Webmedcentral - Genetics ArticlesThe Genetics articles published by Webmedcentral
http://www.webmedcentral.com
2024-03-29T15:09:08+01:00webmedcentral logo
http://www.webmedcentral.com/
http://www.webmedcentral.com/images/Header_Logo.giftext/html2015-03-20T07:27:50+01:00http://www.webmedcentral.com/Dr. Clyde WintersInference of Ancient Black Mexican Tribes and DNA
http://www.webmedcentral.com/article_view/4856
Background: Controversy surrounds the time period when Indigenous Mexican-African admixture occurred. Most researchers assume this admixture took place after the Atlantic Slave Trade. But, Spanish eyewitness accounts, Mayan skeletons with sickle cell anemia, and West African skeletal remains generally,indicate that there were Black Native Mexican and Meso-American communities in Meso-America before 1492. Using genetic association studies of available Indigenous Mexican and African genome-wide SNP genotypes and HLA we infer the probable pre-or post Columbian date for the admixture. Here we analyze the historical and archaeogentic literature relating to the American foundational haplogroups and HLA to extract ancestry information detailing when Indigenous Mexican-African admixture took place.
Results: Indigenous Mexican and African archaeogenetic, DNA and HLA resources were analyzed to determine to what extent admixture had occurred between these populations. The sample indicated that Indigenous Mexican-African admixture has taken place across Mexican fundamental male and female lineages; and that Africans and Indigenous Mexicans share HLA alleles. In addition, archaeogenetic evidence including, African [Mande] inscriptions, Mande substratum in Mayan languages, Africans depicted in Mayan murals at San Bartolo and Xultun, African skeletons generally, and ancient Mayan skeletons with sickle cell anemia support Spanish eyewitness accounts of Black Native American tribes [Otomi, Chontal (Mayan speaking group) ,Yarura and etc.] in Meso-America when they arrived on the scene.
Conclusion: We demonstrate that given the age of the African skeletons, excavated at Meso-American archaeological sites and Spanish eyewitness accounts of Black Mexicans, Indigenous Mexican- African admixture occurred prior to the European discovery of America. The date for the African skeletons indicate that there were several waves of West Africans who probably introduced African haplotypes into the Americas. The 25,000 Malians who sailed to America in 1310 probably had a major influence on the exchange of African genes in the Americas.text/html2010-09-08T19:13:05+01:00http://www.webmedcentral.com/Prof. Guenter Albrecht-BuehlerThe Evolution Of Alu Mutations In The Human Genome
http://www.webmedcentral.com/article_view/565
The article reports the frequency distributions of the mutants of Alu elements in the human genome. They are remarkably complex and, yet, almost identical for each chromosome, suggesting a universal mechanism for base substitutions in Alu-elements and, possibly, other retro-transposons as well. Conceivably, these mutations of the Alu-elements effectively reduced or even crippled their proliferation which, otherwise, might have fragmented and destroyed the host genome. The article proposes a simple mathematical model that simulates the observed distributions and offers(a) a quantitative reconstruction of the evolutionary past of the number of Alu-mutants,(b) a determination of the times in their past when new copies of the Alu-elements inserted with full capacity to proliferate (‘seedings’), arguably giving rise to new sub-families,(c) a new and simple determination of the evolutionary age of Alu-mutants and, thus, of a minimal age of the domains of the host chromosome in which they were found.text/html2011-07-29T18:28:52+01:00http://www.webmedcentral.com/Dr. James C FoglemanFine Mapping of an Amyotrophic Lateral Sclerosis Modifier Locus to a Single BAC
http://www.webmedcentral.com/article_view/2044
Mutations in the Cu/Zn superoxide dismutase (SOD1) gene are responsible for 15-20% of familial amyotrophic lateral sclerosis (FALS) cases. Severity of the ALS phenotype is dependent on genetic background for mice carrying the mG86R SOD1 transgene. A BAC (149m19) containing several candidate genes (Serf, Smn, Naip2 and Naip5) and derived from 129Sv genomic DNA was used to investigate whether these genes partially rescue the mG86R SOD1 (FVB/NJ) ALS phenotype by delaying ALS onset. Two single-insertion BAC lines were produced and both mRNA and protein for BAC genes were shown to be elevated. Mice heterozygous for mG86R SOD1 and BAC149m19 in the FVB/NJ background were shown to have significantly delayed ALS onset compared to mG86R SOD1 controls. BAC 149m19 did not significantly delay ALS onset for mice carrying the human G93A SOD1 mutation in the FVB/NJ background. Delayed ALS onset for BAC/mG86R mice was not due to reduced SOD1 expression. Overexpression of one or more of the BAC genes appears to be linked to the severity of ALS phenotype in mice, but in a mutation specific manner.text/html2012-07-31T18:28:17+01:00http://www.webmedcentral.com/Dr. Atanu K DuttaA New PCR-RFLP Method for Diagnosing PNPLA3 rs738409 Polymorphism
http://www.webmedcentral.com/article_view/2928
Background:PNPLA3 rs738409 (C10109G) polymorphism has been identified as a predisposingfactor for nonalcoholic fatty liver disease, fibrosis, alcoholic cirrhosis and elevation of serumalanine transaminase in the human. However, no simple method for its assay is available. Hence, this research work was undertaken to develop PCR-RFLP method for the assay of PNPLA3 rs738409.Methods:PCR primers were designed using NCBI primer Blast and restriction endonuclease was identified using NEB Cutter 2 software. PCR-RFLP based genotyping was confirmed by sequencing both strands of PCR amplicons of a normal homozygote, a heterozygote and a mutant homozygote.Results:Amplification of genomic DNA with specific primers demonstrated 333 bp fragment. PCR-RFLP of DNA from a normal homozygote demonstrated 200 and 133 bp fragments, of a heterozygote 333, 200 and 133 bp fragments and of a mutant homozygote 333 bp fragment. Sequencing of DNA from a normal homozygote, a heterozygote and a mutant homozygote demonstrated C, C/G and G with sense primer and G, C/G and C with anti sense primer, respectively.Conclusion:A simple PCR-RFLP method for the assay of PNPLA3 rs738409 has been developed and its validity confirmed by DNA sequencing. This shall facilitate genotyping of PNPLA3 rs738409.text/html2012-02-25T08:47:42+01:00http://www.webmedcentral.com/Dr. Jian-min ChenIs the SPINK1 p.Asn34Ser Missense Mutation Per se the True Culprit within its Associated Haplotype?
http://www.webmedcentral.com/article_view/3084
Although SPINK1, which encodes the pancreatic secretory trypsin inhibitor (PSTI), has been firmly established as a chronic pancreatitis-predisposing gene, the causal variant within the most common c.101A>G (p.Asn34Ser)-containing haplotype remains to be identified. The low penetrance of this haplotype implies a minor effect on gene expression and/or protein function; such a minor effect may not have been readily detectable in the previous studies. Here, we focused on the putative functional effect of the p.Asn34Ser haplotype on pre-mRNA splicing and mRNA stability. Two measures were taken to maximize the relevance and accuracy of our in vitro analysis. First, all five cis-linked variants were analyzed together within a single expression plasmid. Second, a real-time quantitative Reverse Transcription Polymerase Chain Reaction (RT-PCR) assay with high accuracy and reproducibility was developed. The exclusion of a minor effect of the p.AsnN34Ser haplotype on gene expression prompted us to reconsider the possible role of the p.Asn34Ser missense mutation in trypsin inhibition. A survey of previous studies that analyzed the inhibitory activity of purified recombinant wild-type and p.Asn34Ser mutant PSTI peptides revealed that a minor effect of the p.Asn34Ser missense mutation on trypsin inhibition appeared to be overlooked. Moreover, the reduced inhibition of trypsin by the p.Asn34Ser mutant peptide is consistent with findings from analyses of PSTI’s 3D structures and with the presence of an increase in p.Asn34Ser mutants in the urine of p.Asn34Ser heterozygotes. A combination of these diverse lines of evidence strongly suggests that the p.Asn34Ser missense mutation is the true culprit within its associated haplotype. The clarification of this issue is pivotal for developing targeted therapies for pancreatitis.text/html2012-03-08T21:36:03+01:00http://www.webmedcentral.com/Dr. Clyde WintersOrigin of the Niger-Congo Speakers
http://www.webmedcentral.com/article_view/3149
The Niger-Congo (NC) Superfamily of languages is the largest family of languages spoken in Africa. Researchers have assumed that the NC speakers originated in West Africa in the Inland Niger Delta. The research indicates that the NC speakers originated in the Saharan Highlands 12kya and belonged to the Ounanian culture. The NC population cultivated millet from Saharan Africa to South India. Phylogenetically the NC mtDNA haplogroups include L1,L2,L3, U5, L3(M,N). The y-Chromosome haplotypes associated with the NC population were A,B, E1b1a, E1b1b, E2, E3a and R1. A major finding was that the Atlantic, Mande and Dravidian languages of India, form a new NC Subfamily we can designate Indo-African.text/html2014-06-26T07:09:19+01:00http://www.webmedcentral.com/Dr. Matthew D GarciaEvaluation of Candidate Genes and Subsequent Effects Growth and Carcass Traits in Multi-Generational Sired and Modern Sired Angus Females
http://www.webmedcentral.com/article_view/4655
The objective of the current study was to evaluate phenotypic differences and SNP located on three candidate genes for possible associations with growth and carcass traits in a population of Angus cows sired by modern phenotype Angus bulls and multi-generational Angus bulls born from 1960-2006. Quantitative analyses revealed that modern sired Angus cows had significantly larger (P< 0.05) weaning weights, levels of intramuscular fat, levels of back fat, but were not significantly different when comparing rib eye area. The only trait that the multi-generational Angus sired cows were significantly larger (P < 0.05) than the modern sired Angus was in birth weight, which is not optimal due to its strong correlation with dystocia during the parturition process. When evaluating SNP located on the DGAT1, LEPR and CAST gene were also evaluated in the same population for possible SNP associations with growth and carcass traits. While significant SNP were identified on both the DGAT1 and LEPR genes no SNP located on the CAST gene were significantly associated with any traits in the current study. Specifically, when evaluating growth traits three SNP (rs134375381, rs135263435, rs43348659) located on the LEPR and three SNP (rs136875432, rs132699547, rs135423283) located on the DGAT1 gene were significantly associated ( P < 0.05) or exhibited a statistical trend ( P < 0.1) with birth weight and weaning weight respectively. When evaluating carcass traits, a statistical trend( P < 0.1) was observed for the trait of back fat thickness for two SNP (rs134375381,rs135263435) located on the LEPR gene. Furthermore, the two SNP associated with back fat thickness were also associated with birth weight, thus revealing that SNP have the potential to be associated with multiple traits. Results of the current study revealed that modern germplasm is more beneficial to be utilized in current production schemes and that multiple SNP from multiple candidate genes can be associated with both growth and carcass traits. However, prior to utilizing the identified SNP in the current study in selection strategies, the effect of SNP must be verified in other populations, other environments and subsequently many more SNP on numerous candidate genes identified prior to implementation into marker assisted selection strategies.text/html2014-07-18T04:05:56+01:00http://www.webmedcentral.com/Dr. Matthew D GarciaA Quantitative Comparison of Growth and Carcass Traits from Crossbred Calves Sired by a Modern Phenotype Paternal Breed Versus Calves Sired by a Multi-Generational Maternal Breed
http://www.webmedcentral.com/article_view/4664
Dramatic improvements in the beef cattle industry have been made over the last five decades. Specifically, the Angus breed has evolved from a small framed maternal breed to a breed with greater muscling and growth characteristics. Major increases have been observed in traits such as birth weight, weaning weight, yearling weight, and average daily gain. Genetic trends show a 3.8 pound increase in birth weight and a 54 pound increase in weaning weight (http://www.angus.org/Nce/GeneticTrends.aspx). Likewise, the Charolais breed, classified as a paternal breed, has also seen dramatic improvements in production traits. The Charolais breed has reported a five pound decrease in birth weight over the last 21 years and a 32 pound increase in weaning weight (http://www.charolaisusa.com/pdf/2012/09.07/PhenotypicTrendTables.pdf).A study conducted by Williams et al. (2010) utilized production and carcass trait data reported in studies from 1976 to 1996. It was observed that the Charolais breed consistently had higher birth weights, weaning weights and post-weaning gains when compared to maternal breeds of cattle (Williams et al, 2010). Specifically, studies evaluating economically important production traits have reported that the Charolais sired calves had heavier birth weights (Cundiff et al., 1998), weaning weights (Cundiff et al., 1998; Thallman et al., 1999), hip heights (Arango et al., 2002; Thallman et al., 1999), and average daily gains (Gregory et al., 1994) than Angus sired animals. Previous studies evaluating carcass traits have reported that Charolais animals have higher average daily gain (Gregory et al., 1994), heavier hot carcass weights (Gregory et al., 1994; DeRouen et al., 1992), larger rib eye areas, lower back fat thickness (DeRouen et al., 1992), and lower marbling scores (Gregory et al., 1994; DeRouen et al., 1992) when compared to other Bos Taurus breeds of cattle.The objective of this study was to test the effect of sire breed type on growth, performance, and carcass characteristics on a population consisting of Charolais sired calves and multigenerational Angus sired calves.