基因表达与mRNA结构的关系

基因的转录调控和转录后水平的调控在基因表达过程中起着重要作用。mRNA的结构与基因表达调控的关系非常密切。目前对于mRNA结构对表达的影响因素,主要集中于起始密码子和S-D序列的结构和间隔长度、基因和基因间的间隔区序列和长度,5’末端与3’末端非翻译区、多聚（A）尾、内含子序列对翻译起始效率、发夹结构对mRNA的稳定性的影响和mRNA翻译起始区等对基因表达影响。     

tRNA丰度与基因表达的关系

tRNA作为蛋白质合成过程中重要参与成分之一 ,其种类和含量的多少会在一定程度上直接或间接地影响到基因表达的速率和时空性 ,是生物在长期进化过程中调节和控制基因表达的主要手段之一。对tRNA丰度与基因表达的关系进行了综述 ,并指出其在基因工程中的重要地位。     

The Impact of Gene Expression Variation on the Robustness and Evolvability of a Developmental Gene Regulatory Network

Regulatory interactions buffer development against genetic and environmental perturbations, but adaptation requires phenotypes to change. We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocentrotus purpuratus. We find extensive variation in gene expression in this network throughout development in a natural population, some of which has a heritable genetic basis. Switch-like regulatory interactions predominate during early development, buffer expression variation, and may promote the accumulation of cryptic genetic variation affecting early stages. Regulatory interactions during later development are typically more sensitive (linear), allowing variation in expression to affect downstream target genes. Variation in skeletal morphology is associated primarily with expression variation of a few, primarily structural, genes at terminal positions within the network. These results indicate that the position and properties of gene interactions within a network can have important evolutionary consequences independent of their immediate regulatory role.     

形目12种鸟类线粒体细胞色素b基因序列差异及其系统发育关系

采用PCR直接测序方法首次对形目 (Charadriiformes) 12种鸟类 :蒙古沙 (Charadriusmongolus)、环颈(Charadriusalexandrinus)、大杓鹬 (Numeniusmadagascariensis)、白腰杓鹬 (Numeniusarquata)、中杓鹬 (Numeniusphaeo pus)、红脚鹬 (Tringatotanus)、林鹬 (Tringaglareola)、翘嘴鹬 (Xenuscineres)、翻石鹬 (Arenariainterpres)、大滨鹬 (Calidristenuirostris)、反嘴鹬 (Recurvirostraavosetts)和砺鹬 (Haematopusostralensis)线粒体cytb基因全序列进行测定 ,并以白鹳(Ciconiaciconia)的同源序列作为外群构建系统发生树。经比对 ,形目 12种鸟类线粒体cytb基因全序列均包括1143bp ,序列间未见有插入和缺失 ,共有 381个变异位点 ,种间序列差异值为 5 16 %～ 16 0 1%。重建的系统树将形目 12种鸟类分为 2个支系 :第 1支系包括红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬、中杓鹬、大杓鹬和白腰杓鹬 ,其中红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬聚为一支 ,中杓鹬、大杓鹬和白腰杓鹬聚为另一支 ;第 2支系包括蒙古沙、环颈、反嘴鹬和砺鹬 ,其中反嘴鹬与砺鹬互为姐妹群 ,然后再与属的两个种蒙古沙和环颈组成的姐妹群构成并系群。分子证据提示 :第 1支系中各属间及种间的系统关系与形态学研     

The Relationship between Species Diversity and Genetic Structure in the Rare Picea chihuahuana Tree Species Community,Mexico

Species diversity and genetic diversity, the most basic elements of biodiversity, have long been treated as separate topics, although populations evolve within a community context. Recent studies on community genetics and ecology have suggested that genetic diversity is not completely independent of species diversity. The Mexican Picea chihuahuana Martínez is an endemic species listed as “Endangered” on the Red List. Forty populations of Chihuahua spruce have been identified. This species is often associated with tree species of eight genera in gallery forests. This rare Picea chihuahuana tree community covers an area no more than 300 ha and has been subject of several studies involving different topics such as ecology, genetic structure and climate change. The overall aim of these studies was to obtain a dataset for developing management tools to help decision makers implement preservation and conservation strategies. However, this unique forest tree community may also represent an excellent subject for helping us to understand the interplay between ecological and evolutionary processes in determining community structure and dynamics. The AFLP technique and species composition data were used together to test the hypothesis that species diversity is related to the adaptive genetic structure of some dominant tree species (Picea chihuahuana, Pinus strobiformis, Pseudotsuga menziesii and Populus tremuloides) of the Picea chihuahuana tree community at fourteen locations. The Hill numbers were used as a diversity measure. The results revealed a significant correlation between tree species diversity and genetic structure in Populus tremuloides. Because the relationship between the two levels of diversity was found to be positive for the putative adaptive AFLP detected, genetic and species structures of the tree community were possibly simultaneously adapted to a combination of ecological or environmental factors. The present findings indicate that interactions between genetic variants and species diversity may be crucial in shaping tree communities.     

(行鸟)形目12种鸟类线粒体细胞色素b基因序列差异及其系统发育关系

采用PCR直接测序方法首次对Hang形目(Charadriiformes)12种鸟类：蒙古沙Hang(Charadrius mongolus)、环颈Hang(Charadrius alexandrinus)、大杓鹬(Numenius madagascariensis)、白腰杓鹬(Numenius arquata)、中杓鹬（Numenius phaeo-pus）、红脚鹬（Trina totanus）、林鹬（Trina alareola）、翘嘴鹬（Xenus cineres）、翻石鹬（Arenaria interpres）、大滨鹬（Calidris teruarostris)、反嘴鹬（Recurvirostra avosetts)和砺鹬（Haematopus ostralensis)线粒体cyt b基因全序列进行测定,并以白鹳（Ciconia ciconia)的同序列作为外群杓建系统发生树。经比对,Hang形目12种鸟类线粒体cyt b基因全序列均包括1143bp,序列间未见有插入和缺失,共有381个变异位点,种间序列差异值为5．16％—16．01％。重建的系统树将Hang形目12种鸟类分为2个支系：第1支系包括红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬、中杓鹬、大杓鹬和白腰杓鹬,其中红脚鹬、林鹬、翻石鹬、大滨鹬、翘嘴鹬聚为一支,中杓鹬、大杓鹬和白腰杓鹬聚为另一支;第2支系包括蒙古沙Hang、环颈Hang、反嘴鹬和硕鹬,其中反嘴鹬与砺鹬互为姐妹群,然后再与Hang属的两个种蒙古沙Jamg和环Hang组成的姐妹群构成并系群。分子证据提示：第1支系中各属问及种间的系统关系与形态学研究结果相吻合;第2支系中的反嘴鹬与Hang鹬之间的亲缘关系较近,两者聚为姐妹群,提示将这两个类群合并为一个亚科——反嘴葫亚科更为合理,与码亚科共同组成Hang科,与核型研究结果和Sibley在新分类体系中将码科分为反嘴鹬亚科和Hang亚科、反嘴鹬族和砺鹬族属于反嘴鹬亚科的观点相一致。     

Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis Plants

Gene expression profiling studies are usually performed on pooled samples grown under tightly controlled experimental conditions to suppress variability among individuals and increase experimental reproducibility. In addition, to mask unwanted residual effects, the samples are often subjected to relatively harsh treatments that are unrealistic in a natural context. Here, we show that expression variations among individual wild-type Arabidopsis thaliana plants grown under the same macroscopic growth conditions contain as much information on the underlying gene network structure as expression profiles of pooled plant samples under controlled experimental perturbations. We advocate the use of subtle uncontrolled variations in gene expression between individuals to uncover functional links between genes and unravel regulatory influences. As a case study, we use this approach to identify ILL6 as a new regulatory component of the jasmonate response pathway.     

火与外来植物相互关系的研究进展

入侵种对本地的生态系统和生物多样性均有不良的影响,严重的会造成物种的灭绝和生态系统的崩溃,这已在全球范围引起广泛关注.在植物外来种与火生态因子的作用研究中发现,火与外来种的关系随物种生物学特性、火作用的时间、频度、强度不同而不同,火有时会有效地抑制外来种的生长和入侵,有时会促进一些外来种的生长和入侵.反之,一些外来种会对火的产生起到积极的作用,一些外来种又会抑制火的发生.火作为控制入侵种的一种方法,经科学地运用,可对某些入侵种起到有效的控制作用.     

Characteristics of Neutral and Deleterious Protein-Coding Variation among Individuals and Populations

Whole-genome and exome data sets continue to be produced at a frenetic pace, resulting in massively large catalogs of human genomic variation. However, a clear picture of the characteristics and patterns of neutral and deleterious variation within and between populations has yet to emerge, given that recent large-scale sequencing studies have often emphasized different aspects of the data and sometimes appear to have conflicting conclusions. Here, we comprehensively studied characteristics of protein-coding variation in high-coverage exome sequence data from 6,515 European American (EA) and African American (AA) individuals. We developed an unbiased approach to identify putatively deleterious variants and investigated patterns of neutral and deleterious single-nucleotide variants and alleles between individuals and populations. We show that there are substantial differences in the composition of genotypes between EA and AA populations and that small but statistically significant differences exist in the average number of deleterious alleles carried by EA and AA individuals. Furthermore, we performed extensive simulations to delineate the temporal dynamics of deleterious alleles for a broad range of demographic models and use these data to inform the interpretation of empirical patterns of deleterious variation. Finally, we illustrate that the effects of demographic perturbations, such as bottlenecks and expansions, often manifest in opposing patterns of neutral and deleterious variation depending on whether the focus is on populations or individuals. Our results clarify seemingly disparate empirical characteristics of protein-coding variation and provide substantial insights into how natural selection and demographic history have patterned neutral and deleterious variation within and between populations.     

染色质结构与基因表达调控

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Genetic Factors in Susceptibility: Serum PON1 Variation Between Individuals and Species

In mammals, serum paraoxonase (PON1) is tightly associated with high-density lipoprotein (HDL) particles. In human populations, PON1 exhibits a substrate dependent activity polymorphism determined by an Arg/Gln (R/Q) substitution at amino acid residue 192. The physiological role of this protein appears to be involvement in the metabolism of oxidized lipids. Several studies have suggested that the PON1_R192 allele may be a risk factor in coronary artery disease. PON1 also plays an important role in the metabolism of organophosphates including insecticides and nerve agents. The PON1_R192 isoform hydrolyzes paraoxon rapidly, but diazoxon, soman and sarin slowly compared with the PON1_Q192 isoform. Both PON1 isoforms hydrolyze phenylacetate at approximately the same rate, while PON1_R192 hydrolyzes chlorpyrifos oxon slightly faster than PON_Q192. Animal model studies involving injection of purified rabbit PON1 into mice clearly demonstrated the ability of PON1 to protect cholinesterases from inhibition by OP compounds. The consequence of having low PON1 levels has been addressed with toxicology studies in PON1 knockout mice. These mice showed dramatically increased sensitivity to chlorpyrifos oxon, diazoxon and some increased sensitivity to the respective parent compounds. These observations are consistent with earlier studies that showed a good correlation between high rates of OP hydrolysis by serum PON1 and resistance to specific OP compounds. They are also consistent with the observations that newborns have an increased sensitivity to OP toxicity, due in part to their not expressing adult PON1 levels for weeks to months after birth, depending on the species. Together, these studies point out the importance of considering the genetic variability of PON1₁₉₂ isoforms and levels as well as the developmental time course of PON1 appearance in serum in developing risk assessment models     

基于表达及网络拓扑结构挖掘动脉粥样硬化风险疾病基因

基于功能基因组信息、网络拓扑结构信息整合分析方法,利用基因表达谱数据和蛋白质互作数据挖掘动脉粥样硬化(AS)风险疾病基因,为从基因组层面研究动脉粥样硬化提供了新的视角．经过差异表达分析,支持向量机(SVM)的机器学习方法双重筛选,可以鉴别出可信度水平较高的风险疾病基因,对于研究动脉粥样硬化疾病基因在网络中的拓扑性质,建立基因与疾病发生发展过程的联系,提供了新的思路．得到了巨噬细胞样本中59个风险疾病基因,泡沫细胞中61个风险疾病基因．这些风险基因与已知疾病基因共享大部分动脉粥样硬化病变相关生物学过程及信号通路．并应用到对其他复杂疾病致病机理的研究中．