Award Abstract # 1458262
CSBR: Living Stocks - The Escherichia Coli Genetic Stock Center

NSF Org: DBI
Division of Biological Infrastructure
Recipient: YALE UNIV
Initial Amendment Date: April 1, 2015
Latest Amendment Date: July 19, 2017
Award Number: 1458262
Award Instrument: Continuing Grant
Program Manager: Reed Beaman
rsbeaman@nsf.gov
 (703)292-7163
DBI
 Division of Biological Infrastructure
BIO
 Directorate for Biological Sciences
Start Date: September 15, 2015
End Date: August 31, 2018 (Estimated)
Total Intended Award Amount: $498,749.00
Total Awarded Amount to Date: $498,749.00
Funds Obligated to Date: FY 2015 = $93,651.00
FY 2016 = $204,452.00

FY 2017 = $200,646.00
History of Investigator:
  • John Wertz (Principal Investigator)
    john.wertz@yale.edu
Recipient Sponsored Research Office: Yale University
150 MUNSON ST
NEW HAVEN
CT  US  06511-3572
(203)785-4689
Sponsor Congressional District: 03
Primary Place of Performance: Wertz, John C
New Haven
CT  US  06520-8013
Primary Place of Performance
Congressional District:
03
Unique Entity Identifier (UEI): FL6GV84CKN57
Parent UEI: FL6GV84CKN57
NSF Program(s): BIOLOGICAL RESEARCH COLLECTION
Primary Program Source: 01001516DB NSF RESEARCH & RELATED ACTIVIT
01001617DB NSF RESEARCH & RELATED ACTIVIT

01001718DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 1106
Program Element Code(s): 119700
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.074

ABSTRACT

This award supports the E. coli Genetic Stock Center (CGSC) at Yale University. Escherichia coli is an important model organism and is perhaps the best understood cellular organism from a genetics and biochemistry standpoint. This high degree of understanding has made E. coli not just an important subject of research, but also the laboratory workhorse for studying a broad variety of organisms as well as an invaluable tool for biotechnology. The mission of the CGSC is to act as a central repository for genetically modified strains of E. coli created by the research community, so that they may be readily available to other researchers and educators. To that end, the CGSC maintains a collection of ~28,000 cultures of genetically defined derivatives of E. coli K-12. There are over 8,000 different mutations represented in this strain collection with verified mutations in over 90% of the 4,111 identified genes in the sequenced E. coli K-12 genome. These cultures are distributed to researchers and educators in the US and over 65 countries worldwide. In addition to the distribution of cultures, the CGSC is also an information resource, and provides information about strains, mutations, genes, gene products and genetic maps, in a fully searchable database on the web. Importantly CGSC also acts as a source of expert information and advice for those researchers who have questions about using the E. coli strains in the collection.

The CGSC will continue to maintain and expand its publicly available database on strain genotypes, phenotypes, histories and pedigrees, which is unique to the Stock Center. Information systems will be upgraded to more seamlessly integrate with other E. coli web resources, including the EcoliWiki project, EcoGene and EcoCyc. The CGSC is collaborating with other international culture collection databases such as StrainInfo and the World Data Centre for Microorganisms (WDCM) so that the collection can be indexed by these global strain databases. Over the period of this award, capabilities will be expanded to distribute large systematic strain sets, which are useful for users interested in genomic and proteomic research. Strain construction services will be offered for those users who require a genetically modified strain, but lack the capability of constructing it themselves, particularly to those outside of the traditional bacterial genetics community. Access to the strain collection database, including genotypes, gene function and map location, as well as an extensive bibliography are available at (http://cgsc.biology.yale.edu/).

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Akusobi C, Chan BK, Williams ESCP, Wertz JE, Turner PE "Parallel Evolution of Host-Attachment Proteins in Phage PP01 Populations Adapting to Escherichia coli O157:H7." Pharmaceuticals (Basel) , v.11 , 2018 , p.E60 10.3390/ph11020060
Boundy-Mills, K. and Hess, M. and Bennett, A. R. and Ryan, M. and Kang, S. and Nobles, D. and Eisen, J. A. and Inderbitzin, P. and Sitepu, I. R. and Torok, T. and Brown, D. R. and Cho, J. and Wertz, J. E. and Mukherjee, S. and Cady, S. L. and McCluskey, K "The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections" Appl. Environ. Microbiol , v.81 , 2015 , p.5671 10.1128/AEM.01176-15
Chan BK, Sistrom M, Wertz JE, Kortright KE, Narayan D, Turner PE "Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa" Scientific reports , v.6 , 2016 , p.26717 10.1038/srep26717
Chan BK, Sistrom M, Wertz JE, Kortright KE, Narayan D, Turner PE "Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa" Scientific Reports , v.2016 , 2016 10.1038/srep26717
Kleiner, G. R. and Wibberg, D. and Winkler, A. and Kalinowski, J. and Wertz, J. E. and Friehs, K "Complete Draft Genome Sequence of Escherichia coli JF733" Genome Announc , v.4 , 2016 10.1128/genomeA.00298-16
Kleiner GR, Wibberg D, Winkler A, Kalinowski J, Wertz JE, Friehs K "Complete Draft Genome Sequence of Escherichia coli JF733" Genome Announc. , v.4 , 2016 , p.e00298-16 10.1128/genomeA.00298-16
McCluskey K, Alvarez A, Bennett R, Bokati D, Boundy-Mills K, Brown D, Bull CT, Coffey M, Dreaden T, Duke C, Dye G, Ehmke E, Eversole K, Fenstermacher K, Geiser D, Glaeser JA, Greene S, Gribble L, Griffith MP, Hanser K, Humber R, Johnson BW, Kermode A, Kri "The U.S. Culture Collection Network Lays the Foundation for Progress in Preservation of Valuable Microbial Resources." Phytopathology , v.106 , 2016 , p.532 10.1094/PHYTO-02-16-0074-RVW
McCluskey, K. and Alvarez, A. and Bennett, R. and Bokati, D. and Boundy-Mills, K. and Brown, D. and Bull, C. T. and Coffey, M. and Dreaden, T. and Duke, C. and Dye, G. and Ehmke, E. and Eversole, K. and Fenstermacher, K. and Geiser, D. and Glaeser, J. A. "The U.S. Culture Collection Network Lays the Foundation for Progress in Preservation of Valuable Microbial Resources" Phytopathology , v.106 , 2016 , p.532 10.1094/PHYTO-02-16-0074-RVW
McCluskey, Kevin,Barker, Katharine B.,Barton, Hazel A.,Boundy-Mills, Kyria,Brown, Daniel R.,Coddington, Jonathan A.,Cook, Kevin,Desmeth, Philippe,Geiser, David,Glaeser, Jessie A.,Greene, Stephanie,Kang, Seogchan,Lomas, Michael W.,Melcher, Ulr "The US Culture Collection Network responding to the requirements of the Nagoya Protocol on Access and Benefit Sharing." mBio , v.8 , 2017 , p.e00982-17 10.1128/mBio.00982-17

PROJECT OUTCOMES REPORT

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

The funding from this grant supported the operation of the E. coli Genetic Stock Center at Yale University.  Founded in 1966 with support from the NSF, the primary mission of the Stock Center is to facilitate scientific discovery by providing accurately documented strains of E. coli to the research and teaching community, in a timely fashion and at an affordable cost. Funds from this award supported ~45% of the operating expenses of the Stock Center, with the balance of funds coming from user fees and institutional support.

The CGSC (we were originally called the "Coli Genetic Stock Center", and the abbreviation is so entrenched in the literature that we still use it), distributes genetically documented cultures of non-pathogenic laboratory strains of E. coli. The vast majority of our strains are derivations of the famous K-12 strain used in the discovery of genetic recombination at Stanford in the 1940s.  The demand for these E. coli strains remains robust, and over the 3 year term of the grant, the Stock Center has distributed ~24,000 strains (~15,500 individual cultures and ~8,500 in 96-well plate format) to 2,385 different laboratories worldwide.  One indication of the impact that the Stock Center has on the research community is that in just the 3 years of this grant, E. coli strains from the CGSC were cited in at least 961 publications and 179 patents. 

  The CGSC serves a remarkably broad research community.  Initially the CGSC served primarily the very active microbial genetics and molecular biology community in their work with E. coli as a model organism for basic research on gene function, gene enzyme relationships, elucidation of metabolic pathways and mechanisms of recombination, replication and other aspects of cellular physiology.  But as the popularity of E. coli as a model organism has increased, the diversity of fields served by the CGSC has also expanded. 

  We now regularly receive requests for strains and information from investigators studying mammalian cells, nitrogen fixation, genomics and molecular biology of archaebacteria, eubacteria, protists, fungi, plant and animal species, drug discovery, vaccine development and other pharmaceutical research, a broad range of biotechnology applications, topics related to basic and applied agriculture, food science and environmental research, chemical synthesis, biofuels, systems and synthetic biology, structural biology and microbial evolution.   

            In addition to the distribution of living strains of E. coli, an important part of the Stock Centers mission has been to act as a public source of information about the genetics of E. coli.  Historically this was done by publishing periodic versions of the genetic map of the E. coligenome.  Since that time the genome of E. coliK-12 has been fully sequenced and the information is now available in a number of locations including on our website in a searchable form.  The Stock Center still acts as the acknowledged authority for assigning allele numbers for newly discovered or engineered mutations in E. coli.  We also offer free advice and consulting on strain selection, use and troubleshooting to both researchers and educators who want to use E. coliat both the high school and colligate level.

 

 


Last Modified: 05/20/2019
Modified by: John E Wertz

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