植物物种形成的模式与机制

物种形成是指由已有的物种通过各种进化机制进化出新物种的过程。持续不断的物种形成产生了地球上灿烂的生物物种多样性。然而,研究人员对物种形成的模式与机制的了解却非常有限。一直以来,谱系分裂被认为是最重要的物种形成模式,但在植物中,谱系融合,即通过杂交形成新物种的过程,也是一个非常重要的物种形成模式。经过几十年的研究才逐渐认识到,生殖隔离是差异适应和遗传漂变的副产品,而不是物种形成的前提。相比合子形成后隔离,合子形成前的隔离在物种形成过程中更早地发挥作用。合子形成前的隔离,尤其是生态地理的隔离是植物中最重要的隔离机制。一些基于QTLs分析的研究发现,基因组中的少数主效位点在物种形成中起了关键作用,并且这些位点往往受到自然选择的作用。适应性辐射往往发生在隆起的山脉和新形成的岛屿上,很可能与这些地方能够提供很多可利用的生态位有关。最新的物种形成理论认为,基因是物种形成的基本单位,不同的物种可以在非控制物种差异适应性状的位点上存在基因流。这一观点为植物物种形成的研究提供了新的思路。随着植物物种形成研究的深入,越来越多植物物种形成基因被分离,包括花色素苷合成通路和S-基因座上的一些关键基因,揭示了植物物种形成的分子机制。前期的研究主要集中在模式植物和农作物上,许多生态上非常有趣的非模式植物还未得到广泛的研究。在未来的研究中,还需要更多来自非模式植物的例子以全面理解植物物种形成的多样化机制。     

赤链蛇不同组织Sox基因表达的RT-PCR分析

采用RT-PCR技术,研究了赤链蛇不同组织Sox基因的表达。通过PCR产物直接克隆法和SSCP技术筛选阳性克隆,分析了雄性睾丸和雌性卵巢组织中的Sox基因序列。结果显示,在赤链蛇雌雄成体组织中,Sox基因在睾丸、卵巢、脑和脾组织中均有不同程度的表达,而在雌雄成体肌肉组织中均无表达,显示该基因表达有一定的组织特异性。序列分析显示睾丸组织中表达的是DRSox3,卵巢组织中表达的是DRSox22。在Sox家族中,Sox3表达于中枢神经系统和尿生殖嵴的发育过程中;Sox22则表达于多种组织和神经系统中,可横跨CNS和PNS的整个过程。此结果表明Sox基因不仅在性别决定中起作用,还可能在胚胎发育过程中担负重要功能。     

基因流存在条件下的物种形成研究述评:生殖隔离机制进化

物种形成过程是生物多样性形成的基础, 长期以来一直是进化生物学的中心议题之一。传统的异域物种形成理论认为, 地理隔离是物种分化的主要决定因子, 物种形成只有在种群之间存在地理隔离的情况下才能发生。近年来, 随着种群基因组学的发展和溯祖理论分析方法的完善, 种群间存在基因流情况下的物种形成成为进化生物学领域新的研究焦点。物种形成过程中是否有基因流的发生?基因流如何影响物种的形成与分化?基因流存在条件下物种形成的生殖隔离机制是什么?根据已发表的相关文献资料, 作者综述了当前物种形成研究中基因流的时间和空间分布模式、基因流对物种分化的影响以及生殖隔离机制形成等问题, 指出基因流存在条件下的物种形成可能是自然界普遍发生的一种模式。     

肿瘤-睾丸-脑抗原家族新成员PNMA5的克隆和表达谱分析

综合运用几种生物信息学数据库 ,分析了人类X染色体上可能的未知基因 ,筛选获得一个新的肿瘤抗原基因并克隆鉴定了它的全长cDNA .该基因全长为 3194bp ,编码一个 4 48个氨基酸残基的蛋白质 ,它与肿瘤 睾丸 脑抗原家族成员PNMA1、PNMA2及PNMA3有很高的同源性 ,命名为PNMA5 .在 16种人正常组织中 ,PNMA5仅在睾丸与脑中表达 ;而在所检测的肝癌、胃癌、肠癌、肺癌、乳腺癌与头颈部肿瘤 ,PNMA5在肠癌中表达 .PNMA5是肿瘤 睾丸 脑抗原家族的一个新成员 .认识这些肿瘤 睾丸 脑抗原的意义在于它们在肿瘤组织的表达可能是肿瘤破坏机体免疫耐受的一种机制 ,其相关神经副肿瘤综合症可能是一些隐匿肿瘤的早期表现 .     

大鼠中心体蛋白家族基因的克隆及其在睾丸中的表达特征

centrin是进化上高度保守的中心体蛋白家族, 已从多种生物中克隆到其同源基因, 但基因文库中尚无大鼠centrin序列的报道. 采用RT-PCR从大鼠睾丸组织中克隆到centrin-1, -2和 -3 cDNA片段, 对其衍生的氨基酸序列进行同源性比较, 结果显示, 人、小鼠、大鼠中相应的centrin蛋白同源性很高. 采用半定量RT-PCR技术研究了它们在大鼠精子发生过程中的表达特征. 结果表明, centrin-1的表达具有睾丸组织和生精细胞特异性, 并呈现出发育阶段相关的规律, 它仅在减数分裂开始后转录, 其mRNA水平在圆形精子细胞中达到高峰. centrin-2和centrin-3在睾丸精原细胞中有高表达, 进入减数分裂后其mRNA水平迅速降低, 同时在一些体细胞中也有表达. 推测centrin-1可能在减数分裂或精子细胞变态分化过程中发挥作用, 而centrin-2, -3可能与有丝分裂有关.     

内含子的进化及基因表达调节

由于内含子(intron)的进化目前还没有一致的观点,一般认为内含子的进化是基因进化的重要部分,是与物种形成相适应的过程.内含子参与基因的组织特异性表达、蛋白质变异、基因转录等多种生物学过程.     

协同物种形成及其生物学意义

自达尔文与华莱士以来的每位生物学家都承认种间生态学作用对进化的意义。1964年,埃利希和雷文提出了协同进化理论。它反映了生态学相关的不同物种之间的相互作用引起的相互进化。这一理论引起了研究者的广泛重视。近年来,随着进化生态研究的深入发展,学者们对进化过程的生态机制以及生态特性与生态关系进化规律、种间生态学作用引起的物种形成有了进一步的认识。本文仅从协同物种形成的概念出发,对协同物种形成的生态机制以及生物学意义作一简要概述。协同物种形成的概念进化在本质上是一种生态过程,是生物与环境、生物与生物之间相互作用的结果。种群分化的生态机制和物种形成的本质在于对生存条件的逐步适应。按照协同进化理论,物种间的相互作用引起的协同适应     

多肽∶N-寡糖酶在小鼠人工隐睾中表达下调

真核多肽∶N-寡糖酶(peptide∶N-glycanase或PNGase)可切除错误折叠糖蛋白上的N-寡糖链,并可与内质网关联降解(endoplasmic reticulum-associated degradation,ERAD)途径中的多种关键成分相结合.然而,对于PNGase的生理功能及其与疾病的关系尚无明确报道.本研究利用重组技术表达和纯化了包含人PNGase N末端片段的融合蛋白,并经融合蛋白免疫与亲和层析纯化家兔抗血清,制备了PNGase的特异性抗体.利用该抗体和Western印迹技术研究了PNGase在小鼠组织中的表达.结果显示PNGase在7种小鼠组织(脑、心、肺、肝、脾、肾、睾丸)中均有不同程度的表达,其中表达量最高者为睾丸;PNGase表达水平在不同品系小鼠(C57BL/6N、BALB/cAnN和昆明小鼠)间有显著差异.在小鼠单侧隐睾模型中首次观察到,与对照侧阴囊内的正常睾丸相比,隐睾内PNGase含量明显下降,提示PNGase在睾丸生精过程中可能有重要作用.     

犏牛精子发生阻滞的比较转录组研究

犏牛是牦牛与普通牛的杂交后代,其雄性不育是牦牛杂交改良中的一大难题.运用高通量测序技术对健康成年犏牛和牦牛的睾丸组织进行转录组测序和比较研究,探讨了犏牛激素调节、精子发生及细胞凋亡等相关基因的表达情况.结果表明,犏牛、牦牛睾丸组织中分别有17784和18529个基因表达,在犏牛中表达显著上调和下调的基因分别有5000和4089个.犏牛睾丸组织中睾酮合成相关基因和抑制素基因表达均显著上调,认为前者的表达上调可能促进睾丸内睾酮分泌和后者的表达,而后者的表达上调可能分别抑制和几乎不影响脑垂体前叶合成、分泌促卵泡刺激素和黄体生成素.比较睾丸组织中细胞标记基因在两种牛间的表达差异,发现犏牛精原干细胞、支持细胞、间质细胞、肌样细胞(睾丸纤维化)和已分化精原细胞的标记基因分别呈显著表达上调和下调,而减数分裂后期或精子形成期呈极显著下调.精原干细胞自我更新与分化异常可能导致犏牛精子发生障碍,认为其与视黄酸信号通路障碍密切相关.Syce3,Fkbp6和Dmrt7等在犏牛睾丸组织中极显著表达下调与同源染色体间、尤其是性染色体间的联会复合体数量减少有关.Spo11和Dmc1分别参与双链断裂和同源修复过程,其在犏牛睾丸中表达下调分别可能使联会复合体减少和同源修复失常.参与高度浓缩细胞核的相关基因,尤其是Tnp2,Hmgb4和H1fnt等几乎不表达,其调控表达基因Crem,GRTH/DDX25等极显著表达下调,该现象与犏牛生精细胞最终只能分化至圆形精子细胞阶段的结果相符.促凋亡相关基因,如p53,TNF-α,Trail,Bmp8b,Bax,Caspase-3,Caspase-6和Caspase-7表达均显著上调,而抑凋亡基因,如survivin,Bcl-2等显著下调,这可能是导致犏牛睾丸组织中有更多的生精细胞发生凋亡的原因之一.通过对生殖相关基因的表达分析研究,为揭示犏牛雄性不育机理以及牦牛杂交改良研究提供了理论基础.     

黑色素瘤抗原编码基因家族新成员MAGE-D1的组织表达谱研究

MAGE D1是黑色素瘤抗原编码基因家族 (MAGE)中MAGE D亚家族的新成员 .为了研究该基因的性质及其可能功能 ,采用Northernblot和Dotblot杂交技术研究了其组织表达谱 .结果发现 ,该基因在多种肿瘤组织和正常组织中均广泛表达 .在所检测的 4 8种肿瘤组织中 ,经与对应正常组织进行比较发现 ,该基因在 13种肿瘤组织中的表达显著增高 ,而在 7种肿瘤组织中的表达则显著降低 .进一步分析提示该基因在多种胚胎组织中的表达高于成年组织 .由于MAGE A、 B、 C亚家族均具有在肿瘤组织 睾丸中特异表达的特点 ,而作为MAGE D亚家族成员的MAGE D1并非在肿瘤组织中特异表达 ,提示需要对MAGE基因家族进行深入的功能研究 .     

Transcriptomic analyses support the similarity of gene expression between brain and testis in human as well as mouse

We previously revealed similarity in gene expression patterns between human brain and testis, based on digital differential display analyses of 760 human Unigenes. In the present work, we reanalyzed the gene expression data in many tissues of human and mouse for a large number of genes almost covering the respective whole genomes. The results indicated that both in human and in mouse, the gene expression profiles exhibited by brain, cerebellum and testis are most similar to each other compared with other tissues.     

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse

Protein-coding genes evolve at different rates, and the influence of different parameters, from gene size to expression level, has been extensively studied. While in yeast gene expression level is the major causal factor of gene evolutionary rate, the situation is more complex in animals. Here we investigate these relations further, especially taking in account gene expression in different organs as well as indirect correlations between parameters. We used RNA-seq data from two large datasets, covering 22 mouse tissues and 27 human tissues. Over all tissues, evolutionary rate only correlates weakly with levels and breadth of expression. The strongest explanatory factors of purifying selection are GC content, expression in many developmental stages, and expression in brain tissues. While the main component of evolutionary rate is purifying selection, we also find tissue-specific patterns for sites under neutral evolution and for positive selection. We observe fast evolution of genes expressed in testis, but also in other tissues, notably liver, which are explained by weak purifying selection rather than by positive selection.     

Do the constraints of human speciation cause expression of the same set of genes in brain, testis, and placenta?

Evolution appears to be especially rapid during speciation, and the genes involved in speciation should be evident in species such as humans that have recently speciated or are presently in the process of speciation. Haldane's rule is that when one sex is sterile or inviable in interspecific F(1) hybrids, it is usually the heterogametic sex. For mammals, this implicates genes on the X chromosome as those particularly responsible for speciation. A preponderance of sex- and reproduction-related genes on the X chromosome has been shown repeatedly, but also mental retardation genes are more frequent on the X chromosome. We argue that brain, testis, and placenta are those organs most responsible for human speciation. Furthermore, the high degree of complexity of the vertebrate genome demands coordinate evolution of new characters. This coordination is best attained when the same set of genes is redeployed for these new characters in the brain, testis, and placenta.     

Brain and testis: more alike than previously thought?

Several strands of evidence indicate the presence of marked similarities between human brain and testis. Understanding these similarities and their implications has become a topic of interest among the scientific community. Indeed, an association of intelligence with some semen quality parameters has been reported and a relation between dysfunctions of the human brain and testis has also been evident. Numerous common molecular features are evident when these tissues are compared, which is reflected in the huge number of common proteins. At the functional level, human neurons and sperm share a number of characteristics, including the importance of the exocytotic process and the presence of similar receptors and signalling pathways. The common proteins are mainly involved in exocytosis, tissue development and neuron/brain-associated biological processes. With this analysis, we conclude that human brain and testis share several biochemical characteristics which, in addition to their involvement in the speciation process, could, at least in part, be responsible for the expression of a huge number of common proteins. Nonetheless, this is an underexplored topic, and the connection between these tissues needs to be clarified, which could help to understand the dysfunctions affecting brain and testis, as well as to develop improved therapeutic strategies.     

Global, comparative analysis of tissue-specific promoter CpG methylation

Understanding cell-type-specific epigenetic codes on a global level is a major challenge after the sequencing of the human genome has been completed. Here we applied methyl-CpG immunoprecipitation (MCIp) to obtain comparative methylation profiles of coding and noncoding genes in three human tissues, testis, brain, and monocytes. Forty-four mainly testis-specific promoters were independently validated using bisulfite sequencing or single-gene MCIp, confirming the results obtained by the MCIp microarray approach. We demonstrate the previously unknown somatic hypermethylation at many CpG-rich, testis-specific gene promoters, in particular in ampliconic areas of the Y chromosome. We also identify a number of miRNA genes showing tissue-specific methylation patterns. The comparison of the obtained tissue methylation profiles with corresponding gene expression data indicates a significant association between tissue-specific promoter methylation and gene expression, not only in CpG-rich promoters. In summary, our study highlights the exceptional epigenetic status of germ-line cells in testis and provides a global insight into tissue-specific DNA methylation patterns.     

Splicing factor and exon profiling across human tissues

It has been shown that alternative splicing is especially prevalent in brain and testis when compared to other tissues. To test whether there is a specific propensity of these tissues to generate splicing variants, we used a single source of high-density microarray data to perform both splicing factor and exon expression profiling across 11 normal human tissues. Paired comparisons between tissues and an original exon-based statistical group analysis demonstrated after extensive RT-PCR validation that the cerebellum, testis, and spleen had the largest proportion of differentially expressed alternative exons. Variations at the exon level correlated with a larger number of splicing factors being expressed at a high level in the cerebellum, testis and spleen than in other tissues. However, this splicing factor expression profile was similar to a more global gene expression pattern as a larger number of genes had a high expression level in the cerebellum, testis and spleen. In addition to providing a unique resource on expression profiling of alternative splicing variants and splicing factors across human tissues, this study demonstrates that the higher prevalence of alternative splicing in a subset of tissues originates from the larger number of genes, including splicing factors, being expressed than in other tissues.