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Biological Identification

Book Description

Biological identification systems are a vital component in countering the threats to life and health posed by natural pathogens, toxins, and bioterrorism agents. It is essential that such systems are fast, accurate, reliable and easy to use. It is also important to employ the most suitable technology in dealing with any particular threat. This book provides a detailed review of the technologies available and the potential for future developments.

Part one covers the essentials of DNA and RNA sequencing for the identification of pathogens, including next generation sequencing (NGS), polymerase chain reaction (PCR) methods, isothermal amplification and bead array technologies. Part two addresses a variety of approaches to making identification systems portable, tackling the special requirements of smaller, mobile systems in fluid movement, power usage, and sample preparation. Part three focuses in on a range of optical methods and their advantages. Finally, part four describes a unique approach to sample preparation and a promising approach to identification using mass spectroscopy.

Biological Identification will be a useful resource for academics and engineers involved in the microelectronics and sensors industry, and for companies, medical organisations and military bodies looking for biodetection solutions.



  • Covers DNA sequencing of pathogens, lab-on-chip and portable systems for biodetection and analysis
  • Provides an in-depth description of optical systems and explores sample preparation and mass spectrometry-based biological analysis

Table of Contents

  1. Cover image
  2. Title page
  3. Copyright
  4. Contributor contact details
  5. Woodhead Publishing Series in Electronic and Optical Materials
  6. Preface
  7. Part I: Technology for DNA and RNA analysis of pathogens
    1. 1. Nucleic acid sequencing for characterizing infectious and/or novel agents in complex samples
      1. Abstract:
      2. 1.1 Pathogen sequencing and applications in public health and biosecurity
      3. 1.2 Next-generation sequencing (NGS) technologies and the sequencing landscape
      4. 1.3 Characterization of known pathogens
      5. 1.4 Discovery of novel agents
      6. 1.5 Future trends
      7. 1.6 Acknowledgments
      8. 1.7 References
    2. 2. Multiplexed, lateral flow, polymerase chain reaction (PCR) techniques for biological identification
      1. Abstract:
      2. 2.1 Introduction
      3. 2.2 Real-time PCR: development and description
      4. 2.3 Considerations when developing a real-time PCR assay
      5. 2.4 Real-time PCR instrument platforms
      6. 2.5 References
    3. 3. Isothermal amplification of specific sequences
      1. Abstract:
      2. 3.1 Introduction
      3. 3.2 Melting temperature (Tm) estimation and categories of isothermal amplification technologies
      4. 3.3 Isothermal amplification based on DNA polymerases
      5. 3.4 Isothermal amplification based on RNA polymerases
      6. 3.5 Future prospects
      7. 3.6 References
    4. 4. Bead array technologies for genetic disease screening and microbial detection
      1. Abstract:
      2. 4.1 Introduction
      3. 4.2 Luminex® xMAP® Technology
      4. 4.3 Illumina VeraCode
      5. 4.4 NanoString nCounter
      6. 4.5 Applications
      7. 4.6 Conclusion
      8. 4.7 References
  8. Part II: Lab-on-chip and portable systems for biodetection and analysis
    1. 5. Electrochemical detection for biological identification
      1. Abstract:
      2. 5.1 Introduction
      3. 5.2 Electrochemical techniques for bioanalysis
      4. 5.3 Electrochemical biosensors for pathogens
      5. 5.4 Conclusions
      6. 5.5 References
    2. 6. Conductometric biosensors
      1. Abstract:
      2. 6.1 Introduction
      3. 6.2 Conductometry in enzyme catalysis
      4. 6.3 Conductometric enzyme biosensors based on direct analysis – I: Biosensors for biomedical applications
      5. 6.4 Conductometric enzyme biosensors based on direct analysis – II: Biosensors for environmental applications
      6. 6.5 Conductometric enzyme biosensors based on direct analysis – III: Biosensors for agribusiness applications
      7. 6.6 Conductometric enzyme biosensors based on inhibition analysis
      8. 6.7 Whole cell conductometric biosensors
      9. 6.8 DNA-based conductometric biosensors
      10. 6.9 Conductometric biosensors for detection of microorganisms
      11. 6.10 Conclusions
      12. 6.11 References
    3. 7. Bio-chem-FETs: field effect transistors for biological sensing
      1. Abstract:
      2. 7.1 Introduction
      3. 7.2 The field effect transistor (FET)
      4. 7.3 Chemical compounds and biological units as sensing elements in Bio-chem-FETs
      5. 7.4 Nanomaterials and nanoengineering in the design of Bio-chem-FETs
      6. 7.6 References
    4. 8. Microfluidic devices for rapid identification and characterization of pathogens
      1. Abstract:
      2. 8.1 Introduction
      3. 8.2 Challenges and technical as well as commercial solutions
      4. 8.3 Pathogens and analytes
      5. 8.4 Chip-based analysis of protein-based analytes in microfluidic devices
      6. 8.5 Chip-based analysis of nucleic acid-based analytes in microfluidic devices
      7. 8.6 Future trends
      8. 8.7 Acknowledgements
      9. 8.8 References
  9. Part III: Optical systems for biological identification
    1. 9. Optical biodetection using receptors and enzymes (porphyrin-incorporated)
      1. Abstract:
      2. 9.1 Introduction
      3. 9.2 Prior research/literature
      4. 9.3 Binding of cells
      5. 9.4 Binding of a receptor to a simulated ‘toxin’
      6. 9.5 Binding of the simulated 'toxin' to the receptor
      7. 9.6 Binding of a specific antigen diagnostic of cancer to a receptor
      8. 9.7 Binding of cholera toxin
      9. 9.8 Binding of influenza
      10. 9.9 Conclusion
      11. 9.10 References
    2. 10. Overview of terahertz spectral characterization for biological identification
      1. Abstract:
      2. 10.1 Introduction
      3. 10.2 Fundamentals of terahertz vibrational spectroscopy for biological identification of large biological molecules and species
      4. 10.3 Overview
      5. 10.4 Recent and future trends
      6. 10.5 Approach for computational modeling of vibrational frequencies and absorption spectra of biomolecules
      7. 10.6 The problem with a poor convergence of simulation
      8. 10.7 Other problems: dissipation time scales
      9. 10.8 Statistical model for <em xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops">Escherichia coli</em> DNA sequence DNA sequence
      10. 10.9 Component-based model for <em xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops">Escherichia coli</em> cells cells
      11. 10.10 Experimental sub-terahertz spectroscopy of biological molecules and species
      12. 10.11 Conclusions and future trends
      13. 10.12 Acknowledgments
      14. 10.13 References
    3. 11. Raman spectroscopy for biological identification
      1. Abstract:
      2. 11.1 Introduction
      3. 11.2 Experimental methods used to capture intensive variability
      4. 11.3 Multivariate spectral analysis methods
      5. 11.4 Species-level biological identification results
      6. 11.5 Conclusions
      7. 11.6 Acknowledgments
      8. 11.7 References
    4. 12. Lidar (Light Detection And Ranging) for biodetection
      1. Abstract:
      2. 12.1 Introduction
      3. 12.2 The value of early warning
      4. 12.3 The essentials of Bio-Lidar
      5. 12.4 How Bio-Lidar is used
      6. 12.5 Bio-Lidar value-added
      7. 12.6 Areas for improvement
      8. 12.7 The value of integration
      9. 12.8 Conclusions and future trends
      10. 12.9 References
  10. Part IV: Sample preparation and mass spectrometry-based biological analysis
    1. 13. Electrophoretic approaches to sample collection and preparation for nucleic acids analysis
      1. Abstract:
      2. 13.1 Introduction
      3. 13.2 Separation parameters for nucleic acids for use in sample preparation
      4. 13.3 Electrophoresis using uniform electric fields for sample preparation and analysis
      5. 13.4 Electrophoresis using non-uniform electric field gradients for sample preparation and analysis
      6. 13.5 Comparison of electrophoretic techniques for sample preparation and contaminant rejection
      7. 13.6 Future trends
      8. 13.7 Sources of further information and advice
      9. 13.8 Acknowledgments
      10. 13.9 References
    2. 14. Mass spectrometry-based proteomics techniques for biological identification
      1. Abstract:
      2. 14.1 Introduction
      3. 14.2 Bacterial proteome handling, processing and separation methods
      4. 14.3 Sample ionization and introduction for mass spectrometry (MS) analysis
      5. 14.4 Mass spectral proteomic methods
      6. 14.5 Computational and bioinformatics approaches for data mining and discrimination of microbes
      7. 14.6 Peptide mass fingerprinting (PMF) and matrix-assisted laser desorption/ionization-tandem mass spectrometry (MALDI-MS/MS) of peptides
      8. 14.7 Analysis of MALDI-MS spectra
      9. 14.8 Analyses of double-blind bacterial mixtures
      10. 14.9 Conclusions
      11. 14.10 References
  11. Index