On the future of genomic data

Many of the challenges in genomics derive from the informatics needed to store and analyze the raw sequencing data that is available from highly multiplexed sequencing technologies. Because single week-long sequencing runs today can produce as much data as did entire genome centers a few years ago, the need to process terabytes of information has become de rigueur for many labs engaged in genomic research. The availability of deep (and large) genomic data sets raises concerns over information access, data security, and subject/patient privacy that must be addressed for the field to continue its rapid advances.     

Molecular genetic markers of DNA polymorphism and their genomic positioning

A comparative analysis of polymorphism of DNA fragments flanked by terminal regions of retrotransposon-like elements of the R175 family in rice and wheat varieties is performed. Differences are revealed in the distribution and polymorphism of such regions, attesting to the characteristics of their mutual positioning. The need in gene pool investigations to take into account the belonging of molecular genetic markers to various families of genomic elements differing in localization, structural and functional organization, conservatism/polymorphism, and evolution is shown.     

Aging in the natural world: comparative data reveal similar mortality patterns across primates

Human senescence patterns-late onset of mortality increase, slow mortality acceleration, and exceptional longevity-are often described as unique in the animal world. Using an individual-based data set from longitudinal studies of wild populations of seven primate species, we show that contrary to assumptions of human uniqueness, human senescence falls within the primate continuum of aging; the tendency for males to have shorter life spans and higher age-specific mortality than females throughout much of adulthood is a common feature in many, but not all, primates; and the aging profiles of primate species do not reflect phylogenetic position. These findings suggest that mortality patterns in primates are shaped by local selective forces rather than phylogenetic history.     

数据库技术在海洋生物资源与生物栖息环境数据管理中的应用

讨论了如何建立和管理符合地理信息系统需要的海洋生物资源与生物栖息环境数据库。数据库采用Access开发平台，开发操作界面清晰明了，开发的功能有数据录入、导入、导出、查询、修改、汇总统计、打印等，系统界面用户可视化，清晰、直观地显示查询结果，其适用范围是针对海上勘测海洋生物资源与生物栖息环境的专业数据管理，能胜任数据库的日常维护与管理。同时介绍了数据库技术在数据管理中的作用。数据库在日后的海洋渔业资源与环境的研究、评价中必将得到广泛的应用。     

数据库技术在海洋生物资源与生物栖息环境数据管理中的应用

讨论了如何建立和管理符合地理信息系统需要的海洋生物资源与生物栖息环境数据库。数据库采用Access开发平台，开发操作界面清晰明了，开发的功能有数据录入、导入、导出、查询、修改、汇总统计、打印等，系统界面用户可视化，清晰、直观地显示查询结果，其适用范围是针对海上勘测海洋生物资源与生物栖息环境的专业数据管理，能胜任数据库的日常维护与管理。同时介绍了数据库技术在数据管理中的作用。数据库在日后的海洋渔业资源与环境的研究、评价中必将得到广泛的应用。     

Detection of genomic signatures for pig hairlessness using high-density SNP data

Hair provides thermal regulation for mammals and protects the skin from wounds, bites and ultraviolet (UV) radiation, and is important in adaptation to volatile environments. Pigs in nature are divided into hairy and hairless, which provide a good model for deciphering the molecular mechanisms of hairlessness. We conducted a genomic scan for genetically differentiated regions between hairy and hairless pigs using 60K SNP data, with the aim to better understand the genetic basis for the hairless phenotype in pigs. A total of 38405 SNPs in 498 animals from 36 diverse breeds were used to detect genomic signatures for pig hairlessness by estimating between-population (F_ST) values. Seven diversifying signatures between Yucatan hairless pig and hairy pigs were identified on pig chromosomes (SSC) 1, 3, 7, 8, 10, 11 and 16, and the biological functions of two notable genes, RGS17 and RB1, were revealed. When Mexican hairless pigs were contrasted with hairypigs, strong signatures were detected on SSC1 and SSC10, which harbor two functionally plausible genes, REV3L and BAMBI. KEGG pathway analysis showed a subset of overrepresented genes involved in the T cell receptor signaling pathway, MAPK signaling pathway and the tight junction pathways. All of these pathways may be important in local adaptability of hairless pigs. The potential mechanisms underlying the hairless phenotype in pigs are reported for the first time. RB1 and BAMBI are interesting candidate genes for the hairless phenotype in Yucatan hairless and Mexico hairless pigs, respectively. RGS17, REV3L, ICOS and RASGRP1 as well as other genes involved in the MAPK and T cell receptor signaling pathways may be important in environmental adaption by improved tolerance to UV damage in hairless pigs. These findings improve our understanding of the genetic basis for inherited hairlessness in pigs.     

水稻白叶枯病菌糖基化岛GI基因的分子鉴定

为了阐述水稻白叶枯病菌(Xanthomonas oryzae pv.oryzae,Xoo)糖基化岛(Glycosylation Island,GI)基因的结构特征以及可能的生物学功能,研究通过基因克隆和序列分析,对GI基因结构特征进行了鉴定;通过与铜绿假单胞菌(Pseudomonas aeruginosa,Pa)a型短GI基因的比较,对XooGI基因进行了功能推测分析。用特异性引物进行PCR扩增,从野生型菌株PXO99A基因组中克隆了10个GI基因序列。该GI插在鞭毛基因簇中,上游为转录调控因子基因fleQxoo,下游为鞭毛基体蛋白基因fliExoo。GI基因均为单拷贝,转录方向相同。GI基因核苷酸序列在Xoo和Paa型短岛中同源性达41.98%~78.58%,其中糖基转移酶基因rbfC具有保守结构域(Glycos_transf_2),在病原黄单胞中同源性较高。在GI基因启动子中存在σ54保守结合序列GG-(N10)-GC和转录调控因子FleQxoo结合序列CC-(N4)-C-(N4)-T。因此,XooGI可能具有进化上的结构和功能保守性;其基因转录可能受到σ54和FleQxoo的直接调控。     

Mutation pressure and the evolution of organelle genomic architecture

The nuclear genomes of multicellular animals and plants contain large amounts of noncoding DNA, the disadvantages of which can be too weak to be effectively countered by selection in lineages with reduced effective population sizes. In contrast, the organelle genomes of these two lineages evolved to opposite ends of the spectrum of genomic complexity, despite similar effective population sizes. This pattern and other puzzling aspects of organelle evolution appear to be consequences of differences in organelle mutation rates. These observations provide support for the hypothesis that the fundamental features of genome evolution are largely defined by the relative power of two nonadaptive forces: random genetic drift and mutation pressure.     

分子间的作用及其结构适应性

某些分子间的作用无法的用范德华力、氢键、介电常数、偶极矩等化学基本理论来加以解释，引入控制论的方法对这些分析间的作用进行研究后的结果表明，选择性分析间引力很可能是分子是最强的物理作用，而分子间的化学作用亦与分子间的结构适应性密切相关。     

通过多基因组比较的方法在5种绿球蓝细菌中识别基因组岛(英文)

为探索水平基因转移在绿球蓝细菌基因组多样性中的作用,5个高光适应性绿球蓝细菌基因组被比较.先用BLASTP两两最佳匹配搜索和基因位置保守性的方法预测直系同源基因,并进一步计算每个基因组中所有基因在其他4种绿球蓝细菌基因组中直系同源基因的数量,从而达到识别外源基因的目的;而基因组岛是指由1个或几个连续外源基因组成的区域.结果表明:在5个绿球蓝细菌基因组中共识别出了16至52个不等的基因组岛,它们中的许多基因在病毒基因组或富含病毒的环境样本中都有同源基因.以上这些结果显示,在绿球蓝细菌中,病毒可能介导了基因的水平转移,从而导致了基因组的多样性.     

Functional organization of the second cortical visual area in primates

The functional organization of the second cortical visual area was examined with three different anatomical markers: 2-[14C]deoxy-D-glucose, cytochrome oxidase, and various myelin stains. All three markers revealed strips running throughout the area, parallel to the cortical surface. The boundaries of these strips provide an anatomical criterion for defining the borders of this extrastriate region. Further, the demonstration of these strips allows a functional and anatomical analysis of modules in the area, just as the recent demonstration of spots in the primary visual cortex has allowed an analysis of modules there. The strips differ structurally and functionally from interstrip regions and these differences are similar to those seen between the spots and the interspot regions in the primary visual cortex. In the macaque the strips and spots differ with regard to binocular organization.     

Living relative of the microfossil Kakabekia

A living, ammonia-obligate, umbellate form, similar to the Precambrian microfossil Kakabekia umbellata Barghoorn, has been isolated from two soil specimens collected at Harlech, Wales. This organism is amenable to culture on agar and in broth. The two soil specimens are similar in that they differ from a typical clay loam in high content of carbon, hydrogen, and organic nitrogen and low levels of sodium, potassium, and titanium. In all other constituents, such as calcium, magnesium, and iron, they are quite dissimilar. Kakabekia-like forms can be grown in glucose-anmonia media with the latter as the sole source of nitrogen, but they can also be grown on peptone and silicate in glucose-free media. Ammonia is necessary, and growth is always slow without glucose. The fission process was not observed, but the enlargement and differentiation of a preumbellate structure into its "mature" form, followed by disintegration (senescence) of this stage, was seem. An ontogeny is proposed in which the stalk and basal bulb of the complete umbellate structure are assumed to be part of the reproductive appartus.     

Red-green cone interactions in the increment-threshold spectral sensitivity of primates

Threshold spectral sensitivity of primate eyes is the upper envelope of the sensitivity of three response channels. Sensitivity in the green and red channels is modeled as linear difference functions reflecting neural interaction between cones containing photopigments with 535- and 575-nanometer peaks. Sensitivity in the blue channel seems determined by a single class of cones containing a 445-nanometer photopigment.     

园艺植物种质资源试管保存与鉴定

试管保存是种质资源的重要保存方式之一 ,目前已广泛应用到植物种质保存中。综述了园艺植物试管保存方法、影响因素及保存后存活率和遗传性的鉴定等 ,并分析了当前存在的问题及解决策略     

二化螟抗药性监测方法及相对敏感基线

选用安徽太湖县二化螟 (ChilosuppressalisWalker)自然种群 ,用 6种药剂对 6龄幼虫进行毒力测定 ,并与国内外已知敏感品系的LD50 值比较 ,在证实了该种群具有较高的敏感水平后 ,经室内纯化和连续饲养近 2 0代 ,育成相对敏感品系(TH S)。为提高试验准确性 ,简化操作 ,使用 4龄幼虫进行抗药性研究。用于测试的 4龄幼虫形态特征为头宽 (0 86±0 0 4)mm ,体重 (8 5± 1 5 )mg ,前胸与头宽之比 1 19± 0 0 4,体长 (10 0± 0 8)mm。在详细观察 4龄幼虫发育历期和形态特征后 ,选用该龄幼虫 ,建立了包括沙蚕毒素、有机磷、杂环类和生物制剂等类的 6种杀虫剂的相对敏感基线。     

Sequencing and analysis of Neanderthal genomic DNA

Our knowledge of Neanderthals is based on a limited number of remains and artifacts from which we must make inferences about their biology, behavior, and relationship to ourselves. Here, we describe the characterization of these extinct hominids from a new perspective, based on the development of a Neanderthal metagenomic library and its high-throughput sequencing and analysis. Several lines of evidence indicate that the 65,250 base pairs of hominid sequence so far identified in the library are of Neanderthal origin, the strongest being the ascertainment of sequence identities between Neanderthal and chimpanzee at sites where the human genomic sequence is different. These results enabled us to calculate the human-Neanderthal divergence time based on multiple randomly distributed autosomal loci. Our analyses suggest that on average the Neanderthal genomic sequence we obtained and the reference human genome sequence share a most recent common ancestor approximately 706,000 years ago, and that the human and Neanderthal ancestral populations split approximately 370,000 years ago, before the emergence of anatomically modern humans. Our finding that the Neanderthal and human genomes are at least 99.5% identical led us to develop and successfully implement a targeted method for recovering specific ancient DNA sequences from metagenomic libraries. This initial analysis of the Neanderthal genome advances our understanding of the evolutionary relationship of Homo sapiens and Homo neanderthalensis and signifies the dawn of Neanderthal genomics.     

Functional genomic analysis of the Wnt-wingless signaling pathway

The Wnt-Wingless (Wg) pathway is one of a core set of evolutionarily conserved signaling pathways that regulates many aspects of metazoan development. Aberrant Wnt signaling has been linked to human disease. In the present study, we used a genomewide RNA interference (RNAi) screen in Drosophila cells to screen for regulators of the Wnt pathway. We identified 238 potential regulators, which include known pathway components, genes with functions not previously linked to this pathway, and genes with no previously assigned functions. Reciprocal-Best-Blast analyses reveal that 50% of the genes identified in the screen have human orthologs, of which approximately 18% are associated with human disease. Functional assays of selected genes from the cell-based screen in Drosophila, mammalian cells, and zebrafish embryos demonstrated that these genes have evolutionarily conserved functions in Wnt signaling. High-throughput RNAi screens in cultured cells, followed by functional analyses in model organisms, prove to be a rapid means of identifying regulators of signaling pathways implicated in development and disease.