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Title: Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains

Abstract

The overall objective of this project was to use a systems biology approach to evaluate the potentials of a number of cyanobacterial strains for photobiological production of advanced biofuels and/or their chemical precursors. Cyanobacteria are oxygen evolving photosynthetic prokaryotes. Among them, certain unicellular species such as Cyanothece can also fix N 2, a process that is exquisitely sensitive to oxygen. To accommodate such incompatible processes in a single cell, Cyanothece produces oxygen during the day, and creates an O 2-limited intracellular environment during the night to perform O 2-sensitive processes such as N 2-fixation. Thus, Cyanothece cells are natural bioreactors for the storage of captured solar energy with subsequent utilization at a different time during a diurnal cycle. Our studies include the identification of a novel, fast-growing, mixotrophic, transformable cyanobacterium. This strain has been sequenced and will be made available to the community. In addition, we have developed genome-scale models for a family of cyanobacteria to assess their metabolic repertoire. Furthermore, we developed a method for rapid construction of metabolic models using multiple annotation sources and a metabolic model of a related organism. This method will allow rapid annotation and screening of potential phenotypes based on the newly available genomemore » sequences of many organisms.« less

Authors:
 [1]
  1. Washington Univ., St. Louis, MO (United States)
Publication Date:
Research Org.:
Washington Univ., St. Louis, MO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1314041
Report Number(s):
DOE-WUSTL-0006870
DOE Contract Number:
SC0006870
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
10 SYNTHETIC FUELS

Citation Formats

Pakrasi, Himadri. Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains. United States: N. p., 2016. Web. doi:10.2172/1314041.
Pakrasi, Himadri. Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains. United States. doi:10.2172/1314041.
Pakrasi, Himadri. 2016. "Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains". United States. doi:10.2172/1314041. https://www.osti.gov/servlets/purl/1314041.
@article{osti_1314041,
title = {Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains},
author = {Pakrasi, Himadri},
abstractNote = {The overall objective of this project was to use a systems biology approach to evaluate the potentials of a number of cyanobacterial strains for photobiological production of advanced biofuels and/or their chemical precursors. Cyanobacteria are oxygen evolving photosynthetic prokaryotes. Among them, certain unicellular species such as Cyanothece can also fix N2, a process that is exquisitely sensitive to oxygen. To accommodate such incompatible processes in a single cell, Cyanothece produces oxygen during the day, and creates an O2-limited intracellular environment during the night to perform O2-sensitive processes such as N2-fixation. Thus, Cyanothece cells are natural bioreactors for the storage of captured solar energy with subsequent utilization at a different time during a diurnal cycle. Our studies include the identification of a novel, fast-growing, mixotrophic, transformable cyanobacterium. This strain has been sequenced and will be made available to the community. In addition, we have developed genome-scale models for a family of cyanobacteria to assess their metabolic repertoire. Furthermore, we developed a method for rapid construction of metabolic models using multiple annotation sources and a metabolic model of a related organism. This method will allow rapid annotation and screening of potential phenotypes based on the newly available genome sequences of many organisms.},
doi = {10.2172/1314041},
journal = {},
number = ,
volume = ,
place = {United States},
year = 2016,
month = 9
}

Technical Report:

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  • Cyanobacteria have been shown to be capable of producing a variety of advanced biofuels; however, product yields remain well below those necessary for large scale production. New genetic tools and high throughput metabolic engineering techniques are needed to optimize cyanobacterial metabolisms for enhanced biofuel production. Towards this goal, this project advances the development of a multiple promoter replacement technique for systems-level optimization of gene expression in a model cyanobacterial host: Synechococcus sp. PCC 7002. To realize this multiple-target approach, key capabilities were developed, including a high throughput detection method for advanced biofuels, enhanced transformation efficiency, and genetic tools for Synechococcusmore » sp. PCC 7002. Moreover, several additional obstacles were identified for realization of this multiple promoter replacement technique. The techniques and tools developed in this project will help to enable future efforts in the advancement of cyanobacterial biofuels.« less
  • One of the great challenges facing current and future generations is how to meet growing energy demands in an environmentally sustainable manner. Renewable energy sources, including wind, geothermal, solar, hydroelectric, and biofuel energy systems, are rapidly being developed as sustainable alternatives to fossil fuels. Biofuels are particularly attractive to the U.S., given its vast agricultural resources. The first generation of biofuel systems was based on fermentation of sugars to produce ethanol, typically from food crops. Subsequent generations of biofuel systems, including those included in the CABS project, will build upon the experiences learned from those early research results and willmore » have improved production efficiencies, reduced environmental impacts and decreased reliance on food crops. Thermodynamic models predict that the next generations of biofuel systems will yield three- to five-fold more recoverable energy products. To address the technological challenges necessary to develop enhanced biofuel systems, greater understanding of the non-equilibrium processes involved in solar energy conversion and the channeling of reduced carbon into biofuel products must be developed. The objective of the proposed Center for Advanced Biofuel Systems (CABS) was to increase the thermodynamic and kinetic efficiency of select plant- and algal-based fuel production systems using rational metabolic engineering approaches grounded in modern systems biology. The overall strategy was to increase the efficiency of solar energy conversion into oils and other specialty biofuel components by channeling metabolic flux toward products using advanced catalysts and sensible design:1) employing novel protein catalysts that increase the thermodynamic and kinetic efficiencies of photosynthesis and oil biosynthesis; 2) engineering metabolic networks to enhance acetyl-CoA production and its channeling towards lipid synthesis; and 3) engineering new metabolic networks for the production of hydrocarbons required to meet commercial fuel standards.« less
  • Advanced Public Transit Systems (APTS) are advanced navigation and communication technologies that are used in all aspects of public transportation. These include the application of advanced electronic technologies to the deployment and operation of high occupancy, shared-ride vehicles, conventional buses, rail vehicles, and the entire range of para-transit vehicles. Three basic APTS subsystems are available for deployment in support of transit travelers and operations. These include Smart Traveler technology, Smart Vehicle technology, and Smart Intermodal Systems. This report provides documentation of APTS technologies and reviews the approaches used in evaluation. The Intelligent Vehicle Highway Systems (IVHS) Intelligent Transportation Systems (ITS)more » literature concerning evaluation of operational tests, shows that evaluation plans generally consist of two components: measures of effectiveness (MOEs) and an evaluation methodology. Various lessons have been learned from this research effort. These lessons highlight the need for modifications in the approaches that are represented in this research. Modifications that will improve the accuracy, reliability, and usefulness of these approaches are encouraged. Perhaps the most significant lesson learned from this research effort is the need for further development in the area of subjective evaluation or Cost-Benefit Analysis (CBA).« less
  • Increased utility reliance on demand-side management (DSM) has created a need to understand and evaluate actual DSM program performance. This report explores statistical techniques used to quantitatively synthesize, accumulate, and compare research findings. In addition, the report provides a database of Wisconsin DSM program evaluations and marketing studies. The project team reviewed approximately 100 evaluation studies, including both process and impact evaluations of DSM programs in Wisconsin. Using PARADOX database software, with annotations appended to database elements, they classified reports into 10 evaluation-type categories. These included program and evaluation descriptions, methods and data employed, and results and recommendations. The teammore » also assessed the applicability of statistical techniques, specifically meta-analytic methods for pooling and leveraging results of DSM evaluations. Recorded database information includes a report abstract; basic program information; study design and method; sample and data collection; and a list of the issues addressed and report findings, with the location of findings by report page number. Analysis of statistical methods produced several promising approaches for combining and leveraging information across studies. The methods, generally termed meta-analytic methods, have the potential to address a number of important DSM research questions. The report includes an example application of these methods. Volume 1 presents the database design, summaries of reports reviewed for database inclusion, and discussion of the statistical techniques analyzed along with their applications to DSM. Volume 2 offers more-detailed summaries of the reports reviewed. Volume 3 provides a printout of the final database, as constructed.« less
  • An important issue facing professionals in the field of Demand-Side Management involves the accumulation and retention of information over time and across multiple studies. Too often, information on evaluation findings and lessons regarding what has worked or not worked in program implementation are difficult to uncover in the literature in the field. Certain protocols for DSM program evaluation require the researcher to assume that essentially nothing is known about the program and work de novo from collected data to assess program implementation and program impacts. While this may be an appropriate paradigm for some evaluations, the accumulation of knowledge onmore » DSM from the many studies being conducted may be able to play an important role in the evaluation of current programs, the modification of existing programs and the design of new programs. This project approaches this issue from two perspectives: First, to develop a data base consolidating the results of roughly 100 DSM evaluations conducted on programs implemented in Wisconsin. As part of the data base effort, information on the evaluations was collected about program type and target market. Second, to examine available methods for synthesizing, accumulating and comparing information for DSM program evaluation literature that encompasses multiple evaluations of program types targeted at specific program sectors. Information on DSM evaluation and reports were recorded in a Paradox data base, with a KMemo attachment. The recorded information included a report abstract, basic program information, study design and method, sample and data collection methods, and a listing of issues addressed and report findings, including the location of those findings by report page number. The data base is easily accessible and the detailed annotation of issues and findings should prove valuable to DSM researchers.« less