniques , Biopsy , Bacterial Proteins/genetics , Colombia/epidemiology , Genes, Bacterial , Gastritis/epidemiology , Gastritis/pathology , Helicobacter Infections/epidemiology , Helicobacter Infections/pathology , Helicobacter pylori/classification , Helicobacter pylori/drug effects , Helicobacter pylori/isolation & purification , Mutation, Missense , Prospective Studies , Sequence Alignment , Sequence Homology, Nucleic Acid