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Madeira PP, Todorov G, Uversky VN, Zaslavsky BY. Solvent polarity and hydrophobicity of solutes are two sides of the same coin. Biochem Biophys Res Commun 2024; 701:149600. [PMID: 38309151 DOI: 10.1016/j.bbrc.2024.149600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024]
Abstract
The hydrophobicity of solutes measures the intensity of a solute's interaction with aqueous environment. The aqueous environment may change with its composition, leading to changes in its solvent properties largely characterized by polarity. As a result, the relative hydrophobicity of a solute is a function of the solute structure and the properties of the water-based solvent determined by the total composition of the aqueous phase. This aspect is commonly ignored by medicinal chemists even though it is essential for drug distribution between different biological tissues. Partitioning of solutes in aqueous two-phase systems provides the relative hydrophobicity estimates for any water-soluble compounds that can be used to improve predictions of the toxicity and other biological effects of these compounds.
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Affiliation(s)
- Pedro P Madeira
- CICECO, Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - German Todorov
- Cleveland Diagnostics, Cleveland, 3615 Superior Ave., OH, USA
| | - Vladimir N Uversky
- Institute for Biological Instrumentation, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL, 33612, USA
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2
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Marchel M, Marrucho IM. Application of Aqueous Biphasic Systems Extraction in Various Biomolecules Separation and Purification: Advancements Brought by Quaternary Systems. SEPARATION & PURIFICATION REVIEWS 2022. [DOI: 10.1080/15422119.2022.2136574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Mateusz Marchel
- Faculty of Chemistry, Department of Process Engineering and Chemical Technology, Gdansk University of Technology, Gdansk, Poland
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Isabel M. Marrucho
- Centro de Química Estrutural and Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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3
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Joshi PU, Turpeinen DG, Schroeder M, Jones B, Lyons A, Kriz S, Khaksari M, O'Hagan D, Nikam S, Heldt CL. Osmolyte enhanced aqueous two-phase system for virus purification. Biotechnol Bioeng 2021; 118:3251-3262. [PMID: 34129733 DOI: 10.1002/bit.27849] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 05/26/2021] [Accepted: 06/02/2021] [Indexed: 01/15/2023]
Abstract
Due to the high variation in viral surface properties, a platform method for virus purification is still lacking. A potential alternative to the high-cost conventional methods is aqueous two-phase systems (ATPSs). However, optimizing virus purification in ATPS requires a large experimental design space, and the optimized systems are generally found to operate at high ATPS component concentrations. The high concentrations capitalize on hydrophobic and electrostatic interactions to obtain high viral particle yields. This study investigated using osmolytes as driving force enhancers to reduce the high concentration of ATPS components while maintaining high yields. The partitioning behavior of porcine parvovirus (PPV), a nonenveloped mammalian virus, and human immunodeficiency virus-like particle (HIV-VLP), a yeast-expressed enveloped VLP, were studied in a polyethylene glycol (PEG) 12 kDa-citrate system. The partitioning of the virus modalities was enhanced by osmoprotectants glycine and betaine, while trimethylamine N-oxide was ineffective for PPV. The increased partitioning to the PEG-rich phase pertained only to viruses, resulting in high virus purification. Recoveries were 100% for infectious PPV and 92% for the HIV-VLP, with high removal of the contaminant proteins and more than 60% DNA removal when glycine was added. The osmolyte-induced ATPS demonstrated a versatile method for virus purification, irrespective of the expression system.
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Affiliation(s)
- Pratik U Joshi
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
| | - Dylan G Turpeinen
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
| | - Michael Schroeder
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA
| | - Bianca Jones
- Department of Biochemistry, University of Detroit-Mercy, Detroit, Michigan, USA
| | - Audrey Lyons
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA
| | - Seth Kriz
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
| | - Maryam Khaksari
- Great Lakes Research Center, Michigan Technological University, Houghton, Michigan, USA
| | | | | | - Caryn L Heldt
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan, USA.,Health Research Institute, Michigan Technological University, Houghton, Michigan, USA
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The solvent side of proteinaceous membrane-less organelles in light of aqueous two-phase systems. Int J Biol Macromol 2018; 117:1224-1251. [PMID: 29890250 DOI: 10.1016/j.ijbiomac.2018.06.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 06/07/2018] [Indexed: 12/29/2022]
Abstract
Water represents a common denominator for liquid-liquid phase transitions leading to the formation of the polymer-based aqueous two-phase systems (ATPSs) and a set of the proteinaceous membrane-less organelles (PMLOs). ATPSs have a broad range of biotechnological applications, whereas PMLOs play a number of crucial roles in cellular compartmentalization and often represent a cellular response to the stress. Since ATPSs and PMLOs contain high concentrations of polymers (such as polyethylene glycol (PEG), polypropylene glycol (PPG), Ucon, and polyvinylpyrrolidone (PVP), Dextran, or Ficoll) or biopolymers (peptides, proteins and nucleic acids), it is expected that the separated phases of these systems are characterized by the noticeable changes in the solvent properties of water. These changes in solvent properties can drive partitioning of various compounds (proteins, nucleic acids, organic low-molecular weight molecules, metal ions, etc.) between the phases of ATPSs or between the PMLOs and their surroundings. Although there is a sizable literature on the properties of the ATPS phases, much less is currently known about PMLOs. In this perspective article, we first represent liquid-liquid phase transitions in water, discuss different types of biphasic (or multiphasic) systems in water, and introduce various PMLOs and some of their properties. Then, some basic characteristics of polymer-based ATPSs are presented, with the major focus being on the current understanding of various properties of ATPS phases and solvent properties of water inside them. Finally, similarities and differences between the polymer-based ATPSs and biological PMLOs are discussed.
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Meti MD, Dixit MK, Tembe BL. Salting-in of neopentane in the aqueous solutions of urea and glycine-betaine. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1431834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manjunath D. Meti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Mayank K. Dixit
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Bhalachandra L. Tembe
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Ferreira LA, Uversky VN, Zaslavsky BY. Phase equilibria, solvent properties, and protein partitioning in aqueous polyethylene glycol-600-trimethylamine N-oxide and polyethylene glycol-600-choline chloride two-phase systems. J Chromatogr A 2018; 1535:154-161. [DOI: 10.1016/j.chroma.2018.01.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/27/2017] [Accepted: 01/03/2018] [Indexed: 12/21/2022]
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Zaslavsky BY, Uversky VN. In Aqua Veritas: The Indispensable yet Mostly Ignored Role of Water in Phase Separation and Membrane-less Organelles. Biochemistry 2018; 57:2437-2451. [PMID: 29303563 DOI: 10.1021/acs.biochem.7b01215] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the common practice of presenting structures of biological molecules on an empty background and the assumption that interactions between biological macromolecules take place within the inert solvent, water represents an active component of various biological processes. This Perspective addresses indispensable, yet mostly ignored, roles of water in biological liquid-liquid phase transitions and in the biogenesis of various proteinaceous membrane-less organelles. We point out that changes in the structure of water reflected in the changes in its abilities to donate and/or accept hydrogen bonds and participate in dipole-dipole and dipole-induced dipole interactions in the presence of various solutes (ranging from small molecules to synthetic polymers and biological macromolecules) might represent a driving force for the liquid-liquid phase separation, define partitioning of various solutes in formed phases, and define the exceptional ability of intrinsically disordered proteins to be engaged in the formation of proteinaceous membrane-less organelles.
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Affiliation(s)
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , Florida 33612 , United States.,Laboratory of New Methods in Biology , Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino , Moscow Region 142290 , Russia
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What are the structural features that drive partitioning of proteins in aqueous two-phase systems? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:113-120. [DOI: 10.1016/j.bbapap.2016.09.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/26/2016] [Accepted: 09/18/2016] [Indexed: 02/07/2023]
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Ferreira LA, Uversky VN, Zaslavsky BY. Role of solvent properties of water in crowding effects induced by macromolecular agents and osmolytes. MOLECULAR BIOSYSTEMS 2017; 13:2551-2563. [DOI: 10.1039/c7mb00436b] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Dipolarity/polarizability of water in polymer mixtures may be additive, reduced or enhanced depending on the composition of the mixture.
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Affiliation(s)
| | - V. N. Uversky
- Department of Molecular Medicine
- Morsant College of Medicine
- University of South Florida
- Tampa
- USA
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Predicting protein partition coefficients in aqueous two phase system. J Chromatogr A 2016; 1470:50-58. [DOI: 10.1016/j.chroma.2016.09.072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/01/2016] [Accepted: 09/30/2016] [Indexed: 01/22/2023]
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Zaslavsky BY, Uversky VN, Chait A. Analytical applications of partitioning in aqueous two-phase systems: Exploring protein structural changes and protein–partner interactions in vitro and in vivo by solvent interaction analysis method. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:622-44. [DOI: 10.1016/j.bbapap.2016.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/16/2016] [Accepted: 02/21/2016] [Indexed: 12/29/2022]
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Interrelationship between partition behavior of organic compounds and proteins in aqueous dextran-polyethylene glycol and polyethylene glycol-sodium sulfate two-phase systems. J Chromatogr A 2016; 1443:21-5. [DOI: 10.1016/j.chroma.2016.03.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/14/2016] [Accepted: 03/14/2016] [Indexed: 01/01/2023]
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Ferreira LA, Povarova OI, Stepanenko OV, Sulatskaya AI, Madeira PP, Kuznetsova IM, Turoverov KK, Uversky VN, Zaslavsky BY. Effects of low urea concentrations on protein-water interactions. J Biomol Struct Dyn 2016; 35:207-218. [DOI: 10.1080/07391102.2015.1135823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Luisa A. Ferreira
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA
| | - Olga I. Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Olga V. Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Pedro P. Madeira
- Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, Porto 4200-465, Portugal
| | - Irina M. Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Konstantin K. Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Biophysics, St. Petersburg State Polytechnic University, St. Petersburg 195251, Russia
| | - Vladimir N. Uversky
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Boris Y. Zaslavsky
- Cleveland Diagnostics, 3615 Superior Ave., Suite 4407B, Cleveland, Ohio 44114, USA
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Ferreira LA, Uversky VN, Zaslavsky BY. Analysis of the distribution of organic compounds and drugs between biological tissues in the framework of solute partitioning in aqueous two-phase systems. MOLECULAR BIOSYSTEMS 2016; 12:3567-3575. [DOI: 10.1039/c6mb00608f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Distribution of organic compounds between different biological tissues may be considered in the framework of solute partitioning in aqueous two-phase systems.
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Affiliation(s)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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Zaslavsky BY, Uversky VN, Chait A. Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics. Expert Rev Proteomics 2015; 13:9-17. [PMID: 26558960 DOI: 10.1586/14789450.2016.1116945] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein-partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein-protein- and protein-partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.
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Affiliation(s)
- Boris Y Zaslavsky
- a Cleveland Diagnostics , 3615 Superior Avenue, Suite 4407B, Cleveland , OH 44114 , USA
| | - Vladimir N Uversky
- b Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine , University of South Florida , Tampa , FL 33612 , USA
| | - Arnon Chait
- a Cleveland Diagnostics , 3615 Superior Avenue, Suite 4407B, Cleveland , OH 44114 , USA
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da Silva NR, Ferreira LA, Madeira PP, Teixeira JA, Uversky VN, Zaslavsky BY. Analysis of partitioning of organic compounds and proteins in aqueous polyethylene glycol-sodium sulfate aqueous two-phase systems in terms of solute-solvent interactions. J Chromatogr A 2015; 1415:1-10. [PMID: 26342872 DOI: 10.1016/j.chroma.2015.08.053] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 12/30/2022]
Abstract
Partition behavior of nine small organic compounds and six proteins was examined in poly(ethylene glycol)-8000-sodium sulfate aqueous two-phase systems containing 0.5M osmolyte (sorbitol, sucrose, trehalose, TMAO) and poly(ethylene glycol)-10000-sodium sulfate system, all in 0.01M sodium phosphate buffer, pH 6.8. The differences between the solvent properties of the coexisting phases (solvent dipolarity/polarizability, hydrogen bond donor acidity, and hydrogen bond acceptor basicity) were characterized with solvatochromic dyes using the solvatochromic comparison method. Differences between the electrostatic properties of the phases were determined by analysis of partitioning of sodium salts of dinitrophenylated (DNP-) amino acids with aliphatic alkyl side-chain. It was found out that the partition coefficient of all compounds examined (including proteins) may be described in terms of solute-solvent interactions. The results obtained in the study show that solute-solvent interactions of nonionic organic compounds and proteins in polyethylene glycol-sodium sulfate aqueous two-phase system differ from those in polyethylene glycol-dextran system.
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Affiliation(s)
- Nuno R da Silva
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Luisa A Ferreira
- Analiza, Inc., 3615 Superior Ave., Cleveland, OH 44114, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Pedro P Madeira
- Laboratory of Separation and Reaction Engineering, Department of Chemical Engineering, Faculty of Engineering of the University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - José A Teixeira
- IBB-Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Boris Y Zaslavsky
- Analiza, Inc., 3615 Superior Ave., Cleveland, OH 44114, USA; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia.
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