Download the Algal Biofuels Roadmap draft document - Sandia

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Although sequencing of large numbers of candidate biofuels algal species is possible,
excess data will result in incomplete interpretation and inefficient progress. It is
recommended that a master plan for genome analysis of species be developed, with an
initial focus on a small number of currently studied species. With these baseline data in
place, the effort can branch out with a survey of major algal classes, and then species
with specific desirable characteristics within the classes (the latter two can overlap). The
information gained with each strain will provide the framework needed to facilitate the
analysis of all subsequent strains.
Establishment of an Integrated Systems Biology and Bioinformatics Framework to
Develop a Fundamental Understanding of Carbon Partitioning in Algae
Identification of important traits: Funnel-through systems analysis
Based on the criteria described above for strain selection, species will be analyzed using
high throughput analysis approaches to determine the underlying cellular processes and
regulation involved in producing the attributes of the strain. High throughput approaches
enable in depth analyses to be performed in a whole cell context. Due to experimental
variability, the highest potential can be realized by performing the various analyses on
extracts from the same culture, and involving researchers from different laboratories in
the process. To ensure the highest reproducibility in comparison between species, a
standardized set of analysis approaches should be decided upon and implemented.
Transcriptomics
New, high-throughput sequencing technologies enable comprehensive coverage of
transcripts, and quantification of their relative abundances. Most transcriptomic
approaches evaluate mRNA levels, however small RNAs play major regulatory roles in
eukaryotes (Bartel 2004; Cerutti and Casas-Mollano 2005), and have been identified in
microalgae (Zhao, Li et al., 2007) and should be considered in investigations of gene
expression regulation, especially with regard to translational regulation.
Proteomics
The cellular complement of protein reflects its metabolic potential. Mass-spectrometrybased
proteomic analysis enables robust evaluation of soluble and membrane-associated
proteins, and not only enables protein identification, but quantification and determination
of whether post-translational modifications are present (Domon and Aebersold 2006;
Tanner, Shen et al., 2007; Castellana, Payne et al., 2008). After annotation, protein
databases on algal biofuel species should be established.
Metabolomics
The metabolome is the collection of small molecular weight compounds in a cell that are
involved in growth, maintenance, and function. Because the chemical nature of
metabolites varies more than for mRNA and proteins, different metabolomic analysis
tools, including LC/MS, GC/MS, and NMR (Dunn, Bailey et al., 2005), have to be
applied. There is a distinction between metabolomics, which involves identification and
analysis of metabolites, and metabonomics which is the quantitative measurement of the
dynamic multiparametric metabolic response of living systems to pathophysiological
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