Population genetic variation in genome-wide gene expression

Evolutionary biologists seek to understand which traits display variation, are heritable, and influence differential reproduction, because such traits respond to natural selection and underlie organic evolution. Selection acts upon individual differences within a population. Whether individual differences within a natural population include variation in gene expression levels has not yet been addressed on a genome-wide scale. Here we use DNA microarray technology for measuring comparative gene expression and a refined statistical analysis for the purpose of comparing gene expression levels in natural isolates of the wine yeast Saccharomyces cerevisiae. A method for the Bayesian analysis of gene expression levels is used to compare four natural isolates of S. cerevisiae from Montalcino, Italy. Widespread variation in amino acid metabolism, sulfur assimilation and processing, and protein degradation-primarily consisting of differences in expression level smaller than a factor of 2-is demonstrated. Genetic variation in gene expression among isolates from a natural population is present on a genomic scale. It remains to be determined what role differential gene expression may play in adaptation to new or changing environments.     

微生物转录组学技术研究进展

随着分子生物技术的不断进步,转录组学技术已广泛应用于生物基因表达水平的研究。近年来,针对微生物转录组学的研究技术也在不断发展。在基因层面上,由片段RNA与微生物样本进行互补验证,发展到直接对全长RNA进行测序得到序列信息;在空间上,由传统群体转录组发展到空间、单细胞以及表观等层面的研究。随着转录组学技术在微生物研究领域中的应用,相应的缺陷也逐渐显现并不断被完善。本文主要是对微生物研究方面传统的和新型的转录组学技术进行了总结归纳,为微生物转录组学研究提供参考。     

Symposium review: International symposium on the implications of salmonid growth variation

In Aberdeen, Scotland, in July 2000, aninternational symposium was held to presentresearch concerning the consequences of growthvariation for the ecology, evolution, andmanagement of salmonid fish. Presentationscovered important topics including linksbetween growth and mortality, interactionsbetween growth and life history, tradeoffsbetween growth and other fitness aspects, andevolutionary implications of growth variation. In addition, the symposium served as a showcaseof new approaches and technologies in salmonidresearch. In this review, I provide anoverview of the presentations, and summarizesome of the major emergent themes of thesymposium.     

Habitat-specific life-history variation in the Caribbean termite Nasutitermes acajutlae (Isoptera: Termitidae)

Abstract.  1. Population and individual colony characteristics of Nasutitermes acajutlae on St John, U.S. Virgin Islands were studied over a 5-year period.
2. Four habitat types (dry forests, moist forests, sparse vegetation, and woodlands) were sampled for N. acajutlae , using quadrat-based methods. Lying dead wood was also quantified in the same sites.
3. Habitats differed significantly in the volume of lying dead wood, and total termite nest volume within quadrats was positively related to wood volume. It was hypothesised that the volume of dead wood affected growth, reproduction, and yearly survival of individual colonies.
4. In a sample of > 100 colonies assessed in 1998, 2000, 2001, and 2002, no significant differences in the growth rate of colonies (= increase in nest volume) could be found between habitat types; however, colonies in sparse vegetation were smaller, less likely to survive, and reproduced at a smaller size compared with those in the other three habitats.
5. Overall nest volume in sparse vegetation was high, compared with dry and moist forest, but colonies showed, on average, poorer survival (interpreted as lower fitness), and produced alates at an early stage of development. Optimum habitat characteristics for N. acajutlae may include not only favourable microclimate but also the reliable acquisition of new dead wood after storms.     

Programs of Gene Expression During the Laying Down of Memory Formation as Revealed by DNA Microarrays

Many experiments in the past have demonstrated the requirement of de novo gene expression during memory formation. In contrast to the initial reductionistic view that genes relevant to learning and memory would be easily found and would provide a simple key to understand this brain function, it is becoming apparent that the genetic contribution to memory is complex. Previous approaches have been focused on individual genes or genetic pathways and failed to address the massively parallel nature of genome activities and collective behavior of the genes that ultimately control the molecular mechanisms underlying brain function. In view of the broad variety of genes and the cross talk of genetic pathways involved in this regulation, only gene expression profiles may reflect the complete behavior of regulatory pathways. In this review we illustrate how DNA microarray-based gene expression profiling may help to dissect and analyze the complex mechanisms involved in gene regulation during the acquisition and storage of memory in the mammalian brain.     

Geographic variation in diapause incidence, life-history traits, and climatic adaptation in Drosophila melanogaster

In Drosophila melanogaster, exposure of females to low temperature and shortened photoperiod can induce the expression of reproductive quiescence or diapause. Diapause expression is highly variable within and among natural populations and has significant effects on life-history profiles, including patterns of longevity, fecundity, and stress resistance. We hypothesized that if diapause expression is associated with overwintering mechanisms and adaptation to temperate environments, the frequency of diapause incidence would exhibit a latitudinal cline among natural populations. Because stress resistance and reproductive traits are also clinal in this species, we also examined how patterns of fecundity and longevity varied with geography and how stress resistance and associated traits differed constitutively between diapause and nondiapause lines. Diapause incidence was shown to vary predictably with latitude, ranging from 35% to 90% among natural populations in the eastern United States Survivorship under starvation stress differed between diapause and nondiapause lines; diapause phenotypes were also distinct for total body triglyceride content and the developmental distribution of oocytes in the ovary following stress exposure. Patterns of longevity, fecundity, and ovariole number also varied with geography. The data suggest that, for North American populations, diapause expression is functionally associated with overwintering mechanisms and may be an integral life-history component in natural populations.     

25-O-乙酰升麻醇-3-0-β-D-木糖苷对HepG2细胞基因表达的影响

研究环菠萝蜜烷三萜化合物25-0-乙酰升麻醇-3-0-β-D-木糖苷对肿瘤细胞HepG2基因表达的影响,探讨其细胞毒作用机制。利用人低密度cDNA microarray研究细胞基因表达的改变,发现9个表达改变基因,6个下调,3个上调。结论表明25—O-乙酰升麻醇-3—0-β-D-木糖苷对HepG2细胞的细胞毒性与MAPK等信号传导途径相关。     

用限制性cDNA文库制作K562细胞基因表达谱芯片探针

以人红白血病K562细胞为材料,应用限制性显示PCR（RD-PCR）技术构建cDNA文库,该文库通过PCR引物3′端延伸两个不同碱基形成136对引物对cDNA进行限制性扩增,得到136组不同的PCR扩增产物,纯化后与载体连接并转化细菌,即为限制性cDNA文库,根据不同的分组进行克隆的鉴定和分离。并进行大量扩增制备cDNA芯片探针,该方法构建的文库因经过了限制性分组扩增,每组均含有特定的cDNA,因而大大加快了随后克隆的分离 和鉴定的速度,为基因芯片探针制备提供了一个新方法。     

应用cDNA微阵列技术筛选大鼠脊髓损伤修复相关基因

脊髓损伤是一类常见的、高致残率的中枢神经系统疾病,由于多种复杂因素影响其损伤后的修复过程,损伤脊髓的再生能力非常有限。本研究采用cDNA微阵列技术筛选大鼠脊髓损伤后出现的差异表达基因。实验组动物在T8-T9进行脊髓全横断手术,对照组动物只打开椎板;4．5d后取脊髓进行RNA提取并在反转录过程中进行Cy3／Cy5标记,然后与预制的、带有4041条特异性探针的芯片进行杂交。Cy5／Cy3信号比值≥2．0视为脊髓损伤后出现差异表达的基因。通过筛选,我们得到了65个上调表达基因（21个已知基因,30个已知EST和14个未知基因）和79个下调基因（20个已知基因,42个已知EST和17个未知基因）。进一步通过半定量RT-PCR对其中的5个上调已知基因（Timpl,Tagln,Vim,Fc gamma receptor,Ctss）和三个下调已知基因（stearyl-CoA desaturase,F2,Ensa）的表达情况进行了验证,结果显示与芯片结果一致。这些基因可能在脊髓损伤后的修复过程中起一定的作用,对其深入研究将有助于揭示脊髓损伤修复的分子机制。     

Do northern riverine anadromous Arctic charr Salvelinus alpinus and sea trout Salmo trutta overwinter in estuarine and marine waters?

By use of acoustic telemetry, the present study showed that both riverine anadromous brown trout (sea trout) Salmo trutta and Arctic charr Salvelinus alpinus in a north Norwegian river descended the river within the first 4 months after spawning in late September and spent long parts of the remaining winter period in the estuary and also possibly partly in salt water. This contradicts the general assumption, based on studies of lake‐dwelling populations, that both species, and in particular S. alpinus, overwinter and spend 9–11 months in fresh water at northern latitudes and the rest of the year in salt water.     

总RNA和mRNA来源的探针与cDNA芯片杂交的差异研究

提取BEP2D细胞的总RNA并按两种方式进行cDNA芯片探针的标记,一种是将100μg BEP2D细胞的总RNA利用逆转录法直接标记成荧光探针,另一种是先从100μg BEP2D细胞的总RNA中分离出mRNA,然后再标记成荧光探针。将两份标记好的探针同时与含有230个基因的cDNA芯片杂交。杂交后的芯片经Axon4100B扫描仪扫描,发现两种方式标记探针的一致性为93．04％,并且mRNA来源探针杂交后的荧光信号值较总RNA的弱。探讨了这两种方法标记探针在基因芯片表达谱研究中的差异性,目的是为利用这两种方法标记探针进行基因表达谱研究提供一些依据。     

Environmental correlates of life-history variation in juvenile chinook salmon, Oncorhynchus tshawytscha (Walbaum)

Throughout its native North Pacific, the chinook salmon, Oncorhynchus tshawytscha (Walbaum), exists as twolife-history types that aredistinguished by the age at which juvenile salmon migrate to sea as smolts. 'Stream-type' chinook migrate seaward after I or more years of feeding in fresh water, whereas 'ocean-type' fish migrate to sea as newly emerged fry or after 2–3 months in fresh water. Stream-type chinook predominate in populations distant from the sea south of 56° N, and in both inland and coastal populations north of this point. By contrast, ocean-type chinook predominate in coastal populations south of 56° N, but are rare in populations in more northerly latitudes. Stream-type populations are associated with areas of low 'growth opportunity' (as measured by temperature and photoperiod regimes) and/or areas distant from the sea compared to ocean-type. Geographic variability in juvenile life history is suggested to result, in part, from environmental modulation of smolting timing via differences in growth opportunity among geo-graphic areas. In addition, differences in migration distance and temperature regime may result in selection for different sizes at migration among populations which, through differences in growth opportunity, might promote geographic variability in age at seaward migration.     

基因芯片表达谱数据的预处理分析

基因芯片数据的预处理是一个十分关键的步骤,通过数据过滤获取需要的数据、数据转换满足正态分布的分析要求、缺失值的估计弥补不完整的数据、数据归一化纠正系统误差等处理为后续分析工作做准备,预处理分析的重要性并不亚于基因芯片的后续分析,它将直接影响后续分析是否能得到预期的结果.本文重点综述了cDNA芯片的数据预处理,简要地概述寡核苷酸芯片的数据预处理.