RESUMEN
Tumor necrosis factor-α (TNF-α) is a proinflammatory cytokine associated with autoimmune and infectious diseases. Importance of TNF-α in P. falciparum malaria and systemic lupus erythematosus (SLE) have been demonstrated. However, association of functional promoter variants with SLE and malaria is lacking in malaria endemic population. A total of 204 female SLE patients and 224 age and sex matched healthy controls were enrolled in the study. Three hundred fourteen P. falciparum infected patients with different clinical phenotypes were included. TNF-α polymorphisms (G-238A & G-308A) were genotyped by PCR-RFLP. Plasma levels of TNF-α was quantified by ELISA. Heterozygous mutants and minor alleles of TNF-α (G-238A and G-308A) polymorphisms were significantly higher in SLE patients compared to healthy controls and associated with development of lupus nephritis. In addition, both promoter variants were associated with severe P. falciparum malaria. SLE patients demonstrated higher levels of plasma TNF-α compared to healthy controls. TNF-α (G-238A and G-308A) variants were associated with higher plasma TNF-α. In conclusion, TNF-α (G-238A & G-308A) variants are associated with higher plasma TNF-α levels in SLE patients residing in malaria endemic areas and could be a contributing factor in the development of SLE and susceptibility to severe P. falciparum malaria.
Asunto(s)
Predisposición Genética a la Enfermedad , Lupus Eritematoso Sistémico/genética , Malaria Falciparum/genética , Polimorfismo Genético , Regiones Promotoras Genéticas , Factor de Necrosis Tumoral alfa/genética , Adulto , Enfermedades Endémicas , Femenino , Humanos , Malaria Falciparum/epidemiología , Masculino , Persona de Mediana EdadRESUMEN
The DNA mismatch repair (MMR) pathway plays a prominent role in the correction of errors made during DNA replication and genetic recombination and in the repair of small deletions and loops in DNA. Mismatched nucleotides can occur by replication error, damage to nucleotide precursors, damage to DNA, or during heteroduplex formation between two homologous DNA molecules in the process of genetic recombination. Defects in MMR can precipitate instability in simple sequence repeats (SSRs), also referred to as microsatellite instability (MSI), which appears to be important in certain types of cancers, both spontaneous and hereditary. Variation in the highly polymorphic alleles of specific microsatellite repeats can be identified using PCR with primers derived from the unique flanking sequences. These PCR products are analyzed on denaturing polyacrylamide gels to resolve differences in allele sizes of more than 2 bp. Although (CA)n repeats are the most abundant class among dinucleotide SSRs, trinucleotide and tetranucleotide repeats are also frequent. These polymorphic repeats have the advantage of producing band patterns that are easy to analyze and can be used as an indication of a possible MMR defect in a cell. The presumed association between such allelic variation and an MMR defect should be confirmed by molecular analysis of the structure and/or expression of MMR genes.
Asunto(s)
Reparación del ADN , Repeticiones de Microsatélite/genética , Análisis de Secuencia de ADN/métodos , Animales , Disparidad de Par Base , Transformación Celular Neoplásica/genética , Daño del ADN , Electroforesis en Gel de Poliacrilamida , Humanos , Pérdida de Heterocigocidad/genética , Reacción en Cadena de la PolimerasaRESUMEN
Single-strand conformation polymorphism (SSCP) for screening mutations/single-nucleotide polymorphisms (SNPs) is a simple, cost-effective technique, saving an expensive exercise of sequencing each and every PCR reaction product and assisting in choosing only the amplicons of interest with expected mutation. The principle of detection of small changes in DNA sequences is based on the changes in single-strand DNA conformations. The changes in electrophoretic mobility that SSCP detects are sequence-dependent. The limitations faced in SSCP range from the routine polyacrylamide gel electrophoresis (PAGE) problems to the problems of resolving mutant DNA bands. Both these problems could be solved by controlling PAGE conditions and by varying physical and environmental conditions such as pH, temperature, voltage, gel type and percentage, addition of additives or denaturants, and others. Despite much upgrading of the technology for mutation detection, SSCP continues to remain the method of choice to analyze mutations and SNPs in order to understand genomic variations, spontaneous and induced, and the genetic basis of diseases.
Asunto(s)
Análisis Mutacional de ADN/métodos , Electroforesis en Gel de Poliacrilamida/métodos , Polimorfismo Conformacional Retorcido-Simple , Análisis de Secuencia de ADN/métodos , Animales , Humanos , Mutación/genética , Conformación de Ácido Nucleico , Desnaturalización de Ácido Nucleico/genética , Reacción en Cadena de la PolimerasaRESUMEN
A study of three different Y-specific microsatellites (Y-STRs) in the populations from Uttar Pradesh (UP), Bihar (BI), Punjab (PUNJ), and Bengal (WB), speaking modern indic dialects with its roots in Indo-Aryan language, and from South of India (SI), speaking the South Indian languages with their root in Dravidian language, has shown that the predominant alleles observed represent the whole range of allelic variation reported in different population groups globally. These results indicate that the Indian population is most diverse. The similarity between the allelic variants between the populations studied by others in Africa and Asia and in this study between WB, PUNJ, UP, BI, and SI are of interest. It demonstrates that these population groups, housed in eight states of the country in different geographic locations, broadly correspond with Indo-Aryan and Dravidian language families. Further, our analyses based on haplotype frequency of different marker loci and gene diversity reveals that none of the population groups have remained isolated from others. High levels of haplotype diversity exist in all the clusters of population. Nonsignificant results based on Markov chain steps and Slatkin's linearized genetic distances indicate that there has been migration to and from in these population groups. However, some of the marginally significant interpopulation differences could be attributed to one or more of the castes with high diversity embedded within the population groups studied. Haplotype sharing between populations, F(ST) statistics, and phylogenetic analysis identifies genetic relatedness to be more between individuals belonging to two different states of India, WB and PUNJ, followed by UP and BI, whereas SI branched out separately.
Asunto(s)
Cromosomas Humanos Y/genética , Etnicidad/genética , Lenguaje , Repeticiones de Microsatélite , Alelos , Análisis de Varianza , Secuencia de Bases , ADN/genética , Frecuencia de los Genes , Genética de Población , Haplotipos , Humanos , India , Masculino , FilogeniaRESUMEN
The DNA mismatch repair (MMR) pathway plays a prominent role in the correction of errors made during DNA replication and genetic recombination and in the repair of small deletions and loops in DNA. Mismatched nucleotides can occur by replication errors, damage to nucleotide precursors, damage to DNA, or during heteroduplex formation between two homologous DNA molecules in the process of genetic recombination. Defects in MMR can precipitate instability in simple sequence repeats (SSRs), also referred to as microsatellite instability (MSI), which appears to be important in certain types of cancers, both spontaneous and hereditary. Variations in the highly polymorphic alleles of specific microsatellite repeats can be identified using PCR with primers derived from the unique flanking sequences. These PCR products are analyzed on denaturing polyacrylamide gels to resolve differences in allele sizes of >2 bp. Although (CA)n repeats are the most abundant class among dinucleotide SSRs, trinucleotide and tetranucleotide repeats are also frequent. These polymorphic repeats have the advantage of producing band patterns that are easy to analyze and can be used as an indication of a possible MMR defect in a cell. The presumed association between such allelic variation and an MMR defect should be confirmed by molecular analysis of the structure and/or expression of MMR genes.
Asunto(s)
Reparación de la Incompatibilidad de ADN , Inestabilidad de Microsatélites , Neoplasias de la Mama/sangre , Neoplasias de la Mama/genética , ADN/genética , ADN/aislamiento & purificación , Análisis Mutacional de ADN , Electroforesis en Gel de Poliacrilamida , Escherichia coli , Femenino , Humanos , Reacción en Cadena de la PolimerasaRESUMEN
Interferon (IFN)-gamma is an important Th1 cytokine, which plays a role in immune surveillance and anti-tumor activity. A case-control study involving 54 sporadic breast cancer patients and 144 healthy controls was carried out to explore if the genotype variation of a proposed non-specific enhancer element with a dinucleotide (CA)n repeat in intron 1 has a role in the susceptibility to promote sporadic breast cancer. Genotype analysis carried out by single-strand length polymorphism and confirmed by sequencing showed an increased frequency of (CA)12 allele (P<0.001) and decreased frequencies of (CA)15 (P<0.01) and (CA)>15 (p<0.001) alleles in sporadic breast cancer patients as compared to controls. Further, in vitro reporter assays for (CA)12 and (CA)15 alleles suggested these to be associated with decreased and increased expressions, respectively, suggesting the (CA)12/(CA)12 background to act as one of the factors that could lead to low production of IFN-gamma. The study concludes that such genetic background for a proposed non-specific enhancer element with (CA)n repeat within intron 1 of the IFNG gene might put the individuals with this genotype at higher risk to promote the development of sporadic breast cancer due to a resultant compromised immune surveillance.
Asunto(s)
Neoplasias de la Mama/genética , Neoplasias de la Mama/inmunología , Interferón gamma/genética , Polimorfismo Genético , Alelos , Secuencia de Bases , Estudios de Casos y Controles , Línea Celular , ADN de Neoplasias/genética , Repeticiones de Dinucleótido , Elementos de Facilitación Genéticos , Femenino , Genes Reporteros , Variación Genética , Humanos , Interferón gamma/biosíntesis , Intrones , Células Jurkat , Polimorfismo Conformacional Retorcido-SimpleRESUMEN
Four binary polymorphisms and four multiallelic short tandem repeat (STR) loci from the nonrecombining region of the human Y-chromosome were typed in different Indian population groups from Uttar Pradeh (UP), Bihar (BI), Punjab (PUNJ), and Bengal (WB) speaking the Indo-Aryan dialects and from South India (SI) with the root in the Dravidian language. We identified four major haplogroups [(P) 1+, (C and F) 2+, (R1a) 3, (K) 26+] and 114 combinations of Y-STR haplotypes. Analyses of the haplogroups indicated no single origin from any lineage but a result of a conglomeration of different lineages from time to time. The phylogenetic analyses indicate a high degree of population admixture and a greater genetic proximity for the studied population groups when compared with other world populations.
Asunto(s)
Cromosomas Humanos Y/genética , Alelos , Etnicidad/genética , Evolución Molecular , Frecuencia de los Genes , Variación Genética , Humanos , India , Masculino , Polimorfismo Genético , Secuencias Repetidas en Tándem , Población Blanca/genéticaRESUMEN
We have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.
Asunto(s)
ADN Mitocondrial/genética , Efecto Fundador , Etnicidad , Femenino , Genética de Población , Humanos , India , Lenguaje , MasculinoRESUMEN
We have screened the basal promoter region, of KRTHB6 gene involving CAAT and TATA boxes in randomly selected 125 individuals of Indian origin by PCR-SSCP and DNA sequencing. We observed a novel promoter polymorphism (-71C>T) which could be differentiated by using LweI restriction enzyme. The frequency of -71 C allele, allele A (Accession no AY203963), was observed to be higher ( 0.712) in comparison to -71 T allele, allele B (0.288) (Accession no. AY037552).