Using FISH for karyotyping coast redwood
Rasmus Nielsen, Professor
Integrative Biology
Applications for Spring 2025 are closed for this project.
The Fluorescence In Situ Hybridization (FISH) technique is a molecular cytogenetic method used to detect and localize the presence or absence of specific DNA sequences on chromosomes. It is widely used for karyotyping to visualize and map chromosomal abnormalities such as translocations, deletions, duplications, and aneuploidies. In Nielsen lab, we've discovered a coast redwood (Sequoia sempervirens) clone that is missing a copy of chromosome 4 so the clone is deemed tenative aneuploid. Aneuploidy is a condition when a genome of an invididual has an abnormal number of chromosomes as compared to the base number of chromosomes. So for a hexaploid, that number is 6 and deviations (up or down) is considered an aneuploidy. This finding was made using short read sequencing data, and computational methods to normalize read depth. However, we need to confirm this chromosomal abnormality via FISH technique. Since the lab is mostly computational, this project will involve some trial and error, and will require a fair amount of literature reading and spending time in a wet lab.
Role: Undergrads in this project will learn wet laboratory techniques to "paint" chromosomes of coast redwood. This will involve collaborating with the RCNR Biological Imaging Facility at UC Berkeley, learning how to use the instruments and follow detailed protocols. Some amount of computational work is expected as this project will involve probe development (identifying target sequences from reference genome data).
Qualifications: Some familiarity with laboratory work is recommended but not required. You will need to complete basic UC Berkeley training on laboratory safety if you haven't already done so (All lab workers are required to successfully complete EHS 101: Fundamentals of Laboratory Safety training offered online at the UC Learning Center. EHS 103: Fundamentals of Laboratory Safety Refresher is required at a minimum of every three (3) years. See the EH&S training webpage for details.). In addition, you might need to complete training specifically required for working at the imaging lab. We expect that you either already have or intend to get some ecology and computational methods background.
Day-to-day supervisor for this project: Sasha Nikolaeva, Post-Doc
Hours: 9-11 hrs
Related website: https://nielsen-lab.github.io/pdfs/Undergrad_mentorship_expectations.pdf
Related website: https://nielsen-lab.github.io/pdfs/Undergrad_mentorship_expectations.pdf