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Microbial systems biology : methods and protocols / edited by Ali Navid.

Contributor(s): Navid, AliMaterial type: TextTextSeries: Methods in molecular biology (Clifton, N.J.) ; v. 881.Publication details: New York : Humana Press, ©2012. Description: 1 online resourceContent type: text Media type: computer Carrier type: online resourceISBN: 9781617798276; 1617798274; 1617798266; 9781617798269Subject(s): Systems biology | Microbiology | Phenomena and Processes | Computational Biology | Biology | Biological Science Disciplines | Natural Science Disciplines | Disciplines and Occupations | Systems Biology | Microbiological Phenomena | Microbiology | Systems biology | Life sciences | Biological models | Microbiology | Systems Biology | levenswetenschappen | microbiologie | systeembiologie | Biology (General) | Biologie (algemeen)Genre/Form: Electronic books. Additional physical formats: Print version:: Microbial systems biology.DDC classification: 570.1/13 LOC classification: QH324.2 | .M53 2012NLM classification: W1 | QW 25Online resources: Click here to access online
Contents:
pt. I. Sample preparation and identification. -- 1. Flow cytometry in environmental microbiology: a rapid approach for the isolation of single cells for advanced molecular biology analysis / Belinda C. Ferrari, Tristrom J. Winsley, Peter L. Bergquist, and Josie Van Dorst ; 2. Pressure cycling technology in systems biology / Bradford S. Powell, Alexander V. Lazarev, Greta Carlson, Alexander R. Ivanov, and David A. Rozak ; 3. Targeted isolation of proteins from natural microbial communities living in an extreme environment / Steven W. Singer ; 4. Bacterial identification and subtyping using DNA microarray and DNA sequencing / Sufian F. Al-Khaldi, Magdi M. Mossoba, Marc M. Allard, E. Kurt Lienau, and Eric D. Brown -- pt. II. Experimental genomic analysis. -- 5. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans / Harry R. Beller, Tina C. Legler, and Stacie R. Kane ; 6. Genome-wide mapping of the binding sites of proteins that interact with DNA / Stephen Spiro -- pt. III. Protein and lipid analysis. -- 7. Microbial proteomics using mass spectrometry / Harry B. Hines ; 8. Fourier transform infrared spectroscopy for molecular analysis of microbial cells / Jesús J. Ojeda and Maria Dittrich -- pt. IV. Metabolomic analyses. -- 9. Mass spectrometery-based microbial metabolomics / Edward E.K. Baidoo, Peter I. Benke, and Jay D. Keasling ; 10. Fast sampling of the cellular metabolome / Walter M. Van Gulik, Andre B. Canelas, Hilal Taymaz-Nikeel, Rutger D. Douma, Lodewijk P. de Jonge, and Joseph J. Heijnen -- pt. V. -- 11. Metabolic pathway determination and flux analysis in nonmodel microorganisms through ¹³C-isotope labeling / Xueyang Feng, Wei-Qin Zhuang, Peter Colletti, and Yinjie J. Tang ; 12. Biolog phenotype microarrays / April Shea, Mark Wolcott, Simon Daefler, and David A. Rozak ; 13. NanoSIP: nanoSIMS applications for microbial biology / Jennifer Pett-Ridge and Peter K. Weber -- pt. VI. Kinetic modeling of cellular processes -- 14. Electrophysiological-metabolic modeling of microbes: applications in fuel cells and environment analysis / Max Fontus and Peter Ortoleva ; 15. Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods / A. Singharoy, H. Joshi, S. Cheluvaraja, Y. Miao, D. Brown, and P. Ortoleva -- pt. VII. -- 16. Bacterial genome annotation / Nicholas Beckloff, Shawn Starkenburg, Tracey Freitas, and Patrick Chain ; 17. LeishCyc: a guide to building a metabolic pathway database and visualization of metabolomic data / Eleanor C. Saunders, James I. MacRae, Thomas Naderer, Milica Ng, Malcolm J. McConville, and Vladimir A. Likić ; 18. Development of constraint-based system-level models of microbial metabolism / Ali Navid ; 19. Complex network analysis in microbial systems: theory and examples / Zahra Zavareh and Eivind Almaas ; 20. Modeling a minimal cell / Michael L. Shuler, Patricia Foley, and Jordan Atlas.
Summary: Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being directed toward examining systems biology in complex multi-cellular organisms, the bulk of system-level analyses conducted to date have focused on the biology of microbes. In, Microbial Systems Biology: Methods and Protocols expert researchers in the field describe the utility and attributes of different tools (both experimental and computational) that are used for studying microbial systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Systems Biology: Methods and Protocols introduces and aids scientists in using the various tools that are currently available for analysis, modification and utilization of microbial organisms.
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Includes index.

Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being directed toward examining systems biology in complex multi-cellular organisms, the bulk of system-level analyses conducted to date have focused on the biology of microbes. In, Microbial Systems Biology: Methods and Protocols expert researchers in the field describe the utility and attributes of different tools (both experimental and computational) that are used for studying microbial systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Systems Biology: Methods and Protocols introduces and aids scientists in using the various tools that are currently available for analysis, modification and utilization of microbial organisms.

pt. I. Sample preparation and identification. -- 1. Flow cytometry in environmental microbiology: a rapid approach for the isolation of single cells for advanced molecular biology analysis / Belinda C. Ferrari, Tristrom J. Winsley, Peter L. Bergquist, and Josie Van Dorst ; 2. Pressure cycling technology in systems biology / Bradford S. Powell, Alexander V. Lazarev, Greta Carlson, Alexander R. Ivanov, and David A. Rozak ; 3. Targeted isolation of proteins from natural microbial communities living in an extreme environment / Steven W. Singer ; 4. Bacterial identification and subtyping using DNA microarray and DNA sequencing / Sufian F. Al-Khaldi, Magdi M. Mossoba, Marc M. Allard, E. Kurt Lienau, and Eric D. Brown -- pt. II. Experimental genomic analysis. -- 5. Genetic manipulation of the obligate chemolithoautotrophic bacterium Thiobacillus denitrificans / Harry R. Beller, Tina C. Legler, and Stacie R. Kane ; 6. Genome-wide mapping of the binding sites of proteins that interact with DNA / Stephen Spiro -- pt. III. Protein and lipid analysis. -- 7. Microbial proteomics using mass spectrometry / Harry B. Hines ; 8. Fourier transform infrared spectroscopy for molecular analysis of microbial cells / Jesús J. Ojeda and Maria Dittrich -- pt. IV. Metabolomic analyses. -- 9. Mass spectrometery-based microbial metabolomics / Edward E.K. Baidoo, Peter I. Benke, and Jay D. Keasling ; 10. Fast sampling of the cellular metabolome / Walter M. Van Gulik, Andre B. Canelas, Hilal Taymaz-Nikeel, Rutger D. Douma, Lodewijk P. de Jonge, and Joseph J. Heijnen -- pt. V. -- 11. Metabolic pathway determination and flux analysis in nonmodel microorganisms through ¹³C-isotope labeling / Xueyang Feng, Wei-Qin Zhuang, Peter Colletti, and Yinjie J. Tang ; 12. Biolog phenotype microarrays / April Shea, Mark Wolcott, Simon Daefler, and David A. Rozak ; 13. NanoSIP: nanoSIMS applications for microbial biology / Jennifer Pett-Ridge and Peter K. Weber -- pt. VI. Kinetic modeling of cellular processes -- 14. Electrophysiological-metabolic modeling of microbes: applications in fuel cells and environment analysis / Max Fontus and Peter Ortoleva ; 15. Simulating microbial systems: addressing model uncertainty/incompleteness via multiscale and entropy methods / A. Singharoy, H. Joshi, S. Cheluvaraja, Y. Miao, D. Brown, and P. Ortoleva -- pt. VII. -- 16. Bacterial genome annotation / Nicholas Beckloff, Shawn Starkenburg, Tracey Freitas, and Patrick Chain ; 17. LeishCyc: a guide to building a metabolic pathway database and visualization of metabolomic data / Eleanor C. Saunders, James I. MacRae, Thomas Naderer, Milica Ng, Malcolm J. McConville, and Vladimir A. Likić ; 18. Development of constraint-based system-level models of microbial metabolism / Ali Navid ; 19. Complex network analysis in microbial systems: theory and examples / Zahra Zavareh and Eivind Almaas ; 20. Modeling a minimal cell / Michael L. Shuler, Patricia Foley, and Jordan Atlas.

Includes bibliographical references and index.

English.

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