Small but influential: the role of microRNAs on gene regulatory network and 3 ' UTR evolution

MicroRNAs (miRNAs) are endogenous similar to 22 nucleotide noncoding RNAs that regulate the expression of complementary messenger RNAs (mRNAs). Thousands of miRNA genes have been found in diverse species, and many of them are highly conserved. With the mi

Adaptive evolution of primate TRIM5 alpha, a gene restricting HIV-1 infection

Recent studies showed that nonhuman primate TRIM5 alpha can efficiently block HIV-1 infection in human cell lines. It can also restrict other retroviruses, therefore, suggested as a general defender against retrovirus infection. Here, we present an evolutionary analysis of TRIM5 alpha in primates. Our results demonstrated that TRIM5a has been evolving rapidly in primates, which is likely caused by Darwinian positive selection. The SPRY domain of TRM5 alpha, which may be responsible for recognition of incoming viral capsids showed higher nonsynonymous/synonymous substitution ratios than the non-SPRY domain, indicating that the adaptive evolution of TRIM5a ill primates might be an innate strategy developed in defending retrovirus infection during primate evolution. In addition, the comparative protein sequence analysis suggested that the amino acid substitution pattern at a single site (344R/Q/P) located in the SPRY domain may explain the differences in Susceptibilities of HIV-1 infection in diverse primate species. (c) 2005 Elsevier B.V. All rights reserved.

Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup

A transmembrane protein gene, c1orf37-dup, was identified as a young gene specific to humans. It was derived from the conserved c1orf37 gene through retroposition after the divergence of human and chimpanzee. This gene has evolved rapidly driven by positi

Bombinakinin M gene associated peptide, a novel bioactive peptide from skin secretions of the toad Bombina maxima

A novel 28-amino acid peptide, termed bombinakinin-GAP, was purified and characterized from skin secretions of the toad Bombina maxima. Its primary structure was established as DMYEIKQYKTAHGRPPICAPGEQCPIWV-NH2, in which two cysteines form a disulfide bond. A FASTA search of SWISS-PROT databank detected a 32% sequence identity between the sequences of the peptide and a segment of rat cocaine- and amphetamine-regulated transcript (CART). Intracerebroventricular (i.c.v.) administration of the peptide induced a significant decrease in food intake in rats, suggesting that it played a role in the control of feeding by brain. Analysis of its cDNA structure revealed that this peptide is coexpressed with bombinakinin M, a bradykinin-related peptide from the same toad. Bombinakinin-GAP appears to be the first example of a novel class of bioactive peptides from amphibian skin, which may be implicated in feeding behavior. (C) 2003 Elsevier Science Inc. All rights reserved.

The First Gene-encoded Amphibian Neurotoxin

Many gene-encoded neurotoxins with various functions have been discovered in fish, reptiles, and mammals. A novel 60-residue neurotoxin peptide (anntoxin) that inhibited tetrodotoxin-sensitive (TTX-S) voltage-gated sodium channel (VGSC) was purified and c

Gene admixture in the Silk Road region of China: Evidence from mtDNA and melanocortin 1 receptor polymorphism

Mitochondrial DNA control region segment I sequences and melanocortin 1 receptor (MC1R) gene polymorphism were examined in ethnic populations in the silk road region of China. Both the frequencies of the MC1R variants and the results of mtDNA data in this region presented intermediate values between those of Europe and East and Southeast Asia, which suggested extensive gene admixture in this area and was in general agreement with previous studies. Phylogenetic analysis of the ethnic populations in the Silk Road region that based on mtDNA data didn't show expected cluster pattern according to their ethnogenesis. We suspect that a high migration rate in female among these closely related populations and other three demographic events might account for it.

Cloning and characterization of the first amphibian bradykinin gene

More than ten bradykinin-related peptides and their cDNAs; have been identified from amphibians, but their genes are unknown. In present study, four cDNAs encoding one, two, four and six copies of bradykinin-related peptides were cloned from the frog (Odorrana grahami) skin cDNA library, respectively. Three bradykinin-related peptides (bradykinin, Thr6-bradykinin, Leu5Thr6-bradykinin) were deduced from these four cDNA sequences. Based on the cDNA sequence, the gene sequence encoding an amphibian bradykinin-related peptide from O. grahami was determined. It is composed of 7481 base pairs including two exons and two introns. The first exon codes signal peptide and the second exon codes acidic spacer peptide and Thr6-bradykinin. The promoter region of the bradykinin gene contains several putative recognition sites for nuclear factors, such as SRY, GATA-1, LYF-1, DeltaE, CDXA, NKX-2.5, MIF1 and S8. The current work may facilitate to understand the regulation and possible functions of amphibian skin bradykinin-related peptides. (C) 2009 Elsevier Masson SAS. All rights reserved.

Developmental Expression of an Amphioxus (Branchiostoma belcheri) Gene Encoding a GATA Transcription Factor

GATA基因在脊椎动物和非脊椎动物的发育中行使重要的功能,该家族的成员在进化上也足非常保守的.脊椎动物的GATA基因分为两个亚群:GATA1/2/3和GATA4/5/6.通过生物信息分析,在文吕鱼的基因缓中找到了3个GATA基因:一个GATA1/2/3业家族基因,两个GATA4/5/6亚家族基因:还找到一个类GATA基因.还克隆了白氏文昌鱼(Branchiostoma belcheri)GATA123的一段序列,并研究了它在早期胚胎发育中的表达图式.结果表明GATA123在原肠胚的中内胚层表达,而在神经胚晚期和幼体早期,GATA123在脑泡和消化道中部区域表达.这种表达模式与头部发育的重要基因Otx相类似.结果提示在文吕鱼脑泡的发育过程中GATA123和Otx很可能共同发挥着重要的作用.

Expansion of the Actin Gene Family in Amphioxus

肌动蛋白是一种分布广泛而且在进化上十分保守的蛋白,是构成细胞骨架的关键组分.肌动蛋白通常被分成肌肉型和胞质型两种类型,各自行使着不同的功能.在此,作者对弗罗里达文昌鱼基因组中的肌动蛋白基因家族进行了系统分析,发现文昌鱼中该基因家族成员多达30多个,其中很多都是连锁分布的.基因结构趋于多样,分别包含2～7个外显子.进化分析的结果显示,文昌鱼的肌动蛋白基因家族可能通过串联重复而发生了扩增.作者还克隆了厦门文昌鱼两个不同的肌肉犁肌动蛋白基因,并比较了它们在文昌鱼早期胚胎中的表达图式.结果显示,这两个基因在表达上有着细微的差别,提示文昌鱼肌动蛋白基因家族成员在功能上的分化.上述结果将有助于阐明肌动蛋白基因家族及其功能在脊索动物中的演化.

Temporal and Spatial Expression Patterns of Sox1 Gene in Xenopus laevis

克隆了非洲爪蟾的Sox1基因并研究了它在非洲爪蟾早期发育过程中的时空表达图式,比较了Sox1-3基因在发育的脑和眼中的表达图式.序列比对分析显示Sox1-3蛋白在其HMG框结构域具有高度的保守性.通过RT-PCR方法分析了Sox1基因在爪蟾早期不同发育时段的表达情况,结果显示Sox1基因从未受精卵到尾芽期均有表达,但表达强度有所差异.原位杂交结果显示,在早期卵裂阶段和囊胚期,Sox1基因主要在动物极表达;从神经板期开始,Sox1基因主要在中枢神经系统和眼原基中表达.在蝌蚪期,Sox1与Sox2、Sox3在脑部和眼睛的表达区域有所不同.对于爪蟾Sox1基因时空表达图式的研究将有助于阐明SoxB1基因家族在脊椎动物神经系统发生过程中的作用.

Embryonic stages and eye-specific gene expression of the local cyprinoid fish Anabarilius grahami in Fuxian Lake, China

Anabarilius grahami is a cyprinoid fish endemic to Fuxian Lake, Yunnan, China. In this study, a comprehensive staging series of A. grahami was produced. The embryonic development of A. grahami was divided into six main periods: zygote period, cleavage per

The intraspecific difference of the triose phosphate isomerase ( tim) gene from Giardia lamblia

目的　探讨蓝氏贾第鞭毛虫 (Giardialamblia)磷酸丙糖异构酶基因种内差异。方法　提取虫体总DNA ,对所有虫株磷酸丙糖异构酶 (tim)基因部分片段进行PCR扩增。测定序列后 ,用简约法和NJ法构建系统树进行系统发育分析。结果　共有 12 4个位点存在变异 (占所有测定序列中的 2 3% ) ,且大多数为发生在密码子的同义突变。两种构树方法所得二树的分枝结构相似 ,均将受试的 16株蓝氏贾第虫分为明显的两组。结论　宿主及地理因素对蓝氏贾第虫群体的遗传多样性影响不大。在DNA分子进化水平上 ,自然选择的影响十分显著。可将tim基因作为蓝氏贾第虫群体遗传结构一个十分有效的遗传标记。

Study on Mitochondrial DNA Cytochrome b Gene of Chinese sea bass, Lateolabrax sp.

参考鳗鲡等鱼类线粒体 DNA序列进行了中国花鲈线粒体 DNA细胞色素 b基因片断的引物设计、PCR扩增及其序列测定。得到中国花鲈的碱基序列为 4 10 bp,其 A、T、G、C含量分别为 10 1bp(2 4 .6 3% )、112 bp(2 7.32 % )、72 bp(17.56 % )、12 5bp(30 .4 9% ) ,与鳗鲡等其他鱼类相同基因片断序列碱基含量相似。

A phylogeny of Chinese leaf monkeys using mitochondrial ND3-ND4 gene sequences

The phylogeny of Chinese leaf monkeys, especially the snub-nosed monkeys (Rhinopithecus), has not been thoroughly investigated using molecular sequence data, perhaps due to their rarity in the wild and their poor representation in institutional collections. Despite several proposed classifications, systematic relationships of these species remain poorly defined and this has hindered their conservation. To clarify the phylogenetic relationships of the leaf monkey clade in China, we sequenced the mitochondrial ND3, ND4L, ND4, tRNA(Arg), tRNA(His), tRNA(Ser), and tRNA(Leu) genes for Rhinopithecus bieti, R. roxellana, Trachypithecus francoisi, T. f. leucocephalus, and T. phayrei as well as Pygathrix nemaeus and Colobus guereza. We included a rotal of 2252 characters for each individual, excluding gaps in primary sequences. Our interpretation of the results from character- and distance-based phylogenetic analyses suggest that (1) Pygathrix nemaeus is sister to Rhinopithecus rather than to Trachypithecus though it is quite divergent from the former; (2) the Yunnan snub-nosed monkey, Rhinopithecus bieti, represents a valid species; (3) the white-headed leaf monkey is not a distinct species, but instead is a subspecies of Trachypithecus francoisi (T. f. leucocephalus), though it should still be considered a separate evolutionarily significant unit (ESU); and (4) because two individuals of the Phayrei's leaf monkey, T. phayrei, are genetically distinct from one another, a more extensive revision of the taxonomy of this putative species in China is needed. These results, plus ongoing work on the molecular systematics of the entire Asian leaf monkey radiation, can provide a sound basis for identifying the appropriate units of conservation for this endangered group of primates.

Mitochondrial cytochrome b gene sequences of Old World monkeys: With special reference on evolution of Asian colobines

The classification and phylogenetic relationships of the Old World monkeys are still controversial. For Asian colobines, from three to nine genera were recognized by different primatologists. In the present study, we have sequenced a 424 bp mitochondrial tRNA(Thr) gene and cytochrome b gene fragment from Macaca mulatta, Mandrillus sphinx, Mandrillus leucophaeus, Semnopithecus entellus, Trachypithecus vetulus, T. johnii, T. phayrei, T. francoisi, Pygathrix nemaeus, Rhinopithecus roxellanae, R. bieti, R. avunculus, Nasalis larvatus, and Colobus polykomos in order to gain independent information on the classification and phylogenetic relationships of those species. Phylogenetic trees were constructed with parsimony analysis by weighting transversions 5 or 10 fold greater than transitions. Our results support the following conclusions: (1) the Old World monkeys are divided into two subfamilies; (2) that among the colobines, Colobus, the African group, diverged first, and Nasalis and Rhinopithecus form a sister clade to Pygathrix; (3) that there are two clades within leaf monkeys, i.e. 1) S. entellus, T. johnii, and T. vetulus, and 2) T, phayrei and T. francoisi; (4) that Rhinopithecus avunculus, R. roxellanae, and R. bieti are closely related to each other, and they should be placed into the same subgenus; (5) that Rhinopithecus is a distinct genus; and (6) that the ancestors of Asian colobines migrated from Africa to Asia during the late Pliocene or early Pleistocene.