伪狂犬病病毒基因编码区碱基组成与密码子使用偏差

由于伪狂犬病病毒(PRV)中G C含量高达74％,至今尚没有一个毒株完成全基因组测序。对已知的68个PRV基因编码区序列碱基组成及密码子使用现象进行了统计分析,结果发现PRV基因中存在非常强的密码子使用偏差。所有68个PRV基因编码区密码子第三位总的G C含量为96．24％,其中UL48基因高达99．52％。PRV基因偏向于使用富含GC的密码子,特别是以C或G结尾的密码子。此外,还发现PRV中G C含量变化较大的UL48、UL40、UL14和IE180等基因附近正好与已知的PRV基因组复制起始区相对应。根据基因功能将PRV基因分为6类进行分析发现,基因功能相同或相近的基因其密码子使用模式相似,其中调节基因的同义密码子相对使用度(RSCU)与其他基因有显著差异,在调节基因中以C结尾的密码子的RSCU值远大于其他同义密码子。最后,对PRV基因氨基酸组成差异进行多元分析,发现不同功能的PRV基因在对应分析图上分布不同,表明PRV基因密码子使用模式可能与基因功能相关。     

Optimal foraging constrains macroecological patterns: body size and dietary niche breadth in lizards

Aim  To explore and identify probable mechanisms contributing to the relationships among body size, dietary niche breadth and mean, minimum, maximum and range of prey size in predaceous lizards.
Location  Our data set includes species from tropical rainforests, semi-arid regions of Brazil, and from deserts of the south-western United States, Australia and the Kalahari of Africa.
Methods  We calculated phylogenetic and non-phylogenetic regressions among predator body size, dietary breath and various prey size measures.
Results  We found a negative association between body size and dietary niche breadth in 159 lizard species sampled across most evolutionary lineages of squamate reptiles and across major continents and habitats. We also show that mean, minimum, maximum and range of prey size were positively associated with body size.
Main conclusions  Our results suggest not only that larger lizards tend to eat larger prey, but in doing so offset their use of smaller prey. Reduction of dietary niche breadth with increased body size in these lizards suggests that large predators target large and more profitable prey. Consequently, the negative association between body size and niche breadth in predators most likely results from optimal foraging. Though this result may appear paradoxical and runs counter to previous studies, resources for predators may be predictably more limited than resources for herbivores, thus driving selection for more profitable prey.     

Optimal moult strategies in migratory birds

Avian migration, which involves billions of birds flying vast distances, is known to influence all aspects of avian life. Here we investigate how birds fit moult into an annual cycle determined by the need to migrate. Large variation exists in moulting patterns in relation to migration: for instance, moult can occur after breeding in the summer or after arrival in the wintering quarters. Here we use an optimal annual routine model to investigate why this variation exists. The modelled bird's decisions depend on the time of year, its energy reserves, breeding status, experience, flight feather quality and location. Our results suggest that the temporal and spatial variations in food are an important influence on a migratory bird's annual cycle. Summer moult occurs when food has a high peak on the breeding site in the summer, but it is less seasonal elsewhere. Winter moult occurs if there is a short period of high food availability in summer and a strong winter peak at different locations (i.e. the food is very seasonal but in opposite phase on these areas). This finding might explain why only long-distance migrants have a winter moult.     

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection. They are thus incapable of inferring whether mutation or selection is responsible for evolution at silent sites. Here we implement a few population genetics models of codon substitution that explicitly consider mutation bias and natural selection at the DNA level. Selection on codon usage is modeled by introducing codon-fitness parameters, which together with mutation-bias parameters, predict optimal codon frequencies for the gene. The selective pressure may be for translational efficiency and accuracy or for fine-tuning translational kinetics to produce correct protein folding. We apply the models to compare mitochondrial and nuclear genes from several mammalian species. Model assumptions concerning codon usage are found to affect the estimation of sequence distances (such as the synonymous rate d(S), the nonsynonymous rate d(N), and the rate at the 4-fold degenerate sites d(4)), as found in previous studies, but the new models produced very similar estimates to some old ones. We also develop a likelihood ratio test to examine the null hypothesis that codon usage is due to mutation bias alone, not influenced by natural selection. Application of the test to the mammalian data led to rejection of the null hypothesis in most genes, suggesting that natural selection may be a driving force in the evolution of synonymous codon usage in mammals. Estimates of selection coefficients nevertheless suggest that selection on codon usage is weak and most mutations are nearly neutral. The sensitivity of the analysis on the assumed mutation model is discussed.     

Social and maternal factors affecting duckling survival in eiders Somateria mollissima

1. With the aid of a novel survivorship model, an 8-year field study of social and maternal factors affecting duckling survival in eiders (Somateria mollissima) revealed that duckling survival probability varies in accordance with maternal brood-rearing strategy. This variability in survival provides compelling evidence of different annual fitness consequences between females that share brood-rearing and those that tend their broods alone. Consequently, as prebreeding survival is often a major source of individual variation in lifetime reproductive success, a female's annual, state-dependent (e.g. condition) choice of a brood-rearing strategy can be a critical fitness decision. 2. Variance in duckling survival among lone tender broods was best explained by a model with significant interannual variability in survival, and survivorship tending to increase with increasing clutch size at hatch. Clutch size was correlated positively with female condition. Hatch date and female body condition together affected duckling survival, but their contributions are confounded. We were unable to identify a relationship between female age or experience and duckling survival. 3. Variance in duckling survival among multifemale brood-rearing coalitions was best explained by a model that included the number of tenders, the number of ducklings and interannual variation in how their ratio affected survivorship. Hatch date did not significantly influence survival. 4. Expected duckling survival is higher in early life for lone tenders when compared with multifemale brood-rearing coalitions. However, as ducklings approach 2-3 weeks of age, two or three females was the optimal number of tenders to maximize daily duckling survival. The survivorship advantage of multifemale brood-rearing coalitions was most evident in years of average survival. 5. The observed frequency distribution of female group sizes corresponds with the distribution of offspring survival probabilities for these groups. Evidence for optimal group sizes in nature is rare, but the most likely candidates may be groups of unrelated animals where entry is controlled by the group members, such as for female eiders. 6. Our study demonstrates that differences in social factors can lead to different predictions of lifetime reproductive success in species with shared parental care of self-feeding young.     

Laboratory appraisal of optimal gaseous conditions for growth of zoonotic Helicobacter felis ATCC 49179

An attempt was made to assess the hitherto undescribed optimal gaseous conditions for growth of zoonotic Helicobacter felis, focusing on the ratio of spiral-forms amongst the whole cells examined. The largest mean colony diameter was obtained under the gaseous condition of O₂ 12% and CO₂ 10%. In analyzing the five day old colonies, the highest percentage of spiral forms (85.5%) was observed under the condition of O₂ 18% and CO₂ 5%. In contrast, the lowest percentage of spiral forms (2.3%) was demonstrated under the condition of O₂ 1% and CO₂ 10%. The condition of O₂ 12% and CO₂ 10% was concluded to be optimal for obtaining cells with the largest colony sizes, although colonies proliferated under such conditions definitely contain many more coccoid cells than spiral forms. In culturing H. felis strains, optimal gaseous conditions should be employed according to the purposes or preferences of study designs.     

Polymorphisms of p53 codon 72 and MDM2 promoter 309 and the risk of endometrial cancer

Genetic polymorphisms of p53 and its negative regulator murine double minute 2 homolog (MDM2) have been shown to be closely associated with tumorigenesis in a variety of human cancers. In the present study, single nucleotide polymorphism (SNP) at p53 codon 72 and MDM2 promoter 309 was examined for germline DNA samples from 102 endometrial cancer cases and 95 controls using polymerase chain reaction-based fragment analysis. There were no significant differences in the genotype and allele prevalence between control subjects and endometrial cancer patients for p53 codon 72. The GG genotype frequency of MDM2-SNP309 was statistically higher in endometrial cancer patients than that in normal healthy women when compared with the TG genotype ( P = 0.0088). However, no statistically significant differences were found between the TT and TG or GG genotype frequencies and allele prevalence. Interestingly, the combination of the homozygous Arg/Arg genotype of p53 codon 72 and homozygous GG genotype of MDM2 SNP309 polymorphisms was significantly associated with the risk of endometrial cancer (odds ratio = 3.28, 95% confidence interval = 1.13 to 9.53, P = 0.0212). The homozygous variants of wild p53 codon 72 and mutant MDM2 promoter 309 may cooperatively increase the risk of endometrial cancer in a Japanese population.     

Parent–offspring conflict and selection on egg size in turtles

The trade‐off between offspring size and number can present a conflict between parents and their offspring. Because egg size is constrained by clutch size, the optimal egg size for offspring fitness may not always be equivalent to that which maximizes parental fitness. We evaluated selection on egg size in three turtle species (Apalone mutica, Chelydra serpentina and Chrysemys picta) to determine if optimal egg sizes differ between offspring and their mothers. Although hatching success was generally greater for larger eggs, the strength and form of selection varied. In most cases, the egg size that maximized offspring fitness was greater than that which maximized maternal fitness. Consistent with optimality theory, mean egg sizes in the populations were more similar to the egg sizes that maximized maternal fitness, rather than offspring fitness. These results provide evidence that selection has maximized maternal fitness to achieve an optimal balance between egg size and number.