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ChunXi Hou ShouJing Zhao* ,Jian Xue, Lixin Xu, XiaoYan Wu, HuiYun Du. College of Biological and Agricultural Engineering,Jilin University Changchun 130022, China Correspondence author: Shoujing Zhao E-mail:swgc@jlu.edu.cn Pnanx ginseng is an oriental herbal possessing ginsenosides as its main bioactivity component, having many pharmacological effects, Including immune system modulation, antistress activities, antihyperglycemic activities, anti-inflammatory activities, and so on. Ginsenosides biosynthesis is achieved through a sequence of catalysis and modification in MVA pathway. A partial length Cdna encoding 3-hydroxy-3-methylglutoryl-Coenzyme A reductase (HMGR; GenBank Accession NO. GQ455990), which catalyzes the first committed step of isoprenoids biosynthesis inMVA pathway, was isolated from young leaves of Panax ginseng. The partial cDNA of HMGR was 360 bp containing a ORF encoding 120amino acids .Database seatches exhibited that PGHMGR shows identification to Bupleurum chinense HMGR(88%), Picrorhiza kurrooa HMGR(84%)and Hevea brasiliensisHMGR(82%). These sequences provide a strong evolutionary conservation to maintain amino acid residues at specific positions, indicating that the conserved motifs might play important roles in the catalytic properties of the enzyme. Southern blot analysis indicated that at one or two copies of PGHMGR gene existed in Panax ginseng genome. Tissue expression analysis revealed that PGHMGR expressed more strongly in roots than in stems and leaves.In panax ginseng root explants,HMGR mRNA increased in response to wounding, but was suppressed treated by methyl jasmonat�e (MeJA), in agreement with some previous reports[1-8]. This study showed the Panax ginseng HMGR gene was differentially expressed in various tissues under different physiological conditions, which may contribute to the regulation of ginsenodedes synthesis in ginseng species. Key words: Panax ginseng, hmgr, HMG-CoA reductase, cloning, ginsenosides, biosynthesis �Thermodynamic constraints and model reduction for signal transduction networks Holger Conzelmann, Michael Ederer and Ernst Dieter Gilles Max-Planck-Institute for Complex Technical Systems, Magdeburg, Germany Many signal transduction networks are characterized by a ligand induced formation of multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species and possible reactions in these processes is enormous. The dynamics of the underlying complex reaction networks are strongly restricted by thermodynamic constraints that follow from the principle of detailed balance. Using common modeling strategies, compliance with thermodynamic constraints requires that kinetic model parameters fulfill certain mathematical restrictions given by the Wegscheider condition. A violation of the Wegscheider condition corresponds to a violation of the law of energy conservation. Systematic analyses reveal that these constraints have a descriptive interpretation for multi-domain proteins. They restrict possible interactions between distinct binding domains. A detailed analysis of these restrictions also facilitates considerable model reductions. The developed reduction approach allows us to reduce a detailed model of EGF and insulin receptor cross-talk consisting of over five thousand ordinary differential equations (ODEs) to a size of only 41 ODEs. Theoretical study of two-photon absorption property of chromophore consisting in green
fluorescent protein ng, W.-D. Cheng* a M.-Y. Zhang, J.-Y. Wa State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Yangqiao Street, Fuzhou 350002,China Green fluorescent protein (GFP) has been shown to be a good flurophore for two-photon excitation, readily excited by 780- to 800-nm laser pulses. n ate second 1-3 The two-photon absorption cross section of GFP is usually obtained by chemically synthesized chromophore compound previously, which did not consider the protein environment influence. This kind of chromphore is close to planar, but whe protein matrix exist, chrompore would be exerted some strain away from planarity. Here we calcul the two-photon absorption properties of cis-trans isomerization of the chromphore. And then through rotating the exocyclic double bond to breakout the planarity as complements of the protein matrix effect, we calculate the two-photon absorption cross section of GFP at differently rotate angles. We further show that, GFP has great intrinsic two-photon absorption cross section when no restrict to planar structure, as Sean et al. reported by considering the larger protein structure. 1 Two-photon absorption cross section δ is directly related to the imaginary part of the hyperpolarizability (;,,)γωωωω−− as follow 242203()Im[(;,,)]2Lncωδωγωωωωε=−h γ ─── third-order molecular polarizability, 0ε ─── the vacuum electric permittivity, L ─── the local-field factor ─── the refractive index of the medium. JFeature: A Java package for extracting global sequence features from proteins for functional classification X. Chen1,* and H.Y. Xu1, 1Department of bioinformatics,College of Life Sciences, Zhejiang University, P.R.China. *To whom correspondence shall be addressed. Email: xinchen@zju.edu.cn Both authors made equal contributions. Conflict of Interest: none declared Prediction of various functional aspects of proteins has long been a central theme of bioinformatics in the post-genomic era. Statistical learning, in addition to analysis based on similarity, was proven successful to detect complex sequence-function associations in many applications. We present JFeature as an integrated Java tool to facilitate extraction of global sequence features and preparation of example sets for statistical learning studies of sequence-function relationships. With a friendly graphical interface, it computes the composition, distribution, transition and auto-correlation features from sequences, as well as helps to assemble a negative example set based on the most-dissimilar principle. The Java package and supplementary documentations are available at http://www.cls.zju.edu.cn/rlibs/software/jfeature.html. Keywords: Machine Learning, Feature Extraction, Java Package, Software, Protein Sequence Codin. PO-009 Size Effect on Protein Encapsulation in Carbon Nanotubes Lijun Liang, Qi Wang, Tao Wu, Yu Kang Department of Chemistry, Zhejiang University, Hangzhou 310027, P. R. China Recently, the ability of CNTs to serve as biocompatible transporters for drug delivery has aroused great expectation. Based on the exciting potentials, we try to focus on the spontaneous phenomenon of the
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