An Amino Acid Substitution Matrix for Protein Conformation Identification

Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

Clemaps: Multiple Alignment Of Protein Structures Based On Conformational Letters

CLEMAPS is a tool for multiple alignment of protein structures. It distinguishes itself from other existing algorithms for multiple structure alignment by the use of conformational letters, which are discretized states of 3D segmental structural states. A letter corresponds to a cluster of combinations of three angles formed by C-alpha pseudobonds of four contiguous residues. A substitution matrix called CLESUM is available to measure the similarity between any two such letters. The input 3D structures are first converted to sequences of conformational letters. Each string of a fixed length is then taken as the center seed to search other sequences for neighbors of the seed, which are strings similar to the seed. A seed and its neighbors form a center-star, which corresponds to a fragment set of local structural similarity shared by many proteins. The detection of center-stars using CLESUM is extremely efficient. Local similarity is a necessary, but insufficient, condition for structural alignment. Once center-stars are found, the spatial consistency between any two stars are examined to find consistent star duads using atomic coordinates. Consistent duads are later joined to create a core for multiple alignment, which is further polished to produce the final alignment. The utility of CLEMAPS is tested on various protein structure ensembles.

盐渍条件下野大豆群体的DNA变异

当前分子生物学的方法以惊人的速度渗透到生命科学研究的各个领域。植物对不断变化的环境逐步适应的过程中，积累了丰富的遗传多样性。与此同时，人类活动空间的不断扩大已经严重威胁到其他生命的生存和繁衍，越来越多的物种以越来越快的速度在我们还没有来得及认识它们时就已经永远地消失了。加快物种鉴定和保护的步伐就必须发展更多能充分揭示物种遗传多样性的实验技术，从具有丰富遗传多样性的野生资源中寻找到更多能够服务于人类可持续发展的基因资源。本文以杨树杂交后代过氧化物同工酶和RAPD分析为基础，论证了我们改进的RAPD方法用于遗传分析的可行性。在前期工作的基础上，进一步测定了野大豆自然群体的耐盐性变异，并且用微卫星和RAPD分析的方法研究分子标记与DXA变异、植株耐盐性之间的关系。对四个可能与抗盐性有关的RAPD片段进行克隆、测序，并进行序列比较。由此得出以下结论： 1、在本文的实验条件下，杨树同工酶和RAPD分析均表明，RAPD标记在亲本及其杂交后代中性状比例符合孟德尔遗传规律，尽管有时也会出现遗传负载等机制引起的基因分布扭曲现象。 2、初步研究了个体发育阶段和环境条件对植株耐盐性的影响。结果表明，植物耐盐性不仅仅与外界的盐度有关，而且受发育阶段和其它环境条件（如，温度）的影响。但也发现了某些个体在各种条件下都具有较高的耐盐性，而且，不易受到其它环境条件的影响。 3、微卫星标记的结果表明，10对引物中的8对引物共检测到时17个等位基因，平均每对引物2.125个等位基因。本文的实验条件下，双核苷酸和三核苷酸的引物对扩增产物都没有出现“ghosts"条带或“打滑”现象。 4、有4个RAPD标记可能与野大豆群体的耐盐性有关，分别是OPCO8460bp、OPCO8213bp、OPCO2690bp、以及OPCO5270bp。测序结果与GenBank中的序列作同源性比较，结果显示，OPCO2_(690bp)与小麦、松树等植物的吉普赛性的逆转录转座子的部分区域（24－－53）有很高的同源性（86－89％）。此外，OPCO2690bp与栽培大豆胞质谷氨酰胺合成酶（gs15）基因的启动子有高达95％的同源性。 5、本文实验条件下，RAPD扩增产物在限制性内切酶消化后，消化产物的多态性未见增大，也没有发现与耐盐性相关的多态位点。 6、野大豆自然群体DNA变异的研究中也可以应用SWAPP方法。

Comparative study and expression analysis of the interferon gamma gene locus cytokines in Xenopus tropicalis

Using bioinformatics approach, the genome locus containing interleukin (IL)-22, IL-26, and interferon gamma (IFN-gamma) genes has been identified in the amphibian, Xenopus tropicalis. Like that in other vertebrates such as fish, birds, and mammals, the Xenopus IL-22, IL-26, and IFN-gamma are clustered in the same chromosome and the adjacent genes are conserved. The genomic structures of the Xenopus IL-22, IL-26, and IFN-gamma gene were identical to that of their mammalian counterparts. The Xenopus IL-22 and IL-26 genes contained five exons and four introns while the Xenopus IFN-gamma gene consisted of four exons and three introns. The Xenopus IL-22, IL-26, and IFN-gamma share 14.1-41.6%, 14.6-31.2%, and 23.7-36.5% identity to their counterparts in other species, respectively. Reverse-transcription polymerase chain reaction (PCR) and real-time quantitative PCR analyses revealed that the expression of IL-22, IL-26, and IFN-gamma genes was significantly upregulated after simulation with bacterial polyliposaccharide and/or synthetic double-stranded poly(I:C), suggesting these cytokines like those in other vertebrates play an important role in regulating immune response in Xenopus.

Design and path planning for a remote-brained service robot

This article introduced an effective design method of robot called remote-brain, which is made the brain and body separated. It leaves the brain in the mother environment, by which we mean the environment in which the brain's software is developed, and talks with its body by wireless links. It also presents a real robot TUT06-B based on this method which has human-machine interaction, vision systems, manipulator etc. Then it discussed the path planning method for the robot based on ant colony algorithm in details, especially the Ant-cycle model. And it also analyzed the parameter of the algorithm which can affect the convergence. Finally, it gives the program flow chat of this algorithm.

achieving on-time delivery: a two-stage probabilistic scheduling strategy for software projects

Chinese Academy of Sciences (ISCAS)

etl workflow analysis and verification using backwards constraint propagation

University of Twente; Centre for Telematics and Information Technology; Netherlands Organisation for Scientific Research; Jacquard; Capgemini

Antifungal Activity of Quaternized Carboxymethyl Chitosan

Quaternized carboxymethyl chitosan (QCMC) were synthesized and their antifungal activities against Alternaria Solani (A. Solani) and Physalospora piricola Nose (P. piricola Nose) were investigated. The results indicated that the quaternized carboxymethyl chitosan derivatives had better inhibitory effects than CMC, and the antifungal activities should be affected by the cation in these compounds.

a new client-to-client password-authenticated key agreement protocol

Natl Univ Defen Technol, China & Nanyang Technol Univ, NUDT

stochastic process algebra based software process simulation modeling

Chinese Acad Sci, ISCAS Lab Internet Software Technologies