Role of genetic variability in Mendelian and multifactorial diseases

The first draft of the human genome sequencing published in 2001 reported a large number of single nucleotide polymorphisms (SNPs). Given that these polymorphisms could practically represent all the variability involved in the susceptibility, protection, severity, among other aspects, of various common diseases, as well as in their response to medications, it was thought that they might be “the biomarkers of choice” in personalized genomic medicine. With the new information obtained from the sequencing of a larger number of genomes, we have understood that SNPs are only an important part of the genetic markers involved in these traits. In addition to SNPs, other variants have been identified, such as insertions/deletions (INDELs) and copy number variants (CNVs), which – in addition to classic variable number tandem repeats (VNTRs) and short tandem repeats (STRs) – originate or contribute to the development of diseases. The use of these markers has served to identify regions of the genome involved in Mendelian diseases (one gene-one disease) or genes directly associated with multifactorial diseases. This review has the purpose to describe the role of STRs, VNTRs, SNPs, CNVs and INDELs in linkage and association studies and their role in Mendelian and multifactorial diseases.

Diversidad genética de cepas extraintestinales de Escherichia coli productoras de las betalactamasas TEM, SHV y CTX-M asociadas a la atención en salud / Genetic diversity of extraintestinal Escherichia coli strains producers of beta-lactamases TEM, SHV and CTX-M associated with healthcare

RESUMEN Introducción. En Venezuela existen pocos reportes que describan las bases genéticas del potencial patogénico y filogenético de las cepas de Escherichia coli provenientes de hospitales. Objetivo. Determinar la diversidad genética de cepas extraintestinales de E. coli productoras de las betalactamasas TEM, SHV y CTX-M asociadas a la atención de salud. Materiales y métodos. Se estudió una colección de 12 cepas extraintestinales de E. coli con sensibilidad disminuida a las cefalosporinas de amplio espectro. La sensibilidad antimicrobiana se determinó por concentración inhibitoria mínima. La detección de los grupos filogenéticos, de los factores de virulencia y de los genes que codifican la resistencia antimicrobiana se hizo mediante la técnica de reacción en cadena de la polimerasa y la relación clonal se estableció mediante reacción en cadena de la polimerasa de elementos palindrómicos extragénicos repetitivos (Repetitive Element Palindromic-PCR, rep-PCR). Resultados. Todas las cepas analizadas presentaron resistencia a las cefalosporinas, y resistencia conjunta a quinolonas y aminoglucósidos. La distribución filogenética evidenció que los grupos A y B1 fueron los más frecuentes, seguidos por D y B2; en este último, se detectaron todos los factores de virulencia evaluados, y el gen más frecuente fue el fimH. En todas las cepas analizadas, se encontró bla CTX-M, con predominio de las bla CTX-M-8, y en dos de estas cepas se evidenció la presencia simultánea de bla CTX-M-9, variantes bla CTX-M-65 y bla CTX-M-147. Conclusión. Las cepas estudiadas demostraron diversidad genética y albergaron diferentes genes de virulencia y betalactamasas de espectro extendido (BLEE) sin predominio de ningún filogrupo en particular. Este estudio constituye el primer reporte de la variante bla CTX-M-65 en Venezuela y de la variante bla CTX-M-147 en el mundo, en cepas no relacionadas genéticamente aisladas de hospitales, situación que merece atención y la racionalización del uso de los antimicrobianos.

ABSTRACT Introduction: There are few reports from Venezuela describing the genetic basis that sustains the pathogenic potential and phylogenetics of Escherichia coli extraintestinal strains isolated in health care units. Objective: To establish the genetic diversity of extraintestinal E. coli strains producers of beta-lactamases TEM, SHV and CTX-M associated with healthcare. Materials and methods: We studied a collection of 12 strains of extraintestinal E. coli with diminished sensitivity to broad-spectrum cephalosporins. Antimicrobial susceptibility was determined by minimum inhibitory concentration. We determined the phylogenetic groups, virulence factors and genes encoding antimicrobial resistance using PCR, and clonal characterization by repetitive element palindromic-PCR rep-PCR. Results: All strains showed resistance to cephalosporins and joint resistance to quinolones and aminoglycosides. The phylogenetic distribution showed that the A and B1 groups were the most frequent, followed by D and B2. We found all the virulence factors analyzed in the B2 group, and fimH gene was the most frequent among them. We found bla CTX-M in all strains,with a higher prevalence of bla CTX-M-8; two of these strains showed coproduction of bla CTX-M-9 and were genetically identified as bla CTX-M-65 and bla CTX-M-147 by sequencing. Conclusion: The strains under study showed genetic diversity, hosting a variety of virulence genes, as well as antimicrobial resistance with no particular phylogroup prevalence. This is the first report of bla CTX-M alleles in Venezuela and in the world associated to non-genetically related strains isolated in health care units, a situation that deserves attention, as well as the rationalization of antimicrobials use.

Cardiac markers in five different breeds of rabbits (Oryctolagus cuniculus Linnaeus, 1758) used for cardiovascular research / Marcadores cardíacos em cinco diferentes raças de coelhos (Oryctolagus cuniculus Linnaeus, 1758) utilizados para pesquisa cardiovascular

Cardiac biomarkers for clinical and experimental heart diseases have previously been evaluated in rabbits. However, several laboratory assays performed and reported with inconsistent results. This study aimed to assess the effects of breed on serum ANP, CRP, and ACE and establish reference interval (RI) for these biomarkers in a large population of healthy rabbits. Ninety-seven adult rabbits from five breeds were included in this study. Assays were performed using specific ELISA commercial kits. The results were statistically analyzed using ANOVA, Tukey test (p<0.05), arithmetic mean, RI of mean, and standard deviation. A significant effect of breed was shown, indicating different RI between breeds for each biomarker. In conclusion, this study demonstrated that breed is an important physiological variable influencing the normal values of cardiac markers in healthy rabbits.(AU)

Biomarcadores cardíacos têm sido avaliados em coelhos para avaliação clínica e experimental das doenças cardíacas. Entretanto diferentes testes laboratoriais têm sido utilizados e relatados, sem uma confluência de resultados. Os objetivos deste estudo foram verificar os efeitos de diferentes raças de coelhos sobre as concentrações séricas de ANP, CRP e ACE, além de estabelecer intervalor de referência para estes biomarcadores em uma população de coelhos saudáveis. Foram utilizados noventa e sete coelhos de cinco diferentes raças. Os exames foram realizados pela metodologia de ELISA, por meio de kits comerciais específicos. Os resultados foram analisados estatisticamente os testes de ANOVA e Tukey (p<0,05), média aritmética, intervalo de referência da média e desvio padrão. Um efeito significativo da raça foi observado sobre as variáveis estudadas, indicando diferentes intervalos de referência entre as raças para cada biomarcador. Em conclusão, este estudo demonstrou que a raça é uma variável fisiológica importante que influencia os valores normais destes biomarcadores em coelhos saudáveis.(AU)

Genetic diversity of Arapaima gigas (Schinz, 1822) (Osteoglossiformes: Arapaimidae) in the Araguaia-Tocantins basin estimated by ISSR marker

The genetic diversity of the specimens of four natural populations of Arapaima from Araguaia-Tocantins basin was assessed within and among these stocks, using five primers for ISSR. COI (cytochrome c oxidase subunit I) partial sequences confirmed that the specimens belongs to Arapaima gigas. The ISSR provided 168 loci, of which 165 were polymorphic. However, the number of loci for each population and expected heterozygosity values were low. AMOVA showed 52.63% intra-population variation and 47.37% inter-population variation. The F ST was high among all populations (F ST ≥ 0.25), however, the cluster analysis (PCoA) and Bayesian inference showed three major groups: Araguaiana-MT + São Félix do Araguaia-MT, Novo Santo Antônio-MT and Itupiranga-PA. The genetic distance was not correlated with geographical distance. The ISSR marker revealed that the populations of the Araguaia-Tocantins are structured and have a low genetic diversity. These are the first data from a population analysis using molecular markers for A. gigas of Araguaia-Tocantins basins and may be used to define the best management strategies and conservation projects for this species.

A diversidade genética dos espécimes de quatro populações naturais de Arapaima coletados na bacia do Araguaia-Tocantins foi avaliada com base em cinco primers para marcadores moleculares ISSR. A sequência parcial do COI (cytochrome c oxidase subunit I) confirmou que os espécimes pertencem à espécie Arapaima gigas. Os ISSR forneceram 168 loci, dos quais 165 polimórficos. No entanto, para cada população, os valores de heterozigosidade esperada foram baixos. A AMOVA mostrou 52,63% de variação intrapopulacional e 47,37% interpopulacional. O F ST foi alto entre todas as populações (F ST ≥ 0,25); entretanto, a análise de agrupamento e a inferência Bayesiana mostraram três grandes grupos: Araguaiana-MT + São Félix do Araguaia-MT, Novo Santo Antônio-MT e Itupiranga-PA. A distância genética não teve correlação com a distância geográfica. Os ISSRs se mostraram eficientes para determinar a diversidade genética para a A. gigas, revelando que as populações da bacia Araguaia-Tocantins estão estruturadas e com baixa diversidade genética. Estes são os primeiros dados de análise populacional utilizando ISSR para A. gigas da bacia Araguaia-Tocantins e poderão ser utilizados para definir as melhores estratégias de manejo e projetos de conservação dessa espécie.

Position and blood supply of the carotid body in a Kenyan population / Posición y suministro sanguíneo del cuerpo carotídeo en una población de Kenia

Position and source of blood supply to the human carotid body displays population variations. These data are important during surgical procedures and diagnostic imaging in the neck but are only scarcely reported and altogether missing for the Kenyan population. The aim of this study was to describe the position and blood supply of the carotid body in a Kenyan population. A descriptive cross-sectional study at the Department of Human Anatomy, University of Nairobi, was designed. 136 common carotid arteries and their bifurcations were exposed by gross dissection. The carotid body was identified as a small oval structure embedded in the blood vessel adventitia. Position and source of blood supply were photographed. Data are presented by tables and macrographs. 138 carotid bodies were identified. Commonest position was carotid bifurcation (75.4 percent) followed by external carotid artery (10.2 percent), internal carotid artery (7.2 percent) and ascending pharyngeal artery (7.2 percent). Sources of arterial blood supply included the carotid bifurcation (51.4 percent), ascending pharyngeal (21.0 percent), external carotid (17.4 percent) and internal carotid (10.2 percent) arteries. Position and blood supply of the carotid body in the Kenyan population displays a different profile of variations from those described in other populations. Neck surgeons should be aware of these to avoid inadvertent injury.

La posición y la fuente de suministro sanguíneo del cuerpo carotídeo humano muestra variaciones en la población. Estos datos son importantes durante los procedimientos quirúrgicos y de diagnóstico por imagen en el cuello, pero son poco informados e inclusive faltan por completo en la población de Kenia. El objetivo de este estudio fue describir la posición y el aporte sanguíneo del cuerpo carotídeo en una población de Kenia. Se diseñó un estudio descriptivo de corte transversal en el Departamento de Anatomía Humana de la Universidad de Nairobi. 136 arterias carótidas comunes y sus bifurcaciones fueron expuestas mediante disección simple. El cuerpo carotídeo fue identificado como una pequeña estructura oval ubicada en la adventicia del vaso sanguíneo. La posición y la fuente de suministro sanguíneo fueron fotografiados. Los datos obtenidos fueron presentados en las tablas y fotomacrografías. 138 cuerpos carotídeos fueron identificados. La posición más frecuente fue la bifurcación carotídea (75,4 por ciento), seguida de la arteria carótida externa (10,2 por ciento), arteria carótida interna (7,2 por ciento) y la arteria faríngea ascendente (7,2 por ciento). Las fuentes de suministro sanguíneo arterial incluyeron la bifurcación carotídea (51,4 por ciento), arteria faríngea ascendente (21,0 por ciento), arteria carótida externa (17,4 por ciento) y arterias carótidas internas (10,2 por ciento). La posición y el suministro sanguíneo del cuerpo carotídeo en la población de Kenia muestra un perfil de variaciones diferente a las descritos en otras poblaciones. Los cirujanos de cuello deben conocer estas variaciones para así evitar lesiones accidentales.

Desencuentros institucionales sobre la investigación en diversidad genética: [editoriales] / Institutional disagreements about research on genetic diversity: [editorial]

En Colombia (y la Comunidad Andina) las actividades sobre diversidad biológica como investigación, prospección, conservación, aplicación industrial o aprovechamiento comercial, requieren autorización por parte del Ministerio de Ambiente, Vivienda y Desarrollo Territorial (MAVDT). La aplicación industrial o el aprovechamiento comercial de recursos biológicos pasan por alto este tipo de autorización; sin embargo en los últimos años y en forma creciente, los investigadores han mostrado interés en tramitar la autorización de Acceso a Recursos Genéticos (ARG) de los cuales Colombia es país de origen. A pesar de los esfuerzos por cumplir el régimen legal los resultados obtenidos, antes que alentar, pueden desmotivar aún más a los investigadores y a las instituciones de investigación...

Association between genetic variations of the transforming growth factor beta receptor type III and asthma in a Korean population

Transforming growth factor-beta (TGF-beta) and its receptors have been suggested to play key roles in the pathogenesis of asthma. The aim of this study was to evaluate the effects of genetic variations in the TGF-beta receptor type III (TGFBR3) on asthma and on its related phenotypes in the general population. A cohort of 2,118 subjects aged from 10 to 18 years responded to a questionnaire concerning asthma symptoms and risk factors. Methacholine airway hyperresponsiveness (AHR), skin test responses to common aeroallergens, and serum total IgE levels were evaluated in the cohort. A total of 19 SNPs for TGFBR3 were found using direct re-sequencing in 24 healthy adults. Of these, informative SNPs [+44T>C (S15F) and +2753G>A at 3'UTR] were selected and scored using the high throughput single base extension method. Atopy was identified in subjects with 44T>C allele [P = 0.04, OR (95% CI) = 0.79 (0.62-0.99)] and in subjects with Ht1 (CG) more frequently than in subjects with other haplotypes [P = 0.04, OR (95% CI) = 1.27 (1.01-1.59)]. The A allele in 2753G>A was more common in subjects with non-atopic asthma [OR (95% CI) = 1.76 (1.01-3.05)]. A significant association was found between non-atopic asthma and 44T_2753A [OR (95% CI) = 2.16 (1.22-3.82)]. Genetic variations in TGFBR3 appear to be associated with a genetic predisposition to development of asthma and to phenotypes of asthma. Also, the minor allele 2753G and the haplotype TA in the TGFBR3 gene were associated with a pathogenesis of non-atopic asthma.

Phenotypic effects of genetic variability in human clock genes on circadian and sleep parameters.

Circadian rhythms and sleep are two separate but intimately related processes. Circadian rhythms are generated through the precisely controlled, cyclic expression of a number of genes designated clock genes. Genetic variability in these genes has been associated with a number of phenotypic differences in circadian as well as sleep parameters, both in mouse models and in humans. Diurnal preferences as determined by the selfreported Horne-Ostberg (HO) questionnaire, has been associated with polymorphisms in the human genes CLOCK, PER1, PER2 and PER3. Circadian rhythm-related sleep disorders have also been associated with mutations and polymorphisms in clock genes, with the advanced type cosegrating in an autosomal dominant inheritance pattern with mutations in the genes PER2 and CSNK1D, and the delayed type associating without discernible Mendelian inheritance with polymorphisms in CLOCK and PER3. Several mouse models of clock gene null alleles have been demonstrated to have affected sleep homeostasis. Recent findings have shown that the variable number tandem polymorphism in PER3, previously linked to diurnal preference, has profound effects on sleep homeostasis and cognitive performance following sleep loss, confirming the close association between the processes of circadian rhythms and sleep at the genetic level.