May 18, 2019

Duke iGEM Team Awarded Grants for Synthetic Biology Research and Outreach

A Bass Connections project, Duke Undergraduate International Genetically Engineered Machine (iGEM) Team, has received two external grants to support its work.

The Duke iGEM team is led by faculty members Nicolas BuchlerCharles Gersbach and Michael Lynch. Student team members have varied backgrounds in biomedical engineering, biology, computer science and public policy studies. Their goal is to identify a particular challenge in such areas as health, sustainability or bioenergy, then apply advanced synthetic biology and metabolic engineering methodologies to create a solution.

The project’s policy component asks team members to explore synthetic biology’s legal, ethical and economic impact and to develop innovative tools to improve access and education.

Building with Biology Grant

With a grant from the Museum of Science in Boston, the iGEM team will present a student-led outreach event at Duke. “Should We Edit the Genome? When, Why and How Much?” will take place on Saturday, September 3, from 5:00 to 7:00 p.m. in Perkins Library Room 217. Duke faculty and student team members will lead the discussion, which is free and open to the public.

The Building with Biology grant was also for using simple demonstrations, games and toys to teach young children about synthetic biology. Duke iGEM members volunteered at the Marbles Kids Museum in Raleigh.

GenScript Grant

One of the team’s summer activities has been to characterize guide RNA (gRNA) sequences in the CRISPR/Cas9 genome editing system. The initial order of almost 13,000 guides will be placed into different strains of the E. coli bacteria and tested to determine whether or not each guide cuts the E. coli chromosomal DNA sufficiently fast to prevent E. coli growth.

The collected data about each of the guides will then be analyzed using different machine learning methods to isolate an algorithm that fits the collected data and can robustly predict other guides chosen to modify DNA in E. coli.

“Thus far, we have selectively isolated over 12,000 specific guide sequences to test in two strains of E. coli,” said team member Adam Yaseen. “We have received a grant from GenScript to help in the initial order of the guide sequences.”

iGEM is a nonprofit organization dedicated to education and collaboration around synthetic biology. “In October the Duke iGEM team will present its final project at the iGEM competition in Boston,” said team member Attyat Mayans.

Images courtesy of Adam Yaseen. 1, 2: team members in Raleigh; 3: A) A plasmid library in which each plasmid contains a unique gRNA will be prepared using Q5 mutagenesis. B) Bacteria will be grown to early log phase at which point Cas9 will be induced. Samples will be taken just prior to induction as well as three times post-induction as the cells continue to grow. C) The plasmids will be purified and sequenced using Next Generation Sequencing. The sequencing data, in combination with sequence-specific features of both the gRNA and target site, will be used to train machine learning algorithms in order to develop a gRNA selection algorithm that will enable robust, reliable Cas9 cleavage.

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