Volume 7
Editorial
Worldwide Scientists
Anniversary
New Books
Knowledge Discovery in Bioinformatics - Techniques, Methods, and Applications
Bioinformatics - Genomics and Post-Genomics
Forthcoming Events
First call for the 21th international symposium on bioprocess systems 2008 - BIOPS’08
Bioprocess Systems
Development and Automation of Microturbulence Intensifying Systems and Biosynthesis Conditions in Bioreactors1-8
Uldis Viesturs
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Results of the investigation applying newly developed methods: a Stirring Intensity Measuring Device (SIMD), a counterflow mixing system, identification of the state of turbohypobiosis, counterflow bioreactor’s design and a process controller BIO-3 have been analysed. Special attention has been given to the phenomena on the liquid-cell interface area. A combination of the above-mentioned methods with conventional ones does not provide the scale up and scale down of bioreactors when geometrical dissimilarity occurs. Special adjustment is necessary for each case and culture.
Modeling Biodegradation Kinetics on Benzene and Toluene and Their Mixture9-22
Daniela E.G. Trigueros, Aparecido N. Módenes, Alexander D. Kroumov
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The objective of this work was to model the biodegradation kinetics of toxic compounds toluene and benzene as pure substrates and in a mixture. As a control, Monod and Andrews models were used. To predict substrates interactions, more sophisticated models of inhibition and competition, and SKIP (sum kinetics interactions parameters) model were applied. The models evaluation was performed based on the experimental data from Pseudomonas putida F1 activities published in the literature. In parameter identification procedure, the global method of particle swarm optimization (PSO) was applied. The simulation results show that the better description of the biodegradation process of pure toxic substrate can be achieved by Andrews’ model. The biodegradation process of a mixture of toxic substrates is modeled the best when modified competitive inhibition and SKIP models are used. The developed software can be used as a toolbox of a kinetics model catalogue of industrial wastewater treatment for process design and optimization.
Biosorption of the Copper and Cadmium Ions - a Study through Adsorption Isotherms Analysis23-33
Marcia R. Fagundes-Klen, Luiz G. L. Vaz, Marcia T. Veit, E. Borba, Edson A. Silva, Alexander D. Kroumov
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In this work, the biosorption process of copper-cadmium ions binary mixture by using marine algae Sargassum filipendula was investigated. A set of experiments was performed to obtain equilibrium data for the given batch operational conditions - T=30°C, pH=5. The interpretation of equilibrium data was based on the binary adsorption isotherms models in the Langmuir and Freundlich forms. To evaluate the models parameters, nonlinear identification procedure was used based on the Least Square statistical method and SIMPLEX local optimizer. An analysis of the obtained results showed that the marine algae biomass has higher affinity to copper ions than to cadmium ones. The biomass maximum adsorption capacity for the binary system was about 1.16 meq/g.
Mathematical Description of Functional States in E. coli Fed-batch Cultivation Processes34-45
Olympia Roeva, Kalin Kosev, Stoyan Tzonkov
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This paper presents an overview of a biochemical correspondence to defined functional states based on specific metabolic mechanisms. For Escherichia coli fed-batch cultivation processes a set of four functional states is considered. It is shown that the process can be divided into several functional states by considering the cell metabolism in more detail. As a result through the proposed functional states the changes in metabolic pathways can be described accurately. For each functional state a respective local model is proposed. Simulations of the E. coli cultivation process with functional state modelling are presented. Furthermore different functional states in a real E. coli MC4110 fed-batch cultivation process are identified and local models are developed. By simulations and comparing results to experimental data is shown that the concept of functional state modelling works in practice and leads to more precise and adequate mathematical description.
An Evaluation of Kinetic Parameters of Cadmium and Copper Biosorption by Immobilized Cells46-56
Dessislava Marinkova, Iren Tsibranska, Lyubov Yotova, Nelly Georgieva
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Bioremediation is the use of living organisms to reduce or eliminate environmental hazards resulting from the accumulation of toxic chemicals and other hazardous wastes. This technology is based on the utilization of microorganisms to transform organic and inorganic compounds. The filamentous yeast Trichosporon cutaneum strain R57, immobilized and free cells was cultivated as batch culture on a liquid medium in the presence of various concentrations of cadmium and copper ions. The simultaneous uptake and accumulation of Cd2+ and Cu2+ ions by Tr. cutaneum cells depending on the initial concentration of Cd2+ and Cu2+ in the medium were studied. The potential use of the free and immobilized cells of Trichosporon cutaneum to remove cadmium and copper ions, from aqueous solutions was evaluated. Two important physicochemical aspects for the evaluation of the sorption process as a unit operation are the equilibrium of sorption and the kinetics. The Cd2+ and Cu2+ ions biosorption capacities of all tested adsorbent were presented as a function of the initial concentration of metal ions within the aqueous biosorption medium. The individual, as well as bicomponent sorption kinetics of copper and cadmium ions by immobilised cells of Trichosporon cutaneum R57 is presented. A second order kinetic model obtains kinetic parameters for the copper and cadmium ions.
Near-native Protein Structure Simulation57-63
Stefka Fidanova
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The protein folding problem is a fundamental problem in computational molecular biology and biochemical physics. The high resolution 3D structure of a protein is the key to the understanding and manipulating of its biochemical and cellular functions. All information necessary to fold a protein to its native structure is contained in its amino-acid sequence. Proteins structure could be calculated from knowledge of its sequence and our understanding of the sequence-structure relationships. Various optimization methods have been applied to formulation of the folding problem. There are two main approaches. The one is based on properties of homologous proteins. Other is based on reduced models of proteins structure like hydrophobic-polar (HP) protein model. After that, the folding problem is defined like optimization problem. It is a hard optimization problem and most of the authors apply Monte Carlo or metaheuristic methods to solve it. In this paper other approach will be used. By HP model is explained the structures of proteins conformation observed by biologists and is studied the correspondence between the primary and tertiary structures of the proteins.
Biomedical Systems
On an Intuitionistic Fuzzy Approach for Decision Making in Medicine: Part 264-69
Ludmila Todorova, Krassimir Atanassov, Stefan Hadjitodorov, Peter Vassilev
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An idea presented in [6, 7] has been developed further, and the patients readiness for weaning form long-term mechanical ventilation has been determined in the sense of intuitionistic fuzzy logic [1]. In the present paper it is solved as pattern recognition problem. As a final estimate of the classification an estimate aggregated from four estimates, obtained by four different procedures: Stepwise discriminant analysis (SDA), stepwise logistic regression (SLR), “intuitionistic fuzzy” Voronoi diagrams (IFVD) and nonpulmonary weaning index (NPWI), is taken. The aggregation of estimates is executed by the application of the second algorithm, proposed in [7]. A comparison between the two algorithms has been made.
Modelling of Enzymatic Action in Heterogeneous Phase Assay70-89
Kiril Tenekedjiev
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Thrombolysis is based on the action of a fluid-phase enzyme (plasminogen activator) on a gel-phase bound plasminogen with subsequent generation of an active protease (plasmin), which dissolves the gel matrix (fibrin). The design of new therapeutic tools requires adequate in silico models of the process for efficient preliminary testing and characterization of the thrombolytic agents. The present study describes an approach for simulation of the heterogeneous phase enzymatic process and identification of model parameters for the enzymes.
Stability Analysis of Time Delay Model of Crosstalk between ERK and STAT5a Interaction90-98
Vladimir Kotev, Svetoslav Nikolov
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In this paper we investigate the qualitative behavior of a time delay model of the crosstalk between ERK and STAT5. We apply linear approximation to study the time delay model. The influence of some parameters on the dynamics of the model is analyzed analytically and numerically. Our qualitative results show that the model is structurally unstable. Relating this result to the physiological nature of the studied mathematical model, we prove mathematically the appearance of a crosstalk between the signaling pathways ERK and STAT in some cancer cells. This pathology appears when the process of homeostasis is disturbed and it has a non-reverse character.
Prevalence of Extended-spectrum β-lactamase in Latvia99-103
Ruta Paberza, Solvita Selderiņa, Sandra Leja, Jelena Storoženko, Lilija Lužbinska, Aija Žileviča
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A total of 507 strains of the Enterobacteriaceae family were tested for the production of ESBL using mini API, ATB Expert system as a screening method, as well as the double disk method and E-test for confirmation. The prevalence of ESBL producing E. coli is 5.95%, Klebsiella spp. strains 37.7%. All ESBL- producing isolates are susceptible to imipenem and clavulanate. The susceptibility to other antimicrobials varies from 36 to 92%.
Virtual Ligand Screening for Structure-based Drug Design: Approaches and Progress104-121
Maria A. Miteva, Olivier Sperandio, Bruno O. Villoutreix
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Recent progress in human genomics and proteomics has significantly increased the number of macromolecular targets potentially involved in drug discovery campaigns. Today technologies like combinatorial chemistry and high-throughput screening (HTS) authorize biological assays of a large number of small molecules against the therapeutically relevant targets. However the escalating costs highlight the need of developing novel approaches while still allowing one to explore larger chemical diversity. In this respect, virtual ligand screening (VLS) is established as an attractive approach to handle large sets of compounds and to improve the “hit-rate” of drug discovery programs. Here, we review the main VLS techniques applied for structure-based drug design and we focus on key concepts in the molecular docking–scoring methodology.

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