Allele frequencies for candidate genes in atherosclerosis and diabetes among Trinidadian neonates

Trinidadians of South Asian origin have a high prevalence of cardiovascular disease and diabetes compared to Trinidadians of African origin. The degree to which these differences are related to genetic and/or environmental factors is unclear. To determine whether there might be a genetic basis for this difference in prevalence of deleterious phenotypes we examined allele frequencies for candidate genes in atherosclerosis and diabetes. We genotyped 81 consecutive neonates of African origin and 103 consecutive neonates of South Asian origin. We evaluated common polymorphisms in 11 candidate genes for atherosclerosis and diabetes. We found differences between the two subpopulations in the allele frequencies of several candidate genes, including APOE, LIPC, APOC3, PON1, PON2, and PPP1R3. However, the differences in the allele frequencies were not all consistent with the pattern of CHD expression between these two ethnic groups in adulthood. Thus, differences in genetic architecture alone may not explain the wide disparities in disease prevalence between these two subpopulations. It is very likely that environmental factors, or unmeasured genetic factors, influence the genetic susceptibility to disease in these subpopulations.     

Contribution of TGFβ1 Codon 10 Polymorphism to High Myopia in an Ethnic Kashmiri Population from India

This study looks at novel variants of the TGFβ1 gene and their potential association with high myopia in an ethnic population from Kashmir, India. Allele frequencies of 247 Kashmiri subjects (from India) with high myopia and 176 ethnically matched healthy controls were tested for Hardy–Weinberg disequilibrium. The genotype and allele frequencies were evaluated using chi-square or Fisher’s exact tests. One of the three SNPs in codon 10 showed a significant difference between patients and control subjects (rs1982073: p genotype = 0.003, p allele = 0.001). There were no statistically significant differences between patients and control subjects for the other two SNPs, rs1800471 at codon 25 and a novel variant at codon 52. SNP rs1982073, substituting proline with leucine, appeared to be significantly associated with high myopia (p < 0.05). In silico predictions show that substitutions are likely to have an impact on the structure and functional properties of the protein, making it imperative to understand their functional consequences in relation to high myopia.     

Association of Central Obesity With the Severity and Audiometric Configurations of Age‐related Hearing Impairment

To investigate the effect of central obesity on the severity and characteristics of age‐related hearing impairment (ARHI), we recruited 690 adult subjects with normal or symmetrical sensorineural hearing loss (SNHL). The effects of age, gender, morphometry, habits, systemic diseases, and environmental noise exposure on average pure tone hearing level at low frequencies (pure tone audiometry (PTA)‐low) and high frequencies (PTA‐high) were analyzed. After adjusting for age, gender, systemic disease, and other variables, waist circumference (WC) showed a significant positive association with PTA‐low and PTA‐high. In females, PTA‐low and PTA‐high only showed significant positive association with age, but not with WC or other variables. However, PTA‐high showed a positive association with borderline significance with WC in female subjects older than 55. In males, WC as well as age and noise exposure showed significant positive associations with both PTA‐low and PTA‐high, primarily in subjects younger than 55. When both WC and BMI were taken into account in a backward stepwise multivariate linear regression analysis, WC, but not BMI, showed a significant positive association with PTA‐low and PTA‐high in males younger than 55, and with PTA‐high with borderline significance in females older than 55. However, the audiogram patterns were not significantly affected by central obesity in either age or gender. Our results suggest that WC was, even after adjustment for BMI, an independent risk factor of ARHI, particularly for low and high frequencies in males younger than 55 and for high frequencies in female subjects older than 55.     

Characterization of Fecal Microbiota across Seven Chinese Ethnic Groups by Quantitative Polymerase Chain Reaction

The human gut microbiota consists of complex microbial communities, which possibly play crucial roles in physiological functioning and health maintenance. China has evolved into a multicultural society consisting of the major ethnic group, Han, and 55 official ethnic minority groups. Nowadays, these minority groups inhabit in different Chinese provinces and some of them still keep their unique culture and lifestyle. Currently, only limited data are available on the gut microbiota of these Chinese ethnic groups. In this study, 10 major fecal bacterial groups of 314 healthy individuals from 7 Chinese ethnic origins were enumerated by quantitative polymerase chain reaction. Our data confirmed that the selected bacterial groups were common to all 7 surveyed ethnicities, but the amount of the individual bacterial groups varied to different degree. By principal component and canonical variate analyses of the 314 individuals or the 91 Han subjects, no distinct group clustering pattern was observed. Nevertheless, weak differences were noted between the Han and Zhuang from other ethnic minority groups, and between the Heilongjiang Hans from those of the other provinces. Thus, our results suggest that the ethnic origin may contribute to shaping the human gut microbiota.     

大苞鞘石斛原球茎玻璃化超低温保存技术的研究

本文研究建立了大苞鞘石斛(Dendrobium wardianum Warner)原球茎玻璃化法超低温保存的技术体系。结果发现,预处理和玻璃化溶液(plant vitrification solution 2,PVS2)装载脱水是影响大苞鞘石斛原球茎相对存活率的两个关键步骤,高渗与低温-高渗两种预处理方法测定的相对存活率具有显著性差异;玻璃化溶液的种类以及脱水时间对冻后存活率具有重要的影响。基于此,建立了大苞鞘石斛原球茎的超低温保存体系,即:以继代培养60 d的大苞鞘石斛原球茎为材料,1/2MS+0.8 mol/L蔗糖的培养基上4℃低温预处理6 d后,转至1/2 MS+2 mol/L甘油+0.4 mol/L蔗糖的装载液中室温下装载40 min,在0℃下装载PVS2脱水40 min,然后转入装有新鲜PVS2冷冻管中并迅速投入液氮。在液氮保存1 h后放在40℃水浴中快速解冻1 min,利用含1.2 mol/L蔗糖的1/2MS培养液洗涤3次,每次间隔10 min;待恢复培养30 d后统计存活率,可使大苞鞘石斛原球茎超低温保存后存活率达到20.0%。     

Investigations on the ethnic variability of the ABO blood group polymorphism in Iran

112 Iranian population samples with a total of 600954 individuals are analyzed concerning the ethnic variability of ABO allele frequencies. The genetic heterogeneity within and between these population samples is considerable. This heterogeneity is discussed with regard to the ethnohistory of Iran. The most striking ABO allele frequencies are observed in Assyrians, Armenians and Zoroastrians, which differ extremely from that of all the other hitherto studied ethnic groups of Iran. Obviously varying ABO allele frequencies are seen also in Yazdis as well as in Turkomans and Arabs living in Iran. And finally the Iranian Jews reveal clear frequency differences in comparison with all the other Iranian population groups. It can be assumed that the specific ABO allele frequencies found in the above mentioned ethnic groups are connected with their different geographical origin as well as with their marked endogamy.     

Diversity in palmar pattern ridge counts among 12 Iranian populations

Bilateral palmar prints of 604 male individuals from 12 Iranian groups, six Mongoloid and six Caucasoid, have been analyzed for palmar pattern ridge counts (PPRC). Highly significant variation has been observed in the size of the palmar patterns in all the configurational areas among the Iranian groups. The distance analysis based on PPRCs differentiated the Iranian Mongoloid from the Iranian Caucasoid groups into distinct clusters. The pattern of differentiation based on PPRCs explained the ethnohistoric relationships between the Iranian groups as well as between the Iranian and the 20 Caucasoid groups from India much better than the palmar pattern frequencies. The results of this study demonstrate the existence of variation in the size of the palmar patterns across different populations within an ethnic group, as well as that among different ethnic groups, and seems to be a better indicator of interpopulational diversity than the palmar pattern frequencies.     

中国人群5—羟色胺2A受体基因中T102C多态性与精神分裂症的联系

在研究５－羟色胺２Ａ受体基因多态性与精神分裂症的关联分析中,调查了２０２例精神分裂症患者及２０２例正常对照。各相匹配组间比较未发现基因型和等位基因频率的显著性差异。结果提示,在中国人群中５－羟色胺２Ａ受体的静态Ｔ１０２Ｃ突变与精神分裂症之间不存在关联。     

西藏藏族起源初探——来自掌指纹的线索

本文采用分层整群抽样的调查方法捺印1183名藏族青少年的掌指纹, 分析掌指纹参数,然后与其他56个群体的掌指纹参数进行聚类分析, 进而从肤纹学角度探讨藏族的起源。发现藏族指纹以斗型纹为主(52.89%), 其次为箕型纹(42.95%), 弓形纹出现频率最低(4.16%); 总指嵴线计数为139.01(其中男性为144.75, 女性为133.87); atd角在男性为42.95°, 女性为43.28°。掌指纹参数聚类分析显示: 藏族与汉族和氐羌氏族的后裔(门巴族、普米族、羌族等)等我国北方人群聚在一起。因而从肤纹学角度推断藏族与汉族和氐羌氏族的亲缘关系较近, 而与印度人和孟加拉人的亲缘关系较远。     

Life-History Characteristics and Fitness in Descendents of Parthenogenetic and Ex-Ephippio Females of Daphnia Magna

Daphnids of ex-ephippial and parthenogenetic origin differ substantially in life-history. Possible maternally transmitted ex-diapause effects of differing female origin on the fitness of their offspring were studied across multiple clones in Daphnia magna. Ex-ephippial daphnids responded in egg size to different constant food concentrations with the same pattern as parthenogenetic females. Significant differences in egg characteristics between females of different origin were only found for the first clutch produced under high food. The smaller size of eggs in ex-ephippial females, however, did not translate into size differences of first-clutch neonates. A trend for lower mass density per body volume was detected in offspring from ex-ephippial females in comparison with parthenogenetic daphnids. Hence, an ex-diapause effect transmitted by ex-ephippial mothers to their parthenogenetic offspring is likely. However, there was no difference in life-histories and fitness between offspring produced by females of ex-ephippial and parthenogenetic origin at both, high and low food concentrations across multiple clones. Thus, a significant ex-diapause effect on fitness in successive parthenogenetic generations may not be expected in D. magna at the population level.     

Cholesteryl ester transfer protein (CETP) ?629C/A polymorphism and it,s effects on the serum lipid levels in metabolic syndrome patients

Metabolic syndrome is a relatively common disorder with significant morbidity worldwide. Cholesteryl ester transfer protein (CETP) plays a central role in the metabolism of lipoproteins. In this study the effect of -629C/A polymorphism on the concentration of CETP and plasma lipids pattern was elicited in metabolic syndrome patients and control subjects. For this, a sample of 200 patients diagnosed with metabolic syndrome disorder was studied in comparison with 200 healthy controls. This study was performed by using polymerase chain reaction and restriction fragment length polymorphisms. Genotype distribution and allelic frequencies were determined and compared in metabolic syndrome and healthy controls. To determine the relationship between -629C/A polymorphism and lipid levels, lipids and CETP concentration were measured in metabolic syndrome and normal subjects. The results showed a significant difference between two groups in terms of FBS, cholesterol, TG, HDL-C, LDL-C levels as well as BMI, waist circumference, systolic and diastolic blood pressure. The genotype frequencies for this polymorphism differed significantly between metabolic syndrome patients and controls (in control group: CC%?20.5, CA%?76, AA%?3.5 and in patient group: CC%?28.5, CA%?53.5, AA%?18) (p?相似文献   

3H]muscimol binding sites increased in autopsied brains of chronic schizophrenics

[3H]muscimol binding and glutamic acid decarboxylase (GAD) activity in the prefrontal cortex and caudate nucleus of autopsied brains from 19 chronic schizophrenics and 17 control subjects were investigated. In the schizophrenics, saturation analysis with varying concentrations of [3H]muscimol revealed an increase in the number of GABAA receptors, but there was no significant difference in the affinity. In addition, the enhancement of [3H]muscimol binding by diazepam was significantly greater in schizophrenics than in controls. GAD activity did not differ between controls and schizophrenics. The possibility that GABAergic mechanisms might play a role in case of chronic schizophrenia should be given further attention.     

Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases

Many disease-susceptible SNPs exhibit significant disparity in ancestral and derived allele frequencies across worldwide populations. While previous studies have examined population differentiation of alleles at specific SNPs, global ethnic patterns of ensembles of disease risk alleles across human diseases are unexamined. To examine these patterns, we manually curated ethnic disease association data from 5,065 papers on human genetic studies representing 1,495 diseases, recording the precise risk alleles and their measured population frequencies and estimated effect sizes. We systematically compared the population frequencies of cross-ethnic risk alleles for each disease across 1,397 individuals from 11 HapMap populations, 1,064 individuals from 53 HGDP populations, and 49 individuals with whole-genome sequences from 10 populations. Type 2 diabetes (T2D) demonstrated extreme directional differentiation of risk allele frequencies across human populations, compared with null distributions of European-frequency matched control genomic alleles and risk alleles for other diseases. Most T2D risk alleles share a consistent pattern of decreasing frequencies along human migration into East Asia. Furthermore, we show that these patterns contribute to disparities in predicted genetic risk across 1,397 HapMap individuals, T2D genetic risk being consistently higher for individuals in the African populations and lower in the Asian populations, irrespective of the ethnicity considered in the initial discovery of risk alleles. We observed a similar pattern in the distribution of T2D Genetic Risk Scores, which are associated with an increased risk of developing diabetes in the Diabetes Prevention Program cohort, for the same individuals. This disparity may be attributable to the promotion of energy storage and usage appropriate to environments and inconsistent energy intake. Our results indicate that the differential frequencies of T2D risk alleles may contribute to the observed disparity in T2D incidence rates across ethnic populations.     

How does farmer connectivity influence livestock genetic structure? A case‐study in a Vietnamese goat population

Assessing how genes flow across populations is a key component of conservation genetics. Gene flow in a natural population depends on ecological traits and the local environment, whereas for a livestock population, gene flow is driven by human activities. Spatial organization, relationships between farmers and their husbandry practices will define the farmer's network and so determine farmer connectivity. It is thus assumed that farmer connectivity will affect the genetic structure of their livestock. To test this hypothesis, goats reared by four different ethnic groups in a Vietnamese province were genotyped using 16 microsatellites. A Bayesian approach and spatial multivariate analysis (spatial principal component analysis, sPCA) were used to identify subpopulations and spatial organization. Ethnic group frequencies, husbandry practices and altitude were used to create cost maps that were implemented in a least-cost path approach. Genetic diversity in the Vietnamese goat population was low (0.508) compared to other local Asian breeds. Using a Bayesian approach, three clusters were identified. sPCA confirmed these three clusters and also that the genetic structure showed a significant spatial pattern. The least-cost path analysis showed that genetic differentiation was significantly correlated (0.131–0.207) to ethnic frequencies and husbandry practices. In brief, the spatial pattern observed in the goat population was the result of complex gene flow governed by the spatial distribution of ethnic groups, ethnicity and husbandry practices. In this study, we clearly linked the livestock genetic pattern to farmer connectivity and showed the importance of taking into account spatial information in genetic studies.     

Perceived contrast following adaptation: the role of adapting stimulus visibility

The issue of whether contrast adaptation can reduce the perceived contrast of gratings oriented orthogonal to the adapting stimulus to a greater extent than parallel gratings has been the subject of considerable debate (Snowden and Hammett, 1992; Ross and Speed, 1996). We compared the reductions in perceived contrast of various test gratings oriented parallel and orthogonal to the adapting stimulus across a range of spatial frequencies (2.25-9 c/deg) and adaptation contrasts (0.19-1.0). Our results show that when the adapting stimulus is low in contrast, parallel adaptation effects are always greater than the effects of orthogonal adaptation. When the adapting contrast is increased, however, the difference between parallel and orthogonal effects is reduced. Further increases in adapting contrast can produce a situation where cross-orientation adaptation effects exceed iso-orientation effects. This was observed at low spatial frequencies (2.25 and 4.5 c/deg) only. The difference in the pattern of results obtained at low and high spatial frequencies can be explained in terms of the adapting stimulus visibility. We conclude that cross-orientation adaptation effects can be greater than iso-orientation effects, but only when the adapting stimulus is highly suprathreshold.     

Haplotype frequency distribution for 7 microsatellites in chromosome 8 and 11 in relation to the metabolic syndrome in four ethnic groups: Tehran Lipid and Glucose Study

Introduction

Different variants of haplotype frequencies may lead to various frequencies of the same variants in individuals with drug resistance and disease susceptibility at the population level.

Materials and methods

In this study, the haplotype frequencies of 4 STR loci including the D8S1132, D8S1779, D8S514 and D8S1743, and 3 STR loci including D11S1304, D11S1998 and D11S934 were investigated in 563 individuals of four Iranian ethnic groups in the capital city of Iran, Tehran. One hundred thirty subjects had the metabolic syndrome. Haplotype frequencies of all markers were calculated.

Results

There were significant differences in the haplotype frequencies in short and long alleles between the metabolic affected subjects and controls. In addition, haplotype frequencies were significant in the four ethnic groups in both chromosomes 8 and 11.

Conclusion

Our findings show a relation between the short allele of D8S1743 in all related haplotype frequencies of subjects with metabolic syndrome. These findings may require more studies of some candidate genes, including the lipoprotein lipase gene, in this chromosomal region.     

Male fitness of oilseed rape (Brassica napus), weedy B. rapa and their F(1) hybrids when pollinating B. rapa seeds

The likelihood that two species hybridise and backcross may depend strongly on environmental conditions, and possibly on competitive interactions between parents and hybrids. We studied the paternity of seeds produced by weedy Brassica rapa growing in mixtures with oilseed rape (B. napus) and their F(1) hybrids at different frequencies and densities. Paternity was determined by the presence of a transgene, morphology, and AFLP markers. In addition, observations of flower and pollen production, and published data on pollen fertilisation success, zygote survival, and seed germination, allowed us to estimate an expected paternity. The frequency and density of B. napus, B. rapa, and F(1) plants had a strong influence on flower, pollen, and seed production, and on the paternity of B. rapa seeds. Hybridisation and backcrossing mostly occurred at low densities and at high frequencies of B. napus and F(1), respectively. F(1) and backcross offspring were produced mainly by a few B. rapa mother plants. The observed hybridisation and backcrossing frequencies were much lower than expected from our compilation of fitness components. Our results show that the male fitness of B. rapa, B. napus, and F(1) hybrids is strongly influenced by their local frequencies, and that male fitness of F(1)hybrids, when pollinating B. rapa seeds, is low even when their female fitness (seed set) is high.     

Ancestral alleles and population origins: inferences depend on mutation rate.

Previous studies have found that at most human loci, ancestral alleles are "African," in the sense that they reach their highest frequency there. Conventional wisdom holds that this reflects a recent African origin of modern humans. This paper challenges that view by showing that the empirical pattern (of elevated allele frequencies within Africa) is not as pervasive as has been thought. We confirm this African bias in a set of mainly protein-coding loci, but find a smaller bias in Alu insertion polymorphisms, and an even smaller bias in noncoding loci. Thus, the strong bias that was originally observed must reflect some factor that varies among data sets--something other than population history. This factor may be the per-locus mutation rate: the African bias is most pronounced in loci where this rate is high. The distribution of ancestral alleles among populations has been studied using 2 methods. One of these involves comparing the fractions of loci that reach maximal frequency in each population. The other compares the average frequencies of ancestral alleles. The first of these methods reflects history in a manner that depends on the mutation rate. When that rate is high, ancestral alleles at most loci reach their highest frequency in the ancestral population. When that rate is low, the reverse is true. The other method--comparing averages--is unresponsive. Average ancestral allele frequencies are affected neither by mutation rate nor by the history of population size and migration. In the absence of selection and ascertainment bias, they should be the same everywhere. This is true of one data set, but not of 2 others. This also suggests the action of some factor, such as selection or ascertainment bias, that varies among data sets.     

Adaptive significance of amylase polymorphism in Drosophila I. The geographical pattern of allozyme polymorphism at the amylase locus in Drosophila subobscura

Allelic variation at the Amy locus was studied in eight natural populations from the central and northern range of D. subobscura, and the geographical pattern of Amy polymorphism over the range of this species was described. Even though regional and local differences in gene frequencies were found, in general the same alleles occur at high, intermediate and low frequencies, in nearly all populations. There are no significant differences in allele frequencies, but there is significant difference in the degree of heterozygosity among groups of populations from the northern, central and southern range. An analysis of population subdivision indicates that heterogeneity within populations is higher than between populations. Genetic distance values indicate that there is a variable degree of geographical differentiation between local populations. Variability within and between continental and insular populations is also discussed.     

Distribution of AB0 and RH blood group alleles in different populations of southern Punjab, Pakistan.

The analysis of a sample of 1632 individuals from patients of the Nishtar Teaching Hospital, Multan, suggests that different ethnic groups (Araeen, Mughals, Syed, Jat, Rajputs, Baloch and Pathan) are not significantly different from another with regard to the distribution of RH blood group alleles (RH*d around 0.30). The distributions of the AB0 blood group alleles suggest that different ethnic groups are not significantly different from the average alele frequencies (AB0*A = 0.23, AB0*B = 0.33, AB0*0 = 0.47) except for the Pathan ethnic group (AB0*A = 0.35, AB0*B = 0.47, AB0*0 = 0.27). The populations of different geographic areas are not significantly different from the average allele frequencies, except for the southern district of Rahim Yar Khan (AB0*A = 0.12) and the northern district of Sahiwal (AB0*A = 0.19). The populations of Sahiwal (RH*d = 0.35) and Muzaffargarh (RH*d = 0.36) yield significantly different allele frequencies at the RH locus. The interpopulation differences can be explained by the geographic distance. There is a significant difference in the frequencies of the AB0 alleles between rural and urban populations, suggesting that rural populations maintain their isolation from urban populations. Rural and urban populations are not significantly different from one another concerning the allele frequencies at the RH locus.