© 2016

Hydrocarbon and Lipid Microbiology Protocols

Synthetic and Systems Biology - Tools

  • Terry J. McGenity
  • Kenneth N. Timmis
  • Balbina Nogales


  • Offers readily-reproducible step-by-step laboratory methods

  • Provides helpful tips and tricks supporting the protocols

  • Includes troubleshooting advice

  • Contains practical laboratory guidance to promote successful results


Part of the Springer Protocols Handbooks book series (SPH)

Table of contents

  1. Front Matter
    Pages i-x
  2. Christopher D. Hirst, Catherine Ainsworth, Geoff Baldwin, Richard I. Kitney, Paul S. Freemont
    Pages 9-26
  3. Ana Mafalda Cavaleiro, Morten T. Nielsen, Se Hyeuk Kim, Susanna Seppälä, Morten H. H. Nørholm
    Pages 27-37
  4. Klaus Hornischer, Susanne Häussler
    Pages 83-96
  5. Marina G. Kalyuzhnaya, Song Yang, David A. C. Beck, Ludmila Chistoserdova
    Pages 97-118
  6. M. A. Valderrama-Gomez, S. G. Wagner, A. Kremling
    Pages 153-184

About this book


This Volume presents generic protocols for wet experimental and computer-based systems and synthetic biology approaches relevant to the field of hydrocarbon and lipid microbiology. It complements a second Volume that describes protocols for systems and synthetic biology applications. The wet experimental tools presented in this Volume include protocols for the standardisation of transcriptional measurements, application of uracil excision-based DNA editing for, inter alia, multi-gene assembly, the use of fluxomics to optimise “reducing power availability”, and the incorporation of non-canonical amino acids into proteins for optimisation of activities. Phenome-ing microbes, using a combination of RNA-seq and bioinformatic algorithms, is presented, as is an illustration, using methylotrophs as an example, of how the different key omics approaches constitute a pipeline for functional analysis, acquisition of a systems overview, and metabolic optimisation. Complementary computational tools that are presented include protocols for probing the genome architecture of regulatory networks, genome-scale metabolic reconstruction, and bioinformatic approaches to guide metabolic engineering. The Volume also includes an overview of how synthetic biology approaches can be used to improve biocontainment.
Hydrocarbon and Lipid Microbiology Protocols
There are tens of thousands of structurally different hydrocarbons, hydrocarbon derivatives and lipids, and a wide array of these molecules are required for cells to function. The global hydrocarbon cycle, which is largely driven by microorganisms, has a major impact on our environment and climate. Microbes are responsible for cleaning up the environmental pollution caused by the exploitation of hydrocarbon reservoirs and will also be pivotal in reducing our reliance on fossil fuels by providing biofuels, plastics and industrial chemicals. Gaining an understanding of the relevant functions of the wide range of microbes that produce, consume and modify hydrocarbons and related compounds will be key to responding to these challenges. This comprehensive collection of current and emerging protocols will facilitate acquisition of this understanding and exploitation of useful activities of such microbes.


Environmental transcription factors Expression systems Fluxomics and metabolics Higher-structure genomic organisation Tools for methylotrophs

Editors and affiliations

  • Terry J. McGenity
    • 1
  • Kenneth N. Timmis
    • 2
  • Balbina Nogales
    • 3
  1. 1.University of Essex Dept. Biological SciencesColchesterUnited Kingdom
  2. 2.Institute of MicrobiologyTechnical University BraunschweigBraunschweigGermany
  3. 3.Department of BiologyUniversity of the Balearic Islands and Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC)Palma de MallorcaSpain

Bibliographic information

  • Book Title Hydrocarbon and Lipid Microbiology Protocols
  • Book Subtitle Synthetic and Systems Biology - Tools
  • Editors Terry J. McGenity
    Kenneth N. Timmis
    Balbina Nogales
  • Series Title Springer Protocols Handbooks
  • Series Abbreviated Title Springer Protocols Handbooks
  • DOI
  • Copyright Information Springer-Verlag Berlin Heidelberg 2016
  • Publisher Name Springer, Berlin, Heidelberg
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-3-662-50430-7
  • Softcover ISBN 978-3-662-57058-6
  • eBook ISBN 978-3-662-50432-1
  • Series ISSN 1949-2448
  • Series E-ISSN 1949-2456
  • Edition Number 1
  • Number of Pages X, 199
  • Number of Illustrations 0 b/w illustrations, 0 illustrations in colour
  • Topics Microbiology
    Biochemical Engineering
  • Buy this book on publisher's site
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