Association of Klotho Gene Polymorphism with Cerebral Infarction

Background: We aimed to investigate the expression of Klotho gene in peripheral blood of patients with cerebral infarction (CI) and the association of its polymorphisms with the occurrence of CI. Methods: A total of 60 CI patients (CI group) and 20 healthy people receiving physical examination (control group) were enrolled as the research subjects. The expression of Klotho gene in CI group and control group was determined using enzyme-linked immunosorbent assay kit. Single nucleotide polymorphisms (rs192031, rs200131 and rs102312) in the promoter region of the Klotho gene were typed via conformational difference gel electrophoresis. Besides, whether the distribution frequencies of Klotho genotypes conformed to Hardy-Weinberg equilibrium was evaluated by chi-square test. Meanwhile, the associations of Klotho alleles and gene polymorphisms with CI occurrence were analyzed. Results: The protein expression level of Klotho in the peripheral blood was remarkably lower in patients in CI group than that in control group (P<0.05). Hardy-Weinberg equilibrium analysis revealed that Klotho gene polymorphisms (rs192031, rs200131 and rs102312) conformed to the genetic equilibrium distribution (P>0.05). Gene-based association analysis manifested that only rs192031 polymorphism and alleles were correlated with CI occurrence (P<0.05). Systolic blood pressure and high-density lipoprotein cholesterol were notably higher in CI patients with TT genotype of Klotho gene polymorphism rs192031 than those in control group (P<0.05). Furthermore, there were no associations of rs200131 and rs102312 polymorphisms and alleles with the occurrence of CI (P>0.05). Conclusions: The expression level of Klotho is evidently reduced in the peripheral blood of CI patients. Rs192031 in the promoter region of the Klotho gene is associated with the occurrence of CI, while rs200131 and rs102312 have no relations with CI.

Polymorphism of Insulin-induced gene 1 (INSIG1) of three local beef cattle in Indonesia

Insulin-induced gene 1 (INSIG1) encoded protein that blocked of proteolysis activity from protein sterol regulatory element binding proteins (SREBP). The role gene plays of cholesterol, fatty acid, and glucose metabolism. Indonesia has many several beef cattle which has good quality of growth trait. The aim of this study was to identify polymorphism of INSIG1 gene (SNP 4366 (A>G) and 4534 (T>C)) of three local beef cattle in Indonesia (Bali, Pasundan and Ongole Decendent). One hundred and twenty seven samples were used in this study consisting of Bali cattle (46) from Pulukan Bali Island, Pasundan (36) from UPTD BPPT Beef cattle Ciamis West Java and Ongole Grade (OD) (45). DNA was extracted from whole blood using High Salt method then genotyping used PCR-RFLP method with RsaI and TaqI enzymes. Parameters in this study were genotype and allele frequencies, heterozigosity observed (Ho), expected (He), Hardy-Weinberg Equilibrium (HWE) and Polymorphism Information Content (PIC). Result showed that a 428 bp of DNA fragment was successfully amplified and digested. Three variant of genotypes with two alleles were identified. For SNP 4366 (A>G) were AA, AG and GG with dominant of G allele while SNP 4534 (T>C) were CC, CT and TT with dominant C allele. Both of SNPs in each of breed populations was in Hardy-Weinberg Equilibrium and polymorphic. Additionally, PIC value reached moderate. In conclusion, polymorphism was found in beef cattle and it could be early study for genetic diversity

LRFN5 locus structure is influenced by the individual’s sex and associated with autism

BackgroundLRFN5 is a brain-specific gene needed for synaptic development and plasticity. It is the only gene in a large 5.4 Mb topologically associating domain (TAD) on chromosome 14, which we term the LRFN5 locus. This locus is highly conserved, but has extensive copy number variation. MethodsLocus structure was studied by chromatin immunoprecipitation (chIP-onchip) in fibroblasts from individuals with autism and controls, supplemented with a capture-HiC determination of TAD structures in a family trio. LRFN5 expression was studied in foetal brain cell cultures. In addition, locus interaction was studied in four large and independent cohorts by measuring deviations from Hardy-Weinberg equilibrium of a common deletion polymorphism. ResultsWe found that locus structural changes are associated with developmental delay (DD) and autism spectrum disorders (ASD). In a large family, ASD in males segregated with a chromosome 14 haplotype carrying a 172 kb deletion upstream of LRFN5 . In a fibroblast capture-HiC study on an ASD-patient-parent trio, the ASDsusceptible haplotype (in the mother and her autistic son) had a TAD pattern different from both the father and a female control. When the trimethylated histone-3-lysine-9 chromatin (H3K9me3) profiles in fibroblasts from control males (n=6) and females (n=7) were compared, a male-female difference was observed around the LRFN5 gene itself (p<0.01). Intriguingly, in three cohorts of individuals with DD (n=8757), the number of heterozygotes of a common deletion polymorphism upstream of LRFN5 was 20-26% lower than expected from Hardy-Weinberg equilibrium. This indicates early allelic interaction, and the genomic conversions from heterozygosity to wildtype or deletion homozygosity were of equal magnitudes. In a control group of medical students (n=1416), such conversions were three times more common than in the DD-patient cohorts (p=0.00001). Hypothetically, such allelic interaction is needed to establish monoallelic expression, which we found in foetal brain cell cultures. LimitationsThe male-female difference in H3K9me3 profiles was based on fibroblast data from a small number of individuals, and the monoallelic expression data on a single experiment. ConclusionsTaken together, allelic interaction, monoallelic expression and sexdependent differences make the LRFN5 locus attractive for exploring the genetic basis of synaptic memory and high-functioning male autism.

A Significant Genetic Admixture in Farmed Populations of the Noble Scallop Chlamys nobilis Revealed by Microsatellite DNA Analysis in Southern China

The noble scallop, Chlamys nobilis, is an important bivalve mollusk with high commercial value and is usually farmed in the waters of southern China. To date, very little is known about the genetic diversity and population structure of C. nobilis. In this study, 10 microsatellite loci of four farmed C. nobilis populations were compared with one another and compared wild population in southern China. A total of 83 alleles were found. Surprisingly, the level of genetic diversity of the farmed C. nobilis populations was higher than that of the wild population. Although the population genetic of wild population was completely in the Hardy–Weinberg equilibrium, due to heterozygote deficiency, significant deviations from the Hardy–Weinberg equilibrium were found in all farmed populations, suggesting a genetic admixture caused by the mixing of seeds from various hatcheries. The Fst and AMOVA values showed significant genetic differences between wild and farmed populations. The Bayesian assignment also confirmed that genetic admixture was significant and widespread in artificial breeding of C. nobilis. Furthermore, the UPGMA tree topology and PCA demonstrated that the genetic diversity of wild population can be clearly distinguished from farmed populations. In a nutshell, the findings of this study not only fill the knowledge gaps in genetic diversity of wild and farmed C. nobilis populations, but also serve as a guide for maintaining the genetic diversity of C. nobilis in both farmed and wild populations.

A Misconception About the Hardy–Weinberg Law

The Hardy–Weinberg law of population genetics is usually associated with the notion of random mating of parents. A numerical example for a triallelic autosomal locus shows that an uncountable set of mating combinations can maintain Hardy–Weinberg proportions. Therefore, one cannot infer random mating in a population from the observation of Hardy–Weinberg equilibrium. The mating system which ensures that the genotypic distribution of offspring is the same as that of the parents is specified.

Commonly used Hardy-Weinberg equilibrium filtering schemes impact population structure inferences using RADseq data

Reduced representation sequencing (RRS) is a widely used method to assay the diversity of genetic loci across the genome of an organism. The dominant class of RRS approaches assay loci associated with restriction sites within the genome (restriction site associated DNA sequencing, or RADseq). RADseq is frequently applied to non-model organisms since it enables population genetic studies without relying on well-characterized reference genomes. However, RADseq requires the use of many bioinformatic filters to ensure the quality of genotyping calls. These filters can have direct impacts on population genetic inference, and therefore require careful consideration. One widely used filtering approach is the removal of loci which do not conform to expectations of Hardy-Weinberg equilibrium (HWE). Despite being widely used, we show that this filtering approach is rarely described in sufficient detail to enable replication. Furthermore, through analyses of in silico and empirical datasets we show that some of the most widely used HWE filtering approaches dramatically impact inference of population structure. In particular, the removal of loci exhibiting departures from HWE after pooling across samples significantly reduces the degree of inferred population structure within a dataset (despite this approach being widely used). Based on these results, we provide recommendations for best practice regarding the implementation of HWE filtering for RADseq datasets.

Teaching Hardy-Weinberg Equilibrium using Population-Level Punnett Squares: Facilitating Calculation for Students with Math Anxiety

The effectiveness of teaching Punnett squares as a calculation aid for Hardy-Weinberg equilibrium with a quasi-experimental design was tested. On its own, this aid may allow for increased calculation success, and it may increase mastery of equation derivation when taught before the equations. Benefits for students with math anxiety are discussed.

Effects of genetic variation in the 20th intron of Sansui duck ATP2A2 gene on eggshell quality

In order to explore the influence of the polymorphism in the 20 intron region of the Sansui duck ATP2A2 gene on the eggshell quality, this study used Primer Premier 5 software to design and synthesize a pair of primers in the 20 intron region, two-way direct sequencing and sequence alignment to mine SNPs Sites, SPSS 18.0 software was used to analyze the relationship between SNP sites and eggshell quality of Sansui duck. Results Three SNP sites were found in the 20 intron region of the ATP2A2 gene: g.40874 T>C, g.40920 G>A and g.40990 T=C, all of which were moderately polymorphic, at the site g.40874 T ＞C and g.40920 G＞A both deviated significantly from Hardy-Weinberg equilibrium (P>0.05), position g.40990 T=C accords with Hardy-Weinberg equilibrium (P<0.05), and position g.40874 T＞C There is a strong linkage disequilibrium between g.40990 T=C; a total of 4 haplotypes and 9 double types were detected at 3 SNP loci; the results of association analysis show that g.40874 T＞C mutation has an effect on eggshell strength The eggshell strength of CC genotype was significantly higher than that of TC and TT genotypes (P<0.05), and the eggshell weight of CC genotype was significantly higher than that of TC genotype (P<0.05), g. The 40990 T=C mutation has a significant effect on the eggshell strength, and the eggshell strength of the TC genotype is significantly higher than that of the TT genotype (P<0.05). In summary, the g.40874 T>C and g.40990 T=C found in the 20th intron region of the Sansui duck ATP2A2 gene may be the marker sites that affect the quality of the eggshell.

Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy–Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy–Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.