Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

The kinetochore is the macromolecular protein complex that mediates chromosome segregation. The Dsn1 component is crucial for kinetochore assembly and is phosphorylated by the Aurora B kinase. We found that Aurora B phosphorylation of Dsn1 promotes the interaction between outer and inner kinetochore proteins in budding yeast.     

Hormonal Correlates of Maternal Style in Captive Macaques (Macaca fuscata and M. mulatta)

Previous studies on nonhuman primate maternal styles showed that variation in infant-directed behavior falls along two dimensions, traditionally labeled as protectiveness and rejection. We investigated maternal styles in rhesus (Macaca mulatta) and Japanese (M. fuscata) macaques living in analogous captive social groups, and correlated them with the levels of estrogen metabolites excreted in female feces during the perinatal period. We focally observed mother-infant pairs 3 hours per week during the first 12 weeks of infant life. We collected fecal samples twice a week from each mother, starting 4 weeks before delivery and ending 4 weeks after delivery. Three significant components were extracted by principal component analysis from 15 different infant directed behaviors, each reflecting a different aspect of mothering style: rejection is correlated with behavioral measures of maternal opposition to contact; protectiveness is correlated with maternal solicitude; and independence is correlated with time in contact, grooming and cradling. Levels of estrogen metabolites are significantly correlated to rejection but not to protectiveness or independence, indicating that, in nonhuman primates, individual endocrine changes related to maternal behavior might specifically affect the timing of contact interruption.     

促进人工饲养实验猕猴心理康乐

目的促进实验猕猴心理康乐,既能减少动物异常行为的发生、获得可靠的科学数据,同时也是实现这一珍贵非人灵长类实验动物福利的重要内容。实验猕猴社会化集群、环境优化、婴猴饲养方式是影响动物心理康乐几个较大的因素,本文对其研究进展进行了综述,对推进我国灵长类实验动物福利具有积极作用。     

Rates and Genomic Consequences of Spontaneous Mutational Events in Drosophila melanogaster

Because spontaneous mutation is the source of all genetic diversity, measuring mutation rates can reveal how natural selection drives patterns of variation within and between species. We sequenced eight genomes produced by a mutation-accumulation experiment in Drosophila melanogaster. Our analysis reveals that point mutation and small indel rates vary significantly between the two different genetic backgrounds examined. We also find evidence that ∼2% of mutational events affect multiple closely spaced nucleotides. Unlike previous similar experiments, we were able to estimate genome-wide rates of large deletions and tandem duplications. These results suggest that, at least in inbred lines like those examined here, mutational pressures may result in net growth rather than contraction of the Drosophila genome. By comparing our mutation rate estimates to polymorphism data, we are able to estimate the fraction of new mutations that are eliminated by purifying selection. These results suggest that ∼99% of duplications and deletions are deleterious—making them 10 times more likely to be removed by selection than nonsynonymous mutations. Our results illuminate not only the rates of new small- and large-scale mutations, but also the selective forces that they encounter once they arise.     

弓形虫（Toxoplasma gondii）的PCR检测方法在笼养猕猴群中的应用

目的建立快速、灵敏、特异及检测结果易判断的PCR方法,并应用于大规模猕猴种群的弓形虫常规检测中。同时比较巢式PCR和单一PCR的一致性。方法根据弓形虫保守基因p30（SAG1）设计了内、外两对进行巢式PCR扩增以及B1基因设计一对引物进行单一PCR扩增,将DNA样本进行10倍倍比稀释,以检测巢式PCR反应的灵敏度;并对医学生物学研究所自繁猕猴共150只进行了弓形虫检测。结果巢式PCR检测法检测限度可达10^-3ng/uL,而且方法特异。两种PCR法检测结果基本一致,其中巢式PCR检测阳性率（10％）稍高于单一PCR检测阳性率（8．67％）。结论巢式PCR和一次PCR方法都可应用于猕猴弓形虫的常规检测中,并提示巢式PCR比单一PCR更敏感、检出率更高。     

Body fat,rank, and nutritional status in a captive group of Rhesus Macaques

Using weight and skinfold thickness to calculate relative body fat, the fat content of 21 captive female rhesus macaques was estimated. Although age and. pregnancy had no effect on fat, rank was significant, especially during winter, with high-rank females having the highest fat scores. Rank therefore has a significant effect on the health of captive animals and may also affect the health of individuals in feral groups.     

Rhesus macaque (Macaca mulatta) group formation and housing: wounding and reproduction in a specific pathogen free (SPF) colony.

In the present report, we examined the effects of group formation strategy and corral design on wounding and reproduction rates in rhesus macaques. Specifically, we examined group formation using a staged strategy, in which small groups of animals were introduced incrementally over a period of weeks, and a rapid formation strategy, in which all animals were introduced in 1 day. We also examined group formation using a divided corral design that facilitated visual and social separation of individuals, and an undivided corral design that did not facilitate visual or social separation. Dependent measures were wounding and reproductive rates over each of the 2 years that followed group formation. Results indicate that incrementally releasing subgroups of animals, and using a corral design that provides for visual and social separation of individuals, are effective strategies for reducing rates of traumatic wounding when forming multimale-multifemale rhesus macaque breeding groups. However, it must be noted that differences in formation strategy and corral design did not lead to higher reproductive rates. We conclude that incrementally releasing animals in hierarchical subgroups, and using a divided vs. undivided housing design, reduced intra-group wounding and associated demands on veterinary and animal management resources following formation of rhesus macaque breeding groups.     

Birth Patterns in Wild and Captive Lion-Tailed Macaques (Macaca silenus)

During a 5-yr study of lion-tailed macaques in their natural habitat, we found that: 1) most births occurred from January to April (70%) and from September to December (19%), showing a bimodal pattern with a major and a minor birth peak; 2) the period of peaks remained the same over 5 yr; and 3) a similar pattern of birth peaks occurred both in groups in large forest complexes that had overlapping home ranges with other groups and in single groups that were isolated in forest fragments in the same region but with similar ecological conditions. The results suggest more of a birth seasonality than mere breeding synchronization in the wild lion-tailed macaques. We also analyzed data on births in captivity in European Zoos for 10 yr. We observed no seasonality or peaks in births, and the pattern was the same over the years. Data on rainfall suggest that resource availability in the wild habitat may not be uniform throughout the year; hence, ecological factors may play an important role in determination of birth patterns in the natural habitats of lion-tailed macaques.     

Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize

Grain produced from cereal crops is a primary source of human food and animal feed worldwide. To understand the genetic basis of seed-size variation, a grain yield component, we conducted a genome-wide scan to detect evidence of selection in the maize Krug Yellow Dent long-term divergent seed-size selection experiment. Previous studies have documented significant phenotypic divergence between the populations. Allele frequency estimates for ∼3 million single nucleotide polymorphisms (SNPs) in the base population and selected populations were estimated from pooled whole-genome resequencing of 48 individuals per population. Using F_ST values across sliding windows, 94 divergent regions with a median of six genes per region were identified. Additionally, 2729 SNPs that reached fixation in both selected populations with opposing fixed alleles were identified, many of which clustered in two regions of the genome. Copy-number variation was highly prevalent between the selected populations, with 532 total regions identified on the basis of read-depth variation and comparative genome hybridization. Regions important for seed weight in natural variation were identified in the maize nested association mapping population. However, the number of regions that overlapped with the long-term selection experiment did not exceed that expected by chance, possibly indicating unique sources of variation between the two populations. The results of this study provide insights into the genetic elements underlying seed-size variation in maize and could also have applications for other cereal crops.     

Temperament in Rhesus,Long‐Tailed,and Pigtailed Macaques Varies by Species and Sex

Temperament differs among individuals both within and between species. Evidence suggests that differences in temperament of group members may parallel differences in social behavior among groups or between species. Here, we compared temperament between three closely related species of monkey—rhesus (Macaca mulatta), long‐tailed (M. fascicularis), and pigtailed (M. nemestrina) macaques—using cage‐front behavioral observations of individually housed monkeys at a National Primate Research Center. Frequencies of 12 behaviors in 899 subjects were analyzed using a principal components analysis to identify temperament components. The analysis identified four components, which we interpreted as Sociability toward humans, Cautiousness, Aggressiveness, and Fearfulness. Species and sexes differed in their average scores on these components, even after controlling for differences in age and early‐life experiences. Our results suggest that rhesus macaques are especially aggressive and unsociable toward humans, long‐tailed macaques are more cautious and fearful, and pigtailed macaques are more sociable toward humans and less aggressive than the other species. Pigtailed males were notably more sociable than any other group. The differences observed are consistent with reported variation in these species’ social behaviors, as rhesus macaques generally engage in more social aggression and pigtailed macaques engage in more male–male affiliative behaviors. Differences in predation risks are among the socioecological factors that might make these species‐typical behaviors adaptive. Our results suggest that adaptive species‐level social differences may be encoded in individual‐level temperaments, which are manifested even outside of a social context. Am. J. Primatol. 75:303‐313, 2013. © 2012 Wiley Periodicals, Inc.     

ORIGINAL ARTICLE: Epithelioid hemangioendothelioma in the right auricle of an adult,male Rhesus macaque (Macaca mulatta)

Abstract Background A 9‐year‐old, male castrate, Rhesus macaque was euthanized following a prolonged history of chronic renal failure. Results Necropsy revealed a proliferative lesion within the right cardiac auricle composed of neoplastic epithelioid cells which infiltrated the myocardium and frequently exhibited intracytoplasmic luminae. Cells multifocally exhibited strong cytoplasmic immunoreactivity for Factor VIII‐related protein (von Willebrand’s factor). Conclusions The histological characteristics of this tumor are consistent with a diagnosis of epithelioid hemangioendothelioma, an intermediate‐grade vasoformative neoplasm which has to our knowledge not previously been reported in the heart of a non‐human species.     

SHIV-XJ02170感染恒河猴后期的传代特点和env基因变异

目的研究SHIV-XJ02170在中国恒河猴感染后期传代过程中病毒和宿主的变化特点,并分析env基因的序列变异。方法将感染中国恒河猴G0401V后期（5年）的SHIV-XJ02170病毒垂直传代2只猴（G0401V→G0402V→0403V）,同时,剔除G0401V猴CD8＋T细胞使潜伏的病毒大量复制后传代1只猴（G0401V→G0404V）,应用流式细胞术、病毒载量测定、序列分析等方法研究该病毒在猴体内长期适应后的病毒和免疫学指标及序列变异特点。结果 G0401V在感染后期仍能稳定传代,且表现出毒力增强的特点。其传代猴G0402V在传代后41 d死亡,外周血CD4＋T淋巴细胞衰竭,仅为43个/mL,符合艾滋病感染猴快速进展型的特征。剔除体内CD8＋T细胞之后的传代猴G0404V的表现类似G0401V,即长期低水平的病毒血症水平。env基因序列分析发现SHIV-XJ02170在G0401V体内长期适应后发生了可遗传的序列变异,并引起糖基化位点的改变。结论 SHIV-XJ02170在猴体长期适应后的传代过程中表现出向强毒株过渡的特征,为进行SHIV-XJ02170感染性克隆的构建奠定了良好的实验基础。     

Marfan syndrome: whole-exome sequencing reveals de novo mutations,second gene and genotype–phenotype correlations in the Chinese population

Marfan syndrome (MFS) is a dominant monogenic disease caused by mutations in fibrillin 1 (FBN1). Cardiovascular complications are the leading causes of mortality among MFS. In the present study, a whole-exome sequencing of MFS in the Chinese population was conducted to investigate the correlation between FBNI gene mutation and MFS. Forty-four low-frequency harmful loci were identified for the FBN1 gene in HGMD database. In addition, 38 loci were identified in the same database that have not been related to MFS before. A strict filtering and screening protocol revealed two patients of the studied group have double mutations in the FBN1 gene. The two patients harboring the double mutations expressed a prominent, highly pathological phenotype in the affected family. In addition to the FBN1 gene, we also found that 27 patients had mutations in the PKD1 gene, however these patients did not have kidney disease, and 16 of the 27 patients expressed aortic related complications. Genotype-phenotype analysis showed that patients with aortic complications are older in the family, aged between 20 and 40 years.     

A cross-disorder dosage sensitivity map of the human genome

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SHIV1157ipd3N4细胞适应株的制备及其生物特性

目的体外制备SHIV1157ipd3N4病毒中国恒河猴细胞适应株,在细胞水平和中国恒河猴体内评价其生物学特性。方法用SHIV1157ipd3N4病毒阴道感染中国恒河猴,在血浆病毒载量高峰期采血分离外周血单核淋巴细胞（PBMCs）,与正常中国恒河猴PBMCs共培养。定期测定培养液中的P24抗原水平。当病毒复制达高峰期时收集培养上清,分装并冻存。测定病毒RNA载量、P24抗原浓度和TCID50。静脉感染中国恒河猴,研究该批次SHIV1157ipd3N4在体内的病毒学、免疫学指标变化及变异情况,分析其基本的生物学特性。结果本研究共制备了243 mL SHIV1157ipd3N4病毒原液,gp120序列分析表明病毒未发生变异,CCR5的嗜性也未发生改变。病毒载量为1.586×108 copies/mL,P24抗原水平为1.16×103 pg/mL,TZM-bl细胞测定病毒的TCID50为3.16×103/mL。1 mL SHIV1157ipd3N4静脉成功感染中国恒河猴G1004V,高峰期病毒载量达到1.0×106 copies/mL以上。结论此次制备的SHIV1157ipd3N4细胞适应株生物学特性稳定,适合作为毒种库构建SHIV1157ipd3N4/中国恒河猴模型。     

Allozyme Variation Patterns and Multiple Hybridization Origins: Clonal Variation Among Four Sibling Parthenogenetic Caucasian Rock Lizards

Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexualis, D.uzzelli, D.sapphirina, and D.bendimahiensis found seven clones and five variable loci. The data supported the hypothesis that D.raddei and D.valentini are the parental species of all four parthenogens. Variation patterns in Darevskia were summarized. Species that originated from a single F₁ typically consisted of one widespread clone with a few rare clones. Species with multiple origins displayed variation only slightly higher than species with a single origin. This is contrary to other genera of parthenogenetic lizards, in which cases massive clonal variations were observed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Current challenges and solutions of de novo assembly

Background: Next-generation sequencing (NGS) technologies have fostered an unprecedented proliferation of high-throughput sequencing projects and a concomitant development of novel algorithms for the assembly of short reads. However, numerous technical or computational challenges in de novo assembly still remain, although many new ideas and solutions have been suggested to tackle the challenges in both experimental and computational settings.Results: In this review, we first briefly introduce some of the major challenges faced by NGS sequence assembly. Then, we analyze the characteristics of various sequencing platforms and their impact on assembly results. After that, we classify de novo assemblers according to their frameworks (overlap graph-based, de Bruijn graph-based and string graph-based), and introduce the characteristics of each assembly tool and their adaptation scene. Next, we introduce in detail the solutions to the main challenges of de novo assembly of next generation sequencing data, single-cell sequencing data and single molecule sequencing data. At last, we discuss the application of SMS long reads in solving problems encountered in NGS assembly.Conclusions: This review not only gives an overview of the latest methods and developments in assembly algorithms, but also provides guidelines to determine the optimal assembly algorithm for a given input sequencing data type.     

The influence of birth timing upon infant growth and survival in Captive Rhesus Macaques (Macaca mulatto)

Weights, growth rates, and mortality data of 815 captive-born Macaca mulattainfants were studied to determine if date of birth influences infant growth and survival. The six groups studied displayed a unimodal spring-summer birth season that has become systematically more restricted since 1977. Males exhibited higher rates of stillbirth and neonatal death and were more frequently born outside the normal birth season, when infant mortality was more common. Within the normal birth season, infant weight increased linearly with birth date, and infant growth rate declined linearly with birth date. Female infants with weights and growth rates near the developmental norm, especially those born in the middle of the birth season, have the greatest probability of survival. Males are more likely to survive if their weights and growth rates exceed the developmental norm, and thus male infants might be initially more costly to produce than female infants. These results are inconsistent with the hypothesis that offspring of high-ranking males, which conceived predominantly in the first third of the breeding season, enjoy a selective advantage.