Genome sequencing and conservation genomics in the Scandinavian wolverine population.

Genetic approaches have proved valuable to the study and conservation of endangered populations, especially for monitoring programs, and there is potential for further developments in this direction by extending analyses to the genomic level. We assembled the genome of the wolverine (Gulo gulo), a mustelid that in Scandinavia has recently recovered from a significant population decline, and obtained a 2.42 Gb draft sequence representing >85% of the genome and including >21,000 protein-coding genes. We then performed whole-genome resequencing of 10 Scandinavian wolverines for population genomic and demographic analyses. Genetic diversity was among the lowest detected in a red-listed population (mean genome-wide nucleotide diversity of 0.05%). Results of the demographic analyses indicated a long-term decline of the effective population size (Ne ) from 10,000 well before the last glaciation to <500 after this period. Current Ne appeared even lower. The genome-wide FIS level was 0.089 (possibly signaling inbreeding), but this effect was not observed when analyzing a set of highly variable SNP markers, illustrating that such markers can give a biased picture of the overall character of genetic diversity. We found significant population structure, which has implications for population connectivity and conservation. We used an integrated microfluidic circuit chip technology to develop an SNP-array consisting of 96 highly informative markers that, together with a multiplex pre-amplification step, was successfully applied to low-quality DNA from scat samples. Our findings will inform management, conservation, and genetic monitoring of wolverines and serve as a genomic roadmap that can be applied to other endangered species. The approach used here can be generally utilized in other systems, but we acknowledge the trade-off between investing in genomic resources and direct conservation actions.

Interaction between angiotensin-converting enzyme gene rs4343 polymorphism, environment factors, and angiotensin II level on susceptibility to knee osteoarthritis.

OBJECTIVES: Osteoarthritis (OA) is a complex multifactorial disease. The association of knee OA risk with ACE gene rs4343 polymorphism, gene environment synergistic effect, and angiotensin II serum level has not been previously examined. Therefore, we investigate the ACE gene rs4343 polymorphism in knee OA, and its association with severity of knee OA, and angiotensin II serum level. METHODS: Using a case-control design, we recruited 200 subjects (100 cases and 100 controls) and all were subjected to genotyping of rs4343 SNP by real-time polymerase chain reaction and assay of serum angiotensin II level by ELISA. RESULTS: G containing genotypes (AG and GG) and G allele frequencies of the ACE rs4343 polymorphism were significantly higher in the case group than that in the control group. There was significant association between ACE rs4343 genotypes and risk of knee OA under the following genetic inheritance models: GG vs. AA (P=0.003), AA vs. GG/AG (P=0.014), AG/AA vs. GG (P=0.037), and G vs. A (P<0.001). Stratified analyses showed ACE rs4343 polymorphism was evidently associated with a significantly increased risk of knee OA among those had BMI≥25% (adjusted OR=3.016; 95% CI 1.052-8.648; P=0.040). Additionally, knee OA patients with GG genotype had greater knee specific WOMAC index, Kellgren score, and serum angiotensin II level than those with AA or GA genotypes. CONCLUSION: The investigated polymorphism in the ACE gene rs4343 may reflect the risk and severity of knee OA in the Egyptian population, particularly with the GG genotype. The interaction between ACE gene rs4343 polymorphism and obesity further increased the risk of knee OA. Moreover, the higher angiotensin II level may be involved in the pathogenesis of knee OA.

Association of the rs5186 polymorphism of the AGTR1 gene with decreased eGFR in patients with type 2 diabetes from Mexico City.

BACKGROUND: Early biomarkers search for Diabetic Kidney Disease (DKD) in patients with Type 2 Diabetes Mellitus (T2DM), as genetic markers to identify vulnerable carriers of the disease even before Glomerular Filtration Rate (GFR) decline or microalbuminuria development, has been relevant during the last few years. The rs5186 (A116C) polymorphism of the Angiotensin II Receptor Type I gene (AGTR1), has been associated to multiple effects of renal injury risk, commonly detected in patients with Diabetes Mellitus (DM). It has been described that rs5186 could have an effect in stability proteins that assemble Angiotensin II Receptor Type I (AT1), modifying its action, which is why it should be considered as a risk factor for Chronic Kidney Disease (CKD), characterized by a GFR progressive reduction. Even though, the association between rs5186 AGTR1 gene polymorphism and DKD in patients with T2DM has been controversial, inconclusive, and even absent. This disputable issue might be as a result of association studies in which many and varied clinical phenotypes included are contemplated as CKD inductors and enhancers. Although, the sample sizes studied in patients with T2DM are undersized and did not have a strict inclusion criteria, lacking of biochemical markers or KDOQI classification, which have hindered its examination. OBJECTIVE: The aim of our study was to establish an association between rs5186 AGTR1 gene polymorphism and GFR depletion, assessed as a risk factor to DKD development in patients with T2DM. METHODS: We analyzed 297 not related patients with T2DM, divided into 221 controls (KDOQI 1) and 76 cases (KDOQI 2). Arterial pressure, anthropometric and biochemical parameters were measured. rs5186 of AGTR1 genotyping was performed by TaqMan assay real-time PCR method. Allele and genotype frequencies, and Hardy-Weinberg equilibrium were measured. Normality test for data distribution was analyzed by Shapiro-Wilk test, variable comparison by Student's t-test for continuous variables, and Chi-squared test for categorical variables; ANOVA test was used for mean comparison of more than two groups. Effect of rs5186 to DKD was estimated by multiple heritability adjustment models for risk variables of DKD. Statistical significance was indicated by p<0.05. Data was analyzed using Statistical Package STATA v11 software. RESULTS: Dominant and Over-dominant models showed a likelihood ratio to GFR depletion of 1.89 (1.05-3.39, p=0.031) and 2.01 (1.08-3.73, p=0.023) in patients with T2DM. Risk factor increased to 2.54 (1.10-5.89) in women in Over-dominant model. CONCLUSION: In clinical practice, most of nephropathies progress at a slow pace into a total breakdown of renal function, even asymptomatic. This is the first study, reporting that rs5186 polymorphism of AGTR1 gene contribution to GFR depletion, and this could be evaluated as a predisposing factor for DKD in patients with T2DM.

The rs1800795 single nucleotide polymorphism in the IL6 gene is not associated with primary open angle glaucoma in Mexican population.

PURPOSE: Interleukin-6 (IL-6) is a proinflammatory cytokine with pleiotropic effects which has been related to primary open angle glaucoma (POAG) due to its particular effect of protecting the retinal ganglion cells (RGc) from the apoptosis. Different single nucleotide polymorphisms (SNP) have been associated with POAG. The aim of this study was to determine whether an association between IL-6 rs1800795 (-174 G>C) SNP and a higher risk for POAG is present in western Mexican population. METHODS: One hundred and sixty-five unrelated Mexican mestizo patients with POAG and 108 control subjects were included. Genomic DNA was extracted from leukocytes and purified, followed by genotyping and amplification by polymerase chain reaction (PCR) with Taqman Biosystem probes. Allelic and genotypic diversity was evaluated between cases and control subjects. RESULTS: There was no statistically significant association between allele and genotype frequencies, neither with dominant nor recessive genetic association models (p > 0.05). CONCLUSION: Even though there is a role of IL6 in the pathophysiology of POAG, our results ruled out the association between IL-6 and the rs1800795 SNP showing not to be an index of higher risk for POAG in Mexican population.

The association between interleukin-6 promoter polymorphisms and rheumatoid arthritis by ethnicity: A meta-analysis of 33 studies.

OBJECTIVE: We performed a meta-analysis to determine the effect Interleukin-6 (IL-6) promoter polymorphism (-174 G>C, -572 G>C, and -597 G>A) have on the development rheumatoid arthritis (RA) by ethnicity. MATERIAL AND METHODS: PubMed, EBSCO, LILACS, and Scopus databases were searched for studies exploring the association between any IL6 polymorphisms and RA until November 2018. Genotype distributions were extracted and, depending on the level heterogeneity, determined by the ψ2-based Q test and the Inconsistency Index (I2), fixed-effects or random-effects models were used to calculate pooled odds ratios (ORs) with 95% confidence intervals (95%CIs) for the heterozygous, homozygous, dominant, recessive, and allelic genetic models. RESULTS: From 708 identified publications, 33 were used in this analysis. For the -174 polymorphism, Asians (ORheterozygous=7.57, 95%CI: 2.28-25.14, ORhomozygous=5.84, 95%CI: 2.06-16.56, ORdominant=7.21, 95%CI: 2.30-22.63, ORrecessive=5.04, 95%CI: 1.78-14.28, ORallelic=6.60, 95%CI: 2.26-19.28, p<.05) and Middle East countries (ORheterozygous=2.30, 95%CI: 1.10-4.81, ORdominant=2.27, 95%CI: 1.22-4.22, ORallelic=2.29, 95%CI: 1.24-4.23, p<.05) were associated with a significant risk of developing RA. Whereas, for Latinos, the C-allele was associated with a benefit (ORhomozygous=0.26, 95%CI: .08-.82, ORrecessive=.25, 95%CI: .08-.80, p<.05). For the -572 polymorphism, Asians demonstrated a significant association for the homozygous and recessive genetic models (8 studies, ORhomozygous=1.56, 95%CI: 1.16-2.09, ORrecessive=1.63, 95%CI: 1.08-2.45, p<.05). For the -597 polymorphism, no association was observed. CONCLUSIONS: Here, the -174 G>C polymorphism increased the risk of developing RA in Asians and Middle East populations. Interestingly, for Latinos, the polymorphism was associated with a benefit. For the -572 polymorphism, only the Asian population showed an increased risk of developing RA for the CC genotype.

The Association Between Interleukin-6 Promoter Polymorphisms and Rheumatoid Arthritis by Ethnicity: A Meta-Analysis of 33 Studies.

OBJECTIVE: We performed a meta-analysis to determine the effect Interleukin-6 (IL-6) promoter polymorphism (-174 G>C, -572 G>C, and -597 G>A) have on the development rheumatoid arthritis (RA) by ethnicity. MATERIAL AND METHODS: PubMed, EBSCO, LILACS, and Scopus databases were searched for studies exploring the association between any IL6 polymorphisms and RA until November 2018. Genotype distributions were extracted and, depending on the level heterogeneity, determined by the ψ2-based Q test and the Inconsistency Index (I2), fixed-effects or random-effects models were used to calculate pooled odds ratios (ORs) with 95% confidence intervals (95%CIs) for the heterozygous, homozygous, dominant, recessive, and allelic genetic models. RESULTS: From 708 identified publications, 33 were used in this analysis. For the -174 polymorphism, Asians (ORheterozygous=7.57, 95%CI: 2.28-25.14, ORhomozygous=5.84, 95%CI: 2.06-16.56, ORdominant=7.21, 95%CI: 2.30-22.63, ORrecessive=5.04, 95%CI: 1.78-14.28, ORallelic=6.60, 95%CI: 2.26-19.28, p<.05) and Middle East countries (ORheterozygous=2.30, 95%CI: 1.10-4.81, ORdominant=2.27, 95%CI: 1.22-4.22, ORallelic=2.29, 95%CI: 1.24-4.23, p<.05) were associated with a significant risk of developing RA. Whereas, for Latinos, the C-allele was associated with a benefit (ORhomozygous=0.26, 95%CI: .08-.82, ORrecessive=.25, 95%CI: .08-.80, p<.05). For the -572 polymorphism, Asians demonstrated a significant association for the homozygous and recessive genetic models (8 studies, ORhomozygous=1.56, 95%CI: 1.16-2.09, ORrecessive=1.63, 95%CI: 1.08-2.45, p<.05). For the -597 polymorphism, no association was observed. CONCLUSIONS: Here, the -174 G>C polymorphism increased the risk of developing RA in Asians and Middle East populations. Interestingly, for Latinos, the polymorphism was associated with a benefit. For the -572 polymorphism, only the Asian population showed an increased risk of developing RA for the CC genotype.

Association of -319 C/T and +49 A/G polymorphisms of CTLA-4 gene in patients with hepatitis C virus infection. / Asociación de los polimorfismos −319 C/T y +49 A/G del gen CTLA-4 en pacientes con infección por el virus de la hepatitis C.

INTRODUCTION AND OBJECTIVE: Molecular changes in the CTLA-4 gene can modify the ability to control T lymphocyte proliferation, and promote the persistence or elimination of the hepatitis C virus (HCV). We aimed to investigate the frequency and association of -319 C/T and +49 A/G polymorphism in the CTLA-4 gene in patients infected with HCV. METHODS: The CTLA-4 gene polymorphisms (-319 C/T in the promoter region, and +49 A/G in exon 1) were analysed by T-ARMS-PCR in 420 individuals, including 205 chronic HCV infected patients and 215 healthy subjects. RESULTS: We found a positive association of +49G allele with HCV infection (OR 1.48; 95% CI 1.09-2.02; p=.02), and with males (OR 1.80; 95% CI 1.16-2.79; p=.02), both in chronic disease (without cirrhosis). Also, significant differences in +49 A/G genotypes distribution between HCV infected patients and healthy subjects were shown in a dominant genetic model (GG+GA versus AA; OR 1.57; 95% CI 1.05-2.33; p=.04). No significant differences were observed in the -319 C/T polymorphism between HCV infected patients and healthy subjects. Moreover, -319C/+49G haplotype confers susceptibility to HCV genotype 3 infection (OR 10.68; 95% CI 1.17-96.97; p=.04). CONCLUSIONS: The +49G allele confers susceptibility to HCV infection and with male gender, both in chronic disease. In addition, the -319C/+49G haplotype confers susceptibility to HCV genotype 3 infection. Our results support an important role of the -319 C/T and +49 A/G polymorphisms in HCV infection.

Asociación del polimorfismo rs5186 del gen AGTR1 con disminución de la TFGe en pacientes con diabetes tipo 2 de la Ciudad de México / Association of the rs5186 polymorphism of the AGTR1 gene with decreased eGFR in patients with type 2 diabetes from Mexico City

Antecedentes: La búsqueda de biomarcadores tempranos de enfermedad renal diabética (ERD) en pacientes con diabetes mellitus tipo 2 (DMT2), como los marcadores genéticos para identificar pacientes vulnerables de la enfermedad, incluso antes de la presencia de una disminución de la estimación de tasa de filtrado glomerular (TFGe) o presencia de microalbuminuria ha cobrado importancia en los últimos años. El polimorfismo rs5186 (A1166C) presente en el gen receptor tipo 1 de la angiotensina II (AGTR1) ha sido asociado a distintos efectos del riesgo de daño renal que suelen estar presentes en pacientes con diabetes mellitus (DM). Se ha descrito que el rs5186 podría influir en la estabilidad de las proteínas que conforman al receptor de la angiotensina II tipo 1 (AT1) alterando su actividad, por lo que podría ser considerado como un factor de riesgo a enfermedad renal crónica (ERC) caracterizada por una disminución progresiva de la TFG. Sin embargo, la asociación del polimorfismo rs5186 del gen AGTR1 con ERD en pacientes con DMT2 ha sido controversial, no concluyente, incluso nula. Las controversias podrían ser por los estudios de asociación y estimación del riesgo del rs5186 previamente reportados incluyen distintos fenotipos clínicos considerados como inductores y potenciadores de ERC, además, los tamaños de las muestras analizadas en pacientes con DMT2 eran pequeñas y no tenían un control estricto en su inclusión, careciendo incluso de marcadores bioquímicos o estadificación KDOQI que han dificultado su análisis. Objetivo: Determinar la asociación del rs5186 del gen AGTR1 con la disminución de TFGe considerada como riesgo al desarrollo de ERD en pacientes con DMT2.(AU)

Background: Early biomarkers search for Diabetic Kidney Disease (DKD) in patients with Type 2 Diabetes Mellitus (T2DM), as genetic markers to identify vulnerable carriers of the disease even before Glomerular Filtration Rate (GFR) decline or microalbuminuria development, has been relevant during the last few years. The rs5186 (A116C) polymorphism of the Angiotensin II Receptor Type I gene (AGTR1), has been associated to multiple effects of renal injury risk, commonly detected in patients with Diabetes Mellitus (DM). It has been described that rs5186 could have an effect in stability proteins that assemble Angiotensin II Receptor Type I (AT1), modifying its action, which is why it should be considered as a risk factor for Chronic Kidney Disease (CKD), characterized by a GFR progressive reduction. Even though, the association between rs5186 AGTR1 gene polymorphism and DKD in patients with T2DM has been controversial, inconclusive, and even absent. This disputable issue might be as a result of association studies in which many and varied clinical phenotypes included are contemplated as CKD inductors and enhancers. Although, the sample sizes studied in patients with T2DM are undersized and did not have a strict inclusion criteria, lacking of biochemical markers or KDOQI classification, which have hindered its examination.Objective: The aim of our study was to establish an association between rs5186 AGTR1 gene polymorphism and GFR depletion, assessed as a risk factor to DKD development in patients with T2DM. (AU)

[Characterisation of three polymorphisms of the tryptophan hydroxylase 2 gene in a sample of Colombian population with major depressive disorder]. / Caracterización de tres polimorfismos del gen de la triptófano hidroxilasa 2 en una muestra de población colombiana con trastorno depresivo mayor.

OBJECTIVE: Identify whether rs11179000, rs136494 and rs4570625 polymorphisms of the tryptophan hydroxylase 2 gene, are associated with a major depressive disorder in a sample of the Colombian population. METHODS: Case-control study was conducted in which a comparison was made between subjects diagnosed with major depressive disorder at some point in adulthood or active symptoms at the time of evaluation, and subjects with no psychiatric disease. Subjects were studied in the Department of Psychiatry, Faculty of Medicine and the Institute of Genetics at the National University of Colombia. Polymorphisms were genotyped using Taqman probes in real time PCR. As well as studying the association between major depressive disorder and these (single nucleotide polymorphisms (SNPs), the association with other factors previously associated with depression were also analysed. RESULTS: No statistically significant association between genotypic and allelic frequencies of each polymorphism and major depressive disorder was found. Association between sex and complication during pregnancy / childbirth and major depressive disorder was observed. Association between sex and complication during pregnancy / childbirth and major depressive disorder was observed. CONCLUSIONS: There was no association between any polymorphism and major depressive disorder.

The association between interleukin-6 promoter polymorphisms and rheumatoid arthritis by ethnicity: A meta-analysis of 33 studies / Asociación entre los polimorfismos del promotor de la interleucina-6 y la artritis reumatoide analizado por etnicidad: un metaanálisis de 33 estudios

Objective: We performed a meta-analysis to determine the effect Interleukin-6 (IL-6) promoter polymorphism (−174 G>C, −572 G>C, and −597 G>A) have on the development rheumatoid arthritis (RA) by ethnicity. Material and methods: PubMed, EBSCO, LILACS, and Scopus databases were searched for studies exploring the association between any IL6 polymorphisms and RA until November 2018. Genotype distributions were extracted and, depending on the level heterogeneity, determined by the ψ2-based Q test and the Inconsistency Index (I2), fixed-effects or random-effects models were used to calculate pooled odds ratios (ORs) with 95% confidence intervals (95%CIs) for the heterozygous, homozygous, dominant, recessive, and allelic genetic models. Results: From 708 identified publications, 33 were used in this analysis. For the −174 polymorphism, Asians (ORheterozygous=7.57, 95%CI: 2.28–25.14, ORhomozygous=5.84, 95%CI: 2.06–16.56, ORdominant=7.21, 95%CI: 2.30–22.63, ORrecessive=5.04, 95%CI: 1.78–14.28, ORallelic=6.60, 95%CI: 2.26–19.28, p<.05) and Middle East countries (ORheterozygous=2.30, 95%CI: 1.10–4.81, ORdominant=2.27, 95%CI: 1.22–4.22, ORallelic=2.29, 95%CI: 1.24–4.23, p<.05) were associated with a significant risk of developing RA. Whereas, for Latinos, the C-allele was associated with a benefit (ORhomozygous=0.26, 95%CI: .08–.82, ORrecessive=.25, 95%CI: .08–.80, p<.05). For the −572 polymorphism, Asians demonstrated a significant association for the homozygous and recessive genetic models (8 studies, ORhomozygous=1.56, 95%CI: 1.16–2.09, ORrecessive=1.63, 95%CI: 1.08–2.45, p<.05). For the −597 polymorphism, no association was observed. Conclusions: Here, the −174 G>C polymorphism increased the risk of developing RA in Asians and Middle East populations. Interestingly, for Latinos, the polymorphism was associated with a benefit. For the −572 polymorphism, only the Asian population showed an increased risk of developing RA for the CC genotype.(AU)

Objetivos: Realizamos un meta-análisis para determinar el efecto de los polimorfismos del promotor de interleucina-6 (IL-6) (-174 G>C, -572 G>C, y -597 G>A) sobre el desarrollo de artritis reumatoide (RA) analizado por etnicidad. Materiales y métodos: En las bases de datos PubMed, EBSCO, LILACS y Scopus se buscaron estudios con la asociación entre polimorfismo de IL-6 y RA publicados hasta noviembre 2018. se obtuvieron las distribuciones de genotipo y de acuerdo al nivel de heterogeneidad el efecto fijo o aleatorio fueron utilizados para calcular los Odds Ratio (OR) con intervalos de confianza del 95% para los modelos genéticos heterocigoto, homocigoto, dominante, recesivo y alélico. Resultados: De 708 estudios identificados, 33 fueron utilizados para este análisis. Para el polimorfismo -174, los países Asiáticos (ORheterocigoto=7,57, 95%CI: 2,28–25,14, ORhomocigoto=5,84, 95%CI: 2,06-16,56, ORdominante=7,21, 95%CI: 2,30-22,63, ORrecesivo=5,04, 95%CI: 1,78-14,28, ORalélico=6,60, 95%CI: 2,26-19,28, p<0,05) y del Medio Oriente (ORheterocigoto=2,30, 95%CI: 1,10-4,81, ORdominante=2,27, 95%CI: 1,22-4,22, ORalélico=2,29, 95%CI: 1,24-4,23, p<0,05) están asociados con el riesgo de desarrollar RA significativamente. Mientras que, para los Latinos, el alelo-C está asociado con un beneficio (ORhomocigoto=0,26, 95%CI: 0,08-0,82, ORrecesivo=0,25, 95%CI: 0,08-0,80, p<0,05). Para el polimorfismo -572, los Asiáticos están asociados significativamente con los modelos genéticos homocigoto y recesivo (8 estudios, ORhomocigoto=1,56, 95%CI: 1,16-2,09, ORrecesivo=1,63, 95%CI: 1,08-2,45, p<0,05). Para el polimorfismo -597, no se observó asociación. Conclusiones: El polimorfismo -174 G>C aumenta el riesgo de desarrollar RA en población Asiática y Medio Oriente. Curiosamente, para los Latinos el polimorfismo está asociado con un beneficio. Para el polimorfismo -572, solo la población Asiática demuestra una aumento en el riesgo de desarrollar RA con el genotipo CC.(AU)

rs11613352 polymorphism (TT genotype) associates with a decrease of triglycerides and an increase of HDL in familial hypercholesterolemia patients.

INTRODUCTION AND OBJECTIVES: Recent genome-wide association studies have identified a locus on chromosome 12q13.3 associated with plasma levels of triglyceride and high-density lipoprotein cholesterol, with rs11613352 being the lead single nucleotide polymorphism in this genome-wide association study locus. The aim of the study is to investigate the involvement of rs11613352 in a population with high cardiovascular risk due to familial hypercholesterolemia. METHODS: The single nucleotide polymorphism was genotyped by Taqman(®) assay in a cohort of 601 unrelated familial hypercholesterolemia patients and its association with plasma triglyceride and high-density lipoprotein cholesterol levels was analyzed by multivariate methods based on linear regression. RESULTS: Minimal allele frequency was 0.17 and genotype frequencies were 0.69, 0.27, and 0.04 for CC, CT, and TT genotypes, respectively. The polymorphism is associated in a recessive manner (TT genotype) with a decrease in triglyceride levels (P=.002) and with an increase in high-density lipoprotein cholesterol levels (P=.021) after adjusting by age and sex. CONCLUSIONS: The polymorphism rs11613352 may contribute to modulate the cardiovascular risk by modifying plasma lipid levels in familial hypercholesterolemia patients.

Influence of genetic markers on the feeding behavior of yearling bulls / Influencia de los marcadores genéticos en el comportamiento alimentario de toretes de un año / Influência de marcadores genéticos no comportamento alimentar de touros de um ano

Abstract Background: The search for gene and marker effects on economically important traits is aimed not only to understanding the genetic architecture of complex traits but also to applying the information to breeding schemes. Objective: To analyze the effect of two temperament-related SNPs (rs109576799 located in the DRD3 gene, and rs43696138 in the HTR2A gene) on feeding performance of Mexican beef cattle. Methods: One hundred and thirty-six young beef bulls were included in a centralized feed efficiency performance test based on residual feed intake (RFI), with 20 d for adaptation and 70 d of feed efficiency testing. In addition to feeding traits, temperament was assessed at the beginning of the trial using pen score (PS) and exit velocity (EV). All animals were genotyped with two markers located in the HTR2A and DRD3 genes, and an association analysis was conducted between these genotypes and the measured traits. Results: For Brangus breed, a significant association was obtained between average daily gain (ADG; p=0.019), and the rs43696138 marker, resulting in higher gains for homozygous genotype GG (1.69 ± 0.04 kg), when compared to the heterozygous genotype GA (1.54 ± 0.04 kg). Conclusion: The previously reported association of these markers with temperament was not confirmed in the evaluated breeds; however, the rs43696138 marker showed an effect on a feeding performance trait. Further studies are needed to determine the effect of this and other markers on both RFI and temperament.

Resumen Antecedentes: La búsqueda de efectos genéticos y marcadores de rasgos económicamente relevantes no solo se basa en el interés biológico de comprender la arquitectura genética de rasgos complejos, sino también en aplicar la información en los esquemas prácticos de mejoramiento. Objetivo: Analizar el efecto de dos SNPs relacionados con el temperamento (rs109576799 localizado en el gen DRD3, y rs43696138 localizado en el gen HTR2A) sobre la eficiencia alimenticia en el ganado bovino mexicano. Métodos: Ciento treinta y seis toretes de carne jóvenes fueron sometidos a una prueba de comportamiento alimenticio basada en el consumo residual de alimento (RFI), con 20 d de adaptación y 70 d de prueba para la eficiencia alimenticia. Además de los rasgos de comportamiento alimenticio, se evaluó el temperamento de los animales al inicio de la prueba, mediante la evaluacion de comportamiento en el corral (PS), y la velocidad de salida (EV). Todas las muestras se tipificaron con dos marcadores localizados en los genes DRD3 y HTR2A para posteriormente realizar un análisis de asociación de los genotipos con los rasgos evaluados. Resultados: En la raza Brangus, se observó una asociación significativa de la media de ganancia diaria de peso (ADG, p=0,019) con el marcador rs43696138, localizado en el gen HTR2A, resultando en mayores ganancias para el genotipo GG (1,69 ± 0,04 kg) en comparación con los toros heterocigóticos GA (1,54 ± 0,04 kg). Conclusión: No se confirmó la asociación de estos marcadores previamente reportados con el temperamento en las razas evaluadas; sin embargo, el marcador rs43696138 mostró efecto en un rasgo de comportamiento alimenticio. Se necesitan más estudios para determinar el efecto de éste y otros marcadores en el consumo residual de alimento (RFI) y el temperamento.

Resumo Antecedentes: A busca de efeitos genéticos e marcadores de características economicamente relevantes não se baseia apenas no interesse biológico de compreender a arquitetura genética de traços complexos, mas também na aplicação da informação nos esquemas práticos de melhoria. Objetivo: Analisar o efeito de dois SNPs relacionados ao temperamento (rs109576799 localizado no gene DRD3 e rs43696138 localizado no gene HTR2A) sobre a eficiência nutricional no gado mexicano. Métodos: Cento e trinta e seis touros jovens foram submetidos a um teste de comportamento alimentar com base na entrada de alimentação residual (RFI), com 20 d de adaptação e 70 d de teste para eficiência de alimentação. Além dos traços de comportamento alimentar, o temperamento dos animais foi avaliado no início do teste, através da avaliação do comportamento na caneta (PS) e da velocidade de saída (EV). Todas as amostras foram digitadas com dois marcadores localizados nos genes DRD3 e HTR2A para posteriormente realizar uma análise de associação dos genótipos com os traços avaliados. Resultados: Na raça Brangus, observou-se uma associação significativa do ganho diário médio (ADG, p = 0,019) com o marcador rs43696138, localizado no gene HTR2A, resultando em maiores ganhos para o genótipo GG (1,69 ± 0,04 kg), em comparação com os touros heterozigóticos GA (1,54 ± 0,04 kg). Conclusão: A associação destes marcadores previamente relatados com o temperamento nas raças avaliadas não foi confirmada; no entanto, o marcador rs43696138 mostrou um efeito sobre uma característica de comportamento alimentar. Mais estudos são necessários para determinar o efeito deste e outros marcadores com ingestão alimentar residual (RFI) e temperamento.

Effect of the polymorphism BDNF rs6265 G/A in Mexican outpatient children with autism spectrum disorders / Efecto del polimorfismo rs6265 G/A del gen BDNF en niños mexicanos ambulatorios con trastornos del espectro autista

Abstract: Introduction: The study of autistic spectrum disorders (ASD) at the genetic level is extremely important to understand their origin. In Mexico, there are few works addressed from this perspective. Objective: We investigated the role of the Brain Derived Neurotrophic Factor (BDNF) gene variant rs6265 G/A for single nucleotide polymorphism analysis in Mexican children with ASD using a case-control association design. Method: We made a pilot study by case-control analysis adjusting by gender, age, and ancestry. Results: Our study found no association between the BDNF rs6265 gene polymorphism and ASD [p = .419, OR = 1.597 (.514, 4.967)] Discussion and conclusion: Worldwide, the results of case-control association studies with the rs6265 of BDNF are controversial and do not always replicate. This may be due to the ethnicity of our population and additional factors not studied in the present work. Our study suggests that the SNP rs6265 is not contributing for ASD susceptibility in Mexican population.

Resumen: Introducción: El estudio de los trastornos del espectro autista a nivel genético es de suma importancia para entender su origen. En México existen pocos trabajos abordados desde esta perspectiva. Objetivo: Investigamos el papel de la variante del gen rs6265 G/A del factor neurotrófico derivado del cerebro (BDNF) para el análisis del polimorfismo de un solo nucleótido en niños mexicanos con TEA por medio de un diseño de asociación de casos y controles. Método: Realizamos un estudio piloto mediante un análisis de casos y controles ajustando por género, edad y ancestría. Resultados: Nuestro estudio no encontró asociación entre el polimorfismo del gen BDNF rs6265 y TEA [p = .419, OR = 1.597 (.514, 4.967)]. Discusión y conclusión: A nivel mundial, los resultados de estudios de asociación caso-control con el rs6265 de BDNF son controvertidos y no siempre se replican. Esto puede deberse a la etnicidad de nuestra población y a otros factores no estudiados en el presente trabajo. El estudio sugiere que el SNP rs6265 no contribuye a la susceptibilidad al TEA en población mexicana.

Polimorfismos genéticos asociados a la inmunidad innata y la susceptibilidad genética a la tuberculosis / Genetic polymorphisms associated with innate immunity and to genetic susceptibility to tuberculosis

Resumen La tuberculosis es un problema de salud mundial exacerbado por la ausencia de una vacuna eficaz y la emergencia de cepas multidrogo resistentes. La inmunidad innata, clave en la susceptibilidad a tuberculosis, está asociada a polimorfismos genéticos en TLRs (Toll Like Receptors), VDR (Vitamin D Receptor), INF-γ, TNF-α, entre otros. Recientemente, también a nueve genes causantes de susceptibilidad mendeliana a enfermedades micobacterianas (MSMD), incluyendo genes autosómicos y ligados al cromosoma X. Después de décadas de exitoso manejo, Chile reportó mantención de la mortalidad, aumento en la incidencia de tuberculosis en todas sus formas y casos multidrogo resistentes. La incidencia es mayor en Norte y Centro, donde la Región Metropolitana mostró incremento de población migrante latinoamericana. Consecuentemente, la alta persistencia de la incidencia en tales zonas geográficas, podría asociarse a poblaciones portadoras de polimorfismos de un solo nucleótido (SNP)s y/o MSMD, confiriendo susceptibilidad genética a tuberculosis y/o a BCG diseminada y otros patógenos intramacrofágicos, similar a lo descrito en poblaciones de Europa, Asia, África y América. En conclusión, proponemos considerar la predisposición genética de la población actual, al momento de diseñar políticas nacionales de salud pública para erradicar la tuberculosis.

Tuberculosis is a global health problem exacerbated by the absence of an effective vaccine and emergence of extensive antibiotic-resistant strains. Innate immunity is key to tuberculosis susceptibility, since it is associated with genetic polymorphisms in TLRs (Toll Like Receptors), VDR (Vitamin D Receptor), INF-γ, TNF-α, among others. Recently, also to nine Mendelian Susceptibility Mycobacterial Diseases (MSMD) -causing genes, including autosomal and X-linked genes. After decades of successful management, Chile reported maintenance of mortality and increase in tuberculosis under 15 years and multidrug resistant cases incidence. Moreover, incidence is higher in the North and the Center, where Metropolitan Region showed a sustained increment of the Latin American migrant population. Consequently, the high incidence persistence in such geographic areas could be associated with populations carrying SNPs genetic polymorphisms types and/or MSMD that confer genetic susceptibility to tuberculosis and/or BCG dissemination and other intramacrophagic pathogens, similar to that described in certain populations in Europe, Asia, Africa and America. Corollary, we propose to consider genetic predisposition of the current population, at the time of designing national public health policies to eradicate tuberculosis.

Diagnóstico molecular de tuberculosis multidrogorresistente en muestras de esputo mediante el análisis de curvas de melting / Molecular diagnosis of multidrug-resistant tuberculosis in sputum samples by melting curve analysis

RESUMEN Objetivos. Analizar curvas de melting para el diagnóstico de tuberculosis multidrogorresistente a partir de muestras de esputo. Materiales y métodos. Se colectaron muestras de esputo (n = 250) de pacientes con sospecha clínica de tuberculosis pulmonar según resultado de baciloscopia y cultivados en medio sólido Lowenstein Jensen. Según el método de referencia se trabajó con 124 muestras sensibles a rifampicina e isoniacida, 24 resistentes a rifampicina, 33 resistentes a isoniacida y 69 multidrogorresistentes. Se evaluó por PCR en tiempo real y luego por las curvas de melting, se utilizó el gen rpoB como biomarcador de resistencia a rifampicina, y el gen katG y región promotora inhA como biomarcadores de resistencia a isoniacida. La cepa H37Rv fue considerada como control sensible a drogas. Se compararon los resultados del método de referencia y los resultados del análisis de curvas de melting para evaluar los parámetros de sensibilidad, especificidad, valor predictivo positivo y valor predictivo negativo. Resultados. La resistencia a rifampicina mostró una sensibilidad de 90,3 %, especificidad de 90,4 %, valor predictivo positivo de 84,8 % y valor predictivo negativo de 94,0 %. La resistencia a isoniacida mostró una sensibilidad de 90,2 %, especificidad de 93,9 %, valor predictivo positivo de 91,1 % y valor predictivo negativo de 93,3 %. La detección de tuberculosis multidrogorresistente mostró valores de 89,9 %, 90,6 %, 78,5 % y 95,9 % para sensibilidad, especificidad, valor predictivo positivo y valor predictivo negativo, respectivamente. Conclusiones. El análisis de curvas de melting mostró ser seguro y confiable para ser utilizado en el diagnóstico rápido de tuberculosis multidrogorresistente en muestras de esputo.

ABSTRACT Objectives. To analyze melting curves for the diagnosis of multidrug-resistant tuberculosis from sputum samples. Materials and Methods. Sputum samples (n = 250) were collected from patients with clinical suspicion of pulmonary tuberculosis as a result of bacilloscopy and cultured in solid medium Lowenstein Jensen. According to the reference method, 124 samples sensitive to rifampicin and isoniazid, 24 resistant to rifampicin, 33 resistant to isoniazid, and 69 multidrug-resistant were used. It was evaluated by real-time PCR and then by melting curves, the rpoB gene was used as a biomarker of rifampicin resistance, and the katG gene and inhA promoter region were used as biomarkers of isoniazid resistance. The H37Rv strain was considered a drug-sensitive control. The results of the reference method and the results of the melting curve analysis were compared to evaluate the parameters of sensitivity, specificity, positive predictive value and negative predictive value. Results. Rifampicin resistance showed a sensitivity of 90.3%, specificity of 90.4%, positive predictive value of 84.8% and negative predictive value of 94.0%. Isoniazid resistance showed a sensitivity of 90.2%, specificity of 93.9%, positive predictive value of 91.1% and negative predictive value of 93.3%. The detection of multidrug-resistant tuberculosis showed values of 89.9%, 90.6%, 78.5% and 95.9% for sensitivity, specificity, positive predictive value and negative predictive value, respectively. Conclusions. The melting curve analysis showed to be safe and reliable to be used in the rapid diagnosis of multidrug-resistant tuberculosis in sputum samples.

El polimorfismo de un solo nucleótido rs1800795 en el gen IL6 no está asociado con el glaucoma primario de ángulo abierto en la población mexicana / The rs1800795 single nucleotide polymorphism in the IL6 gene is not associated with primary open angle glaucoma in Mexican population

Objetivo La interleucina 6 (IL-6) es una citoquina proinflamatoria con efectos pleiotrópicos que se ha relacionado con el glaucoma primario de ángulo abierto (GPAA) debido a su efecto particular de protección de las células ganglionares de la retina (CGR) contra la apoptosis. Se han asociado diferentes polimorfismos de un solo nucleótido (PSN) con el GPAA. El objetivo de este estudio fue determinar si existe una asociación entre el PSN de IL-6 rs1800795 (−174 G>C) y un mayor riesgo de padecer GPAA en la población mexicana occidental. Métodos Se incluyeron 165 pacientes mestizos mexicanos no emparentados con GPAA y 108 sujetos de control. Se extrajo el ADN genómico de los leucocitos y se purificó, seguido de la genotipificación y la amplificación por reacción en cadena de la polimerasa (PCR) con sondas TaqMan® Biosystem®. Se evaluó la diversidad alélica y genotípica entre los casos y los sujetos de control. Resultados No hubo asociación estadísticamente significativa entre las frecuencias alélicas y genotípicas, ni con modelos de asociación genética dominante ni recesiva (p>0,05). Conclusiones Aunque existe un papel de la IL6 en la fisiopatología del GPAA, nuestros resultados descartan la asociación entre la IL-6 y el PSN rs1800795 mostrando no ser un índice de mayor riesgo de GPAA en la población mexicana (AU)

Purpose Interleukin-6 (IL-6) is a proinflammatory cytokine with pleiotropic effects which has been related to primary open angle glaucoma (POAG) due to its particular effect of protecting the retinal ganglion cells (RGc) from the apoptosis. Different single nucleotide polymorphisms (SNP) have been associated with POAG. The aim of this study was to determine whether an association between IL-6 rs1800795 (−174 G>C) SNP and a higher risk for POAG is present in western Mexican population. Methods One hundred and sixty-five unrelated Mexican mestizo patients with POAG and 108 control subjects were included. Genomic DNA was extracted from leukocytes and purified, followed by genotyping and amplification by polymerase chain reaction (PCR) with Taqman Biosystem probes. Allelic and genotypic diversity was evaluated between cases and control subjects. Results There was no statistically significant association between allele and genotype frequencies, neither with dominant nor recessive genetic association models (P>.05). Conclusion Even though there is a role of IL6 in the pathophysiology of POAG, our results ruled out the association between IL-6 and the rs1800795 SNP showing not to be an index of higher risk for POAG in Mexican population (AU)

Characterisation of three polymorphisms of the tryptophan hydroxylase 2 gene in a sample of Colombian population with major depressive disorder / Caracterización de tres polimorfismos del gen de la triptófano hidroxilasa 2 en una muestra de población colombiana con trastorno depresivo mayor

ABSTRACT Objective: Identify whether rs11179000, rs136494 and rs4570625 polymorphisms of the tryptophan hydroxylase 2 gene, are associated with a major depressive disorder in a sample of the Colombian population. Methods: Case-control study was conducted in which a comparison was made between subjects diagnosed with major depressive disorder at some point in adulthood or active symptoms at the time of evaluation, and subjects with no psychiatric disease. Subjects were studied in the Department of Psychiatry, Faculty of Medicine and the Institute of Genetics at the National University of Colombia. Polymorphisms were genotyped using Taqman probes in real time PCR. As well as studying the association between major depressive disorder and these single nucleotide polymorphisms (SNPs), the association with other factors previously associated with depression were also analysed. Results: No statistically significant association between genotypic and allelic frequencies of each polymorphism and major depressive disorder was found. Association between sex and complication during pregnancy/childbirth and major depressive disorder was observed. Association between sex and complication during pregnancy/childbirth and major depres sive disorder was observed. Conclusions: There was no association between any polymorphism and major depressive disorder.

RESUMEN Objetivo: Identificar si los polimorfismos rs11179000, rs136494 y rs4570625 del gen de la triptófano hidroxilasa 2 están asociados a trastorno depresivo mayor en una muestra de población colombiana. Métodos: Estudio de casos y controles en el que se comparó a sujetos con trastorno depresivo mayor diagnosticado en algún momento de la vida adulta o con síntomas activos en el momento de la valoración y sujetos sin enfermedad psiquiátrica. Se estudió a los sujetos en el Departamento de Psiquiatría de la Facultad de Medicina y en el Instituto de Genética de la Universidad Nacional de Colombia. Se genotipificaron los polimorfismos usando reacción en cadena de la polimerasa en tiempo real y sondas Taqman. Además de buscar asociación entre trastorno depresivo mayor y estos polimorfismos de un solo nucleótido, se exploró asociación con otros factores relacionados previamente con depresión. Resultados: No se encontró asociación estadísticamente significativa entre las frecuencias genotípicas o alélicas de cada polimorfismo y el trastorno depresivo mayor. Se observó asociación entre sexo y complicaciones durante el embarazo/parto y trastorno depresivo mayor. Conclusiones: No se halló asociación entre polimorfismo alguno y el trastorno depresivo mayor.

NAT2 gene polymorphisms in three indigenous groups in the Colombian Caribbean Coast region / Polimorfismo del Gen NAT2 en tres grupos indígenas de la región Caribe Colombiana

Objective: To study the NAT2 gene polymorphisms 481T, 590A and 857A in the Chimila, Wiwa and Wayuu indigenous groups of the Colombian Caribbean to determine the frequencies of the alleles NAT2*4, NAT2*5, NAT2*6, and NAT2*7 and to determine the types of acetylators present in these populations. Methods: A total of 202 subjects were studied: 47 Chimila, 55 Wiwa, and 100 Wayuu. The polymorphisms were identified using a real-time PCR method for allelic discrimination designed using Taqman of Applied Biosystems. Results: The following alleles were found at the highest frequency in the following groups: the NAT2*4 allele (wild type) in the Wayuu group (55.3%), the NAT2*5 allele in the Wiwa group (34.5%), and the NAT2*7 allele in the Chimila group (24.2%). A higher frequency of the rapid acetylator status was found in the Wayuu group (31.3%) and Chimila group (29.5%) compared with the Wiwa group (12.7%). The intermediate acetylator status distribution was very similar in all three groups, and the frequency of the slow acetylator status was higher in the Wiwa group (32.7%) compared with the Chimila and Wayuu groups (20.5% and 21.2%, respectively). Conclusion: The results demonstrated the allelic distribution and pharmacogenetic differences of the three groups studied and revealed the most frequent acetylator status and phenotype. Because of the high prevalence of slow acetylators, a greater incidence of tuberculosis (TB) drug-induced hepatotoxicity is predicted in these populations, with a higher frequency in the Wiwa group.

Objetivo: Estudiar los polimorfismos tipo SNP (del inglés- single nucleotide polymorphism) 481T, 590A y 857A del gen NAT2, en los grupos indígenas Chimila, Wiwa y Wayúu del Caribe Colombiano para determinar las frecuencias de los alelos NAT2*4, NAT2*5, NAT2*6 y NAT2*7 y caracterizar el tipo de acetiladores presentes en estas poblaciones. Métodos: Se estudiaron 202 individuos en total, 47 Chimila, 55 Wiwa y 100 Wayúu. Los polimorfismos se determinaron mediante la técnica de PCR en tiempo real por el método de discriminación alélica Taqman de Applied Biosystems. Resultados: El alelo NAT2*4 (wild type) mostró una mayor frecuencia en el grupo Wayúu (55.3%), el alelo NAT2*5 en el grupo Wiwa (34.5%) y el alelo NAT2*7 en el grupo Chimila (24.2%). Se encontró una mayor frecuencia del estado acetilador rápido en el grupo Wayúu (31.3%) y en el grupo Chimila (29.5%) al compararse con el grupo Wiwa (12.7%). La distribución del estado acetilador intermedio es muy similar en los tres grupos, y para el estado acetilador lento observamos que en el grupo Wiwa la frecuencia es mayor (32.7%) con respecto a Chimila y Wayúu con 20.5% y 21.2% respectivamente. Conclusiones: Los resultados permitieron conocer la distribución alélica y el componente farmacogenético de los tres grupos estudiados; igualmente, deducir el estado acetilador y/o fenotipo más frecuente. Debido a la alta prevalencia de acetiladores lentos, se podría predecir un aumento de la incidencia de hepatotóxicidad inducida por medicamentos antituberculosos como la Isoniacida indicados en estas poblaciones y en mayor frecuencia en el grupo Wiwa.

Uso de la técnica SSCP para detectar mutaciones puntuales del ADN mitocondrial humano

En el presente trabajo se evalúa la técnica de SSCP (polimorfismo de conformación de cadena individual de ADN) para detectar mutaciones puntuales, tanto por su sensibilidad en la detección (alrededor 80% en condiciones ideales), como por su implementación fácil y económica. Se utilizaron como controles positivos y negativos, ADN de voluntarios caracterizados previamente para las mutaciones puntuales de 5 RFLPs mitocondriales. Para la optimización de la prueba fueron ensayadas concentraciones variables del tampón TBE (1X y 0,5X) y del glicerol (10%, 5% y 0) en geles de poliacrilamida. Cuatro de los 5 RFLPs fueron detectados en las condiciones utilizadas y pueden ser usados en estudios de rutina sin usar enzimas de restricción. Además, la técnica SSCP permitió determinar mutaciones desconocidas en un segmento de 394 nucleótidos de la región hipervariable (HVI) del ADNmt. Diferencias en correspondencia a los distintos haplotipos fueron detectados e incluso permitió discernir grupos dentro del mismo subtipo. La secuenciación de dos muestras del subtipo B1 con migración diferencial en SSCP, corroboró la existencia de siete nucleótidos distintos.

We evaluate the use of SSCP (single strand conformational polymorphism), a relatively easy and inexpensive technique for the detection of point mutations with a sensibility around 80% under ideal conditions. To test the technique, we used samples of volunteers whose DNA had been previously characterized for the presence or absence of 5 mitochondrial RFLPs. Optimization of the tests included variations in TBE (1X and 0,5X) and of glycerol concentration (10%, 5% and no glycerol) in polyacrylamide gels. Four out of five RFLPs were detected under the conditions used and could be applied routinely without using restriction enzymes. In addition, the SSCP technique allowed detection of unknown mutations in a 394 bp nucleotide segment of the hypervariable (HVI) region of mtDNA. Differences corresponding to different haplotypes were detected, helping to distinguish groups within the same subtype. Sequencing of two samples of subtype B1 with differential migration on SSCP gels, proved the existence in seven different nucleotides.