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A Web Enabled Database for Rapid Metagenomic Biocatalyst Discovery and Validation

Award Information
Agency: Department of Health and Human Services
Branch: National Institutes of Health
Contract: 2R44GM113357-02
Agency Tracking Number: R44GM113357
Amount: $1,291,276.00
Phase: Phase II
Program: SBIR
Solicitation Topic Code: 300
Solicitation Number: PA14-071
Timeline
Solicitation Year: 2014
Award Year: 2016
Award Start Date (Proposal Award Date): 2016-04-01
Award End Date (Contract End Date): 2018-03-31
Small Business Information
2430 5TH ST., SUITE D, Berkeley, CA, 94710-2451
DUNS: 078535589
HUBZone Owned: N
Woman Owned: Y
Socially and Economically Disadvantaged: Y
Principal Investigator
 JEFFREY KIM
 (510) 450-0761
 customerservice@amyris.com
Business Contact
 JEFFREY KIM
Phone: (917) 660-8166
Email: jeffhkim@gmail.com
Research Institution
N/A
Abstract
DESCRIPTION provided by applicant Radiant Genomics proposes to develop an integrated enzyme discovery service the Enzyme Variant Engine EVE built upon the largest cloned metagenomic sequence collection reported to date The goal is to combine a publicly accessible search engine richly annotated sequence database arrayed sample library and LIMS automation platform to deliver novel enzyme variants to end users for lower cost in less time and from a greater pool of biodiversity than alternative options such as DNA synthesis Importantly this service overcomes a major bottleneck in enzyme discovery that has traditionally focused on easily cultivated organisms which are now known to represent less than of biodiversity Phase I research and development milestones were met or exceeded In particular we successfully demonstrated a high efficiency sequencing workflow that will allow us to sequence and assemble our clone library which is predicted to encode M genes andgt of which are derived from uncultivated and essentially unstudied organisms We next demonstrated a combinatorial barcoding strategy that yields assemblies with an average length of andgt kilobases a dramatic improvement in metagenomic contiguity This feature enables the discovery of clusters of functionally related genes such as those that encode complex natural products and nutrient fixation These services were successfully integrated into an online search engine and e commerce platform available at www eve bio Finally we developed and demonstrated infrastructure for an automated LIMS gene recovery system that can recover thousands of genes of interest from our arrayed library per week The success of Phase I research was complemented by general improvements in sequencing cost efficiency and cloud computing The EVE service has gained commercial traction and we believe further development will benefit basic research while positively impacting a broad range of biomanufacturing processes Based on customer feedback the aims of this proposal are continued sequencing of the library using contiguity preserving strategies scaling of computational infrastructure development of advanced enzyme selectors and third party database integration The overall outcome of this program will be a centralized search engine which allows end users to rapidly select and receive genes identified in bioinformatic analyses These genes will be accessible for lower cost in less time and from a greater pool of genetic diversity than existing services Overall we believe that our platform will improve our understanding of sequence to function relationships and annotation for metagenomic environments helping to bridge the gap between in silico and biochemical characterization from unexplored pools of genetic diversity PUBLIC HEALTH RELEVANCE Bio based manufacturing is poised to become a major economic driver due to advances in genetic and metabolic engineering Most enzymes involved in biomanufacturing however are derived from the less than of total biodiversity that is easily cultivated To address this we aim to make genes encoded in our metagenomic clone library the largest and most diverse reported to date accessible through a public search engine and delivery service providing researchers with access to orders of magnitude more enzyme diversity for lower cost than competing methods

* Information listed above is at the time of submission. *

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