307 results on '"Haplotipos"'
Search Results
2. Análisis y revisión de la variación del MHC-B (complejo mayor de Histocompatibilidad) en pollos. Síntesis del trabajo en líneas sintéticas INTA
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Gabriela Marisa Iglesias
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complejo mayor de histocompatibilidad ,pollos ,gallus gallus ,mhc ,aves ,snps ,haplotipos ,campero inta ,Veterinary medicine ,SF600-1100 - Abstract
El complejo mayor de Histocompatibilidad (MHC del inglés: Major histocompatibility complex) en pollos (Gallus gallus) se encuentra localizado en un micro cromosoma, el 16 del genoma aviar. Así como ocurre en otras especies tiene una fuerte asociación con la resistencia genética a enfermedades. Esta característica multigénica es particularmente deseada para la selección de esta especie, en particular por su relación con el bienestar animal. En este trabajo se pretende revisar los conocimientos sobre el análisis de la variabilidad del MHC-B en pollos y sus metodologías de análisis y una síntesis de los trabajos realizados en pollos Campero INTA
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- 2022
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3. Genetic structure of drug-resistant Mycobacterium tuberculosis strains in Peru based on haplotypes obtained from a line probe assay
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David Santos-Lazaro, Zully M. Puyen, and Ronnie G. Gavilan
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mycobacterium tuberculosis ,tuberculosis resistente a múltiples medicamentos ,genotipo ,haplotipos ,perú. ,Medicine ,Medicine (General) ,R5-920 - Abstract
Objective. To determine the genetic structure of drug-resistant strains of Mycobacterium tuberculosis that circulated throughout Peru during the years 2011-2015, by using haplotypes obtained from a line probe assay. Materials and methods. A total of 6589 samples that were admitted to the Instituto Nacional de Salud for routine diagnosis using the GenoType® MTBDRplus v2 assay were analyzed during the study period. Resistant haplotypes were created by concatenating 21 polymorphic sites of the evaluated genes using the line probe assay; and the association analysis was carried out with phenotypes obtained by the 7H10 agar ratio method. Results. The most frequent mutations were: rpoB S531L (55.4%) and rpoB D516V (18.5%) for rifampicin resistance, and katG S315T (59.5%) and inhA c-15t (25.7%) for isoniazid resistance. We obtained 13 representative haplotypes (87.8% of analyzed samples), 6 corresponded to the multidrug-resistant genotype, 4 to the isoniazid mono-resistant genotype and 3 to the rifampicin mono-resistant genotype. Eighteen regions and the province of Callao showed high haplotype diversity; four showed moderate diversity and two showed low diversity. Conclusions. Most regions showed high haplotype diversity; in addition, most drug-resistant strains of Mycobacterium tuberculosis were concentrated in the cities of Lima and Callao. Likewise, drugresistant Mycobacterium tuberculosis strains circulating in Peru mainly contain the genetic markers with the highest prevalence worldwide, which are associated with resistance to rifampicin and isoniazid.
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- 2021
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4. Nuevos haplotipos de Diaphorina citri, vector de Candidatus Liberibacter en zonas citrícolas de México.
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Ceballos Ceballos, Augusto Gil, Cerna Chavez, Ernesto, Ochoa Fuentes, Yisa María, and Rodríguez Pagaza, Yolanda
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GENE amplification ,MITOCHONDRIAL DNA ,INSECT collection & preservation ,HAPLOTYPES ,NUCLEOTIDES ,CITRUS greening disease - Abstract
Copyright of Revista Mexicana de Ciencias Agrícolas is the property of Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2022
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5. NUEVOS REGISTROS DE CALOMYS TENER (RODENTIA: CRICETIDAE, SIGMODONTINAE) QUE AMPLÍAN LA DISTRIBUCIÓN Y DIVERSIDAD GENÉTICA CONOCIDA PARA MISIONES, ARGENTINA.
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Burgos, Eliana F., Labaroni, Carolina, Lanzone, Cecilia, Urdapilleta, Mara, and Gómez Villafañe, Isabel E.
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CYTOCHROME b , *COLONIZATION (Ecology) , *SPECIES distribution , *HAPLOTYPES , *RODENTS - Abstract
Misiones province has a great diversity of rodents, some of them, such as Calomys tener, have few records and their presence in the province has been widely discussed. The aims of this work were to: a) provide information on a new locality of presence, b) describe morphologically, and c) analyze the molecular variability of cytochrome b of Calomys tener. Based on sampling seasons carried out in 2017 and 2018, four individuals were captured and identified morphologically and molecularly as C. tener. This new records extend the species distribution to the north of the province of Misiones. The sequences of C. tener obtained in this study, together with those available in GenBank from Paraguay, Brazil, Bolivia and Argentina, show that the haplotypes found in Misiones are divergent, suggesting multiple colonization from different geographic areas. [ABSTRACT FROM AUTHOR]
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- 2022
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6. ESTRUCTURA GENÉTICA DE CEPAS DROGORRESISTENTES DE Mycobacterium tuberculosis EN PERÚ BASADA EN HAPLOTIPOS OBTENIDOS DE UN ENSAYO CON SONDAS EN LÍNEA.
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Santos-Lazaro, David, Puyen, Zully M., and Gavilan, Ronnie G.
- Abstract
Objective. To determine the genetic structure of drug-resistant strains of Mycobacterium tuberculosis that circulated throughout Peru during the years 2011-2015, by using haplotypes obtained from a line probe assay. Materials and methods. A total of 6589 samples that were admitted to the Instituto Nacional de Salud for routine diagnosis using the GenoType® MTBDRplus v2 assay were analyzed during the study period. Resistant haplotypes were created by concatenating 21 polymorphic sites of the evaluated genes using the line probe assay; and the association analysis was carried out with phenotypes obtained by the 7H10 agar ratio method. Results. The most frequent mutations were: rpoB S531L (55.4%) and rpoB D516V (18.5%) for rifampicin resistance, and katG S315T (59.5%) and inhA c-15t (25.7%) for isoniazid resistance. We obtained 13 representative haplotypes (87.8% of analyzed samples), 6 corresponded to the multidrug-resistant genotype, 4 to the isoniazid mono-resistant genotype and 3 to the rifampicin mono-resistant genotype. Eighteen regions and the province of Callao showed high haplotype diversity; four showed moderate diversity and two showed low diversity. Conclusions. Most regions showed high haplotype diversity; in addition, most drug-resistant strains of Mycobacterium tuberculosis were concentrated in the cities of Lima and Callao. Likewise, drugresistant Mycobacterium tuberculosis strains circulating in Peru mainly contain the genetic markers with the highest prevalence worldwide, which are associated with resistance to rifampicin and isoniazid. [ABSTRACT FROM AUTHOR]
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- 2021
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7. Genetic diversity and population structure of Anopheles triannulatus s. l. in the department of Córdoba, Colombia, using DNA barcoding
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María Atencia, Angie Toro-Cantillo, and Richard Hoyos-López
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Anopheles/genética ,variación genética ,haplotipos ,flujo génico ,Colombia ,Medicine ,Arctic medicine. Tropical medicine ,RC955-962 - Abstract
Introduction: Anopheles triannulatus is not incriminated as a vector of malaria transmission in Colombia despite recent reports of infection with Plasmodium spp. in populations related to the northwestern and southeastern lineages. Genetic diversity can delimit information about gene flow and population differentiation in localities with malaria. Objective: To estimate the genetic diversity of An. triannulatus in five municipalities with high and low incidence of malaria in the department of Córdoba. Materials and methods: The entomological collections were done between August and November, 2016, in Tierralta, Puerto Libertador, Montelíbano, Sahagún, and Planeta Rica. We used the COI barcoding fragment as molecular marker. The genetic analysis included the estimation of genetic parameters such as the diversity haplotype, the genetic structure, the gene flow, the Tajima’s D test, the haplotype network, and the phylogenetic relationship. Results: We obtained 148 sequences with a length of 655 nucleotides of the COI gene, from which we derived 44 haplotypes. The H2 and H21 haplotypes were the most frequent in the populations. The values of the Tajima’s D test were negative and not significant (p>0.10). The genetic structure index (FST=0.01427) and the gene flow (Nm=17.27) evidenced no differentiation between sampled populations due to the high exchange of migrants. Using phylogenetic inferences and the haplotype network, we identified one single species without geographic differentiation or lineages in the geographic range studied. Conclusions: The genetic diversity calculated for An. triannulatus in this context indicated stable populations in constant exchange.
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- 2018
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8. LEPR polymorphisms and haplotypes in Mexican patients with colorectal cancer.
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Partida, Miriam, Gutiérrez, Melva, de la Luz Ayala, María, Macias, Nelly Margarita, Alvizo, Calos Rogelio, and Peregrina, Jorge
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Introduction: Obesity and colorectal cancer (CRC) could be linked by adipocytokines, proteins associated with cell proliferation. High level of adipocytokine leptin, through its receptor, promote the development of CRC. Objective: To determine the association between c.326A>G and c.668A>G LEPR gene polymorphisms and CRC. Materials and methods: DNA was extracted from peripheral blood of 147 patients with sporadic CRC and 134 healthy people. The genotypes were obtained by PCR-RFLP and the association was determinated by Odds Ratio (OR) test in the SPSS v10.0 program. Haplotypes frequencies and linkage disequilibrium (LD) were estimated by the Arlequin software v3.5. Results: Both polymorphisms were in Hardy-Weinberg equilibrium. Only the c.326A>G heterozygous genotype revealed an increased risk for CRC development (OR=1.81, 95% CI=1.04-3.16, p=0.04). The AG haplotype showed a significant association with CRC: OR=0.58 and CI=0.35-0.96 (p<0.03), LD between the variants was only evident for patients group (r²=0.36). Conclusion: Our results suggest that heterozygous AG individuals for the c.326A>G LEPR variant have a higher risk for CRC development whereas the AG haplotype (c.326A/c.668G) has a protective effect in the Mexican population. [ABSTRACT FROM AUTHOR]
- Published
- 2019
9. Análisis filogenético del murciélago hematófago Desmodus rotundus en el Valle del Cauca Colombia
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Fernando Favian Castro castro, Jaime Eduardo Muñoz Flores, and Wilson Uieda
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ADN ,Clados Genbank ,Haplotipos ,Patagio ,16SL ,16SH ,Agriculture - Abstract
En los municipios La Victoria, Águila, Obando, Cartago, Zarzal, San Pedro, Cerrito y Palmira del depar-tamento Valle del Cauca; Mercaderes en el Cauca; y Puerto Nariño en el departamento del Amazonas Amazonas, se realizó el análisis de filogenia del murciélago hematófago Desmodus rotundus. Las mues-tras de tejido epitelial fueron tomadas en el patagio del quiróptero, fueron amplificadas por PCR utilizan-do cebadores 16SL y 16SH, se amplificó ADN mitocondrial, y se secuenciaron 50 individuos de murciéla-gos hematófagos. Después de la secuenciación se encontraron ocho haplotipos y se encontró que el más frecuente se presenta en 43 individuos. Se utilizaron dos métodos, máxima verisimilitud y parsimonia. Utilizando el Genbank se revisaron secuencias de marcadores mitocondriales s16 rRNA de Brasil, Vene-zuela y Costa Rica. Se encontró un acercamiento de estos individuos de Costa Rica y Venezuela con murciélagos hematófagos de los departamentos del Valle del Cauca y Cauca, ubicados en el sur occidente de Colombia. Se revisan aspectos genéticos como relaciones filogeográficas entre las poblaciones y se encontró en el estudio que existe una conexión entre los diferentes haplotipos de los clados existentes reflejado en los árboles filogénicos y red de haplotipos, que se formó en varias generaciones producto po-siblemente de migraciones de los murciélagos hematófagos a lo largo de las cordilleras y ríos que atraviesan Colombia.
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- 2016
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10. Presencia de haplotipos no africanos incrementa la diversidad genética en pacientes con anemia falciforme en Colombia
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Cristian Fong and Guillermo Barreto
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Beta globina ,Desequilibrio de ligamiento ,Haplotipos ,Mestizaje ,Biology (General) ,QH301-705.5 - Abstract
El objetivo de este estudio fue identificar la frecuencia de haplotipos dentro del cluster de Beta globina presente en pacientes con anemia falciforme en Colombia, establecer la presencia de haplotipos no africanos en esta población, así como verificar variaciones en el patrón de desequilibrio de ligamiento dentro del cluster de Beta globina. Se analizaron 83 individuos con anemia falciforme, los haplotipos se formaron utilizando cinco sitios de restricción dentro del cluster de Beta globina, se estableció la frecuencia de haplotipos, se calculó el grado de desequilibrio de ligamiento entre los sitios de restricción, así como la similitud genética de esta población con otra de afectados en América. Los haplotipos más frecuentes en la población fueron Benín ( 35,1 %) y Bantú (26, 5 %), ambos africanos. Sin embargo, haplotipos presentes en poblaciones indígenas americanas y europeas alcanzaron frecuencias entre el 2 – 10 %, así como haplotipos que no han sido reportados en otras poblaciones. Los sitios de restricción presentaron bajo o nulo desequilibrio de ligamiento entre ellos. Al compararse con otras poblaciones, la población colombiana presentó mayor similitud con la población de Venezuela en donde Benin y Bantú son también predominantes. Nuestros resultados muestran que el mestizaje ha facilitado el paso de la mutación para la anemia falciforme a un contexto genético no africano (amerindio y europeo). Además, el mestizaje también ha alterado el patrón de desequilibrio de ligamiento dentro del cluster de Beta globina generando modificaciones que pueden tener influencia en estudios de asociación dentro de esta población de afectados.
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- 2018
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11. VARIABILIDAD DEL GEN NUCLEAR G3PDH EN JATROPHA CURCAS L.
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Sonia Castro Guzmán, Ogata Aguilar Nisao, Leticia M. Cano Asseleih, and Odilón Sánchez Sánchez
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gen G3pdh ,diversidad genética ,haplotipos ,Botany ,QK1-989 - Abstract
Jatrophacurcas L.es una especie nativa de América tropical; en nuestro país se ha venido utilizando principalmente como medicinal y alimenticia desde la época prehispánica. Actualmente el aceite extraído de sus semillas ha adquirido importancia internacional ya que puede ser transformado a biodiesel. El conocimiento que existe sobre la variabilidad genética de la especie es escaso. Un gen utilizado con éxito para el estudio de patrones de variación y origen de la yuca (ManihotesculentaL.) y del caco (Theobromacacao L.) es el gen nuclearG3pdh(Gliceraldehído3 fosfato deshidrogenasa) involucrado en la fotosíntesis. Con base en ello, en este trabajo se exploró la variabilidad del gen G3pdh en individuos deJ. curcasprovenientes de 15 poblaciones de los estados de Veracruz, Campeche, Yucatán y Quintana Roo. Para obtener el gen G3pdh completo de alrededor de 1000 pares de bases, se amplificó utilizando losprimersdiseñados porStrandet al. (1997) y los dosprimersinternos reverse diseñados porOlsenySchaal(1999) para obtener segmentos más cortos, de 600 y 800 pares de bases aproximadamente. Por primera vez se amplificaron aproximadamente 500pby los resultados demuestran que el gen G3pdh es útil para analizar la variabilidad deJ. curcas, y con un importante potencial para evaluar la distribución y evolución de sus poblaciones en México, conocer las relaciones ancestro descendiente a nivel poblacional y explicar las causas de la distribución de los distintoshaplotipos.
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- 2015
12. ZIKV-envelope proteins induce specific humoral and cellular immunity in distinct mice strains
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Victória Alves Santos Lunardelli, Juliana de Souza Apostolico, Higo Fernando Santos Souza, Fernanda Caroline Coirada, Jéssica Amaral Martinho, Renato Mancini Astray, Silvia Beatriz Boscardin, and Daniela Santoro Rosa
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Immunity, Cellular ,Mice ,HAPLOTIPOS ,Multidisciplinary ,Viral Envelope Proteins ,Zika Virus Infection ,Animals ,Zika Virus ,CD8-Positive T-Lymphocytes ,Antibodies, Viral ,Antibodies, Neutralizing ,Recombinant Proteins ,Immunity, Humoral - Abstract
Recent outbreaks of Zika virus (ZIKV) infection have highlighted the need for a better understanding of ZIKV-specific immune responses. The ZIKV envelope glycoprotein (EZIKV) is the most abundant protein on the virus surface and it is the main target of the protective immune response. EZIKV protein contains the central domain (EDI), a dimerization domain containing the fusion peptide (EDII), and a domain that binds to the cell surface receptor (EDIII). In this study, we performed a systematic comparison of the specific immune response induced by different EZIKV recombinant proteins (EZIKV, EDI/IIZIKV or EDIIIZIKV) in two mice strains. Immunization induced high titers of E-specific antibodies which recognized ZIKV-infected cells and neutralized the virus. Furthermore, immunization with EZIKV, EDI/IIZIKV and EDIIIZIKV proteins induced specific IFNγ-producing cells and polyfunctional CD4+ and CD8+ T cells. Finally, we identified 4 peptides present in the envelope protein (E1–20, E51–70, E351–370 and E361–380), capable of inducing a cellular immune response to the H-2Kd and H-2Kb haplotypes. In summary, our work provides a detailed assessment of the immune responses induced after immunization with different regions of the ZIKV envelope protein.
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- 2022
13. PRESENCIA DE HAPLOTIPOS NO AFRICANOS INCREMENTA LA DIVERSIDAD GENÉTICA EN PACIENTES CON ANEMIA FALCIFORME EN COLOMBIA.
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FONG, Cristian and BARRETO, Guillermo
- Abstract
The objective of this study was identify the frequency of Beta globin cluster's haplotypes present in sickle cell anemia patients in Colombia, to establish the presence of non-African haplotypes in this population, to verify variations in the pattern of linkage disequilibrium in the Beta globin cluster. It was analyzed 83 individuals affected with sickle cell anemia, the haplotypes were formed using five restriction sites into Beta globin cluster. The haplotype frequency was calculated, as well as the linkage disequilibrium among restriction sites, the genetic similarity among Colombian population and other affected American population was determined. The haplotypes most frequent were Benin (35.1 %) and Bantu (26.5 %), both African. However, haplotypes present in American indigenous and European populations got frequency between two to ten percent, as well as haplotypes not reported in others population were observed in our population. The restriction sites showed low or null linkage disequilibrium. When compare with other populations, the Colombian population showed higher similarity with Venezuelan population where Benin and Bantu are predominant too. Our results showed that admixture has facilitated the move of sickle cell mutation to a non-African genetic context (Amerindian and European). Further, the admixture has also modified the pattern of linkage disequilibrium into the Beta globin cluster generating modifications that could have influence in association studies in this affected population.The objective of this study was identify the frequency of Beta globin cluster's haplotypes present in sickle cell anemia patients in Colombia, to establish the presence of non-African haplotypes in this population, to verify variations in the pattern of linkage disequilibrium in the Beta globin cluster. It was analyzed 83 individuals affected with sickle cell anemia, the haplotypes were formed using five restriction sites into Beta globin cluster. The haplotype frequency was calculated, as well as the linkage disequilibrium among restriction sites, the genetic similarity among Colombian population and other affected American population was determined. The haplotypes most frequent were Benin (35.1 %) and Bantu (26.5 %), both African. However, haplotypes present in American indigenous and European populations got frequency between two to ten percent, as well as haplotypes not reported in others population were observed in our population. The restriction sites showed low or null linkage disequilibrium. When compare with other populations, the Colombian population showed higher similarity with Venezuelan population where Benin and Bantu are predominant too. Our results showed that admixture has facilitated the move of sickle cell mutation to a non-African genetic context (Amerindian and European). Further, the admixture has also modified the pattern of linkage disequilibrium into the Beta globin cluster generating modifications that could have influence in association studies in this affected population. [ABSTRACT FROM AUTHOR]
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- 2018
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14. Diversidad genética y estructura poblacional de Anopheles triannulatus s.l. en Córdoba, Colombia, determinadas mediante el método de región de código de barras de ADN.
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Atencia-Pineda, María, Toro-Cantillo, Angie, and Hoyos-López, Richard Onalbi
- Abstract
Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2018
- Full Text
- View/download PDF
15. Diversidad de haplotipos del complejo principal de histocompatibilidad en equinos de la raza Árabe de la República Argentina
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S. A. Sadaba, C. M. Corbi Botto, M. E. Zappa, M. H. Carino, E. E. Villegas Castagnasso, P. Peral García, and S. Díaz
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Haplotipos ,complejo principal de histocompatibilidad ,equinos Árabes ,Animal culture ,SF1-1100 ,Veterinary medicine ,SF600-1100 - Abstract
La diversidad de los genes del complejo principal de histocompatibilidad (MHC) es clave en su función en la presentación de antígenos en el sistema inmune. La tipificación indirecta basada en microsatélites (STR) del MHC aporta información de la variabilidad genética y de la estructura poblacional y es una estrategia para conocer procesos selectivos y evolutivos. Con el fin de caracterizar una población de caballos de raza Árabe, se identificaron los haplotipos del MHC sobre la base de tres microsatélites (UM011, DRB2-STR2 y COR112) abarcando una región de ~1Mpb. El ADN genómico se extrajo de sangre y pelo de 30 caballos de cinco haras de la provincia de Buenos Aires y los STRs se amplificaron con cebadores fluorescentes para tipificar en secuenciador automático. Se estimaron parámetros poblacionales y de diversidad y la detección de haplotipos se realizó mediante análisis de segregación y con el programa de reconstrucción de haplotipos PHASE. Se reconocieron 24 haplotipos; entre ellos, 12 se verificaron por segregación en los registros de pedigree del Stud Book. Los resultados obtenidos demostraron la existencia de ligamiento con alelos conocidos de genes de clase II del equine leukocyte antigen (ELA) y la cantidad de haplotipos identificada permitió expandir la valoración de la diversidad del MHC equino. Esta metodología constituye una herramienta de utilidad y un método alternativo para la tipificación del MHC en linajes de caballos y en estudios poblacionales relacionados con la inmunidad.
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- 2017
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16. Diversidade genética de Xylella fastidiosa em regiões produtoras de citros na Bahia
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Vinicius Oliveira Casais, Epaminondas do Patrocínio, Saulo Alves Santos de Oliveira, Alessandra Selbach Schnadelbach, Cristiane de Jesus Barbosa, and Luciana Veiga Barbosa
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Citrus sinensis ,bactéria fitopatogênica ,CVC ,haplótipos ,microssatélites ,Agriculture (General) ,S1-972 - Abstract
O objetivo deste trabalho foi avaliar, por meio de marcadores SSR, a diversidade genética de Xylella fastidiosa no Estado da Bahia. Foram estudadas duas das principais regiões produtoras de citros no Estado, o Litoral Norte e o Recôncavo Sul. Para fins comparativos, utilizaram-se dez amostras provenientes do Estado de São Paulo. Foram empregados os seguintes iniciadores: ASSR20, OSSR9, OSSR17, CSSR4, CSSR12 e CSSR20, dos quais os quatro últimos permitiram identificar 22 loci polimórficos. As populações de X. fastidiosa presentes em citros no Estado da Bahia apresentam elevada diversidade genética, com base nos marcadores SSR, com pools gênicos distintos e agrupamento geográfico. No Litoral Norte, as populações do isolado apresentam maior diversidade genética do que as da região do Recôncavo Sul da Bahia.
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- 2014
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17. KIR2DL4 genetic diversity in a Brazilian population sample: implications for transcription regulation and protein diversity in samples with different ancestry backgrounds
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Erick C. Castelli, Juliana Rodrigues Lara, Heloisa S. Andrade, Michelle A. Paz, Emiliana Weiss, Iane O. P. Porto, Celso T. Mendes-Junior, Andreia S. Souza, Nayane S. B. Silva, Camila Ferreira Bannwart Castro, Thálitta H. A. Lima, Rejane Maria Tommasini Grotto, Eduardo Antônio Donadi, Universidade Estadual Paulista (Unesp), and Universidade de São Paulo (USP)
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0301 basic medicine ,KIR genes ,Immunology ,Second-generation sequencing ,Biology ,03 medical and health sciences ,Exon ,0302 clinical medicine ,parasitic diseases ,Genotype ,Genetics ,Gene family ,Allele frequency ,Gene ,Genetic association ,Genetic diversity ,HAPLOTIPOS ,Haplotype ,HLA ,030104 developmental biology ,Haplotypes ,Evolutionary biology ,KIR2DL4 ,Natural killer cells ,Polymorphisms ,geographic locations ,030215 immunology - Abstract
Made available in DSpace on 2021-06-25T10:53:00Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-06-01 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) KIR2DL4 is an important immune modulator expressed in natural killer cells; HLA-G is its main ligand. We have characterized the KIR2DL4 genetic diversity by considering the promoter, all exons, and all introns in a highly admixed Brazilian population sample and by using massively parallel sequencing. We introduce a molecular method to amplify and to sequence the complete KIR2DL4 gene. To avoid the mapping bias and genotype errors commonly observed in gene families, we have developed and validated a bioinformatic pipeline designed to minimize these errors and applied it to survey the variability of 220 individuals from the State of São Paulo, southeastern Brazil. We have also compared the KIR2DL4 genetic diversity in the Brazilian cohort with the diversity previously reported by the 1000Genomes consortium. KIR2DL4 presents high linkage disequilibrium throughout the gene, with coding sequences associated with specific promoters. There are few but divergent promoter haplotypes. We have also detected many new KIR2DL4 sequences, all bearing nucleotide exchanges in introns and encoding previously described proteins. Exons 3 and 4, which encode the external domains, are the most variable. The ancestry background influences the KIR2DL4 allele frequencies and must be considered for association studies regarding KIR2DL4. Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit School of Medicine São Paulo State University (UNESP) Genetics Program Institute of Biosciences of Botucatu São Paulo State University (UNESP) Pathology Program School of Medicine São Paulo State University (UNESP) School of Agronomical Sciences São Paulo State University (UNESP) Department of Medicine Ribeirão Preto Medical School University of São Paulo (USP) Departamento de Química Faculdade de Filosofia Ciências E Letras de Ribeirão Preto Universidade de São Paulo Molecular Genetics and Bioinformatics Laboratory - Experimental Research Unit School of Medicine São Paulo State University (UNESP) Genetics Program Institute of Biosciences of Botucatu São Paulo State University (UNESP) Pathology Program School of Medicine São Paulo State University (UNESP) School of Agronomical Sciences São Paulo State University (UNESP) FAPESP: 2017/05042-4 FAPESP: 2017/19223-0
- Published
- 2021
18. Haplotypes in CCR5-CCR2, CCL3 and CCL5 are associated with natural resistance to HIV-1 infection in a Colombian cohort.
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Vega, Jorge A., Villegas-Ospina, Simón, Aguilar-Jiménez, Wbeimar, Rugeles, María T., Bedoya, Gabriel, and Zapata, Wildeman
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HIV infections , *GENETIC polymorphisms , *GENE expression , *SINGLE nucleotide polymorphisms , *CHEMOKINE receptors - Abstract
Introduction: Variants in genes encoding for HIV-1 co-receptors and their natural ligands have been individually associated to natural resistance to HIV-1 infection. However, the simultaneous presence of these variants has been poorly studied. Objective: To evaluate the association of single and multilocus haplotypes in genes coding for the viral co-receptors CCR5 and CCR2, and their ligands CCL3 and CCL5, with resistance or susceptibility to HIV-1 infection. Materials and methods: Nine variants in CCR5-CCR2, two SNPs in CCL3 and two in CCL5 were genotyped by PCR-RFLP in 35 seropositive (cases) and 49 HIV-1-exposed seronegative Colombian individuals (controls). Haplotypes were inferred using the Arlequin software, and their frequency in individual or combined loci was compared between cases and controls by the chi-square test. A p' value <0.05 after Bonferroni correction was considered significant. Results: Homozygosis of the human haplogroup (HH) E was absent in controls and frequent in cases, showing a tendency to susceptibility. The haplotypes C-C and T-T in CCL3 were associated with susceptibility (p'=0.016) and resistance (p'<0.0001) to HIV-1 infection, respectively. Finally, in multilocus analysis, the haplotype combinations formed by HHC in CCR5-CCR2, T-T in CCL3 and G-C in CCL5 were associated with resistance (p'=0.006). Conclusion: Our results suggest that specific combinations of variants in genes from the same signaling pathway can define an HIV-1 resistant phenotype. Despite our small sample size, our statistically significant associations suggest strong effects; however, these results should be further validated in larger cohorts. [ABSTRACT FROM AUTHOR]
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- 2017
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19. Determinación del polimorfismo de HLA-A, -B y -DRB1 en donantes de órganos con muerte encefálica representativos de la población general colombiana, 2007-2014.
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Arias-Murillo, Yazmín, Osorio-Arango, Karime, Bayona, Brayan, Ercilla, Guadalupe, and Beltrán-Durán, Mauricio
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Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2017
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20. DIVERSIDAD Y ESTRUCTURA GENÉTICA DE ARTIBEUS JAMAICENSIS (CHIROPTERA: PHYLLOSTOMIDAE) EN CHIAPAS, MÉXICO.
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LLAVEN MACÍAS, VIRIDIANA, RUIZ MONTOYA, LORENA, GARCÍA BAUTISTA, MARICELA, GORDILLO, JULIA LESHER, and MACHKOUR M'RABET, SALIMA
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ARTIBEUS jamaicensis , *BATS , *SPECIES diversity , *ANIMAL genetics , *HAPLOTYPES , *BIODIVERSITY - Abstract
Deforestation causes fragmentation of habitats, which in turn affects the composition, abundance and demography of species, and therefore the population isolation of many species. The impacts of fragmentation will depend on the responsiveness of the species to disturbances in their habitat, and the configuration and structure of landscape. In some populations, habitat fragmentation can cause long-term population isolation by the reduction in population size and the weakening of relations between individuals, even in highly mobile species like bats. In Mexico, A. jamaicensis is the most studied bat; however, few studies focused on the knowledge of the impacts of habitat modification in its diversity and genetic structure. Therefore, the objective of this study was to evaluate the diversity, structure and genetic differentiation, and analyze demographic history of A. jamaicensis in two different habitats, using a 396 bp fragment of the mitochondrial Dloop region. Haplotype network revealed 34 unique haplotypes of 34 individuals analyzed. Haplotype diversity was high (h = 1) for both populations, and nucleotide diversity was relatively low (< 0.03). The analysis of the distribution of pairwise differences between sequences and negative values of statistical tests based on neutrality suggest a process of recent and sudden demographic expansion of A. jamaicensis. A moderate genetic differentiation points to the existence of genetic structure of A. jamaicensis. [ABSTRACT FROM AUTHOR]
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- 2017
21. Variantes del ADNmt en isleños del lago Titicaca: máxima frecuencia del haplotipo B1 y evidencia de efecto fundador
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José Sandoval, Bedsabé Delgado, Luis Rivas, Bertha Bonilla, Daniel Nugent, and Ricardo Fujita
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ADN mitocondrial ,isleños del Lago Titicaca ,haplotipos ,RFLP ,Science ,Biology (General) ,QH301-705.5 - Abstract
Los polimorfismos del ADN mitocondrial son herramientas en el estudio comparativo de poblaciones modernas y antiguas. Entre los más usados están los haplotipos mitocondriales basados en RFLP (polimorfismo de longitud de fragmentos de restricción) y un sistema de inserción /deleción. El presente estudio establece la frecuencia de estos haplotipos y compara un total de 144 individuos representativos de las islas Taquile y Amantaní (lengua quechua) y de las islas de Los Uros y Anapia (lengua aymara) del lago Titicaca, Perú. Nuestros resultados revelan la predominancia del haplotipo B1: 100% en Taquile (n=57); 88,6% en Amantaní (n=35); 75% en Los Uros (n=28) y 87,5% en Anapia (n=24), siendo las frecuencias más altas registradas en el mundo. Otros haplotipos se observan en menor proporción: 17,9% de A2 y 7,1% de D1 en Los Uros; 11,4% de la variante C1 en Amantaní; 4,2% de cada haplotipo C1, C2 y D1 en Anapia. La alta frecuencia de B1 indica que las poblaciones de Taquile, Amantaní y Anapia provienen de un grupo fundador reducido. Aunque hay afinidad entre las poblaciones aymaras de Anapia y Los Uros; la proporción de algunos alelos en los últimos, sugiere la persistencia de un acervo genético uru en contraposición a la idea de su extinción.
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- 2013
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22. Variabilidad genética del Aedes aegypti determinada mediante el análisis del gen mitocondrial Nd4 en once áreas endémicas para dengue en el Perú
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Pamela Yáñez, Enrique Mamani, Jorge Valle, María Paquita García, Walter León, Pablo Villaseca, Dina Torres, and César Cabezas
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Aedes ,Haplotipos ,Linaje ,ADN Mitocondrial ,Perú ,Medicine ,Medicine (General) ,R5-920 - Abstract
Con el objetivo de establecer la variabilidad genética de Aedes aegypti determinada por el análisis del gen mitocondrial ND4, se analizaron 51 especímenes de Ae. aegypti en once regiones endémicas para dengue en el Perú. La variabilidad genética se determinó mediante la amplificación y secuenciación de un fragmento de 336 pares de bases del gen mitocondrial ND4. El análisis de filogenia intraespecífica se realizó con el programa Network Ver. 4.6.10; y el análisis filogenético, con el método de distancia Neighbor Joining. Se identificó la presencia de cinco haplotipos de Ae. aegypti agrupados en dos linajes: el primero agrupa a los haplotipos 1, 3 y 5 y el segundo agrupa los haplotipos 2 y 4, se muestra además la distribución geográfica de cada uno de los haplotipos encontrados. Se concluye que esta variabilidad se debe tanto a la migración activa de este vector como a la migración pasiva mediada por la actividad humana.
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- 2013
23. Frequency of MYO9B polymorphisms in celiac patients and controls Frecuencia de polimorfismos del gen MYO9B en pacientes celiacos y en sujetos controles
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Tamara Loeff, Magdalena Araya, and Francisco Pérez-Bravo
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Gen MYO9B ,Enfermedad celiaca ,Haplotipos ,MYO9B gene ,Celiac disease ,Haplotypes ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Introduction: the MYO9B gene contributes to the maintenance of the intestinal barrier and it has been postulated as a risk factor of celiac disease (CD). The objective of this study was to compare the frequency and association rs2305764, rs2305767and rs1457092 MYO09B polymorphisms in pediatric CD patients from Chile and Argentina. Patients and methods: the study was made in 104 CD pediatric patients (Chilean and Argentineans) and 104 controls subjects. MYO9B gene polymorphisms were analyzed by Taqman allelic probes. We evaluated the Hardy-Weinberg equilibrium by means of Chi-square and compared the haplotypes distribution using Fisher test. Results: SNPs rs2305767 and rs1457092 were associated with celiac disease (CD); TT genotype in rs2305767 would be a protective factor (p < 0.000, OR = 0.19 CI 0.1-0.4) and the CT genotype would be a risk factor (p < 0.0001, OR = 4.9 CI 2.2 to 11.3). CC genotype in rs1457092 also showed a protective effect for celiac (p < 0.000, OR = 0.07 CI 0.0 to 0.3). Conclusion: our findings suggest that genetic variation MYO9B gene is associated with CD, as a protective or a risk factor depending on the polymorphism studied.Introducción: el gen miosina IX B (MYO9B) participa en el mantenimiento de la barrera intestinal y se postula que puede aportar riesgo para desarrollar enfermedad celiaca (EC). El objetivo de este estudio fue comparar la frecuencia y la asociación de los polimorfismos rs 2305764, rs 2305767 y rs 1457092 del gen MYO9B en pacientes pediátricos con EC procedentes de Chile y Argentina. Pacientes y métodos: el estudio se realizó en 104 pacientes pediátricos con EC (chilenos y argentinos) y en 104 sujetos controles. El análisis de los polimorfismos del gen MYO9B se realizó mediante ensayos Taqman de discriminación alélica. Se evalúo equilibrio de Hardy-Weinberg mediante Chi-cuadrado y comparación de haplotipos según prueba de Fisher. Resultados: los polimorfismos de un solo nucleótido (SNPs) rs2305767 y rs1457092 mostraron asociación con la EC. El genotipo TT del rs2305767 sería un factor protector (p < 0,0001, OR = 0,19 IC 0,1-0,4) mientras que el genotipo CT sería un factor de riesgo (p < 0,0001, OR = 4,9 IC 2,2-11,3). En el rs1457092, el genotipo CC resultó también un factor protector frente a esta enfermedad (p < 0,0001, OR = 0,07 IC 0,0-0,3). Conclusión: nuestros hallazgos sugieren que la variación genética del gen MYO9B estaría asociada a la EC en este grupo de pacientes, constituyendo un factor tanto de protección como a susceptibilidad dependiendo del polimorfismo en cuestión.
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- 2012
24. Noninvasive prenatal paternity determination using microhaplotypes: a pilot study
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Renato David Puga, Jaqueline Yu Ting Wang, Martin R. Whittle, Anatoly Yambartsev, Helder I. Nakaya, and André Fujita
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Genetic Markers ,Male ,0301 basic medicine ,lcsh:Internal medicine ,lcsh:QH426-470 ,Noninvasive Prenatal Testing ,Population ,Paternity ,Pilot Projects ,Single-nucleotide polymorphism ,Computational biology ,Biology ,Noninvasive ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,0302 clinical medicine ,Pregnancy ,Genetics ,False positive paradox ,Humans ,Prenatal ,Genetic Testing ,030216 legal & forensic medicine ,1000 Genomes Project ,education ,lcsh:RC31-1245 ,Genetics (clinical) ,education.field_of_study ,HAPLOTIPOS ,Massive parallel sequencing ,Probability of paternity ,Microhaplotype ,High-Throughput Nucleotide Sequencing ,DNA ,Single nucleotide polymorphism ,lcsh:Genetics ,030104 developmental biology ,Technical Advance ,Haplotypes ,Genetic marker ,Female - Abstract
Background The use of noninvasive techniques to determine paternity prenatally is increasing because it reduces the risks associated with invasive procedures. Current methods, based on SNPs, use the analysis of at least 148 markers, on average. Methods To reduce the number of regions, we used microhaplotypes, which are chromosomal segments smaller than 200 bp containing two or more SNPs. Our method employs massively parallel sequencing and analysis of microhaplotypes as genetic markers. We tested 20 microhaplotypes and ascertained that 19 obey Hardy–Weinberg equilibrium and are independent, and data from the 1000 Genomes Project were used for population frequency and simulations. Results We performed simulations of true and false paternity, using the 1000 Genomes Project data, to confirm if the microhaplotypes could be used as genetic markers. We observed that at least 13 microhaplotypes should be used to decrease the chances of false positives. Then, we applied the method in 31 trios, and it was able to correctly assign the fatherhood in cases where the alleged father was the real father, excluding the inconclusive results. We also cross evaluated the mother-plasma duos with the alleged fathers for false inclusions within our data, and we observed that the use of at least 15 microhaplotypes in real data also decreases the false inclusions. Conclusions In this work, we demonstrated that microhaplotypes can be used to determine prenatal paternity by using only 15 regions and with admixtures of DNA.
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- 2020
25. Evidencias fotográfica, biológica y genética de la presencia actual de jaguaroundi (Puma yagouaroundi) en Michoacán, México Photographic, biological and genetic evidences of the presence of jaguaroundi (Puma yagouaroundi) at the moment in Michoacán, Mexico
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Tiberio C. Monterrubio-Rico, Juan Felipe Charre-Medellín, María Guadalupe Zavala-Paramo, Horacio Cano-Camacho, Mario Quetzal Pureco-Rivera, and Livia Leon-Paniagua
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distribución observada ,Felidae ,haplotipos ,onza ,observed distribution ,haplotypes ,Biology (General) ,QH301-705.5 - Abstract
El jaguaroundi, a pesar de su amplia distribución neotropical, es uno de los felinos menos estudiados del continente y se carece de estudios genéticos sobre la especie. Para el estado de Michoacán ha existido la sospecha de su presencia y no obstante que sólo se tenía un registro del año 1970, los mapas de distribución de la especie en México incluyen al estado. Combinando métodos de campo (trampas cámara, recolección de campo, transectos) y genotipificación molecular, obtuvimos evidencia fotográfica, biológica y genética que confirma la presencia actual de jaguaroundi (Puma yagouaroundi) en 3 regiones del estado de Michoacán, México. Se obtuvieron 11 registros fotográficos en 7 localidades con bosque tropical y 7 de estos registros, revelaron que la especie está activa principalmente por la tarde, que existen 2 fases de pelaje, predominando la fase clara y que se reproduce en el estado. Con base en las distancias e independencia entre registros de los municipios de Arteaga y Lázaro Cárdenas, se plantea la hipótesis de que la distribución continúa a lo largo de la sierra Madre del Sur y la costa del Pacífico de Michoacán, aunque se desconoce si hay conectividad hacia la depresión del Balsas. Se obtuvieron 2 secuencias de 1089 y 1096 pb del gen de citocromo b que actualmente son las más largas que se han obtenido para la especie en México y el norte del continente. Las secuencias indican que hay 2 haplotipos distintos. La presencia de la especie en 3 regiones y los 2 haplotipos permiten suponer que en Michoacán puede contar con importante diversidad genética, aunque hace falta ampliar el tamaño de muestra para confirmarlo. Las secuencias obtenidas permitirán la comparación con individuos de otras regiones del país para conocer mejor la variabilidad genética en la especie y auxiliarán en la identificación de poblaciones para conservación.The jaguaroundi is one of the least studied felids on the American continent, despite its wide neotropical distribution. Genetic studies concerning the species are also inexistent. For the state of Michoacán, it has always been assumed as present, since the distribution maps for the species in Mexico include the state, but only one record existed from 1970. Combining survey methods (camera traps, skulls and tissue found in the field, and transects) and molecular genotyping, we obtained photographic, biological and genetic evidence that confirms the actual presence of the jaguaroundi (Puma yagouaroundi) in 3 regions of Michoacán, Mexico. Eleven records were obtained from 7 localities that present tropical forests. Seven photographic records revealed that the species main activity period is during the afternoon, that both pelage phases occur in the state with a greater proportion in the clear pelage phase, and that breeding activity occurs in the state. Based on the distance and independence among Arteaga and Lázaro Cárdenas records, we hypothesize a continuous distribution of a population along the Sierra Madre del Sur and Pacific coast of Michoacán. We are unaware if a continuous distribution occurs as well along the Balsas basin. 1 089 and 1 096 pb cytochrome b gene sequences were obtained and constitute the longest sequences reported for the species in Mexico and to the north of the continent. The sequences also revealed the presence of 2 distinct haplotypes. The presence of species in 3 regions and the presence of 2 haplotypes allow us to hipothezise that in Michoacán the species may possess important genetic diversity, although a greater sample size is required for confirmation. The sequences obtained will allow the comparison with individuals from other regions of the country in order to increase the knowledge on the species genetic variability, and will provide support for the identification of populations of conservation interest.
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- 2012
26. Diversidad genética y ancestría del ganado Hartón del Valle mediante ADN mitocondrial Estimação da ancestralidade e da diversidade genética no gado Hartón del Valle utilizando DNA mitocondrial Assessing the genetic diversity and ancestry of Hartón del Valle cattle using mitochondrial DNA
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Luz A Álvarez, Víctor J Vera, Heiber Cárdenas, and Guillermo Barreto
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filogenia ,ganadocriollo ,haplotipos ,linajes ,gadonativo ,haplótipos ,linhagens ,creolecattle ,haplotypes ,lineages ,phylogeny ,Animal culture ,SF1-1100 - Abstract
El Hartón del Valle (HV),es una raza adaptada a las condiciones del Valle del Cauca(Colombia) que está catalogada como “vulnerable” y cuya población ha descendido drásticamente en los últimos dos años. Objetivo: debido al futuro incierto y a la importancia como recurso potencial en la seguridad alimentaria regional se abordó el estudio de la diversidad, la estructura genética y la ancestría del HV, mediante ADN mitocondrial (ADNmt). Métodos: se amplificó y secuenció un fragmento de 350 pb en 72 animales HV, provenientes de nueve poblaciones y de controles de las razas Brahman y Holstein. Para analizar la ancestría las secuencias fueron comparadas con 560 secuencias de 50 razas Bos taurus y Bos indicus, depositadas en el GenBank. Resultados: de acuerdo con su origen español, se encontró una marcada influencia del ADNmt europeo (91.7%) y baja participación de taurinos de origen africano (5.5%) y del cercano Oriente (2.7%). La diversidad haplotípica promedio fue 0.65 ± 0.05. El hato más antiguo fue el único que mostró los tres linajes mitocondriales, sin embargo, este ha sido liquidado recientemente. Se observó proximidad entre el HV con las razas colombianas Romosinuano y Costeño con Cuernos. La comparación con las secuencias depositadas en el GenBank con diferentes razas reveló la presencia de 37 haplotipos, de los cuales siete fueron únicos en el HV. Conclusiones: las razas ibéricas más cercanas al HV fueron: Tudanca, Rubia Gallega, Negra Serrana, Murciana, Pajuna, Avileña, Garvonesa y Mertolenga. El árbol filogenético confirmó la ancestralidad ibérica y la influencia africana en las razas criollas de América Latina.O Hartón del Valle (HV) é uma raça adaptada às condições da região pertencente ao departamento do Valle del Cauca (Colombia). A raça está catalogada como vulnerável já que sua população tem sido reduzida drasticamente nos últimos dois anos. Objetivo: devido a incerteza no futuro da raça e a sua importancia como recurso potencial na segurança alimentaria regional, abordou-se o estudo da diversidade, a estrutura genética e a ancestralidade do gado HV, utilizando DNA mitocondrial (mtDNA). Métodos: para isto, se amplificou e sequenciou um fragmento de 350 pares de bases em 72 animais provenientes de nove populações e também de controles das raças Brahman e Holandesa. Para analizar a ancestralidade das sequências, estas foram comparadas com outras 560 de 50 raças Bos taurus y Bos indicus depositadas no genebank. Resultados: de acordo com sua origem espanhola, foi encontrada uma marcada influência do DNA mitocondrial europeu (91.7%), e baixa participação de taurinos de origem africana (5.5%) e do Oriente Próximo (2.7%). A média da diversidade haplotípica foi de 0.65 ± 0.05. A população de gado HV mais antiga foi a única que apresentou as três linhagens mitocondriais encontradas; embora, esta população foi terminada recentemente. Observou-se também proximidade do gado HV com as raças colombianas da região Caribe, Romosinuano e Costeño con Cuernos. A comparação com as sequências depositadas no genebank com diferentes raças revelou a presença de 37 haplotipos, dos quais sete foram únicos no HV. Conclusões: as raças ibéricas mais aproximadas do HV foram: Tudanca, Rubia Gallega, Negra Serrana, Murciana, Pajuna, Avileña Garvonesa e Mertolenga. A árvore filogenética confirmou sua ancestralidade ibérica e a influência africana nas raças crioulas da América Latina.The Hartón del Valle(HV)cattleisa Criollo breed of Spanish descent that has adapted to the conditionsof the Cauca valley (Colombia). This breed is currently listed as “vulnerable” because its population has dramatically declined in the last two years. Prompted by the uncertain future of this breed and its importance as a potential resource of valuable genes. Objective: this study addressed the diversity, genetic structure and ancestry of HV cattle using mitochondrial DNA (mtDNA). Methods: a 350-bp fragment was amplified and sequenced from 72 HV animals in 9 separate farms and from animals of Brahman and Holstein breeds. To analyze the breed's ancestry, the sequences were compared with 560 sequences available in the GenBank, representing 50 Bos taurus and Bos indicus breeds. Results: in accordance with the Spanish origin of the HV breed, there was a high representation of European mtDNA (91.7%) and a low representation of African (5.5%) and Middle Eastern mtDNA (2.7%). The average haplotype diversity was 0.65 ± 0.05. The farm with the oldest ancestry was the only population in which three mitochondrial lineages were observed; unfortunately, it was recently depopulated. Proximity was observed between HV and two Columbian breeds, the Romosinuano and Costeño con Cuernos. A comparative analysis with the sequences deposited in the GenBank from numerous breeds revealed the presence of 37 haplotypes, seven of which were unique to HV. Conclusions: the following Iberian breeds were found to be most closely related to HV: Tudanca, Rubia Gallega, Negra Serrana, Murciana, Pajuna, Avileña, Garvonesa and Mertolenga. Phylogenetic analysis confirmed the Iberian ancestry and some African influence on this Latin American Criollo breed.
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- 2012
27. Sickle cell disease: acute clinical manifestations in early childhood and molecular characteristics in a group of children in Rio de Janeiro Manifestações clínicas agudas na primeira e segunda infâncias e características moleculares da doença falciforme em um grupo de crianças do Rio de Janeiro
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Isaac Lima da Silva Filho, Georgina Severo Ribeiro, Patrícia Gomes Moura, Monica Longo Vechi, Andréa Cony Cavalcante, and Maria José de Andrada-Serpa
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Anemia falciforme ,Talassemia alfa ,Haplótipos ,Triagem neonatal ,Evolução clínica ,Anemia, sickle cell ,Alpha-thalassemia ,Haplotypes ,Neonatal screening ,Clinical evolution ,Diseases of the blood and blood-forming organs ,RC633-647.5 - Abstract
OBJECTIVE: To describe clinical events of sickle cell disease and the correlation with β-globin haplotypes and α-thalassemia in under 6-year-old children. METHODS: A retrospective study was conducted of under 6-year-old children from the neonatal screening program in Rio de Janeiro. Forty-eight male and 48 female children were enrolled in this study, 79 with sickle cell anemia and 17 with hemoglobin SC. The mean age was 29.9 (standard deviation = 20.9) months, 62 (16.2 ± 8.6) were aged between 0-3 years old and 34 (54.9 ± 11.3) were from 3-6 years old. Painful events, acute splenic sequestration, hemolytic crises, hand-foot and acute chest syndromes and infections were evaluated. RESULTS: The events were more frequent in under 3-year-old children, 94% of children had at least one episode. Infection was the most common event affecting 88.5% of children. Acute splenic sequestration took place earlier, while painful crises and acute chest syndromes in under 6-year-old children. Thal-α 3.7 was observed in 20.9% of cases. Bantu was the most frequent haplotype found, followed by Benin. No correlation was observed between clinical events and β-globin haplotypes. Children with sickle cell anemia and α-thalassemia have less infectious events. No correlation was found among these polymorphisms and clinical events, however, the majority of children with Bantu/Bantu and without α-thalassemia had more clinical events.OBJETIVO: Avaliar a expressão clínica da anemia falciforme (AF) e sua relação com os haplótipos da globina beta e talassemia alfa (Tal) em crianças na primeira e segunda infâncias. MÉTODOS: Foi realizado um estudo descritivo e retrospectivo de série de casos em crianças na primeira e segunda infâncias provenientes da triagem neonatal do Rio de Janeiro. Um total de 96 crianças, 79 com AF e 17 com HbSC, 48 homens e 48 mulheres, média de idade de 29,9 (DP+/-20,9) meses, sendo 62 (16,2+/-8,6) na primeira e 34 (54,9+/-11,3) na segunda infância. Foram avaliados: crises dolorosas (CD), de sequestro esplênico (SE) e hemolítica (CH), síndromes mão-pé (SMP) e torácica aguda (STA) e infecções. RESULTADOS: Os eventos foram mais frequentes na primeira infância; 94% das crianças apresentaram ao menos um episódio. Infecção foi o evento mais frequente, acometendo 88,5% das crianças, SE ocorreu mais na primeira infância, enquanto CD e STA mais na segunda. A Tal alfa 3.7 foi observada em 20,9% dos casos. O haplótipo mais frequente foi o Bantu (73,7%), seguido de Benin (23,0%). Não foi observada associação entre eventos clínicos e haplótipos da globina. Crianças com AF e Tal apresentaram menos eventos infecciosos. Não foi possível associar os polimorfismos com a expressão clínica, porém, a maioria das crianças Bantu/Bantu e sem Tal apresentou mais eventos clínicos.
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- 2012
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28. Associations between polymorphic variants of the tryptophan hydroxylase 2 gene and obsessive-compulsive disorder Associação entre polimorfismos do gene da triptofano hidroxilase 2 e o transtorno obsessivo-compulsivo
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Felipe Filardi da Rocha, Nathália Bueno Alvarenga, Naira Vassalo Lage, Marco Aurélio Romano-Silva, Luiz Armando de Marco, and Humberto Corrêa
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Psiquiatria ,Transtorno obsessivo-compulsivo ,Polimorfismo genético ,Triptofano hidroxilase ,Haplótipos ,Psychiatry ,Obsessive-compulsive disorder ,Polymorphism, genetic ,Tryptophan hydroxylase ,Haplotypes ,RC435-571 - Abstract
OBJECTIVE: A substantial body of evidence suggests that obsessive-compulsive disorder has a genetic component, and substantial candidate genes for the disorder have been investigated through association analyses. A particular emphasis has been placed on genes related to the serotonergic system, which is likely to play an important role in the pathogenesis of obsessive-compulsive disorder. The gene for tryptophan hydroxylase 2, which is a rate limiting enzyme in serotonin synthesis, is considered an important candidate gene associated with psychiatric disorders. METHOD: Our sample consisted of 321 subjects (107 diagnosed with obsessive-compulsive disorder and 214 healthy controls), which were genotyped for eight tagSNPs (rs4448731, rs4565946, rs11179000, rs7955501, rs10506645, rs4760820, rs1487275 and rs10879357) covering the entire human tryptophan hydroxylase 2 gene. Statistical analyses were performed using UNPHASED, version 3.0.12, and Haploview®. RESULTS: Single markers, genotype analysis did not show a significant genetic association with obsessive-compulsive disorder. A significant association between the T-C-T (rs4448731, rs4565946, rs10506645) and C-A-T (rs4565946, rs7955501, rs10506645) haplotypes and obsessive-compulsive disorder was observed, as well as a strong linkage disequilibrium between SNPs rs4448731 and rs4565946, and SNPs rs10506645 and 4760820. DISCUSSION: Our research has not demonstrated the existence of associations between the eight SNPs of TPH2 and obsessive-compulsive disorder. However, two LD and two haplotypes areas were demonstrated, thus suggesting that more studies in TPH2 are needed to investigate the role of tryptophan hydroxylase 2 variants in obsessive-compulsive disorder.OBJETIVO: Diversos estudos demonstram que o transtorno obsessivo-compulsivo apresenta considerável contribuição genética, com diversos genes candidatos tendo sido estudados por meio de estudos de associação. Como alterações do sistema serotonérgico estão associadas ao transtorno obsessivo-compulsivo, o gene da triptofano hidroxilase 2, enzima limitante da síntese da serotonina, é plausível candidato para estudos. MÉTODO: Nossa amostra é composta de 321 sujeitos (107 pacientes com transtorno obsessivo-compulsivo e 214 controles) e investigamos oito tagSNPs (rs4448731, rs4565946, rs11179000, rs7955501, rs10506645, rs4760820, rs1487275 e rs10879357) do gene da triptofano hidroxilase 2. Análise estatística foi realizada com os programas UNPHASED e Haploview. RESULTADOS: Análise de frequência alélica e genotípica entre casos e controles não evidenciaram diferenças estatisticamente significativas. No entanto, observamos maior prevalência dos haplótipos T-C-T (rs4448731, rs4565946, rs10506645) e C-A-T (rs4565946, rs7955501, rs10506645) entre os pacientes, assim como duas regiões com importantes desequilíbrios de ligação (SNPs rs4448731 e rs4565946; SNPs rs10506645 e 4760820). DISCUSSÃO: Nossos achados não demonstraram uma associação entre os SNPs do gene da TPH2 e o transtorno obsessivo-compulsivo, porém mais estudos são necessários, já que fortes desequilíbrios de ligação foram demonstrados, assim como dois haplótipos.
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- 2011
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29. CHARACTERIZATION OF Phytophthora infestans POPULATIONS IN ANTIOQUIA, COLOMBIA CARACTERIZACIÓN DE LAS POBLACIONES DE Phytophthora infestan EN ANTIOQUIA, COLOMBIA
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Elizabeth Gilchrist Ramelli, Sonia Jaramillo Villegas, Lucia Afanador Kafuri, and Rafael Eduardo Arango Isaza
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Tizón tardío ,linaje clonal ,Sur América ,haplotipos ,grupo de compatibilidad ,Late blight ,clonal lineage ,South America ,haplotypes ,mating type ,Agriculture ,Agriculture (General) ,S1-972 - Abstract
From the Phytophthora infestans collection of the Universidad Nacional de Colombia, the isolates collected in different locations in Antioquia, Colombia between 1994 and 2000 were evaluated. These isolates were obtained from late blight lessons in different hosts. In 2000, these isolates were characterized by mating type, mitochondrial haplotype and virulence races. All isolates were of the A1 mating type and two mitochondrial haplotypes were identified: IIa, present in isolates from all the hosts tested, and Ib present only in isolates from tomato and water cucumber (Solanum muricatum). The Antioquia population of P. infestans showed a large complexity of virulence factors (10 out 11), especially those isolates collected from potato, while the tomato population was less complex. The A1 mating type and the mitochondrial haplotype IIa has been associated with the EC1 population that possibly is replacing the US1 population.De la colección de Phytophthora infestans de la Universidad Nacional de Colombia, se evaluaron aquellos aislamientos provenientes de diferentes localidades de Antioquia, Colombia entre 1994 y 2000. Dichos aislamientos fueron obtenidos de lesiones de tizón tardío en diferentes hospederos. En el año 2000 se caracterizaron por el tipo de apareamiento, haplotipo mitocondrial y razas de virulencia. Todos los aislamientos correspondieron al tipo de apareamiento A1 y se presentaron dos haplotipos mitocondriales: IIa, en aislamientos de todos los hospederos evaluados, y Ib solamente en aislamientos colectados de tomate y pepino de agua (Solanum muricatum). La población antioqueña de P. infestans presenta una amplia complejidad de factores de virulencia (10 de 11), especialmente para los aislamientos colectados de papa, mientras que la población de tomate fue menos compleja. El tipo de apareamiento A1 y el haplotipo mitocondrial IIa han sido asociados a la población EC1 que posiblemente está desplazando la población US1.
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- 2009
30. Análise dos haplótipos da anemia falciforme em Fortaleza revela as origens étnicas da população cearense Analysis of sickle cell anemia haplotypes in Fortaleza reveals the ethnic origins of Ceará state population
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Lilianne Brito da Silva, Romélia Pinheiro Gonçalves, and Sílvia Helena Barem Rabenhorst
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Haplótipos ,βS-globina ,Anemia falciforme ,Haplotypes ,βS-globin ,Sickle cell anemia ,Pathology ,RB1-214 - Abstract
Os haplótipos ligados ao gene da βS-globina foram analisados em uma amostra de 68 cromossomos de pacientes de Fortaleza, capital do Ceará, com anemia falciforme (AF), com a finalidade de fornecer informações sobre a distribuição das frequências dos haplótipos, contribuindo para o estudo das origens da formação étnica da população cearense. A distribuição dos haplótipos do gene da βS-globina foi 66,2% do tipo Bantu, 22% do Benin e 11,8% do atípico. Houve diferença estatisticamente significativa entre o presente estudo e os resultados de outros pesquisadores no Ceará. A distribuição das frequências dos haplótipos do gene da βS-globina no presente estudo está condizente com a história da formação da população brasileira. Conforme dados históricos sobre as origens da população negra trazida ao Ceará, o haplótipo Bantu seria o mais prevalente, seguido pelo Benin e Senegal. Estes resultados são relevantes para o estudo das rotas de tráfico dos escravos no Brasil e para entendermos as origens étnicas da população brasileira.In a sample of 68 chromosomes from sickle cell anemia patients from the population of Fortaleza, capital of Ceará State - Brazil, the haplotypes connected with βS-globin gene were analyzed with the aim to provide further information on haplotype frequency distribution, which ultimately contributed to the investigation into the ethnic origins of the state's population. The haplotype distribution of βS-globin gene was 66.2% Bantu type, 22% Benin type and 11.8% atypical. There was a significant statistical difference between the results of the present study and those achieved by other researchers in Ceará. The distribution of haplotype frequencies of βS-globin gene in the present study is consistent with the history of the Brazilian population origins. According to historical data on the origins of the slave population brought to Ceará State, Bantu haplotype would be the most prevalent, followed by Benin and Senegal. These results are relevant to the study of the slave traffic routes in Brazil and to understand the ethnic origins of Brazilian population.
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- 2009
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31. Determinantes genéticos e Acidente Vascular Encefálico em crianças com doença falciforme.
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Rodrigues, Daniela O. W., Ribeiro, Luiz C., Sudário, Lysla C., Teixeira, Maria T. B., Martins, Marina L., Pittella, Anuska M. O. L., and de O. Fernandes Junior, Irtis
- Abstract
Copyright of Jornal de Pediatria is the property of Sociedade Brasileira de Pediatria and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2016
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32. Sickle cell disease in western Sudan: genetic epidemiology and predictors of knowledge attitude and practices.
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Daak, Ahmed A., Elsamani, Elfatih, Ali, Eltigani H., Mohamed, Fatma A, Abdel‐Rahman, Manar E., Elderdery, Abozer Y., Talbot, Octavious, Kraft, Peter, Ghebremeskel, Kebreab, Elbashir, Mustafa I., and Fawzi, Wafaie
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SICKLE cell anemia , *GENETIC epidemiology , *CROSS-sectional method , *HAPLOTYPES , *CONSANGUINITY , *BLOOD cell count , *CHILD mortality , *CLUSTER analysis (Statistics) , *CAUSES of death , *DEMOGRAPHY , *HEALTH attitudes , *INTERVIEWING , *MOLECULAR epidemiology , *PARENTS , *SOCIAL classes , *EDUCATIONAL attainment , *DISEASE prevalence - Abstract
Objective: To investigate the epidemiology of sickle cell disease (SCD) and determinants of knowledge, attitudes and practices (KAP) towards SCD in western Kordofan State, Sudan.Methods: A community-based, descriptive, cross-sectional study was conducted in three towns. Three hundred and seventy-two households were polled, and blood samples for haemoglobin phenotyping were collected from 1116 individuals. Sociodemographic, socio-economic and KAP data were collected using investigator-administered questionnaires. Descriptive, frequency distribution and multiple regression analyses were performed.Results: About 50.9% of the study population were Misseriya tribes. Consanguineous marriages were reported by 67.5% of the households. The highest percentage of homozygous SCD was 2.8% among children under 5 years of age. About 24.9% were carriers of HbS allele (HbAS). HbS allele frequency was highest in children aged 5-11 years (18.3%, CI: 13.7-22.9%) and lowest in males >15 years old (12.0%, CI: 6.1-17.9%). The average HbS frequency across all age groups was 14.5% (95% CI: 12.2-16.8%). The most frequent β-globin gene cluster haplotype was the Cameroon (30.8%), followed by the Benin (21.8%), the Senegal (12.8%) and the Bantu (2.2%) haplotypes. About 17.0% of all-cause child deaths were due to SCD. The estimated change in log odds of having the SS genotype per year increase in age was (-) 0.0058 (95% CI -0.0359, 0.0242). This represents a non-statistically significant 2.9% increase in 5-year mortality for individuals with the SS genotype relative to those with AS and AA genotypes. About 46.9% of the households had poor knowledge, 26.1% had satisfactory knowledge, and 26.9% had good knowledge about sickle cell disease. Mothers' and fathers' educational levels were significant predictors of good knowledge about SCD (P < 0.05). About 48.0% had a satisfactory attitude towards sickle cell disease while 30.7% had poor attitude and only 21.3 showed good attitudes. Poor knowledge about SCD and low socio-economic status were the strongest positive predictors of poor attitude and practices towards SCD (P < 0.01).Conclusions: Sickle cell disease is a major health problem in West Kordofan, Sudan. Knowledge, attitude and practices towards the disease are not satisfactory. The development of public health programs is highly recommended to control and manage SCD in western parts of Sudan. [ABSTRACT FROM AUTHOR]- Published
- 2016
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33. Análisis filogenético del murciélago hematófago Desmodus rotundus en el Valle del Cauca Colombia.
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Castro Castro, Fernando Favian, Muñoz Flores, Jaime Eduardo, and Uieda, Wilson
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Phylogenetic analyses of the hematophagous bat Desmodus rotundus were performed in villages belonging to Valle del Cauca, Cauca and Amazonas regions. Samples were mainly collected at hematophagous bat shelters located in Victoria, Águila, Obando, Cartago, Zarzal, San Pedro, Cerrito and Palmira villages belonging to Valle del Cauca region, two samples at Mercaredes which belong to Cauca, two samples at Puerto Nariño which is part of Amazonas region. Epithelial tissue samples were collected from bat's patagium, and submitted to PCR using primers 16 SL and 16SH amplifying mitochondrial DNA of 50 vampires, these products were sequencing resulting in eight haplotypes being the most common presented in 43 individuals. Two methods to reach maximum likelihood and parsimony were used. GENBANK sequences of mitochondrial markers s16 rRNA from Brazil, Venezuela and Costa Rica were used for comparison. Higher similarity between vampire bats from Valle del Cauca and Cauca region, located in the southwest Colombia and vampire bats from Costa Rica and Venezuela was found. In the present study the genetic profiles correlated with the phylogeographic aspects of different populations was performed and a connection between different haplotypes of existing clades was found according to the phylogenetic tree and haplotype net, possible being generated during hematophagous bats migration over the mountain-chain and rivers crossing Colombia. [ABSTRACT FROM AUTHOR]
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- 2016
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34. Morphological and Genetic Variation in Mexican Wild Populations of Tamarixia radiata (Hymenoptera: Eulophidae).
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Peña-Carrillo, Kenzy I., González-Hernández, Alejandro, López-Arroyo, J. Isabel, Mercado-Hernández, Roberto, and Favela-Lara, Susana
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JUMPING plant-lice , *HYMENOPTERA behavior , *EULOPHIDAE , *HETEROGENEITY , *HAPLOTYPES - Abstract
We analyzed the morphological and genetic variation of the Asian citrus psyllid nymphal ectoparasitoid Tamarixia radiata (Waterston) (Hymenoptera: Eulophidae) in 2 regions of Mexico, in the northeast (represented by the states of Nuevo León and Tamaulipas) and the west (represented by the states of Colima and Michoacán). We found that the morphological variation of the specimens lay mainly in body color traits. The morphometric study indicated that in comparison with females, males presented heterogeneity, and it was concentrated in the state of Colima. Despite the morphological variation found in the species, it was not exclusively associated with any of the geographical regions. Molecular analysis revealed the presence of 2 haplotypes (H1 and H2), which were the same found in previous research among strains introduced to Florida. Haplotype H2 was found in both studied regions and more frequently than haplotype H1, which was collected only in the northeast (Tamaulipas state), suggesting possible points of gene flow between Mexico and the USA. Our results have implications for the extensive use of T. radiata in biological control programs of the Asian citrus psyllid. [ABSTRACT FROM AUTHOR]
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- 2015
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35. Clinical, hematological, and molecular characterization of sickle cell anemia pediatric patients from two different cities in Brazil Caracterização clínica, hematológica e molecular de crianças portadoras da anemia falciforme em duas diferentes cidades do Brasil
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Isa Menezes Lyra, Marilda Souza Gonçalves, Joseffina A. Pellegrinei Braga, Maria de Fátima Gesteira, Maria Helena Carvalho, Sara Terezinha Olalla Saad, Maria Stella Figueiredo, and Fernando Ferreira Costa
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Anemia Falciforme ,Talassemia Alfa ,Haplotipos ,Pediatria ,Sickle Cell Anemia ,Alpha-Thalassemia ,Haplotypes ,Pediatrics ,Medicine ,Public aspects of medicine ,RA1-1270 - Abstract
This study focused on clinical, hematological, and molecular aspects of sickle cell anemia pediatric patients from two different cites in Brazil. Seventy-one patients from São Paulo and Salvador, aged 3 to 18 years, were evaluated. Hematological analyses, betaS globin gene haplotypes, and alpha2 3.7kb-thalassemia were performed. Numbers of hospitalizations due to vaso-occlusive crises, infections, stroke, and cholelithiasis were investigated. São Paulo had more hospitalizations from vaso-occlusion, cholelithiasis, and stroke than Salvador. The Ben/CAR genotype predominated in both cities. alpha2 3.7kb-thalassemia had a frequency of 28.2% in Salvador, mostly with Ben/CAR genotype (45.0%), while São Paulo had 22.5% with similar frequencies of the Ben/ CAR and CAR/CAR genotypes. Sickle cell anemia patients from São Paulo also had more episodes of stroke, which was observed among CAR/CAR, atypical, and BEN/CAR haplotypes. In Salvador stroke was only observed in the Ben/CAR genotype. Cholelithiasis had similar frequencies in the two cities. These data suggest a milder phenotype among patients in Salvador, possibly due to genetic, environmental, and socioeconomic factors. Further studies are needed to elucidate modulating factors and phenotype association.O objetivo desse estudo foi avaliar aspectos clínicos, hematológicos e moleculares de pacientes pediátricos portadores de anemia falciforme em duas cidades brasileiras: Salvador e São Paulo. Foram estudados 71 pacientes com idades variando entre 3 a 18 anos, analisando-se os seguintes aspectos: perfis hematológicos, haplótipos dos genes da globina beta, presença de talassemia alfa-2(3.7kb), número de internações por vaso-oclusão, infecção, presença de acidente vascular cerebral e litíase biliar. O genótipo Ben/CAR predominou nas duas cidades. Talassemia alfa-2(3.7kb) teve freqüência de 28,2% em Salvador e 22,5% em São Paulo. Os pacientes de São Paulo apresentaram um número maior de internações por vaso-oclusão nos diferentes genótipos. Esses dados sugeriram um fenótipo com menor gravidade clínica nos pacientes de Salvador, possivelmente relacionados a fatores genéticos, ambientais e sócio-econômicos. Estudos adicionais necessitam ser realizados com intuito de elucidar os efeitos moduladores na expressão gênica da doença.
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- 2005
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36. Influencia dos polimorfismos do elemento regulatorio maior dos genes do cluster da globina alfa humana na expressão genica in vitro
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Ribeiro, Daniela Maria, Sonati, Maria de Fátima, 1958, Salzano, Francisco Mauro, Silva, Márcio José da, Melo, Mônica Barbosa de, Mello, Maricilda Palandi de, Universidade Estadual de Campinas. Faculdade de Ciências Médicas, Programa de Pós-Graduação em Ciências Médicas, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Haplotypes ,Haplótipos ,Globinas ,Globins - Abstract
Orientador: Maria de Fatima Sonati Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Resumo: A expressão dos genes do cluster da globina a em humanos é regulada pelo a-MRE ( a-Major Regulatory Element), um elemento localizado 40 kb à montante do respectivo cluster na região telomérica do braço curto do cromossomo 16. O a-MRE é geneticamente polimórfico e seis diferentes haplótipos, nomeados de A a F, foram determinados em alguns grupos populacionais da África, Europa e Ásia e em indivíduos pertencentes a duas populações indígenas brasileiras. As substituições de base que resultaram nestes haplótipos estão localizadas entre sítios de ligação para fatores nucleares ou em um sítio não ocupado in vivo, exceto no caso do haplótipo D, em que o polimorfismo altera a seqüência de um dos sítios ocupado in vivo pelo fator NF-E2. Não há, de nosso conhecimento, nenhum estudo experimental feito para avaliar se essa variabilidade pode influenciar a expressão gênica. Assim, no presente trabalho foi analisada e comparada a expressão do gene repórter da luciferase em células K562 transientemente transfectadas com construções que tiveram como enhancers os diferentes haplótipos do a-MRE, além de 3 dos polimorfismos isoladamente (+130, +199 e +209). Os resultados revelaram redução da expressão do gene da luciferase com todas as construções em relação à do haplótipo selvagem A: os haplótipos B e C corresponderam a 19% do grau de expressão do haplótipo A, o D a 21%, o E a 15%, o F a 3%, o polimorfismo +130 a 24%, o +199 a 32% e o +209 a 3%. Em seu conjunto, eles demonstram que os polimorfismos responsáveis pelos diferentes haplótipos do a-MRE, em sua maioria situados nas seqüências flanqueadoras dos sítios de ligação para proteínas regulatórias, reduzem a expressão gênica in vitro Abstract: The expression of human a-like globin genes is regulated by the a-MRE (a-Major Regulatory Element), an element located 40 kb upstream of the a cluster in the short arm of chromosome 16. The a-MRE is genetically polymorphic and six different haplotypes, named A to F, have been identified in some population groups from Europe, Africa and Asia and in native Indians from two Brazilian Indian tribes. The base substitutions that resulted in these haplotypes are located between binding sites for nuclear factors or in a site that is considered not to be active in vivo, with the exception of haplotype D, in which the polymorphism changes the first binding site for the NF-E2 factor occupied in vivo. To our knowledge, there are no experimental studies evaluating whether this variability may influence gene expression. Thus, the present work analyzed and compared the expression of the luciferase reporter gene in K562 cells transiently transfected with constructs that have, as enhancers, the different a-MRE haplotypes, besides three isolated polymorphisms (+130, +199 and +209). The results demonstrated a reduction in luciferase gene expression with all the constructs compared with the wild type a-MRE (A haplotype): the B and C haplotypes corresponded to 19% of the A haplotype expression, the D to 21%, the E to 15%, the F to 3%, the polymorphism +130 to 24%, the +199 to 32% and the +209 to 3%. They demonstrate that the polymorphisms responsible for the a-MRE haplotypes, most located in the flanking sequences of the regulatory protein binding sites, decrease in vitro gene expression Doutorado Ciências Biomédicas Doutor em Ciências Médicas
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- 2021
37. Relevancia de polimorfismos geneticos para concentrações sanguineas e plasmaticas de chumbo na gravidez
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Dias, Vania Braghini de Rezende, Tanus-Santos, Jose Eduardo, Rocha, João Batista Teixeira da, Funayama, Carolina Araújo Rodrigues, Ramos, Ester Silveira, Sabha, Maricene, Universidade Estadual de Campinas. Faculdade de Ciências Médicas, Programa de Pós-Graduação em Farmacologia, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Sintase do portobilinogenio ,Lead ,Pregnancy ,Toxicologia genética ,Haplotype ,Polimorfismo (Genética) ,Gravidez ,Haplótipos ,Porphobilinogen Synthase ,Polymorphism ,Toxicogenetics ,Chumbo - Abstract
Orientador: Jose Eduardo Tanus dos Santos Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Resumo: Mulheres grávidas constituem um grupo de indivíduos particularmente mais susceptíveis aos efeitos tóxicos associados ao chumbo (Pb)[1]. O chumbo é um metal pesado que se acumula nos tecidos mineralizados. Possui um comportamento similar ao cálcio, o que explica sua toxicidade. Durante a gravidez, o remodelamento ósseo promove a migração do chumbo para o plasma e como resultado, o metal é transferido para o feto, mesmo se a mãe foi exposta há vários anos [2]. Durante a exposição materna, cerca de 99% do chumbo absorvido, aqui referenciado como Pb-Sangue Total, permanece associado a enzima acido d-aminolevulinico desidratase (ALAD) no eritrócito. O restante (cerca de 1%), aqui referenciado como Pb-Plasma (e/ou Soro), permanece livre e eventualmente se deposita nos tecidos mineralizados (ossos e dentes)[2]. O Pb-Sangue Total e Pb-Plasma (ou Soro) são naturalmente correlacionados, mas essa correlação ainda não está bem compreendida, sendo essencial a medida dos dois parâmetros para esclarecer esses processos. Além disso, os fatores genéticos são de crucial importância, com alguns genes como o da ALAD e o do receptor da vitamina D (VDR) tendo sido associados a diferentes concentrações sanguíneas e plasmáticas de chumbo em indivíduos expostos[3]. A dinâmica do chumbo durante a gravidez também tem um papel importante nesse processo e deve ser considerada. Até o momento, nenhum trabalho havia estudado os fatores genéticos acima citados, numa população especialmente exposta e susceptível aos efeitos deletérios do chumbo. Mesmo quando a exposição materna cessa, o chumbo permanece alojado nos ossos por vários anos e será mobilizado através do remodelamento ósseo, contaminando o feto. Haveria um grupo de gestantes, segundo genótipos, predisposto a maiores ou menores aumentos do metal no plasma e fração plasmática? Teriam maior re-exposição ao chumbo durante períodos de acentuado remodelamento ósseo? Para responder a essas questões, esse estudo concentrou nas medidas do metal no Sangue e Plasma e/ou Soro (sendo o Soro equivalente ao plasma) e na avaliação da susceptibilidade genética das grávidas através do estudo dos polimorfismos dos genes ALAD e VDR, além da análise de polimorfismos agrupados em haplótipos. Nós não encontramos diferenças significativas para o grupo de genótipos da ALAD, nem mesmo para os genótipos do VDR. Porém, as principais descobertas foram que o grupo de haplótipos H8 do VDR (f, a, b) estão associados às mais baixas concentrações de Pb no Soro e na razão Pb-Soro/Pb-Sangue Total. Esses resultados sugerem que esse grupo de gestantes, mesmo expostas às mesmas concentrações de Pb, acumula e/ou reabsorvem menos Pb que os grupos com outros haplótipos. Além disso, é importante ressaltar que analisando apenas a concentração de Pb no sangue total, não seria possível chegar a essa conclusão. Abstract: Pregnant women constitute a group of subjects particularly susceptible to toxic effects due to exposure to lead (Pb). Lead is a heavy metal which accumulates in bone tissues and has a behavior that is similar to calcium, thus explaining its toxicity. In particular, the increase in bone resorption processes that take place during pregnancy cause lead migration into the maternal plasma. As a result, lead transference to the fetus may take place even years after the mother's last exposure. During maternal exposure, most (99%) of the absorbed lead (here referred to as Pb-Blood) remains associated to d - aminolevulinic acid dehydratase within erytrocytes. The remaining (2% to 10%, here referred to as Pb-Plasma) lead remains free and is eventually deposited - and accumulated - in the bone tissues (teeth and bones). The Pb-Blood and Pb-Plasma are naturally correlated, but the correlation is not well understood, making it essential to measure both quantities in studies aimed at clarifying these processes. Also of crucial importance are genetic factors, with some genes such as ALAD and VDR been associated with Pb-Blood and Pb-Plasma concentrations. The dynamics of lead migration during pregnancy also plays a major role in the process and therefore must also be considered. Even after the mother's exposure has ceased, lead remains accumulated in the teeth and bones for many years and is mobilized by processes of bone resorption such as those taking place during pregnancy. Is there a group of pregnant women, according to genotypes, that is more prone to higher or lower Pb concentations in plasma? Is that group more exposed to Pb due to greater Pb absorption or reabsorption through bone remodeling? To address these questions, this study focused on the measurement of Pb-Blood and Pb-Serum (the same of plasma) and on genetic susceptibility of pregnant women. We found no significant differences among different ALAD or VDR genotype groups. However, the main findings reported here are that haplotype H8 of VDR (f, a, b) is associated with lower Pb-Serum concentration and lower Pb-Serum/Pb-Blood ratios. Therefore, pregnant women with this haplotype have lower Pb-serum, even when exposed to the same Pb-Blood concentrations. Interestingly, we would not have make this conclusion by assessing only Pb-Blood concentrations. Doutorado Farmacologia Doutor em Farmacologia
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- 2021
38. The dystrophinopathies in Costa Rica
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Jorge Azofeifa
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distrofia muscular ,Duchenne ,Becker ,cromosoma X ,portadoras ,deleciones ,haplotipos ,Muscular dystrophy ,X chromosome ,carriers ,deletions ,haplotypes ,Biology (General) ,QH301-705.5 - Abstract
A five-years long study aiming to describe the basic genetic epidemiology of the dystrophinopathies in Costa Rica recruited 31 patients with clinical symptoms of DMD/BMD at the National Children’s Hospital (HNN). This center is the obligate reference hospital of the national health system for genetic diseases, however, the geographic origin of the patients, a low percentage of deletions and a high proportion of de novo mutations found among them indicate that a significant ascertainment bias impedes a substantial scientific approach to confront and alleviate the problems posed by these severe diseases in Costa Rica. Rev. Biol. Trop. 52(3): 485- 490. Epub 2004 Dic 15.Un estudio de cinco años tendiente a describir la epidemiología genética básica de las distrofinopatías en Costa Rica detectó 31 pacientes con sintomatología de DMD o de BMD en el Hospital Nacional de Niños (HNN), el centro de referencia del sistema nacional de salud para enefrmedades hereditarias, sin embargo, la distribución geográfica de los pacientes, un bajo porcentaje de deleciones y una muy elevada proporción de mutaciones de novo indican que un significante sesgo de averiguación impide el estudio científico de riguroso tendiente a disminuir el impacto de estas enfermedades en Costa Rica.
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- 2004
39. Aspectos moleculares da anemia falciforme
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Gentil Claudino de Galiza Neto and Maria da Silva Pitombeira
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Anemia falciforme ,Hemoglobinopatia ,Globina betaS ,Haplótipos ,Pathology ,RB1-214 - Abstract
No presente artigo abordaram-se vários aspectos relacionados à natureza molecular da anemia falciforme, desordem hematológica de caráter hereditário que acomete expressivo número de indivíduos em várias regiões do mundo. As pesquisas realizadas em torno desta patologia da hemácia, ao longo de quase um século, a partir de 1910, cooperaram para a criação de um novo e importante segmento da ciência, denominado biologia molecular. A descoberta dos polimorfismos da mutação (GAT->GTG) no gene que codifica a cadeia beta da hemoglobina, originando diferentes haplótipos da doença, permitiu um melhor e mais amplo conhecimento em torno da heterogeneidade clínica nos pacientes falcêmicos. Analisando a hemoglobina na sua estrutura normal e mutante, sua produção e evolução, pode-se ter um entendimento mais completo da fisiopatologia desta doença e da sua complexidade clínica.
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- 2003
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40. Aspectos moleculares da anemia falciforme
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Galiza Neto Gentil Claudino de and Pitombeira Maria da Silva
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Anemia falciforme ,Hemoglobinopatia ,Globina betaS ,Haplótipos ,Pathology ,RB1-214 - Abstract
No presente artigo abordaram-se vários aspectos relacionados à natureza molecular da anemia falciforme, desordem hematológica de caráter hereditário que acomete expressivo número de indivíduos em várias regiões do mundo. As pesquisas realizadas em torno desta patologia da hemácia, ao longo de quase um século, a partir de 1910, cooperaram para a criação de um novo e importante segmento da ciência, denominado biologia molecular. A descoberta dos polimorfismos da mutação (GAT->GTG) no gene que codifica a cadeia beta da hemoglobina, originando diferentes haplótipos da doença, permitiu um melhor e mais amplo conhecimento em torno da heterogeneidade clínica nos pacientes falcêmicos. Analisando a hemoglobina na sua estrutura normal e mutante, sua produção e evolução, pode-se ter um entendimento mais completo da fisiopatologia desta doença e da sua complexidade clínica.
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- 2003
41. Organización, arquitectura y plasticidad genómica de Trypanosoma cruzi.
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Greif, Gonzalo, Sanz, Carlos, Álvarez-Valín, Fernando, Robello, Carlos, and Berná, Luisa
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Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2022
42. Caracterização de aspectos geneticos e imunologicos envolvidos no desenvolvimento de inibidores em hemofilia A e B
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Santos, Andrey dos, Ozelo, Margareth Castro, 1970, Rezende, Suely Meireles, Justo, Giselle Zenker, Saad, Sara Teresinha Olalla, Traina, Fabíola, Universidade Estadual de Campinas. Faculdade de Ciências Médicas, Programa de Pós-Graduação em Clínica Médica, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Hemofilia ,Immune system ,Haplotypes ,Haplótipos ,Hemophilia ,Sistema imunológico ,Etnia - Abstract
Orientador: Margareth Castro Ozelo Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Resumo: Uma complicação decorrente do tratamento da hemofilia é a formação de anticorpos neutralizadores da atividade coagulante do fator VIII ou IX (inibidores). Diversos fatores estão relacionados com o desenvolvimento desses inibidores em indivíduos com hemofilia, incluindo fatores genéticos e ambientais. Entre os fatores genéticos, a mutação associada ao diagnóstico da hemofilia é um fator de risco bem documentado. Recentemente foi observada a maior ocorrência de inibidores em indivíduos da etnia negra. O objetivo deste trabalho foi analisar os aspectos genéticos e não genéticos envolvidos no desenvolvimento de inibidores. Foram incluídos nesse estudo 411 pacientes hemofílicos, sendo 321 com hemofilia A (HA) (238 famílias) e 99 com hemofilia B (HB) (59 famílias). A presença de inibidores foi constatada apenas entre os pacientes HA graves. Do total de 220 HA graves desse estudo, 46 (20,9%) apresentaram inibidor detectado em pelo menos uma ocasião após sua inclusão no estudo. Mutações consideradas de alto-risco para o desenvolvimento de inibidores foram identificadas em 125/220 pacientes HA graves (58,8%), e 33 deles desenvolveram inibidores (26,4%). Considerando o grupo étnico de acordo com traços físicos e ancestralidade, 38% dos pacientes HA graves foram classificados como negros. A incidência de inibidores foi maior nesse grupo de pacientes (31% do total de pacientes HA graves classificados como negros) quando comparada aos pacientes caucasóides (20% do total de pacientes HA graves classificados como caucasóides). Recentemente, foi observado que a maior incidência de inibidores em uma população norte-americana de pacientes com HA, estava relacionada com a presença de determinados haplótipos no gene do fator VIII. Esta observação poderia ser explicada pelo fato dos as proteínas expressas pelos haplótipos que aparecem exclusivamente entre a população negra (denominados H3 e H4), estarem ausentes nos concentrados de fator VIII recombinantes utilizados rotineiramente no tratamento desses pacientes. Em nossa análise a presença desses haplótipos não está relacionada com a maior freqüência de inibidor na população negra desse estudo. Além disso, a distribuição dos diferentes haplótipos do gene do fator VIII, classificados de H1 a H6, foi distinta entre todos os grupos étnicos brasileiros e norte-americanos. Essa observação pode ser explicada pela origem distinta entre os negros que imigraram da África para o Brasil e para a América do Norte, assim como o alto índice de miscigenação de nossa população. Em outra fase desse estudo, foi realizada a análise comparativa da expressão gênica a partir de amostras de RNA mensageiro (RNAm) extraídas em pool leucocitário de pacientes com HA grave, com ou sem a presença de inibidores. Na avaliação que incluiu numa primeira análise pacientes de uma mesma família discordante para a presença de inibidor e, em uma segunda fase, indivíduos não relacionados, foram observados 50 genes mais expressos e 16 genes menos expressos em pacientes com inibidor em comparação aos sem inibidor. Dentre esses genes foram selecionados dez, levando-se em conta sua participação na resposta imune ou sua correlação prévia com o desenvolvimento de inibidores em outros estudos. Pela técnica de PCR em tempo real, observou-se que os genes da interleucina 8 (IL-8) e da cistatina F (CST7) demonstraram ser mais expressos em pacientes com inibidor, enquanto que o gene da interleucina 10 (IL-10) foi menos expresso nesse grupo de pacientes. Dessa forma, nossos resultados fortalecem a idéia de que o mecanismo de desenvolvimento de inibidores em hemofilia é complexo e ainda não totalmente esclarecido e que existe um grande envolvimento de diversos genes relacionados com sistema imune na formação desses inibidores. O estudo em diferentes populações é uma importante etapa para o entendimento dos fatores de risco para o desenvolvimento de inibidores. Esse foi o primeiro trabalho realizado no Brasil incluindo pacientes de diversas regiões e analisando simultaneamente diferentes fatores e seu envolvimento com o desenvolvimento de inibidores. A determinação desses fatores de risco ajudará no futuro a determinar um tratamento diferenciado para o controle e sobretudo prevenção do desenvolvimento de inibidores Abstract: The most serious complication of the treatment of hemophilia is the development of neutralizing antibodies to coagulation activity of factor VIII or IX (inhibitors). Several risk factors are related to the development of these inhibitors in patients with hemophilia, including genetic and environmental factors. Among genetic factors, the mutation associated with the diagnosis of hemophilia is a risk factor well documented. Recently, it was observed a higher incidence of inhibitors in African ancestry patients. The aim of this study was to analyze the genetic and non-genetic factors involved in the development of inhibitors. The study included 411 hemophilia patients, of which 321 with hemophilia A (HA) and 99 with hemophilia B (HB), belonging to a total of 238 and 59 families, respectively. The inhibitors were observed only in severe HA patients. From the 220 severe HA, 46 (20.9%) had inhibitor. The high risk mutation for the development of inhibitors were identified in 125 / 220 (58.8 %) severe HA patients, and 33 (26.4 %) of them developed inhibitors. Considering the ethnic group according to physical traits and ancestry, 38 % of severe HA patients were classified as black. The incidence of inhibitors is higher in this group of patients (31%) when compared to Caucasian patients (20%). The higher risk of inhibitor among African-Brazilians, could not be explained by the presence of the distinct factor VIII haplotypes, such as H3 and H4, as suggested in previous study. In fact, the prevalence rates of these haplotypes were distinct between Brazilians and North Americans, probably due to the fact that migrations of blacks to Brazil and to North America were originated from different geographic areas of Africa. In another phase of this study, we performed a comparative analysis of gene expression in samples of messenger RNA (mRNA) extracted from leukocytes of inhibitor and non-inhibitor patients with severe HA was performed. The evaluation consisted of an initial analysis of severe HA patients siblings, or from the same family, discordant for inhibitor development and in a second phase a group of unrelated individuals. Using the bioarrays technology 50 genes were upregulated and 16 were downregulated in inhibitor patients compared with non-inhibitor patients. Ten genes were selected among them, which are involved in immune response and were related to inhibitors development in other studies. It was observed by real time PCR that the genes for interleukin 8 (IL-8) and cystatin F (CST7) were upregulated and for interleukin 10 (IL-10) was downregulated in inhibitor patients. In conclusion, our results strengthen the idea that the mechanism of inhibitor development in hemophilia is complex, not clear and there is a large involvement of several genes related to the immune system in the development of these inhibitors. The study in different populations is important to understand the risk factors for the development of inhibitors. This is the first work in Brazil, to study patients from various regions and to performe analysis of different factors and their involvement in the development of inhibitors. The determination of these risk factors will help in the future to determine differential treatment for the control and in particular, for preventing the development of inhibitors Doutorado Clínica Médica Doutor em Clínica Médica
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- 2021
43. Estudio de las variantes genéticas de diaphorina citri, vector de candidatus liberibacter spp. en cítricos
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Ceballos Ceballos, Augusto Gil, Cerna Chávez, Ernesto, Ochoa Fuentes, Yisa María, Hernández Juárez, Agustín, and Flores Dávila, Mariano
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Diaphorina citri ,Psílido ,Haplotipos ,CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA - Abstract
"El presente trabajo se basó en técnicas moleculares para la detección de Candidatus Liberibacter de las especies americana y asiática, se utilizó la técnica PCR punto final y se aplicó a muestras vegetales y de insectos usando los iniciadores BK-DY2F (5´- CGCGTATGCAATACGAGCGGCA-3´) Y BK-DY2R (3´- GCCTCGCGACTTCGCAACCCAT-5´) para la especie asiática y BK-DY1F (5´- AGTCGAGCGAGTACGCAAGTACT-3´) y BK-DY1R (3´- CAACTTAATGATGGCAAATATAG-5´) para la especie americana. No se detectó presencia de Huanglongbing en ninguno de los casos, se concluyó que esto pudo deberse a que no se eligieron plantas con sintomatología aparente. Se sugiere el uso de PCR Tiempo Real o PCR anidada y se propuso que los muestreos sean basados en plantas con sintomatología aparente. La técnica que se usó para la identificación de haplotipos del Psílido Asiático de los Cítricos (PAC) fue PCR punto final. La amplificación del ADN se realizó con los iniciadores específicos DCITRI COI-L y DCITRI COI-R, el producto de la reacción PCR fue secuenciado en el Instituto Potosino de Investigación Científica y Tecnológica A. C. (IPICYT), obteniendo 22 secuencias finales que se analizaron con los programas Oligo analizer y Clustal Omega. Las secuencias obtenidas se compararon con las que se encuentran reportadas en el GenBank y se determinó que existe una línea matriz que corresponde al haplotipo Dcit-1 con número de identificación FJ190306, sin embargo, también existen algunos individuos con diferencias en dos nucleótidos y que corresponden a los sitios de muestreo donde no hay estudios previos. Se identificaron dos nuevos posibles haplotipos a los que se les denominó DcitACC-1 y DcitACC-2. La distribución de las nuevas variantes corresponde a estados que no se han estudiado anteriormente, el haplotipo Dcit-1 ya se ha reportado en Nuevo León (Fuentes et al., 2018). Las nuevas posibles variantes pueden estar relacionadas con las condiciones climáticas a las que habita el PAC. Se sugirió realizar muestreos más amplios en zonas donde el PAC no haya sido estudiado, esto con la finalidad de describir todas las variantes distribuidas en el país." "The present work was based on molecular techniques for the detection of Candidatus Liberibacter of the American and Asian species, endpoint PCR technique was used and applied to plant and insect samples using the primers BK-DY2F (5'- CGCGTATGCAATACGAGCGGCA-3') and BK-DY2R (3'- GCCTCGCGACTTCGCAACCCAT-5') for the Asian species and BK-DY2R for the Asian species. GCCTCGCGACTTCGCAACCCAT-5') for the Asian species and BK-DY1F (5'- AGTCGAGCGAGCGAGTACGCAAGTACT-3') and BK-DY1R (3'- CAACTTAATGATGGATGGCAAATATATAG-5') for the American species. The presence of Huanglongbing was not detected in any of the cases, it was concluded that this could be due to the fact that plants with apparent symptomatology were not selected. The use of Real Time PCR or nested PCR is suggested and it was proposed that sampling be based on plants with apparent symptomatology. The technique used for the identification of Asian citrus psyllid (ACP) haplotypes was endpoint PCR. DNA amplification was performed with the specific primers DCITRI COI-L and DCITRI COI-R, the product of the PCR reaction was sequenced at the Instituto Potosino de Investigación Científica y Tecnológica A. C. (IPICYT), obtaining 22 final sequences that were analyzed with the Oligo analyzer and Clustal Omega programs. The sequences obtained were compared with those reported in GenBank and it was determined that there is a parent line that corresponds to the Dcit-1 haplotype with identification number FJ190306, however, there are also some individuals with differences in two nucleotides and that correspond to sampling sites where there are no previous studies. Two new possible haplotypes were identified and named DcitACC-1 and DcitACC-2. The distribution of the new variants corresponds to states that have not been previously studied; the Dcit-1 haplotype has already been reported in Nuevo León (Fuentes et al., 2018). The new possible variants may be related to the climatic conditions at which the CAP inhabits. It was suggested to conduct broader sampling in areas where PAC has not been studied, this with the aim of describing all variants distributed in the country."
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- 2021
44. Influencia dos polimorfismos T6235C e A4889G, do gene CYP1A1, e dos haplotipos NAT1*3, NAT1*4 e NAT1*10 do gene NAT1, associados com o metabolismo de carcinogenos, na susceptibilidade ao adenocarcinoma colorretal esporadico
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Angelo, Sandro Nunes, Lima, Carmen Silvia Passos, 1957, Coy, Claudio Saddy Rodrigues, 1961, Saad, Luiz Henrique Cury, Fagundes, João Jose, Universidade Estadual de Campinas. Faculdade de Ciências Médicas, Programa de Pós-Graduação em Cirurgia, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Haplotypes ,Polimorfismo (Genética) ,Haplótipos ,Polymorphism - Abstract
Orientadores: Carmen Silvia Passos Lima, Claudio Saddy Rodrigues Coy Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Resumo: A exposição das células do cólon e do reto a substâncias carcinogênicas está associada ao consumo de alimentos que constituam fonte de substratos, como aminas aromáticas e hidrocarbonetos aromáticos policiclícos. Enzimas como a mono-oxigenase do citocromo P450, codificada pelo gene CYP1A1 e a N-acetiltransferase, codificada pelo gene NAT1, estão relacionadas com o metabolismo dessas substâncias. Os polimorfismos T6235C e A4889G, do gene CYP1A1, e o haplótipo NAT1*10, do gene NAT1, foram associados ao risco do câncer colorretal (CC) em indivíduos do hemisfério norte. Não há descrições sobre as influências desses polimorfismos no risco do CC em nossa população, sendo este o objetivo do estudo. O DNA de 254 pacientes com adenocarcinoma colorretal esporádico (ACE) e 255 controles foi analisado por meio da reação em cadeia da polimerase e digestão enzimática. Foi avaliado também, o padrão dietético de pacientes e controles por meio do recordatório de freqüência alimentar. Houve risco maior de ocorrência do ACE em indivíduos com os genótipos variantes dos polimorfismos T6235C e A4889G do gene CYP1A1 e com consumo excessivo de carnes. A frequência do haplótipo NAT1*10 foi maior em pacientes do que em controles, havendo risco maior de ocorrência do ACE nesses indivíduos. Maior risco de ocorrência da doença foi também observado em indivíduos com os haplótipos NAT1*10 do gene NAT1 e consumo excessivo de carnes e escasso de verduras e frutas. Os resultados deste estudo sugerem que as vias herdadas do metabolismo de carcinógenos, CYP1A1 e NAT1, associadas ao padrão da dieta influenciam o risco de ocorrência do ACE em nosso meio. Abstract: The exposure of the cells of the colon and rectum to carcinogenic substances is associated with the consumption of foods that are source of substrates, such as aromatic amines and polycyclic aromatic hydrocarbons. Enzymes such as cytochrome P450 monooxygenase, encoded by the CYP1A1 gene, and acetyltransferase, encoded by the NAT1 gene, are related to the metabolism of these substances. T6235C and A4889G polymorphisms, of the CYP1A1 gene, and NAT1*10 haplotype of the gene NAT1 were associated with incidence of colorectal cancer (CC). There are no descriptions about the influences of these polymorphisms on the risk for the CC in our population, which is the objective of the study. DNA from 254 sporadic colorectal adenocarcinoma (SCA) patients and 255 controls were analysed by polymerase chain reaction and restriction digestion. It was also assessed the dietary pattern pacients and controls through the recall of food frequency. There was a greater risk of the occurrence of SCA in individuals with the variant genotypes of the T6235C and A4889G polymorphisms, of the CYP1A1 gene, associated with high consumption of meat. The frequency of the NAT1*10 haplotype was greater in pacients than in controls, with increased risk of occurrence of SCA these individuals. Increased risk of occurrence of the disease was also observed in individuals with NAT1*10 haplotype of the gene NAT1 and excessive consumption of meat and little vegetables and fruits. The results of the study suggest that the pathaway inherited from the metabolism of carcinogens, CYP1A1 and NAT1, associated with the pattern of diet influences the risk of occurrence of SCA in our country. Mestrado Cirurgia Mestre em Cirurgia
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- 2021
45. Análise da variação molecular de Poecilia vivipara (Cypronodontiformes: Poecillidea)
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Tonhatti, Carlos Henrique, 1983, Reis, Sérgio Furtado dos, 1952, Souza, Anete Pereira de, Araújo, Marcio Silva, Universidade Estadual de Campinas. Instituto de Biologia, Programa de Pós-Graduação em Genética e Biologia Molecular, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Control region ,Haplotypes ,Population genetics ,DNA mitocondrial ,Região de controle ,Haplótipos ,Genética de populações ,Poecilia vivipara ,Mitochondrial DNA - Abstract
Orientador: Sérgio Furtado dos Reis Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia Resumo: Os poecilídeos são um excelente sistema modelo para estudos de evolução de história de vida seleção natural e sexual, evolução e coevolução experimental e evolução fenotípica em gradientes ecológicos. Os poecilídeos são também excelentes modelos para o estudo de processos ecológicos e evolutivos associados como a invasão e colonização de novos ambientes. As populações de Poecilia vivípara que ocorrem no sistema lagunar de Campos de Goytacazes no norte do estado do Rio de Janeiro são um exemplo notável de invasão e colonização de novos ambientes. Nesse sistema, a origem das lagoas deve-se a processos geomorfológicos associados com a formação do delta do rio Paraíba do Sul durante o Holoceno. Para este sistema formulamos a hipótese que a história geológica da região influenciou a variação genética atual em Poecilia vivípara. Deste modo, uma população de uma outra bacia hidrográfica seria diferente das populações da bacia do rio Paraíba do Sul. Uma população do rio Paraíba do Sul de uma região com formação mais antiga seria diferente das populações de regiões com história mais recente. Dentre as mais recentes as que vivem na área de influência marinha seriam diferentes das que vivem na área fluvial. A hipótese foi testada usando sequências da região de controle da replicação mitocondrial de 8 populações com 30 indivíduos cada. Os resultados mostraram uma grande diversidade genética dentro e entre as populações, estruturação genética entre as populações antigas recentes do rio Paraíba do Sul e que não houve mudanças no tamanho efetivo das populações recentemente. A partir dos resultados a hipótese formulada não foi refutada. Assim, existe relação entre a história geológica da região e a variação genética atual do P. vivípara. Há evidências que o regime de inundação característico da região também age sobre a variação genética destas populações aumentando o fluxo genético entre as mesmas Abstract: The fishes of Poeciliidae family are an excellent model system for studies of life history evolution of natural and sexual selection, experimental evolution and coevolution in phenotypic evolution and ecological gradients. These are also excellent models for the study of ecological and evolutionary processes associated as the invasion and colonization of new environments. Populations of Poecilia vivipara occurring in the lagoon system of Goytacazes fields in northern Rio de Janeiro state are a notable example of invasion and colonization of new environments. In this system, the origin of the lakes due to geomorphological processes associated with the formation of the delta of the River Paraíba do Sul during the Holocene. For this system we hypothesized that the geological history of the region influenced the genetic variation present in Poecilia vivipara. Thus, a population of another watershed would be different populations of river basin Paraíba do Sul A population of Paraíba do Sul River in a region with older formation would be different regions with populations of more recent history. Among the most recent ones that live in the area of marine influence would be different from those who live in the river. The hypothesis was tested using sequences of the control region of mitochondrial replication of 8 populations with 30 individuals each. The results showed a high genetic diversity within and among populations, genetic structure among populations older times recent Paraíba do Sul river and that there were no changes in effective population size recently. From the results the hypothesis was not refuted. Thus, there is a relationship between the geological history of the region and genetic variation of the current P. vivipara. There is evidence that the flooding regime characteristic of the region also acts on the genetic variation of these populations increasing gene flow between them Mestrado Genética Animal e Evolução Mestre em Genética e Biologia Molecular
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- 2021
46. Haplotipos da região genica CFTR em nucleos familiares de pacientes com fibrose cistica
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Furgeri, Daniela Tenório, 1983, Bertuzzo, Carmen Sílvia, 1963, Ribeiro, Antonio Fernando, Soma, Mithitaka, Universidade Estadual de Campinas. Faculdade de Ciências Médicas, Programa de Pós-Graduação em Farmacologia, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Haplotypes ,Diagnóstico ,Diagnosis ,Genetics ,Polimorfismo (Genética) ,Fibrose cística ,Haplótipos ,Polymorphism ,Genética ,Cystic fibrosis - Abstract
Orientador: Carmen Silvia Bertuzzo Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciencias Medicas Resumo: A Fibrose Cística (FC) é uma doença genética de padrão de herança autossômica recessiva com incidência de 1/2.500 indivíduos e uma freqüência de portadores de 1/25 nos indivíduos caucasóides. A doença é progressiva e apresenta como manifestação clínica a obstrução respiratória crônica, infertilidade masculina e deficiência de ganho de peso pelo dano ao pâncreas exócrino. A maioria dos pacientes tem níveis elevados de eletrólitos no suor. O gene responsável pela doença foi localizado no cromossomo 7, possui 27 éxons e é denominado CFTR (¿Cystic Fibrosis Transmembrane Conductance Regulator Gene¿). Existem mais de 1.000 mutações descritas em todo o gene, a mais freqüente, a ?F508, é caracterizada como uma deleção de três pares de bases, o que determina a perda de uma fenilalanina na posição 508 da proteína CFTR, a qual forma um canal para o transporte do íon cloro. O defeito básico está associado com a diminuição da condução de íons cloro através da membrana apical de células epiteliais. O objetivo desse trabalho foi verificar em uma amostra de núcleos familiares de pacientes com fibrose cística, os haplótipos existentes, a possibilidade de utilização de polimorfismos para diagnóstico pré-natal e pré-implantação e correlacionar a mutação ?F508 com os haplótipos encontrados. A análise de polimorfismos GATT foi realizada através da técnica da reação em cadeia da polimerase (PCR) e a análise dos polimorfismos MP6-D9, TUB09 e TUB18 foi realizada através da PCR e digestão enzimática específica. Em nossa casuística, nove haplótipos diferentes foram encontrados em 39 cromossomos. Vinte e cinco estão ligados à mutação ?F508 e 14 ligados a outras mutações (não-?F508). O haplótipo 6, +; G; C (GATT, MP6D9, TUB09 e TUB18) foi o mais freqüente (48%) em cromossomos com o gene CFTR alterado e está fortemente ligado à mutação ?F508 (64%). Em 43% das famílias analisadas pelo menos um polimorfismo informativo foi encontrado para o diagnóstico pré-natal ou pré-implantação. Em conclusão, estes polimorfismos constituem um excelente grupo de marcadores genéticos, úteis para observar a transmissão dos alelos mutados em famílias de pacientes com fibrose cística, onde não é possível estabelecer o genótipo completo. De acordo com os resultados obtidos, estes polimorfismos poderão ser amplamente utilizados para o diagnóstico pré-natal e pré-implantação, cumprindo com o objetivo do trabalho Abstract: Cystic Fibrosis (FC) is a genetic autossomic recessive disease with an incidence of 1/2.500 life births and a carrier frequency of 1/25 in the caucasian population. The disease is progressive and present as a clinical manifestation the respiratory chronic blockage, male infertility and deficiency to gain weight caused for the damage to the exocrine pancreas. The majority of the patients has raised electrolyte levels in the sweat. The gene responsible is located in chromosome 7, and it has 27 éxons, and is called CFTR ("Cystic Fibrosis Transmembrane Conductance Regulator Gene"). Over 1.200 mutations have been described all over the gene and the mutation ?F508 is the most frequent, and is characterized as a deletion of three bases pairs, which determines the loss of a phenylalanine in position 508 of protein CFTR. The basic defect is associated with the reduction of the conduction of ions Cl- through the apical membrane of epithelial cells. The CFTR forms a channel for the transport of this ion. The aim of this work was to determine to verify in a cystic sample of nuclei familiates of patients with cystic fibrosis, the existing haplotypes, the possibility of use polymorphisms for prenatal and preimplantacion diagnosis and to correlate the mutation ?F508 with the joined haplotypes. The analysis of polymorphism GATT was performed by polymerase chain reaction (PCR) and the analysis of polymorphisms MP6-D9, TUB09 and TUB18 polymorphism was performed by PCR and enzymatic digestion. In our casuistic, nine differents haplotypes had been found in 39 chromosomes. Twenty-five with ?F508 mutation and 14 with other mutations (not-?F508), haplotype 6, +; G; C (GATT, MP6-D9, TUB09 and TUB18) was most frequent (48%) in chromosomes with mutated CFTR gene and is strong linked to the ?F508 mutation (64%). In 43% families analyzed at least an informative polymorphism were found for the prenatal diagnosis or preimplantacion. In conclusion, these polymorphisms constitute an excellent group of genetic useful markers to observe the transmission of the mutateds alleles in families of patients with cystic fibrosis, where it is not possible to establish the complete genotype. In accordance with the gotten results, these polymorphisms could be used for the prenatal and preimplantacion diagnosis, fulfilling with the objective of the work Mestrado Mestre em Farmacologia
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- 2021
47. Associação entre haplótipos de metaloproteinase-9 de matriz extracelular (MMP-9) e obesidade infantil
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Belo, Vanessa de Almeida, Tanus-Santos, Jose Eduardo, Sonati, Maria de Fátima, Krieger, Jose Eduardo, Casella Filho, Antônio, Velloso, Licio Augusto, Universidade Estadual de Campinas. Faculdade de Ciências Médicas, Programa de Pós-Graduação em Farmacologia, and UNIVERSIDADE ESTADUAL DE CAMPINAS
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Matrix metalloproteinase ,Aterosclerose ,Pharmacogenetic ,Farmacogenética ,Haplotype ,Polimorfismo (Genética) ,Haplótipos ,Metaloproteinases da matriz ,Polymorphism ,Atherosclerosis - Abstract
Orientador: José Eduardo Tanus dos Santos Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas Resumo: A obesidade em crianças e adolescentes constitui-se num importante fator de risco para doenças cardiovasculares, em especial, aterosclerose. Esta condição é caracterizada por acúmulo de lipídeos e elementos fibrosos em artérias de grande calibre em que mecanismos inflamatórios e remodelamento vascular estão envolvidos. Neste contexto, a metaloproteinase-9 de matriz extracelular (MMP-9) - endopeptidase capaz de degradar componentes da matriz extracelular - e seu inibidor endógeno preferencial, inibidor tecidual de MMP (TIMP-1) são importantes mediadores deste remodelamento e um equilíbrio entre MMP-9 e TIMP-1 deve existir a fim de manter a integridade do sistema cardiovascular. Ademais, níveis aumentados de MMP-9 são observados em pacientes com doenças cardiovasculares e estudos genéticos têm mostrado ainda que polimorfismos funcionais no gene da MMP-9 têm sido relacionados à presença e severidade de doenças cardiovasculares. Contudo, ainda não se sabe como a associação desses polimorfismos com a obesidade infantil pode afetar as concentrações de MMP-9 no plasma. Logo, os objetivos desse trabalho foram: 1) comparar as concentrações plasmáticas de MMP-9, TIMP-1 e razão MMP-9/TIMP-1 (atividade líquida da MMP-9) entre crianças e adolescentes obesos e controles; 2) comparar as frequências genotípicas e haplotípicas dos polimorfismos C-1562T, -90(CA)14-24 e Q279R da MMP-9 entre obesos e controles e 3) correlacionar as concentrações de MMP-9 aos genótipos e haplótipos da MMP-9. Inicialmente, determinaram-se os níveis de pro-MMP-9 e no plasma, por zimografia, e as concentrações plasmáticas de MMP-9 e TIMP-1 em obesos e controles por ELISA. Nós não encontramos diferenças nas concentrações plasmáticas de MMP-9 e razão MMP-9/TIMP-1 entre obesos e controles. No entanto, nossos resultados revelaram que em obesos houve diminuição de TIMP-1. Em seguida, extraiu-se o DNA dos voluntários e determinaram-se as frequências genotípicas dos polimorfismos C -1562T e (CA)n, por PCR seguida de eletroforese, do polimorfismo Q279R, por PCR em tempo real, e as frequências haplotípicas, pelo programas PHASE. Não houve diferenças nas frequências genotípicas e haplotípicas entre os grupos. Nós avaliamos a relevância de diferentes genótipos e haplótipos nas concentrações plasmáticas de MMP-9. Para os polimorfismos C-1562T e Q279R, nós encontramos que no grupo de obesos, portadores dos genótipos CC apresentaram menores níveis de MMP-9 quando comparados aos portadores dos genótipos CT+TT e aos controles com mesmo genótipo. No grupo de obesos, portadores do genótipo QQ apresentaram menores níveis de MMP-9 quando comparados aos portadores do genótipo RR e aos controles com mesmo genótipo. Para o polimorfismo -90(CA) 14-24 não observamos diferenças nos níveis de MMP-9 entre os grupos genotípicos. Em relação aos haplótipos, no grupo de obesos, portadores do haplótipo H2 apresentaram menores concentrações de MMP-9 e da razão MMP-9/TIMP-1 (atividade líquida de MMP-9) quando comparados aos outros haplótipos e aos controles com mesmo haplótipo. No grupo controle, não observamos influência dos genótipos e haplótipos nas concentrações plasmáticas de MMP-9. Portanto, nossos achados que sugerem que genótipos (CC e QQ) e o haplótipo H2 podem diminuir os níveis circulantes de MMP-9 em crianças e adolescentes obesos, mas não em crianças saudáveis, consequentemente, estes genótipos e haplótipo poderiam oferecer proteção contra doenças cardiovasculares somente em crianças obesas Abstract: The childhood obesity is important risk factor for cardiovascular diseases, in particular, atherosclerose. This condition is characterized by the accumulation of lipids and fibrous elements in the large arteries in which inflammatory mechanisms and vascular remodeling are involved. In this context, matrix metalloproteinase 9 (MMP-9) - endopeptidade capable of degrading components of extracellular matrix - and its endogenous inhibitor preferential, the tissue inhibitors of MMP (TIMP-1) are important mediators of this remodeling and a critical equilibrium between MMP-9 and TIMP-1 must exist in order to maintain the integrity of cardiovascular system. Moreover, elevated levels of MMP-9 have been reported in patients with cardiovascular diseases, and genetic studies showing that functional polymorphism MMP-9 gene were related to presence and severity of cardiovascular diseases. However, it remains unclear how the association of these polymorphisms with childhood obesity can affect MMP-9 plasma concentrations. Thus, the objectives of this study were: 1) to compare plasma MMP-9, TIMP-1 and MMP-9/TIMP-1(activity) ratio between obese and control groups; 2) to compare the genotype and haplotype frequencies of MMP-9 polymorphisms (C-1562T and (CA)14-24 and Q279R) between obese and control and, 3) correlate the MMP-9 concentrations with MMP-9 genotypes and haplotypes. To achieve our first goal, we determined the plasma pro-MMP-9 levels by zymography, and plasma MMP-9 and TIMP-1 concentrations by ELISA in obese and control. We not found differences in MMP-9 plasma concentratios and MMP-9/TIMP-1 between obese and control. However, our results showed that obese had lower plasma TIMP-1 concentrations than control. Moreover, to achieve our second goal, we firstly extracted DNA from volunteers, and then we determined the genotype frequencies of C-1562T and (CA)14-24 polymorphisms by PCR followed by electrophoresis, of and Q279R polymorphism by real time PCR, and the haplotype frequencies by the programs PHASE. We found similar genotype and allelic distribution for the three polymorphisms when study groups were compared. We evaluated the relevance of different genotypes in plasma MMP-9 concentrations in study groups. To the C-1562T and Q279R polymorphisms, we found that in the obese group, CC genotype carries had lower MMP-9 levels when compared with CT+TT genotype carries and control with the same genotype. In the obese group, QQ genotype carries had lower MMP-9 levels when compared with RR genotype carries and control the same genotype. To the -90(CA)14-24 polymorphism, we did not observe differences in the MMP-9 levels among different genotypic groups. In relation to haplotypes, we found that in the obese group, H2 haplotype carriers had lower MMP-9 levels and MMP-9/TIMP-1 ratio when compared other haplotypes and control with the same haplotype. Therefore, our findings suggest that (CC and QQ) genotypes and H2 haplotype decrease circulating MMP-9 levels in obese but not in healthy children, thus genotypes and haplotype could offer protection against cardiovascular diseases in those children Mestrado Farmacologia Doutor em Farmacologia
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- 2021
48. Low MBL-associated serine protease 2 ( MASP-2) levels correlate with urogenital schistosomiasis in Nigerian children.
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Ojurongbe, Olusola, Antony, Justin S., Van Tong, Hoang, Meyer, Christian G., Akindele, Akeem A., Sina ‐ Agbaje, Olawumi R., Kremsner, Peter G., and Velavan, Thirumalaisamy P.
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SERINE proteinases , *SCHISTOSOMIASIS in children , *NIGERIANS , *MANNOSE-binding lectins , *BLOOD serum analysis , *GENETIC polymorphisms , *DISEASES - Abstract
Objectives The human mannose-binding lectin ( MBL) and ficolins ( FCN) are involved in pathogen recognition in the first line of defence. They support activation of the complement lectin cascade in the presence of MBL-associated serine protease 2 ( MASP-2), a protein that cleaves the C4 and C2 complement components. Recent studies found that distinct MBL2 and FCN2 promoter variants and their corresponding serum levels are associated with relative protection from urogenital schistosomiasis. Methods We investigated the contribution of MASP-2 levels and MASP2 polymorphisms in a Nigerian study group, of 163 individuals infected with Schistosoma haematobium and 183 healthy subjects. Results MASP-2 serum levels varied between younger children (≤12 years) and older children (>12 years) and adults ( P = 0.0001). Younger children with a patent infection had significantly lower MASP-2 serum levels than uninfected children ( P = 0.0074). Older children and adults (>12 years) with a current infection had higher serum MASP-2 levels than controls ( P = 0.032). MBL serum levels correlated positively with MASP-2 serum levels ( P = 0.01). MASP2 secretor haplotypes were associated with MASP-2 serum levels in healthy subjects. The heterozygous MASP2 p.P126L variant was associated with reduced serum MASP-2 levels ( P = 0.01). Conclusions The findings indicate that higher MASP-2 serum levels are associated with relative protection from urogenital schistosomiasis in Nigerian children. [ABSTRACT FROM AUTHOR]
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- 2015
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49. Cambios genéticos temporales y microgeográficos de Aedes aegypti en Medellín, Colombia.
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Cadavid, Jorge Mario, Rúa, Guillermo, Campo, Omer, Bedoya, Gabriel, and Rojas, Winston
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Copyright of Biomédica: Revista del Instituto Nacional de Salud is the property of Instituto Nacional de Salud of Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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- 2015
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50. Comparación de las técnicas de secuenciación y algoritmos de detección de variantes estucturales y haplotipos utilizados en el diagnóstico genético
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Cañizares Sales, Joaquín, Blanca Postigo, José Miguel, Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia, Universitat Politècnica de València. Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural - Escola Tècnica Superior d'Enginyeria Agronòmica i del Medi Natural, Carrión García, Ana Esther, Cañizares Sales, Joaquín, Blanca Postigo, José Miguel, Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia, Universitat Politècnica de València. Escuela Técnica Superior de Ingeniería Agronómica y del Medio Natural - Escola Tècnica Superior d'Enginyeria Agronòmica i del Medi Natural, and Carrión García, Ana Esther
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[ES] El ser capaz de identificar el haplotipo de un individuo, así como las numerosas variaciones estructurales que se pueden encontrar en las secuencias genéticas, es uno de los desafíos primordiales con los que se enfrenta la genómica y quizás en mayor medida la bioinformática actualmente. Desde que se secuenciara la primera cadena de material genético, hasta hoy en día, las tecnologías de secuenciación han evolucionado inmensamente, como también lo han hecho la cantidad de datos que somos capaces de obtener con una sola secuenciación. Es por ello, que se han desarrollado y se están desarrollando numerosas aproximaciones y algoritmos, capaces de ordenar y analizar estos datos, de los que posteriormente extraer ciertas conclusiones (detección de haplotipos y variantes estructurales). Es aquí dónde nos encontramos con uno de los objetivos principales de este trabajo de revisión: hacer un estudio exhaustivo tanto de las tecnologías de secuenciación que están siendo utilizadas actualmente como de los algoritmos asociados y comprarlos entre ellos. Además, examinaremos la aplicación de estas tecnologías genómicas, desde un punto de visto clínico y particular: el proto-onco gen RET. Este gen que codifica para un receptor de membrana de tipo tirosina-quinasa y es diana de muchas mutaciones, causantes de diversas enfermedades, entre ellas el síndrome Hirschsprung. Desde que se propusiera este gen como candidato de estas enfermedades, se han llevado a cabo numerosos estudios que han realizado aproximaciones genómicas para determinar cuáles son las variantes estructurales responsables de dichas enfermedades. Nuestra intención es entender como la diversidad de aproximaciones y algoritmos han hecho posible obtener un diagnóstico, con metodologías distintas, dependiendo tanto de las características de las experiencias realizadas como del momento temporal de cada de estudio. Por último, se pretende también poner en práctica los conocimientos bibliográficos obtenidos, para propon, [EN] Determining which variants have a common inheritance and where they are located in the genome is known as haplotype assembly. Knowing an individual's haplotype greatly facilitates the work capacity of association studies, being a great tool in phylogenetics and clinical diagnosis, however, it is not a simple task. Many efforts have been done for years on the determination of haplotypes, since the first genome haplotype map (HapMap) was created in 2003. Today the predominant approaches are those based on the molecular readings generated by sequencing technologies. This means that being able to determine the haplotype depends greatly on the type of sequence being worked with. Up to a few year ago, the algorithms were programmed to work with short readings produced by 'Next Generation Sequencing' technologies, being able to cope with the most common errors in these readings. However, these sequences cause a lot of information to be lost throughout the genome, as most of them are incapable of covering more than one heterozygous variant, in addition to their difficulty in mapping complex genomes such as the human one, directly affecting the quality of the haplotype that can be generated from this type of reading. For this and other reasons, haplotype assembly algorithms have evolved to be able to work with long readings produced by third generation technologies, avoiding the limitations of short readings, but coping with others, such as the high error rate of some of these technologies. In the present review it is proposed to analyze and explain each of the algorithms developed for this purpose, as well as to compare their operation and impact on the scientific literature. Furthermore, how the quality of the final haplotype can vary is also studied, with the combination of the most innovative sequencing methodologies such as Hi-C and StrandSeq. An approach deduced as optimal from the literature is also proposed.
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- 2020
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