| NSF Org: |
MCB Division of Molecular and Cellular Biosciences |
| Recipient: |
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| Initial Amendment Date: | August 14, 2019 |
| Latest Amendment Date: | August 4, 2021 |
| Award Number: | 1915154 |
| Award Instrument: | Continuing Grant |
| Program Manager: |
David Rockcliffe
drockcli@nsf.gov (703)292-7123 MCB Division of Molecular and Cellular Biosciences BIO Directorate for Biological Sciences |
| Start Date: | August 15, 2019 |
| End Date: | June 30, 2024 (Estimated) |
| Total Intended Award Amount: | $622,199.00 |
| Total Awarded Amount to Date: | $622,199.00 |
| Funds Obligated to Date: |
FY 2021 = $420,112.00 |
| History of Investigator: |
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| Recipient Sponsored Research Office: |
2221 UNIVERSITY AVE SE STE 100 MINNEAPOLIS MN US 55414-3074 (612)624-5599 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
1445 Gortner Ave St. Paul MN US 55108-1095 |
| Primary Place of
Performance Congressional District: |
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| Unique Entity Identifier (UEI): |
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| Parent UEI: |
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| NSF Program(s): |
Infrastructure Capacity for Bi, Systems and Synthetic Biology |
| Primary Program Source: |
01002122DB NSF RESEARCH & RELATED ACTIVIT 01002223DB NSF RESEARCH & RELATED ACTIVIT |
| Program Reference Code(s): |
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| Program Element Code(s): |
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| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.074 |
ABSTRACT
This project will generate physical and data resources that will dramatically advance understanding of the functions of thousands of genes in photosynthetic organisms. Photosynthetic organisms provide food and energy for nearly all life on Earth, yet most of their genes remain uncharacterized. This project will expand the availability of mutants needed to study the functions of genes in the single-celled model photosynthetic alga Chlamydomonas reinhardtii. The new project will use the newly generated mutants to identify relationships between genes and observable characteristics and will allow genes to be assigned to genetic pathways on an unprecedented scale. The resulting mutants will be available to the research community via the Chlamydomonas Resource Center, and the resulting data will be searchable on a website. The basic knowledge and resources generated by this project will lay the groundwork for advances in biotechnology, agriculture, and health. The placement of thousands of genes into pathways will identify new opportunities for pathway engineering in photosynthetic organisms. Mutants with enhanced or deficient growth in specific environments will reveal genetic targets for enhancing resistance of crops to a broad range of stresses. Mutants with defects in cilia will advance our structural and molecular understanding of these organelles, which play key roles in development and disease. The project will enhance infrastructure for research and education by providing urgently needed high-quality disruption mutants for many genes. The project will directly contribute to the training of many undergraduates, college graduates, and a postdoctoral fellow, and will advance the training of countless young researchers as they use the resources produced.
The project builds on the team's success in developing the existing Chlamydomonas mutant resource and extensive preliminary studies demonstrating that mutant phenotypes can be assessed in pools, where each mutant's growth rate is tracked by measuring the abundance of its unique DNA barcode. High confidence in a genotype-phenotype relationship requires three independent high-confidence alleles disrupting the gene of interest. The first aim of this project is to increase from 9% to 84% the percentage of genes covered with three high-confidence disruptions by improving the mapping accuracy of existing mutants and by generating additional mutants. The second aim is to systematically assign genes to pathways by identifying high-confidence genotype-phenotype relationships across the genome. The phenotypes of 70,000 mutants will be determined under hundreds of conditions, half of which will be selected by the community. Genes will be clustered into pathways based on the principle that mutants affected in in the same pathway show a similar pattern of phenotypes across a broad range of conditions. The third aim is to make the resulting mutants and data broadly available to the research community. Mutants generated by the project will complement the Chlamydomonas Resource Center's existing collection by providing coverage for genes not currently represented. Insertion sites, mutant and gene phenotypes, and gene pathway assignments will be searchable online. This project will transform our understanding of photosynthetic organisms by producing a comprehensive genotype-phenotype map. The availability of mutants and phenotypes will allow the community to make rapid progress on determining the molecular functions of uncharacterized genes and the proteins they encode.
This award was jointly funded by the Systems and Synthetic Biology Program and the Genetic Mechanisms Program in the Division of Molecular and Cellular Biosciences and by the Infrastructure Capacity for Biology Program / Collections in Support of Biological Research in the Division of Biological Infrastructure. All three programs are in the Biological Sciences Directorate.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
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.
This award supported the maintenance and distribution by the Chlamydomonas Resource Center (CRC) of more than 73,000 mutants generated by the new Chlamydomonas Library Project (CLiP2). This project seeks to generate and characterize mutant lines of Chlamydomonas reinhardtii with mapped insertions in thousands of Chlamydomonas genes, producing a powerful genetic resource for understanding biochemical pathways and processes in this unique photosynthetic eukaryote.
As its part of the overall project the CRC has replicated, in triplicate, 192 plates of up to 384 colonies per plate, and we are in the process of freezing the entire collection in liquid nitrogen, in duplicate. Early in the project we collaborated with the Jonikas laboratory to identify the best host strain to use for the insertional mutagenesis used to generate the library. By comparing growth, flagellar motility and mating of candidate strains our labs settled on strain 21gr mating type +, commonly known as the "g1" strain routinely used in laboratories that study flagellar motility. The names and descriptions of the mutants have been entered into the database maintained by the CRC. Within a month this database will be linked to the CLiP2 database maintained by the Jonikas labortory at Princeton, after which time orders will be received at Princeton, then forwarded to the CRC which will send the strains to users.
Throughout the funding period of this project the CRC has continued to receive and fill orders for the original CLiP mutant library, as well as orders for strains from the "core" collection of mutant strains, as well as plasmids, educational kits, and cell growth reagents in our catalogue. During the period covered by this report the CRC shipped 3177 CLiP mutant strains, along with along with 3942 strains from the Core collection of non-CLiP mutants. Also provided during this period, with the support of this grant were 799 plasmids, including large insert BAC and fosmid clones. Other resources provided to the community during this period were 366 shipments of media components, and 147 educational kits providing instructions, cells and reagents for conducting experiments for teaching labs at secondary and post-secondary schools. We have also continued to receive new plasmid clones and Chlamydomonas strains provided by users, and to make these resources available to the community. Users are asked to provide detailed information about the characteristics and histories of each strain or plasmid received and this information is available on our web page (chlamycollection.org).
Last Modified: 10/14/2024
Modified by: Paul A Lefebvre
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