Frank Harmon, Professor

Closed (1) Project 1: Discovering transcript splicing mechanisms with mutants in the plant Arabidopsis thaliana

Applications for fall 2021 are now closed for this project.

Splicing of transcripts (mRNAs) is fundamental to gene expression in eukaryotes, including all crop plants. The goal of this project is to learn the function of poorly characterized splicing-associated proteins in the model plant Arabidopsis thaliana. This project identifies novel mutants in genes encoding splicing-associated proteins and subsequently characterizes how the mutants alter transcript splicing and impact development and growth. Due to the conservation of the transcript splicing process, the findings from this project will give insight into transcript splicing mechanisms in both plant and animal cells.

Students will find novel mutants, combine mutants to make new double mutants, and identify transgenic lines. Work will involve screening for the desired lines in large plant populations with molecular biology techniques. Successful discovery of mutant and transgenic plant lines will lead to characterization of these plants at the molecular and whole plant levels. Students will learn genetic and molecular biology techniques applicable to many branches of biology and gain experience working with a complex eukaryotic organism.

Qualifications: Students should be reliable, diligent, highly motivated, and interested in learning about scientific inquiry. Seeking juniors or seniors with 3.0 GPA that are biological science majors. Molecular biology experience is helpful but not necessary, as we will train students to perform the necessary tasks. Applicants should be available for 9-12 hours or more a week and will need large blocks of time (3-4 hours) to successfully complete the project.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: The lab is located off-campus at the Plant Gene Expression Center in Albany, about 3 miles from campus. The street address in 800 Buchanan Street. Public transit options include the RFS shuttle and the AC Transit 52L bus, which stops within a block of the lab. The building also has a large parking lot and secure bike parking.

Related website: https://harmonlab.berkeley.edu/
Related website: https://pgec.berkeley.edu/harmon-lab-0

Closed (2) Computational identification of shared and unique transcriptional regulatory modules in the crop plants sorghum, maize, and Setaria

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Transcriptional regulatory modules organize the pattern of gene expression that, in turn, controls the behavior of cells, tissues, and whole organisms. This project seeks to identify shared and unique transcriptional regulatory modules in three grass plants (sorghum, maize, and Setaria) through analysis of an RNA-seq gene expression dataset. The goal of this project is to learn the structure of the regulatory networks organizing gene expression in these three grass crops.

This a fully computational project, where the undergraduate student will work with existing gene expression datasets. It will be necessary for the student to learn how to run published bioinformatic analysis pipelines in R, as well use command line scripting to manipulate text-based datasets.

Qualifications: The ideal candidate will be reliable, diligent, and highly motivated. Seeking juniors or seniors with a GPA of 3.0 or higher. Experience with command line scripting and R are required. A biology background is desirable but not essential. Applicants should be able to commit 9-12 hours a week to the project.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: The lab is located off-campus at the Plant Gene Expression Center in Albany, about 3 miles from campus. The street address in 800 Buchanan Street. Public transit options include the RFS shuttle and the AC Transit 52L bus, which stops within a block of the lab. The building also has a large parking lot and secure bike parking.

Related website: https://harmonlab.berkeley.edu/
Related website: https://pgec.berkeley.edu/harmon-lab-0

Closed (3) Project 3: Characterizing the maize circadian clock with mutants.

Applications for fall 2021 are now closed for this project.

The project involves identifying and characterizing mutants in maize that affect the circadian clock. Corn, know also as maize, is the largest production crop in the United States. Besides serving as important source of food, feed, and fuel, maize is also an established experimental model for plant biology. The endogenous molecular timer, the circadian clock, is important for correct plant growth and development. A genetic understanding of maize circadian rhythms is sorely lacking. We are seeking to define the genes driving maize circadian rhythms. The intern will be involved in sample collection, genotyping, and studying gene expression.

Qualifications: Sophomore, junior, or senior with a GPA 3.0 and Biological Science major. Applicants should be available for 9-12 hours or more a week and will need large blocks of time (3-4 hours) to successfully complete the project. We are looking for reliable and diligent individuals who are interested in learning about scientific inquiry. Molecular biology experience is helpful but not necessary.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: The lab is located off-campus at the Plant Gene Expression Center in Albany, about 3 miles from campus. The street address in 800 Buchanan Street. Public transit options include the RFS shuttle and the AC Transit 52L bus, which stop within a block of the lab. The building also has a large parking lot.

Related website: http://pmb.berkeley.edu/profile/fharmon
Related website: http://www.pgec.usda.gov/Harmon/FHlab.html