美洲大蠊变应原Per a 2的生物信息学分析

目的：了解美洲大蠊变应原Per a 2的分子生物学特征。方法：从Genbank中获得Per a 2的核酸序列,用ExPaSy、EBI和NCBI网站的在线软件推导出编码氨基酸序列及其理化性质、空间结构、功能位点,并在Blastp比对后选择不同物种同源序列计算井刖双率、构建分子进化树。结果：Per a 2由351个氨基酸细戍,分子量为38119Da、等电点为490、分子式为C1217H1825N285O297S18,为细胞外疏水性蛋白、属于肽酶a家族,信号肽位于1～20氨基酸处,三个跨膜螺旋区域依次位于1～19aa、51～78aa、282～300aa处;二级结构由α-螺旋（9．4％）、β延伸（28．49％）、随机线圈（62．11％）组成;美洲大蠊和德国小蠊相似率为55％、与马德拉蜚蠊相似率为51％,三者在Per a 2与不同物种的同源序列构建的分子进化树中聚成一簇。结论：通过对Per a 2的生物信息学分析获得了该变应原分子特征．为进一步研究奠定基础。     

美洲大蠊变应原Pera2的生物信息学分析

目的:了解美洲大蠊变应原Per a 2的分子生物学特征。方法:从Genbank中获得Per a 2的核酸序列,用ExPaSy、EBI和NCBI网站的在线软件推导出编码氨基酸序列及其理化性质、空间结构、功能位点,并在Blastp比对后选择不同物种同源序列计算相似率、构建分子进化树。结果:Pera2由351个氨基酸细戍,分子量为38119Da、等电点为4.90、分子式为C1217H1825N285O297S18,为细胞外疏水性蛋白、属于肽酶a家族,信号肽位于1～20氨基酸处,三个跨膜螺旋区域依次位于1～19aa、51～78aa、282～300aa处;二级结构由α-螺旋(9.4%)、β延伸(28.49%)、随机线圈(62.11%)组成;美洲大蠊和德国小蠊相似率为55%、与马德拉蜚蠊相似率为51%,三者在Pera2与不同物种的同源序列构建的分子进化树中聚成一簇。结论:通过对Per a 2的生物信息学分析获得了该变应原分子特征,为进一步研究奠定基础。     

Pla a 1序列分析及三维结构建模

联合运用多种方法预测Pla a 1的亲水性及其二级结构,利用同源建模法建构Pla a 1的三维结构模型,在nb数据库中进行BLAST并构建同源进化树,在Scan Prosite数据库中进行Motif预测,对Pla a 1进行序列分析并进行三维结构建模。该蛋白是一个主要为α β结构的亲水性蛋白,预测其具有一个蛋白激酶C的磷酸化位点,一个N豆蔻酰化位点和三个酪蛋白激酶Ⅱ磷酸化位点。Pla a 1具有较强的信号转导作用,且与拟南芥的果胶(甲)酯酶抑制剂在进化上具有较近的亲缘关系;所预测的三维结构基本能反映出Pla a 1真实的空间构象,这将为今后进一步理解和掌握Pla a 1结构和功能上的关系打下理论基础。     

三种隐孢子虫钙依赖蛋白激酶的生物信息学分析

对三种隐孢子虫(C.parvum Iowa II、C.hominis TU502和C.muris RN66)钙依赖蛋白激酶(Calcium-dependent protein kinases,CDPKs)进行生物信息学分析,探索该蛋白的结构并预测其功能,为其基因功能的研究提供一定的理论基础。通过隐孢子虫基因组数据库收集数据,获得三种隐孢子虫CDPKs蛋白的序列信息,通过生物信息学软件进行分析,预测该蛋白的理化性质、翻译后修饰位点、功能域、亚细胞定位、二级结构、亲/疏水性、抗原表位等。隐孢子虫CDPKs的蛋白性质不稳定,理论分子量从59.76 k Da到76.63 k Da,p I值为5.33~6.09,CDPKs不具有跨膜区和信号肽,不是跨膜分泌性蛋白,都具有蛋白激酶C磷酸化位点、酪氨酸激酶Ⅱ磷酸化位点、酪氨酸激酶磷酸化位点、c AMP和c GMP依赖蛋白激酶磷酸化位点、N-端糖基化位点、N-端肉豆蔻酰化位点和EF-hand钙结合域,二级结构主要以α螺旋和无规卷曲为主;CDPKs主要存在虫体细胞内,均有20多个潜在的抗原表位。在隐孢子虫中,CDPKs蛋白不仅可单独发挥作用,而且还能通过相互结合发挥其生物学效应;同时,CDPKs有望成为候选疫苗及潜在药物靶点。     

美洲大蠊3-磷酸甘油醛脱氢酶基因的克隆及表达

旨在通过5’-RACE获得美洲大蠊3-磷酸甘油醛脱氢酶(GAPDH)基因的全长cDNA序列,进行生物信息学分析,构建原核表达载体,诱导重组蛋白表达,为进一步研究其功能奠定基础.通过3’-RACE技术,PCR扩增获取编码美洲大蠊GAPDH蛋白的全长cDNA序列;采用生物信息学方法推导出该序列编码的氨基酸序列及其理化性质;预测信号肽、蛋白疏水性、可溶性、跨膜区结构、二级结构、三级结构,并构建系统发育树;构建原核表达载体pET28a-GAPDH,IPTG诱导重组蛋白表达,并用Histag抗体Western blotting验证.结果显示,美洲大蠊GAPDH基因,其完整阅读框含999个碱基,编码332个氨基酸.序列分析显示,该蛋白与家蚕GAPDH相似性为89％,具有GAPDH保守功能域,经IPTG诱导获得重组蛋白.     

产气荚膜梭菌青海分离株virS基因序列分析与蛋白结构预测

为了探究产气荚膜梭菌virS基因的结构及其编码蛋白的功能,本研究提取了产气荚膜梭菌青海分离株基因组DNA,PCR扩增virS基因、测序并分析序列与蛋白结构,使用在线服务器对VirS蛋白进行功能位点、三级结构、信号肽以及跨膜结构域预测。研究表明,产气荚膜梭菌分离株virS基因长度为1323 bp,编码440个氨基酸;分离株virS基因与JIR4025菌株、FORC-025菌株、Del1菌株、FORC-003菌株、LLY-N11菌株、CP15菌株、13菌株、ATCC13124菌株、JP55菌株、JP838菌株、EHE-NE18菌株以及SM101菌株等参考产气荚膜梭菌比对后,显示其核苷酸序列同源性依次为99.2%、99.5%、99.4%、99.4%、99.3%、99.3%、99.2%、99.0%、98.9%、98.2%、97.9%以及95.4%,氨基酸序列同源性依次为99.1%、99.5%、99.8%、99.5%、99.5%、99.5%、99.1%、99.5%、99.5%、98.2%、97.7%以及94.6%;二级结构预测表明分离株VirS蛋白主要由α螺旋组成,其次是β折叠;三级结构预测显示分离株VirS蛋白有5种结构,蛋白功能位点预测表明分离株virS蛋白具有5个N-糖基化位点、2个N-豆蔻酰化位点、5个蛋白激酶C磷酸化位点、2个酪蛋白激酶Ⅱ磷酸化位点、2个酪氨酸激酶磷酸化位点和1个糖基水解酶家族V。     

大熊猫核糖体蛋白S11亚基基因(RPS11)cDNA的克隆及序列分析

RPS11是核糖体小亚基40S的组成部分,由RPS11基因所编码,属于核糖体蛋白S17p家族,主要存在于真核生物中.为了解大熊猫核糖体蛋白亚基RPS11基因的结构特点及其与已报道的人和其他哺乳动物核糖体蛋白亚基RPS11 基因的异同,本研究根据已报道的部分哺乳动物核糖体蛋白S11亚基基因(RPS11)的相关信息设计引物,运用RT-PCR 技术从大熊猫的肌肉组织总RNA中成功克隆了核糖体蛋白亚基RPS11基因,并进行了测序和序列分析.结果表明:大熊猫RPS11亚基基因的开放阅读框(ORF)长为477 bp,编码158 个氨基酸的蛋白质,该蛋白的相对分子量为18.4275 kDa,pI为10.96.拓扑预测显示该蛋白含有14个功能位点:即2 个N-糖基化位点,6个蛋白激酶C磷酸化位点,4个酪蛋白激酶Ⅱ磷酸化位点,1个酪氨酸激酶磷酸化位点和1个核糖体蛋白S17 signature位点.进一步分析发现,大熊猫RPS11基因与已报道的部分哺乳动物的表达序列及其编码的氨基酸序列都具有很高的相似性.本研究结果为丰富和完善哺乳动物RPS11基因资源库提供了基础资料.     

油菜花粉发育相关基因RALFbn的克隆与表达分析

根据美国NCBI数据库中快速碱化因子(RALF)类基因序列的已知信息,克隆了油菜的快速碱化因子基因RALFbn,对其核酸序列及预测蛋白进行了生物信息学分析,并在油菜多种组织内观测其表达情况.结果表明:(1)经克隆获得油菜RALFbn基因的cDNA序列全长为510 bp,无内含子,编码79个氨基酸.(2)生物信息学分析发现,油菜RALFbn蛋白具有RALF类蛋白保守的“YIXY”区和4个保守的半胱氨酸残基,并且含有N豆蔻酰化位点、酪氨酸激酶Ⅱ磷酸化位点、蛋白激酶C磷酸化位点、和酪氨酸激酶磷酸化位点等多个生物活性位点,说明该蛋白在油菜中潜在的生理调节能力较为活跃.(3) RT-PCR检测RALFbn基因在油菜生殖器官中的表达结果发现,RALFbn主要在油菜雄蕊中表达,而在雌蕊、花瓣和萼片中没有表达.提示RALFbn基因极可能与油菜雄蕊中花粉的发育相关.     

藏羊GM-CSF基因的RT-PCR扩增、序列分析及蛋白结构预测

为了研究藏羊GM-CSF基因及其编码蛋白的功能,提取藏羊脾脏总RNA,应用RT-PCR技术对藏羊GM-CSF基因进行扩增及测序,并利用DNA Star软件进行序列分析及编码蛋白结构预测。测试表明,藏羊GM-CSF基因长度为381 bp,编码127个氨基酸;藏羊GM-CSF基因与参考绵羊、藏羚羊、山羊和水牛的GM-CSF基因的核苷酸序列同源性依次为100%、99.2%、98.7%和92.1%,氨基酸序列同源性依次为100%、97.6%、96.9%和81.0%。蛋白结构预测表明GM-CSF蛋白具有1个N-糖基化位点、1个N-豆蔻酰化位点、1个粒细胞-巨噬细胞集落刺激因子信号、2个蛋白激酶C磷酸化位点、3个酪蛋白激酶Ⅱ磷酸化位点;综合二、三级结构预测得出,该蛋白主要由α螺旋组成,其次是β转角和无规则卷曲,而β折叠相对较少。研究成果可为青海藏羊GM-CSF基因抗病功能的研究提供参考。     

Endophilin B1 基因及蛋白的生物信息学分析

目的:利用生物信息学方法分析人Endophilin B1基因以及蛋白的结构,为进一步研究其功能和参与的调控机制提供一定的理论依据。方法:通过GenBank搜索Endophilin B1基因及蛋白序列,采用生物信息学方法分析该基因在不同物种中的差异,分析该蛋白的亚细胞定位,二级结构,功能域以及抗原表位。结果:该基因编码一个长度为365个氨基酸的蛋白,具有两个BAR和SH3两个功能域。Endophilin B1蛋白理论分子量为40796.3,理论等电点为5.78。二级结构中α螺旋(H)占56.44%,β折叠(E)占5.48%,无规卷曲占38.08%。Endophilin B1蛋白含有4个可能的N连接糖基化位点,5个潜在的酪蛋白激酶II磷酸化位点,7个豆蔻酰基化位点,3个PKC磷酸化位点以及2个酪氨酸激酶磷酸化位点。并进一步利用DNAstar软件分析了了该蛋白的抗原表位。结论:利用生物信息学预测出的结构和功能信息,能为Endophin B1蛋白的相关研究提供一定的信息基础。     

Metaproteomics: Evaluation of protein extraction from activated sludge

Metaproteomic studies of full‐scale activated sludge systems require reproducible protein extraction methods. A systematic evaluation of three different extractions protocols, each in combination with three different methods of cell lysis, and a commercial kit were evaluated. Criteria used for comparison of each method included the extracted protein concentration and the number of identified proteins and peptides as well as their phylogenetic, cell localization and functional distribution and quantitative reproducibility. Furthermore, the advantage of using specific metagenomes and a 2‐step database approach was illustrated. The results recommend a protocol for protein extraction from activated sludge based on the protein extraction reagent B‐Per and bead beating. The data have been deposited to the ProteomeXchange with identifier PXD000862 ( http://proteomecentral.proteomexchange.org/dataset/PXD000862 ).     

利用系统进化树对H7N9大数据预测传播模型的评估

活禽贸易和H7N9禽流感病毒传播之间存在关联,应用大数据技术分析活禽交易网络数据,可进行疫情溯源并预测未来传播趋势。从流感研究数据库中获取了截止至2013年分离得到的H7N9毒株的血凝素基因核酸序列,构建系统进化树推断2013年上半年疫情中H7N9在各省及城市间的传播情况,并与大数据推断结果进行对比分析。结果表明,系统进化树推断结果更为准确,但大数据分析能够提供更多地区的信息且具有更好的时效性,同时推断的传播模型准确度较高,在H7N9疫情的应对中具有较高的应用价值。     

Effect of dietary oils enriched with n-3 fatty acids on survival of mice

Female mice were fed a conventional diet, shifted at 119 days of age to a diet supplemented with 10 wt % lard (Lar), high-linoleic (n-6) safflower oil (Saf), rapeseed oil (low-erucic, Rap), high-alpha-linolenic (n-3) perilla oil (Per) or a mixture (1:9) of ethyl docosahexaenoate (n-3) and soybean oil (DHA/Soy). Weight gain was less in the Per group than in the other groups at 497 days of age. In the Rap group, proteinuria was more severe than in the Saf, Per and DHA/Soy group, and hepatic triacylglycerol accumulation was greater than in the other groups. The mean survival time of the DHA/Soy group (753 days) was significantly longer than in the Lar group (672 days) and Saf group (689 days); the differences among other groups (e.g., 701 days in the Per group and 712 days in the Rap group) were not statistically significant. Although DHA is more susceptible to auto-oxidation than other major fatty acids in the air, an oil containing DHA was found to increase the survival of mice. Rapeseed oil that decreases the survival time of SHRSP rats was found to be safe in the mouse strain used in this study when survival was an end point.     

Intercellular coupling confers robustness against mutations in the SCN circadian clock network

Molecular mechanisms of the mammalian circadian clock have been studied primarily by genetic perturbation and behavioral analysis. Here, we used bioluminescence imaging to monitor Per2 gene expression in tissues and cells from clock mutant mice. We discovered that Per1 and Cry1 are required for sustained rhythms in peripheral tissues and cells, and in neurons dissociated from the suprachiasmatic nuclei (SCN). Per2 is also required for sustained rhythms, whereas Cry2 and Per3 deficiencies cause only period length defects. However, oscillator network interactions in the SCN can compensate for Per1 or Cry1 deficiency, preserving sustained rhythmicity in mutant SCN slices and behavior. Thus, behavior does not necessarily reflect cell-autonomous clock phenotypes. Our studies reveal previously unappreciated requirements for Per1, Per2, and Cry1 in sustaining cellular circadian rhythmicity and demonstrate that SCN intercellular coupling is essential not only to synchronize component cellular oscillators but also for robustness against genetic perturbations.     

Comparative Analysis of <Emphasis Type="Italic">Period</Emphasis> Genes in Teleost Fish Genomes

Period (Per) is a canonical circadian clock gene. The fruit fly, an invertebrate, has one per gene, while the human, a tetrapod vertebrate, has three Per genes. Per1, Per2, and Per3 of the tetrapods were generated from two rounds of ancient genome duplications from the ancestral chordate Per gene. Searching for five teleost fish genomes in a combination of phylogenetic, splicing site, and syntenic analyses revealed that zebrafish have two per1 genes, per1a and per1b, one per2, and one per3; medaka, fugu, and tetraodon each have two per2 genes, per2a and per2b, one per1, and one per3; sticklebacks also have per2a, per2b, and one per1 but lack per3; and per1a/per1b in zebrafish and per2a/per2b in madaka, fugu, tetraodon, and stickleback are ancient duplicates. While the dN/dS ratios of the five fish per duplicates are all <1, suggesting that they likely have been subject to purifying selection, the Tajima relative rate test showed that zebrafish per1a/per1b and fugu and medaka per2a/per2b have asymmetric evolutionary rates, implicating that one of these duplicates might have been under positive selection or relaxed functional constraint. Further, in situ hybridization showed that zebrafish per1a and per1b clearly have distinct patterns of temporal and spatial expression. These results support the notion that extra copies of teleost per genes were generated from the fish-specific genome duplication, and divergent resolution after the duplication resulted in retention of different per duplicates in different fish, most of which have diverged significantly.     

厦门附近海域浮游甲藻类的分布

本文报道了厦门附近海域浮游甲藻类49种,并对其生态特性以及与海洋环境因素的关系进行了详细研究与讨论。分析的204号样品,系1980年9月至1981年8月,逐月采自厦门海域的浔江区(Ⅰ区),西港区(Ⅱ区)和九龙江口区(Ⅱ区)。     

利用线粒体16S rRNA基因全序列分析直翅目主要类群的系统发生关系

为了构建稳健的直翅目主要类群间的系统发生关系并探讨16S rRNA基因序列在构建直翅目昆虫不同分类阶元系统发生关系时的可行性、功效以及性能,文章测定了直翅目4总科9科18种昆虫的16S rRNA基因全序列,联合已知该基因全序列的其他40种昆虫,构建了直翅目主要类群之间的系统发生关系,并分析了16SrRNA基因全序列的系统发生性能和功效。结果表明,直翅目昆虫的16S rRNA基因全长平均为1 310 bp;除生活方式特化的蚤蝼总科和蝼蛄总科的地位无法确定外,直翅目其他主要类群系统发生关系比较稳定;蝗总科下除了斑翅蝗科和槌角蝗科外,剑角蝗科、斑腿蝗科、网翅蝗科都不是单系群,且用不同的方法构建的系统发生树中聚类情况完全一致,各科间遗传距离差异不大,建议将其合为一科;锥头蝗科、瘤锥蝗科和癞蝗科间的遗传距离差异也不大;在构建系统发生树时,16S rRNA基因环区的信息量要比茎区的大;16S rRNA基因可以构建可靠的直翅目属与种水平和目与亚目高级阶元的系统发生关系,但对科和总科阶元缺乏足够的分辨力。     

ANCAC: amino acid, nucleotide, and codon analysis of COGs -- a tool for sequence bias analysis in microbial orthologs

ABSTRACT: BACKGROUND: The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. RESULTS: Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. CONCLUSIONS: Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.