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SURF: Announcements of Opportunity

Below are Announcements of Opportunity posted by Caltech faculty and JPL technical staff for the SURF program. Additional AOs for the Amgen Scholars program can be found here.

Specific GROWTH projects being offerred for summer 2019 can be found here.

Each AO indicates whether or not it is open to non-Caltech students. If an AO is NOT open to non-Caltech students, please DO NOT contact the mentor.

Announcements of Opportunity are posted as they are received. Please check back regularly for new AO submissions! Remember: This is just one way that you can go about identifying a suitable project and/or mentor.

Announcements for external summer programs are listed here.

Students pursuing opportunities at JPL must be
U.S. citizens or U.S. permanent residents.

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Project:  Programmable Conditional CRISPR/Cas9 Regulators for Scalable Synthetic Biology
Disciplines:  Bioengineering, Synthetic Biology
Mentor:  Niles A. Pierce, Professor, (BBE),, Phone: x8834
Mentor URL:  (opens in new window)
AO Contact:  Jining Huang,
Background:  Traditional synthetic biology regulators have relied on protein:protein and protein:DNA interactions mined from existing genomes, posing challenges to scalability due to crosstalk and the limited number of available regulators. Exploiting principles from dynamic RNA nanotechnology and molecular programming [1,2], the Pierce Lab is working to rationally design libraries of orthogonal CRISPR/Cas9 regulators for scalable engineering of closed-loop control circuits.
Description:  A standard guide RNA (gRNA) directs the activity of a Cas9 effector to enable silencing or activation of a target gene of choice [3,4]. To enable programmable spatiotemporal control over gRNA activity, we have engineered novel conditional guide RNAs (cgRNAs) that can be toggled ON->OFF or OFF->ON by programmable RNA triggers. Programmable conditional cgRNA regulators provide a platform for scalable synthetic biology. This SURF project will focus on expanding the functional vocabulary of the cgRNA regulators in E. coli by engineering them to operate with new Cas9 variants.
References:  Signal transduction via dynamic RNA nanotechnology
1. Hochrein, L. M., Schwarzkopf, M., Shahgholi, M., Yin, P. & Pierce, N. A. Conditional Dicer Substrate Formation via Shape and Sequence Transduction with Small Conditional RNAs. Journal of the American Chemical Society 135, 17322–17330 (2013).

Reaction pathway engineering with NUPACK
2. Wolfe, B. R., Porubsky, N. J., Zadeh, J. N., Dirks, R. M. & Pierce, N. A. Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. Journal of the American Chemical Society 139, 3134–3144 (2017).

Silencing dCas9
3. Qi, L. S. et al. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell 152, 1173–1183 (2013).

Activating dCas9
4. Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Research 41, 7429–7437 (2013).
Student Requirements:  Strong preference for students that are eager to begin lab work during the spring term and are familiar with or willing to learn molecular cloning techniques.
Programs:  This AO can be done under the following programs:

  Program    Available To
       Amgen Scholars    Non-Caltech students only  
       SURF    both Caltech and non-Caltech students 

Click on a program name for program info and application requirements.

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