Applications: - Applications of Microbial Cell Sensors, by Mifumi Shimomura-Shimizu and Isao Karube - Whole-Cell Bioreporters for the Detection of Bioavailable Metals, by Anu Hynninen and Marko Virta - Bacteriophage-Based Pathogen Detection, by Steven Ripp - Cell-Based Genotoxicity Testing, by Georg Reifferscheid and Sebastian Buchinger - Cytotoxicity and Genotoxicity Reporter Systems Based on the Use of Mammalian Cells, by Christa Baumstark-Khan, Christine E. Hellweg, and Günther Reitz - Live Cell Optical Sensing for High Throughput Applications, by Ye Fang - Cyanobacterial Bioreporters as Sensors of Nutrient Availability, by George S. Bullerjahn, Ramakrishna Boyanapalli, Mark J. Rozmarynowycz, and R. Michael L. McKay - Application of Microbial Bioreporters in Environmental Microbiology and Bioremediation, by E. E. Diplock , H. A. Alhadrami , and G. I. Paton

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

Table of Contents Reporter cells: - Yeast Based Sensors by Mifumi Shimomura-Shimizu and Isao Karube - Mammalian Cell-Based Sensor Systems by Pratik Banerjee, Briana Franz, and Arun K. Bhunia - Fluorescent and Bioluminescent Cell-Based Sensors: Strategies for Their Preservation by Amol Date, Patrizia Pasini, and Sylvia Daunert - Electrochemical Cell-Based Sensors by Eliora Z. Ron and Judith Rishpon - Microbial Cell Arrays by Tal Elad, Jin Hyung Lee, Man Bock Gu, and Shimshon Belkin Devices: - Surface Functionalization for Protein and Cell Patterning by Pascal Colpo , Ana Ruiz , Laura Ceriotti , and François Rossi - Fiber-Optic Based Cell Sensors by Evgeni Eltzov and Robert S. Marks - Electronic Interfacing with Living Cells by James T. Fleming - On-Chip Detection of Cellular Activity by R. Almog , R. Daniel , S. Vernick , A. Ron , H. Ben-Yoav, and Y. Shacham-Diamand

Bacterial reporters are live, genetically engineered cells with promising application in bioanalytics. They contain genetic circuitry to produce a cellular sensing element, which detects the target compound and relays the detection to specific synthesis of so-called reporter proteins (the presence or activity of which is easy to quantify). Bioassays with bacterial reporters are a useful complement to chemical analytics because they measure biological responses rather than total chemical concentrations. Simple bacterial reporter assays may also replace more costly chemical methods as a first line sample analysis technique. Recent promising developments integrate bacterial reporter cells with microsystems to produce bacterial biosensors. This lecture presents an in-depth treatment of the synthetic biological design principles of bacterial reporters, the engineering of which started as simple recombinant DNA puzzles, but has now become a more rational approach of choosing and combining sensing, controlling and reporting DNA 'parts'. Several examples of existing bacterial reporter designs and their genetic circuitry will be illustrated. Besides the design principles, the lecture also focuses on the application principles of bacterial reporter assays. A variety of assay formats will be illustrated, and principles of quantification will be dealt with. In addition to this discussion, substantial reference material is supplied in various Annexes. Table of Contents: Short History of the use of Bacteria for Biosensing and Bioreporting / Genetic Engineering Concepts / Measuring with Bioreporters / Epilogue

Microbial Biodegradation and Bioremediation brings together experts in relevant fields to describe the successful application of microbes and their derivatives for bioremediation of potentially toxic and relatively novel compounds. This single-source reference encompasses all categories of pollutants and their applications in a convenient, comprehensive package. Our natural biodiversity and environment is in danger due to the release of continuously emerging potential pollutants by anthropogenic activities. Though many attempts have been made to eradicate and remediate these noxious elements, every day thousands of xenobiotics of relatively new entities emerge, thus worsening the situation. Primitive microorganisms are highly adaptable to toxic environments, and can reduce the load of toxic elements by their successful transformation and remediation. - Describes many novel approaches of microbial bioremediation including genetic engineering, metagenomics, microbial fuel cell technology, biosurfactants and biofilm-based bioremediation - Introduces relatively new hazardous elements and their bioremediation practices including oil spills, military waste water, greenhouse gases, polythene wastes, and more - Provides the most advanced techniques in the field of bioremediation, including insilico approach, microbes as pollution indicators, use of bioreactors, techniques of pollution monitoring, and more

Transcriptome Analysis, by Frank Stahl, Bernd Hitzmann, Kai Mutz, Daniel Landgrebe, Miriam Lübbecke, Cornelia Kasper, Johanna Walter und Thomas Scheper Transcriptome Data Analysis for Cell Culture Processes, by Marlene Castro-Melchor, Huong Le und Wei-Shou Hu Modeling Metabolic Networks for Mammalian Cell Systems: General Considerations, Modeling Strategies, and Available Tools, by Ziomara P. Gerdtzen Metabolic Flux Analysis in Systems Biology of Mammalian Cells, by Jens Niklas und Elmar Heinzle Advancing Biopharmaceutical Process Development by System-Level Data Analysis and Integration of Omics Data, by Jochen Schaub, Christoph Clemens, Hitto Kaufmann und Torsten W. Schulz Protein Glycosylation and Its Impact on Biotechnology, by Markus Berger, Matthias Kaup und Véronique Blanchard Protein Glycosylation Control in Mammalian Cell Culture: Past Precedents and Contemporary Prospects, by Patrick Hossler Modeling of Intracellular Transport and Compartmentation, by Uwe Jandt und An-Ping Zeng Genetic Aspects of Cell Line Development from a Synthetic Biology Perspective, by L. Botezatu, S. Sievers, L. Gama-Norton, R. Schucht, H. Hauser und D. Wirth.

Light Microscopic Analysis of Mitochondrial Heterogeneity in Cell Populations and Within Single Cells, by S. Jakobs, S. Stoldt, and D. Neumann * Advanced Microscopy of Microbial Cells, by J. A. J. Haagensen, B. Regenberg, and C. Sternberg * Algebraic and Geometric Understanding of Cells, Epigenetic Inheritance of Phenotypes Between Generations, by K. Yasuda * Measuring the Mechanical Properties of Single Microbial Cells, by C. R. Thomas, J. D. Stenson, and Z. Zhang * Single Cell Analytics: Pushing the Limits of the Doable, by H. Kortmann, L.M. Blank, and A. Schmid * Cultivation-Independent Assessment of Bacterial Viability, by F. Hammes, M. Berney, and T. Egli * Resolution of Natural Microbial Community Dynamics by Community Fingerprinting, Flow Cytometry and Trend Interpretation Analysis, by P. Bombach, T. Hübschmann, I. Fetzer, S. Kleinsteuber, R. Geyer, H. Harms, and S. Müller *Multivariate Data Analysis Methods for the Interpretation of Microbial Flow Cytometric Data, by H.M. Davey, and C.L. Davey * From Single Cells to Microbial Population Dynamics: Modelling in Biotechnology Based on Measurements of Individual Cells, by T. Bley