Mentor Name:
James Gagnon

Mentor Position:
Assistant Professor

School of Biological Sciences



Project Description:

**This project is a part of the Summer Program for Undergraduate Research (SPUR), which provides undergraduate students with an intensive 10-week research experience under the mentorship of a University of Utah faculty member. SPUR 2022 begins on May 25 and ends on August 4. If you are interested in this project, please review all program information on the SPUR site. If you wish to apply to this project, you must apply using the SPUR 2022 application.**

Embryos develop from a pool of equivalent “stem cells” into adults composed of thousands of different cell types organized into tissues and organs. What are the mechanisms that choreograph such a complex process, such that that majority of embryos develop correctly into healthy adults? How do these mechanisms go wrong in diseases? Over the past century, developmental geneticists have carefully studied these mechanisms one gene at a time, to understand their role in this larger process. Our lab is taking a different approach adapted from systems biology. We have developed CRISPR tools for large-scale perturbation of gene regulatory networks in embryos, and combined them with single-cell sequencing methods for sensitive and detailed descriptions of the consequences of each perturbation. Now that we have these tools in hand, we are focused on the network of genes that control mesoderm specification and diversification. Mesoderm is formed early in the embryo, and diversifies during development to generate muscles, skeletal tissue, and organs such as the kidney, ovary and testis in adults. While we can appreciate the importance of mesoderm, we have a poor understanding of the gene regulatory networks that underlie its formation and diversification.

Opportunity Type:

This is a paid research position

Student Role:

This summer, a SPUR student will be an integral part of our team that is implementing these technologies to understand mesoderm. The student will learn experimental and computational methods from our expert team. On the experimental side, this includes breeding zebrafish, our model organism of choice, and injecting their embryos, as well as CRISPR experimental design and embryo manipulation. On the computational side, the student will be generating sequencing data and using software packages to analyze these data to understand mesoderm gene expression in normal and CRISPR-perturbed embryos. The student will use these new skills to understand how an interconnected network of transcription factors controls mesoderm development. Together, this project will combine extensive learning and front-line experience in a supportive and fast-moving science environment.

Student Benefits:

Biology is rapidly transitioning into an interdisciplinary field of study which mixes experimental and computational approaches that pull from other fields for experience and inspiration. A rapidly growing sector of pharma, biotech and startups is desperate for students who are fluent in both “wet” and “dry” lab approaches. In addition, these skills are highly sought-after in PhD programs nationwide. This project will teach a variety of cutting-edge technologies, including CRISPR, sequencing, and computational analysis, to accelerate skill acquisition. Since the student will be an essential component of our team, if successful, this project is highly likely to result in peer-reviewed manuscripts with the student as a co-author. In the past, undergraduates in the Gagnon lab have been co-authors and even lead authors on papers, and many have continued on to medical or graduate school.

Project Duration:

35-40 hours per week on research and program-related activities, begins May 25, 2022, and ends August 4, 2022

Minimum Requirements:

Admission to the program is competitive. Applicants must meet all of the following criteria: 1) be a matriculated, degree-seeking undergraduate student in the Fall 2022 semester (beginning or continuing college career in Fall 2022 and not graduating before December 2022; concurrent enrollment while in high school does not meet this eligibility requirement). Applicants do not need to be a University of Utah student. 2) eligible to work in the United States: If you are a University of Utah Dreamer (with or without DACA), you are eligible to participate. U Dreamers with DACA will be hired and paid through U payroll. U Dreamers without DACA who graduated from a Utah high school will be compensated via a different mechanism. If you are a Dreamer from a different institution: If you have DACA, you are eligible to participate and will be hired and paid though U payroll. If you do not have DACA, you are able to participate and gain research experience, but we do not currently have a mechanism that allows us to compensate you. For more information, please contact Megan Shannahan at megan.shannahan@utah.edu or 801-581-2478. If you are an international student or scholar, you must either a) be a degree-seeking undergraduate student at the University of Utah, OR b) possess documentation that establishes your eligibility to work in the United States (if you hold US citizenship, it is likely you have these documents). 3) able to commit to approximately 35-40 hours per week of employment at the University of Utah for the entire duration of the program (May 25-August 4, 2022). 4) at least 18 years old by May 23, 2022 (required if you wish to use on-campus housing; preferred if you will not be using on-campus housing).