Two human valyl-tRNA synthetase-encoding cDNA sequences deposited in GenBank display extensive differences

Five blocks of significant differences exist between two published sequences of the cDNA encoding human valyl-tRNA synthetase (GenBank X59303 and M98326). By comparison with the partial sequence of rat valyl-tRNA synthetase (GenBank M98327) the correct sequence can be deduced for two such blocks. The possible origin of the diversity for the two sequences is discussed.     

传染性法氏囊病病毒中国强毒株A节段cDNA基因的克隆和序列分析

以来自哈尔滨传染性法氏囊病病毒（ＩＢＤＶ） 强毒株（Ｈａｒｂｉｎ 毒株,Ｈ） 的基因组ＲＮＡ为模板,用反转录聚合酶链反应（ＲＴ－ ＰＣＲ） 的方法得到了其Ａ 节段的全长ｃＤＮＡ 片段,分５＇端（１ ６５９ｂｐ） 和３＇端（１ ４４４ｂｐ） 上下两段分别克隆到ｐＧＥＭＢ○Ｒ － Ｔ 载体上,测定了其核苷酸顺序,在长为３ １０１ ｂｐ 中含有两个阅读框ＯＲＦＡ１ 和ＯＲＦＡ２ ,分别编码１ ０１２ 个氨基酸的前体蛋白（ＶＰ２ － ４ －３） 和１４５ 个氨基酸的ＶＰ５,ＯＲＦＡ１ 和ＯＲＦＡ２ 有部分的重叠。将核苷酸序列及推测出的氨基酸序列与已报道的ＩＢＤＶ 血清Ⅰ型和Ⅱ型毒株的相应序列进行了比较,结果表明：Ｈ 毒株与其它血清Ⅰ型毒株之间,在核苷酸水平上存在２５ｂｐ － ２６７ｂｐ 的差异;在氨基酸水平上存在１７ ～４０ 个氨基酸的差异。在ＶＰ２ － ４ － ３ 内比较显示,Ｈ 毒株与Ｐ２ 、Ｃｕ－ １ 之间氨基酸的差异最小为１ ．７％ ,Ｈ 毒株与ＵＫ６６１ 之间氨基酸的差异最大为３ ．９ ％ 。变异主要发生在ＶＰ２ 的可变区（２０６ － ３５０ 位氨基酸） ,在Ｈ 毒株所特有的１２ 个氨基酸当中,该区就占５ 个,代表１ ．７６ ％ 的变异。ＶＰ４、ＶＰ３ 和ＶＰ５区各有     

Sequence boundary and related sedimentary and diagenetic facies formed on Middle Permian mid-oceanic carbonate platform: Core observation of Akiyoshi Limestone,Southwest Japan

Detailed core observation of the Akiyoshi Limestone, Southwest Japan, reveals a sequence boundary and related sedimentary and diagenetic facies formed on a late Murgabian (Middle Permian) mid-oceanic carbonate platform. The sequence boundary lies upon karstified bioclastic grainstone and is overlain by peritidal lime- and dolo-mudstone. The karstified bioclastic grainstone, which had been affected by subaerial exposure and early diagenetic processes, is characterized by crystal silts, prismatic, bladed and dogtooth cements, blackened limestone features, and alveolar textures. The overlying peritidal lime- and dolo-mudstone is 8 m thick and exhibits fenestrae, fissures, laminations, black pebbles, and low-diversity biota composed exclusively of ostracodes and calcispherids. The sequence boundary almost coincides with a major fusulinoidean biostratigraphic boundary. A sea-level fall in the late Murgabian resulted in a biotic turnover and formed the sequence boundary and the karst textures. The following relatively slow transgression resulted in the deposition of the thick transgressive peritidal unit.     

Geographic distribution and recombination of genomic fragments on the short arm of chromosome 2 of Arabidopsis thaliana

Abstract: Range expansion from Pleistocene refugia and anthropogenic influences contribute to the present distribution pattern of Arabidopsis thaliana. We scored a genome-wide set of CAPSs and found two markers with an east-west geographic distribution across the Eurasian range of the species. Regions around the two SNPs were sequenced in 98 accessions, including newly collected plants from Middle Asia and Western Siberia. These regions correspond to a gene (∼ 1500 bp) and a non-coding region (∼ 500 bp) 300 kbp apart on chromosome 2. Nucleotide diversities, π, of the two sequenced fragments were 0.0032 and 0.0130. The haplotypes of both sequences belonged to one of two groups: a rather uniform "Asian" and a more variable "European" haplotype group, on the basis of non-disjunct clusters of SNPs. Recombination between "Asian" and "European" haplotypes occurs where they meet. Especially in the "European" haplotype, many rare SNP variants representing independent mutations are scattered among the shared haplotype-specific SNPs. This agrees with previous suggestions of two large haplotype groups in A. thaliana and the post-glacial colonization of central Europe from the east and the west. A clear correlation between climatic factors and the haplotype distribution may reflect the dispersal history rather than local climate adaptation. The pattern of SNP variation within the contiguous sequences explains why only a minority of SNPs selected across the genome show evidence of this geographic pattern.     

Sequencing, expression, and characterization of cDNA expressed flavin-containing monooxygenase 2 from mouse

The cDNA clone of mouse flavin-containing monooxygenase 2 (FMO2) was obtained as an expressed sequence tag (EST) isolated from a female mouse kidney cDNA library from the I.M.A.G.E. consortium (I.M.A.G.E. CloneID 1432164). Complete sequencing of the EST derived a nucleotide sequence for mouse FMO2, which contains 112 bases of 5' flanking region, 1607 bases of coding region, and 309 bases of 3' flanking region. This FMO2 sequence encodes a protein of 535 amino acids including two putative pyrophosphate binding sequences (GxGxxG/A) beginning at positions 9 and 191. Additionally, this mouse FMO protein sequence shows 87 and 86% homology to rabbit and human FMO2 respectively. The mouse FMO2 sequence was subcloned into the expression vector pJL-2, a derivative of pKK233-2 and used to transform XL1-Blue Escherichia coli. FMO activity in particulate fractions isolated from isopropyl-beta-D-thiogalactopyanoside (IPTG) induced cells was heat stable (45 degrees C for 5 min) and demonstrated optimal activity at a relatively high pH of 10.5. The expressed FMO2 enzyme showed catalytic activity towards the FMO substrate methimazole and further analysis of E. coli fractions utilizing NADPH oxidation demonstrated that the mouse FMO2 enzyme also exhibits catalytic activity towards thiourea, trimethylamine, and the insecticide phorate.     

Genomics of steroid hormones: in silico analysis of nucleotide sequence variants (polymorphisms) of the enzymes involved in the biosynthesis and metabolism of steroid hormones

Alterations of steroid hormone biosynthesis and metabolism are suspected to be involved in the pathogenesis of several diseases. Several polymorphisms of the enzymes involved in these processes have already been described and some could be associated with certain diseases. We attempted to examine the sequence variants of these genes in order to find novel variants by an in silico analysis. We analyzed the known human nucleotide sequences of the enzymes p450 side-chain cleavage enzyme, steroid 17-alpha-hydroxylase/17,20-lyase, 3-beta-hydroxysteroid dehydrogenase types 1 and 2, 21-hydroxylase, 11-beta-hydroxylase, aldosterone synthase, aromatase, 11-beta-hydroxysteroid dehydrogenase types 1 and 2, steroid 5-alpha-reductase types 1 and 2, steroid 5-beta-reductase, dehydroepiandrosterone sulfotransferase, 17-beta-hydroxysteroid dehydrogenase types 1–3. The analysis was performed using the National Center for Biotechnology Information Database by the search tool blastn. We found numerous sequence variants in both coding and non-coding sequences. The majority of these sequence variants have already been described, nevertheless, some appear as novel variants. Some of these may also have functional significance. We hypothesize over the possible significance of these findings and briefly review the available literature.     

The Hansenula polymorpha (strain CBS4732) genome sequencing and analysis

The methylotrophic yeast Hansenula polymorpha is a recognised model system for investigation of peroxisomal function, special metabolic pathways like methanol metabolism, of nitrate assimilation or thermostability. Strain RB11, an odc1 derivative of the particular H. polymorpha isolate CBS4732 (synonymous to ATCC34438, NRRL-Y-5445, CCY38-22-2) has been developed as a platform for heterologous gene expression. The scientific and industrial significance of this organism is now being met by the characterisation of its entire genome. The H. polymorpha RB11 genome consists of approximately 9.5 Mb and is organised as six chromosomes ranging in size from 0.9 to 2.2 Mb. Over 90% of the genome was sequenced with concomitant high accuracy and assembled into 48 contigs organised on eight scaffolds (supercontigs). After manual annotation 4767 out of 5933 open reading frames (ORFs) with significant homologies to a non-redundant protein database were predicted. The remaining 1166 ORFs showed no significant similarity to known proteins. The number of ORFs is comparable to that of other sequenced budding yeasts of similar genome size.