Annual Meeting – Session Descriptions

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Enzymes for Hydrolysis of Lignocellulosics

Convener: Debbie Yaver, Regine Behr (Novozymes)
To enable second generation ethanol and chemical production from lignocellulosic biomass cost effective biocatalysts for hydrolysis are essential. This session will focus on recent discoveries in both enzymes and microorganisms for biomass hydrolysis including synergy between commercial cellulases and cellulosomes, bacteria that can metabolize lignin and enzymes that can degrade native lignin molecules. New insights into mechanisms and structures of cellulases will also be discussed.
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Microbial consortia / Population synergies

Convener: Cynthia Collins (Rensselaer Polytechnic Institute, Chemical and Biological Engineering)
The potential of microbial consortia for use in biotechnology, bioprocessing and other applications has reemerged as an active area of research. Like their natural counterparts, engineered microbial consortia can perform complex functions by distributing tasks. Combinations of microbes have also been observed to exhibit increased production rates and metabolic efficiency compared to monoculture systems. Challenges in this nascent field include our ability to reliably control community composition and function. This session will highlight both novel approaches for coordinating microbial community behavior and application that use microbial communities. Topics of interest include, experimental and computational tools for screening and predicting community behavior, cell-cell communication and synthetic biology approaches for understanding or controlling ecosystem behavior, and metabolic engineering at the community level.
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Miniature bioreactors in strain development

Conveners: Goutham Vemuri (BioAmber), Katy Kao (Texas A&M)
Rational design of proteins or metabolic network itself has not matured to enable targeted engineering of biological systems. Therefore, there is a substantial amount of dependent on mutagenesis to create diversity. With the advancement of high throughput and miniature bioreactors, there is a ripe opportunity to develop excellent screens and also test a broad variety of conditions. This session will focus on the role of miniature bioreactors in screening and strain development process. In addition, the application of small-scale bioreactors for use in evolutionary engineering will also be discussed. The engineering aspects of the miniature bioreactors, fabrication and validation are also within the scope of this session.
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Genomic stability in fermentation processes

Conveners: Chandresh Thakker (Rice Univ.), Clementina Dellomonaco (DuPont)
Maintaining genome stability is crucial for the success of industrial fermentation processes. This session will focus on the impact of fermentation modes and environmental conditions, metabolites, and stress on host and plasmid stability. Additionally, it will provide insights into new approaches and methodology for developing genetically robust strains to improve fermentation performance.
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Beer and Wine Fermentation

Conveners: Noel Fong (Nucelis), Torben Bruck (Pfenex)
Beer and winemaking are the oldest fermentations known. In this session, we will provide updates on strain characterization and modification, chemistry during the fermentation, substrate effects on flavor, and predictors of quality.
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Biopharmaceutical Production

Conveners: Thomas Kelleher (Amgen), Tiffany Rau (Eli Lilly)
Changes in Regulatory Expectations, Production Systems, Safety Standards and Cost Structures are driving a much deeper understanding of Biopharmaceutical Manufacturing. Commercial production opportunities and issues, which directly impact product quality, have emerged from these drivers. The exploration of quality is enabled by a revolution in communication, analytical science, and process monitoring. Our ability to discern and control more parameters is having wide-ranging impact as commercial biopharmaceutical manufacturing moves into a Global future.
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Production of Biochemicals

Conveners: Daniel Solaiman (USDA/ARS) and Robert Fireovid (USDA/ARS)
Fermentative production of biochemicals in a biorefinery setting will be emphasized in this session. Biorefinery takes its root from the well-developed petroleum-refinery process in which every output-stream is efficiently utilized either “as-is” (fuels) or as feedstocks for petrochemicals (detergents, plastics, etc.). Thus, in a broad sense, a biorefinery feeds on renewable plant- or animal-based biofeedstocks to produce multiple biobased products (which could include fuels) for industrial application. Within this context, presentations in this session will showcase various fermentation processes that can be or have potential to be incorporated into a biorefinery, so as to maximize the utilization of incoming biofeedstock materials for the production of value-added biobased products.
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Integrated Approaches for Sustainable and Cost-Efficient Biofuels Production

Convener: Andreas Schirmer (LS9)
The major driver for future success of biofuels is the development of cost-efficient and scalable processes based on sustainable feedstocks. Rising feedstock costs, moderate crude oil prices and other macroeconomic factors have made this endeavor a formidable challenge. Overcoming the obstacles for sustainable and cost-efficient biofuels production will require interdisciplinary and integrated approaches. This session focuses on contributions that aim at combining state-of-the art Metabolic Engineering with exploiting low-cost feedstocks and/or leveraging innovative production technologies towards biofuels.
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Metabolic Engineering and Synthetic Biology Approaches for Advanced Biofuels Synthesis

Convener: Cong T. Trinh (Univ. of Tennessee)
Recent research has focused on engineering microbial biocatalysts to synthesize “drop-in” advanced biofuels. The challenges are that these biocatalysts have low yields, titers, and productivities and are engineered under conditions that are not practical for industrial scale-up processes (e.g., simple sugars, complex medium, aerobic condition, free of inhibitors). This section will focus on contributions that present the state-of-the-art metabolic engineering and synthetic biology approaches to address these challenges.
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Metabolic Engineering for Basic and Intermediate Chemicals Production

Convener: Steve van Dien (Genomatica)
Industrial chemicals are the building blocks for a multitude of polymers that make up many of the products we use in our daily life, and are currently produced almost exclusively from petrochemical feedstocks. The use of microorganisms to convert biobased feedstocks to these same products is emerging as a transformational technology for sustainable chemical production. Rapid advances in metabolic engineering, systems biology, and synthetic biology have contributed to recent success in this field. This session will cover development of microorganisms and fermentation processes for the production of commodity chemicals from sugars or other biobased feedstocks, and the approaches used to develop them. Various stages of the research workflow will be covered, from proof-of-concept research to commercial success stories.
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Metabolic Engineering for the Production of Fine Chemicals and Pharmaceutical Precursors

Convener: David Nielsen (Arizona State University)
Fine chemicals and pharmaceutical precursors are used as building blocks to produce many important specialty products and drugs. Today, however, these products are produced almost exclusively from petrochemical feedstocks according to chemocatalytic production routes. Alternatively, microorganisms can be engineered and used as biocatalysts to convert biobased feedstocks to the same fine chemicals and pharmaceutical precursors. As the use of biocatalysts can reduce energy and solvent consumption while also offering higher chemo-, regio-, and stereo-specificity, this approach is emerging as a transformational and sustainable technology. Rapid advances in metabolic engineering, systems biology, and synthetic biology have contributed to recent success in this field. This session will cover development of microorganisms and fermentation processes for the production of fine chemicals and pharmaceutical precursors from sugars or other biobased feedstocks, and the approaches used to develop them. Various stages of the research workflow will be covered, from proof-of-concept research to commercial success stories.
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New Developments in Natural Product Biosynthesis

Convener: Brian Bachmann (Vanderbilt)
A renaissance is underway in the field of natural product biosynthesis. The combination of the sudden availability of staggering amounts of secondary metabolic genomic sequence data, breakthroughs in structural biology of long intractable biosynthetic systems, advances in analytical methodologies, and an explosion of powerful methods in synthetic biology have converged to underline the centrality of natural product biosynthetic studies in such chemical biological research. Remarkably, these breakthroughs are completely synergistic and it is becoming commonplace for research programs to integrate biosynthetic studies with synthetic biology, natural product discovery (new and unnatural), evolutionary biology, ecological chemistry and structural biology. This session exemplifies interdisciplinary research programs representative of this renaissance period in secondary metabolite research.
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New Methodologies for Natural Products Chemistry

Conveners: Paul Jensen (Scripps Institute of Oceanography), Eric Schmidt (Univ. Utah)
The National Institutes of Health have long supported the field of natural products research. This has proven particularly important in an era where large pharma has moved away from natural products as a drug discovery platform. This session derives its name from an ongoing NIH-supported program designed to “reinvigorate the investigation of nature as a prolific source of small-molecules” and to “stimulate the development of a new generation of methods for natural products chemistry”. This session will feature new approaches to natural products research, ranging from genomics to mass spectroscopy, that are being explored as part of this NIH funded program.
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Cyanobacterial Natural Products and Metabolic Engineering

Convener: William Gerwick (Scripps Institute of Ocenaography)
Marine cyanobacteria have been revealed to be extraordinarily rich sources of novel organic molecules with utility to both drug discovery and biofuel applications. In the drug discovery area, the metabolites of these organisms have an amazing diversity of molecular architectures that are largely created from the modular Polyketide Synthase (PKS) and Non-Ribosomal Peptide Synthetase (NRPS) biosynthetic pathways. As a result, these metabolites possess novel pharmacological properties with potential biomedical utility to many human diseases, including cancer, inflammation and infectious diseases. Moreover, as modular pathways, they are amenable to genetic manipulation and pathway engineering. On the biofuels focus, cyanobacteria have been revealed to produce a wide range of hydrocarbon oils with drop-in-ready fuel characteristics. At least two distinct biosynthetic pathways are utilized by cyanobacteria to make these distinctive molecular species, and these also are amenable to manipulation through genetic engineering. Hence, this session will explore through six exceptional presentations the chemistry, biosynthesis and metabolic engineering of marine cyanobacterial metabolites with applications in medicine and next-generation biofuels.
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The Future of Natural Products in Drug Discovery: Roundtable

Convener: William Fenical (Scripps/UCSD)
This session will focus on the changing dynamics of microbial drug discovery in the “Omics Era.” This session will be composed of four 30 minute presentations from experts in the field of microbial drug discovery. Topics will encompass innovations in the cultivation of “uncultured” strains, the increasing role of genomic mining and using genomic probes in the discovery of novel bioactives, and innovative ways in which natural products can be translated into drugs. The presentations will be followed by a Round Table discussion with audience participation to amplify and probe aspects of these topics.
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Synthetic Biology II: Applications

Convener: Kirsten Benjamin (Amyris)
This session will highlight diverse recent applications of synthetic biology for industrial and biomedical solutions. Industrial applications include novel microbial production of chemicals and materials. Biomedical applications include drug production and delivery, environmental sensors, biofilm modulation, and more.
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63 SIMB Annual Meeting Conference Location: San Diego, CA Conference Dates: August 11 - 15, 2013 Show Dates: August 11 - 14, 2013
Thanks to our 2013 Sponsors!