Using maximum likelihood method to detect adaptive evolution of HCV envelope protein-coding genes

The basic process of adaptive evolution by natural selection is the replacement of one allele gene by an- other with a higher fitness in a population. Detecting the adaptive evolution would be helpful for better un- derstanding of bio-evolutionary mechani…     

小兴安岭3种原始红松混交林土壤nirK型反硝化微生物群落特征

【目的】分析小兴安岭地区3种典型原始红松林下土壤nirK型反硝化微生物的群落结构和多样性,探索影响原始红松林土壤nirK型反硝化微生物群落的关键土壤理化因子。【方法】在黑龙江省伊春市小兴安岭凉水自然保护区内采集3种原始红松林(云冷杉红松林、椴树红松林和枫桦红松林)林下土壤样品,提取土壤微生物总DNA,PCR扩增反硝化过程中的关键酶——硝酸盐还原酶的编码基因nirK高变区片段,采用Illumina MiSeq技术对其进行测序,并运用生物信息学技术分析nirK反硝化微生物的群落结构和多样性。【结果】共获得3种林型土壤nirK型基因的848 312条有效序列,761 912条优质序列,平均长度为320 bp。3种原始红松林土壤nirK型反硝化微生物分属于三界(细菌、古菌和无明确分类地位)。3种林型土壤中均含有大量未被鉴定的nirK型基因序列,在已鉴定的nirK型反硝化微生物中各林型均以变形菌门(Proteobacteria)为主,核心菌属为慢生根瘤菌属(Bradyrhizobium)、红假单胞菌属(Rhodopseudomonas)、固氮螺菌属(Azospirillum)和伯霍尔德杆菌属(Burkholderia)。α多样性分析显示:3种原始红松林nirK型反硝化微生物的4种α多样性指数(Shannon指数、Simpson指数、Ace指数和Chao1指数)没有显著差异。但β多样性分析显示:3种林型土壤nirK型反硝化微生物群落组成差异显著(R=0.25,P<0.05)。Metastats分析表明:3种林型土壤中丰度存在显著差异的是拟杆菌门(Bacteroidetes)、广古菌门(Euryarchaeota)和变形菌门(Proteobacteria)。土壤铵态氮和全氮含量是显著影响林下土壤nirK型反硝化微生物群落组成的主要理化因子(P<0.05)。【结论】3种原始红松林土壤理化性质差异没有对nirK型反硝化微生物的α多样性指数产生显著影响,但导致β多样性差异显著,其中铵态氮和全氮含量是显著影响3种原始红松林土壤nirK型反硝化微生物群落组成的主要因子。     

Characterization of the 1918 influenza virus polymerase genes

The influenza A viral heterotrimeric polymerase complex (PA, PB1, PB2) is known to be involved in many aspects of viral replication and to interact with host factors, thereby having a role in host specificity. The polymerase protein sequences from the 1918 human influenza virus differ from avian consensus sequences at only a small number of amino acids, consistent with the hypothesis that they were derived from an avian source shortly before the pandemic. However, when compared to avian sequences, the nucleotide sequences of the 1918 polymerase genes have more synonymous differences than expected, suggesting evolutionary distance from known avian strains. Here we present sequence and phylogenetic analyses of the complete genome of the 1918 influenza virus, and propose that the 1918 virus was not a reassortant virus (like those of the 1957 and 1968 pandemics), but more likely an entirely avian-like virus that adapted to humans. These data support prior phylogenetic studies suggesting that the 1918 virus was derived from an avian source. A total of ten amino acid changes in the polymerase proteins consistently differentiate the 1918 and subsequent human influenza virus sequences from avian virus sequences. Notably, a number of the same changes have been found in recently circulating, highly pathogenic H5N1 viruses that have caused illness and death in humans and are feared to be the precursors of a new influenza pandemic. The sequence changes identified here may be important in the adaptation of influenza viruses to humans.     

Avian flu: multiple introductions of H5N1 in Nigeria

As the avian influenza virus H5N1 swept from Asia across Russia to Europe, Nigeria was the first country in Africa to report the emergence of this highly pathogenic virus. Here we analyse H5N1 sequences in poultry from two different farms in Lagos state and find that three H5N1 lineages were independently introduced through routes that coincide with the flight paths of migratory birds, although independent trade imports cannot be excluded.     

onc sequences (v-fes) of Snyder-Theilen feline sarcoma virus are derived from noncontiguous regions of a cat cellular gene (c-fes)

Type C sarcoma viruses are genetic recombinants containing portions of replication-competent helper viruses linked to sarcoma virus-specific sequences (generically designated onc genes) which are thought to be required for acute fibroblast transformation. The onc elements of different avian and mammalian sarcoma viral isolates are each homologous to subsets of cellular DNA sequences which have no well-defined role in normal cells. Because of the lack of significant homology between helper viral genes and cellular onc sequences, the recombinational mechanisms which facilitate the formation of sarcoma viral genomes remain unclear. In Moloney murine sarcoma virus, viral onc (or v-mos) and cellular onc (or c-mos) sequences exhibit complete and uninterrupted homology as determined by heteroduplex and restriction enzyme analyses of molecularly cloned DNA. By contrast, the cellular counterparts of the onc elements of Rous sarcoma virus (G. Cooper and R. Parker, personal communication), avian erythroblastosis virus (B. Vennstrom, personal communication), Abelson leukaemia virus (D. Baltimore, personal communication), Harvey sarcoma virus (E. Scolnick, personal communication) and simian sarcoma virus (R. Gallo, personal communication) are now known to contain intervening sequences which do not appear in the respective viral genomes. Here we report the use of the Southern blot technique to examine cat cellular DNA sequences (c-fes) homologous to the onc gene (v-fes) of Snyder-Theilen feline sarcoma virus (ST-FeSV). We used cloned DNA 'probes' containing defined portions of the ST-FeSV genome to show that v-fes sequences originate from at least four noncontiguous sequences in cat cellular DNA, separated from each other by intervening sequences.     

鄂尔多斯盆地城华地区长3油组高分辨率层序地层学分析

运用高分辨率层序地层学的基准面旋回原理,以钻井、测井资料的综合研究为基础,对鄂尔多斯盆地城华地区长3油层组进行高分辨率层序地层学分析,将其划分为超短期、短期和中期3个级次的基准面旋回层序.各级基准面旋回可进一步分为向上"变深"和向上"变浅"非对称型与对称型两大类3种基本层序类型和更多的亚类型.重点论述了超短期基准面旋回层序沉积背景、叠加式样和沉积动力学过程.在研究超短期和短期旋回叠加和分布规律的基础上,总结出短期基准面旋回的分布模式.研究表明自水下分流河道向河口坝中期基准面旋回层序结构稳定的变化规律,与处于三角洲强烈进积期的长3油层组沉积演化特征是一致的.     

Multiple sclerosis and human T-cell lymphotropic retroviruses

A combination of different types of data suggests that some multiple sclerosis patients respond immunologically to, and have cerebrospinal T cells containing, a retrovirus that is related to, but distinct from, the three types of human T-cell lymphotropic viruses. The role of this virus in multiple sclerosis is uncertain.     

A relationship between the yeast cell cycle genes CDC4 and CDC36 and the ets sequence of oncogenic virus E26

We report here significant primary sequence homology among the predicted translational products of three genes: CDC4 , CDC36 and ets. CDC4 and CDC36 are Saccharomyces cerevisiae cell division cycle genes, while ets is a transformation-specific sequence of avian erythroblastosis virus E26. The deduced primary structures of the three gene products were compared by computer to a large data base of known and predicted protein sequences. The search revealed 22.0-25.5% identity over regions of 140-206 codons, respectively between the different pairwise combinations. For these particular sequences, these identity scores fall 3.4-4.0 standard deviations above the empirically-determined mean values of fortuitous similarity. S. cerevisiae calls require CDC36 and CDC4 in order to complete two early events in the cell cycle: execution of start ( CDC36 ) and spindle pole body separation ( CDC4 ). In virus E26, the ets sequence is linked in frame with delta gag and mybE in the tripartite structure 5'-delta gag- mybE -ets-3', comprising the E26 transforming oncogene. The homologies described here suggest that the biochemical functions or regulation of the CDC4 , CDC36 and ets products may be related.     

Speciation- induced heritable cytosine methylation changes in polyploid wheat

To study possible epigenetic changes accompanying polyploid speciation, genomic DNA from natural polyploid wheats and their putative diploid progenitors were digested with a pair of isoschizomers Hpa II / Msp I and hybridized to 21 different types of low-copy DNA sequences. It was found that cytosine methylation changes were abundant in natural polyploid wheats after their speciation. The hybridization of the same set of sequences to a synthetic hexaploid wheat along with its parental lines indicated that the extensive DNA methylation changes already existed in the early generations (S5, S6 and Sy) of this plant. Moreover, the high similarity of the changed restriction fragment length polymorphism (RFLP) patterns among three randomly chosen individual plants suggested that the methylation changes occurred even earlier, and/or were of a nonrandom nature. The changed patterns were stably inherited in the three successive selfed generations. Though methylation changes are probably a genome-wide occurrence, they appeared to be confined to the specific types of DNA sequences. The possible implications of the rapid and extensive cytosine methylation changes for several attributes of allopolyploid genome evolution, such as genetic diploidization and gene diversification, are discussed .     

基于 MPEG 国际标准压缩视频流的镜头切分算法

镜头切分是实现对动态视频基于内容检索的第一步，以检测出来的镜头作为基本单元，可以进一步对视频内容进行分析和建立索引。从实用角度看，目前越来越多的动态视频资料都是以压缩形式存储和传输，所以，研究基于压缩视频流的算法更有实际意义。本文旨在提出一种基于ＭＰＥＧ国际标准压缩视频流的镜头自动切分算法，通过利用ＭＰＥＧ数据流中已有的信息，如离散余弦变换（ＤＣＴ）系数和运动向量，只进行最小程度的解码，来检测镜头间的边界，从而实现镜头切分。针对实际视频流中镜头切换方式的复杂性，本文提出了三个算法分别处理不同情况，并将这三个算法以树形分类器的方式组织在一起，形成一个系统。通过对十段不同类型的ＭＰＥＧ－Ⅰ压缩视频节目进行镜头切分实验，取得了９０％以上的正确率。     

长江三角洲晚第四纪地层层序特征

通过289口钻孔资料的分析,以下切河谷底部的侵蚀面及河间地古土壤层顶面为层序界面,据此将长江三角洲晚第四纪地层划分为三个层序,古河谷和古河间地的层序界面埋深相差较大,但所划分的三个层序在横向上可以进行对比,长江三角洲晚第四纪地层存在古河谷相序和古河间地等两类相序以及四种层序组合方式,其中三期古河谷充填层序具有套叠式结构,证明古河谷的发育具有继承性,且规模逐渐缩小,长江晚第四纪古河谷经历了“下切—充填—海泛—三角洲进积—再下切”的周期性发育过程     

Nucleotide sequence of chicken c-myb complementary DNA and implications for myb oncogene activation

Avian myeloblastosis virus (AMV), like other acute transforming viruses, arose by recombination between its helper virus and host cellular sequences. The latter sequences, termed v-myb, are responsible for the oncogenic properties of the virus. AMV causes acute myeloblastic leukaemia in chickens and transforms a specific class of haematopoietic cells in vitro, but does not induce morphological transformation of cultured fibroblasts, suggesting that only a restricted target-cell population is responsive to its transforming gene product. The normal cellular counterpart of v-myb, c-myb, is highly conserved and is present in all vertebrate and some invertebrate species examined. DNA rearrangements and altered expression of the myb oncogene have been reported in mouse lymphoid tumours and human myeloid and colon tumours. The mechanism of activation of the cellular proto-oncogenes is thought to involve the structural alteration of the coding regions that result in either the synthesis of an altered gene product or the enhanced expression of a proto-oncogene caused by alterations in its regulatory elements. To distinguish between these two mechanisms, we have cloned and sequenced the chicken c-myb complementary DNA and compared it with that of v-myb sequences. We demonstrate that during the transduction of the cellular sequences and/or viral passage a substantial portion of the coding region of the c-myb gene has been lost from both the 5' and 3' ends, resulting in the generation of a truncated gene product that mediates the transforming function of the virus.     

百色盆地百49块百岗组三段高分辨率层序地层学分析

以高分辨率层序地层学理论为指导，通过地表露头、岩芯、测井资料的综合研究，并结合地震剖面资料，分析了百色盆地塘寨油田百49块古近系百岗组三段不同级别的层序界面和湖泛面特征及识别标志，划分出1个长期、3个中期、14个短期基准面旋回层序。在此基础上，详细讨论了各级次基准面旋回层序的垂向序列、岩性岩相组合、结构类型及更加样式等特征，并探讨了高分辨率层序地层学的研究成果在区块油气开发工程中的应用前景。     

基于动态算法的序列分析

为了获得2009年新型甲型H1N1流感病毒与2008流感病毒的基因序列及氨基酸序列的一致性，以便对一个基因家族的生物学特征有一个简明扼要的了解，针对目前流行的新型甲型H1N1流感病毒的基因序列及其所编码的氨基酸序列，采用动态规划算法对其一级序列进行序列相似度分析，获得了2009年新型甲型H1N1流感病毒的NA和M基因片段以及2008年猪源性甲型H1N1流感病毒的相应基因片段同源性高、在有些位点发生了基因突变增添和突变缺失等重要基因信息。为此次新型甲型H1N1流感病毒的研究提供了依据。     

伪距离空间中一些广义压缩型映象的不动点

本文在完备的伪距离空间中,讨论了具两种广义压缩型条件的可换双映象对的公共严格周期点和不动点的问题,得到两个主要定理.在此基础上,还讨论了三种类型的映象列的严格周期点和不动点问题,相应地得到六个推论.