过表达miR-9对黄鳝受精卵中基因转录组水平的影响

为了更深入地研究鱼类天然性逆转的生理学机制, 研究通过克隆黄鳝(Monopterus albus) miR-9的前体序列, 及在黄鳝受精卵中过表达miR-9的生物学研究, 最终筛选得到157个基因与miR-9的过表达相关, 其中松弛素信号通路(ko04926)为显著富集的KEGG条目。tektin 4基因(tekt4)、环腺苷酸环化酶合成酶2a(adcy2a)、Ⅰ型细胞骨架角蛋白13(k1c13)和视黄醇脱氢酶5(rdh5)等基因的表达量在miR-9过表达后出现不同程度的升高; 成纤维细胞生长因子13b(fgf13b)和促甲状腺激素释放激素受体2(trhr2)等基因的表达量在miR-9过表达后出现不同程度的降低。rdh5基因在黄鳝眼睛中具有最高的表达水平(P<0.01), 而在脑、血液、精巢和卵巢中几乎没有表达(P<0.01)。松弛素家族基因rln3a和rln3b在黄鳝成鱼中的组织表达模式类似, 均在脑和精巢组织中具有较高的表达水平。推测miR-9可能与黄鳝视觉功能的发育或维持相关; miR-9可能通过松弛素信号通路调控黄鳝精巢的发育过程。研究有助于探讨miR-9对内分泌系统相关基因的调控通路, 为阐明黄鳝性别分化的分子机制提供理论依据。     

黄鳝P-450芳香化酶基因的克隆及序列分析

P-450芳香化酶(P450arom)是催化雄激素生物合成雌激素的关键酶。本文采用RT-PCR和RACE(Rapid amplifi- cation of cDNA ends)法,首次分离和克隆了雌雄同体鱼黄鳝卵巢中P450 arom基因。该基因cDNA全长1802bp(不包 括poly(A)),5'端非翻译区有49bp,3'端202bp(不包含poly(A)),阅读框(Open reading frame,ORF)1551bp,翻译成517 个氨基酸,计算的蛋白质分子量58．2kDa。同源性分析显示,黄鳝卵巢P450arom的氨基酸序列与其他鱼卵巢 P450arom具有63％-80％同源性,与其他鱼脑P450arom为58％-60％同源,与人胚盘和鸡卵巢P450arom则为 50％-52％同源;但在芳香化酶高保守区(包括1-螺旋区,芳香化酶特异保守区和血红素结合区)的同源性高达 76％-92％。系统发育分析表明芳香化酶基因是单起源,黄鳝卵巢芳香化酶基因与鳉鱼卵巢的关系最近,与鱼类卵 巢P450arom属于同一分支的,与鱼类脑及鸡和人的属于不同分支。     

Medaka--a model organism from the far East

Genome sequencing has yielded a plethora of new genes the function of which can be unravelled through comparative genomic approaches. Increasingly, developmental biologists are turning to fish as model genetic systems because they are amenable to studies of gene function. Zebrafish has already secured its place as a model vertebrate and now its Far Eastern cousin--medaka--is emerging as an important model fish, because of recent additions to the genetic toolkit available for this organism. Already, the popularity of medaka among developmental biologists has led to important insights into vertebrate development.     

黄鳝激素敏感性脂肪酶基因Hsl染色体原位杂交定位

动物脂肪组织中的甘油三酯在数量上是最重要的储存能源。Hsl基因所编码的激素敏感性脂肪酶是一种多功能酶。它通过催化水解储存在脂肪组织中的甘油三酯,以及卵巢、肾上腺、睾丸和胎盘中的胆固醇酯,在机体能量供应和类固醇生成作用中发挥重要作用。本研究以放射性同位素和地高辛标记重组质粒pBS中所含猪Hsl基因作为探针,分别与Pst Ⅰ酶切的黄鳝基因组总DNA和有丝分裂染色体标本进行Southern杂交和荧光原位杂交(FISH)。结果显示,Southern杂交呈现一条带,片段长度约为11.5kb。同时,应用FISH定位Hsl基因于黄鳝5号染色体,相对着丝粒距离为78.35±1.26。该定位结果与应用“特定染色体DNA池”定位黄鳝Hsl基因结果相符,且定位结果更为精细。表明在淡水鱼类黄鳝基因组中存在Hsl基因,另一方面也首次提供黄鳝5号染色体上FISH杂交信息,从而为增加黄鳝染色体组中已知的遗传标记和建立高精度遗传图谱奠定基础。 Abstract:Adipose tissue triacylglycerols are the quantitatively most important source of stored energy in animals.Hormone-sensitive lipase encoded by hormone-sensitive lipase gene (Hsl) is a multifunctional enzyme that catalyzes the hydrolysis of triacylglycerol stored in adipose tissue and cholesterol esters in the adrenals,ovaries,testes and macrophages.Using pig Hsl gene inserted into pBS labeled by the radioactive isotope and the digoxigenin as the probes respectively,one band,11.5kb,has been shown to hybridized with total DNA of rice field eel digested with Pst Ⅰby Southern blotting and Hsl gene has been assigned to metaphase chromosome 5,at the position of 78.35±1.26 from the c entromere in rice field eel by fluorescent in situ hybridization (FISH).The mapping results are corresponding to that of “specific-chromosomal DNA pool”obtained by chromosome microisolation used to map gene and the mapping result is more accurate.The results of the study further illustrate the importance of the presence of Hsl gene in rice field eel genome and provide the first FISH mapping data for rice field eel chromosome 5.The current studies would advance the addition of known genetic markers and the construction of high resolution genetic map in rice field eel genome.     

ZFX基因同源序列在黄鳝基因组中的检出及其染色体定位

以大熊猫锌指蛋白基因Zfx为探针 ,在黄鳝基因组DNA中检测到一条长约 9 5kb的杂交带。依据哺乳类和爬行类动物锌指蛋白基因 (ZFX/Zfc)编码第 7～ 13个锌指结构的DNA序列保守性设计引物 ,在黄鳝基因组DNA中仅扩增到一条 5 12bp的DNA片段。将此片段克隆至载体 pBS中 ,从雌性、雄性个体中分别挑选 4个含有插入片段的白色克隆进行测序。测序结果表明 ,这些克隆中插入片段的核苷酸序列一致。该DNA片段在核苷酸水平上与人类ZFX和ZFY分别具有 88%和 87%同源性 ,但其与美洲鳄鱼Zfc的同源性可达 90 % ,而在氨基酸水平上则分别存在 95 9%、95 9%和 93 5 %的同源性 (170个氨基酸 )。该基因命名为黄鳝锌指蛋白基因Zfa ,并运用FISH将其定位于黄鳝 1号染色体 ,距离着丝粒的相对位置为 6 0 1± 0 38。通过进一步研究证明 ,黄鳝 1号染色体上存在有真兽类哺乳动物X染色质同源的保守片段 ,该保守片段有可能就是哺乳动物X染色体起源和进化的原始物质基础之一。应用哺乳动物X染色体连锁的其他基因在鱼类开展染色体比较定位研究 ,将有望促进脊椎动物性染色体进化的深入研究     

黄鳝体表溃疡病病原菌的分离与鉴定

研究首次报道从患体表溃疡病黄鳝的肝脏、肾脏、脾脏等分离到1株细菌, 经动物回归试验鉴定其为病原菌。形态学观察、生理生化试验和16S rRNA基因鉴定, 结果证实该病原菌株为温和气单胞菌(Aeromonas sobria)。通过致病性试验证明其对鲤鱼和泥鳅均有致病力;药敏试验结果表明:分离菌株对头孢氨噻肟、头孢曲松钠、丙氟哌酸、洛美沙星、甲氧苄啶、氟哌酸、壮观霉素等高度敏感,而对氨苄青霉素、乙酰螺旋霉素等药物不敏感。       

Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome

Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.     

Outlook for development of high-throughput cryopreservation for small-bodied biomedical model fishes

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach.     

Outlook for development of high-throughput cryopreservation for small-bodied biomedical model fishes

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach.     

Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes.     

Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome

Owing to their phylogenetic position, cartilaginous fishes (sharks, rays, skates, and chimaeras) provide a critical reference for our understanding of vertebrate genome evolution. The relatively small genome of the elephant shark, Callorhinchus milii, a chimaera, makes it an attractive model cartilaginous fish genome for whole-genome sequencing and comparative analysis. Here, the authors describe survey sequencing (1.4× coverage) and comparative analysis of the elephant shark genome, one of the first cartilaginous fish genomes to be sequenced to this depth. Repetitive sequences, represented mainly by a novel family of short interspersed element–like and long interspersed element–like sequences, account for about 28% of the elephant shark genome. Fragments of approximately 15,000 elephant shark genes reveal specific examples of genes that have been lost differentially during the evolution of tetrapod and teleost fish lineages. Interestingly, the degree of conserved synteny and conserved sequences between the human and elephant shark genomes are higher than that between human and teleost fish genomes. Elephant shark contains putative four Hox clusters indicating that, unlike teleost fish genomes, the elephant shark genome has not experienced an additional whole-genome duplication. These findings underscore the importance of the elephant shark as a critical reference vertebrate genome for comparative analysis of the human and other vertebrate genomes. This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes.     

黄鳝β-actin基因的克隆及其在鱼类中的系统发生分析

β-actin是actin家族的一员,在维持细胞结构,细胞内运动,细胞分裂等细胞生理活动方面发挥着重要的作用。克隆的黄鳝β-actin基因的cDNA全长1860bp,编码375个氨基酸,在脊椎动物中不同物种的β-actin基因之间的序列同源性超过了98％。RT-PCR表明克隆的黄鳝β-actin基因在睾丸、卵巢、心、肝、脾、脑等组织中广谱表达。基于目前已知的全部鱼类β-actin cds,构建了进化树。星形辐射的树型结构一致支持将鱼类β-actin基因划分为4类。到目前为止,所有的鱼都没有发现拥有全部4个β-actin基因。这暗示伴随着鱼类的辐射式进化历程,可能发生了种系特异性的β-actin的丢失。     

Alternative splicing and differential expression of P450c17 (CYP17) in gonads during sex transformation in the rice field eel

Several mechanisms were used in determination of the development of the male or female of vertebrates. The genes for determination of sequential hermaphrodite sex are unknown. Here, we reported cloning, alternative splicing, and expression patterns of the CYP17 gene of the rice field eel, a teleost fish with a characteristic of nature sex reversal. The CYP17 gene of the rice field eel was clustered into the CYP17 gene group of all the other vertebrates, especially into the fish subgroup. Four isoforms of the CYP17 were generated in gonads by alternative splicing and polyadenylation. Alternative splicing events of all these isoforms occurred in 3(') regions, which encoded three different sizes (517, 512, and 159aa) of proteins. RT-PCR results indicate specific expression in gonads of these isoforms. Northern blot analysis shows that expression patterns of the CYP17 (dominantly expressed in testis, less in ovary, and the least in ovotestis) are consistent with the sex reversal process of the rice field eel. In situ hybridization further shows its specific expression in germinal lamellae, the gonadal epithelium of the gonads. These findings indicate that CYP17 is differentially regulated in a sex- and developmentally specific manner, suggesting that the CYP17 potentially has important roles in gonad differentiation during sex reversal of the rice field eel.     

脊椎动物中的一种解剖学新模型——黄鳝外周嗅觉系统

除单鼻型的圆口类外, 脊椎动物的左、右两侧嗅觉器官和嗅神经皆互为独立地分布于头前端, 而且它们的前鼻孔(外鼻孔)、嗅腔、嗅觉副囊腔(部分鱼具嗅觉副囊)与后鼻孔(或内鼻孔)也都互为相通, 且多呈开放状态。它们还通常具有一个体积相对较大且较稳定的嗅腔, 而嗅上皮则多位于嗅腔的一侧。此外, 鱼类的嗅囊与鼻窝之间通常也无明显间隙。然而, 运用常规的解剖学方法发现, 黄鳝(Monopterus albus)外周嗅觉系统(嗅觉器官和嗅神经)在解剖结构上已发生如下重大变化: (1)虽然具有前、后鼻孔, 但两者互不相通, 而嗅腔仅靠前鼻孔通至外界; (2)两侧嗅囊的末端及两侧嗅神经的前段均分别发生了合并。此外, 在该鱼上还发现:(1)嗅囊为一柔软而扁塌的长管囊结构, 其唯一的开口(即位于前鼻孔球上的前鼻孔)却常呈关闭状, 故此时该嗅腔实际上是一个体积被压扁到最小且暂时被封闭的空间; (2)嗅囊纵向地贴附于长鼻窝的内侧壁上, 它仅占鼻窝的一小部分空间, 故鼻窝显得相对很宽敞; (3)嗅觉副囊不与嗅腔相通, 而与鼻窝共同经后鼻孔通至外界; (4)两侧嗅囊的末端相向地穿越鼻窝内侧壁, 进入筛骨与额骨之间的“筛-额横管”, 在那里发生嗅囊合并;(5)嗅囊壁周缘几乎都内衬着嗅上皮, 且具数个褶窝(说明该嗅囊有扩张的可能)。因此, 黄鳝的这套解剖学特征不同于包括鱼类在内的所有脊椎动物的外周嗅觉系统。研究所发现的黄鳝这套形态学特征不仅为脊椎动物外周嗅觉系统的研究提供了一个独特的解剖学新模型, 同时也为动物进化研究提供了一个有关前、后鼻孔互不相通的进化特例。此外, 研究还依据上述发现提出嗅囊扩张-压缩假说以解释气味媒质进出于黄鳝这种特殊嗅腔的动力学机制。       

Medakafish as a model system for vertebrate developmental genetics

Several teleosts, such as the zebrafish and the medakafish or medaka (Oryzias latipes), are used as vertebrate model systems in various fields of biology. The medaka is suitable for use in genomic studies because of its small genome size. Moreover, our recent results of small-scale mutagenesis in the medaka indicate that it is possible to identify mutations, the phenotypes of which could not be found in zebrafish mutants obtained by large-scale mutagenesis. An example is Oot (One-sided optic tectum), a maternal-effect mutation. In the Oot phenotype, bilateral symmetry is broken in the optic tectum in the early developmental stages, and either the left or right morphology is duplicated on both sides. Medaka inbred strains can be produced and used to study quantitative traits in vertebrate development. Data presented support the use of medaka as another important fish model for the study of vertebrate developmental genetics.     

The Genomic and Genetic Toolbox of the Teleost Medaka (Oryzias latipes)

The Japanese medaka, Oryzias latipes, is a vertebrate teleost model with a long history of genetic research. A number of unique features and established resources distinguish medaka from other vertebrate model systems. A large number of laboratory strains from different locations are available. Due to a high tolerance to inbreeding, many highly inbred strains have been established, thus providing a rich resource for genetic studies. Furthermore, closely related species native to different habitats in Southeast Asia permit comparative evolutionary studies. The transparency of embryos, larvae, and juveniles allows a detailed in vivo analysis of development. New tools to study diverse aspects of medaka biology are constantly being generated. Thus, medaka has become an important vertebrate model organism to study development, behavior, and physiology. In this review, we provide a comprehensive overview of established genetic and molecular-genetic tools that render medaka fish a full-fledged vertebrate system.     

Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements

With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents.     

Expression of a duplicate Na,K-ATPase beta(1)-isoform in the European eel (Anguilla anguilla)

Recent studies on teleost fish have suggested that their genomes have undergone ancient polyploidization events resulting in the duplication of the genome. A duplicate copy of the Na,K-ATPase beta(1)-isoform (called beta(233)) has been identified in the European eel (Anguilla anguilla). The beta(233)-isoform shares high levels of nucleotide (74.8%) and amino acid (69.9%) homology with the eel beta(1)-subunit as well as other vertebrate beta(1)-sequences. Compared with the widely expressed beta(1)-isoform, expression of beta(233)-mRNA is mainly restricted to epithelial tissues. Seawater acclimation induced increases in beta(233)-mRNA levels in kidney, gill, and intestine of migratory "silver" but not the nonmigratory "yellow" adult eels, suggesting that the factors responsible for this upregulation are themselves developmentally regulated. Expression of a variably glycosylated 40- to 52-kDa beta(233)-protein in both gill "chloride" and intestinal epithelial cells suggests that the beta(233)-isoform of Na,K-ATPase may play an important functional role in the major osmoregulatory tissues of euryhaline fish such as the eel.     

Ubiquitin C-terminal hydrolase-L1 (Uch-L1) correlates with gonadal transformation in the rice field eel

The ubiquitin-proteasome pathway is crucial for a variety of biological processes, including spermatogenesis. Ubiquitin C-terminal hydrolase-L1 (Uch-L1) is thought to associate with monoubiquitin to control ubiquitin levels. Here, we report the identification of Uch-L1 cDNA from the testis of the rice field eel, a natural sex reversal vertebrate, by using cDNA microarray analysis. Uch-L1 encodes a protein of 220 amino acids that shows high homology to Uch-L1 of vertebrates, especially fish species. Both mRNA and protein are mainly expressed in testis, ovotestis and ovary, as well as in the brain. Immunohistochemistry analysis revealed differential expression of Uch-L1 in three kinds of gonads. In the ovary, expression of Uch-L1 was observed mainly in the developing ovary and slightly in the mature ovary. In ovotestis during the intersex stage, Uch-L1 was expressed in the male gonad epithelium and degraded ovary. In testis, expression was observed in developing germ cells, including spermatogonia and spermatocytes. Furthermore, Uch-L1 was upregulated during gonadal transformation, especially from the beginning of the intersex stage onwards. Native-PAGE showed that Uch-L1 underwent dimerization and oligomerization in gonads, and that the relative level of dimerization/oligomerization decreased during gonadal transformation. Simultaneously, ubiquitin polypeptide expression was upregulated during this process. These results suggest that Uch-L1, via the ubiquitin-proteasome system, may play an important role not only in gametogenesis, but also in the gonadal transformation process in the rice field eel.