不同传染性法氏囊病病毒分离株VP2基因部分核酸序列及其编码蛋白的比较

根据已报告的传染性法氏囊病病毒（ Ｉ Ｂ Ｄ Ｖ） ｃ Ｄ Ｎ Ａ 序列，在病毒 Ｖ Ｐ２ 区域，设计 １ 对引物，并在 ２ 引物上分别加 Ｐｓｔ Ⅰ和 Ｅｃｏ Ｒ Ｉ酶切位点。对 ２ 个 Ｉ Ｂ Ｄ Ｖ 分离株 Ｊ Ｓ３ 和 Ｊ Ｓ４，用异硫氰酸胍酚氯仿抽提一步法提取病毒 Ｒ Ｎ Ａ，然后进行逆转录和 Ｐ Ｃ Ｒ 扩增，将扩增片段经酶切纯化后克隆于 ｐ Ｕ Ｃ１８ 质粒载体中，以双脱氧链末端终止法测定 ｃ Ｄ Ｎ Ａ 序列。将测定的分离株与标准对照株（ Ｓ１） Ｉ Ｂ Ｄ Ｖ Ｖ Ｐ２ 基因片段的核苷酸序列进行计算机分析比较， Ｊ Ｓ３ 与 Ｓ１ 的同源性为 ９７％ ， Ｊ Ｓ４ 与 Ｓ１ 的同源性为 ９７％ ， Ｊ Ｓ３ 与 Ｊ Ｓ４ 的同源性为 ９９％ 。推导编码蛋白氨基酸序列， Ｊ Ｓ３ 和 Ｓ１ 的同源性为 ９７％ ， Ｊ Ｓ４ 与 Ｓ１ 的同源性为 ９６％ ， Ｊ Ｓ３ 和 Ｊ Ｓ４ 的同源性为 ９８％ 。这表明在我国流行的 Ｉ Ｂ Ｄ Ｖ 毒株与标准毒株相比不仅在免疫学反应上有差异，而且在病毒核酸序列上有变异，这种变异是造成疫苗免疫失败或免疫逃避的分子基础。

不同血清型腺相关病毒衣壳蛋白氨基酸残基序列分析

目的:分析不同血清型腺相关病毒衣壳蛋白(VP1)氨基酸残基序列,建立相似性比较方法和数据库,预测VP1氨基酸残基序列突变后可能隶属的血清型。方法:对不同血清型腺相关病毒VP1氨基酸残基序列分析,找出共同序列,并对序列进行对齐。分别对疏水氨基酸残基、亲水氨基酸残基和酸/碱氨基酸残基进行单独赋值,赋值参数包括侧链长度、基团数量和解离/结合强度等,再用相关系数法和差值法计算相似度。规定全局电荷决定界值,判断电荷的变化是否会引起蛋白质周围电场的显著变化。最后综合考虑四者的关系,给出与已知血清型VP1氨基酸残基序相似度。通过其他已知血清型的VP1氨基酸残基序进行验证。结果:基本上可以区分不同的血清型,并且对相同血清型中的不同亚型具有一定的容忍度。结论:对腺相关病毒衣壳蛋白VP1氨基酸残基序列与其血清型间的联系进行了探讨,希望对重组腺相关病毒为载体的基因治疗研发提供支持。

不同物种间胰岛素及其编码mRNA,DNA序列比较与分析

通过PSI BLAST搜索与人类胰岛素原 (含有 86个氨基酸 )相似的蛋白质序列 ,并进行比对 ,计算比对矩阵的相似得分和期望值 ,同时运用ClustalW算法对不同物种编码前胰岛素原mRNA及其翻译的蛋白质和DNA序列进行多重比对 .结果发现 ,脊椎动物的胰岛素蛋白质一级结构 (A链和B链 )和mRNA非常相似 ,但部分动物C肽的部分序列有差异 ;系统进化分析表明 ,人和猴、小鼠和大鼠编码胰岛素的mRNA在进化上关系相近 .各物种间编码相同氨基酸的核苷酸序列 (CDS)相同 ,但编码胰岛素的DNA序列不同 .各物种胰岛素原蛋白质序列中 ,A链和B链序列保守 ,C肽有一定的差异 ;

Micro-heterogeneity of Storage Glutelin in Rice Seed

The storage glutelin in rice ( Oryza sativa L.) seeds could be separated at least into more than 13 acidic and 19 basic polypeptides by two dimensional electrophoresis. Rice glutelin might be mainly controlled by about six major genes according to the expression of glutelin polypeptides. The acidic polypeptide of glutelin could be clearly separated into two groups by peptide mapping and N-terminal amino acid sequence analysis. These two groups were just in accord with the GluA and GluB subfamilies exactly.

Bioinformatics Analysis of Zinc Transporter from Baoding Alfalfa

[Objective] This study aimed to perform the bioinformatics analysis of Zinc transporter （ZnT） from Baoding Alfalfa. [Method] Based on the amino acid sequence, the physical and chemical properties, hydrophilicity/hydrophobicity, secondary structure of ZnT from Baoding alfalfa were predicted by a series of bioinformatics software. And the transmembrane domains were predicted by using different online tools. [Result] ZnT is a hydrophobic protein containing 408 amino acids with the theoretical pl of 5.94, and it has 7 potential transmembrane hydrophobic regions. In the sec- ondary structure, co-helix （Hh） accounted for 48.04%, extended strand （Ee） for 9.56%, random coil （Cc） for 42.40%, which was accored with the characteristic of transmembrane protein. [Conclusion] mZnT is a member of CDF family, responsible for transporting Zn^2＋ out of the cell membrane to reduce the concentration and toxicity of Zn^2＋.

Monopterus albus Contains a Sequence Homolous to the 5'cDNA of the Rat Tyrosine Kinase Receptor-encoding Gene, ptk3

From the. genome of the Rice-field Eel,Monopterus alubs partial DNA sequence has been obtained that shows homology to the 5'cDNA sequence of the gene encoding rat tyrosine kinase receptor ptk3. Southern blots revealed identical hybridization patterns in both sex.

The Full-length Genome Analysis of a Street Rabies Virus Strain Isolated in Yunnan Province of China

The epidemic of rabies has rapidly increased and expanded in Yunnan province in recent years. In order to further analyze and understand the etiological reasons for the rapid expansion of rabies in Yunnan, a strain of rabies virus CYN1009D in Yunnan was isolated, and the complete genomic sequencing was carried out, and the bioimfomative analysis on genes/encoded proteins and phylogeny with reference to sequences in GenBank was performed. The complete genome of CYN1009D was 11923 nt in length and belonged to genotype I. The genes encoding different structural proteins were all conserved in their lengths, in comparison to other strains in China. The amino acid sequence was conserved at different antigen sites of NP, but the variation was detected at the secondary phosphorylation site of position 375; variations were also detected in the phosphorylation sites at positions 63-63 and 162 of PP; the sites playing important roles in virus synthesis, budding and viral morphology in MP were conserved; two glycosylation sites were detected at Asn37 and Ash319 in GP, the neutralizing antigen sites in GP were conserved; the initial amino acid of LP （ML） was different from that of most of the strains in China （MM）; the variations in G-L region in the intergenic region were significant. The phylogenic tree showed that CYN1009D has a closer genetic relationship to the strains in Southeast Asia, indicating that prevention and control on rabies in borderland areas should be reinforced meanwhile efforts are made to control rabies in China.

The RACE amplifying and sequence analyzing of secreted aspartic proteinase gene SA76 of Trichoderma harzianum

Total RNA was isolated from mycelium of T. harzianum by Total RNA extraction kit, and two clear bands of rRNA （28S and 18S） were observed in agarose electrophoresis. By joining the 3＇end sequence with the known SA76 EST from cDNA library of T. harzianum, a full-length cDNA sequence of 2019bp was obtained, whose open reading frame contained 1593bp, a stop codon TAA, a 5＇untranslated region （5＇UTR） of 266bp, a 3＇untranslated region （3＇UTR） of 201bp, and poly （A） 29 encoded a protein of 530 amino acids, had a signal peptide. T. harzianum shared 53% identity of secreted aspartic proteinase gene with G. zeae, 37% with N. crassa and 36% with C. globosum. The full-length cDNA sequence of secreted aspartic proteinase gene from T. harzianum was cloned for the first time by using BD SMART RACE technique, which provides a foundation to obtain and validate functional genes of T. harzianum.

A cadmium metallothionein gene of ridgetail white prawn Exopalaemon carinicauda(Holthuis,1950) and its expression

Metallothioneins （MTs） are a group of low molecular weight cysteine-rich proteins capable of binding heavy metal ions. A cadmium metallothionein （EcMT-Cd） cDNA with a 189 bp open reading frame （ORF） that encoded a 62 amino acid protein was obtained from Exopalaemon carinicauda. Seventeen cysteines were in the deduced amino acid sequence, and the cysteine （Cys）-rich characteristic was revealed in different metallothioneins in other species. In addition, the deduced amino acid sequence did not contain any aromatic amino acid residues, such as tyrosine （Tyr）, tryptophan （Trp）, and phenylalanine （Phe）. EcMT- Cd mRNA was expressed in all tested tissues （the ovary, muscle, stomach, and hepatopancreas）, and its expression profiles in the hepatopancreas were very different when shrimps were exposed to seawater containing either 50 pmol/L CuSO4 or 2.5 gmol/L CdC12. The expression of EcMT-Cd was significantly up-regulated in shrimp exposed to CuSO4 for 12 h and down-regulated in shrimps exposed to CdC12 for 12 h. After 24 h exposure to both metals, its expression was down-regulated. By contrast, at 48 h the EcMT-Cd was up-regulated in test shrimps exposed to CdC12. The transcript of EcMT-Cd was very low or even absent before the zoea stage, and the expression of EcMT-Cd was detected from mysis larvae-I, then its expression began to rise. In conclusion, a cadmium MT exists in E. carinicauda that is expressed in different tissues and during different developmental stages, and responds to the challenge with heavy metal ions, which provides a clue to understanding the function of cadmium MT

Molecular Characterization of the Duck Enteritis Virus UL4 Gene

Duck enteritis virus(DEV) is a herpesvirus that causes an acute,contagious and fatal disease. In the present article,the DEV UL4 gene was cloned and sequenced from a vaccine virus. A degenerate oligonucleotide primer for the consensus site of herpesvirus UL3 gene and a specific primer located in UL5 were used in the polymerase chain reaction(PCR) to amplify a DNA product 2 086 bp in size. DNA sequence analysis revealed that a 714 bp open reading frame(ORF) of DEV encoding a 237 amino acid polypeptide is homologous to the family of herpesvirus UL4 proteins and therefore has been characterized as a DEV UL4 gene. Alignment of the DEV UL4 protein sequence with those of other alphaherpesviruses showed that 10 amino acid residues are completely conserved. Phylogenetic tree analysis showed that the seventeen alphaherpesviruses viruses analyzed were classified into four large groups,and the duck enteritis virus branched separately,closely related to the Mardiviruses group comprising Gallid herpesvirus 2(GaHV-2) ,Gallid herpesvirus 3(GaHV-3) and Meleagrid herpesvirus 1(MeHV-1) . The present study showed that the evolutionary relationship of the UL4 protein could be used for classification of alphaherpesviruses.

Characterization and expression of sweetfish （Plecoglossus altivelis） cathepsin D

Cathepsin D （CTSD） is a lysosomal acidic endoproteinase that plays an important role in immune response, In this study, we obtained sweetfish （Plecoglossus altivelis） CTSD （PaCTSD） via de-novo transcriptome sequencing of sweetfish macrophages. The full length cDNA sequence of PaCTSD was 1955 bp encoding a propeptide of 397 amino acids. The deduced protein had a calculated molecular weight of 43.17x 103. Multiple alignment with other known CTSD amino acid sequences revealed amino acid conservation through the teleosts. Phylogenetic tree analysis showed that PaCTSD grouped tightly with other fish CTSD, and was close to that of Atlantic salmon and rainbow trout. Subsequently, PaCTSD was prokaryotically expressed and refolded by the urea gradient method on a nickel-nitrilotriacetic acid column. Enzyme activity analysis showed that PaCTSD exhibited pH-dependent proteolytic activity. Quantitative real-time PCR showed that PaCTSD mRNA was expressed in all detected tissues in healthy sweetfish. The highest expression was observed in the spleen and white blood cells, followed by liver, head-kidney, kidney, intestine, gill, and muscle. After Listonella anguillarum infection, PaCTSD transcripts were up-regulated significantly in liver, spleen, white blood cells, and head-kidney of sweetfish. In summary, PaCTSD has proteolytic activity and is closely involved in the immune response of sweetfish.

Bioinformatic Analysis of zm ERECTA-LIKE2Gene from Zea mays

Zm ERECTA-LIKE2 sequences were isolated according to the Zea mays genome. The study indicates that zm ERECTALIKE2 is composed of 2 410 nucleotides and encodes a receptor-like kinase which consists of 774 amino acids by biological analysis. The results show that zm ERECTA-LIKE2 protein contains 13 domains of leucine-rich repeats and belongs to the PKclike family, it is a liposoluble protein, with a conserved transmembrane region.

New Software for the Identification and Characterization of Peptides Generated during Fontina Cheese Ripening Using Mass Spectrometry Data

The aim of this work was to design and implement a new bioinformatics software which is able to identify the protein peptides from the peaks which arise from in-source or MS/MS fragmentation. The oligopeptide fraction was extracted from Fontina cheese at different ages of ripening and subsequently analyzed by LC/MS/MS. On the resulting total ion chromatograms, the peptides were identified by a method based both on the in-source fragmentation detectable with a single-quadrupole mass analyzer and by a new software which was developed. This software performs an in-silieo digestion of the major milk proteins, it calculates all the possible peptide fragments which are generated by the loss of the first N- or C-terminal amino acids, and finally, it matches the experimental ion chromatogram with the in-silico which generated theoretical spectrum to identify the exact amino-acid protein sequence of the unknown oligopeptide. With this tool, the useful insights into the proteolytic processes which occur during Fontina cheese aging are obtained, which leads to a better knowledge about the functional features of the proteolysis end product.

Purification and Partial Characterization of an Antibacterial Protein Tz1

A strain (T3) of Bacillus has been screened from paddy field. It secretes large amount of antibacterialproteins which show a strong inhibiting activity against several pathogens of rice. This paper presentsa systematic study of the inhibition spectrum and characteristics of T3 proteins. Total proteins wereprecipitated with ammonium sulfate at 70% saturation from cell-free culture. One of the proteins(Tzl) was purified from the crude extracts with Sephadex G-100, DEAE52 and FPLC Superose 12columns. A single band was demonstrated in both 15% SDS-PAGE and IEF, with an apparent MWof 6,9 kd and a pI of 7.8. Its amino acid composition was analyzed and part of its sequence,determined.

Activation of Prophenol Oxidase PHOX-S with Limited Proteolysis in Drosophila Melanogaster

Prophenol oxidase isoform A1 was isolated from Drosophila melanogaster （The sequence has been deposited in GenBank data base under accession number AB557586） PHOX-S strain, and its characteristics and activation mechanism were determined. The NH2-terminal region of PHOX-S A1 was determined to be comprised of 15 amino acids with the following sequence MTNMKMKMKAMMR. Comparison of an alignment in the known prophenol oxidase protein sequences from Drosophila melanogaster strains showed high homology in the copper-binding sequences at the Cu （A） site of the active center. Limited proteolysis takes place between Arg-50 and Val-51. Therefore, it is concluded that prophenol oxidase PHOX-S protein was evolved at the upstream, but no evolved at the central site in Drosophila melanogaster.

Vero细胞培养传代后的2株SARS冠状病毒基因组序列变异分析

RNA病毒在复制时有易出错的倾向, 因此SARS病毒在传染或传代过程中易发生突变而产生不同的毒株, 这种机制也利于病毒逃脱宿主的免疫系统而生存下来. 许多研究也表明, 不同的SARS病毒分离株的全基因组序列存在不同程度的差异, 这些差异的研究无疑对SARS病毒疫苗的研制具有重要的指导意义. 同时, 对SARS病毒在传代过程中的遗传稳定性及核酸特性的分析, 是SARS疫苗研制不可或缺的环节. 采用PCR产物直接测序的方法, 对2株用Vero细胞培养经过多次传代的SARS病毒进行了全基因组序列的测定, 通过比较分析发现该病毒在传代过程中具有高遗传稳定性, 其中检定参比株(Sino1株)2和11代全基因组序列比较有4个碱基的变化, 而候选疫苗株(Sino3株)3与10代的基因组全序列仅有1个碱基的差异. SARS病毒在Vero细胞上传代的遗传稳定性表明, 以此制备的灭活病毒疫苗是稳定的.

A Gibbs free energy formula for protein folding derived from quantum statistics

The fundamental law for protein folding is the thermodynamic principle.The amino acid sequence of a protein determines its native structure and the native structure has the minimum Gibbs free energy.Lacking of a Gibbs free energy formula is the reason that all ab initio protein structure prediction only empirical and various empirical energy surfaces or landscapes are introduced to fill the gap.We make a quantum mechanics derivation of the Gibbs free energy formula G(X)using quantum statistics for a single conformation X.For simplicity,only monomeric self folding globular proteins are considered.

PREDICTING SUBCHLOROPLAST LOCATIONS OF PROTEINS BASED ON THE GENERAL FORM OF CHOU＇S PSEUDO AMINO ACID COMPOSITION： APPROACHED FROM OPTIMAL TRIPEPTIDE COMPOSITION

Chloroplasts are organelles found in plant cells that conduct photosynthesis. The subchloroplast locations of proteins are correlated with their functions. With the availability of a great number of protein data, it is highly desired to develop a com- putational method to predict the subchloroplast locations of chloroplast proteins. In this study, we proposed a novel method to predict subchloroplast locations of proteins using tripeptide compositions. It first used the binomial distribution to optimize the feature sets. Then the support vector machine was selected to perform the prediction of subchloroplast locations of proteins. The proposed method was tested on a reliable and rigorous dataset including 259 chloroplast proteins with sequence identity ≤ 25%. In the jack-knife cross-validation, 92.21% envelope proteins, 93.20% thylakoid mem- brane, 52.63% thylakoid lumen and 85.00% stroma can be correctly identified. The overall accuracy achieves 88.03% which is higher than that of other models. Based on this method, a predictor called ChloPred has been built and can be freely available from http：//cobi.uestc.edu.cn/people/hlin/tools/ChloPred/. The predictor will provide important information for theoretical and experimental research of chloroplast proteins.

On Using Physico-Chemical Properties of Amino Acids in String Kernels for Protein Classification via Support Vector Machines

String kernels are popular tools for analyzing protein sequence data and they have been successfully applied to many computational biology problems. The traditional string kernels assume that different substrings are independent. However, substrings can be highly correlated due to their substructure relationship or common physico-chemical properties. This paper proposes two kinds of weighted spectrum kernels： The correlation spectrum kernel and the AA spectrum kernel. We evMuate their performances by predicting glycan-binding proteins of 12 glycans. The results show that the correlation spectrum kernel and the AA spectrum kernel perform significantly better than the spectrum kernel for nearly all the 12 glycans. By comparing the predictive power of AA spectrum kernels constructed by different physico-chemical properties, the authors can also identify the physico- chemical properties which contributes the most to the glycan-protein binding. The results indicate that physico-chemical properties of amino acids in proteins play an important role in the mechanism of glycamprotein binding.