The Effect of a Selected Locus on Linked Neutral Loci

The effects produced on linked neutral loci as a selected locus evolves towards its equilibrium value are considered. Significant effects on the neutral loci arise if the recombination fraction between the neutral and selected loci is smaller than the order of magnitude of the selective differences at the selected locus. The effect on gene frequencies at the neutral loci, that is, the hitchhiking effect, is determined, as well as the linkage disequilibrium generated by this hitchhiking effect. One of the more important findings is that significant disequilibrium can be generated between two neutral loci by the evolution of a linked selected locus. Consideration is given to the problem of determining how the effect of selection operating in natural populations can be detected, the question of the establishment of inversions in populations, and also to the nonequilibrium properties of populations.     

The Effect of Change in Population Size on DNA Polymorphism

The expected number of segregating sites and the expectation of the average number of nucleotide differences among DNA sequences randomly sampled from a population, which is not in equilibrium, have been developed. The results obtained indicate that, in the case where the population size has changed drastically, the number of segregating sites is influenced by the size of the current population more strongly than is the average number of nucleotide differences, while the average number of nucleotide differences is affected by the size of the original population more severely than is the number of segregating sites. The results also indicate that the average number of nucleotide differences is affected by a population bottleneck more strongly than is the number of segregating sites.     

Genealogy of Neutral Genes and Spreading of Selected Mutations in a Geographically Structured Population

In a geographically structured population, the interplay among gene migration, genetic drift and natural selection raises intriguing evolutionary problems, but the rigorous mathematical treatment is often very difficult. Therefore several approximate formulas were developed concerning the coalescence process of neutral genes and the fixation process of selected mutations in an island model, and their accuracy was examined by computer simulation. When migration is limited, the coalescence (or divergence) time for sampled neutral genes can be described by the convolution of exponential functions, as in a panmictic population, but it is determined mainly by migration rate and the number of demes from which the sample is taken. This time can be much longer than that in a panmictic population with the same number of breeding individuals. For a selected mutation, the spreading over the entire population was formulated as a birth and death process, in which the fixation probability within a deme plays a key role. With limited amounts of migration, even advantageous mutations take a large number of generations to spread. Furthermore, it is likely that these mutations which are temporarily fixed in some demes may be swamped out again by non-mutant immigrants from other demes unless selection is strong enough. These results are potentially useful for testing quantitatively various hypotheses that have been proposed for the origin of modern human populations.     

The Amount of DNA Polymorphism Maintained in a Finite Population When the Neutral Mutation Rate Varies among Sites

The expectations of the average number of nucleotide differences per site (π), the proportion of segregating site (s), the minimum number of mutations per site (s*) and some other quantities were derived under the finite site models with and without rate variation among sites, where the finite site models include Jukes and Cantor's model, the equal-input model and Kimura's model. As a model of rate variation, the gamma distribution was used. The results indicate that if distribution parameter α is small, the effect of rate variation on these quantities are substantial, so that the estimates of θ based on the infinite site model are substantially underestimated, where θ = 4Nv, N is the effective population size and v is the mutation rate per site per generation. New methods for estimating θ are also presented, which are based on the finite site models with and without rate variation. Using these methods, underestimation can be corrected.     

The Age of a Neutral Mutant Persisting in a Finite Population

Formulae for the mean and the mean square age of a neutral allele which is segregating with frequency x in a population of effective size N(e) have been obtained using the diffusion equation method, for the case of 4N(e)v<1 where v is the mutation rate. It has been shown that the average ages of neutral alleles, even if their frequencies are relatively low, are quite old. For example, a neutral mutant whose current frequency is 10% has the expected age roughly equal to the effective population size N(e) and the standard deviation 1.4N(e) (in generations), assuming that this mutant has increased by random drift from a very low frequency. Also, formulae for the mean "first arrival time" of a neutral mutant to a certain frequency x have been presented. In addition, a new, approximate method has been developed which enables us to obtain the condition under which frequencies of "rare" polymorphic alleles among local populations are expected to be uniform if the alleles are selectively neutral.-It was concluded that exchange of only a few individuals on the average between adjacent colonies per generation is enough to bring about such a uniformity of frequencies.     

The Hitchhiking Effect on the Site Frequency Spectrum of DNA Polymorphisms

The level of DNA sequence variation is reduced in regions of the Drosophila melanogaster genome where the rate of crossing over per physical distance is also reduced. This observation has been interpreted as support for the simple model of genetic hitchhiking, in which directional selection on rare variants, e.g., newly arising advantageous mutants, sweeps linked neutral alleles to fixation, thus eliminating polymorphisms near the selected site. However, the frequency spectra of segregating sites of several loci from some populations exhibiting reduced levels of nucleotide diversity and reduced numbers of segregating sites did not appear different from what would be expected under a neutral equilibrium model. Specifically, a skew toward an excess of rare sites was not observed in these samples, as measured by Tajima's D. Because this skew was predicted by a simple hitchhiking model, yet it had never been expressed quantitatively and compared directly to DNA polymorphism data, this paper investigates the hitchhiking effect on the site frequency spectrum, as measured by Tajima's D and several other statistics, using a computer simulation model based on the coalescent process and recurrent hitchhiking events. The results presented here demonstrate that under the simple hitchhiking model (1) the expected value of Tajima's D is large and negative (indicating a skew toward rare variants), (2) that Tajima's test has reasonable power to detect a skew in the frequency spectrum for parameters comparable to those from actual data sets, and (3) that the Tajima's Ds observed in several data sets are very unlikely to have been the result of simple hitchhiking. Consequently, the simple hitchhiking model is not a sufficient explanation for the DNA polymorphism at those loci exhibiting a decreased number of segregating sites yet not exhibiting a skew in the frequency spectrum.     

The Accumulation of P-Element-Induced Recombinants in the Germline of Male Drosophila Melanogaster

P-element-induced recombination in Drosophila melanogaster occurs premeiotically. Recombinants are therefore expected to accumulate in the stem cells of the germline of P-element-carrying males. We show that both the recombination frequency and the incidence of ``clustering' increase with the age of males carrying various P-element derivatives. The combination of end-deleted elements can lead to average recombination frequencies >50% with individual instances of 100% recombination. These elements also lowered the fertility of the carriers. We investigated these features by constructing an analytical and a computer simulation model of the course of events in the germline, incorporating the recently proposed hybrid element insertion (HEI) model of P-element activity. The model is able to predict extreme recombination levels, segregation ratio biases and lowered fertility through cell death in a single analysis.     

The Effects of Hitchhiking on a Gene for Recombination

This paper proposes that alleles increasing recombination rates may be selected for as a result of the perturbing effects of the spread of selectively favored alleles on neighboring loci maintained polymorphic by sleection. The recombination genes are favored since their presence increases the production of selectively advantageous types of gametes with which they tend to remain associated. Numerical examples are presented, and some consequences of this model discussed. One such consequence is the wicespread existence of polymorphism for genes affecting recombination values.     

新疆维吾尔族HLA-Cw基因座遗传多态性调查 The Study of HLA-Cw Polymorphism in Uygur Population

采用序列特异性寡核苷酸探针杂交技术（PCR-SSOP）对146位新疆维吾尔族无关个体HLA-Cw基因座进行基因分型,研究该民族HLA-Cw基因座遗传多态性,建立新疆维吾尔族HLA-Cw基因频率数据库。检出18种等位基因,基因频率分布在0.0069~02460,其中HLA-Cw*04、07、08、14基因频率比较高,基因频率分别为02460、0.1151、0.1010、0.1202,共占新疆维吾尔族可检出等位基因的58.23%,PCR-SSOP分型技术使新疆维吾尔族HLA-Cw基因座空白基因频率降至0.0064。经χ2检验,基因型分布符合Hardy-Weinberg平衡定律。建立民族HLA-Cw基因座基因频率数据库,为临床器官移植配型、人类学、法医学提供重要的群体遗传学资料。 Abstract:The HLA-Cw loci polymorphism in Uygur population was investigated using the PCR- sequence specific oligonucleotide probe (SSOP) method,and the genetic database on the distribution of gene frequency of the HLA-Cw loci was established.From 146 individuals of Uygur population,18 HLA-Cw alleles were detected.The gene frequency was from 0.0069 to 0.2460.The four most common alleles were HLA-Cw*04(24.60%)、07(11.51%)、08(1010%)、14(12.02%),and they covered 58.23% of total alleles detected from Uygur population.We have made a survey of HLA-Cw alleles frequencies in a Uygur population,with blank frequency being lowered to 0.0064.The distribution of genotype frequencies met the law of Hardy-Weinberg equilibrium by hi-square test.The frequency data can be used in forensic and paternity tests to estimate the frequency of a DNA profile in the Uygur population,transplant matching and anthropology.     

MiR-34c在奶山羊雄性生殖干细胞增殖分化过程中的作用

microRNA (miRNA)在奶山羊雄性生殖细胞和精子发生过程有重要的调控功能。为研究miR-34c对雄性生殖干细胞增殖与分化中的作用,本文利用视黄酸效应基因8（Stra8）在雄性生殖细胞中随年龄增长,以其表达量上调的表达特征为指针,使用实时定量PCR技术筛选分析miRNAs。结果发现,miR-34c与Stra8的表达规律基本一致。在无精症奶山羊的睾丸组织中,发现miR-34c在无精症奶山羊睾丸组织中表达缺失。利用miR-34c模拟物及抑制剂转染奶山羊雄性生殖干细胞,体外转染miR-34c模拟物及其抑制剂,发现miR-34c能够下调Rarg、Stra8与c-Myc基因的表达,减缓奶山羊雄性生殖干细胞的增殖。结果提示,miR-34c可能具有调控奶山羊雄性生殖干细胞的减数分裂的作用,同时抑制其增殖。     

REV-ERB ALPHA Polymorphism Is Associated with Obesity in the Spanish Obese Male Population

REV-ERB ALPHA has been shown to link metabolism with circadian rhythms. We aimed to identify new polymorphisms in the promoter of REV-ERB ALPHA and tested whether these polymorphisms could be associated with obesity in the Spanish population. Of the 1197 subjects included in our study, 779 were obese (BMI 34.38±3.1 kg/m²) and 418 lean (BMI 23.27±1.5 kg/m²). In the obese group, 469 of the 779 had type 2 diabetes. Genomic DNA from all the subjects was obtained from peripheral blood cells and the genotyping in the REV-ERB ALPHA promoter was analyzed by High Resolution Melting. We found six polymorphisms in the REV-ERB ALPHA promoter and identified rs939347 as a SNP with the highest frequency in the total population. We did not find any association between rs939347 and type 2 diabetes (p = 0.101), but rs939347 was associated with obesity (p = 0.036) with the genotype AA exhibiting higher frequency in the obese (5.2% in total obese vs 2.4% in lean). This association was found only in men (p = 0.031; 6.5% AA-carriers in obese men vs 1.9% AA-carriers in lean men), with no association found in the female population (p = 0.505; 4.4% AA-carriers in obese women vs 2.7% AA-carriers in lean women). Our results suggest that the REV-ERB ALPHA rs939347 polymorphism could modulate body fat mass in men. The present work supports the role of REV-ERB ALPHA in the development of obesity as well as a potential target for the treatment of obesity.     

The Intersection of Inheritance and Metastasis: The Role and Implications of Germline Polymorphism in Tumor Dissemination

Metastasis is an enormously complex process that involves both spatial and temporal barriers. Metastatic cells must not only acquire all of the characteristics of a primary tumor, but additionally must be capable of invasion, survival during transit and in the secondary site, interact productively with a novel microenvironment and proliferate to form a clinically relevant lesion 1. Adding complexity to the process is the fact that it can be years or even decades after diagnosis of the primary tumor before the secondary tumors are apparent. A number of models have been proposed to explain the origins of metastasis. However, while all of the models can account for some aspects of the experimental observations, suggesting they may be at least in part true, none adequately explain all of the data. This implies that the existing models are likely to be too simplistic and additional factors must be considered to adequately account for existing and newly emerging data.     

PLZF与哺乳动物雄性生殖干细胞的发育分化

早幼粒细胞白血病锌指蛋白（promyelocytic leukemia zinc finger,PLZF）,也被称为ZBTB16(zinc finger and BTB domain containing 16,ZBTB16)或锌指蛋白145(zinc finger protein 145,ZFP145),是我国学者发现与人类疾病相关的蛋白质.人类PLZF的是由673个氨基酸残基组成的转录抑制因子,属于蛋白质超家族. 该超家族以N端的BTB/POZ（bric-à-brac, tramtrack, brad complex(BTB)/poxvirus zinc finger (POZ) domain）结构为特征. PLZF蛋白的BTB/POZ结构与个体发育、胚胎发生、染色体的重构等事件相关.近年发现,PLZF在哺乳动物雄性生殖干细胞（male germline stem cells,mGSCs）发育分化过程中也发挥重要作用.探讨PLZF的生物学功能和作用机制,将有助于理解其在mGSCs发育过程中的重要作用. 本文就PLZF在维持mGSCs自我更新和在发育分化调控中的作用给予综述.     

The Effect of Age on a Sexually Selected Acoustic Display

Models of sexual selection suggest that females should prefer to mate with older males because old age is evidence of heritable high viability. In a longitudinal analysis, we demonstrate that male field crickets (Gryllus campestris) alter their calling song with age. Carrier frequency, a calling song character related to growing condition and the main song component under female preference, changed towards higher sexual attractiveness with age. Body mass decreased slightly with age, while chirp rate, an indicator of current condition, remained stable. By choosing males singing at a low frequency, female field crickets would base their mate choice decision on a sexual trait that indicates superior growing conditions as juvenile and on viability, i.e. enhanced current condition as adult.     

Positive Periodic Solution for a Neutral Delay Model in Population

IIntroductionIn1993,KuangY［11gavetheopenp毗fern9．2：恤tainsufficientCOnditionsfortheeds－tenceofpO8ltlvependIc劝utionsinN”（t）＝N（t）［a（t）一B（t）N（）一b（t）N（t—r（t））－c（t）N”（t一巾》】（1）wherea（t）,尸（t）,b（t）,c（t）,,（t）are。＂negativecontinuouspo。odlcfunctionswithpenodT．Inthispaper,weconsideraspecialcasewheng（t）。0,b（t）＞0,c（t）。c,r（t）。,,i．e．O鹏idertheexlstenceOfp用tlvependicdutionsOftkforirlBynsf叩ofsomenewtechnicsandtoPOloglcaldeg…     

The Relationship between Gene Polymorphism and CRP Level in a Chinese Han Population

We investigated the relationships among the +1444C/T polymorphism in the C-reactive protein (CRP) gene and the concentration of CRP and the risk of coronary heart disease. Using polymerase chain reaction-restriction fragment length polymorphism, we analyzed the frequency distribution of genotypes and alleles of the +1444C/T polymorphism in samples from 128 patients with coronary heart disease (coronary stenosis more than 50%) and 119 unrelated normal individuals. The plasma levels of CRP and lipids in the subjects were also measured. The frequencies of the genotypes were CC 89.1%, CT 10.9%, and TT 0% in patients and CC 89.9%, CT 10.1%, and TT 0% in controls. The frequency of allele C was 94.5% in patients and 95.0% in controls, and allele T was 5.5% in patients and 5.1% in controls. The distribution of genotypes and alleles in the Chinese Han population was significantly different from that of the Caucasian population. There were no significant differences between frequencies of genotype and allele of controls and those of patients (P>0.05), but in controls the concentrations of CRP in the CC genotype subgroup were significantly higher than those in the CT genotype subgroup (P<0.05). This suggests that the +1444C/T variant in the CRP gene influences the basal CRP level in normal people. These findings imply that there may eventually be a need to establish genotype-specific risk thresholds of the CRP level.