182 results on '"Base Sequence"'
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2. Análisis genómico comparativo con especies y subgenotipos del apicomplexa Cryptosporidium
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Arias Agudelo, Laura Marcela and Galván Díaz, Ana Luz
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Cryptosporidium parvum ,Biología molecular ,id.nlm.nih.gov/mesh/D016785 [http] ,Molecular biology ,Genómica ,Secuenciación de nucleótidos de alto rendimiento ,id.nlm.nih.gov/mesh/D019295 [http] ,Cryptosporidium ,Genomics ,id.nlm.nih.gov/mesh/D001483 [http] ,Variación genética ,Base sequence ,id.nlm.nih.gov/mesh/D014644 [http] ,id.nlm.nih.gov/mesh/D003458 [http] ,id.nlm.nih.gov/mesh/D023281 [http] ,Computational biology ,id.nlm.nih.gov/mesh/D059014 [http] ,Biología computacional ,Secuencia de bases ,Genetic variation ,id.nlm.nih.gov/mesh/D008967 [http] ,High-throughput nucleotide sequencing - Abstract
RESUMEN: Cryptosporidium es un apicomplexa asociado con diarrea, principalmente en niños y pacientes inmunocromprometidos. En la actualidad se describen 38 especies que difieren en cuanto a la especificidad de hospedero, hábitat, distribución geográfica y virulencia. Además, se han descrito subgenotipos que representan variaciones intraespecie basadas en el polimorfismo del gen gp60. Aunque se tienen disponibles genomas de diferentes especies y subgenotipos, son escasos los análisis comparativos que estudien las bases genéticas que expliquen las diferencias interespecie e intragenotípicas descritas para este protozoo. Teniendo en cuenta lo anterior, y con el propósito de contribuir al conocimiento de la genómica y taxonomía en este género, se realizó un estudio comparativo y filogenómico con 23 genomas de las especies más frecuentes en humanos: C. hominis, C. parvum y C. meleagridis. Los genomas analizados presentaron un tamaño aproximado de 9,0Mb. Se observaron porcentajes de identidad frente al genoma de referencia C. parvum Iowa II del 96,8% en los aislados de C. hominis y 91,5% en C. meleagridis. En C. parvum se identificaron porcentajes de identidad entre un 99,7 y 99,9% para aislados zoonóticos y del 99,5% para antroponóticos. Además, en esta especie se identificó una mayor acumulación de variantes de un solo nucleótido (SNVs) en aislamientos antroponóticos en comparación con los zoonóticos. La mayoría de los SNVs e inserciones y deleciones (indels) se encontraron en regiones codificantes, observándose una distribución homogénea en los cromosomas de C. parvum, mientras que en C. hominis y C. meleagridis predominaron en los cromosomas 1 y 3. Los genes con cambios deletéreos e indels anotados, están asociados con el procesamiento de la información genética, procesos enzimáticos y metabólicos; no obstante, alrededor del 50% de los genes codifican proteínas hipotéticas. El análisis filogenómico se realizó a partir de una matriz generada con 800.861 SNVs. El árbol obtenido mostró tres cladas monofiléticas para todos los aislados, observándose la presencia de dos ramas separadas para los aislados antroponóticos y zoonóticos de C. parvum. Todos los genomas de C. hominis y C. parvum se agruparon de acuerdo con la familia de subgenotipos basada en el gen gp60. Hasta el momento, este estudio es el análisis filogenómico y comparativo más robusto realizado en el género Cryptosporidium, que incluye genomas completos de diferentes aislados, familias alélicas y subgenotipos de las tres principales especies intestinales de Cryptosporidium asociadas con infección en el hombre. ABSTRACT: Cryptosporidium is an apicomplexan associated with diarrhea mainly in children and immunocompromised patients. Currently, there are 38 species that differ in host specificity, habitat, geographic distribution, and virulence. Additionally, subtype families that show intraspecies variations based on the polymorphism of the gp60 gene are described. Although genomes of several species and subtypes are available, a comparative analysis that explores the genetic bases of the phenotypic differences within the genus are scarce. According to the above, and to contribute to the knowledge of genomics and taxonomy in Cryptosporidium, a comparative and phylogenomic study was conducted with 23 genomes of the most frequent species in humans: C. hominis, C. parvum, and C. meleagridis
- Published
- 2020
3. Genetic variability of Aedes aegypti in the department of Sucre, Colombia, by analysis of the nucleotide sequence of the mitochondrial ND4 gene
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Maria Claudia Atencia, María de Jesús Pérez, Sandy Milena Caldera, María Cristina Jaramillo, and Eduar Elias Bejarano
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lcsh:Arctic medicine. Tropical medicine ,Base Sequence ,lcsh:RC955-962 ,fungi ,lcsh:R ,lcsh:Medicine ,Genetic Variation ,ADN mitocondrial ,Colombia ,DNA, Mitochondrial ,dengue ,Aedes/genetics ,Culicidae ,Aedes ,DNA mitocondrial ,Animals ,Aedes/genética - Abstract
Resumen Introducción. Aedes aegypti es la especie de mosquito de mayor relevancia en América por transmitir los virus del dengue, del Zika, del chikungunya y de la fiebre amarilla. Tanto factores ecológicos como el control químico, pueden influir en la composición genética de las poblaciones de Ae. aegypti, por lo cual es necesaria su caracterización. Objetivo. Determinar la variabilidad genética de las poblaciones de Ae. aegypti en cuatro municipios del departamento de Sucre, Colombia. Materiales y métodos. Larvas de Ae. aegypti, recolectadas en los municipios de Sincelejo, Sampués, Corozal y Guaranda del departamento de Sucre, fueron criadas en laboratorio hasta el estado adulto. Como marcador genético, se utilizó un segmento del gen mitocondrial ND4, que codifica para la subunidad 4 de la enzima NADH-deshidrogenasa. El análisis genético incluyó la estimación de parámetros de diversidad de nucleótidos, haplotipos, de estructura genética y de flujo de genes. Resultados. Se obtuvieron 108 secuencias parciales de 357 nucleótidos y cuatro haplotipos de nucleótidos del gen ND4 de Ae. aegypti. Se encontró una diferenciación genética significativamente alta entre las poblaciones de Sampués y Guaranda mediante el índice de fijación (F ST =0,59467), las de Sincelejo y Sampués (F ST = 0,25637), y las de Corozal y Guaranda (F ST = 0,22237). Se evidenció un gran flujo de genes (Nm=infinito) entre las poblaciones de Sincelejo y Corozal. Conclusión. Existen diferencias genéticas entre las poblaciones del mosquito Ae. aegypti de los municipios del departamento de Sucre. Se registra la presencia de un nuevo haplotipo del gen mitocondrial ND4 de Ae. aegypti en Colombia, el cual fue detectado en el municipio de Sincelejo. Abstract Introduction. Aedes aegypti is the most important mosquito species in America for the transmission of viruses of dengue, Zika, Chikungunya and yellow fever. Ecological factors as well as chemical controls can affect the genetic composition of Ae. aegypti populations, which is why its genetic characterization is necessary. Objective. To determine the genetic variability of Ae. aegypti populations in four municipalities of Sucre department, Colombia. Materials and methods. Larvae of Ae. aegypti, collected in the municipalities of Sincelejo, Sampués, Corozal and Guaranda, Sucre department, were reared under laboratory conditions to adult stage. A segment of the mitochondrial ND4 gene which codes for the subunit 4 of the enzyme NADH-dehydrogenase was used as genetic marker. The genetic analysis included the estimation of parameters of nucleotide and haplotype diversity, genetic structure and gene flow. Results. One hundred and eight partial sequences of 357 nucleotides and four nucleotide haplotypes of the ND4 gene of Ae. aegypti were obtained. A significantly high genetic differentiation was found between the Sampués and Guaranda populations (F ST =0.59467),Sincelejo and Sampués (F ST =0.25637), and Corozal and Guaranda (F ST =0.22237). A high gene flow (Nm=infinite) was observed among the populations of Sincelejo and Corozal. Conclusion. There are genetic differences between the Ae. aegypti populations from the municipalities of Sucre department. The presence of a new haplotype of the mitochondrial ND4 gene of Ae. aegypti in Colombia was recorded, detected in the municipality of Sincelejo.
- Published
- 2018
4. Especies de flebotomíneos (Diptera: Psychodidae) recolectados en reservas naturales de las regiones del Darién y del Pacífico en Colombia
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María Angélica Contreras, Iván D. Vélez, Sandra Uribe, Juan David Suaza, Rafael José Vivero, and Charles H. Porter
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0301 basic medicine ,natural reservations, Colombia ,lcsh:Arctic medicine. Tropical medicine ,lcsh:RC955-962 ,Parks, Recreational ,030231 tropical medicine ,Leishmaniasis, Cutaneous ,lcsh:Medicine ,Zoology ,Colombia ,Forests ,General Biochemistry, Genetics and Molecular Biology ,Electron Transport Complex IV ,03 medical and health sciences ,0302 clinical medicine ,Species Specificity ,Genus ,Sequence Homology, Nucleic Acid ,medicine ,Animals ,Psychodidae ,Neighbor joining ,Phylogeny ,Leishmania ,Base Sequence ,Ecology ,biology ,lcsh:R ,Dendrogram ,Leishmaniasis ,Vegetation ,biology.organism_classification ,medicine.disease ,Insect Vectors ,reservas naturales, Colombia ,030104 developmental biology ,Geography ,Vector (epidemiology) ,Insect Proteins ,Animal Distribution ,Sequence Alignment - Abstract
Resumen Introducción. Los departamentos de Chocó y Antioquia en Colombia presentan condiciones climáticas y de vegetación que favorecen el establecimiento de especies de vectores del género Lutzomyia y la transmisión de Leishmania spp. a poblaciones humanas que ingresan a ambientes selváticos conservados. Objetivo. Reportar las especies de flebotomíneos presentes en tres reservas naturales de las regiones del Darién y del Pacífico en Colombia. Materiales y métodos. Los flebotomíneos se recolectaron en las reservas naturales El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) y Tulenapa (Carepa, Antioquia). La recolección se hizo con trampas de luz CDC, mediante búsqueda activa en sitios de reposo y con trampas Shannon. La determinación taxonómica de especies se basó en las claves taxonómicas. En algunas especies de interés taxonómico, se evaluó el uso de secuencias parciales de la región 5’ del gen COI. Resultados. Se recolectaron 611 flebotomíneos adultos: 531 en Acandí, 45 en Carepa y 35 en Bahía Solano. Se identificaron 17 especies del género Lutzomyia, tres del género Brumptomyia y una del género Warileya. Las distancias genéticas (K2P) y los soportes de agrupación (>99 %) en el dendrograma de neighbor joining correspondieron a la mayoría de unidades taxonómicas operacionales moleculares (Molecular Operational Taxonomic Units, MOTU) establecidas para el grupo Aragaoi y confirmaron claramente la identidad de Lu. coutinhoi. Conclusión. Se identificaron especies que tienen importancia en la transmisión de la leishmaniasis en Acandí, Bahía Solano y Carepa. Se confirmó la presencia de Lu. coutinhoi en Colombia. Abstract Introduction: The departments of Chocó and Antioquia in Colombia show climatic and vegetation conditions favoring the establishment of vector species of the genus Lutzomyia and the transmission of Leishmania spp. to human populations entering conserved forest environments. Objective: To report the species of Phlebotomine sandflies present in three natural reserves in the Darien and Pacific regions of Colombia. Materials and methods: Sand flies were collected specifically in the natural reserves El Aguacate (Acandí, Chocó), Nabugá (Bahía Solano, Chocó) and Tulenapa (Carepa, Antioquia). Sand flies were collected with CDC light traps, active search in resting places and Shannon traps. The taxonomic determination of species was based on taxonomic keys. For some species of taxonomic interest, we evaluated the partial sequences of the 5’ region of COI gene. Results: A total of 611 adult sand flies were collected: 531 in Acandí, 45 in Carepa and 35 in Bahía Solano. Seventeen species of the genus Lutzomyia, three of the genus Brumptomyia and one of the genus Warileya were identified. The genetic distances (K2P) and grouping supported (>99%) in the neighbor joining dendrogram were consistent for most established molecular operational taxonomic units (MOTU) of the Aragaoi group and clearly confirmed the identity of Lu. coutinhoi. Conclusion: Species that have importance in the transmission of leishmaniasis in Acandí, Bahía Solano and Carepa were identified. The presence of Lu. coutinhoi was confirmed and consolidated in Colombia.
- Published
- 2017
5. SARS-CoV-2 sequencing: The technological initiative to strengthen early warning systems for public health emergencies in Latin America and the Caribbean
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Álvarez-Díaz DA, Laiton-Donato K, Franco-Muñoz C, and Mercado-Reyes M
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- Base Sequence, COVID-19, Caribbean Region, Communicable Diseases, Emerging, Coronavirus Infections prevention & control, Coronavirus Infections virology, Disaster Planning, Disease Outbreaks, Humans, Latin America epidemiology, Molecular Epidemiology methods, Pneumonia, Viral prevention & control, Pneumonia, Viral virology, Procedures and Techniques Utilization, Public Health, RNA-Seq, SARS-CoV-2, Sustainable Development, Virus Diseases epidemiology, Betacoronavirus genetics, Coronavirus Infections epidemiology, Genome, Viral, Information Dissemination, Molecular Epidemiology trends, Pandemics prevention & control, Pneumonia, Viral epidemiology, Population Surveillance, RNA, Viral genetics, Sequence Analysis, RNA
- Abstract
The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.
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- 2020
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6. Prevalencia y factores asociados a la infección por toxoplasma gondii en carne procedente de plantas de beneficio animal con destino nacional
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Franco Hernández, Erika Natalia, Gómez Marín, Jorge Enrique (Thesis advisor), and Cortés Vecino, Jesús Alfredo
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Polymerase Chain Reaction (PCR) ,ADN ,Meet ,57 Ciencias de la vida ,Biología / Life sciences ,biology ,Toxoplasma gondii ,Reacción en cadena de la polimerasa (PCR) ,35 Administración pública y ciencia militar / Public administration and military science ,Base sequence ,Carne ,61 Ciencias médicas ,Medicina / Medicine and health ,Prevalence ,59 Animales / Animals ,Secuencia de bases ,Prevalencia - Abstract
La toxoplasmosis es la enfermedad parasitaria causada por Toxoplasma gondii, un protozoario de vida intracelular obligado que, en animales de sangre caliente como hospederos intermediarios, se encuentra en forma de quistes tisulares, con manifestaciones clínicas oculares y en sistema nervioso en personas inmunosuprimidas y en recién nacidos que la adquieren de forma congénita. El estudio buscó determinar la prevalencia de Toxoplasma gondii en la carne procesada en plantas de beneficio animal con destino a todo el país, usando la Prueba de Reacción en Cadena de la Polimerasa (PCR). Se realizó un estudio descriptivo de corte transversal. En muestras de carne se utilizó la prueba de PCR para detectar el gen B1, adicionalmente se secuenciaron algunas muestras positivas. También se realizó la trazabilidad de la procedencia de los animales. Se encontró una prevalencia de infección de T. gondii en la carne de 43,9%, en bovinos de 36,7%, en porcinos de 40% y en aves de 55%. Se confirmó la presencia del gen B1 en las secuencias amplificadas, lo que sugiere que la carne es una importante fuente de infección a considerar en los humanos si se consume poco cocinada o cruda. Abstract. Toxoplasmosis is the parasitical disease caused by Toxoplasma gondii, a protozoan of compelled intracellular life that, in warm blood animals as intermediary host, it is found as tisular cyst, with clinical ocular manifestations and in nervous system of immune suppressed people and in newborn that acquire it by congenital way. The research consist in determine Toxoplasma gondii prevalence in processed meat on animal profit plants destined to the whole country, using the polymerase chain reaction test (PCR). It was made a transverse section descriptive research. PCR was used in meat samples for gene B1 detection, some positive samples were arranged in sequence additionally. Animals origin traceable research was also did. It was found a prevalence of T. gondii infection in meat of 43,9%, in bovines of 36,7%, in hog of 40% and in poultry of 55%. Presence of gene B1 was confirmed on amplified sequences which suggest that meat is an infection source in human beings to consider if it´s consumed undercooked or raw. Maestría
- Published
- 2015
7. A common Salmonella Enteritidis sequence type from poultry and human gastroenteritis in Ibagué, Colombia
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Fandiño LC and Verjan N
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- Animals, Base Sequence, Colombia epidemiology, Cross-Sectional Studies, Drug Resistance, Microbial, Egg Shell microbiology, Feces microbiology, Gastroenteritis epidemiology, Gastroenteritis veterinary, Humans, Multilocus Sequence Typing, Phylogeny, Poultry, Poultry Diseases epidemiology, Salmonella Food Poisoning epidemiology, Salmonella Infections, Animal epidemiology, Salmonella enteritidis classification, Salmonella enteritidis drug effects, Salmonella enteritidis isolation & purification, Sequence Analysis, DNA, Serogroup, DNA, Bacterial genetics, Gastroenteritis microbiology, Poultry Diseases microbiology, Salmonella Food Poisoning microbiology, Salmonella Infections, Animal microbiology, Salmonella enteritidis genetics
- Abstract
Salmonella Enteritidis es una de las mayores causas de salmonelosis en el mundo, siendo los huevos contaminados y la carne de pollo cruda sus principales fuentes de infección. En Ibagué, Colombia, se identificaron los principales serovares circulando en granjas, superficies de huevos y canales de pollo, sin embargo, se desconoce si esos serovares son responsables de gastroenteritis. Objetivo. Evaluar la relación genética entre aislamientos de Salmonella Enteritidis de aves de corral y humanos con gastroenteritis mediante multilocus sequence typing (MLST). Materiales y métodos. Se aisló Salmonella spp., de casos clínicos de gastroenteritis (n=110). Se realizó test de sensibilidad antibiótica, seguido de serotipificación y tipificación por medio de MLST y se comparó S. Enteritidis de humanos frente a S. Enteritidis de granjas ponedoras y de huevo comercializado (n=6). Resultados. Se aislaron 10 cepas de Salmonella spp., a partir de heces de humanos con gastroenteritis. Se obtuvo una prevalencia de Salmonella spp. de 9.09%, siendo S. Enteritidis (n=4), S. Typhymurium (n=2), S. Newport (n=1), S. Grupensis (n=1), S. Uganda (n=1) y S. Braenderup (n=1) los serotipos presentes en pacientes con gastroenteritis. El MLST indico que un tipo de secuencia común (ST11) de S. Enteritidis estuvo presente en todas las tres fuentes y mostraron el mismo patrón de resistencia antibiótica. Conclusión. S. Enteritidis ST11 constituye un vínculo entre el consumo/manipulación de huevos contaminados y gastroenteritis humana en Ibagué. Son necesarios estudios complementarios para conocer si otros serovares de Salmonella aislados de carne de pollo cruda también se asocian con la gastroenteritis humana.
- Published
- 2019
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8. Comparative evaluation of the identification of rapidly growing non-tuberculous mycobacteria by mass spectrometry (MALDI-TOF MS), GenoType Mycobacterium CM/AS assay and partial sequencing of the rpoβ gene with phylogenetic analysis as a reference method.
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Costa-Alcalde JJ, Barbeito-Castiñeiras G, González-Alba JM, Aguilera A, Galán JC, and Pérez-Del-Molino ML
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- Bacteriological Techniques methods, Base Sequence, DNA, Bacterial analysis, Genotype, Humans, Nontuberculous Mycobacteria physiology, Phylogeny, Bacterial Proteins genetics, DNA-Directed RNA Polymerases genetics, Nontuberculous Mycobacteria genetics, Nontuberculous Mycobacteria isolation & purification, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Abstract
Introduction: The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant non-tuberculous mycobacteria (NTM) should be identified to the species level in order to determine their clinical significance. The aim of this study was to evaluate identification of rapidly growing NTM (RGM) isolated from clinical samples by using MALDI-TOF MS and a commercial molecular system. The results were compared with identification using a reference method., Methods: We included 46 clinical isolates of RGM and identified them using the commercial molecular system GenoType
® CM/AS (Hain, Lifescience, Germany), MALDI-TOF MS (Bruker) and, as reference method, partial rpoβ gene sequencing followed by BLAST and phylogenetic analysis with the 1093 sequences available in the GeneBank., Results: The degree of agreement between GenoType® and MALDI-TOF MS and the reference method, partial rpoβ sequencing, was 27/43 (62.8%) and 38/43 cases (88.3%) respectively. For all the samples correctly classified by GenoType® , we obtained the same result with MALDI-TOF MS (27/27). However, MALDI-TOF MS also correctly identified 68.75% (11/16) of the samples that GenoType® had misclassified (p=0.005)., Conclusions: MALDI-TOF MS classified significantly better than GenoType® . When a MALDI-TOF MS score >1.85 was achieved, MALDI-TOF MS and partial rpoβ gene sequencing were equivalent. GenoType® was not able to distinguish between species belonging to the M. fortuitum complex. MALDI-TOF MS methodology is simple, rapid and associated with lower consumable costs than GenoType® . The partial rpoβ sequencing methods with BLAST and phylogenetic analysis were not able to identify some RGM unequivocally. Therefore, sequencing of additional regions would be indicated in these cases., (Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.)- Published
- 2019
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9. Identification of a new variant of Chlamydia trachomatis in Mexico.
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Escobedo-Guerra MR, Katoku-Herrera M, Lopez-Hurtado M, Villagrana-Zesati JR, de Haro-Cruz MJ, and Guerra-Infante FM
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- Bacterial Outer Membrane Proteins genetics, Bacterial Proteins genetics, Base Sequence, Chlamydia Infections epidemiology, Chlamydia trachomatis genetics, Chlamydia trachomatis isolation & purification, Computer Simulation, Female, Genotype, Humans, Infertility, Female epidemiology, Infertility, Female microbiology, Integrases genetics, Mexico epidemiology, Phylogeny, Plasmids genetics, Polymerase Chain Reaction, Sequence Alignment, Sequence Deletion, Sequence Homology, Nucleic Acid, Serogroup, Uterine Cervicitis epidemiology, Uterine Cervicitis microbiology, Chlamydia Infections microbiology, Chlamydia trachomatis classification, DNA, Bacterial genetics, Open Reading Frames genetics
- Abstract
Introduction: Chlamydia trachomatis is one of the main etiological agents of sexually transmitted infections worldwide. In 2006, a Swedish variant of C. trachomatis (Swedish-nvCT), which has a deletion of 377bp in the plasmid, was reported. In Latin America, Swedish-nvCT infections have not been reported. We investigated the presence of Swedish-nvCT in women with infertility in Mexico., Methods: Swedish-nvCT was searched in 69C. trachomatis positive samples from 2339 endocervical specimens. We designed PCR primers to identify the deletion in the plasmid in the ORF1, and the presence of a repeated 44bp in the ORF3. The sample with the deletion was genotyped with the genes of the major outer membrane protein A (ompA) and the polymorphic membrane protein (pmpH)., Results: The deletion was detected in one of the 69 samples positive C. trachomatis of 2339 endocervical exudates. The nucleotide sequence analysis of the ompA shows a high degree of similarity with the Swedish nvCT (98%), however the variant found belongs to serovar D. The nucleotide sequence of the pmpH gene associates to the variant found in the genitourinary pathotype of the Swedish-nvCT but in different clusters., Conclusions: Our results revealed the presence of a new variant of C. trachomatis in Mexican patients. This variant found in Mexico belongs to serovar D based on the in silico analysis of the ompA and pmpH genes and differs to the Swedish-nvCT (serovars E). For these variants of C. trachomatis that have been found it is necessary to carry out a more detailed analysis, although the role of this mutation has not been demonstrated in the pathogenesis., (Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.)
- Published
- 2019
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10. Endocrine disruption in thicklip grey mullet (Chelon labrosus) from the Urdaibai Biosphere Reserve (Bay of Biscay, Southwestern Europe)
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Pilar Aragón, Carmen Domínguez, Denise Fernandes, Cinta Porte, Julia Atienza, Miren P. Cajaraville, Eunate Puy-Azurmendi, Marta Villagrasa, Ángel Maquieira, Josep M. Bayona, Damià Barceló, Maren Ortiz-Zarragoitia, Marina Kuster, Rosa Puchades, and Miren López de Alda
- Subjects
Male ,endocrine system ,medicine.medical_specialty ,Geologic Sediments ,Environmental Engineering ,Gonad ,Transcription, Genetic ,Disorders of Sex Development ,Estrogen receptor ,Enzyme-Linked Immunosorbent Assay ,Vitellogenin ,Endocrine Disruptors ,Gas Chromatography-Mass Spectrometry ,Vitellogenins ,Expression of aromatase and nuclear receptors ,Internal medicine ,QUIMICA ANALITICA ,medicine ,Environmental Chemistry ,Endocrine system ,Animals ,RNA, Messenger ,Waste Management and Disposal ,DNA Primers ,Endocrine disruptors in sediments and fish bile ,biology ,Base Sequence ,Chelon ,Urdaibai Biosphere Reserve ,Thicklip grey mullet Chelon labrosus ,biology.organism_classification ,Pollution ,Smegmamorpha ,Europe ,medicine.anatomical_structure ,Endocrinology ,Endocrine disruptor ,biology.protein ,Female ,Intersex gonad ,Thicklip grey mullet ,Estuaries ,Water Pollutants, Chemical ,Hormone - Abstract
Endocrine disruptors (EDs) interfere with the development and functioning of the endocrine system, causing reproductive disturbance in aquatic wildlife. The aim of the present work was to determine the presence of EDs in sediments and to investigate possible exposure and effects of EDs in the estuary of the Urdaibai Biosphere Reserve (Gernika) in comparison with the Arriluze marina. For this, gonad histology, plasma vitellogenin (VTG) protein levels and mRNA levels of vitellogenin (vtg), cyp19 aromatases, estrogen receptor (er) and retinoid X receptor (rxr) were studied in Chelon labrosus. The presence of alkylphenols (APs) in fish bile was also assessed. In sediments, estrogenic hormones were below the detection limit and levels of bisphenol A were very low. In Gernika organotin compounds were low but in Arriluze levels of up to 12 μg/g were found. Moderate levels of APs and phthalate levels of up to 8 μg/g were found in sediments. In fish, a high prevalence up to 33% of intersex gonads was found in Gernika, whereas only one intersex was found in Arriluze. Accordingly, mullets from Gernika showed higher concentrations of APs in bile. VTG protein levels were detected not only in females but also in some undifferentiated, male and intersex fish. mRNA of vtg was detected in one male from Gernika. mRNA of er and rxr showed significant differences between seasons. In conclusion, the present study demonstrated that C. labrosus from the Urdaibai estuary were exposed to EDs and showed clear signs of endocrine disruption., This work was supported by Catedra UNESCO of the University of the Basque Country (UPV/EHU) through the project DERBiUr (UNESCO06/19), by the University of the Basque Country through a grant to the Unit of Formation and Research (UFI 11/37), by the Basque Government through the project ETORTEK-IMPRES and a grant to consolidated research groups (GIC07/26-IT-393-07), and by MICINN through the projects CEMAGUA (CGL2007-64551/HID) and SCARCE (Consolider-Ingenio 2010 CSD2009-00065). Denise Fernandes acknowledges a postdoctoral fellowship (SFRH/BPD/34289/2006) from the Portuguese Fundacao para a Ciencia e Tecnologia (FCT) of the Ministry of Science and Technology of Portugal. The help of Drs. T. Serrano and M.C. Barbero with the examination of gonad preparations is greatly acknowledged.
- Published
- 2013
11. Production of the biotechnologically relevant AFP from Aspergillus giganteus in the yeast Pichia pastoris
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José G. Gavilanes, James M. Manning, Vivian de los Ríos, Blanca San Segundo, Ana Moreno, Álvaro Martínez-del-Pozo, and Belén López-García
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Bioquímica ,Antifungal Agents ,Molecular Sequence Data ,Mutagenesis (molecular biology technique) ,Peptide ,Pichia ,Pichia pastoris ,Fungal Proteins ,Fusarium ,Amino Acid Sequence ,Cysteine-rich ,Peptide sequence ,neoplasms ,chemistry.chemical_classification ,Fungal protein ,Antifungals ,Biología molecular ,biology ,Base Sequence ,digestive, oral, and skin physiology ,biology.organism_classification ,Yeast ,digestive system diseases ,Amino acid ,Aspergillus ,chemistry ,Biochemistry ,embryonic structures ,Antimicrobial ,Biotechnology - Abstract
El pdf del artículo es la versión pre-print., The mould Aspergillus giganteus produces a basic, low molecular weight protein (AFP) showing in vitro and in vivo antifungal properties against important plant pathogens. AFP is secreted as an inactive precursor containing an amino-terminal extension of six amino acids (If-AFP) which is later removed to produce the active protein. The molecular basis to explain this behavior and the features that determine the fungal specificity of this protein are not completely solved. In this work, the mature AFP (AFP*) and a version of AFP with an extended amino-terminal (proAFP) have been cloned and produced in the yeast Pichia pastoris. The two proteins have been purified to homogeneity and characterized from structural and functional points of view. AFP* produced is practically indistinguishable from the natural fungal protein in terms of its spectroscopic and antifungal properties while proAFP is mostly inactive under identical assay conditions. The availability of an active AFP protein produced in P. pastoris will allow getting further insights into the mode of action and targeting specificity of AFP by using site-directed mutagenesis approaches., This work was supported by Grants BFU2006- 04404 and BIO2006-05583 from the Ministerio de Educación y Ciencia (MEC) (Spain) and within the center CONSOLIDER on Agrigenomics (MEC) and the Xarxa de referencia en Biotecnología (Generalitat de Catalunya).
- Published
- 2010
12. Isla de patogenicidad de Vibrio parahaemolyticus en cepas chilenas clínicas y ambientales
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Harold Núñez, Carlos G. Osorio, María Teresa Ulloa, and Fabiola Guerra
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Vibrio parahaemolyticus ,Hemolysis, Vibrio ,Virulence ,food and beverages ,Hemolysin ,Genome, viral ,General Medicine ,Biology ,Pathogenicity ,biology.organism_classification ,law.invention ,Microbiology ,law ,Base sequence ,Polymerase chain reaction - Abstract
Background: Most clinical isolates of Vibrio parahaemolyticus produce a major virulence factor known as the thermostable direct hemolysin (TDH). TDH is encoded by the tdh gene which is located in a genomic pathogenicity island (PAI). Most environmental isolates are described as tdh negative. Aim: To assess if environmental strains lack the full pathogenicity island or if only the tdh gene is deleted. Material and methods: Thirty eight clinical and 66 environmental strains of Vibrio parahaemolyticus were studied. PAI was characterized by polymerase chain reaction (PCR). The presence of tdhA and tdhS genes, was determined by Southern blot. Results: Fifty three environmental strains (80%) lacked a full PAI when compared with clinical strains. In environmental strains, Southern blot and sequence analysis showed that a genetic región of 80 kilobase pairs including genes from VPA1310 to VPA1396 was missing. Conclusions: These results highlight the genetic dynamism of Vibrio parahaemolyticus pathogenecity island región and suggest that new pathogenic strains could appear by horizontal transfer of the island between toxigenic and non-toxigenic strains.
- Published
- 2009
13. [Differentiation of pathogenic leptospires spp by PCR of ligB gene and sequencing].
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Martínez ML, Grune Loffler S, Romero GN, and Brihuega BF
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- Animals, Base Sequence, Cattle, DNA Primers, Leptospira interrogans, Rats, Swine, Leptospira genetics, Leptospirosis diagnosis, Polymerase Chain Reaction
- Abstract
Leptospirosis is a zoonosis having worldwide distribution. The objective of this work was to develop a molecular technique to differentiate pathogenic Leptospira spp. A region of adhesin ligB, present only in the pathogenic species was amplified by PCR and sequenced. ligBRpet and ligBFpet primers were used, which amplified the target DNA from pathogenic L. interrogans reference strains serovars Pomona strain Pomona, Canicola strain Hond Utrecht IV, Copenhageni strain M 20, Wolffi strain 3705, Pyrogenes strain Salinem, Hardjo strain Hardjoprajitmo, L. borgpetersenii serovar Castellonis strain Castellon 3 and 4 pathogenic strains isolated from bovines, pigs, rats and opossums. L. biflexa serovars Patoc strain Patoc I and Andamana strain Andamana were not amplified. Sequencing of the amplified products exhibited sufficient variation among serovars, which differentiates them., (Copyright © 2017 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.)
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- 2018
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14. A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.
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Fernández-Caballero Rico JÁ, Chueca Porcuna N, Álvarez Estévez M, Mosquera Gutiérrez MDM, Marcos Maeso MÁ, and García F
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- Adult, Anti-HIV Agents pharmacology, Base Sequence, Drug Resistance, Viral genetics, HIV-1 classification, HIV-1 drug effects, Humans, Phylogeny, Sequence Analysis, DNA, Consensus Sequence, DNA, Viral genetics, HIV-1 genetics, High-Throughput Nucleotide Sequencing, Molecular Epidemiology methods
- Abstract
Objective: To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies., Material and Methods: Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies., Results: At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100)., Conclusion: A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies., (Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.)
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- 2018
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15. Multiple regulatory mechanisms act on the 5′ untranslated region of the S-Layer gene from Thermus thermophilus HB8
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Cristina Vallés, José Berenguer, Miguel A. de Pedro, Heinz Schwarz, Pablo Castán, Cristina Risco, and Luis Ángel Fernández
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Untranslated region ,Genética ,Five prime untranslated region ,Mutant ,Molecular Sequence Data ,Genetics and Molecular Biology ,Microbiology ,Bacterial Proteins ,Transcription (biology) ,Thermophilic ,Thermus ,Molecular Biology ,Gene ,Sequence Deletion ,Biologia molecular ,Regulation of gene expression ,Membrane Glycoproteins ,biology ,Base Sequence ,Three prime untranslated region ,Thermus thermophilus ,Membrane Proteins ,Gene Expression Regulation, Bacterial ,biology.organism_classification ,Molecular biology ,Genes, Bacterial ,5' Untranslated Regions ,Bacterias - Abstract
Producción Científica, The role of the 5′ untranslated region (5′UTR) of the S-layer gene from Thermus thermophilus was analyzed through the isolation of Δ5′UTR mutants. In these mutants the half-life ofsplA mRNA was strongly reduced and slpAtranscription was no longer subjected to growth phase-dependent repression. Overproduction and detachment of the external envelopes of the mutants were observed in stationary phase., Comisión Interministerial de Ciencia y Tecnología (Project BIO108-0183), Ministerio de Educación, Cultura y Deporte y Unión Europea (Proyect 2FD97-0127- C02-01)
- Published
- 2001
16. Prevalence of the Rhizobium etli-like allele in genes coding for 16S rRNA among the indigenous rhizobial populations found associated with wild beans from the Southern Andes in Argentina
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María Verónica López, Orlando Mario Aguilar, Matías Pagano, Pablo M. Riccillo, Daniel Horacio Grasso, Gabriel Favelukes, Ramón Bautista Gonzalez, and Alfred Pühler
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Rhizobiaceae ,Molecular Sequence Data ,Argentina ,Biology ,medicine.disease_cause ,Applied Microbiology and Biotechnology ,DNA, Ribosomal ,Phaseolus vulgaris ,Rhizobium etli ,Rhizobium leguminosarum ,Rhizobia ,Plant Microbiology ,RNA, Ribosomal, 16S ,Botany ,Nitrogenase ,medicine ,16S rRNA ,Symbiosis ,Ribosomal DNA ,Alleles ,Phylogeny ,Ciencias Exactas ,Plants, Medicinal ,Ecology ,Base Sequence ,food and beverages ,Fabaceae ,Genes, rRNA ,biochemical phenomena, metabolism, and nutrition ,biology.organism_classification ,DNA Fingerprinting ,Genes, Bacterial ,Rhizobium ,bacteria ,Phaseolus ,Oxidoreductases ,Food Science ,Biotechnology ,Plasmids - Abstract
A collection of rhizobial isolates from nodules of wild beans,Phaseolus vulgaris var. aborigineus, found growing in virgin lands in 17 geographically separate sites in northwest Argentina was characterized on the basis of host range, growth, hybridization to a nifH probe, analysis of genes coding for 16S rRNA (16S rDNA), DNA fingerprinting, and plasmid profiles. Nodules in field-collected wild bean plants were largely dominated by rhizobia carrying the 16S rDNA allele of Rhizobium etli. A similar prevalence of the R. etli allele was observed among rhizobia trapped from nearby soil. Intragroup diversity of wild bean isolates with either R. etli-like or Rhizobium leguminosarum bv. phaseoli-like alleles was generally found across northwest Argentina. The predominance of the R. etli allele suggests that in this center of origin of P. vulgaris the coevolution of Rhizobium spp. and primitive beans has resulted in this preferential symbiotic association, Instituto de Biotecnologia y Biologia Molecular
- Published
- 1998
17. [Phylogenetic analysis of South American sequences of the nonstructural protein-1 (ns1) of dengue serotype 2 associated with severe clinical bleeding].
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Castro-Orozco R, Castro-García LR, and Gómez-Camargo DE
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- Amino Acid Sequence, Base Sequence, Bayes Theorem, Humans, Serogroup, Severe Dengue complications, Viral Nonstructural Proteins classification, Dengue Virus genetics, Hemorrhage virology, Phylogeny, Severe Dengue virology, Viral Nonstructural Proteins genetics
- Abstract
Objective The objective of this in silico study was to compare nucleotide and amino acids DENV-2-NS1 sequences isolated from febrile patients, with and without disease severity, from different South American countries. Matherials and Methods A bayesian MCMC phylogenetic analysis was carried out using 28 complete sequences of the gene NS1 of the DENV-2 serotype (1 056 bp), using MrBayes v.3.2.0 software, with the model SYM+G (2.5 million generations). We also carried out a phylogenetic analysis with Neighbor-Joining method (Jukes-Cantor model). In addition, the amino acids sequences were aligned and compared with each other, using Clustal W included in MEGA v.5.2 software. Results In the amino acids sequences associated with bleeding, the most frequent substitution was isoleucine → threonine at posicion 93. These sequences showed a high percentage (94.6 %) of amino acid homology in comparison with the percentage of amino acids homology (74 %) of DENV-2 isolates not associated with bleeding. Five clades were identified that group the vast majority of the DENV-2-NS1 sequences analyzed (19/24; 79.2 %) with posterior probability values greater than or equal to 58 %. Seven sequences (87.5 %) associated with bleeding were phylogenetically related within clades 4 and 5, the posterior probability values were 58 % and 97 %, respectively. Conclusion Neither phylogenetic characteristics nor differences between amino acids of the DENV-2-NS1 sequences studied were found that could be associated directly with severity of the disease.
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- 2016
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18. [Epigenetics in atherosclerosis].
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Guardiola M, Vallvé JC, Zaina S, and Ribalta J
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- Base Sequence, Disease Progression, Gene-Environment Interaction, Humans, Atherosclerosis genetics, Epigenesis, Genetic, Genetic Predisposition to Disease
- Abstract
The association studies based on candidate genes carried on for decades have helped in visualizing the influence of the genetic component in complex diseases such as atherosclerosis, also showing the interaction between different genes and environmental factors. Even with all the knowledge accumulated, there is still some way to go to decipher the individual predisposition to disease, and if we consider the great influence that environmental factors play in the development and progression of atherosclerosis, epigenetics is presented as a key element in trying to expand our knowledge on individual predisposition to atherosclerosis and cardiovascular disease. Epigenetics can be described as the discipline that studies the mechanisms of transcriptional regulation, independent of changes in the sequence of DNA, and mostly induced by environmental factors. This review aims to describe what epigenetics is and how epigenetic mechanisms are involved in atherosclerosis., (Copyright © 2015 Sociedad Española de Arteriosclerosis. Published by Elsevier España. All rights reserved.)
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- 2016
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19. Statins and atherosclerosis: the role of epigenetics.
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Storino Farina M, Rojano Rada J, Molina Garrido A, Martínez X, Pulgar A, Paniagua R, and Garrido J
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- Atherosclerosis genetics, Atherosclerosis pathology, Base Sequence, Disease Progression, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors pharmacology, Inflammation drug therapy, Inflammation genetics, Inflammation pathology, Plaque, Atherosclerotic drug therapy, Plaque, Atherosclerotic pathology, Atherosclerosis drug therapy, Epigenesis, Genetic, Hydroxymethylglutaryl-CoA Reductase Inhibitors therapeutic use
- Abstract
Atherosclerosis is an immune-inflammatory disease, in which pathophysiological mechanisms include inflammation patterns and epigenetic changes that alter gene expression of several inflammatory and non-inflammatory mediators. Epigenetics is offering explanations on how diet, environmental factors and lifestyle can influence the onset and progression of the disease, and how these alterations can be transmitted to the following generations without any changes in DNA sequences. Statins, through their pleiotropic effects, provide a useful tool in controlling the progression of plaques and their subsequent impact.
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- 2015
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20. [Identification of variants in LMF1 gene associated with primary hypertriglyceridemia].
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Lamiquiz-Moneo I, Bea AM, Mateo-Gallego R, Baila-Rueda L, Cenarro A, Pocoví M, Civeira F, and de Castro-Orós I
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- Adult, Aged, Base Sequence, Exons, Female, Gene Frequency, Humans, Lipoprotein Lipase metabolism, Male, Middle Aged, Mutation, Polymorphism, Genetic, Young Adult, Genetic Variation, Hypertriglyceridemia genetics, Membrane Proteins genetics
- Abstract
The majority of severe primary hypertriglyceridemia (HTG) are diagnosed in adults, and their molecular bases have not yet been fully defined. The promoter, coding regions and intron-exon boundaries of LMF1 were sequenced in 112 patients with severe primary hipertrigliceridemia (defined as TG above 500mg/dl). Five patients (4.46%) were carriers of four rare variants in the LMF1 gene associated with HTG, which participate in lipoprotein lipase (LpL) function. Also, we have identified two common variants, c.194-28 T>G and c.729+18C>G that were associated with HTG, with a different allelic frequency to that observed in the general population. A bioinformatic analysis of all found variants was conducted, defining the following as potentially harmful: p.Arg364Gln, p.Arg451Trp, p.Pro562Arg and p.Leu85Leu. Our results suggest that LMF1 mutations are involved in a substantial proportion of cases with severe HTG, putting together the moderate-aggressive effect of rare mutations with polymorphisms classically associated with this disease., (Copyright © 2014 Sociedad Española de Arteriosclerosis. Published by Elsevier España. All rights reserved.)
- Published
- 2015
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21. [Delta⁰-thalassemia by insertion of 27 base pairs in δ-globin gene with decreased hemoglobin A₂ levels].
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González Borrachero ML, de la Fuente-Gonzalo F, González FA, Nieto JM, Villegas A, and Ropero P
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- Base Sequence, Biomarkers blood, Female, Hemoglobin A2 genetics, Hemoglobins, Abnormal genetics, Humans, Middle Aged, Sequence Deletion, Spain, alpha-Globins genetics, delta-Thalassemia blood, delta-Thalassemia diagnosis, Hemoglobin A2 metabolism, Hemoglobins, Abnormal metabolism, Mutagenesis, Insertional, delta-Globins genetics, delta-Thalassemia genetics
- Abstract
Background and Objective: We describe a novel delta-thalassemia mutation causing decreased hemoglobin (Hb) A2 levels associated with Hb Watts, variant Hb resulting from a trinucleotide deletion in Spain., Patients and Method: Hb variant analysis was performed by cation-exchange high performance liquid chromatography (HPLC) and capillary zone electrophoresis. Polymerase chain reaction and DNA sequence analyses were used to identify mutations in the δ- and α-globin genes., Results: Abnormal Hb was observed on capillary zone electrophoresis in Z6 and by cation-exchange HPLC a slower peak than HbA was observed at an retention time of 4.19min. This variant Hb is called Hb Watts [α2 74(EF3)Asp->0 or α2 75(EF4)Asp->0; HBA2:c.226_228delGAC]. The decreased HbA2 percentage owes to an insertion of 27nt between nt 83 and 84 of IVS-I of the δ-globin gene., Conclusions: When analyzing a chromatogram, the possibility of the existence of delta-thalassemia or an HbA2 variant should be considered, apart from alfa-, beta-thalassemia and structural haemoglobinopathies. To this end, each of the peaks and their percentages should be considered to allow for correct interpretation and to avoid misdiagnosis as much as possible., (Copyright © 2014 Elsevier España, S.L.U. All rights reserved.)
- Published
- 2015
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22. Description of alpha-1-antitrypsin deficiency associated with PI*Q0ourém allele in La Palma Island (Spain) and a genotyping assay for its detection.
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Hernández Pérez JM, Ramos Díaz R, Fumero García S, and Pérez Pérez JA
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- Adult, Aged, Alleles, Base Sequence, Endoplasmic Reticulum-Associated Degradation, Female, Humans, Male, Middle Aged, Molecular Sequence Data, Phenotype, Sequence Analysis, DNA, Spain, alpha 1-Antitrypsin analysis, Genotyping Techniques, alpha 1-Antitrypsin genetics, alpha 1-Antitrypsin Deficiency genetics
- Abstract
By analysis of a case of discrepancy between serum alpha-1-antitrypsin (AAT) level and genotype for the most common defective alleles associated with AAT deficiency (PI*S and PI*Z), a patient carrying the allele PI*Q0ourém has been identified for the first time outside of Portugal. This null allele has been implicated in cases of severe pulmonary emphysema. After developing a clinical assay for detection of c.1130insT mutation, based on fluorescent probes (HybProbe®), another 4 carriers of PI*Q0ourém allele were identified among 43 patients with abnormally low serum AAT levels based on their genotypes for PI*S and PI*Z alleles. Since 4 out 5 cases are from the same locality (La Palma Island, Spain), it is advisable to conduct genetic analyses of affected families and, possibly, a focused population screening., (Copyright © 2013 SEPAR. Published by Elsevier Espana. All rights reserved.)
- Published
- 2015
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23. [Gene polymorphisms in the dihydrofolate reductase ( dhfr ) and dihydropteroate synthase ( dhps ) genes and structural modelling of the dhps gene in Colombian isolates of Toxoplasma gondii].
- Author
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Cortés LJ, Duque S, López MC, Moncada D, Molina D, Gómez-Marín JE, and Gunturiz ML
- Subjects
- AIDS-Related Opportunistic Infections cerebrospinal fluid, AIDS-Related Opportunistic Infections parasitology, Amino Acid Substitution, Animals, Base Sequence, Cerebrospinal Fluid parasitology, Cloning, Molecular, Colombia, DNA, Protozoan genetics, DNA, Recombinant genetics, Dihydropteroate Synthase chemistry, Exons genetics, Humans, Male, Mice, Models, Molecular, Molecular Sequence Data, Protein Conformation, Protozoan Proteins chemistry, Sequence Alignment, Sequence Homology, Nucleic Acid, Toxoplasma genetics, Toxoplasma isolation & purification, Toxoplasmosis, Animal parasitology, Toxoplasmosis, Cerebral cerebrospinal fluid, Toxoplasmosis, Cerebral parasitology, Dihydropteroate Synthase genetics, Polymorphism, Single Nucleotide, Protozoan Proteins genetics, Tetrahydrofolate Dehydrogenase genetics, Toxoplasma enzymology
- Abstract
Introduction: There are no reports describing polymorphisms in target genes of anti- Toxoplasma drugs in South American isolates., Objective: This study sought to perform cloning and sequencing of the dihydrofolate reductase ( dhfr ) and dihydropteroate-synthase ( dhps ) genes of the reference Rh strain and two Colombian isolates of Toxoplasma gondii ., Materials and Methods: Two isolates were obtained from the cerebrospinal fluid of HIV-infected patients with cerebral toxoplasmosis. A DNA extraction technique and PCR assay for the dhfr and dhps genes were standardized, and the products of amplification were cloned into Escherichia coli and sequenced., Results: One polymorphism (A « G) was found at position 235 of exon 2 in the dhps gene. In addition, two polymorphisms (G « C) at positions 259 and 260 and one polymorphism (T « G) at position 371 within exon 4 of the dhps gene were detected. In this last exon, a bioinformatic analysis revealed a non-synonymous polymorphism in the coding region that could lead to the substitution of Glu (CAA or CAG) for His (encoded by codons AAU or AAC). A structural model of the T. gondii DHPS protein was calculated, and the results revealed modifications in secondary structure due to mutations., Conclusions: The methods described in this study can be used as a tool to search for polymorphisms in samples from patients with different clinical manifestations of toxoplasmosis and to examine their relationship with the therapeutic response.
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- 2014
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24. [Lymnaea cousini , intermediate host of Fasciola hepatica in the Colombian high tropical Andes, and its new haplotypes confirmed with the mitochondrial marker cytochrome oxidase I].
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Uribe N, Becerra WM, and Velásquez LE
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- Animals, Base Sequence, Biomarkers, Colombia, DNA genetics, DNA, Mitochondrial genetics, Electron Transport Complex IV genetics, Haplotypes genetics, Lymnaea enzymology, Lymnaea genetics, Molecular Sequence Data, Phylogeny, Protein Subunits, Sequence Alignment, Sequence Homology, Nucleic Acid, Disease Vectors classification, Electron Transport Complex IV analysis, Fasciola hepatica, Lymnaea classification
- Abstract
Introduction: Fasciolosis is the disease transmitted by vectors with the highest latitudinal, longitudinal, and altitudinal distribution due to the colonizing capacity of the parasite Fasciola hepatica and its intermediate hosts, Lymnaeidae mollusks. These snails are under research due to their epidemiological importance, but their taxonomic identification is difficult given their interspecific phenotypical similarity. For this reason, there is uncertainty regarding Lymnaea cousini -a host of F. hepatica in Colombia- due to the morphological similarity it has with Lymnaea meridensis , recently described for Venezuela., Objective: To confirm with the COI marker (ADNmt) the taxonomic status of individuals morphologically identified as L. cousini from Nariño, Norte de Santander, and Santander (Colombia), deposited in the Vector Mollusks Collection VHET No. 37 of Universidad de Antioquia., Materials and Methods: The amplification of the mitochondrial COI required total DNA extraction of each individual´s foot using the DNeasy Blood and Tissue Kit (Qiagen®). Products amplified were sent for sequencing to Macrogen Inc., Korea. Twenty seven sequences generated in this research were compared to sequences published in the GenBank, including sequences of the type locality of L. cousini ., Results: Two new haplotypes of L. cousini were obtained for Colombia. Specimens from Nariño correspond to haplotype A, referenced for Ecuador, and specimens from Santander and Norte de Santander belong to a new haplotype we called haplotype D., Conclusion: By using the mitochondrial COI marker, we confirmed that the species under study did correspond to L. cousini . The number of known haplotypes of the species for Colombia has been duplicated and its geographical distribution has been extended to the southwest and northeast of the Colombian high Andean region.
- Published
- 2014
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25. [Identification and differential expression of the microphthalmia-associated transcription factor in heart and isolated cardiomyocytes from Guinea pigs: possible role in hypertrophy and viability].
- Author
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Gunturiz ML and Gómez LA
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, Cardiomyopathy, Hypertrophic genetics, Cell Survival, Cells, Cultured, DNA, Complementary genetics, Female, Gene Expression Regulation, Guinea Pigs, Ischemic Preconditioning, Myocardial, Microphthalmia-Associated Transcription Factor antagonists & inhibitors, Microphthalmia-Associated Transcription Factor biosynthesis, Microphthalmia-Associated Transcription Factor genetics, Molecular Sequence Data, Myocardial Ischemia genetics, Myocardial Ischemia metabolism, Myocytes, Cardiac pathology, Oxygen pharmacology, Protein Isoforms biosynthesis, Protein Isoforms genetics, Protein Isoforms physiology, RNA Interference, RNA, Small Interfering pharmacology, Sequence Alignment, Sequence Homology, Cardiomyopathy, Hypertrophic metabolism, Microphthalmia-Associated Transcription Factor physiology, Myocardium metabolism, Myocytes, Cardiac metabolism
- Abstract
Introduction: The microphthalmia -associated transcription factor ( MITF ) regulates the expression of specific genes and its cardiac expression and function is not known., Objectives: To identify the expression of MITF in hearts and isolated cardiomyocytes from Guinea pigs, to describe morphological changes associated with mRNA interference of MITF and to evaluate their relative changes in expression in isolated cardiomyocytes under ischemic preconditioning., Materials and Methods: The cardiac specific isoform, MITF-H, and relative expression level analysis, was determined by semi-quantitative real time PCR, sequencing and Western blotting. Reduction of mRNA-MITF-H was induced by transduction of specific-MITF-shRNAi interference. The cardiac morphological changes, diameter and number of cardiac fibers were evaluated by direct observation and light microscopy., Results: A cDNA fragment of 281 bp was amplified from heart and isolated ventricular cardiac myocytes. Sequence analysis confirmed the identity of the isoform MITF-H, exon 1. The MITF silencing was associated with an increase in cardiac index (heart weight/body weight vs . 5.46 x 10 -3 vs 4.6 x 10 -3 ) and higher diameter of cardiac fibers (50.2±16 µ m vs 38,7±14,7 µ m p<0.05, n=150). In isolated cardiac myocytes under ischemic preconditioning we observed a higher relative expression compared with that measured in myocytes exposed to normoxia and simulated ischemia (eighty and one hundred times, p <0.05, n = 5). Conclusion. The results suggest that MITF-H isoform may be involved in Guinea pig cardiac hypertrophy, response to stress by ischemia and cardiomyocytes survival.
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- 2014
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26. [Prenatal exclusion of von Hippel-Lindau syndrome in a Mexican family carrying a novel VHL gene mutation].
- Author
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Chacón-Camacho OF, Benitez-Granados J, and Zenteno JC
- Subjects
- Alleles, Base Sequence, DNA genetics, Female, Humans, Mexico, Mutation, Pedigree, Polymerase Chain Reaction, Pregnancy, Young Adult, von Hippel-Lindau Disease genetics, Prenatal Diagnosis methods, Von Hippel-Lindau Tumor Suppressor Protein genetics, von Hippel-Lindau Disease diagnosis
- Abstract
Background: von Hippel-Lindau (VHL) disease is an autosomal dominant and familial multisystemic syndrome that is caused by the inactivation of the VHL gene and it is characterized by diverse types of high vasculated tumours of benign and malign nature. In this work we describe the clinical characteristics and the prenatal diagnosis of a woman with VHL., Objective: Describe the first exclusion prenatal case by DNA analysis of the VHL syndrome in Latinoamerican population., Material and Methods: Analysis of a Mexican familial pedigree showed 5 affected subjects with VHL on 3 consecutive generations. The proband was a 7 weeks pregnancy woman who was referred to our service for familiar and personal history of this disease. Maternal DNA was obtained from peripheral blood leukocytes, while fetal DNA was isolated from amniotic liquid cells on the 15th week. The maternal and fetal DNA analysis were done by the Polymerase Chain reaction (PCR) and the direct nucleotide sequence of the VHL gene., Results: A novel mutation (c. 161_168 dup GGAGGCCG) in the VHL gene was identified in maternal DNA. Fetal DNA analysis indicated that the fetus inherited the wild-type allele from the mother., Conclusion: A novel VHL gene mutation was identified in a familial case of the disease, expanding the mutational spectrum in this disorder. The molecular prenatal testing in the affected woman at 15 weeks of gestation, demonstrated that the fetus did nor inherited the mutated allele. To the best of our knowledge, this is the first example of prenatal-molecular exclusion on VHL syndrome in Latinoamerica population.
- Published
- 2014
27. [Primers for (1,3)-β-glucan synthase gene amplification and partial characterization of the enzyme in Ganoderma lucidum].
- Author
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Guerrero-Torres JV, Mata G, Martínez-Carrera D, Garibay-Orijel C, and Garibay-Orijel R
- Subjects
- Agaricales enzymology, Agaricales genetics, Amino Acid Sequence, Base Sequence, DNA Primers, DNA, Intergenic genetics, Molecular Sequence Data, Molecular Weight, Phylogeny, Reishi genetics, Sequence Alignment, Sequence Homology, Amino Acid, Sequence Homology, Nucleic Acid, DNA, Fungal genetics, Fungal Proteins genetics, Glucosyltransferases genetics, Polymerase Chain Reaction methods, Reishi enzymology
- Abstract
Background: β-(1,3)(1,6)-D-glucan is fungal cell wall component that has demonstrated immunomodulatory and anti-cancer effects. The (1,3)-β-glucan synthase is one of the main enzymes involved in its biosynthesis., Aims: To design primers to partially amplify and characterize the (1,3)-β-glucan synthase gene and to determine them in Ganoderma lucidum (G. Lucidum) strain CP-132., Methods: The primers were designed on the basis of homologous genes in other fungi. Then, using the PCR technique, primers were tested using DNA extracted from the G. lucidum strain CP-382. Amplified sequences were compared with those from the GenBank., Results: Three primer pairs were designed; all of them produced amplicons of the expected size. The sequences obtained with primer pairs BGS2113UmF and BGS3097UmR, and BGS547UmF and BGS2113UmR matched with 2 sections of the (1,3)-β-glucan synthase gene. The deduced amino acid sequences showed high similarity with homologous genes from other fungi, particularly with those of the Agaricomycetes class., Conclusions: The primer design to partially amplify the (1,3)-β-glucan synthase gene of G. lucidum using sequences from homologous genes was successful. These primers will allow to characterize this important enzyme in a wide group of fungi., (Copyright © 2012 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.)
- Published
- 2013
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28. [Patentability of DNA sequences: the debate remains open].
- Author
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Martín Uranga A
- Subjects
- Humans, United States, Base Sequence, DNA, Patents as Topic legislation & jurisprudence, Supreme Court Decisions
- Abstract
The patentability of human genes was from the beginning of the discussion concerning the Directive on the legal protection of biotechnological inventions, an issue that provoked debates among politicians, scientists, lawyers and civil society itself. Although Directive 98/44 tried to settle the matter by stating that to support the patentability of human genes, it should know what role they fulfill, which protein they encode, all of this as an essential requirement to test its industrial application. However, following the judgment of 13 June 2013 (Supreme Court of the United States of America in the case of Association for Molecular Pathology et al. versus Myriad Genetics Inc.) the debate on this issue has been reopened. There are several issues to be considered, taking into account that the patents on DNA & Gene Sequences have played an important incentive to increase the interest in biotechnology applied to human health. On the other hand, this is a paradigm shift in the R & D of biopharmaceutical companies, and it has moved from an in house research model to a model of open innovation, a model of collaboration between large corporations with biotech SMEs and public and private research centers. This model of innovation, impacts on the issue of the industrial property, and therefore it will be necessary to clearly define what each party brings to the relationship and how they are expected to share the results. But all of this, with the ultimate goal that the patients have access to treatments and medications most innovative, safe and effective.
- Published
- 2013
29. [Myths and truths about the human genome].
- Author
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Crámer P and Iusem ND
- Subjects
- Base Sequence, Humans, Genome, Human genetics, Genomics
- Published
- 2013
30. [Hepatitis E: molecular virology, epidemiology and pathogenesis].
- Author
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Rodríguez-Frias F, Jardi R, and Buti M
- Subjects
- Animals, Antiviral Agents therapeutic use, Base Sequence, Female, Food Contamination, Genes, Viral, Genotype, Hepatitis E virus classification, Hepatitis E virus genetics, Hepatitis E virus physiology, Humans, Liver Cirrhosis epidemiology, Liver Cirrhosis etiology, Male, Mammals virology, Molecular Sequence Data, Organ Transplantation adverse effects, Postoperative Complications virology, Pregnancy, Pregnancy Complications, Infectious epidemiology, Pregnancy Complications, Infectious virology, RNA, Viral genetics, Serotyping, Swine, Swine Diseases epidemiology, Swine Diseases virology, Transfusion Reaction, Viral Hepatitis Vaccines, Virus Replication, Zoonoses, Hepatitis E diagnosis, Hepatitis E drug therapy, Hepatitis E epidemiology, Hepatitis E transmission, Hepatitis E veterinary, Hepatitis E virology
- Abstract
Hepatitis E represents a significant proportion of enteric transmitted liver diseases and poses a major public health problem, mainly associated with epidemics due to contamination of water supplies, especially in developing countries. Hepatitis E virus (HEV) is responsible for self-limiting acute liver oral-faecal infections. In industrialised countries, acute hepatitis E is sporadic, detected in travellers from endemic areas but also in sporadic cases with no risk factors. HEV is a non-enveloped virus with a single-stranded RNA genome classified into 4 genotypes and a single serotype. Genotypes 1 and 2 only infect humans, and are predominant in the developing countries, while 3 and 4 are predominant in industrialised countries, and also infect other species of mammals, especially pigs, and multiple evidence classifies HEV as a zoonotic agent. Some HEV chronic infections have recently been reported in kidney and liver transplant patients. The mortality rate of HEV infection is greater than hepatitis A. In addition to faecal-oral transmission, parenteral transmission of HEV has also been reported. Several vaccines are currently in development. The severity of this infection in some groups of patients, especially pregnant women, and the occurrence of chronic hepatitis, even with progression to cirrhosis, have raised interest in the application of interferon and/or ribavirin therapy., (Copyright © 2011 Elsevier España, S.L. All rights reserved.)
- Published
- 2012
- Full Text
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31. [Development of a nested polymerase chain reaction test for the diagnosis of transmissible gastroenteritis of pigs].
- Author
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Rodríguez E, Betancourt A, Relova D, Lee C, Yoo D, and Barrera M
- Subjects
- Animals, Base Sequence, DNA, Viral chemistry, RNA, Viral genetics, RNA, Viral isolation & purification, Swine, Transmissible gastroenteritis virus genetics, Gastroenteritis, Transmissible, of Swine diagnosis, Polymerase Chain Reaction veterinary, Transmissible gastroenteritis virus isolation & purification
- Abstract
The aim of this study was to develop a nested polymerase chain reaction (nested PCR) for the rapid detection of transmissible gastroenteritis virus (TGEV) of pigs. The primers were designed on the basis of highly conserved regions of several TGEV sequences included in the analysis. External primers were used to amplify a fragment of the expected size (441 bp) in all the samples evaluated using reverse transcriptase polymerase chain reaction (RT-PCR), but with very low intensity. In the second amplification (nested PCR), internal primers were used to amplify a fragment of the expected size (168 bp), with good concentration. The performance of the test based on virus isolates in tissue culture and in clinical samples was judged good for the virological diagnosis of transmissible gastroenteritis of pigs.
- Published
- 2012
32. [First world case of -α3,7-associated Hb J-Camagüey].
- Author
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de la Fuente-Gonzalo F, Sala F, Ropero P, and González FA
- Subjects
- Aged, Amino Acid Substitution, Base Sequence, Chromatography, High Pressure Liquid, Female, Hemoglobin J chemistry, Hemoglobin J isolation & purification, Hemoglobinopathies blood, Heterozygote, Humans, Molecular Sequence Data, Mutation, Missense, Sequence Analysis, DNA, alpha-Thalassemia blood, Anemia, Hypochromic etiology, Hemoglobin J genetics, Hemoglobinopathies genetics, Point Mutation, alpha-Globins genetics, alpha-Thalassemia genetics
- Published
- 2012
- Full Text
- View/download PDF
33. [New genovariantes of Chlamydia trachomatis serovar L2 proctitis causing].
- Author
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Guerra-Infante FM, López-Hurtado M, and Villagrana-Zesati R
- Subjects
- Bacterial Proteins genetics, Base Sequence, Chlamydia trachomatis genetics, Female, Genes, Bacterial, Genetic Variation, Genotype, Global Health, Humans, Lymphogranuloma Venereum microbiology, Male, Molecular Sequence Data, Multicenter Studies as Topic, Serotyping, Chlamydia Infections microbiology, Chlamydia trachomatis classification, Proctitis microbiology
- Abstract
Lymphogranuloma venereum (LGV) is a chronic disease of the lymphatic system that is transmitted sexually and whose etiologic agents are L1, L2 and L3 serotypes of Chlamydia trachomatis. Since 2003 in Europe, USA, Canada and Australia have had outbreaks of L2 serotype infection that develops proctitis in place of LGV in men who have sex with men. It appears that these strains are a new genovariant of L2 serotype (L2b) that is developing a different pathology to LGV. However, the analysis of L2b genome not differs significantly to L2 genome (L2/434 UB) for which L2b is considered as a classic L2 strain. Despite this, new genovariantes of L2 and L2b are appearing, which develop or not LGV or proctitis so we need to do an analysis of its genome to identify genetic changes that these strains shown.
- Published
- 2012
34. [Bacillus anthracis: a molecular look at a famous pathogen].
- Author
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Pavan ME, Pettinari MJ, Cairó F, Pavan EE, and Cataldi AA
- Subjects
- Animals, Anthrax epidemiology, Anthrax veterinary, Antigens, Bacterial immunology, Antigens, Bacterial physiology, Bacillus classification, Bacillus anthracis classification, Bacillus anthracis genetics, Bacillus anthracis pathogenicity, Bacterial Capsules physiology, Bacterial Toxins, Bacterial Typing Techniques, Base Sequence, DNA, Bacterial genetics, Genomic Islands physiology, Humans, Membrane Proteins genetics, Membrane Proteins physiology, Microfilament Proteins, Minisatellite Repeats, Molecular Sequence Data, Neoplasm Proteins genetics, Neoplasm Proteins physiology, Plasmids, Polymorphism, Single Nucleotide, Receptors, Cell Surface genetics, Receptors, Cell Surface physiology, Receptors, Peptide, Sequence Alignment, Sequence Homology, Nucleic Acid, Virulence genetics, Virulence physiology, Zoonoses, Anthrax microbiology, Bacillus anthracis physiology
- Abstract
Bacillus anthracis, a gram-positive rod belonging to the Bacillus cereus group, has an extremely monomorphic genome, and presents high structural and physiological similarity with B. cereus and Bacillus thuringiensis. In this work, the new molecular methods for the identification and typing of B. anthracis developed in the last years, based on variable number tandem repeats or on genetic differences detected through sequencing, are described. The molecular aspects of traditional virulence factors: capsule, protective antigen, lethal factor and edema factor are described in depth, together with virulence factors recently proposed, such as the siderophores petrobactin and bacillibactin, the S-layer adhesin and the MntA lipoprotein. It is detailed the molecular organization of megaplasmids pXO1 and pXO2, including the pathogenicity island of pXO1. The genetic skeleton of these plasmids has been observed in related species, and this could be attributed to lateral gene transfer. Finally, the two anthrax toxin protective antigen receptors, ANTXR1/TEM8 and ANTXR2/CMG2, essential for the interaction of the pathogen with the host, are presented. The molecular studies performed in recent years have greatly increased knowledge in different aspects of this microorganism and its relationship with the host, but at the same time they have raised new questions about this noted pathogen.
- Published
- 2011
- Full Text
- View/download PDF
35. [Molecular characterization of Sigmodon hirsutus (Rodentia: Cricetidae) populations in Venezuela].
- Author
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Lessmann J, Arrivillaga J, and Aguilera M
- Subjects
- Animals, Base Sequence, Molecular Sequence Data, Phylogeny, Phylogeography, Sequence Analysis, DNA, Venezuela, Cytochromes b genetics, Genetic Variation genetics, Sigmodontinae genetics
- Abstract
Recent phylogenetic studies based on cytochrome b gene sequence, have determined that the species historically known as Sigmodon hispidus (Rodentia) from South America comprises a species S. hirsutus of paraphyletic origin. The aim of this study was to test the hypothesis that populations from Venezuela, represent the sensu strict form, ancestral haplotypes, and monophyletic subspecieS. For this, 12 individual sequences from three localities of different biogeographic regions in Venezuela were evaluated and sequenced based on cyto b. Additionally, the sequences were used to develop a cladistic analysis and genetic distance calculations, and to compare this information with two individual sequences of Sigmodon specimens available in Genbank. Phylogenetic analyses show that the three populations of S. hirsutus of Venezuela form an ancestral and monophyletic subclade supported by high bootstrap values and significant genetic distance between subclade within the S. hirsutus. Besides, the existence of two lineages suggests two subspecies, S. hirsutus hirsutus from Venezuela, and S. hirsutus mexicanus from Mexico-Central America, but, both species need formal description.
- Published
- 2011
36. [Mutational frequencies in usherin(USH2A gene) in 26 Colombian individuals with Usher syndrome type II].
- Author
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López G, Gelvez NY, and Tamayo M
- Subjects
- Base Sequence, Colombia, DNA Mutational Analysis, Female, Hearing Loss, Sensorineural genetics, Humans, Male, Molecular Sequence Data, Pedigree, Polymorphism, Genetic, Retinitis Pigmentosa genetics, Usher Syndromes pathology, Usher Syndromes physiopathology, Extracellular Matrix Proteins genetics, Mutation, Mutation Rate, Usher Syndromes genetics
- Abstract
Introduction: Usher syndrome is a disorder characterized by progressive retinitis pigmentosa, prelingual sensory hearing loss and vestibular dysfunction. It is the most frequent cause of deaf-blindness in humans. Three clinical types and twelve genetic subtypes have been characterized. Type II is the most common, and among these cases, nearly 80% have mutations in the USH2A gene., Objective: The aim of the study was to establish the mutational frequencies for the short isoform of USH2A gene in Usher syndrome type II., Materials and Methods: Twenty-six Colombian individuals with Usher syndrome type II were included. SSCP analysis for 20 exons of the short isoform was performed and abnormal patterns were sequenced. Sequencing of exon 13 of the USH2A gene was performed for all the individuals because the most frequent mutation is located in this exon., Results: The most frequent mutation was c.2299delG, identified in the 27% (n=8) of the sample. The second mutation, p.R334W, showed a frequency of 15%. A new variant identified in the 5’UTR region, g.129G>T, was present in 1 individual (4%). Four polymorphisms were identified; one of them is a new deletion in exon 20, first reported in this study., Conclusions: Mutations in the usherin short isoform were identified in 38% of a sample of 26 USH2 cases. Molecular diagnosis was established in 7 of the 26.
- Published
- 2011
- Full Text
- View/download PDF
37. [Rapid identification of Histoplasma capsulatum in culture lysates].
- Author
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Ibarra-Camou B, Toranzo AI, Lee W, Davel G, and Canteros CE
- Subjects
- Base Sequence, Chrysosporium genetics, Culture Media, Fungi genetics, Fungi growth & development, Histoplasma genetics, Histoplasma growth & development, In Vitro Techniques, Molecular Sequence Data, Mycology methods, Predictive Value of Tests, Sensitivity and Specificity, Sequence Alignment, Sequence Homology, Nucleic Acid, Species Specificity, Time Factors, DNA, Fungal isolation & purification, Histoplasma isolation & purification, Polymerase Chain Reaction methods
- Abstract
Background: Histoplasma capsulatum is the agent of histoplasmosis, a deep mycosis mainly afflicting immunocompromised patients. Rapid identification of the fungus isolated from clinical specimens allows timely administration of specific treatment., Aim: To assess the ability of a dual PCR system targeting specific H. capsulatum DNA sites to identify fungal species in simple aqueous lysates from cultured fungi., Methods: We analysed the performance of two independent PCR reactions designed to amplify fragments of 111 and 279 bp included in H. capsulatum-specific gene AgM. We used 248 H. capsulatum strains and 68 isolates of other fungal species. Reaction templates consisted of aqueous lysates of cultured fungi (either in mycelial or yeast phase) obtained after three cycles of boiling and immediate cooling at 0°C. Selected strains were submitted to conventional DNA extraction and/or sequencing., Results: Both PCR systems performed identically. Amplification from aqueous lysates was achieved from 239 H. capsulatum strains; the remaining 9 strains only showed specific bands when purified DNA was used as template. Of all other fungal species tested, only 2 Emmonsia crescens strains amplified H. capsulatum-specific bands and sequences of their amplified PCR products matched > 97% with H. capsulatum sequences. Total test time did not exceed 7h with 96% sensitivity, 97% specificity and 99% positive predictive value., Conclusions: The assay is fast, accurate and economical, and can be an alternative method for presumptive identification of H. capsulatum in simple culture lysates., (Copyright © 2010 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.)
- Published
- 2011
- Full Text
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38. [Susceptibility of M. tuberculosis to antituberculosis drugs as determined by two methods, in Sucre state, Venezuela].
- Author
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Mendoza R, De Donato M, de Waard JH, Takiff H, Bello T, and Chirinos G
- Subjects
- Bacterial Proteins analysis, Bacterial Proteins genetics, Base Sequence, DNA-Directed RNA Polymerases, Drug Resistance, Multiple, Bacterial genetics, Ethambutol pharmacology, Humans, Isoniazid pharmacology, Molecular Sequence Data, Morbidity trends, Mutation, Missense, Mycobacterium tuberculosis enzymology, Mycobacterium tuberculosis genetics, Nitrate Reductase analysis, Point Mutation, Prevalence, Rifampin pharmacology, Sequence Alignment, Sequence Homology, Nucleic Acid, Sputum microbiology, Streptomycin pharmacology, Tuberculosis epidemiology, Tuberculosis, Multidrug-Resistant epidemiology, Tuberculosis, Multidrug-Resistant microbiology, Venezuela epidemiology, Antitubercular Agents pharmacology, Drug Resistance, Microbial, Microbial Sensitivity Tests methods, Mycobacterium tuberculosis drug effects, Tuberculosis microbiology
- Abstract
The objective of this study was to evaluate the resistance to isoniazid (INH), rifampicin (RIF), streptomycin (STR) and ethambutol (EMB), with the Canetti's proportions method (PM) and the nitrate reductase assay (NRA) of 59 clinical strains of Mycobacterium tuberculosis, isolated in the period of august 2005 to december 2006, in Sucre state, Venezuela. Primary and acquired drug resistance was 6.3% and 14.3%, respectively. Only one strain was found to be multidrug resistant (MDR). The overall agreement between the NRA and PM was 100% for INH, RIF and EMB, and 96% for STR. The time to obtain results was 10 to 14 days for the NRA, compared to 42 days for the PM. The NRA was easy to perform and therefore represents a useful tool for rapid and accurate determination of drug-resistant M. tuberculosis. The sequence of the rpoB gene of the RIF resistant strain demonstrated a never described mutation (change in the codon 456; TCG > CAG) in the hypervariable region of 81 base pairs where most of the mutations of the RIF resistant strains have been reported. Comparison of our results with those of the last resistance prevalence study carried out in the years 1998-1999, shows a decrease in the studied area.
- Published
- 2010
39. [Presence of mutations associated with ganciclovir resistance in cytomegalovirus UL97 gene].
- Author
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Oyarzún MA, Bustos P, González M, Domínguez MI, Aguayo F, Nervi B, and Ferres M
- Subjects
- Adolescent, Adult, Base Sequence, Child, Child, Preschool, Chile, Cytomegalovirus drug effects, Genome, Viral, Humans, Immunocompromised Host, Middle Aged, Young Adult, Antiviral Agents pharmacology, Cytomegalovirus genetics, Drug Resistance, Viral genetics, Ganciclovir pharmacology, Mutation, Phosphotransferases (Alcohol Group Acceptor) genetics
- Abstract
Background: Long term use of ganciclovir (GCV) is associated with acquired resistance to it. Ninety percent of the responsible mutations occur in cytomegalovirus (CMV) UL 97 gene., Aim: To search for these mutations, comparing nucleotide sequences of CMV-positive samples from post transplant and immunocompromised patients receiving GCV, with sequences of CMV isolates obtained from subjects not exposed to the drug., Patients and Methods: Codons 440 to 465 of gene UL 97, including the most common mutations causing resistance to GCV, were amplified in 33 plasma samples from patients exposed to GCV and in 15 urine samples of newborns. Both populations and their nucleotide sequences were compared with the prototype strain CMV AD169., Results: Samples of exposed patients had multiple mutations but only one had a mutation associated with clinical resistance (M460I). Eight subjects had the D605E mutation, whose role in resistance is controversial. The remaining 150 mutations were silent mutations., Conclusions: A low frequency of mutations associated with CMV resistance to GCV was found in these exposed and unexposed samples. These mutations may reflect coexistence of multiple genetic variants of CMV. The absence of clinical expression of resistance, even with these mutations, can be explained by the use of GCV for a shorter lapse than that associated with the appearance of resistance.
- Published
- 2010
- Full Text
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40. [New mutation in the PSEN1 (E120G) gene associated with early onset Alzheimer's disease].
- Author
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Lladó A, Sánchez-Valle R, Rey MJ, Mercadal P, Almenar C, López-Villegas D, Fortea J, and Molinuevo JL
- Subjects
- Adult, Base Sequence, DNA Mutational Analysis, Exons, Female, Humans, Male, Molecular Sequence Data, Alzheimer Disease genetics, Mutation, Presenilin-1 genetics
- Abstract
Objective: To describe a novel mutation in exon 5 of the presenilin 1 gene (E120G)associated with early-onset autosomal dominant Alzheimer's disease (AD)., Patient and Methods: The proband was a man who began with memory loss and progressive cognitive decline at the age of 34. His father and his sister suffered from early-onset cognitive decline. The genetic study performed on the blood sample using the single strand conformation polymorphism (SSCP) technique did not detect any abnormality suggestive of the presence of a mutation in PSEN1, PSEN2, and APP. In the last stage of the disease the patient had seizures and gait alteration. He died at the age of 44. Coding exons 3-12 of PSEN1 were studied by direct sequencing using isolated DNA from frozen brain tissue of the proband., Results: The neuropathological examination showed the presence of frequent amyloid plaques and neurofibrillary tangles and severe amyloid angiopathy. The direct sequencing of the PSEN1 gene disclosed the presence of the E120G mutation., Conclusions: E120G is a novel mutation in PSEN1 that probably causes early-onset autosomal dominant AD. Absence of genetic alterations in screening techniques (SSCP) does not rule out the presence of mutations. We recommend direct sequencing for the genetic study of patients with early-onset autosomal dominant AD.
- Published
- 2010
41. [Mutations in the BRCA1 gene (185delAG and 5382insC) are not present in any of the 30 breast cancer patients analyzed from eastern Colombia].
- Author
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Sanabria MC, Muñioz G, and Vargas CI
- Subjects
- Adult, Base Sequence, Breast Neoplasms epidemiology, Carcinoma epidemiology, Colombia epidemiology, Contraceptives, Oral, Hormonal, DNA Mutational Analysis, Family Health, Female, Hormone Replacement Therapy, Humans, Middle Aged, Molecular Sequence Data, Mutagenesis, Insertional, Neoplasms, Hormone-Dependent epidemiology, Neoplasms, Hormone-Dependent genetics, Receptors, Estrogen analysis, Receptors, Progesterone analysis, Reproductive History, Sequence Deletion, Surveys and Questionnaires, Breast Neoplasms genetics, Carcinoma genetics, DNA, Neoplasm genetics, Genes, BRCA1
- Abstract
Introduction: Breast cancer is considered a worldwide public health problem, and, in Santander Province, Colombia, it is the first leading cause of morbidity and mortality by cancer in women. All cancers are considered genetic diseases, and mutations in BRCA (BReast CAncer) genes raises the risk for breast cancer by 60%-80%. The current study searched for the two most frequent BRCA1 mutations reported in the Breast Cancer Core Information database., Objective: The presence of specific mutations (185delAG, exon 2 and 5382insC, exon 20) was determined for the BRCA1 gene in women with familial/hereditary breast cancer., Materials and Methods: The sample included 30 female patients using the oncology services in Bucaramanga, eastern Colombia; an informed consent, a questionnaire and a blood sample were obtained from each. The molecular analysis was done with PCR-Mismatch, to detect the insertion or eliminatation of a restriction site, and enzymatic digestion methods (Hinfl or Ddel)., Results: Two of the most frequent BRCA1 mutations in the international database were not found in the 30 patients studied., Conclusion: Additional mutation screening techniques are necessary involving the entire BRCA1 gene, are necessary in order to better characterize the molecular epidemiology of breast cancer in Bucaramanga, Santander, Colombia.
- Published
- 2009
42. [Pathogenicity island region of clinical and environmental strains of Vibrio parahaemolyticus, isolated in Chile].
- Author
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Núñez H, Ulloa MT, Guerra F, and Osorio CG
- Subjects
- Bacterial Toxins genetics, Base Sequence, Chile, DNA, Bacterial isolation & purification, Environmental Microbiology, Humans, Molecular Sequence Data, Polymerase Chain Reaction, Shellfish microbiology, Vibrio parahaemolyticus isolation & purification, Vibrio parahaemolyticus pathogenicity, Virulence Factors, Genomic Islands genetics, Hemolysin Proteins genetics, Vibrio parahaemolyticus genetics
- Abstract
Background: Most clinical isolates of Vibrio parahaemolyticus produce a major virulence factor known as the thermostable direct hemolysin (TDH). TDH is encoded by the tdh gene which is located in a genomic pathogenicity island (PAI). Most environmental isolates are described as tdh negative., Aim: To assess if environmental strains lack the full pathogenicity island or if only the tdh gene is deleted., Material and Methods: Thirty eight clinical and 66 environmental strains of Vibrio parahaemolyticus were studied. PAI was characterized by polymerase chain reaction (PCR). The presence of tdhA and tdhS genes, was determined by Southern blot., Results: Fifty three environmental strains (80%) lacked a full PAI when compared with clinical strains. In environmental strains, Southern blot and sequence analysis showed that a genetic region of 80 kilobase pairs including genes from VPA1310 to VPA1396 was missing., Conclusions: These results highlight the genetic dynamism of Vibrio parahaemolyticus pathogenecity island region and suggest that new pathogenic strains could appear by horizontal transfer of the island between toxigenic and non-toxigenic strains.
- Published
- 2009
- Full Text
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43. [Genetic characterization of the fungus involved in the first case of coccidioidomycosis described by Alejandro Posadas in 1892].
- Author
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Canteros CE, Toranzo A, Suárez-Alvarez R, Davel G, Castañon-Olivares LR, and Nápoli J
- Subjects
- Antigens, Fungal genetics, Argentina, Base Sequence, Cadaver, Coccidioidomycosis microbiology, History, 19th Century, Humans, Molecular Sequence Data, Polymerase Chain Reaction, Coccidioides genetics, Coccidioidomycosis history, DNA, Fungal analysis
- Abstract
In 1892 Alejandro Posadas described the first worldwide case of coccidioidomycosis in a patient named Domingo Escurra. A preserved necropsy piece from the patient's remains is conserved in the Museum of Pathology of the Medical School, Buenos Aires University. Paraffin-embedded specimens obtained from this piece served to identify the fungus involved in the case. Histological slices from different lesion sites were submitted to a genus-specific immunohistochemical staining in order to select the more suited areas in terms of abundance/integrity of fungal esporangia and endospora. Fungal DNA was amplified from selected deparaffinated slices using a nested PCR designed to amplify a segment of the gen Ag2/PRA and differentiate C. immitis from C. posadasii. This PCR was also applied to two reference strains (C. immitis M38-05, C. posadasii 1-NL) and isolates obtained from four recent coccidioidomycosis cases occurred in Argentina. Amplified products were submitted to sequencing of both DNA strands. The obtained sequences were edited, aligned and compared with C. posadasii (Access N degrees AY536446, strain Silveira) and C. immitis (Access N degrees AY536445) deposited in GenBank. DNA sequences from Escurra's lesions were 100% homologous to the recent Argentinean cases and the reference strain 1-NL. A single point C(R)G difference in position 1228 was observed with respect to sequence of strain C. posadasii Silveira. For the first time, Coccidioides DNA is recovered from a museum piece which is more than 100-year-old. Our results confirm that the original case of Posadas's disease was caused by the recently described C. posadasii.
- Published
- 2009
44. [A rare blood group: p phenotype].
- Author
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De La Vega Elena CD, Hellberg A, Bonetti S, Gonzalez CA, Chialina S, Raillon MA, Pivetta MA, Solis EA, and Olsson ML
- Subjects
- Adult, Base Sequence, Blood Transfusion, Female, Glycosyltransferases analysis, Humans, Pregnancy, Erythroblastosis, Fetal blood, Galactosyltransferases genetics, Mutation, Missense, P Blood-Group System genetics, Phenotype
- Abstract
A rare blood group is usually defined as the absence of a high prevalence antigen or the absence of several antigens within a single blood group system. These individuals may develop clinically significant red cell antibodies to the high incidence red cell antigens they lack. A 33-year-old alloimmunized woman was referred to our center at the 12th week of her third pregnancy for evaluation and follow up. The laboratory work-up grouped her as belonging to "p" phenotype, associated with difficulties to find compatible blood for transfusion and a high incidence of recurrent miscarriage. At 36 weeks, a baby girl was born by induced labor due to fetal suffering. With a negative direct antiglobulin test but a positive elution test, she was in the neonatology ward for one week receiving luminotherapy. Homozygosity for a missense mutation at position 752 (c.752C > T) in the A4GALT gene was found to be responsible for the p phenotype. This mutation changes a proline to a leucine at codon 251 of the 4-?-galactosyltransferase. Recently, due to an imminent chirurgical intervention and the impossibility to have compatible blood available for transfusion, an autologous donation plan was designed to satisfy probable demand. This case showed the need for blood bank facilities capable to respond satisfactorily to these situations in Argentina. This would facilitate the storage of cryopreserved blood from individuals with rare blood groups for homologous use or to develop rare blood donors programs.
- Published
- 2009
45. [Mitochondrial DNA analysis on pre-Columbian bone remains of the Herrera period].
- Author
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Silva A, Briceño I, Burgos J, Torres D, Villegas V, Gómez A, Bernal JE, and Rodríguez JV
- Subjects
- Archaeology, Base Sequence, Colombia, Computational Biology, Databases, Nucleic Acid, Haplotypes, History, Ancient, Humans, Polymorphism, Genetic, Bone and Bones cytology, Bone and Bones physiology, DNA, Mitochondrial analysis, Fossils, Paleontology, Sequence Analysis, DNA
- Abstract
Introduction: Ancient bone remains constitute an important source of biological information, and their genetic characterization allows the confirmation or rebuttal of human affiliations proposed on the basis of non-molecular approaches. Pre-Columbian history of the Eastern Andes in Colombia has been divided into three main periods: (i) an early colonization by groups of hunter-gatherers, (ii) an intermediate period "Herrera" characterized by primitive agriculture and (iii) a late stage of Chibcha-speaking groups, with agriculture and ceramics ("agroalfarero")., Objective: The mitochondrial DNA on ancient bone remains of the Herrera period were analyzed for comparison with modern and other ancient DNAs., Materials and Methods: Mitochondrial DNA was extracted from 11 Herrera individuals [approximately 2,000 years before present (YBP)] found in the Madrid 2-41 archaeological site near Bogotá, Colombia. A 192 bp segment of the hypervariable segment I was amplified and sequenced, following stringent archaic DNA authenticity criteria. The sequences were compared with those in American and European databases using bioinformatics tools., Results: All individuals had identical sequences and were classified as haplogroup B. This identity may be related to the type of ritual burial performed in the site, probably exclusively for members of a hierarchically important family of the ancient Herrera society. The search for homologous sequences in the American and European mtDNA data bases produced no identical coincidences, although a Brazilian Amazonic individual (approximately 4,000 YBP) was recorded with a matching sequence., Conclusion: Individuals buried in the Madrid 2-41 site were maternally closely related and showed a mtDNA sequence that is apparently absent in contemporary populations.
- Published
- 2008
46. [Molecular characterization of calicivirus strains detected in outbreaks of gastroenteritis occurring in Argentina during 2005 and 2006].
- Author
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Gomes KA, Stupka JA, Diana A, and Parra GI
- Subjects
- Adolescent, Adult, Aged, Argentina epidemiology, Astroviridae Infections epidemiology, Astroviridae Infections virology, Base Sequence, Caliciviridae genetics, Caliciviridae Infections epidemiology, Child, Child, Preschool, Gastroenteritis epidemiology, Genotype, Humans, Mamastrovirus isolation & purification, Molecular Sequence Data, Norovirus genetics, Norovirus isolation & purification, Phylogeny, Rotavirus isolation & purification, Rotavirus Infections epidemiology, Rotavirus Infections virology, Sapovirus genetics, Sapovirus isolation & purification, Sequence Alignment, Caliciviridae isolation & purification, Caliciviridae Infections virology, Disease Outbreaks, Gastroenteritis virology, RNA, Viral genetics
- Abstract
In order to determine the incidence of calicivirus, rotavirus and astrovirus in outbreaks of gastroenteritis occurring in different regions of Argentina during 2005 and 2006, fecal samples from seven nonbacterial outbreaks were analyzed. A commercial ELISA was used for rotavirus detection, while RT-PCRs were used for calicivirus and astrovirus. Of the 74 samples analyzed, 20 were calicivirus positive, 17 were rotavirus positive and one was astrovirus positive. No mixed infections were detected. A partial region of the RdRp gene was sequenced in five calicivirus positive-samples; 4 of them belonged to Norovirus genus and one to Sapovirus genus. The phylogenetic analysis of norovirus-positive-samples revealed the presence of strains from genogroups GI and GII; genotypes GII-4, GII-b and GII-17 were identified within the latter. Phylogenetic the sapovirus-positive-sample revealed the presence of genotype GI-1. This study represents a follow-up of the of molecular epidemiology analysis of calicivirus associated to gastroenteritis outbreaks that have been carried out by our group since 2004, and constitutes the first report of the circulation of genotype GII-17 in Argentina.
- Published
- 2008
47. [Molecular and immunological analyses suggest the absence of hydrophilic surface proteins in Leishmania (Viannia) panamensis].
- Author
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Marín M, Aguilar YA, Ramírez JR, Triana O, and Muskus CE
- Subjects
- Amino Acid Sequence, Animals, Antigens, Protozoan genetics, Base Sequence, Humans, Leishmania classification, Leishmania genetics, Membrane Proteins genetics, Molecular Sequence Data, Protozoan Proteins genetics, Sequence Alignment, Antigens, Protozoan metabolism, Leishmania metabolism, Membrane Proteins metabolism, Protozoan Proteins metabolism
- Abstract
Introduction: The genus Leishmania is divided into two subgenera: Leishmania and Viannia. The two subgenera present several important differences such as the pathology they cause in susceptible hosts, their in vitro growth behavior, their genetic characteristics, and the expression pattern of several proteins, including those of the hydrophilic surface protein family., Objective: To characterize the hydrophilic surface protein family in Leishmania (Viannia) panamensis., Materials and Methods: The hasp genes were amplified in L. (V.) panamensis, using specific primers previously designed to amplify this gene in Leishmania (Leishmania) major. The PCR products were cloned, sequenced, and the sequences analyzed using common bioinformatics tools. Secondly, a serological screening was undertaken with an enzyme-linked immunosorbent assay and Western blot to detect specific antibodies against the hydrophilic surface recombinant protein from L. (L.) major., Results: A copy of a pseudogene was amplified in L. (V.) panamensis which was 60% homologous with the L. (L.) major orthologous gene. Antibodies responded to the hydrophilic surface recombinant proteins only in sera from patients with visceral leishmaniasis [Leishmania (Leishmania) chagasi]., Conclusion: These results suggest the lack of a functional hasp gene in L. (V.) panamensis, suggesting probably the loss of the complete gene family in this species of the Viannia subgenus.
- Published
- 2008
48. [Epidemiologic and molecular study of Entamoeba histolytica and Entamoeba dispar strains in pacients with diarrhea in Cumana, Sucre state, Venezuela].
- Author
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Mora L, García A, De Donato M, and Urdaneta H
- Subjects
- Adolescent, Adult, Aged, Animals, Base Sequence, Child, Child, Preschool, Diarrhea etiology, Diarrhea parasitology, Dysentery, Amebic epidemiology, Endemic Diseases, Entamoeba genetics, Entamoeba histolytica genetics, Female, Helminthiasis epidemiology, Helminthiasis parasitology, Humans, Infant, Intestinal Diseases, Parasitic epidemiology, Intestinal Diseases, Parasitic parasitology, Male, Middle Aged, Molecular Sequence Data, Polymerase Chain Reaction, Prevalence, Protozoan Infections epidemiology, Protozoan Infections parasitology, Ribotyping, Sequence Alignment, Sequence Homology, Nucleic Acid, Species Specificity, Venezuela epidemiology, Dysentery, Amebic parasitology, Entamoeba isolation & purification, Entamoeba histolytica isolation & purification
- Abstract
An epidemiological and molecular study on E. histolytica and E. dispar was carried out in 428 patients with gastrointestinal symptomatology of diarrhea from different health centers in Cumana, Sucre state. The samples were processed through: direct examination with 0.85% physiological saline solution, temporal lugol staining, trichromic staining and the Ritchie method of concentration; a sucrose gradient was used for cyst isolation. The small subunit of the 16S RNA was amplified by nested, multiplex PCR for the molecular detection. The E. histolytica/E. dispar prevalences according to the direct, Ritchie and trichromic staining methods were 20.09, 13.79 and 12.15%, respectively; while prevalences according to PCR for E. histolytica and E. dispar were 6.31% and 4.44%, respectively, also detecting four cases of mixed infection. Sequencing of the amplified fragments of E. histolytica showed 100% homology with the sequences with strains from Merida (Venezuela), USA, Brazil, Mexico and GenBank. The infections by E. histolytica and E. dispar were statistically associated with age but not with sex. The presence of mucus, blood and abdominal pain were only associated to E. histolytica infection. The moderate prevalence of E. histolytica shows the endemic status of this population and warns about the potential problem as a morbidity and mortality in Sucre state. The frequency of E. dispar in this population suggests the existence of an overestimation problem in the diagnosis of amoebiasis with its clinical and epidemiological implications, and shows the poor knowledge about the true prevalences of this protozoan. The PCR allowed for the differential identification of E. histolytica and E. dispar, as well as the presence of mixed infections, making a great tool for epidemiological amoebiasis studies.
- Published
- 2008
49. [Characterizing the CD3 epsilon chain from the New World primate Aotus nancymaae].
- Author
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Del Castillo H and Vernot JP
- Subjects
- Amino Acid Sequence, Animals, Base Sequence, CD3 Complex genetics, Humans, Lymphocyte Activation immunology, Molecular Sequence Data, Protein Isoforms genetics, Receptor-CD3 Complex, Antigen, T-Cell genetics, Receptor-CD3 Complex, Antigen, T-Cell immunology, Sequence Alignment, Signal Transduction physiology, Aotidae immunology, CD3 Complex immunology, Protein Isoforms immunology
- Abstract
Introduction: The T-cell receptor (TCR)-associated complex, CD3 (d, g, e) and z-chains are essential transmembrane proteins for signal transduction during T cell activation and immune response, as well as during thymocyte development., Objective: This work established the CD3epsilon-chain primary structure for the New World owl monkey Aotus nancymaae., Materials and Methods: Total RNA was isolated from peripheral blood mononuclear cells; CD3epsilon molecule was amplified, cloned and sequenced., Results: The CD3epsilon amino acid sequence was deduced for the owl monkey Aotus nancymaae.> It has an identity for nucleotide and amino acid sequences with the human counterpart of 84% and 76%, respectively. As described in other species, the Aotus CD3-e molecule is very variable in the extracellular region and greatly conserved in the intracellular domain. Even though high variability occurs in the CD3epsilon-extracellular domain, the subregions involved in ectodomain folding are conserved., Conclusions: The primary structure suggested that the Aotus protein has a functional role similar to that of humans, and that the initial T-cell activation steps are also similar. However, the great variation observed in CD3epsilon-extracellular region in humans in contrast to the Aotus (especially in areas that are surface-exposed) indicated that some monoclonal antibodies against the human CD3 complex will not recognize these Aotus determinants.
- Published
- 2008
50. [Analysis of the primary and secondary structure of the mitochondrial serine transfer RNA in seven species of Lutzomyia].
- Author
-
Vivero RJ, Contreras-Gutiérrez MA, and Bejarano EE
- Subjects
- Animals, Base Sequence, Insect Vectors genetics, Molecular Sequence Data, Polymorphism, Genetic, Psychodidae classification, RNA genetics, RNA, Mitochondrial, RNA, Transfer, Ser genetics, Sequence Alignment, Nucleic Acid Conformation, Psychodidae genetics, RNA chemistry, RNA, Transfer, Ser chemistry
- Abstract
Introduction: Lutzomyia sand flies are involved in the transmission of the parasite Leishmania spp. in America. The taxonomy of these vectors is traditionally based on morphological features of the adult stage, particularly the paired structures of the head and genitalia. Although these characters are useful to distinguish most species of Lutzomyia, morphological identification may be complicated by the similarities within subgenera and species group., Objective: To evaluate the utility of mitochondrial serine transfer RNA tRNA Ser for taxonomic identification of Lutzomyia., Materials and Methods: Seven sand fly species, each representing one of the 27 taxonomic subdivisions in genus Lutzomyia, were analyzed including L. trinidadensis (Oswaldoi group), L. (Psychodopygus) panamensis, L.(Micropygomyia) cayennensis cayennensis, L. dubitans (Migonei group), L. (Lutzomyia) gomezi, L. rangeliana (ungrouped) and L. evansi (Verrucarum group). The mitochondrial tRNA Ser gene, flanked by the cytochrome b and NAD dehydrogenase subunit one genes, was extracted, amplified and sequenced from each specimen. Secondary structure of the tRNA Ser was predicted by comparisons with previously described homologous structures from other dipteran species., Results: The tRNA Ser gene ranged in size from 66 base pairs in L. gomezi to 69 base pairs in L. trinidadensis. Fourteen polymorphic sites, including four insertion-deletion events, were observed in the aligned 70 nucleotide positions. The majority of the substitutions were located in the dihydrouridine, ribothymidine-pseudouridine-cytosine and variable loops, as well as in the basal extreme of the anticodon arm., Conclusion: Changes of primary sequence of the tRNASer provided useful molecular characters for taxonomic identification of the sand fly species under consideration.
- Published
- 2007
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