RECENT ADVANCES in BIOLOGY, · research interests are related to biomaterials, drug delivery...

RECENT ADVANCES in BIOLOGY,

BIOPHYSICS, BIOENGINEERING

and COMPUTATIONAL

CHEMISTRY

Proceedings of the 5th WSEAS International Conference on

CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and

BIOENGINEERING (BIO '09)

Proceedings of the 3rd WSEAS International Conference on

COMPUTATIONAL CHEMISTRY (COMPUCHEM '09)

Puerto De La Cruz, Tenerife, Canary Islands, Spain

December 14-16, 2009

Recent Advances in Biology and Biomedicine

A Series of Reference Books and Textbooks

Published by WSEAS Press

www.wseas.org

ISSN: 1790-5125

ISBN: 978-960-474-141-0



and COMPUTATIONAL

CHEMISTRY







December 14-16, 2009 Recent Advances in Biology and Biomedicine

A Series of Reference Books and Textbooks

Published by WSEAS Press

www.wseas.org

Copyright © 2009, by WSEAS Press

All the copyright of the present book belongs to the World Scientific and Engineering Academy and

Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval

system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or

otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy

and Society Press.

All papers of the present volume were peer reviewed by two independent reviewers. Acceptance was

granted when both reviewers' recommendations were positive.

See also: http://www.worldses.org/review/index.html

ISSN: 1790-5125

ISBN: 978-960-474-141-0

World Scientific and Engineering Academy and Society



and COMPUTATIONAL

CHEMISTRY







December 14-16, 2009

Editors:

Prof. Cornelia A. Bulucea, University of Craiova, Romania

Prof. Valeri Mladenov, Technical University of Sofia, Bulgaria

Prof. Emil Pop, University of Petrosani, Romania

Prof. Monica Leba, University of Petrosani, Romania

Prof. Nikos Mastorakis, Technical University of Sofia, Bulgaria

International Program Committee Members:

Jill Mesirov (MIT)

Thomas Lengauer (Saarbrucken)

Alfonso Valencia (CNB, Madrid)

Ceslovas Venclovas (Vilnius)

Martin Vingron (Max Planck Institute, Berlin)

Shoshana Wodak (University of Toronto)

Ralf Zimmer (Saarbrucken)

Haim Wolfson (Tel Aviv University)

Alberto Apostolico (Padova University)

Serafim Batzoglou (Stanford University)

Rita Casadio (Bologna University)

Soren Brunak (Technical University Denmark)

Frank Eisenhaber (IMP, Vienna)

Nir Friedman (Hebrew University of Jerusalem)

Mikhail Gelfand (IITP, Moscow)

Raffaele Giancarlo (Palermo University)

David Gilbert (University of Glasgow)

Concettina Guerra (Padova University)

Roderic Guigo (IMIM, Barcelona)

Sorin Istrail (Brown University)

Simon Kasif (Boston University)

Andrzej Kolinski (Warsaw University)

Gregory Kucherov (LIFL, Lille)

Giuseppe Lancia (Udine University)

Satoru Miyano (Tokyo University)

Pavel Pevzner (San Diego)

Ron Pinter (Technion, Haifa)

Tal Pupko (Tel Aviv University)

Aviv Regev (Harvard University)

Isidore Rigoutsos (TJ Watson Research Center)

Burkhardt Rost (Columbia University)

Mikhail Roytberg (IMPB, Russia)

Marie-France Sagot (Lyon)

Eran Segal (Weizmann Institute of Science)

Ron Shamir (Tel Aviv University)

Roded Sharan (Tel Aviv University)

Steve Skiena (SUNY Stony Brook)

Jeff Skolnick (Georgia Institute of Technology)

Wojciech Szpankowski (Purdue University)

Anna Tramontano (University of Rome) Ron

Unger (Bar Ilan University)

Donald Truhlar (University of Minnesota)

Graham Richards (University of Oxford)

Minhaeng Cho (Korea University)

Modesto Orozco (University of Barcelona)

Pavel Hobza (Czech Republic)

Rebecca Wade (EML Research)

Richard Friesner (Columbia University)

Todd Martinez (University of Illinois)

Walter Thiel (Max Planck Institute)

Wilfred van Gunsteren (ETH)

Alexander Lyubartsev (Stockholm University)

Alexey Mazur (CNRS-UPR9080, IBPC)

Alexey Onufiev (Virginia Tech)

Amedeo Palma (CNR-ISMN)

Andriy Baumketner (UNC Charlotte)

Dieter Hofmann (GKSS Research Centre)

George Shields (Hamilton College)

Hassan Safouhi (University of Alberta)

Jaroslav Koca (Masaryk university, Fac Sci)

Jiri Vanicek (EPFL)

Laurence Leherte (University of Namur) Marie-

Pierre Gaigeot (Universite d'Evry val d'Essonne)

Martin Parker (University of Leeds)

Nick Quirke (Imperial College London)

Paul Smith (Kansas State University)

Robert Woods (Carbohydrate Research Center)

Roberto Lins (Pacific Northwest Laboratory)

Roman Efremov (Shemyakin-Ovchinnikov)

Scott Brown (Abbott Laboratories)

Shina Lynn Kamerlin (Southern California)

Tanja van Mourik (University of St Andrews)

Yaoqi Zhou (Indiana University)

Yingkai Zhang (New York University)

Preface

This year the 5th WSEAS International Conference on CELLULAR and MOLECULAR

BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO'09) and the 3rd WSEAS International

Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM'09) were held at Puerto De

La Cruz, Tenerife, Canary Islands, Spain, December 14-16, 2009. The conferences remain

faithful to their original idea of providing a platform to discuss biology of cell, metabolism,

molecular biology, neural modeling, biophysics, biochemistry, computer biology, genetics,

theoretical chemistry, computational material science, numerical analysis for chemical

engineering and chemistry, computational intelligence tools for chemistry and chemical

engineering, computational molecular science and nanoscience, mathematical molecular

medicine, chemical fluid mechanics, environmental chemical engineering etc. with participants

from all over the world, both from academia and from industry.

Their success is reflected in the papers received, with participants coming from several countries,

allowing a real multinational multicultural exchange of experiences and ideas.

The accepted papers of these conferences are published in this Book that will be indexed by ISI.

Please, check it: www.worldses.org/indexes as well as in the CD-ROM Proceedings. They will

be also available in the E-Library of the WSEAS. The best papers will be also promoted in many

Journals for further evaluation.

Conferences such as these can only succeed as a team effort, so the Editors want to thank the

International Scientific Committee and the Reviewers for their excellent work in reviewing the

papers as well as their invaluable input and advice.

The Editors

Table of Contents

Plenary Lecture 1: Nanoparticles for the Transport of Antiretroviral Drugs across the Blood-

Brain Barrier: A Potential Therapy for the Acquired Immunodeficiency Syndrome

11

Yung-Chih Kuo

Plenary Lecture 2: Creation of Electromagnetic Structure-Creating Spaces to Improve the

Growth of Some Types of Cells and Albumins

12

Vladyslav Vlastopulo

Plenary Lecture 3: A New Way of Natural Oligopeptide Primary Structure Elucidation 13

Alexander A. Zamyatnin

Studies on a Promising Anticancer Molecule of Marine Origin. Results of an Interdisciplinary

Study

15

A. Zovko, T. Turk, M. Faimali, F. Garaventa, E. Chelossi, C. Falugi, M. G. Aluigi, C. Angelini, S.

Trombino, L. Gallus, S. Ferrando, P. Russo, L. Paleari, K. Sepcic

An Intelligent Controller of the Chemical Reactor 24

Jelenka Savkovic-Stevanovic

Evolution of Proliferating Cells under Different Decaying Behaviors of the Total Tumor Cells

During a Course of Treatment

30

Mitra Shojania Feizabadi

A New Way of Natural Oligopeptide Primary Structure Elucidation 33

Alexander A. Zamyatnin

Nitrate Removal from the Cetina Surface Water by using Bacteria Attached to Lewatit M600 39

Lucija Foglar, Ana-Marija Babic, Mario Siljeg

Information Theory-Based Code Optimization of Matrix Elements for Overall Rotation

Angular Momenta

45

Maria Eugenia Castro, Camelia Munoz-Caro, Alfonso Nino

Nanoaggregation and Solubility of Crude Oil Asphaltenes from Molecular Dynamics

Simulations

51

Francesco Frigerio

Computational Study of Nodifloridin-A and Nodiflorifin-B, with Highlight on the Peculiarities

of Acylated Phloroglucinol Derivatives

58

Liliana Mammino, Mwadham M. Kabanda

Mitochondrial DNA Copy Number and Citrate Synthase Activity in Nonalcoholic Fatty Liver

Disease Induced in Rats by a high-fat plus Fructose Diet Fortified or not with

Dehydroepiandrosterone (DHEA)

64

Angela Maria Lezza, Pierluigi Cassano, Raffaella Mastrocola, Pesce Vito, Manuela Aragno, Maria

Nicola Gadaleta

DFT Study of Tautomeric Equilibria of 6-Hydroxy—Flourocytosine 68

Behzad Chahkandi, Sorour Hasani

RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

ISSN: 1790-5125 9 ISBN: 978-960-474-141-0

Investigation of Various Conformations of HCO-Gly-L-Val-Gly-NH2 Tripeptide in Elastin: Ab

Initio and DFT Calculations

74

Behzad Chahkandi, Badrosadat Seyed Hosseini

Nanochannel and its Application in Analytical Chemistry 80

Zenglian Yue, Guoqing Zhao, Bin Peng, Shasheng Huang

On the Numerical Solution of Mathematical Models of Cancer Growth and Optimal Cancer

Therapy

94

Nikos E. Mastorakis

Development of Transgenic Cotton Expressing Modified Bt and CpTI Genes by Pollen Tube

Pathway Mediated-Transformation

105

Jinying Guo, Tianzhen Zhang

High Pest Resistance Transgenic Cotton Transformed with Bt and Sck Gene 110

Guo Jinying, Chen Tao, Zhang Tianzhen

The Genetic Stability of Transgenic Bt and Sck Insect-Resistant Cotton 115

Guo Jinying, Chen Tao, Zhang Tianzhen

Qsar Study of Anthranilic Acid Sulfonamides as Inhibitors of Methionine Aminopeptidase-2

using Different Chemometrics Tools

119

Razieh Sabet, Mohsen Shahlaei, Afshin Fassihi

Virtual Reality Applied to the Management, Planning and Optimization of Surgical

Interventions

126

Cristina Suarez-Mejias, Armando Cabral-Camacho, Daniel Derlinchan-Gonzalez, Tomas Gomez-

Cia, Purificacion Gacto-Sanchez, Manuel Perez-Lorente, Carlos Parra-Calderon, Jose Maria De La

Higuera-Gonzalez

Characterization of Codon Usage Bias in the Newly Identified DEV UL10 Gene 132

Tao Zhou, An-Chun Cheng, Ming-Shu Wang, Dekang Zhu,Renyong Jia, Qihui Luo, Hengmin Cui, Yi

Zhou, Yin Wang, Zhiwen Xu, Zhengli Chen, Xiaoyue Chen, Xiaoyu Wang

Numerical Simulation of Thermal Response of the Skin Tissues 143

Iulia Maria Carstea, Ion Carstea

Authors Index 149


ISSN: 1790-5125 10 ISBN: 978-960-474-141-0

Plenary Lecture 1

Nanoparticles for the Transport of Antiretroviral Drugs across the Blood-Brain Barrier: A

Potential Therapy for the Acquired Immunodeficiency Syndrome

Professor Yung-Chih Kuo

Department of Chemical Engineering

National Chung Cheng University

Chia-Yi, Taiwan 62102, Republic of China

E-mail: [email protected] Abstract: Transport of antiretroviral agents into the central nervous system is an important issue because human

immunodeficiency viruses (HIV) have been found to reside and replicate themselves in the brain parenchyma. This yields a complicated treatment for the acquired immunodeficiency syndrome. Recently, novel nanoparticles (NPs) have been developed for carrying anti-HIV drugs across the blood-brain barrier (BBB). In this presentation, the anti-HIV drugs incorporated with NPs to circumvent the BBB included zidovudine, lamivudine, stavudine, didanosine, delavirdine, and saquinavir. These pharmaceuticals were loaded on the surfaces of polymeric NPs or entrapped in the matrix of solid lipid nanoparticles (SLNs). Polybutylcyanoacrylate, methylmethacrylate-co-sulfopropylmethacrylate, and poly(lactide-co-glycolide) were among the typical polymeric NPs, and various kinds of SLNs with lipid core of tripalmitin, cacao butter, docosanoic acid, stearic acid, and Compritol ATO 888 were also discussed. On the surfaces of the drug carriers, bioactive molecules including polysorbate 80, sorbitan monolaurate, phospatidylcholine, cholesteryl hemisuccinate, taurocholate, stearylamine, dioctadecyldimethyl ammonium bromide, heparin, L-arginine, and transferrin were applied to stabilization or modification. Effects of cold storage, pH value, synthesis duration, stirring speed, lyophilization, and composition on the drug delivery system, and physicochemical characteristics including particle size and shape, molecular weight, zeta potential, mobility, drug distribution, loading and entrapment efficiency, and release kinetics were shown. In addition, confluent monolayer of brain-microvascular endothelial cells (BMECs) from both bovine and human and an in vivo rat model were employed to the evaluation of permeability across the BBB. Presence of the medium chemicals including alcohol and glutamic acid was also considered. It was generally observed that cytotoxicity and transendothelial electrical resistance of BMECs cocultured with NPs were in reasonable range, and dramatic increase in the permeability of NPs-mediated system could be obtained. Moreover, impacts of the exposure to electromagnetic field (EMF) including power, wave type, frequency, modulation or depth of amplitude modulation, and modulation or deviation of frequency modulations were demonstrated. Finally, the evidence of vesicular endocytosis of drug-containing NPs by clathrin-coated endosome and the expression of tight junction and P-glycoprotein on the plasma membranes of BMECs were presented.

Brief Biography of the Speaker:

Dr. Yung-Chih Kuo is a professor at the Department of Chemical Engineering, National Chung Cheng University. His research interests are related to biomaterials, drug delivery system, tissue engineering, blood-brain barrier, nervous regeneration, cancer therapy, biophysics, and colloid and interface science. In these fields, he has authored or coauthored over 100 reviewed journal papers, abstracts, book chapters, and technical reports. He is an honor member of Phi Tau Phi Society and an active life member of Biochemical Engineering Society of Taiwan and Taiwan Institute of Chemical Engineers. He was often invited as a manuscript reviewer for over 20 journals and an external reviewer for academic awards, research grants, faculty recruitments and promotions, and hosting international symposium subsidy.


ISSN: 1790-5125 11 ISBN: 978-960-474-141-0

Plenary Lecture 2

Creation of Electromagnetic Structure-Creating Spaces to Improve the Growth of Some

Types of Cells and Albumins

Dr. Vladyslav Vlastopulo

Research Laboratories VVL

Chief of biophysical department

Str. Gen. Petrova 9\2, app. 44

Odessa, 65065, Ukraine

E-mail: [email protected] Abstract: There are given some constructions of bio-field simulators for creating the electromagnetic structure-

creating spaces and improving the growth of some types of cells and albumins. There are given investigations of such illnesses: outer covering wounds, anaemia, ligamentous disruption, neurology and diabetes mellitus, - with the help of different types of bio-field simulators..


Dr. Vladyslav Vlastopulo is a scientifically-commercial director of biophysical department on creating of new biomedical methods and devices, bio-field simulators in "Research Laboratories VVL", Odessa, Ukraine, and professor of cathedra of ways and methods of struggling with marine corrosion and biological fouling in Odessa Marine University. His research interests are related to biomedical, tribologycal, biotribologycal and mechanical engineering and also biophysics, bio-field simulators, computer fragmentary treatment of diseases demanding the operations, drug abuse patients, obesity patients, the using in video, audio products for creating attracted bioenergetic advertisement, creation of joints on basis of hydrodynamical lubricant theory. He has more than 120 papers, abstracts, book chapters and technical reports in biomedical, tribologycal, biotribologycal and mechanical engineering, and 50 of them are inventions of Soviet Union, Russian Federation and Ukraine. He is a member of more than 20 international conferences on mechanical, biomedical, tribologycal engineering.


ISSN: 1790-5125 12 ISBN: 978-960-474-141-0

Plenary Lecture 3

A New Way of Natural Oligopeptide Primary Structure Elucidation

Professor Alexander A. Zamyatnin

Departamento de Informatica

Universidad Tecnica Federico Santa Maria

1680 av. Espana, Valparaiso V-110

CHILE

also with

Computer Biochemistry Group

A. N. Bach Institute of Biochemistry

Russian Academy of Sciences

33 Leninsky prosp., Moscow 119071

RUSSIAN FEDERATION

E_mail: [email protected] Abstract: For more than a century, natural oligopeptides have attracted scientific attention as important biochemical

regulators. Since that time, thousands natural oligopeptide regulators have been described, and now ~600 new natural oligopeptides emerge annually, out of a literature of >70 000 publications each year on oligopeptide chemistry and biology according to PubMed database. Their primary structure is determined either directly or by translation from nucleotide sequences. Both these ways are experimental and laborous. But there are a lot of unrecognized protein sequences in different public databases which can contain unknown oligopeptide structures. Thereupon we have carried out a theoretical structure–function analysis of known uncharacterized protein amino acid residue sequences in order to identify new oligopeptide primary structures. As an example, grape (Vitis vinifera) proteins were chosen. A special computer analysis was developed for such analysis. The data of GenBank and SwissProt databases containing primary structures of unrecognized grape proteins, EROP-Moscow database containing information on structure and functions of plant regulatory oligopeptides and specially created computer programs for the comparison of GenBank or SwissProt information with EROP-Moscow data were used. This method permitted to reveal new potentially active regulatory oligopeptide sequences after alignment procedure. It was been found 21 grape protein structure sites homologues to known regulatory oligopeptides elucidated from other plant species. Their similarity with other plant oligopeptide primary structures was from 54.4 to 95.7%. They can be characterized as putative antimicrobial oligopeptides and rapid alkalinization factors. The problem of existence of these oligopeptide structures in grape is discussed. It has been proposed that rapid alkalinization factors can also possess antimicrobial activity. This way of oligopeptide structure elucidation can be extended to oligopeptide structures of any functional class.


Alexander A.Zamyatnin is scientist general of A.N.Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russian Federation and associated investigator of Santa Maria Technical University, Valparaiso, Chile. His area of expertise is endogenous oligopeptides (neuropeptides, hormones, toxins, antimicrobial), protein thermodynamics, structure-function relationship, ligand-receptor interaction, biosensors, computer biochemistry and biophysics, biological data bases, and drug design. He authored or co-authored over 200 scientific papers published in reviewed journals or presented at international conferences. He is the author of unique EROP-Moscow oligopeptide database (http://erop.inbi.ras.ru/; A.A.Zamyatnin et al. Nucleic Acids Research, 34, Database Issue, pp. D261-D266, 2006). He is a member of the European Peptide Society (from 1995).


ISSN: 1790-5125 13 ISBN: 978-960-474-141-0

Authors Index

Aluigi, M. G. 15 Gadaleta, M. N. 64 Savkovic-Stevanovic, J 24

Angelini, C. 15 Gallus, L. 15 Sepcic, K. 15

Aragno, M. 64 Garaventa, F. 15 Shahlaei, M. 119

Babic, A.-M. 39 Gomez-Cia, T. 126 Siljeg, M. 39

Cabral-Camacho, A. 126 Guo, J. 105, 110, 115 Suarez-Mejias, C. 126

Carstea, I. 143 Hasani, S. 68 Tao, C. 110, 115

Cassano, P. 64 Hosseini, B. S. 74 Tianzhen, Z. 110, 115

Castro, M. E. 45 Huang, S. 80 Trombino, S. 15

Chahkandi, B. 68, 74 Jia, R. 132 Turk, T. 15

Chelossi, E. 15 Kabanda, M. M. 58 Vito, P. 64

Chen, X. 132 Lezza, A. M. 64 Wang, M.-S. 132

Chen, Z. 132 Luo, Q. 132 Wang, X. 132

Cheng, A.-C. 132 Mammino, L. 58 Wang, Y. 132

Cui, H. 132 Maria Carstea, I. M. 143 Xu, Z. 132

De La Higuera-Gonzalez, J. M. 126 Mastorakis, N. E. 94 Yue, Z. 80

Derlinchan-Gonzalez, D. 126 Mastrocola, R. 64 Zamyatnin, A. A. 33

Faimali, M. 15 Munoz-Caro, C. 45 Zhang, T. 105

Falugi, C. 15 Nino, A. 45 Zhao, G. 80

Fassihi, A. 119 Paleari, L. 15 Zhou, T. 132

Feizabadi, M. S. 30 Parra-Calderon, C. 126 Zhou, Y. 132

Ferrando, S. 15 Peng, B. 80 Zhu, D. 132

Foglar, L. 39 Perez-Lorente, M. 126 Zovko, A. 15

Frigerio, F. 51 Russo, P. 15

Gacto-Sanchez, P. 126 Sabet, R. 119


ISSN: 1790-5125 149 ISBN: 978-960-474-141-0

RECENT ADVANCES in BIOLOGY, · research interests are related to biomaterials, drug delivery...

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