Seasonal cycles of allozyme-by-chromosomal-inversion gametic disequilibrium in Drosophila subobscura

Allozyme loci are frequently found non randomly associated to the chromosomal inversions in which they are included in Drosophila. Two opposite views compete to explain strong allozyme-by-inversion gametic disequilibria: they result from natural selection or, conversely, merely represent remnants of associations accidentally established at the origin of inversions. Empirical efforts aimed at deciding between adaptive and historical scenarios have focused on the spatial distribution of disequilibria. Yet, the evolutionary significance of these associations remains uncertain. I report here the results of a time-series analysis of the seasonal variation of alleles at six allozyme loci (Acph, Lap, Pept-1, Ao, Mpi, and Xdh) in connection with the O chromosomal polymorphisms of D. subobscura. The findings were: (1) in the segment I of the O chromosome, Lap and Pept-1 allozymes changed seasonally in a cyclical fashion within the ST gene arrangement, but they changed erratically within the 3 + 4 gene configuration; (2) the frequencies of Lap1.11 and Pept-1(0.40) within ST dropped to their lowest values in early and late summer, respectively, when the seasonal level of the ST arrangement is lowest. Furthermore, Lap1.11 and Pept-1(0.40) covary with ST only within these seasons, yet in a fashion inconsistent with these alleles having a major influence on the dynamics of the inversion; (3) seasonal cycling of alleles within inversions were not detected at Acph, Ao, Mpi, and Xdh, yet these loci are nearly monomorphic at the study population, and/or their sampled series were shorter than those for Lap and Pept-1; and (4) simply monitoring allozyme frequencies separately for each inversion proved to be superior, for evidencing the seasonal cycles of the disequilibria, to the use of the D' coefficient of association. Observed seasonal cycles of allozymes within inversions likely reflect natural selection.     

A long-term study on seasonal changes of gametic disequilibrium between allozymes and inversions in Drosophila subobscura

Seasonal variation (spring, early summer, late summer, and autumn) of gametic disequilibrium between gene arrangements (OST and O3+4) of the O chromosome and Lap, Pept-1, and Acph allozyme loci, located inside these inversions, has been recorded in a natural population of Drosophila subobscura during seven years over a 15-year period. The length of the study allowed us to investigate the temporal variation of the allozyme-inversion associations by statistical methods of time series analysis. Cyclic seasonal changes of allozyme-inversion associations for both Lap and Pept-1 are detected in the natural population. In both cases, the patterns of seasonal change are due to the seasonal change of frequency of Lap and Pept-1 allozymes occurring exclusively within the OST gene arrangement. In contrast, the allozyme frequencies at these loci within the O3+4 gene arrangement are stable along seasons. The patterns of temporal variation of allozyme-inversion associations for Lap and Pept-1 in the natural population are contrasted with those previously published that correspond to gene arrangements of the O chromosome and nucleotide polymorphism at the rp49 region located inside these inversions, suggesting that natural selection is operating on these allozyme-inversion associations.     

LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci

Large-scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1 Mb bin, we tested independence, effectively an apparent linkage disequilibrium (LD), with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a nonreciprocal translocation between chromosomes (chr.) 7 and 8 resulted in a 5–3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma,” the terminal arm of chr. 4 translocated to the tip of chr. 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, while apparent LD between pericentromeric regions suggested the effect of repeats. This method, LD-CNV, should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.     

The efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage

In a simulation study, different designs were compared for efficiency of fine-mapping of QTL. The variance component method for fine-mapping of QTL was used to estimate QTL position and variance components. The design of many families with small size gave a higher mapping resolution than a design with few families of large size. However, the difference is small in half sib designs. The proportion of replicates with the QTL positioned within 3 cM of the true position is 0.71 in the best design, and 0.68 in the worst design applied to 128 animals with a phenotypic record and a QTL explaining 25% of the phenotypic variance. The design of two half sib families each of size 64 was further investigated for a hypothetical population with effective size of 1000 simulated for 6000 generations with a marker density of 0.25 cM and with marker mutation rate 4 × 10^-4 per generation. In mapping using bi-allelic markers, 42~55% of replicated simulations could position QTL within 0.75 cM of the true position whereas this was higher for multi allelic markers (48~76%). The accuracy was lowest (48%) when mutation age was 100 generations and increased to 68% and 76% for mutation ages of 200 and 500 generations, respectively, after which it was about 70% for mutation ages of 1000 generations and older. When effective size was linearly decreasing in the last 50 generations, the accuracy was decreased (56 to 70%). We show that half sib designs that have often been used for linkage mapping can have sufficient information for fine-mapping of QTL. It is suggested that the same design with the same animals for linkage mapping should be used for fine-mapping so gene mapping can be cost effective in livestock populations.     

Linkage disequilibrium between alleles at highly polymorphic mini- and micro-satellite loci of Theileria parva isolated from cattle in three regions of Kenya

Theileria parva schizont-infected lymphocyte culture isolates from western, central and coastal Kenya were analysed for size polymorphism at 30 T. parva-specific variable number tandem repeat (VNTR) loci using a panel of mini- and micro-satellite markers. The mean number of alleles ranged from 3 to 11 at individual loci and 183 distinct alleles were observed in total, indicating high genetic diversity within the T. parva gene pool in Kenyan cattle. The frequency distribution of the length variation of specific alleles among isolates ranged from normal to markedly discontinuous. Genetic relationships between isolates were analysed using standard indices of genetic distance. Genetic distances and dendrograms derived from these using neighbour-joining algorithms did not indicate significant clustering on a geographical basis. Analysis of molecular variance demonstrated that the genetic variation between individual isolates was 72%, but only 2.3% when isolates from different regions were pooled. Both these observations suggest minimal genetic sub-structuring relative to geographical origin. Linkage disequilibrium was observed between pairs of loci within populations, as in certain Ugandan T. parva populations. A novel observation was that disequilibrium was also detected between alleles at three individual pairs of VNTR loci when isolates from the three regional meta-populations were pooled for analysis.     

The additive genetic variance after bottlenecks is affected by the number of loci involved in epistatic interactions

Abstract We investigated the role of the number of loci coding for a neutral trait on the release of additive variance for this trait after population bottlenecks. Different bottleneck sizes and durations were tested for various matrices of genotypic values, with initial conditions covering the allele frequency space. We used three different types of matrices. First, we extended Cheverud and Routman's model by defining matrices of "pure" epistasis for three and four independent loci; second, we used genotypic values drawn randomly from uniform, normal, and exponential distributions; and third we used two models of simple metabolic pathways leading to physiological epistasis. For all these matrices of genotypic values except the dominant metabolic pathway, we find that, as the number of loci increases from two to three and four, an increase in the release of additive variance is occurring. The amount of additive variance released for a given set of genotypic values is a function of the inbreeding coefficient, independently of the size and duration of the bottleneck. The level of inbreeding necessary to achieve maximum release in additive variance increases with the number of loci. We find that additive-by-additive epistasis is the type of epistasis most easily converted into additive variance. For a wide range of models, our results show that epistasis, rather than dominance, plays a significant role in the increase of additive variance following bottlenecks.     

The effects of selective genotyping on estimates of proportion of recombination between linked quantitative trait loci

Selective genotyping is the marker assay of only the more extreme phenotypes for a quantitative trait and is intended to increase the efficiency of quantitative trait loci (QTL) mapping. We show that selective genotyping can bias estimates of the recombination frequency between linked QTLs — upwardly when QTLs are in repulsion phase, and downwardly when QTLs are in coupling phase. We examined these biases under simple models involving two QTLs segregating in a backcross or F₂ population, using both analytical models and computer simulations. We found that bias is a function of the proportion selected, the magnitude of QTL effects, distance between QTLs and the dominance of QTLs. Selective genotyping thus may decrease the power of mapping multiple linked QTLs and bias the construction of a marker map. We suggest a large proportion than previously suggested (50%) or the entire population be genotyped if linked QTLs of large effects (explain > 10% phenotypic variance) are evident. New models need to be developed to explicitly incorporate selection into QTL map construction.     

The genetic basis of floral traits associated with mating system evolution in Leptosiphon (Polemoniaceae): an analysis of quantitative trait loci

Mapping of quantitative trait loci (QTL) was used to investigate the genetic architecture of divergence in floral characters associated with the mating system, an important adaptive trait in angiosperms. Two species of Leptosiphon (Polemoniaceae), one strongly self-fertilizing (L. bicolor) and the other partially outcrossing (L. jepsonii), were crossed to produce F2 and both backcross progenies. For each crossing population, a linkage map was created using amplified fragment length polymorphism markers, and QTL were identified for several dimensions of floral size. For each of the five traits examined, three to seven QTL were detected, with independent datasets yielding congruent results in some but not all cases. The phenotypic effect of individual QTL was generally moderate. We estimated that many of the QTL were additive or showed dominance toward L. bicolor, whereas comparison of mean trait values for parental and cross progenies showed apparent overall dominance of L. jepsonii traits. Colocalization of QTL for different dimensions of floral size was consistent with high phenotypic correlations between floral traits. Substantial segregation distortion was observed in marker loci, the majority favoring alleles from the large-flowered parent. A low frequency of male sterility in the F2 population is consistent with the Dobzhansky-Muller model for the evolution of reproductive isolation.     

杏品种一年生休眠枝,花,幼果抗寒的相关分析

用电导法并配以Ｌｏｇｉｓｔｉｃ方法对２５个杏品种的抗寒性进行鉴定,结果表明,杏１年生枝的抗守则测试在－２８．５℃～－４０℃,花蕾的抗寒温度在－７．０℃～－１９．０℃,盛开花朵的抗寒温度在－３．０℃～－６．９℃,幼果的抗寒温度在－１．１℃～－２．２℃,枝、花枝和幼果彼此间抗寒性呈显著相关,其抗寒性强弱的顺序为枝〉花〉幼果,同一朵花器官的抗寒性为：花瓣〉雄蕊〉雌蕊。     

HDL/LDL 比值、LP（a）及s-CRP 与冠脉病变程度相关性分析

目的:研究高密度脂蛋白/低密度脂蛋白比值(HDL/LDL比值)、脂蛋白a(LP(a))及超敏C反应蛋白(s-CRP)与冠脉病变程度之间的关系。方法:对120名初发急性STEMI行急诊冠脉造影术并支架植入术患者(<12小时),并于次日晨检测空腹生化血脂分析,测得HDL/LDL比值、LP(a)及s-CRP等相关指标,冠脉造影结果根据Gensini积分系统分轻、中、重度三组,比较三组之间上述三项指标有无差异,并选取冠脉造影正常20例为对照组,比较各组间有无差异。结果:与正常组相比,心梗组HDL/LDL比值明显降低(P<0.05),各组间HDL/LDL比值亦存在差异(P<0.05),LP(a)及s-CRP在不同冠脉分级上亦存在着差异(P<0.05),以上差异均有统计学意义。结论:上述三项指标对冠脉病变严重程度有一定的预测价值。     

The environmental temperature and physiological polymorphism of populations. 4. The effect of heat acclimation on the intensity and the genetic effectiveness of selection caused by heating

Heat acclimation is shown to result in the decrease in the intensity of thermal selection which is more evident at the lower as compared with higher heat doses. Heat acclimation is accompanied by a sharp decrease in the genetic effectiveness of thermal selection. Therefore the directed selection of individuals turns into a poorly selective or even completely non-selective order of death. This effect is achieved in three ways: (1) a decrease in individual variability of organismal heat resistance. (2) a decrease in the heritability of this trait and (3) a change in the order of death of individuals during thermal selection (rearrangement of selectivity).

The change in the intensity (δi) and genetic effectiveness (δE) of thermal selection due to the effect of acclimation demonstrates a functional homeostasis of the population. This homeostatic mechanism maintains population numerical composition and genetic structure under conditions of variable temperature. This can be expressed as follows: H = 1 - δi·δE where H is the level of homeostasis, δi is the organismal and δE the populational components of the total homeostasis.     

Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations

Chlorophyll content, one of the most important physiological parameters related to plant photosynthesis, is usually used to predict yield potential. To map the quantitative trait loci (QTLs) underlying the chlorophyll content of rice leaves, a double haploid (DH) population was developed from an indica/japonica (Zhenshan 97/Wuyujing 2) crossing and two backcross populations were established subsequently by backcrossing DH lines with each of their parents. The contents of chlorophyll a and chlorophyll b were determined by using a spectrophotometer to directly measure the leaf chlorophyll extracts. To determine the leaf chlorophyll retention along with maturation, all measurements were performed on the day of heading and were repeated 30 days later. A total of 60 QTLs were resolved for all the traits using these three populations. These QTLs were distributed on 10 rice chromosomes, except chromosomes 5 and 10; the closer the traits, the more clustering of the QTLs residing on common rice chromosomal regions. In general, the majority of QTLs that specify chlorophyll a content also play a role in determining chlorophyll b content. Strangely, chlorophyll content in this study was found mostly to be lacking or to have a negative correlation with yield. In both backcross F₁ populations, overdominant (or underdominant) loci were more important than complete or partially dominant loci for main-effect QTLs and epistatic QTLs, thereby supporting previous findings that overdominant effects are the primary genetic basis for depression in inbreeding and heterosis in rice.     

动态心电图ST-T 改变诊断冠心病的临床价值研究

目的:探讨心电图ST-T的动态改变对临床诊断冠心病的实用价值。方法:选取2013年10月~2015年10月在我院诊断治疗的有ST-T段改变的患者,观察并记录所有患者的心电图状态,并重点监测ST-T改变的动态情况,并回归性分析及对比检测结果。结果:心电图ST-T改变有动态变化率的冠心病确诊率为67.9%,明显高于无动态变化组32.3%的确诊率。两组确诊率具有统计学意义(P0.05)。结论:心电图有动态改变的ST-T段改变能提高患者冠心病的临床确诊率,值得进一步推广应用。     

新疆塔里木河下游物种多样性与地下水位的关系

依据塔里木河下游7个监测断面36眼地下水位观测井和36个植物样地野外采集的数据,应用Margalef丰富度指数、Shannon-Weiner信息指数、Alatalo均匀度指数和修正的Simpson多样性指数以及含参数的Hill指数,对塔里木河下游物种多样性特征进行了分析。结果表明:塔里木河下游物种多样性与地下水埋深有显著的关联性,随着地下水埋深增大,塔里木河下游物种丰富度和多样性均表现出递减趋势,而均匀度指数的变化趋势则不甚明显;Hill指数的分析表明,以地下水埋深6m和10m为界,多样性变化明显分为3个不同的变化阶段,其中地下水埋深在6m以下时,多样性锐减,且曲线最终趋于平直。综合野外调查和样地资料分析,认为塔里木河下游物种多样性受损的临界地下水位为6m左右。     

桂林漓江沿岸植物区系特点及其与景观的关系

桂林漓江沿岸原生植被受破坏严重 ,植物区系为次生性质 ,其特点 :( 1 )种类丰富 ,共有野生维管束植物 80 8种 ,隶属于 1 5 6科、483属 ;( 2 )植物区系的地理成份复杂 ,可将 45 4个种子植物属归为 1 4个类型 ,以热带、亚热带类型为主 ,温带类型次之 ,中国特有属 6个 ;( 3 )植物区系岩溶特性明显 ,属于东亚植物区、中国—日本森林植物亚区、岭南山地地区的一个小区。植物景观是桂林漓江沿岸风景的重要组成部分 ,具体表现在各类植物群落的外貌和一些重要植物种类的花、果和叶色的季节性变化上。现存的主要植物群落以次生藤刺灌丛为主 ;少见尚存的喀斯特常绿、落叶阔叶混交林 ;独有的喀斯特硬叶常绿阔叶林 :以乌冈栎为建群种的山顶矮林 ,是我国东部湿润亚热带地区罕见的残遗植被类型 ,在构成景观和科研上均有特殊意义。沿河岸分布的植物是最吸引游人注意的重要景观 ,形状各异的灌丛、杂木林、竹林和农田植被等都是风景的重要组成部分     

Relationships between iron and vanadium metabolism: The exchange of vanadium between transferrin and ferritin

The study of possible relationships between iron and vanadium metabolism (E. Sabbioni and E. Marafante, Proc. XIth Int. Conf. Biochem., 13-5-R122, Toronto, Canada) was extended to the vanadium in the biochemical mechanisms which involve the exchange of iron between transferrin and ferritin. The transfer of vanadium between transferrin and ferritin was investigated using ⁴⁸V radiotracer and gel filtration technique. ⁴⁸V labelled human transferrin and horse spleen ferritin, ⁴⁸V plasma from rats injected with ⁴⁸VO²⁺, unlabelled rat liver cytosol, and plasma were used as sources of the two proteins for their incubation under different conditions. The results show that the equilibrium:

occurs in vitro at physiological pH under the conditions of this experiment. No transfer of vanadium between the two proteins, however, occurs when they are incubated simply in a buffer at pH = 7.4. The maximum transfer was observed when transferrin and ferritin were mixed in their natural environments such as plasma and liver cytosol. This suggests that the exchange of the vanadium between the two proteins is affected by biochemical factors which are present in the body. A brief evaluation of the significance on the very low amounts of the element exchanged between the two proteins is also presented     

塔里木河下游胡杨径向生长与地下水的关系

本文通过分析塔里木河下游地区地下水位与胡杨径向生长量的相互关系,建立胡杨径向生长量随地下水位变化的函数模型,并从数理统计学的角度验证了胡杨生长的胁迫水位和临界水位。结果表明：1）随着地下水位的下降,胡杨径向生长量的均值逐渐减小。2）胡杨径向生长量与地下水位之间存在极显著的回归关系,其最佳回归模拟函数为四次多项式Y=0.003X4-0.080X3 0.731X2-3.060X 6.934,判定系数R2为0.857,P值为0.0001。3）通过分析可知：胡杨生长的胁迫水位是4.71 m,临界水位是8.62 m。胡杨正常生长的水位区间为0.5—4.71 m,受到胁迫的水位区间为4.71 m—8.62 m,当地下水位大于8.62 m时,胡杨将会呈现出衰败景象,此时,胡杨径向生长量的变化率逐渐向0接近,表明胡杨径向生长趋向停止。     

Power-laws in the genomic distribution of coding segments in several organisms:: An evolutionary trace of segmental duplications,possible paleopolyploidy and gene loss

Large-scale features of the spatial arrangement of protein-coding segments (PCS) are investigated by means of the inter-PCS spacers' size distributions, which have been found to follow power-laws. Linearity in double-logarithmic scale extends to several orders of magnitude in the genomes of organisms as disparate as mammals, insects and plants. This feature is also present in the most compact eukaryotic genomes and in half of the examined bacteria, despite their very limited non-coding space. We have tried to determine the sequence of events in the course of genomes' evolution which may account for the formation of the observed size distributions. The proposed mechanism essentially includes two types of events: (i) segmental duplications (and possibly paleopolyploidy), and (ii) the subsequent loss of most of the duplicated genes. It is shown by computer simulations that the formulated scenario generates power-law-like inter-PCS spacers' size distributions, which remain robust for a variety of parameter choices, even if insertion of external sequences, such as viruses or proliferating retroelements is included. Moreover, power-laws are preserved after most of the non-coding DNA has been removed, thus explaining the finding of this pattern in genomes as compact as that of Takifugu rubripes.     

The relationship between the presence of ADHD and certain candidate gene polymorphisms in a Turkish sample

Due to the high heritability of attention-deficit hyperactivity disorder (ADHD), parents of children with ADHD appear to represent a good sample group for investigating the genetics of the disorder. The aim of this study was to investigate the association between ADHD and six polymorphisms in five candidate genes [5-HT2A (rs6311), NET1 (rs2242447), COMT (rs4818), NTF3 (rs6332), SNAP-25 (rs3746544) and (rs1051312)]. We included 228 parents of children diagnosed with ADHD and 109 healthy parents as the control group. The polymorphisms were genotyped using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays and analyzed using the chi-square test and the multinomial logit model. SNAP-25 (rs3746544) polymorphism was associated with loading for ADHD, while 5-HT2A (rs6311) and NET1 (rs2242447) polymorphisms were associated with ADHD. On the other hand, there was no significant association between the SNAP-25 (rs1051312), NTF3 (rs6332), or COMT (rs4818) gene polymorphisms and ADHD.