California Initiative for Large Molecule Sustainable Fuels (CILMSF)

In 2011, The California Energy Commission awarded the then San Diego Center for Algae Biotechnology a three-year, two million dollar grant to support innovative collaborative projects that advance sustainable biofuels production. These projects are intended to maintain California as a leader in developing sustainable biofuels, from both algae and other promising alternative sources.

Download the CILMSF Final Report.

Technical Advisory Committee (TAC)

The Technical Advisory Committee (TAC) for the CILMSF was created to provide strategic guidance to the CILMSF through meetings, calls and participation in the CILMSF Roadmap meeting. The guidance included scope of research, research methodologies, timing, and coordination with other research. The TAC was composed of researchers, academic experts, algae biotechnology industry representatives, biofuels industry representatives, and policy experts.

TAC Membership

  • Jeffrey Jacobs (VP, Biofuels & Business Chevron Technology Ventures)
  • Todd Peterson (VP R&D Genomics NAP, Life Technologies)
  • Alex Aravanis (Chief Technology Officer, Sapphire Energy)
  • Eric Mathur (VP & Chief Technologist, SG Biofuels)
  • Anastasios Melis (Professor of Plant and Microbial Biology, University of California, Berkeley)
  • Anthony Eggert (Executive Director, Policy Institute for Energy, Environment and the Economy University of California, Davis)
  • Joseph Norbeck (Director, Environmental Research Institute, University of California, Riverside)
  • James Liao (Professor of Chemistry and Biomolecular Engineering, University of California, Los Angeles)

Biofuel Life Cycle Analysis

The CILMSF is tasked with developing robust life cycle analyses (LCA) for large molecule biofuel production.

LCAs provide an objective assessment of the environmental aspects and potential impacts associated with production of sustainable alternative large molecule fuels. For each biofuel production process, the associated inputs and releases are factored into an evaluation of potential impacts. Such impacts include demands on natural resources, environmental impacts, and increased or decreased burdens upon other industries. The results of the LCAs are the basis for informed decision-making and promote greater public understanding about biofuel production. The analyses also help to identify aspects of the processes and externalities that may need improvement or reconsideration.


Part of the Initiative is to develop a long-term strategy for the identification and development of new research areas and technologies that may be useful for the sustainable production of LMSFs. The roadmap, held at UC San Diego in October 2012, was developed with community input from biofuels researchers and other stakeholders in the public and private sectors. The presentations and meetings have encouraged ongoing communication to address issues such as the allocation of research resources and the identification and incorporation of new technologies (from, for example, agriculture science, aquaculture engineering, and fuel processing) into research projects. Here are the links for the CILMSF Roadmap Meeting and the Executive Summary.

High Throughput (HT) Processes

The incorporation of HT processes for biomolecule manipulation and analysis has enabled enormous advances in the biomedical sector over the last ten years, but similar processes have yet to be developed for biofuels organisms. The goal is to develop HT processes (high-volume capacity) for rapid selection and evaluation of biofuel organisms.

This includes designing and creating HT analytical techniques to identify potential biofuel production strains, identifying and classifying potential biofuel organism species for their commercial potential, and creating a curated collection of these strains.


  1. Elizabeth A. Specht and Stephen P. Mayfield. Synthetic Oligonucleotide Libraries Reveal Novel Regulatory Elements in Chlamydomonas Chloroplast mRNAs. ACS Synthetic Biology.

  2. Specht EA,Nour-Eldin HH, Hoang KTD, and Mayfield, SP. (2014) An improved ARS2-derived nuclear reporter enhances the efficiency and ease of genetic engineering in Chlamydomonas. Biotechnology Journal.

Genetic Toolbox

In order to facilitate the adoption of new biofuel technology by other academic and industrial laboratories, a suite of genetic and molecular tools for non-food biomass organisms for biofuel applications is being developed and made broadly available to others.

This toolbox includes new methods to control gene expression and cell viability, methods for genetic transformation of previously non-transformed species, additional selectable markers and crop protection tools, and combinatorial genetic manipulation for directed evolution in biofuel species.

Algae Expression & Engineering Products By Life Technologies


  1. Beld, J., Sonnenschein, E. C., Vickery, C. R., Noel, J.P., & Burkart, M. D. (2014). The phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life.Natural product reports, 31(1), 61-108.

  2. Ma, A.T., C.M.Schmidt, and J.W Golden. Regulation of gene expression in diverse cyanobacterial species using theophylline-responsive riboswitches.Mbio In prep.

  3. Simkovsky, R. E. Daniels, K. Tang, S. C. Huynh, S. S. Golden, and B. Brahamsha. “Impairment of O-antigen production confers resistance to grazing in a model amoeba–cyanobacterium predator–prey system”. PNAS 2012 109 (41) 16678-16683; published ahead of print September 24, 2012, doi:10.1073/pnas.1214904109.

  4. Simkovsky, R., E. Effner, M.J. Iglesias-Sánchez, K. Tang, J. Kenchel, N. Bearmar, and S.S. Golden. Lipopolysaccharide mutants reveal novel targets for cyanobacterial grazer resistance and tolerance to LPS deletion. In prep.

  5. Taton A., F. Unglaub, N.E. Wright, W.Y. Zeng, B. Brahamsha, B. Palenik, J. Paz-Yepez, T. C. Peterson, F. Haerizadeh, S.S. Golden, and J.W. Golden. Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. NAR. In prep.

Metabolic Engineering

Food crops and livestock have been selectively bred for centuries to obtain the efficient agricultural production species that we use today. A similar process of selection and modification of biofuels organisms is being conducted in order to develop the efficient optimized production species that will be required for economic viability of biofuel production.

To achieve this within a reasonable time frame, new metabolic engineering techniques and strategies are being developed to enable improved accumulation of biofuel molecules in production strains. Genomic (DNA analysis), proteomic (protein analysis), and metabolomic (small molecule analysis) technologies are being used to define target pathways and regulatory systems.


  1. Blatti JL, Beld J, Behnke CA, Mendez M, Mayfield SP, et al. (2012) Manipulating Fatty Acid Biosynthesis in Microalgae for Biofuel through Protein-Protein Interactions. PLoS ONE 7(9): e42949.

  2. Coates RC, Podell S, Korobeynikov A, Lapidus A, Pevzner P, Sherman D, Allen EE, Gerwick L, Gerwick WH (2013) Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways.PLoS One.

  3. Hildebrand, M., RM Abbriano, JEW Polle, JC Traller, EM Trentacoste, SR Smith, AK Davis. “Metabolic and cellular organization in evolutionarily diverse microalgae as related to biofuels production”. Current Opinion in Chemical Biology.

  4. Trentacoste, E. M., Shrestha, R. P., Smith, S. R., Glé, C., Hartmann, A. C., Hildebrand, M. & Gerwick, W. H. (2013). Metabolic engineering of lipidcatabolism increases microalgal lipid accumulation without compromising growth.Proc Natl Acad Sci 110 (49): 19748–197532.

Harvesting and Extraction

Once algae biomass has grown for commercial use, it needs to be harvested and the proteins and lipids need to be taken out. The CILMSF is developing economically viable technologies to collect and purify biofuels from plant and algal biomass. This includes employing genetic engineering to increase oil accumulation and efficient extraction, and creating and evaluating bioreactor and/or aquaculture design to maximize harvesting and extraction.


A large portion of plant and algal biomass is composed of non-fuel molecules, including proteins, carbohydrates, and other water-soluble biomolecules. This non-hydrocarbon biomass may be used for a variety of purposes, including animal feeds and fertilizers, industrial enzymes and a variety of bio-products. Moreover, organisms may be engineered to produce additional value-added co-products within this biomass, including nutritional, therapeutic, or ecologically beneficial biomolecules. The CILMSF is tasked with engineering these value-added products into producer organisms for non-biofuel applications. The potential of these additional products from biomass is a critical factor in making biofuels economically viable.


  1. Barrera, D. J. & Mayfield, S. P. (2013). High Value Recombinant Protein Production in Microalgae. In A. Richmond & Q. Hu (Eds.), Handbook of Microalgal Culture: Applied Phycology and Biotechnology. (2nd Ed., pp.532-544) Wiley.

  2. Gregory, J. A., Topol, A. B., Doerner, D. Z., & Mayfield, S. (2013). Alga-Produced Cholera Toxin-Pfs25 Fusion Proteins as Oral Vaccines. Applied and environmental microbiology,79(13),3917-3925.

  3. Rasala BA, Lee PA, Shen Z, Briggs SP, Mendez M, et al. (2012) Robust Expression and Secretion of Xylanase1 in Chlamydomonas reinhardtii by Fusion to a Selection Gene and Processing with the FMDV 2A Peptide. PLoS ONE 7(8): e43349.

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