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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
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Home › Webinars › Engagement Webinar: What Can You Do With An Approved CSP Functional Genomics Call Proposal?

July 16, 2020

Engagement Webinar: What Can You Do With An Approved CSP Functional Genomics Call Proposal?

Hal Alper, UT Austin
Hal Alper

On July 8, JGI’s DNA Synthesis Science group held a JGI Engagement: Accessing Functional Genomics Capabilities Webinar inviting researchers to submit white papers to the Community Science Program’s Functional Genomics call for proposals. The proposal call is open year-round, but proposals submitted by July 30 will be included in the next review.

“So webinars like this didn’t really fully exist back then,” said Hal Alper, a University of Texas at Austin professor, “but we really first heard about the JGI synthesis grant during a presentation that [DNA Synthesis Science Head] Yasuo [Yoshikuni] gave back in 2016.” Alper’s first approved JGI proposal came through the Functional Genomics (formerly DNA Synthesis) call, and he noted the data had driven his lab’s focus on guide RNA library generation and development and its applications.

Philipp Zerbe, UC Davis
Philipp Zerbe

“I moved to UC Davis in 2014,” recalled Philipp Zerbe of the University of California, Davis. “The work with JGI was one of the first things we actually started doing when starting the lab. It has been, especially from an early career perspective, been absolutely instrumental in a lot of the work that we are doing now.”

Zerbe’s proposal involving six labs at universities around the world was the first of the Functional Genomics call’s approved proposals by a consortium. The consortium looked at how different bioenergy relevant plants can produce species-specific blends of terpenoids, naturally occurring organic chemicals with a wide range of potential applications.

Q&A from the Webinar

Q(uestion): Are the JGI capabilities described in this webinar only offered through the CSP Functional Genomics call?
A(nswer): It’s also possible to access these capabilities in other calls such as the annual large-scale CSP call or through the “Facilities Integrating Collaborations for User Science” (FICUS) initiative. 

Q: What is the difference between “regular” proposal and a consortium-type proposal?
A: Consortium proposals can scale the request size, being permitted to request up to 1.5 megabases (MB) of a synthesis, compared to 0.5 MB for a single lab. 

Q: What is the review process for submitted proposals?  
A: When a proposal is submitted to the JGI, JGI scientists will go over the whole proposal for the technical feasibility first. Prospective users are always welcome to contact one of us about possible proposals if it’s different from what is on offer and to see if it can be done. 
After the technical review, proposals with feasibility notes go to peer review, which is very similar to the regular grant application approval process. And then, once the review panel recommends proposals for acceptance, it will be sent off for internal review to consider the biosecurity, biosafety, and environmental aspects of the proposals. Upon approval from JGI reviewers, the DOE project managers review the proposals. The proposer of approved proposals are notified and a contract is drawn up to begin the work.

Q: What is it that people will physically receive? What is the product that you are providing?
A: It depends on the proposal. For example, if an approved proposal involves a guide RNA library, the researchers will receive a FedEx package with the sequenced, quality controlled population representing the full library.

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Filed Under: Blog, Webinars Tagged With: synthetic biology

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