This Volume presents a comprehensive series of generic protocols for the
genetic and genomic analysis of prokaryotic isolates. Genetic methods
for functional analyses employ the latest cloning vectors, gene fusion
methods and transposon mutagenesis systems, as well as systems for
introducing protease-cleavage sequences into permissive sites in
proteins under investigation. Genomic methods described include
protocols for transcriptomics, shotgun proteomics, interactomics,
metabolic profiling, and lipidomics. Bioinformatic tools for genome
annotation, transcriptome display and the integration of transcriptomic
data into genome-scale metabolic reconstructions are described.
Protocols for 13C-based metabolic flux determinations and
analysis of the hierarchical and metabolic regulation of fluxes through
pathways are included. The Volume thus enables investigators to
functionally analyse an isolate over the entire cellular range spanning
the gene, the genome, the transcript repertoire, the proteome, the
interactome, the metabolic network with its nodes and their regulatory
hierarchies, and the metabolic fluxes and their physiological controls.
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.
