Development of tetra-primer ARMS-PCR protocol to genotype the prolactin receptor SNP 39136666 and assessment of this SNP in Brazilian locally adapted cattle breeds / [Desenvolvimento de protocolo de tetra-primer ARMS- PCR para genotipagem do SNP 39136666 do receptor da prolactina e avaliação desse SNP em raças bovinas brasileiras localmente adaptadas]

As raças taurinas de origem ibérica Limonero e Carora (Bos primigenius taurus) possuem o fenótipo de pelo curto, liso e com baixa densidade folicular, o que confere a esses animais maior tolerância térmica e melhor produtividade em regiões quentes. Diferentes mutações associadas a esse fenótipo foram descritas no gene do receptor de prolactina PRLR, localizado no cromossomo bovino BTA20. Uma mutação recentemente encontrada é a substituição do nucleotídeo C por T, SNP 39136666 (p. R497*), no exon 11, que gera um códon de parada e, consequentemente, uma menor isoforma desse receptor. Neste trabalho, desenvolveu-se um protocolo rápido e de baixo custo para detecção desse SNP, utilizando-se a técnica de tetra-primer ARMS-PCR. Assim, foi possível detectar essa mutação nas raças brasileiras de origem ibérica localmente adaptadas: Caracu, Crioulo Lageano, Mocho Nacional e Pantaneiro. O alelo T foi mais frequente na raça Caracu (80%), enquanto o alelo C foi mais frequente na raça Crioulo Lageano (84%). Essa simples metodologia pode ser usada para genotipar esse SNP e ajudar na aplicação dessas informações moleculares em programas de melhoramento focados na tolerância térmica em bovinos taurinos e seus mestiços.(AU)

Development and application of two novel functional molecular markers of BADH2 in rice

BACKGROUND: Fragrance is one of the most important quality traits in rice, and the phenotype is attributed to the loss-of-function betaine aldehyde dehydrogenase (BADH2) gene. At least 12 allelic variations of BADH2 have been identified, and some of these have been applied to rice fragrance breeding using traditional molecular markers and Sanger sequencing techniques. However, these traditional methods have several limitations, such as being very expensive, imprecise, inefficient, and having security issues. Thus, a new molecular marker technology must be developed to improve rice fragrance breeding. RESULTS: In this study, more than 95% of the cultivated fragrant rice varieties belonged to a 7-bp deletion in exon 2 (badh2-E2) or an 8-bp deletion and 3-bp variation in exon 7 (badh2-E7). Both allelic variations resulted in the loss of function of the badh2 gene. We developed two novel SNP molecular markers, SNP_badh2-E2 and SNP_badh2- E7, related to the alleles. Their genotype and phenotype were highly cosegregated in the natural variation of rice accessions, with 160 of the 164 fragrant rice varieties detected with the two markers. These markers cosegregated with the fragrance phenotype in the F2 population. CONCLUSIONS: Two functional SNP molecular markers of badh2-E2 and badh2-E7 allelic variations were developed. These functional SNP molecular markers can be used for genotype and genetic improvement of rice fragrance through marker-assisted selection and will significantly improve the efficiency of fragrant rice breeding and promote commercial molecular breeding of rice in the future.

Introducción del genotipaje molecular de los antigenos plaquetarios / Introduction of molecular genotypingof plateles antigens

Introducción: Los antígenos plaquetarios humanos (HPA) se expresan en 6 glucoproteínas plaquetarias diferentes. Se ha descrito que estos antígenos pueden estimular la producción de aloanticuerpos una vez expuestos a plaquetas humanas con diferentes HPA, lo que provoca complicaciones clínicas como la trombocitopenia neonatal aloinmune y la púrpura postransfusional. Métodos: Se realizó el estudio a 11 muestras de pacientes en espera de trasplante renal de genotipo de los antígenos HPA-1,2,3 a/b mediante PCR multiplex, mientras que para el estudio de genotipo de los antígenos HPA-5a/b se utilizó la técnica de PCR con secuencia específica de primer. Los productos de ADN amplificados fueron visualizados mediante electroforesis en gel de agarosa y electroforesis capilar. Resultados: El análisis de los fragmentos de ADN amplificados revelaron resultados similares por ambos métodos. Para los antígenos HPA-1,-2, el 63 por ciento de las muestras fueron homocigóticas para el fenotipo (a) mientras que se observó heterocigocidad en todos los casos para el genotipo HPA-3. En el sistema HPA-5, el 54 por ciento fueron homocigóticas para el fenotipo (a) y el 46 por ciento, heterocigóticas. Para el genotipo del HPA-15, el 4 por ciento fueron homocigóticas para el fenotipo (b) mientras que el 96 por ciento resultaron ser heterocigóticas. Conclusiones: Estos resultados muestran similitudes para los genotipos HPA 1, 2,3 a/b, HPA 5a/b y HPA15 a/brespecto a lo planteado en la literatura(AU)

Introduction: Human platelet antigens (HPA) are expressed in 6 different platelet glycoproteins. It has been described that these antigens can stimulate the production of alloantibodies once exposed to human platelets with different HPA, which causes clinical complications such as neonatal alloimmune thrombocytopenia and postransfusional purpura. Methods: The study was performed on 11 samples of patients awaiting kidney transplantation of genotype of the HPA-1,2,3 a/b antigens by multiplex PCR, while for the genotype study of the HPA-5a/b antigens was used the PCR technique with primer-specificsequence. The amplified DNA products were visualized by agarose gel electrophoresis and by capillary electrophoresis. Results: The analysis of DNA fragments amplified by agarose electrophoresis and capillary electrophoresis revealed similar results in both methods. For the HPA-1, -2 antigens, 63 percent of the samples were homozygous for phenotype (a) while heterozygosity was observed in all cases for the HPA-3 genotype. In the HPA-5 system, 54 percent were homozygous for the phenotype (a) and 46 percent were heterozygous. For the genotype of HPA-15, 4 percent were homozygous for phenotype (b) while 96 percent proved heterozygous. Conclusions: These results show similarities for the genotypes HPA 1, 2.3 a/b, HPA 5a/b and HPA15 a/bwith respect to report in literature(AU)

Frecuencia, caracterización y análisis genotípico de Escherichia coli productor de toxina Shiga en frigoríficos de carne bovina de Argentina / Frequency, characterization and genotypic analysis of Shiga toxin-producing Escherichia coli in beef slaughterhouses of Argentina

The objectives of this study were: (1) to estimate STEC frequency in hide and carcass samples taken from beef slaughterhouses supplying the domestic market in Argentina, (2) to establish the pheno-genotypic characteristics of STEC and non-toxigenic Escherichia coli of serogroups O26, O45, O103, O121, O111, O145 or O157 isolated from the analyzed samples and, (3) to study their clonal relatedness. Sixty hides and 60 carcasses were analyzed. At the screening step, 48% of hide and 80% of carcass samples tested positive for the stx gene by endpoint PCR. The STEC isolation rate was 5% for hides and 8% for carcasses. The isolation rate of STEC-positive for O26, O45, O103, O111, O145 or O157 serogroups was 0% for hides and 2% for carcasses. With the purpose of studying the clonal relatedness of isolates, macrorestriction fragment analysis by pulsed-field gel electrophoresis was performed. The results indicated cross-contamination between hides and between carcasses of animals in the same lot and, that the origin of carcass contamination was their own hide, or the hides of other animals in the same lot. The high detection rate at the screening step, especially in carcasses, and the evidence of cross-contamination show the need to apply additional in-plant intervention strategies aimed at preventing carcass contamination.

Los objetivos del presente estudio fueron tres: 1) estimar la frecuencia de Escherichia coli productor de toxina Shiga (STEC) en muestras de cuero y carcasa de bovinos en frigoríficos de consumo interno de Argentina; 2) realizar la caracterización feno-genotípica de las cepas STEC y de Escherichia coli no toxigénicas pertenecientes a los serogrupos O26, O45, 0103, O121, O145 u O157 aisladas a partir de las muestras analizadas; 3) establecer la relación clonal de ese conjunto de cepas. Se analizaron 60 cueros y 60 carcasas. En la etapa de tamizaje, el gen stx se detectó en el 48% de las muestras de cuero y en el 80% de las muestras de carcasa por una PCR de punto final. La frecuencia de recuperación de cepas STEC fue del 5% en cueros y del 8% en carcasas, y la de cepas STEC positivas para los serogrupos O26, O45, O103, O121, O111, O145 u O157 fue del 0% en los cueros y del 2% en las carcasas. La relación clonal de las cepas aisladas se investigó a través de electroforesis de campo pulsado y análisis de los patrones de macrorrestricción generados. Los resultados demostraron la existencia de contaminación cruzada entre cueros y carcasas de animales pertenecientes a un mismo lote, y también que el origen de la contaminación fue el propio cuero del animal o el cuero de otros animales pertenecientes al mismo lote. Los altos porcentajes de detección en la etapa de tamizaje, especialmente en carcasas, y la evidencia de contaminación cruzada ponen de manifiesto la necesidad de evaluar la implementación de estrategias de intervención tendientes a evitar la contaminación de carcasas.

Full Sibling Testing Based on NGS-SNP Genotyping Method and IBS Strategy / 法医学杂志

Objective To evaluate the effectiveness of single nucleotide polymorphism （SNP） genoty-ping in combination with identity by state （IBS） strategy in full sibling testing. Methods Thirty-five blood samples were collected from a four-generation family. Ninety autosomal SNPs were genotyped using Precision ID Identity Panel. The distribution of IBS scores for full siblings and other relationships were calculated and compared. The relationships were determined using Fisher discriminant function and threshold method, respectively. Results Based on family members and previous research, 44, 30, 111, 71 and 1 000 pairs of full siblings （FS）, grandparent-grandchild （GG）, uncle/aunt-nephew/niece （UN）, first cousins （FC） and unrelated individuals （UI） were obtained, respectively. The average IBS scores were 148, 130, 132, 124 and 120, respectively. Except for the GG and UN pairs, the distribution differences among the other relationships had statistical significance （P<0.05）. The false rates of Fisher discriminant function to determine relationships were 1.3%, 22.3%, 17.0% and 38.7% for FS, GG, UN and FC, respectively. Based on the simulation data, the thresholds t1=128 and t2=141 were recommended to determine full sibling relationships （the false rate ≤0.05%）. Conclusion The 90 SNP genetic markers included in the Precision ID Identity Panel meet the testing requirements for full sibling relationships. The threshold method based on IBS has a relatively lower false rate and is more flexible.

Allele and haplotype frequencies of human platelet and leukocyte antigens in platelet donors / Frequência alélica e haplotípica dos antígenos plaquetários e leucocitários humanos em doadores de plaquetas

ABSTRACT Objective To described the allele and haplotype frequencies of human leukocyte antigen genes at the -A, -B loci and human platelet antigen genes for human platelet antigen systems 1 to 9, 11 and 15 in blood. Methods We included 867 healthy unrelated volunteer donors who donated platelets between January 2011 and December 2014. Microarray genotyping was performed using a BeadChip microarray. Medium resolution typing of the human leukocyte antigen at loci A and B was carried out using sequence-specific oligonucleotide probe hybridization. We used multivariate analysis and our human leukocyte antigen population was compared to data from the United States national bone marrow donor program. Human platelet antigen results were compared to a literature review and data from around the world. Results Our human leukocyte antigen haplotype results were more similar to those of hispanics, followed by caucasians. Likewise, our human platelet antigen sample is more similar to those of Argentina, Rio Grande do Sul and Italy. Conclusion This was the first article that discusses human platelet antigen and human leukocyte antigen data together. Rare genotypes or antibody associations can make patient management difficult. A blood bank with genotyped donors allows for optimal transfusion and can contribute to better results. Our information can serve as basis for a database of platelet antigen polymorphisms.

RESUMO Objetivo Descrever as frequências alélicas e haplotípicas de genes dos antígenos leucocitários humanos nos loci -A,- B e dos antígenos plaquetários humanos para os sistemas HPA-1 a 9, 11 e 15. Métodos Foram incluídos 867 doadores voluntários, saudáveis, não relacionados, que doaram plaquetas por aférese entre janeiro de 2011 e dezembro de 2014. A genotipagem foi realizada usando microarray BeadChip. A tipificação de resolução intermediária dos antígenos leucocitários humanos loci A e B foi realizada por meio de hibridização com sonda para oligonucleotídeos por sequência específica. Utilizamos análises multivariadas e o antígeno leucocitário humano de nossa população foi comparado com a do programa nacional de doadores de medula óssea norte-americano. Já os resultados dos antígenos plaquetários humanos foram comparados à revisão da literatura e a dados de populações de outros países. Resultados Os resultados do haplótipo de antígenos leucocitários humanos são mais parecidos com os dos hispânicos, seguidos dos caucasianos. Igualmente, a amostra de antígenos plaquetários humanos foi mais semelhante às da Argentina, do Rio Grande do Sul e da Itália. Conclusão Este foi o primeiro artigo a discutir antígenos plaquetários e leucocitários humanos simultaneamente. Genótipos raros ou associações de anticorpos podem dificultar o manejo clínico do paciente. Um banco de sangue com doadores genotipados permite um melhor resultado e transfusão possíveis. Estas informações podem servir de base para um banco de dados sobre polimorfismos de antígenos plaquetários.

Desempeño de métodos moleculares para la identificación de subtipos poco comunes del virus de la hepatitis C, genotipo 2 / Performance of molecular methods for identification of unusual subtypes of hepatitis C virus genotype 2

Resumen Introducción. El virus de la hepatitis C (HCV) presenta una gran variabilidad genética, con siete genotipos y numerosos subtipos. La determinación del tipo viral ha sido fundamental para la escogencia y la duración del tratamiento antiviral adecuado. En Venezuela, el genotipo 2 del HCV es relativamente diverso, siendo particularmente prevalente el subtipo 2j. Objetivo. Evaluar el desempeño de las metodologías para la determinación del genotipo del HCV, particularmente para la identificación del subtipo 2j. Materiales y métodos. Se determinaron el genotipo y el subtipo del HCV mediante la técnica de hibridación inversa LiPA (Line Probe Assay) y secuenciación de las regiones genómicas 5'NC y NS5B del virus. Resultados. En 65 muestras analizadas, la metodología basada en la amplificación de la región 5'NC mostró mayor sensibilidad (100 %), en comparación con la técnica LiPA (91 %) y la secuenciación de la región NS5B (77 %). La determinación de genotipo, tomando como método de referencia la secuenciación de NS5B, mostró un alto grado de concordancia para la secuenciación de la región 5´NC y la hibridación inversa LiPA, con 100 % en la asignación de genotipos, comparado con 70 % y 66 % para los subtipos, respectivamente. La secuenciación de la región NS5B permitió identificar los subtipos 2j y 2s, los cuales no fueron detectados por las otras metodologías. No se observó un patrón característico para las muestras subtipo 2j en la hibridación inversa LiPA. Conclusión. Aunque es la metodología con menor sensibilidad, la secuenciación de la región NS5B es una herramienta poderosa para la correcta discriminación de los distintos subtipos circulantes del HCV, lo cual reviste importancia epidemiológica.

Abstract Introduction: Hepatitis C virus (HCV) displays high genetic variability, with seven genotypes and numerous subtypes. The determination of the viral type has been essential for the selection and timing of antiviral treatment. In Venezuela, HCV genotype 2 is relatively diverse, being particularly prevalent subtype 2j. Objective: To evaluate the performance of methodologies for genotyping HCV, particularly for identification of subtype 2j. Materials and methods: HCV genotype and subtype were determined by reverse hybridization technique (LiPA) and sequencing of the HCV 5'UTR and NS5B regions. Results: A total of 65 samples from HCV-infected patients were analyzed. PCR amplifications of the 5'UTR region exhibited the highest sensitivity (100% vs 91% for LiPA and 77% for NS5B). Genotype determination, taking as reference test NS5B, showed 100% concordance with the other methods, and 67% and 59% for subtypes with 5´NC and LiPA, respectively. NS5B sequencing allowed the identification of subtypes 2j and 2s, which were not detected by the other methods. A specific LiPA pattern was not observed for HCV subtype 2j. Conclusion: Although being the methodology with lowest sensitivity for amplification of HCV RNA, sequencing NS5B region remains a powerful tool for correct discrimination of the different HCV subtypes, which is of epidemiological relevance.

Molecular studies on African swine fever virus from Brazilian isolates / Estudos moleculares do vírus da peste suína africana de isolados brasileiros

African swine fever (ASF) is a devastating viral infirmity that affects domestic and wild swine caused by the ASF virus (ASFV) that belongs to the family Asfaviridae in the Asfavirus genus. Studies for genotypic and antigenic determination of ASFV including samples from Brazilian outbreaks were carried out outside Brazil. Here, we have reviewed studies on the molecular aspects of Brazilian isolates from 1978 and 1979. Results obtained from restriction fragment analysis, cloning and gene sequencing display the genotypic variation of viral samples. Viral genotyping based on sequences of the 3' region of the p72 gene included in genotype I Brazilian samples, reinforcing the suggestion of the European origin for the virus that infected Brazilian herds and having low virulence potential. Corroborating those findings, at the American station PIADC, the infection of healthy pigs with the Brazilian strain induced ASF sub acute disease with low mortality and a low-virulence. Those results were similar with epidemiological vigilance forms of Brazilian swineherd in good health conditions having at least one ASFV isolation, and the ASF pioneer's studies on the low mortality in the Brazilian herds affected by ASF. The ASFV spreading in Eastern Europe and Russia triggered a greater concern with intensifying the risk of viral dissemination from country to country. The low virulence ASF strains can increase the problem because of hidden viral reservoirs - which further reinforces the need for safety and preventive measures in virus-free countries. Finally, the problem is further compounded by the lack of vaccines and other immunological resources.(AU)

A peste suína africana é uma enfermidade viral devastadora que afeta suínos domésticos e selvagens causada pelo vírus pertencente à família Asfaviridae no gênero Asfavirus. Estudos para determinação genotípica e antigênica do vírus da peste suína africana, incluindo as amostras de surtos brasileiros, foram realizados em laboratórios fora do Brasil. Aqui, revisamos os estudos sobre o aspecto molecular de isolados brasileiros de 1978 e 1979. Os resultados obtidos pela análise de fragmentos de restrição, clonagem e sequenciamento mostram variação genotípica das amostras virais. A genotipagem viral baseada nas sequências da região 3' do gene p72 incluíram amostras brasileiras no genótipo I, reforçando a sugestão da origem europeia do vírus que infectou rebanhos brasileiros e potencialmente de baixa virulência. Corroborando, na estação americana Plum Island Animal Disease Center, a inoculação do vírus da peste suína africana do surtos brasileiros em suínos saudáveis evoluiu para peste suína africana subaguda com baixa mortalidade sugerindo a baixa virulência. Similarmente aos formulários de vigilância epidemiológica de rebanhos em boas condições sanitárias que tiveram pelo menos um isolamento de vírus da peste suína africana e com os estudos pioneiros sobre a baixa mortalidade nos rebanhos afetados pela peste suína africana. A dispersão do vírus da peste suína africana na Europa Oriental e Rússia desencadearam uma preocupação com o risco de disseminação do vírus entre países. O vírus da peste suína africana de baixa virulência pode aumentar o problema porque esconde reservatórios virais e reforça a necessidade de medidas preventivas e de segurança em países livres de vírus. Finalmente, o problema é ainda mais agravado pela falta de vacinas e outros recursos imunológicos.(AU)

Molecular characterization of Mycobacterium tuberculosis and Mycobacterium bovis isolates by Enterobacterial Repetitive Intergenic Consensus-PCR

Tuberculosis (TB) is an infectious disease in which the molecular typing methods allow to have important information about the dynamics of transmission and to assist properly in disease control. Although the ERIC-PCR (Enterobacterial repetitive intergenic consensus-PCR) assay is fast and easy to perform, scarce studies have reported its use in epidemiological studies in TB outbreaks. In this study, we aimed to genotype Mycobacterium tuberculosis and M. bovis isolates by ERIC-PCR and compare its discriminatory power with two other classically used methods: 12 loci-MIRU (Mycobacterial Interspersed Repetitive Units) and Spoligotyping. The M. tuberculosis isolates studied were from northwestern and southwestern and M. bovis from northwestern Parana, Brazil. ERIC-PCR rendered banding patterns with great diversity (1 to 12 bands) of molecular sizes, ranging from 100 to 1600 bp. ERIC-PCR showed to be fast, simple and affordable to differentiate isolates. ERIC-PCR would be an important tool in the epidemiology of TB as screening in case of outbreak, which demands rapid intervention. However if any doubt persist, as it may occur with the application of only one genotypic method, other genotyping methods should be applied and carefully interpreted, always with additional epidemiological information.

A participação da autofagia na regulação da célula-tronco hemopoética em camundongos knockouts para Atg7 e transglutaminase 2 / The participation of autophagy in hemopoietic stem cell regulation in mice Knockouts for Atg7 and transglutaminase 2

A desnutrição é um dos principais problemas de saúde pública do mundo, que contribui significativamente para o aumento da morbidade e mortalidade. Estima-se um total de 815 milhões de pessoas subnutridas no mundo, e apesar da melhoria dos recursos alimentares o número de pessoas desnutridas ainda é alarmante. Estudos de nosso laboratório tem demonstrado, em modelo murino de desnutrição proteica, hipoplasia medular com evidências histológicas de alterações na matriz extracelular (MEC) e permanência da célula-tronco hemopoética (CTH) na fase G0/G1 do ciclo celular em camundongos desnutridos. Dados deste trabalho evidenciaram alterações nas proteínas Akt /mTOR, que podem contribuir para o aumento da expressão autofágica nas CTHs e CTPHs (célula-tronco progenitora). A literatura demonstra que desequilíbrios nutricionais e metabólicos podem induzir ativação autofágica. Autofagia é um processo catabólico que participa da manutenção da homeostase celular, da MEC e na regulação das CTHs, dados deste trabalho demonstram diminuição da quantidade de CTH e CTPH em camundongos desnutridos sem a presença do gene Atg7, proteína participativa no processo autofágico. Já camundongos com deleção da transglutaminase 2 (TG2) e submetidos a privação de nutrientes por 24 horas , apresentou diminuição da quantidade de CTH e aumento da diferenciação da CTPH. A TG2 tem participação na impulsão e formação do fagóforo (processo inicial autofágico). Considerando que a desnutrição proteica leva a comprometimento da hemopoese, alterações no ciclo celular das CTHs e hipoplasia medular com pancitopenia periférica e que privação e ou jejum prolongado de nutrientes pode aumentar a atividade autofágica, concluímos nesse projeto que autofagia é importante para regulação da CTH e diferenciação da CTPH, entretanto a desnutrição proteica e privação de nutrientes estimula de maneira diversa o mecanismo de diferenciação da CTH

Malnutrition is one of the world's major public health problems, which contributes significantly to increased morbidity and mortality. An estimated 815 million people are undernourished in the world, and despite the improvement in food resources the number of undernourished people is still alarming. Studies of our laboratory have demonstrated in murine model of protein malnutrition, medullary hypoplasia with histological evidence of extracellular matrix (ECM) changes and hemopoietic stem cell (HSC) stay in the G0/ G1 phase of the cell cycle in malnourished mice. Data from this work showed alterations in Akt / mTOR proteins, which may contribute to the increase of autophagic expression in HSC and HPC (progenitor stem cell). The literature demonstrates that nutritional and metabolic imbalances can induce autophagic activation. Autophagy is a catabolic process that participates in the maintenance of cellular homeostasis, ECM and in the regulation of HSC, data from this work demonstrate a decrease in the amount of HSC and HPC in malnourished mice without the presence of the Atg7 gene, a participatory protein in the autophagic process. Mice with transglutaminase 2 deletion (TG2) and submitted to nutrient deprivation for 24 hours showed a decrease in the amount of HSC and an increase in the differentiation of HPC. TG2 plays a role in the uptake and formation of phagophore (autophagic initial process). Considering that protein malnutrition leads to hemopoiesis, alterations in the cell cycle of HSC and spinal cord hypoplasia with peripheral pancytopenia, and that prolonged nutrient starvation or fasting may increase the autophagic activity, we conclude in this project that autophagy is important for regulation of HSC and differentiation of HPC, however, protein malnutrition and nutrient deprivation stimulate in a different way the mechanism of differentiation of HSC

Detection and genotyping of human adenovirus and sapovirus in children with acute gastroenteritis in Belém, Pará, between 1990 and 1992: first detection of GI. 7 and GV. 2 sapoviruses in Brazil

Abstract INTRODUCTION: Acute gastroenteritis (AGE) is one of the most common causes of morbidity and mortality, especially among children from developing countries. Human adenovirus (HAdV) and sapovirus (SaV) are among the agents that cause AGE. The present study aimed to detect and genotype HAdV and SaV in 172 fecal samples from children with AGE, collected during a surveillance study carried out in a low-income community in Belém, Pará, between 1990 and 1992. METHODS: HAdV was detected by nested PCR, using primers Hex1deg/Hex2deg and NeHex3deg/NeHex4deg. SaV was assayed by reverse transcription PCR (RT-PCR), nested PCR, and quantitative PCR. The nucleotide sequence was determined by direct cycle sequencing. RESULTS: Overall, 43% (74/172) of samples were positive for HAdV, of which 70.3% (52/74) were sequenced and classified as belonging to five different species, mostly A and F. For SaV, positivity was 5.2% (9/172) and genotypes GI.1, GI.7, GII.1, and GV.2 were detected. CONCLUSIONS: The present results reinforce the need for further studies to obtain epidemiological data about the circulation of these viruses in Brazil, especially in the Amazon Region, where data from the early 1990's are scarce. Furthermore, the study describes for the first time the detection of SaV genotypes GI.7 and GV.2 in Brazil, showing that these types circulated in the region more than 25 years ago.

Descripción de las mutaciones de Mycobacterium tuberculosis que confieren resistencia a rifampicina e isoniacida detectadas mediante GenoType(r) MTBDR plus V.2 en Colombia / Description of Mycobacterium tuberculosis mutations conferring resistance to rifampicin and isoniazid detected by GenoType(r) MTBDR plus V.2 in Colombia

Resumen Introducción: La metodología de GenoType(r) MTBDRplus V.2 es una técnica molecular aprobada por la Organización Mundial de la Salud y la Organización Panamericana de la Salud para la detección de las mutaciones en el gen rpoβ del complejo Mycobacterium tuberculosis, las cuales confieren resistencia a la rifampicina, y las de los genes katG e inhA que la confieren frente a la isoniacida. Debido a la variación genética en las cepas circulantes a nivel mundial, los programas nacionales de control de la tuberculosis deben comprobar el desempeño de los nuevos métodos de diagnóstico para su aplicación como prueba rápida. Objetivo: Describir las mutaciones detectadas mediante la técnica GenoType(r) MTBDRplus V.2 en muestras pulmonares y aislamientos de M. tuberculosis procesados en el Laboratorio Nacional de Referencia del Instituto Nacional de Salud durante el 2014. Materiales y métodos: Se hizo un estudio retrospectivo descriptivo que determinó la expresión de los genes inhA, KatG y rpoβ responsables de la resistencia a isoniacida y rifampicina, utilizando la técnica GenoType(r) MTBDRplus V.2 en 837 muestras y aislamientos de casos de tuberculosis. Resultados. Se obtuvieron 689 resultados de pruebas: 581(84,3 %) sensibles, 58 (8,4 %) resistentes y 50 (7,2 %) multirresistentes. Se detectaron diversas mutaciones en el gen rpoβ, de las cuales la más frecuente fue la Ser531Leu (36,6 %), seguida por la Asp516Val (21,6 %), en tanto que en el gen katG la más frecuente fue la Ser315Thr1 (91,9 %). Conclusiones: Se detectaron varias mutaciones en los casos resistentes reportados en el país, con frecuencias similares a las reportadas en otros países de la región de América del Sur.

Abstract Introduction: The GenoType(r)MTBDRplusV.2 assay is a molecular technique endorsed by the World Health Organization and the Pan American Health Organization that allows for the identification of the Mycobacterium tuberculosis complex and the detection of mutations in the rpoβ gene for rifampicin resistance, and katG and inhA genes for isoniazid resistance. Due to the genetic variability in the circulating strains around the world, the national tuberculosis control programs should assess the performance of these new diagnostic technologies and their use under program conditions as rapid tests. Objective: To describe the mutations identified by the GenoType(r)MTBDRplusV.2 assay in pulmonary samples and Mycobacterium tuberculosis isolates in the Laboratorio Nacional de Referencia of the Instituto Nacional de Salud in 2014. Materials and methods. We conducted a retrospective, descriptive study to detect the expression of inhA, KatG and rpoβ genes, responsible for resistence against isoniazid and rifampicin using the GenoType(r) MTBDRplus V.2 assay in 837 samples and isolates from tuberculosis cases. Results: Several mutations in the rpoβ gene were identified. Ser531Leu was the most frequent (36.6%) followed by Asp516Val (21.6%), while Ser315Thr1 was the most frequent mutation in the katG gene (91.9%). Conclusions: We were able to identify different mutations present in MDR-TB strains in the country, with frequencies similar to those reported in other countries in the South American region.

Relationship between glycemic control and OPG gene polymorphisms with lower bone mineral density in patients with type 1 Diabetes mellitus

ABSTRACT The aim of the present study was to investigate the bone mineral density (BMD) of patients with type 1 Diabetes mellitus (T1DM). We also assessed the association between osteoprotegerin (OPG) genetic polymorphisms and BMD. Genotyping was performed for 1181G>C and 163A>G OPG polymorphisms by allelic discrimination in 119 patients with T1DM and 161 normoglycemic (NG) individuals, aged 6 to 20 years old. Glycemic control, serum parameters of bone metabolism and BMD were evaluated. T1DM patients showed low BMD, poor glycemic control and decreased total calcium values when compared to controls (p < 0.05). For all the polymorphisms studied, the genotype and allele frequencies in patients with T1DM were not significantly different from the controls. In patients with T1DM, carriers of OPG 1181CC showed higher concentrations of ionized calcium compared to patients with GG+GC genotypes. These results suggest that low BMD is associated with poor glycemic control in T1DM. Despite the lack of a detected association between OPG polymorphisms and BMD in these patients, the increased ionized calcium in those carrying OPG 1181CC suggests a possible increase in osteoclastogenesis, a conclusion that may be supported by the lower BMD observed in these subjects.

Design of an allele-specific PCR assay to genotype the rs12255372 SNP in a pilot study of association between common TCF7L2 polymorphisms and type 2 diabetes in Venezuelans

Objective The global burden of diabetes mellitus will impact strongly American countries in the coming decades. Type 2 diabetes mellitus (T2DM) is a multifactorial disease and the basis for its genetic susceptibility remains not fully understood. Different population studies have demonstrated that variants of the TCF7L2 gene are strongly associated with an increased risk of T2DM. Moreover, institutions or countries with limited budget to conduct genetic research need cost effective methods for detecting DNA variants. Subjects and methods We standardized a rapid and simple allele-specific PCR method for genotyping the rs12255372 single nucleotide polymorphism (SNP) in a pilot study exploring the association of three TCF7L2 polymorphisms (rs7903146, rs12255372 and DG10S478) with T2DM in 70 patients and 73 controls from Venezuela. Results The performance of the designed allele-specific PCR reaction for rs12255372 genotyping was reliable and accurate. Patients carrying the TCF7L2 rs7903146 T allele (CT + TT genotypes) and heterozygous CT genotype had a significantly higher risk for T2DM (OR = 2.9 and 2.3, respectively). Although rs12255372 and DG10S478 risk alleles predominated in T2DM group no statistical significance was found. Conclusions We developed a novel allele-specific PCR method for easier and rapid detection of rs12255372 polymorphism without the use of expensive instrumentation and reagents. Our study in a relatively small sample of the Venezuelan population replicated the association of the rs7903146 SNP with T2DM. Further studies with larger sample size and more biochemical data should be conducted to explore the genetic basis of T2DM susceptibility in Venezuela.

ACE I/D Polymorphism in Brazilian Women with Endometriosis / Polimorfismo ACE I/D em Mulheres Brasileiras com Endometriose

Endometriosis is a chronic gynecological disease that displays some features similar to malignancy, such as local invasion, aggressive spread to distant organs and angiogenesis. Polymorphisms of the ACE gene have been linked with some vascular disease. To determine the frequency of the ACE I/D polymorphism in Brazilian patients with endometriosis compared to controls. This case-control study included a total of 134 women (49 endometriosis patients and 85 controls) who had undergone a laparoscopy or laparotomy. Molecular analysis was performed by polymerase chain reaction (PCR). For the statistical analysis, the chi-square and multiple logistic regression tests were used. The I/D ACE genotype frequencies in cases and controls were, respectively: II 16.3% and 16.5%; ID 24.5% and 20%; DD 59.2% and 63.5%. There was no statistically significant difference between cases and controls, either in the genotype frequencies (χ2 = 0.385; p = 0.825) or in the allele frequencies (χ2 = 0.098; p = 0.75) of the ACE I/D polymorphism. However, the genotype distribution was not consistent with the Hardy-Weinberg equilibrium, either in patients (χ2 = 7.84; p = 0.005) or in controls (χ2 = 20.09; p <0.0001). Multiple logistic regression analysis has not shown any differences amongst groups for the polymorphism studied [(OR 1.51; CI 95% 0.52- 4.41); p=0.4523]. Despite of the small sample size, the present study suggests that I/D ACE polymorphism is not related with endometriosis in brazilian patients.(AU)

A endometriose é uma doença ginecológica crônica que apresenta algumas características semelhantes à malignidade, tais como invasão local, disseminação para órgãos distantes e angiogênese. Polimorfismos no gene ACE têm sido relacionados com algumas doenças vasculares. Determinar a frequência do polimorfismo ACE I/D em pacientes brasileiros com endometriose em comparação aos controles. Estudo caso-controle que incluiu um total de 134 mulheres (49 pacientes com endometriose e 85 controles) que se submeteram a uma laparoscopia ou laparotomia. A análise molecular foi realizada por Reação em Cadeia da Polimerase (PCR). A análise estatística utilizou os testes de qui-quadrado e regressão logística. As frequências genotípicas ACE I/D em casos e controles foram, respectivamente: II 16,3% e 16,5%; ID 24,5% e 20%; DD 59,2% e 63,5%. Não houve diferença estatisticamente significativa entre os casos e controles, tanto nas frequências genotípicas (χ2 = 0,385; p = 0,825) ou nas frequências alélicas (χ2 = 0,098; p = 0,75) do polimorfismo ACE I/D. Entretanto, a distribuição genotípica não foi consistente com o equilíbrio de Hardy-Weinberg, tanto nos pacientes (χ2 = 7,84; p = 0,005) ou nos controles (χ2 = 20,09; p <0,0001). A análise de regressão logística não mostrou qualquer diferença entre os grupos para o polimorfismo estudado [(OR 1,51; CI 95% 0,52-4,41); p=0,4523]. Apesar do pequeno número de amostras, o presente estudo mostra que em pacientes brasileiras o polimorfismo ACE I/D não está relacionado com endometriose.(AU)

A human papillomavirus (HPV)-16 or HPV-18 genotype is a reliable predictor of residual disease in a subsequent hysterectomy following a loop electrosurgical excision procedure for cervical intraepithelial neoplasia 3 / 부인종양

OBJECTIVE: This study was conducted using the human papillomavirus (HPV) DNA chip test (HDC), in order to determine whether the HPV genotype is a predictor of residual disease in a subsequent hysterectomy following a loop electrosurgical excision procedure (LEEP) for cervical intraepithelial neoplasia (CIN) 3. METHODS: Between January 2002 and February 2015, a total of 189 patients who underwent a hysterectomy within 6 months of LEEP caused by CIN 3 were included in this study. We analyzed their epidemiological data, pathological parameters, high-risk HPV (HR-HPV) load as measured by the hybrid capture II assay, and HR-HPV genotype as measured by the HDC. A logistic regression model was used to analyze the relationship between covariates and the probability of residual disease in subsequent hysterectomy specimens. RESULTS: Of the 189 patients, 92 (48.7%) had residual disease in the hysterectomy specimen, CIN 2 in seven patients, CIN 3 in 79 patients, IA1 cancer in five patients, and IA2 cancer in one patient. Using multivariate analysis, the results were as follows: cone margin positivity (odds ratio [OR], 2.43; 95% CI, 1.18 to 5.29; p or =220 relative light unit (OR, 2.98; 95% CI, 1.38 to 6.43; p<0.01), positive endocervical cytology (OR, 8.97; 95% CI, 3.81 to 21.13; p<0.001), and HPV-16 or HPV-18 positivity (OR, 9.07; 95% CI, 3.86 to 21.30; p<0.001). CONCLUSION: The HPV-16 or HPV-18 genotype is a reliable predictive factor of residual disease in a subsequent hysterectomy following a LEEP for CIN 3.

Role of a GenoType MTBDRplus line probe assay in early detection of multidrug-resistant tuberculosis at a Brazilian reference center

Resistance to Mycobacterium tuberculosis is a reality worldwide, and its diagnosis continues to be difficult and time consuming. To face this challenge, the World Health Organization has recommended the use of rapid molecular tests. We evaluated the routine use (once a week) of a line probe assay (Genotype MTBDRplus) for early diagnosis of resistance and for assessment of the main related risk factors over 2 years. A total of 170 samples were tested: 15 (8.8%) were resistant, and multidrug resistance was detected in 10 (5.9%). The sensitivity profile took 3 weeks (2 weeks for culture and 1 week for rapid testing). Previous treatment for tuberculosis and the persistence of positive acid-fast smears after 4 months of supervised treatment were the major risk factors observed. The use of molecular tests enabled early diagnosis of drug-resistant bacilli and led to appropriate treatment of the disease. This information has the potential to interrupt the transmission chain of resistant M. tuberculosis.

Vascular endothelial growth factor insertion/deletion gene polymorphism in West Indian patients of type 2 diabetes and diabetic nephropathy.

Diabetic nephropathy (DN) is a major cause of morbidity and mortality in diabetes. Vascular endothelial growth factor (VEGF) is a potent multi-functional cytokine which plays a key role in the pathogenesis of DN. In this study, we evaluated the possible association of the VEGF gene (I/D) polymorphisms with DN in type 2 diabetes patients in West Indian population. Genotyping (I/D) of the VEGF gene polymorphism was done by the polymerase chain reaction. A total of 103 patients with type 2 diabetes, 102 patients with DN, 108 patients with non-diabetic nephropathy and 143 healthy controls were genotyped. The frequency of VEGF genotype distribution and biochemical parameters like creatinine and HbA1c were compared in diabetic, diabetic nephropathy, non diabetic nephropathy and control groups. We found significant difference in creatinine level in DN and NDN groups on comparison with control group. Our study suggests that I/D polymorphism in the promoter region of the VEGF gene is not associated with DN in type 2 diabetes patients, but might have a role in development of non-diabetic nephropathy.

Relationship of the total atrial conduction time to subclinical atherosclerosis, inflammation and echocardiographic parameters in patients with type 2 diabetes mellitus

OBJECTIVES: The aim of our study was to evaluate the total atrial conduction time and its relationship to subclinical atherosclerosis, inflammation and echocardiographic parameters in patients with type 2 diabetes mellitus. METHODS: A total of 132 patients with type 2 diabetes mellitus (mean age 54.5±9.6 years; 57.6% male) and 80 age- and gender-matched controls were evaluated. The total atrial conduction time was measured by tissue-Doppler imaging and the carotid intima-media thickness was measured by B-mode ultrasonography. RESULTS: The total atrial conduction time was significantly longer in the patients with type 2 diabetes mellitus than in the control group (131.7±23.6 vs. 113.1±21.3, p<0.001). The patients with type 2 diabetes mellitus had significantly increased carotid intima-media thicknesses, neutrophil to lymphocyte ratios and high-sensitivity C-reactive protein levels than those of the controls. The total atrial conduction time was positively correlated with the high-sensitivity C-reactive protein level, neutrophil to lymphocyte ratio, carotid intima-media thickness and left atrial volume index and negatively correlated with the early diastolic velocity (Em), Em/late diastolic velocity (Am) ratio and global peak left atrial longitudinal strain. A multiple logistic regression analysis demonstrated that the neutrophil to lymphocyte ratio, carotid intima-media thickness and global peak left atrial longitudinal strain were independent predictors of the total atrial conduction time. CONCLUSIONS: We suggest that subclinical atherosclerosis and inflammation may represent a mechanism related to prolonged total atrial conduction time and that prolonged total atrial conduction time and impaired left atrial myocardial deformation may be represent early subclinical cardiac involvement in patients with type 2 diabetes mellitus. .

Genotyping of High Risk Human Papillomavirus (HPV) Among Cervical Precancer and Cancer Patients.

Introduction: Human papillomavirus (HPV) is a DNA virus which has tropism for epithelial cells, is the major etiological factor for development of cervical precancerous and cancerous lesions. Nearly 100 diff erent types of HPV have been characterized and thereare a large number of other types. HPV infection is one of the most common causes of sexually transmitted disease in both men and women worldwide. It is associated with a variety of clinical conditions that range from innocuous lesions to cancer. Genital HPV types are divided into high and low-risk types, according to the oncogenic potential. Molecular and epidemiologic studies have solidifi ed the association between high risk HPV types (especially HPV-16 and HPV-18) and cervical squamous cell carcinoma. HPV infection is often transient and self-limiting but infection may persists and progress to high grade lesions and cancer. In addition to persistent high-risk HPV infection, other viral factors such as high viral loads, HPV variants, infections with multiple high-risk HPV types and genetic predisposition contribute to the development of cervical cancer. Th e aim of the present study was to detect HPV DNA and identify high risk HPV genotype among women having cervical intraepithelial neoplasia and carcinoma and to evaluate potential effi cacy of prophylactic HPV vaccine. Methods: Cervical swab from histopathologically diagnosed CIN (n=51) and carcinoma (n=39) patients were taken and high risk HPV DNA was detected by HC II assay. Polymerase Chain Reaction was used to identify high risk HPV genotype. Result: HPV DNA was detected in 41 (45.56%) patients by HC II assay. HPV type 16 was detected in 27 (81.82%) followed by type 18 in 3 (9.09%) and type 45 in 2 (6.06%) cases of cervical carcinoma. Among precancerous cases, only type 16 was detected. Conclusion: Knowledge based on HPV prevalence and genotype could be used to predict the effi cacy of cost eff ective prophylactic vaccine, introduction of newer generation vaccine and management of cervical carcinoma.