Why Life Histories Evolve Differently in the Sea

Marine life histories differ from terrestrial life historiesbecause seawater is denser and more viscous than air, becausedesiccation is not a problem for organisms in water, and becausefood is abundant in suspension and solution. (1) Mating andcompetition for paternity in the sea often differs. Female gametesare often spawned freely. Passively dispersed spermatophorescould in some cases provide single paternity to an entire clutchof offspring. Penises of sessile animals reach far for copulation.There are no pollinators. (2) In many clades of benthic marineanimals, greater dispersal of offspring is associated with largeadult size, and greater parental care of offspring and reducedplanktonic larval periods are associated with small adult size.(3) Many benthic marine animals are colonies with modular construction,and these also commonly brood embryos and have short-lived larvae,in contrast to related solitary forms. (4) Unlike dispersalof terrestrial animals, larval dispersal of marine animals isoften obligate with sexual reproduction and often includes aprecompetent period during which larvae cannot settle at goodsites. Unlike terrestrial seeds, marine larvae have no clearadaptations for dispersal, often grow during dispersal, andoften leave bad sites. Feeding planktonic larvae are commonamong marine animals and rare among other aquatic animals, perhapsbecause of persistent aquatic routes between habitable sitesfor marine animals. Peculiarities in marine life histories mayinfluence many aspects of evolution in the sea. Closely relatedsedentary marine animals can differ greatly in larval dispersalwith consequences for recruitment to populations, genetic exchangebetween benthic populations, adaptation to local conditions,sex allocation, interaction with kin, speciation, and extinction.     

Urease-Encoding Genes in Ammonia-Oxidizing Bacteria

Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth. We sequenced the urease operons from two AOB, the β-proteobacterium Nitrosospira sp. strain NpAV and the γ-proteobacterium Nitrosococcus oceani. In both organisms, all seven urease genes were contiguous: the three structural urease genes ureABC were preceded and succeeded by the accessory genes ureD and ureEFG, respectively. Green fluorescent protein reporter gene fusions revealed that the ure genes were under control of a single operon promoter upstream of the ureD gene in Nitrosococcus oceani. Southern analyses revealed two copies of ureC in the Nitrosospira sp. strain NpAV genome, while a single copy of the ure operon was detected in the genome of Nitrosococcus oceani. The ureC gene encodes the alpha subunit protein containing the active site and conserved nickel binding ligands; these conserved regions were suitable primer targets for obtaining further ureC sequences from additional AOB. In order to develop molecular tools for detecting the ureolytic ecotype of AOB, ureC genes were sequenced from several β-proteobacterial AOB. Pairwise identity values ranged from 80 to 90% for the UreC peptides of AOB within a subdivision. UreC sequences deduced from AOB urease genes and available UreC sequences in the public databases were used to construct alignments and make phylogenetic inferences. The UreC proteins from β-proteobacterial AOB formed a distinct monophyletic group. Unexpectedly, the peptides from AOB did not group most closely with the UreC proteins from other β-proteobacteria. Instead, it appears that urease in β-proteobacterial autotrophic ammonia oxidizers is the product of divergent evolution in the common ancestor of γ- and β-proteobacteria that was initiated before their divergence during speciation. Sequence motifs conserved for the proteobacteria and variable regions possibly discriminatory for ureC from β-proteobacterial AOB were identified for future use in environmental analysis of ureolytic AOB. These gene sequences are the first publicly available for ure genes from autotrophic AOB.     

应用显微操作和PCR技术进行基因的染色体定位

介绍了一种将染色体显微操作和ＰＣＲ技术结合起来进行基因染色体定位的方法,具有简便易行,特异性和敏感性很高等特点。分析了这种定位方法的技术特点,以及ＳＳＣＰ和ＤＮＡ序列分析等方法在排除错误结果中的运用。     

Genes on mouse Chromosomes 2 and 9 determine variation in ethanol consumption

Quantitative trait locus (QTL) mapping efforts in alcohol (ethanol) research are beginning to generate promising data that may ultimately lead to the identification of genes influencing alcohol addiction. Rodents have been extensively utilized to study ethanol's rewarding and aversive effects, and to demonstrate the existence of genetic influences on traits such as free-choice ethanol-consumption, ethanol-conditioned place preference and ethanol-conditioned taste aversion. The purpose of the current investigation was to verify or eliminate from further consideration putative QTLs for free-choice ethanol consumption originally identified in BXD Recombinant Inbred (RI) strains and other informative genetic crosses. B6D2F₂ mice were utilized in a verification testing strategy to evaluate the viability of putative ethanol consumption QTLs. When data were combined from BXD RI, B6D2F₂ and short-term selected line (STSL) mapping studies, verification was obtained for two QTLs, one on Chromosome (Chr) 9 (proximal-mid) and another on Chr 2 (distal), and suggestive verification was obtained for QTLs on Chrs 2 (proximal), 3, 4, 7, and 15. In addition, the possible genetic association of ethanol consumption with conditioned place preference was evaluated. Genetic correlations were estimated from BXD RI strain means, and QTL maps for these traits were compared to evaluate the possibility of a genetic association. The correlational analysis yielded a trend (r = 0.34, p = 0.09), but no statistically significant results. However, comparisons of QTL mapping results between phenotypes suggested some possible genetic overlap for these traits, both putative measures of ethanol reward. These data suggest that the determinants of these two measures are genetically diverse, but may share some common genetic elements. Received: 15 September 1998 / Accepted: 8 October 1998     

Tandem Repetitive D Domains of the Sperm Ligand Zonadhesin Evolve Faster in the Paralogue Than in the Orthologue Comparison

Gene duplication is regarded as an important evolutionary mechanism creating genetic and phenotypic novelty. At the same time, the evolutionary mechanisms following gene duplication have been a subject of much debate. Here we analyze the sequence evolution of zonadhesin, a mammalian sperm ligand that binds to the oocyte zona pellucida in a species-specific manner. In pig, rabbit, and primates, precursor zonadhesin comprises, among others, one partial and four complete tandem repetitive D domains. The mouse precursor is distinguished by 20 additional partial D3 domains consisting of 120 amino acids each. This gene structure allows sequence comparison in both paralogues and orthologues. Detailed sequence analysis reveals that D domains evolve faster across paralogues than orthologues. Moreover, at the codon level, partial D3 paralogues of mouse show evidence of positive selection, whereas the corresponding orthologues do not. Individual posttranslational motif patterns and positive selection point to neofunctionalization of partial D3 paralogues of mouse, rather than subfunctionalization. However, as we found additional evidence for homogenization by partial gene conversion, sequence evolution of partial D3 paralogues of mouse might be better described as a combination of divergent and convergent evolution. So far, the divergence at the codon level has outbalanced the convergence at the level of smaller fragments. The probable driving force behind the evolutionary patterns observed is sexual selection. We finally discuss whether the functional determination influences the evolutionary regime acting on sperm ligands and egg receptors, respectively. [Reviewing Editor: Dr. Yves Van de Peer]     

植物病原细菌的hrp基因

hrp基因存在于4类革兰氏阴性植物病原细菌中,决定病原细菌对寄主植物致病性和诱导非寄主及抗病植物过敏性反应。本文从hrp基因族,hrp基因avr基因的关系,hrp基因的编码产物harpin蛋白,hrp基因调控与功能以及hrp基因参与植物-细菌互作等几个方面,较为详细地阐述了当前植物病原细菌hrp基因的研究状况,并分析了hrp基因未来研究的趋势。     

抗砷细菌arsH基因多样性分析

目的:研究含arsH基因抗砷微生物的多样性.方法:从NCBI数据库中收集95条arsH基因序列,通过Clustal W 1.83,Mega 3.0、DOTUR软件分别对95条序列进行多序列比对、构建系统发育树、稀释曲线等分析.结果:这些包含arsH基因的菌株分别归属于α-变形杆茵纲(约40%),γ-变形杆茵纲(35%),β-变形杆茵纲(22%),以及蓝细茵(3%).在涉及的14个科当中,Rhizo-biales所占比例最高(29%);Burkholderiales:次之(22%);Pseudomonadales和Enterobaeteriales占较少的比例,分别为18%和11%.针对数据库已有数据分析显示,含有arsH基因的微生物约89%分布在陆地,6%分布在海洋,还有5%在陆地海洋均有分布.陆地中占总比例的24%分布于土壤中;21%分布于矿山、地下水、气田、油田、受污染环境、矿坑水、淡水等环境中;约1%为植物共生菌,26%为病原微生物.结论:该基因在不同的物种之间存在水平基因转移,目前对于含arsH基因的抗砷微生物的筛选和分离工作还远远不够.     

Finding and Mapping New Genes Faster than Ever: Revisited

This article recounts some of the early days of the Human Genome Project, covering the important and sometimes controversial role that complementary DNA-based approaches played in the discovery and mapping of the majority of human genes. It also describes my involvement in this effort and my lab''s development of methods for rapid sequence identification and mapping of human genes.