Freshman Research Initiative

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RNA Gelvegfaa mutant exhibits mis-migration of trunk intersegmental blood vessels

Learning by Doing! Relating Information from BIOL 212 (Principles of Biology II) to a Research Project:

During Spring 2015, 40 freshmen in three life sciences majors (Biology, Bioinformatics and Computational Biology, and Genetics) participated in the Freshman Research Initiative funded by a grant to ISU faculty from the Howard Hughes Medical Institute.  Twenty Genetics students were among the participants, earning 2 credits which applied to their major requirements.  Students attended a weekly one-hour lab meeting with project leader Dr. Jeff Essner,  Associate Professor, Department of Genetics, Development, and Cell Biology, and spent another 5-6 hours per week working under the supervision of graduate and undergraduate teaching assistants.

Zebrafish were chosen for this experiment.  Zebrafish are great model organisms in which to study vertebrate development with their low cost of culture and transparent bodies.  The zebrafish genome has been sequenced and is publicly available. The goal of the project was to make zebrafish mutants using the CRISPR/Cas 9 system which allows investigators to initiate double strand breaks in a specific DNA sequence.  When these breaks are resolved, a gene may be deleted or otherwise rendered non-functional.

Students chose their gene of interest from a list of genes expected to be involved in either vascular development or the formation of cancer or both.  The first part of the project involved determining what was already known about the gene from the research literature. Next came an exercise in bioinformatics: annotating the gene (finding introns and exons) and designing a pair of oligonucleotides to target unique sequences in the first and last exons of the gene. Double stranded DNA was then synthesized, purified, and transcribed.  Synthesis of both dsDNA and RNA transcripts (guide RNAs) involved careful preparation of reactions and gel electrophoresis to check on products. 

Guide RNAs and Cas9 were then injected into Fli1-egfp transgenic embryos which can express green fluorescent protein; embryos were incubated and scanned for phenotypes over a five day period. Although not every student was able to complete all steps in the process, it was a fabulous learning experience for all as described by one student:

"I did not reach the injection phase with my gene because it would not pass the DNA gel and after five attempts I was paired up with someone else so that I would have a bit more success. I really appreciated having this opportunity to work in a research lab with special interest to my major. Learning the techniques involved in the handling and prep of solutions that need to remain sterile was really rewarding because I got to see my hard work and diligence pay off (minus the DNA gel part of course!) Also I found it valuable to learn the workings of the bioinformatics related to this type of research, which also happened to help in the lecture portion of biology 212!"

What's Next?

Some students are using this experience to jump into longer term research in Dr. Essner's lab and other labs on campus.

Three research streams are planned for the incoming Fall 2015 class of freshmen in Spring 2016 including one using stem cells in Dr. Donald Sakaguchi's lab and one in ecology with Dr. Kevin Roe. 

Overall 75% of freshmen in Genetics gained research experience during the 2014-15 school year.  The remaining 25% chose not to be involved.

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