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Hydrocarbon and Lipid Microbiology Protocols

Statistics, Data Analysis, Bioinformatics and Modelling

  • Book
  • © 2016

Overview

Editors:
  1. Terry J. McGenity

    1. Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, United Kingdom

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  2. Kenneth N. Timmis

    1. Braunschweig, Germany

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    You can also search for this editor in PubMed   Google Scholar

  3. Balbina Nogales Fernández

    1. University of the Balearic Islands , Palma de Mallorca, Spain

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    You can also search for this editor in PubMed   Google Scholar

  • Offers readily reproducible, step-by-step laboratory methods
  • Provides helpful tips and tricks to complement the protocols
  • Includes troubleshooting advice
  • Features practical laboratory guidelines to promote successful results

Part of the book series: Springer Protocols Handbooks (SPH)

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Table of contents (11 protocols)

  1. Front Matter

    Pages i-xii
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  2. Introduction to Computer-Assisted Analysis in Hydrocarbon and Lipid Microbiology

    • Wilfred F. M. Röling
    Pages 1-6

  3. A Brief Review on the Ecological Network Analysis with Applications in the Emerging Medical Ecology

    • Zhanshan (Sam) Ma, Chengchen Zhang, Qingpeng Zhang, Jie Li, Lianwei Li, Linyi Qi et al.
    Pages 7-39

  4. Statistical Tools for Data Analysis

    • Sean M. Gibbons
    Pages 41-57

  5. Statistical Tools for Study Design: Replication

    • Peter E. Larsen
    Pages 59-68

  6. MG-RAST, a Metagenomics Service for the Analysis of Microbial Community Structure and Function

    • Elizabeth M. Glass, Folker Meyer
    Pages 69-87

  7. Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments

    • Luke K. Ursell, Adam Robbins-Pianka, Nicole Scott, Antonio Gonzalez, Dan Knights, Jai Ram Rideout et al.
    Pages 89-113

  8. Biodegradation Prediction Tools

    • Florencio Pazos, Víctor de Lorenzo
    Pages 115-124

  9. Predicting Protein Interactions

    • Florencio Pazos, David de Juan
    Pages 125-134

  10. Syntax and Semantics of Coding in Python

    • Jeremy Meulemans, Tonya Ward, Dan Knights
    Pages 135-154

  11. Protocols for Calculating Reaction Kinetics and Thermodynamics

    • Jan Dolfing
    Pages 155-163

  12. Modelling the Environmental Fate of Petroleum Hydrocarbons During Bioremediation

    • Guozhong Wu, Frédéric Coulon
    Pages 165-180
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Keywords

About this book

This Volume covers protocols for in-silico approaches to hydrocarbon microbiology, including the selection and use of appropriate statistical tools for experimental design replication, data analysis, and computer-assisted approaches to data storage, management and utilisation. The application of algorithms to analyse the composition and function of microbial communities is presented, as are prediction tools for biodegradation and protein interactions. The basics of a major open-source programming language, Python, are explained. Protocols for calculating reaction kinetics and thermodynamics are presented, and modelling the environmental fate of hydrocarbons during bioremediation is explained. With the exception of molecular biology studies of molecular interactions, the use of statistics is absolutely essential for both experimental design and data analysis in microbiological research, and indeed in the biomedical sciences in general. Moreover, studies of highly varying systems call for the modelling and/or application of theoretical frameworks. Thus, while two protocols in this Volume are specific to hydrocarbon microbiology, the others are generic, and as such will be of use to researchers investigating a broad range of topics in microbiology and the biomedical sciences in general.

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 rangeof 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.




Editors and Affiliations

  • Dept. Biological Sciences, University of Essex Dept. Biological Sciences, Colchester, United Kingdom

    Terry J. McGenity

  • Braunschweig, Germany

    Kenneth N. Timmis

  • University of the Balearic Islands , Palma de Mallorca, Spain

    Balbina Nogales Fernández

Bibliographic Information

  • Book Title: Hydrocarbon and Lipid Microbiology Protocols

  • Book Subtitle: Statistics, Data Analysis, Bioinformatics and Modelling

  • Editors: Terry J. McGenity, Kenneth N. Timmis, Balbina Nogales Fernández

  • Series Title: Springer Protocols Handbooks

  • DOI: https://doi.org/10.1007/978-3-662-49310-6

  • Publisher: Springer Berlin, Heidelberg

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer-Verlag Berlin Heidelberg 2016

  • Hardcover ISBN: 978-3-662-49309-0Published: 19 August 2016

  • Softcover ISBN: 978-3-662-57000-5Published: 15 June 2018

  • eBook ISBN: 978-3-662-49310-6Published: 09 August 2016

  • Series ISSN: 1949-2448

  • Series E-ISSN: 1949-2456

  • Edition Number: 1

  • Number of Pages: XII, 180

  • Topics: Microbiology, Biochemical Engineering

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