Computing Degree of Maps Between Manifolds

We determine the degrees of maps between two given closed （n-1）-connected 2n-mamifolds when n ≡ 1 （mod 8）.     

An efficient way of finding good indel seeds for local homology search

Designing good or optimal seeds is a key factor for local homology search in bioinformatics. Continuous seeds have existed for nearly 20 years used by BLAST series programs. Recently, spaced seeds, which were introduced by PattenHunter program, were shown to be more sensitive and faster than continuous seeds under the same similarity level. However, there are 2 main disadvantages for space seeds： （i） It assumes that only matches and mismatches occur within seed alignments, but not insertions and deletions （indels）; （ii） calculating optimal spaced seeds is an NP-hard problem. Introduction for indel seeds solved the first problem, but the second is getting much harder because of its higher exponential level. In this paper, we introduce an efficient way of designing good （even optimal） indel seeds under ＂indel overlap complexity＂ model, and it can be calculated in polynomial time. We calculate indel seeds from weight of 11 to 15. The result shows that indel seeds have higher sensitivities than spaced ones and our algorithm finds good indel seeds very quickly.     

SARS-CoV-2病毒全基因组序列比对及进化分析

SARS-CoV-2病毒株是β属冠状病毒,它包括S、N、E、M4个主要编码蛋白,是造成中国湖北省武汉市爆发重大公共卫生事件的罪魁祸首,目前对该病毒的系统性研究分析并不是很多.运用计算机辅助软件工具来对筛选自NCBI基因文库中的36条来自不同国家地区的SARS-CoV-2病毒株序列进行全序列比对分析,从而找出SARS-C...     

新疆一些根瘤菌的DNA同源性分析

通过分析七株根瘤菌的DNA同源性,证实从新疆新分离到的一些慢生根瘤菌与数值分类选定的新疆慢生根瘤菌群的中心菌株A—IBS的DNA同源性为77—100.3％;与已定种的根瘤菌的模式菌株R.huakii103、R.tropici899 Agorh、Canlinodans571、R.fredii205的DNA同源性分别为66.75％、45.73％、2.61％、30.61％。结果证明,这些菌与原有的已研究的新疆慢生根瘤菌聚成一群,进一步证明新疆慢生根瘤菌群有可能为根瘤菌的一个新种或新属。     

曲霉属糖化酶基因的克隆及其在毕赤酵母中的表达

从黑曲霉、无花果曲霉、米曲霉中提取总RNA,RT-PCR分别获得其糖化酶基因,所得序列在Gen-Bank数据库中注册,注册号分别为AY652617、AY642120和DQ211971.BLAST分析显示,克隆的曲霉属糖化酶基因与GenBank数据库相应序列同源性很高.将这些糖化酶基因与表达载体pPIC9重组后,电转化进毕赤酵母株GS115,均获得了分泌表达糖化酶的酵母工程菌株.甲醇诱导72 h后,糖化酶的分泌量达到最高,分别为(11.6±0.2)、(12.4±0.2)和(10.0±0.2)U/mL.SDS-PAGE显示,分泌表达的糖化酶分子量均约为80 kDa.     

酵母螺旋酶(YRF)基因家族的同源性分析

运用序列对比分析的方法对酵母螺旋酶(Y′helicase protein，YRF)家族基因和类YRF基因的开放阅读框(Open Reading Frame，ORF)进行了比较，比较中考虑了启动区所在序列．纠正了已公布酵母基因组中可能存在的错误，给出了新预测的基因位置．提出了酵母螺旋酶基因进化的过程，并对内含子的进化进行了初步探讨，结论支持内含子早论．     

几株光合细菌DAN的G＋Cmol%及DNA—DNA同源性的测定

对８株新分离的光合细菌从形态，生理及遗传学特性等方面进行了研究，结果表明，８株菌可以分为５个不同的ＤＮＡ同源群，其中菌株１３，１８，３７，４５可以划分为一个同源群，它们与沼泽红假单胞菌（Ｒｈｏｄｏｐｓｅｕｄｏｍｏｎａｓｐａｌｕｓｔｒｉｓ）模式菌株ＡＴＣＣ１７００１的ＤＮＡ同源性在７０％以上，菌株８，４０，５２，５５分别形成另外四个同源群，菌株８与深红红螺菌（Ｒｈｏｄｏｓｐｉｒｉｌｌｕｍｒｕｂｒｕｍ     

Gene Sequence, Soluble Expression and Homologous Comparison of a D-Hydantoinase from Pseudomonas putida YZ-26

A 1440bp open-reading frame encoding D-hydantoinase from Pseudomonas putida YZ-26 was cloned and sequenced（ GenBank AY387829）. The DNA fragment was inserted into Nde and BamHI sites of vector pET-3a, yielding a recombinant plasmid, pET-HDT. After being transferred into the host strain, the artificial strain, pET-HDT/ E. coli BL21 can express the D-hydantoinase as the soluble form in the Lura-Bertani medium without addition of any inducers. The activity of the enzyme toward substrate DL-hydantoin can reach 3000-4000 IU per cells from one-liter bacterial culture incubated at 30 ℃ for 10-12 h. By the comparison of amino acid sequence homology, hydrophobic residues analysis and secondary structure prediction, it was found that D-hydantoinase reported herein is quite similar to that from Pseudomonas putdia CCRC12857, and alike to that from Pseudomonas putdia DSM84 or other bacteria. A rapid and efficient purification procedure of the enzyme was performed by a three-step procedure： ammonium sulfate fractionation, phenyl Sepharose hydrophobic interaction chromatography and Sephacryl S-200 gel filtration. The molecular mass of the monomeric enzyme is 52042 Da as determined by MALDI-TOF mass spectrometry.     

中药决明蛋白质的提取分离及部分一级结构的测定

决明子（Cassia obtusifolia L)的蛋白质含量比较丰富,其中含有人体必需的各种氨基酸,通过十二烷基硫酸钠-聚丙烯酰胺凝胶电泳（SDS-PAGE）分析的结果表明,决明子非还原态蛋白质主要是由相对分子质量（Mr)为42、40和38kd的蛋白质组成,还原态主要由Mr为24和16.5kd的两条肽链组成,采用硫酸铵盐析分级法提取蛋白质的结果表明,当硫酸铵饱和度为40%-55%时,所提取的蛋白质（P55）得率最高,对由P55分离纯化所得的主要组分Ps的N端部分进行测序及同源分的析,结果显示该序列与人体载脂蛋白B有一些相关性,并提示决明子蛋白质或有可能通过参与体内脂质的代谢而起到降脂的作用。     

半滑舌鳎DMRT 1基因的克隆与表达分析

利用同源克隆的方法克隆了半滑舌鳎(Cynoglossus semilaevis)的DMRT 1基因;并用RT-PCR技术检测了该基因在半滑舌鳎不同发育时期以及雌雄成鱼的不同组织的表达情况.结果表明,该基因cDNA序列全长1 232 bp(GenBank登录号为EU007655),包括774 bp开放阅读框,131 bp5′非翻译区以及含poly(A)信号的329 bp的3′非翻译区,编码258个氨基酸.氨基酸序列同源性分析表明,半滑舌鳎DMRT1氨基酸序列与牙银汉鱼、黑鲷、青鳉、河豚和斑马鱼DMRT1氨基酸序列的同源性分别达到了63%、59%、54%、53%和52%;与光滑爪蟾、小鼠和人类的同源性较低分别为38%、42%和41%.RT-PCR分析表明,DMRT 1基因在半滑舌鳎早期胚胎不同发育时期和孵化后5、13、18、22和35 d的仔鱼均有表达,在孵化后22 d表达量最高.在成体鱼中只在雄性精巢中有特异表达,其他组织均无表达,表明该基因可能参与半滑舌鳎雄性性腺的发育或精子的形成.