Introducing The CSH Syn Bio Class of 2015

Today, our fantastic class of students concluded the CSH Synthetic Biology 2015 summer course experience with final presentations on the various projects and a graduation ceremony. There were four core projects that were carried out during week 2 of the course, plus two additional creative cross-disciplinary projects.

Wasti Nurani, Baudoin Delepine, and Bryan St. Germain presented their team’s work on screening GPCR variants in yeast for the ability to BIND, sense and respond to biofuel ligands. They utilized 3D computer modeling of protein structures and ligands to predict strong candidates. Screening of function in live cells (yeast) was done by placing a green fluorescent protein under the control of the GPCR, so that functional candidates would glow green and be collected for further analysis. Their project was led by Pamela Peralta-Yahya and Emily Yasi (TA).


The Bacterial CRISPRi project was presented by Orlando deLange, Trevor Tanner, Wasti Nurani, David Hauser, Will Byrd, and Katherina Garcia Vanegas presented their team’s. They studied CRISPRi (CRISPR-inhibitor) -mediated control of fluorescent reporter genes and the chemotaxis pathway. They used the tremendous flexibility of CRISPRi (only 20 nt of RNA needs to be designed to target virtually any gene at any position) to turn off different genes in the bacterial motility pathway and control bacterial motion in soft agar. They also tested CRISPRi RNA-DNA interactions in a cell-free TXTL system. The project was led by Stanley Qi and Eddie Zhao.


The in vitro cell-free gene circuit characterization project was presented by Helena Shomar, Lin JinAlfonso Rodriguez-Paton, and Arnab Bandyopadhyay. Their team’s goal was to use TXTL to develop a paper-based diagnostic tool to detect toxins in solution. They were able to detect fluorescent protein expression in as fast as 20 minutes! They tested different gene circuit configurations and showed very exciting data. The project was led by Julius Lucks and James Chappell.


Kirsten CouplandKatherina Garcia Vanega, Bryan St Germain, Guanyu Wang, and Will Byrd presented their work on using DNA-cutting CRISPR to edit the genome of cultured, cancer-derived human cells. The team pursued a bevy of projects…reporter-gene replacement in a stable line, landing-pad integration, knock-out of metabolic genes to create a platform for robust selection, and targeting CRISPR to fix disease-linked errors in mitochondrial DNA. The group succeeded in designing dozens of constructs needed to perform the experiments, and generating many of them via PCR and single-pot assembly.


BROCCOLI APTAMER. Khalid Alam presented the results of his mini-project, an investigation of RNA-based fluorophores for live RNA tracking. Broccoli is the latest spin-off from the well-known Spinach aptamer that was published by the Jaffrey Lab.

CRISPRi IN TXTL. Kirsten Coupland reported on all of the creative experiments done by several students (Kirsten, Helena Shomar, Alfonso Rodriguez-Paton, and Katherina Garcia Vanegas) to study CRISPRi in the cell-free TXTL system. This included characterizing repression of a GFP reporter, building an A AND NOT B logic gate, and using fluorescent RNA aptamers for quick turnover of signal.

PHYTOPATHOGEN DETECTION. Orlando deLange and Lin Jin presented their idea and efforts to interface paper-based TXTL with plant biology by engineering TXTL to respond to plant pathogens.

TXTL SENSOR-REPORTER MODELING. Guanyu Wang, a mathematician by training (who now rocks at PCR and cloning), presented her focus-project on building deterministic models for GFP expression over time in the cell-free TXTL system.

PCR BEST PRACTICES. Will Byrd gave a highly informative presentation on best practices for PCR from a first-time-pipetting mathematician’s point of view. Pro tips: do not get lint on the gel cast or else the photo will be noisy, always load a DNA ladder, always make sure the PCR machine is working, do not let the gel air dry, never try to pry open a melted PCR tube with an ink pen, and pen ink fluoresces quite nicely in an agarose gel.

WHAT HAPPENS WHEN YOU MIX DNA WITH CELLS? Inspired by a question from his daughter Stella, Julius Lucks organized a project to explore DNA uptake. The results were beautiful E. coli-agar art.

We concluded the course with a graduation ceremony with a special thanks and awards for our hard-working TAs. Rene Daer received a special “Veteran TA” award as recognition for her commitment to the course for three consecutive years. The Students all received official diplomas signed by the instructors and a commemorative group photo.


Working with this year’s group was exciting, intense, and extremely fun. The students learned, struggled, and triumphed together. Although they credited us (the instructors and TAs) for our work setting up the course, it was the  students’ own great character and creativity that made the experience a true success. The instructors were fortunate to witness the genesis of new relationships, new insights, and hands-on learning in an authentic research environment.


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