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Electron. j. biotechnol ; 51: 8-16, May. 2021. tab, graf, ilus
Article in English | LILACS | ID: biblio-1343314


BACKGROUND: Myogenic regulatory factors (MRFs) such as MyoD, Myf6 and Myf5 play a vital role in the growth and development of muscles. Jeju Native Pig (JNP) is the top ranker in Korea amongst the indigenous livestock reared for meat purpose. Few studies covering transcript abundance of the MRFs and related to their co-expression with Pax7 in JNP have been conducted. Despite having better quality pork, JNP does not have a comparative growth rate with respect to western breeds. Therefore, the present study was designed with the objective to study the relative transcript levels of MRFs in the postnatal myogenesis of longissimus dorsi muscles in JNP and Berkshire breeds. RESULTS: Relative transcript levels were analyzed by qRT-PCR and blot expression analysis through Western blotting. Immunocytochemistry was performed to analyze their expressions at cellular levels. ToppCluster aided in the analysis of gene ontology of biological processes. The quantitative transcript levels of MyoD and Pax7 were significantly (P < 0.05) higher in Berkshire than in JNP. Myotube formation was observed under the co-expression of MyoD and Pax7. ToppCluster helped in the understanding of the linking of biological processes of the MRFs with the different signaling pathways. MyBPH had significantly (P < 0.05) high transcript levels during the chosen age groups in JNP than Berkshire. CONCLUSIONS: The current study can be helpful in understanding the genetic basis for myogenesis in postnatal stage. Moreover, it can act as stepping stone for the identification of marker genes related to body growth and meat quality in JNP.

Animals , Swine , Myogenic Regulatory Factors/metabolism , Muscle Development/genetics , Immunohistochemistry , Genetic Markers , Blotting, Western , Myogenic Regulatory Factors/genetics , PAX7 Transcription Factor/metabolism , Real-Time Polymerase Chain Reaction , Gene Ontology , Pork Meat
Electron J Biotechnol ; 49: 72-81, Jan. 2021. tab, graf
Article in English | LILACS | ID: biblio-1291929


BACKGROUND: Persimmon (Diospyros kaki Thunb.) is the most widely cultivated species of the genus Diospyros. In this study, genetic diversity and variations in persimmon genotypes were investigated using single nucleotide polymorphism (SNP) markers identified by genotyping-by-sequencing (GBS) analysis. RESULTS: Ninety-five persimmon accessions grown in the Pear Research Institute, National Institute Horticultural and Herbal Science, were sequenced using the Illumina Hiseq2500 platform and polymorphic SNPs were detected to develop molecular markers. These reliable SNPs were analyzed using the Kompetitive Allele Specific PCR (KASP) assay to discriminate among persimmon genotypes. GBS generated a total of 447,495,724 trimmed reads, of which 89.7% were raw reads. After demultiplexing and sequence quality trimming, 108,876,644 clean reads were mapped to the reference transcriptome. An average of 1,146,070 genotype reads were mapped. Filtering of raw SNPs in each sample led to selection of a total of 1,725,401 high-quality SNPs. The number of homozygous and heterozygous SNPs ranged from 1,933 to 6,834 and from 846 to 5,927, respectively. CONCLUSIONS: Of the 49 SNPs selected for development of an identification system for persimmons, 15 SNPs were used in the KASP assay to analyze 32 persimmon accessions. These KASP markers discriminated among all accessions.

Polymerase Chain Reaction/methods , Diospyros/genetics , Genetic Variation , Genetic Markers , Chromosome Mapping , Polymorphism, Single Nucleotide/genetics , Alleles , Genotyping Techniques , Homozygote
Electron J Biotechnol ; 49: 50-55, Jan. 2021. tab, graf
Article in English | LILACS | ID: biblio-1291649


BACKGROUND: Euphorbia fischeriana Steud is a very important medicinal herb and has significant medical value for healing cancer, edema and tuberculosis in China. The lack of molecular markers for Euphorbia fischeriana Steud is a dominant barrier to genetic research. For the purpose of developing many simple sequence repeat (SSR) molecular markers, we completed transcriptome analysis with the Illumina HiSeq 2000 platform. RESULTS: Approximately 9.1 million clean reads were acquired and then assembled into approximately 186.3 thousand nonredundant unigenes, 53,146 of which were SSR-containing unigenes. A total of 76,193 SSR loci were identified. Of these SSR loci, 28,491 were detected at the terminal position of ESTs, which made it difficult to design SSR primers for these SSR-containing sequences, and the residual SSRs were thus used to design primer pairs. Analyzing the results of these markers revealed that the mononucleotide motif A/T (44,067, 57.83% of all SSRs) was the most abundant, followed by the dinucleotide type AG/CT (9430, 12.38%). Using 100 randomly selected primer pairs, 77 primers were successfully amplified in Euphorbia fischeriana Steud, and 79 were successfully amplified in three other related species. The markers developed displayed relatively high quality and cross-species transferability. CONCLUSIONS: The large number of EST-SSRs exploited successfully in Euphorbia fischeriana Steud for the first time could provide genetic information for research on linkage maps, variety identification, genetic diversity analysis, and molecular marker-assisted breeding.

Euphorbia/genetics , High-Throughput Nucleotide Sequencing/methods , Plants, Medicinal , Genetic Variation , Genetic Markers
Braz. arch. biol. technol ; 64: e21190007, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153291


HIGHLIGHTS Low genetic similarity in Paspalum notatum accessions. High genetic distance among diploid accessions. The accessions have good potential to breeding program.

Abstract Paspalum notatum is an important forage grass contributing significantly to the coverage of the natural fields of Southern Brazil. Simple sequence repeat (SSR) markers were used to evaluate the genetic similarity of strains within a P. notatum collection. Genomic DNA was extracted in bulk from young leaves of five plants from each accession obtained from the USDA. In the molecular analysis, the eight SSR markers evaluated formed seven distinct groups, and two isolated genotypes, with an average similarity index of 0.29, ranging from zero to 0.83. All the loci were polymorphic and the polymorphism information content ranging from 0.41 to 0.69. The results evidenced a low genetic similarity, which can be explored via parental selection in a breeding program.

Paspalum/genetics , Diploidy , Plant Breeding , Breeding , Genetic Markers , Hybrid Vigor
Article in English | WPRIM | ID: wpr-878372


Objective@#To study the polymorphism in P66 and its human B-cell epitopes of @*Methods@#Polymerase chain reaction (PCR) and sequencing were used to obtain the P66 sequences of 59 Chinese @*Results@#Results showed that genetic and amino acid diversity presented in the 66 kD protein of all 59 Chinese strains, especially in @*Conclusion@#In P66 of 59 Chinese strains, polymorphisms were widely distributed. More importantly, the P66 amino acid sequences of

Bacterial Proteins/genetics , Borrelia burgdorferi/genetics , China , Cluster Analysis , Epitopes, B-Lymphocyte/genetics , Genetic Markers , Genotype , Humans , Mutation , Polymerase Chain Reaction , Polymorphism, Genetic , Porins/genetics
Article in English | WPRIM | ID: wpr-880352


BACKGROUND@#Arsenic is a developmental neurotoxicant. It means that its neurotoxic effect could occur in offspring by maternal arsenic exposure. Our previous study showed that developmental arsenic exposure impaired social behavior and serotonergic system in C3H adult male mice. These effects might affect the next generation with no direct exposure to arsenic. This study aimed to detect the social behavior and related gene expression changes in F2 male mice born to gestationally arsenite-exposed F1 mice.@*METHODS@#Pregnant C3H/HeN mice (F0) were given free access to tap water (control mice) or tap water containing 85 ppm sodium arsenite from days 8 to 18 of gestation. Arsenite was not given to F1 or F2 mice. The F2 mice were generated by mating among control F1 males and females, and arsenite-F1 males and females at the age of 10 weeks. At 41 weeks and 74 weeks of age respectively, F2 males were used for the assessment of social behavior by a three-chamber social behavior apparatus. Histological features of the prefrontal cortex were studied by ordinary light microscope. Social behavior-related gene expressions were determined in the prefrontal cortex by real time RT-PCR method.@*RESULTS@#The arsenite-F2 male mice showed significantly poor sociability and social novelty preference in both 41-week-old group and 74-week-old group. There was no significant histological difference between the control mice and the arsenite-F2 mice. Regarding gene expression, serotonin receptor 5B (5-HT 5B) mRNA expression was significantly decreased (p < 0.05) in the arsenite-F2 male mice compared to the control F2 male mice in both groups. Brain-derived neurotrophic factor (BDNF) and dopamine receptor D1a (Drd1a) gene expressions were significantly decreased (p < 0.05) only in the arsenite-F2 male mice of the 74-week-old group. Heme oxygenase-1 (HO-1) gene expression was significantly increased (p < 0.001) in the arsenite-F2 male mice of both groups, but plasma 8-hydroxy-2'-deoxyguanosine (8-OHdG) and cyclooxygenase-2 (COX-2) gene expression were not significantly different. Interleukin-1β (IL-1β) mRNA expression was significantly increased only in 41-week-old arsenite-F2 mice.@*CONCLUSIONS@#These findings suggest that maternal arsenic exposure affects social behavior in F2 male mice via serotonergic system in the prefrontal cortex. In this study, COX-2 were not increased although oxidative stress marker (HO-1) was increased significantly in arsnite-F2 male mice.

Animals , Arsenic/toxicity , Arsenites/toxicity , Behavior, Animal/drug effects , Environmental Pollutants/toxicity , Female , Gene Expression/drug effects , Genetic Markers , Male , Maternal Exposure/adverse effects , Mice , Mice, Inbred C3H , Oxidative Stress/genetics , Prefrontal Cortex/drug effects , Pregnancy , Prenatal Exposure Delayed Effects/psychology , Reverse Transcriptase Polymerase Chain Reaction , Serotonin/metabolism , Social Behavior , Sodium Compounds/toxicity
Article in Chinese | WPRIM | ID: wpr-878958


Based on the characteristics and ISSR molecular marker technology, the study is aimed to compare and perform genetic diversity analysis on Sparganium stoloniferum from 7 regions. Molecular identification method was established for S. stoloniferum from Hunan province. Differences among Sparganii Rhizoma samples from seven habitats were analyzed via measuring weight, length, width and thickness of them. Genetic diversity of S. stoloniferum from 7 regions was analyzed by screening out primers amplifying clear band and showing rich polymorphism, then a cultivars dendrogram was built. The target primer was screened out, and the specific band was sequenced. Nine ISSR primers were selected to amplified clear band, rich polymorphism. A total of 73 bands were amplified by nine ISSR primers selected from 27 ISSR primers. On average, each primer produced 8.0 bands. A total of 38 bands were polymorphic, which occupied 52.8% of all bands. The cultivars dendrogram showed the genetic similarity was 0.54-0.94. Genetic similarity coefficient of S. stoloniferum from Jiangsu province, Anhui province and Jiangxi province was big, indicating the differences among them were slight on genetic level. S. stoloniferum from Hunan province is quite different from samples from the other six habitats on appea-rance and genetic level. A specific band(327 bp) in S. stoloniferum from Hunan province was obtained via ISSR-857 primer, and was sequenced. According BLASTn database, there were few sequences similar to the gene fragment and had little correlation with the growth process of plant. ISSR molecular marker technology provides a new idea for the identification of S. stoloniferum. This result confirmed the particularity of S. stoloniferum from ancient Jingzhou.

China , Drugs, Chinese Herbal , Genetic Markers/genetics , Genetic Variation , Microsatellite Repeats , Phylogeny , Polymorphism, Genetic
Rev. chil. pediatr ; 91(5): 761-766, oct. 2020. tab
Article in Spanish | LILACS | ID: biblio-1144276


INTRODUCCIÓN: La asociación de casos familiares de epilepsia y discapacidad intelectual (DI) en mujeres fue reportada en 1971. El año 2008, se identificó el rol de variantes patogénicas del gen PCDH19 en algunas familias. La enfermedad se presenta con crisis febriles en cluster, DI y rasgos autistas. La mayoría se debe a variantes de novo, pero hay algunos casos heredados por un modo peculiar de transmisión ligada X. OBJETIVO: Comunicar el caso de una paciente con epilepsia portadora de una variante patogénica en el gen PCDH1 9, revisando la historia natural de la enfermedad y la evidencia disponible para su manejo. CASO CLÍNICO: Paciente femenina, con antecedentes de embarazo y período perinatal normal. A los 6 meses, estando febril, presentó crisis focales motoras en cluster que repitieron a los 14, 18, 21 meses y 3 años siempre asociadas a fiebre, presentando incluso estatus epiléptico. Mantiene biterapia con topiramato y ácido valproico, completando 13 años sin crisis. El estudio del gen SCN1A no mostró anomalías y el estudio del gen PCDH19 reveló una variante patogénica en heterocigosis, "de novo". La paciente ha evolucionado con DI y alteraciones conductuales severas que requieren aten ción de salud mental. CONCLUSIONES: Las variantes patogénicas PCDH19 tienen expresión fenotípica variada. El diagnóstico genético debe sospecharse con la clínica. La morbilidad psiquiátrica a largo plazo puede ser incapacitante.

INTRODUCTION: The association of family cases of epilepsy and intellectual disability in women was reported in 1971. In 2008, the role of pathogenic variants of the PCDH19 gene in some families were identified. The disease presents with febrile seizure clusters, intellectual disability, and autistic features. Most cases are due to de novo variants, however, there are some inherited cases, with an atypical way of X-linked transmission. OBJECTIVE: To report the case of a patient with epilepsy carrier of a pathogenic variant of the PCDH19 gene, reviewing the natural history of this condition and the available evidence for its management. CLINICAL CASE: Female patient, with normal history of pregnancy and perinatal period. At 6 months, while febrile, she presented focal motor seizure clusters that repeated at 14, 18, 21 months and 3 years old, always associated with fever, even presenting status epilepticus. She is on therapy with topiramate and valproic acid, achieving 13 seizure-free years. The analysis of the SCN1A gene showed no abnormalities and the study of the PCDH19 gene revealed a de novo heterozygous pathogenic variant. The patient evolved with intellectual disability and severe behavioral disorders that require mental health team support. CONCLUSIONS: PCDH19 pathogenic variants have varied phenotypic expression. The genetic diagnosis should be guided with the clinical features. Long-term psychiatric morbidity can be disabling.

Humans , Female , Adolescent , Cadherins/genetics , Mutation, Missense , Epilepsy/genetics , Intellectual Disability/genetics , Genetic Markers , Diagnosis, Differential , Epilepsy/complications , Epilepsy/diagnosis , Heterozygote , Intellectual Disability/complications , Intellectual Disability/diagnosis
Rev. bras. ortop ; 55(5): 537-542, Sept.-Oct. 2020.
Article in English | LILACS | ID: biblio-1144207


Abstract The influence of genetic inheritance has been increasingly investigated in shoulder disorders, such as rotator cuff injury, instability and frozen shoulder. Although the initial findings are enlightening, it is necessary to progressively build a database of genetic markers to catalog genomic profiles that, later, may contribute for predicting the risk of the disease, as well as to the development of better diagnostic and treatment tools. The present article seeks to update what is evidence of genetic studies in the literature for these diseases, from polymorphism analyses, expression of candidate genes in tissues and broad genomic association studies (GWAS). However, it is necessary to point out that there is great difficulty in replicating and using the findings, mainly due to the lack of statistical power, the high rate of false-positive results and the large number of variables involved.

Resumo A influência da herança genética tem sido cada vez mais investigada nas afecções do ombro, como a lesão do manguito rotador, instabilidade e ombro congelado. Ainda que os achados iniciais sejam pouco esclarecedores, é necessário construir progressivamente um banco de marcadores genéticos para catalogar perfis genômicos que, mais adiante, poderão contribuir para a previsão do risco da doença, desenvolvimento de melhores ferramentas de diagnóstico e tratamento. O presente artigo busca atualizar o que há de evidências de estudos genéticos na literatura para essas doenças, desde análises de polimorfismos, expressão de genes candidatos em tecidos e estudos de associação genômica ampla (GWAS, na sigla em inglês). Porém, é necessário apontar que existe grande dificuldade na replicação e utilização dos achados, principalmente em razão da falta de poder estatístico, da alta taxa de resultados falso-positivos e da grande quantidade de variáveis envolvidas.

Polymorphism, Genetic , Shoulder , Wounds and Injuries , Bursitis , Genetic Markers , Gene Expression , Incidence , Rotator Cuff , Heredity , Diagnosis , False Positive Reactions , Rotator Cuff Injuries
Rev. cuba. hematol. inmunol. hemoter ; 36(3): e1243, jul.-set. 2020.
Article in Spanish | LILACS, CUMED | ID: biblio-1156443


Las neoplasias hematológicas se caracterizan por un gran número y complejidad de alteraciones genéticas, desde la formación de genes de fusión a partir de translocaciones e inversiones cromosómicas hasta mutaciones génicas y alteraciones epigenéticas que han permitido la identificación de nuevos oncogenes y genes supresores de tumores responsables de su etiología. Al abordar el estudio genético de las leucemias se utilizan múltiples técnicas como la citogenética convencional, citogenética molecular (hibridaciónin situ por fluorescencia (FISH), esta última con una mayor sensibilidad, especificidad y rapidez que permiten el diagnóstico, la estratificación pronóstica y seguimiento de la enfermedad. Las técnicas anteriores se integran con técnicas de biología molecular, secuenciación génica, entre otras, que permiten el hallazgo de nuevos marcadores genéticos con una mejor caracterización de las hemopatías malignas y la posibilidad del desarrollo de nuevos fármacos específicos que actúen sobre la diana molecular. El objetivo fue revisar la utilidad de la citogenética y la secuenciación génica en el estudio de la leucemia mieloide aguda y la leucemia linfocítica crónica. Ante las ventajas, desventajas y limitaciones de estas técnicas genéticas es necesario utilizarlas de forma complementaria y nunca excluyente(AU)

Hematological neoplasms are characterized by a large number and great complexity of genetic disorders, from the formation of fusion genes after chromosomal translocations and inversions to gene mutation and epigenetic disorders that have permitted the identification of new oncogenes and tumor-suppressing genes responsible for their etiology. When addressing the genetic study of leukemias, multiple techniques are used, such as conventional cytogenetics, molecular cytogenetics, and fluorescence in situ hybridization (FISH), the latter having the higher degree of sensitivity, specificity and speed, which allow diagnosis, prognostic stratification and follow-up of the disease. The previous techniques are integrated with molecular biology techniques, gene sequencing, among others, which allow discovery of new genetic markers with better characterization of malignant hemopathies and the possibility of developing new specific drugs against the molecular target. The objective was to review the usefulness of cytogenetics and gene sequencing in the study of acute myeloid leukemia and chronic lymphocytic leukemia. Given the advantages, disadvantages and limitations of these genetic techniques, it is necessary to use them in as complementary but never exclusive management ways(AU)

Humans , Oncogenes , Genetic Markers , In Situ Hybridization, Fluorescence/methods , Hematologic Neoplasms/genetics , Cytogenetics , Epigenomics , Genetic Diseases, Inborn , Molecular Biology , Whole Genome Sequencing/methods
Rev. chil. pediatr ; 91(4): 584-590, ago. 2020. tab, graf
Article in Spanish | LILACS | ID: biblio-1138675


INTRODUCCIÓN: El síndrome IPEX (inmunodesregulación, poliendocrinopatía y enteropatía autoinmune ligada a X) causado por mutaciones en el gen FOXP3, se caracteriza por diarrea prolongada, alteraciones endocrinológicas y dermatitis. El tratamiento consiste en la administración de medicamentos inmunosupresores, siendo el trasplante de médula ósea la única cura potencial. OBJETIVO: Describir una nueva mutación del gen FOXP3, así como los hallazgos y evolución de un paciente con síndrome IPEX. CASO CLÍNICO: Lactante menor masculino que debutó al mes de vida con diarrea cró nica, falla intestinal e infecciones recurrentes. Exámenes de laboratorio y biopsia intestinal sugerentes de enteropatía autoinmune. Durante el seguimiento, el paciente presentó refractariedad al manejo inmunosupresor con esteroides, ciclosporina y tacrolimus, falleciendo a los 7 meses de edad por complicaciones vasculares. Antecedente familiar por línea materna de múltiples muertes en hombres menores de 1 año. Ante la sospecha de síndrome IPEX se realizó exoma en trío que reportó una mutación probablemente patogénica en el gen FOXP3. CONCLUSIÓN: Se documentó una nueva mutación del gen FOXP3 en paciente con síndrome IPEX. A pesar de la baja prevalencia de esta enfermedad, es importante el reconocimiento de síntomas no específicos pero sugerentes del diagnóstico.

INTRODUCTION: The IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked) syn drome is caused by the mutations of the FOXP3 gene, characterized by persistent diarrhea, endo crine disorders, and dermatitis. The treatment is the administration of immunosuppressive drugs, where hematopoietic stem cell transplantation is the only potential cure. OBJECTIVE: To describe a new FOXP3 gene mutation, as well as the findings and evolution of a patient with IPEX syndrome. CLINICAL CASE: Male infant presenting at one month of age with chronic diarrhea, intestinal failure, and recurrent infections. Lab tests and intestinal biopsy suggested autoimmune enteropathy. During follow-up, the patient presented resistance to immunosuppressive treatment with corticosteroids, cyclosporine, and tacrolimus, dying at 7 months of age due to vascular complications. He had a ma ternal family history of multiple deaths of men under 1 year of age. IPEX syndrome was suspected therefore a trio whole-exome sequencing was performed that showed a probably pathogenic FOXP3 gene mutation. CONCLUSION: A new FOXP3 gene mutation is reported in a patient with IPEX syndro me. Despite the low prevalence of this disease, it is important to recognize non-specific but suggestive symptoms for its diagnosis.

Humans , Male , Infant , Genetic Diseases, X-Linked/diagnosis , Diabetes Mellitus, Type 1/congenital , Diarrhea/diagnosis , Forkhead Transcription Factors/genetics , Immune System Diseases/congenital , Pedigree , Genetic Markers , Chronic Disease , Fatal Outcome , Genetic Diseases, X-Linked/genetics , Diabetes Mellitus, Type 1/diagnosis , Diabetes Mellitus, Type 1/genetics , Diarrhea/genetics , Immune System Diseases/diagnosis , Immune System Diseases/genetics , Mutation
Electron. j. biotechnol ; 46: 1-7, jul. 2020. ilus, graf, tab
Article in English | LILACS | ID: biblio-1223252


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.

Oryza/enzymology , Oryza/genetics , Betaine-Aldehyde Dehydrogenase/metabolism , Genetic Markers , Alleles , Genotyping Techniques/methods , Genotype , Odorants
Rev. chil. pediatr ; 91(3): 371-378, jun. 2020. tab, graf
Article in Spanish | LILACS | ID: biblio-1126174


Resumen: Introducción: La obesidad es una enfermedad inflamatoria donde la genética determina cierto nivel de riesgo. Aun cuando existen estudios que reportan asociación entre polimorfismos de FTO (fat-mass associated gene) y adiposidad, existe limitada evidencia en población infantil chilena. Objetivo: determinar la asociación entre el polimorfismo rs9939609 del FTO y marcadores de adiposidad en población in fantil chilena. Pacientes y Método: Estudio de corte transversal incluyó 361 participantes (de 6 a 11 años; 50% niñas). Los datos clínicos y la recolección de muestras de sangre se realizaron entre marzo y junio de 2008. El polimorfismo SNP (rs9939609), del gen FTO, se determinó utilizando ADN genómico extraído de leucocitos, utilizando el Mini Kit QIAamp DNA Blood (Qiagen GmbH, Hilden, Alemania). Los marcadores de adiposidad estudiados fueron, índice de masa corporal (IMC), masa grasa, perímetro de cintura (PC) y razón cintura/talla, y se compararon ajustados por sexo, edad y estadio de Tanner. La asociación entre el polimorfismo estudiado y los marcadores de obesidad se realizó mediante análisis de regresión lineal. Resultados: Al ajustar los marcadores por sexo, edad y estadío de Tanner se observó una asociación significativa entre el polimorfismo e indicadores de adi posidad. Por cada copia extra del alelo de riesgo se encontró un aumento de 2,47 kg de peso corporal, (IC 95%: 1,39-3,55); 1,06 kg/m2 de IMC, (IC 95%: 0,56-1,54); 2,55 cm de PC, (IC 95%: 1,26-3,85) y 1,98% de masa grasa, (IC 95%: 0,78-3,19). Al convertir los marcadores de adiposidad a z-score, la razón perímetro de cintura/talla arrojó la mayor asociación con el alelo de riesgo de FTO. Conclu sión: Este estudio indica asociación entre el polimorfismo rs9939609 del gen FTO con marcadores de adiposidad general y central en población infantil en Chile.

Abstract: Introduction: Obesity is considered a chronic inflammatory disease with an important genetic component. Although several studies have reported an association between the FTO (fat-mass associated gene) and adiposity in children, there is limited evidence in the Chilean population. Objective: To deter mine the association between the polymorphism rs9939609 of the FTO gene and markers of adipo sity in Chilean children. Patients and Method: Cross-sectional study which included 361 children aged between 6 and 11 years (50% were girls). Between March and June 2008, clinical data and blood sample collection was carried out. The rs9939609 single-nucleotide polymorphism (SNP) of the FTO gene, was determined using the genomic DNA extracted from leukocytes, using the QIAamp DNA Blood Mini Kit (Qiagen GmbH, Hilden, Germany).The adiposity markers included were body mass index (BMI), waist circumference (WC), body fat, and WC/H index; which were later compared adjusted by sex, age, and Tanner stage. Linear regression analyses were conducted to detect the association between the polymorphism and obesity markers. Results: After adjusting the models by age, sex, and Tanner stage, we found a significant association between the polymorphism and markers of adiposity. For each extra copy of the risk allele, we found an increase of 2.47 kg body weight (95% CI: 1.39-3.55); 1.06 kg/m2 BMI (95% CI: 0.56-1.54); 2.55 cm WC, (95% CI: 1.26-3.85); and 1.98% body fat (95% CI: 0.78-3.19). When converting adiposity markers to z-score, we found that WC/height index shows the strongest association with the risk allele FTO. Conclusion: This study supports the association between the rs9939609 SNP of the FTO gene and overall and central adiposity markers in Chilean children.

Humans , Male , Female , Child , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Adiposity/genetics , Pediatric Obesity/genetics , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics , Genetic Markers , Linear Models , Chile , Cross-Sectional Studies , Pediatric Obesity/diagnosis , Pediatric Obesity/pathology
Rev. chil. pediatr ; 91(3): 417-423, jun. 2020. graf
Article in Spanish | LILACS | ID: biblio-1126181


Resumen: Introducción: La trombosis senovenosa cerebral neonatal (TSVC), es una patología rara y generalmente grave, de la cual se conoce poco sobre los mecanismos fisiopatológicos responsables y, aunque controvertido, se ha sugerido que la trombofilia genética, puede desempeñar un rol en la patogénesis. Debido a los temores de un sangrado intracraneal el tratamiento anticoagulante con heparina de bajo peso mole cular es controvertido. Objetivo: presentar un recién nacido con una trombosis senovenosa cerebral neonatal, discutir los factores de riesgo trombofílico, y el manejo con heparina de bajo peso molecu lar de la trombosis venosa cerebral. Caso Clínico: Recién nacido de término que debutó a los 8 días de vida con convulsiones clónicas, rechazo al pecho más hipoactividad motora. La neuroimagen con RM mostró una TSVC involucrando múltiples senos venosos, un infarto hemorrágico talámico dere cho y congestión venosa de la sustancia blanca frontal. El estudio de trombofilia puso de relieve una mutación homocigota del gen MTHFR C677T. El tratamiento con heparina de bajo peso molecular se asoció a repermeabilización del seno sagital superior a los 23 días de iniciada la terapia. Conclusio nes: La presentación clínica de la TSVC en el neonato es inespecífica, probablemente en relación con la extensión y gravedad de la lesión y el desarrollo de complicaciones asociadas, como infartos he morrágicos venosos intraparenquimatosos o hemorragia intraventricular. Estas complicaciones son detectables mediante Ecografia o Resonancia Magnética, y deben hacer sospechar una TSVC. En esta experiencia el tratamiento anticoagulante mostró ser seguro y prevenir la extensión de la trombosis.

Abstract: Introduction: Neonatal cerebral sinovenous thrombosis (CSNT) is a rare and generally serious con dition about which there is little knowledge of the responsible pathophysiological mechanisms and, although controversial, it has been suggested that genetic thrombophilia may play a role in its patho genesis. Out of concern for intracranial bleeding, the anticoagulant treatment with low-molecular- weight heparin is controversial. Objective: To present a case of a newborn with neonatal CSNT, to analyze the thrombophilic risk factors, and the management of cerebral venous thrombosis with low-molecular-weight heparin. Clinical Case: Full-term newborn who presented at eight days of life breastfeeding rejection, clonic seizures, and locomotor hypoactivity. The MRI neuroimaging showed a CSNT involving multiple venous sinuses, a right thalamic hemorrhagic infarction, and venous congestion in frontal white matter. Thrombophilia study highlighted a homozygous MTHFR C677T mutation. Treatment with low-molecular-weight heparin was associated with repermeabilization of the superior sagittal sinus after 23 days of starting therapy. Conclusions: The clinical presentation of CSNT in the neonate is nonspecific, probably related to the extent and severity of the injury and the development of associated complications, such as venous hemorrhagic infarctions and intraparenchymal or intraventricular hemorrhage. These complications are detected through ultrasound or MRI, and they should make us suspect a CSNT. In this experience, the anticoagulant treatment proved to be safe and prevents thrombus propagation.

Humans , Female , Infant, Newborn , Sinus Thrombosis, Intracranial/diagnosis , Sinus Thrombosis, Intracranial/etiology , Enoxaparin/therapeutic use , Methylenetetrahydrofolate Reductase (NADPH2)/deficiency , Homocystinuria/diagnosis , Muscle Spasticity/diagnosis , Anticoagulants/therapeutic use , Psychotic Disorders/complications , Psychotic Disorders/diagnosis , Psychotic Disorders/genetics , Sinus Thrombosis, Intracranial/drug therapy , Genetic Markers , Methylenetetrahydrofolate Reductase (NADPH2)/genetics , Homocystinuria/complications , Homocystinuria/genetics , Homozygote , Muscle Spasticity/complications , Muscle Spasticity/genetics , Mutation
Rev. Bras. Saúde Mater. Infant. (Online) ; 20(2): 467-471, Apr.-June 2020. tab
Article in English | SES-SP, LILACS, SES-SP | ID: biblio-1136441


Abstract Objectives: the present study aimed to evaluate the association between the rs1799998 polymorphism of the CYP11B2 gene and the susceptibility to preeclampsia (PE) in a Brazilian population. Methods: the study group comprised 61 women who were diagnosed with PE. The control group included 116 women who did not show changes in their blood pressure levels during their pregnancies. The rs1799998 polymorphism of the CYP11B2 gene was amplified by allele-specific polymerase chain reaction (PCR). A multiple logistic regression analysis was performed using the SNPStat program to evaluate the risk of the CYP11B2 gene rs1799998 polymorphism contributing to PE. Results: the PE group had the following genotypes: 1.64% CC, 91.80% CT, and 6.56% TT. In the control group, the observed genotypic frequencies were: 11% CC, 73% CT, and 16% TT. The genotypic frequency distribution did not fit the Hardy Weinberg Equilibrium (HWE) in either study group. The multiple logistic regression analysis showed a statistically significant difference for the rs1799998 polymorphism in the recessive model. Conclusion: the results suggest an association between the recessive model of C/C genotype of the rs1799998 polymorphism of the CYP11B2 gene and susceptibility to PE.

Resumo Objetivos: avaliar a associação entre o polimorfismo rs1799998 do gene CYP11B2 e a suscetibilidade à PE em uma população brasileira. Métodos: participaram desse estudo 61 mulheres com PE e 116 mulheres normotensas. O polimorfismo rs1799998 do gene CYP11B2 foi amplificado por PCR alelo-específica. O risco do polimorfismo rs1799998 do gene CYP11B2 contribuir com a PE foi avaliado pela análise de regressão logística múltipla. Resultados: as frequências genotípicas observadas foram 1.64% CC, 91.80% CT e 6.56% TT no grupo PE e 11%CC, 73%CT e 16%TT grupo controle. A distribuição da frequência genotípica não estava em Equilíbrio de Hardy Weinberg em nenhum dos grupos estudados. A análise de regressão logística múltipla demonstrou diferença estatisticamente significativa para o polimorfismo rs1799998 no modelo recessivo. Conclusão: o presente trabalho sugere associação do genótipo C/C no modelo recessivo, do polimorfismo rs1799998 do gene CYP11B2 com a suscetibilidade a PE.

Humans , Female , Pregnancy , Polymorphism, Genetic , Pre-Eclampsia/genetics , Cytochrome P-450 CYP11B2 , Cytochrome P-450 Enzyme System , Brazil , Genetic Markers , Logistic Models , Genetic Predisposition to Disease , Genetic Profile
Electron. j. biotechnol ; 44: 25-32, Mar. 2020. graf, tab, ilus
Article in English | LILACS | ID: biblio-1087637


BACKGROUND: Cultivated peanut (Arachis hypogaea. L) represents one of the most important oil crops in the world. Although much effort has been expended to characterize microsatellites or Simple Sequence Repeats (SSRs) in peanut, the quantity and quality of the markers in breeding applications remain limited. Here, genome-wide SSR characterization and marker development were performed using the recently assembled genome of the cultivar Tifrunner. RESULTS: In total, 512,900 microsatellites were identified from 2556.9-Mb genomic sequences. Based on the flanking sequences of the identified microsatellites, 7757 primer pairs (markers) were designed, and further evaluated in the assembled genomic sequences of the tetraploid Arachis cultivars, Tifrunner and Shitouqi, and the diploid ancestral species, A. duranensis and A. ipaensis. In silico PCR analysis showed that the SSR markers had high amplification efficiency and polymorphism in four Arachis genotypes. Notably, nearly 60% of these markers were single-locus SSRs in tetraploid Arachis species, indicating they are more specific in distinguishing the alleles of the A and B sub-genomes of peanut. In addition, two markers closely related with purple testa color and 27 markers near to FAD2 genes were identified, which could be used for breeding varieties with purple testa and high-oleic acid content, respectively. Moreover, the potential application of these SSR markers in tracking introgressions from Arachis wild relatives was discussed. CONCLUSIONS: This study reported the development of genomic SSRs from assembled genomic sequences of the tetraploid Arachis Tifrunner, which will be useful for diversity analysis, genetic mapping and functional genomics studies in peanut

Arachis/genetics , Breeding/methods , Microsatellite Repeats , Polymorphism, Genetic , Genetic Markers , Polymerase Chain Reaction , Genome , Crops, Agricultural
Rev. cuba. invest. bioméd ; 39(1): e336, ene.-mar. 2020. graf
Article in Spanish | LILACS, CUMED | ID: biblio-1126572


Introducción: El género Brucella está incluido en la familia Brucellaceae que pertenece al orden Rhizobiales y es reconocido por su alto grado de patogenicidad. Las bacterias de este género son responsables de la brucelosis, enfermedad que ha sido reportada como una de las zoonosis más importantes a nivel mundial por su incidencia en el ganado y el hombre. Los estudios previos para la clasificación taxonómica del género, se han basado fundamentalmente en el análisis del gen 16S ARNr. Sin embargo, pocas investigaciones se han dirigido a la identificación de marcadores moleculares que distingan a sus miembros de otros grupos de bacterias. Objetivo: Identificar inserciones en secuencias de proteínas conservadas, que pudieran ser utilizados como marcadores moleculares para la taxonomía y diagnóstico de especies del género Brucella. Métodos: Las secuencias homólogas de las proteínas analizadas fueron obtenidas de bases de datos internacionales y, posteriormente, alineadas con el programa ClustalX2, para ello fueron considerados los parámetros sugeridos en la literatura. Resultados: Se identificaron inserciones en las proteínas oxoglutarato deshidrogenasa (componente E1) y ADN ligasa A específicas del género Brucella. Conclusiones: Las inserciones halladas pueden ser empleadas como complemento a los métodos tradicionales de clasificación taxonómica y para el diagnóstico molecular de bacterias incluidas en el género Brucella(AU)

Introduction: Brucella is a genus from the Brucellaceae family, Rhizobiales order. This genus is recognized for its high pathogenicity. Brucella bacteria cause brucellosis, a disease reported as one of the most important zoonoses worldwide due to its incidence in cattle and people. Previous studies on taxonomic classification of the genus have been mainly based on the analysis of gene 16S rDNA. However, few studies have been aimed at identification of molecular markers distinguishing its members from other groups of bacteria. Objective: Identify insertions in preserved protein sequences which could be used as molecular markers for the taxonomy and diagnosis of species from the Brucella genus. Methods: The homologous sequences for the proteins analyzed were obtained from international databases and aligned with the software ClustalX2, considering the parameters suggested in the literature. Results: Insertions were identified in the proteins oxoglutarate dehydrogenase (component E1) and DNA ligase A, specific of the genus Brucella. Conclusions: The insertions found may be used as complements to the traditional methods for taxonomic classification and for the molecular diagnosis of bacteria from the genus Brucella(AU)

Humans , Sequence Homology , Ketoglutarate Dehydrogenase Complex , Brucella/pathogenicity , Genetic Markers/genetics
Mem. Inst. Oswaldo Cruz ; 115: e190407, 2020. tab
Article in English | LILACS | ID: biblio-1101275


BACKGROUND Early diagnosis of tuberculosis (TB) and identification of strains of Mycobacterium tuberculosis resistant to anti-TB drugs are considered the main factors for disease control. OBJECTIVES To standardise a real-time polymerase chain reaction (qPCR) assay technique and apply it to identify mutations involved in M. tuberculosis resistance to Isoniazid (INH) directly in Ziehl-Neelsen (ZN) stained slides. METHODS Were analysed 55 independent DNA samples extracted from clinical isolates of M. tuberculosis by sequencing. For application in TB diagnosis resistance, 59 ZN-stained slides were used. The sensitivity, specificity and Kappa index, with a 95% confidence interval (CI95%), were determined. FINDINGS The agreement between the tests was, for the katG target, the Kappa index of 0.89 (CI95%: 0.7-1.0). The sensitivity and specificity were 97.6% (CI95%: 87.7-99.9) and 91.7% (CI95%: 61.5-99.5), respectively. For inhA, the Kappa index was 0.92 (CI95%: 0.8-1.0), the sensitivity and specificity were 94.4% (CI95%: 72.7-99.8) and 97.3% (CI95%: 85.8-99.9), respectively. The use of ZN-stained slides for drug-resistant TB detection showed significant results when compared to other standard tests for drug resistance. MAIN CONCLUSIONS qPCR genotyping proved to be an efficient method to detect genes that confer M. tuberculosis resistance to INH. Thus, qPCR genotyping may be an alternative instead of sequencing.

Humans , Genetic Markers/genetics , Drug Resistance, Bacterial/genetics , Isoniazid/pharmacology , Mutation/genetics , Mycobacterium tuberculosis/genetics , Antitubercular Agents/pharmacology , DNA, Bacterial/genetics , Microbial Sensitivity Tests , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction , Genotype , Mycobacterium tuberculosis/drug effects
Braz. arch. biol. technol ; 63: e20190511, 2020. tab, graf
Article in English | LILACS | ID: biblio-1132257


Abstract Long-chain non-encoded RNAs (lncRNAs) are important in many life activities and can participate in the occurrence of hepatocellular carcinoma (HCC). Moreover, lncRNAs can be used as basis for developing new strategies to hinder liver cancer. To investigate the utility of lncRNAs in HCC as potential biomarkers for early detection and diagnosis, we mined genomic data from the Cancer Genome Atlas (TCGA), and analyzed the gene expressions from 374 tumor patients and 50 normal patients. The abnormal expressions of 387 differentially expressed lncRNAs (DElncRNAs) were identified from a total of 3099 lncRNAs. Moreover, 18 modules were divided based on WGCNA, and 2 of the 18 modules were positively correlated with stage and grade, and negatively correlated with survival time. Finally, 10 lncRNAs were found and their main functions are the enhancement of cellular metabolic capacity and cell proliferation. These 10 lncRNAs may serve as novel prognostic markers and therapeutic targets, and may help guide subsequent studies on HCC.

Humans , Biomarkers, Tumor/genetics , Genetic Markers/genetics , Carcinoma, Hepatocellular/genetics , RNA, Long Noncoding/genetics , Liver Neoplasms/genetics
Biol. Res ; 53: 15, 2020. tab, graf
Article in English | LILACS | ID: biblio-1100921


BACKGROUND: Current South American populations trace their origins mainly to three continental ancestries, i.e. European, Amerindian and African. Individual variation in relative proportions of each of these ancestries may be confounded with socio-economic factors due to population stratification. Therefore, ancestry is a potential confounder variable that should be considered in epidemiologic studies and in public health plans. However, there are few studies that have assessed the ancestry of the current admixed Chilean population. This is partly due to the high cost of genome-scale technologies commonly used to estimate ancestry. In this study we have designed a small panel of SNPs to accurately assess ancestry in the largest sampling to date of the Chilean mestizo population (n = 3349) from eight cities. Our panel is also able to distinguish between the two main Amerindian components of Chileans: Aymara from the north and Mapuche from the south. RESULTS: A panel of 150 ancestry-informative markers (AIMs) of SNP type was selected to maximize ancestry informativeness and genome coverage. Of these, 147 were successfully genotyped by KASPar assays in 2843 samples, with an average missing rate of 0.012, and a 0.95 concordance with microarray data. The ancestries estimated with the panel of AIMs had relative high correlations (0.88 for European, 0.91 for Amerindian, 0.70 for Aymara, and 0.68 for Mapuche components) with those obtained with AXIOM LAT1 array. The country's average ancestry was 0.53 ± 0.14 European, 0.04 ± 0.04 African, and 0.42 ± 0.14 Amerindian, disaggregated into 0.18 ± 0.15 Aymara and 0.25 ± 0.13 Mapuche. However, Mapuche ancestry was highest in the south (40.03%) and Aymara in the north (35.61%) as expected from the historical location of these ethnic groups. We make our results available through an online app and demonstrate how it can be used to adjust for ancestry when testing association between incidence of a disease and nongenetic risk factors. CONCLUSIONS: We have conducted the most extensive sampling, across many different cities, of current Chilean population. Ancestry varied significantly by latitude and human development. The panel of AIMs is available to the community for estimating ancestry at low cost in Chileans and other populations with similar ancestry.

Humans , Male , Female , Ethnic Groups/genetics , Indians, South American/genetics , Polymorphism, Single Nucleotide/genetics , Population Groups/genetics , Genetics, Population/organization & administration , Saliva , Genetic Markers/genetics , Chile , Phylogeography , Genotyping Techniques , Gene Frequency/genetics , Genotype