Caroline Williams, Professor

Closed (1) Carry over effects of snow on willow leaf beetles

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

Willow leaf beetles (Chrysomela aeneicollis) live in the Sierra Nevada mountain ranges and have been used to study the molecular, biochemical, and physiological mechanisms by which organisms respond to environmental change. We are studying how winter conditions affect both survival and subsequent reproduction, in order to understand how changing winters will alter population dynamics.

We collected beetles last summer as they emerged from the snow, and are looking for a talented and dedicated student to assist with quantifying their energy reserves and investment into reproduction. Students will gain skills in insect husbandry, problem solving, and measuring physiological and life-history parameters to quantify performance.

Undergraduates in the Williams lab attend lab meetings and take part in the intellectual life of the lab. They interact with graduate students and the PI and have the opportunity to form long-term mentoring relationships. For exceptional students, there may be opportunities to contribute to a publication or present at a conference. Students often stay in the lab for multiple semesters and contribute to diverse research projects including independent research and honors theses.

Qualifications: Required: reliable, detail-oriented, excited about science, steady hands. Desirable but not essential: experience reading primary literature, research experience with good references, some ecology or physiology course-work.

Weekly Hours: 9-11 hrs

Closed (2) Life history trade-offs in the field and the laboratory

Applications for Spring 2019 are now closed for this project.

Life history trade-offs occur when limited resources must be allocated among competing traits including reproduction, somatic maintenance, and activity. In the laboratory, high food availability may obscure these trade-offs, because organisms have plenty of energy for all life history traits. We are studying life history trade-offs in the laboratory and the field using wing polymorphic crickets, which have two forms, a dispersal form that flies and invest heavily into the body, and a reproductive form that invest heavily in making eggs.

Measure lipid content of crickets collected from the field and the laboratory. Training in biochemical techniques will be provided.

Qualifications: Required: reliable, detail-oriented, excited about science, steady hands. Desirable but not essential: experience reading primary literature, research experience with good references, some ecology or physiology course work. Undergraduates in the Williams lab attend lab meetings and take part in the intellectual life of the lab. They interact with graduate students and the PI and have the opportunity to form long-term mentoring relationships. For exceptional students, there may be opportunities to contribute to a publication or present at a conference. Students often stay in the lab for multiple semesters and contribute to diverse research projects including independent research and honors theses.

Weekly Hours: 9-11 hrs

Related website: http://cmwilliamslab.com

Closed (3) Functional characterization of proteins underlying cold-tolerance in tardigrades

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

Tardigrades are microscopic aquatic animals that are well known for their extreme tolerance to freezing, high temperature, radiation, and desiccation—yet the molecular mechanisms that underlie these remarkable phenotypes remain less known. In particular, one unresolved question that underlies how tardigrades survive freezing is whether various species produce proteins to control the formation of extra- or intra-cellular ice. In this URAP project, the student will clone several such tardigrade candidate genes into bacterial over-expression vectors and utilize nickel-affinity purification to isolate large quantities of the proteins of interest. Future work will include in vitro and in vivo functional characterization of these candidate genes, among several species of tardigrades that are currently cultured in lab. This project will help the student foster skills in molecular biology, biochemistry, biophysics, and comparative physiology.

1. Student utilizes Gibson assembly cloning methods, to insert candidate gene sequences into E. coli overexpression vectors
2. Student runs DNA gels and prepares cloning constructs for sequencing, to verify DNA sequence
3. Student over-expresses these proteins in large quantities in E. coli, and purifies individual proteins using batch-binding nickel affinity
4. Student runs protein gels and/or prepares samples for Mass-spec, to verify protein sequence
5. If student participates in project long-term: there is an opportunity for the student to be involved in in vitro and in vivo functional characterization of these candidate proteins (including designing and implementing phenotypic assays+RNAi)

Day-to-day supervisor for this project: Ana Lyons

Qualifications: -General interest in biology & evolution, especially the molecular biology and the structure-function relationship of proteins. -Bio 1A, MCB102, experience with molecular cloning+PCR+some protein purification strongly preferred. -MCB110L or other wet lab experience is preferred, but not required. -Strong note-taking, problem-solving, communication skills -Willingness to work with PhD research mentor as part of a collaborative team. Day-to-day supervisor for this project: PhD Student, Ana Lyons Additional qualifications: Required: reliable, detail-oriented, excited about science, steady hands. Desirable but not essential: experience reading primary literature, research experience with good references, molecular biology experience, computational expertise. Undergraduates in the Williams lab attend lab meetings and take part in the intellectual life of the lab. They interact with graduate students and the PI and have the opportunity to form long-term mentoring relationships. For exceptional students, there may be opportunities to contribute to a publication or present at a conference. Students often stay in the lab for multiple semesters and contribute to diverse research projects including independent research and honors theses.

Weekly Hours: 9-11 hrs

Related website: http://cmwilliamslab.com

Closed (4) COMPUTATIONAL BIOLOGY OPPORTUNITY: De novo protein modeling & evolutionary analysis of gene families underlying tardigrade stress-tolerance

Closed. This professor is continuing with Fall 2018 apprentices on this project; no new apprentices needed for Spring 2019.

Exposing the cells of most organisms to extreme conditions of heat, freezing or desiccation would result in cell death, but surprisingly, for the microscopic animal known as the “tardigrade,” this is not the case. Tardigrades are aquatic, microscopic animals (~0.5mm) with complex body structures (8 legs, claws, eyespots, an intricate architecture of smooth-muscle, and a multi-lobed brain). Tardigrades are uniquely classified in their own phylum in the animal kingdom, and the phylum Tardigrada is comprised of 1200+ species—many of are which found in a wide array of environments across the globe. By utilizing a unique molecular toolbox (and in some cases, falling into a reversible form of dormancy known as “cryptobiosis”), tardigrades are uniquely able to withstand temperatures ranging from nearly absolute zero to 151C, up to 6,000 atmospheric pressures, radiation of up to 5000gy, up to 20 years in desiccation, and even survive the vacuum of space, making them one of the most robust metazoans known to science.



Complete genomes and proteomes of various tardigrade species have only recently become publicly available, and these datasets provide a wealth of information that can be utilized to predict what types of genes underlie survival to environmental extremes. More so, it is now possible to study how conserved these candidate genes are across multiple species of tardigrades—and thus evolution. In this work, we will focus on a handful of candidate gene families, whose function we predict underlies tolerance to desiccation, cold/freezing, and/or osmotic stress. Experimental work conducted in lab has helped narrow down this list of candidate genes thought to be involved in tardigrade abiotic stress response, and we now hope to model the 3D structure of these gene products (as proteins) & understand how the conservation of various protein structures within gene families & across the phylum may influence these genes’ function. More specifically, the student will use cutting-edge Rosetta software to model the de novo structures of these candidate proteins & explore various methods to recognize and quantify structural changes in these proteins throughout evolution (with the opportunities to hone skills in protein modeling, protein structure comparison, molecular evolution, and/or evolutionary physiology).

1. Model 3D protein structures for candidate genes (and their various isoforms) underlying tardigrade abiotic stress response, using Rosetta (requires knowledge of running computationally expensive tasks on a remote server and writing/running supporting Python scripts). More info on Rosetta here: https://www.rosettacommons.org/software
-Note: A custom-python wrapper exists for automating the use of Rosetta software on relevant UC Berkeley Servers, but this wrapper may require modification and/or optimization of parameters. The student may also need to optimize parameters/criteria to choose the “best” Rosetta protein model, for each gene candidate.
2. Explore the use of various computational methods to compare structural differences, between various members (and 3D protein structures) of each gene family (within and between tardigrade species)
3. Optional but encouraged: Work with large genomic datasets/population genetics software programs to explore conservation patterns of candidate genes’ primary nucleic acid sequence

Day-to-day supervisor for this project: Ana Lyons

Qualifications: -Proficiency in Python, UNIX & comfort working with remote servers. -Student must have a strong interest in applying computational methods to biological problems. CS 61A & 61B are strongly preferred, and 61C, 70 is helpful but not required. -General interest in biology & evolution, especially the structure-function relationship of proteins. -Bio 1A or MCB102 is helpful, but not required. -If student has a strong interest/background in machine learning & image recognition, this is an additional extension project available. -Willingness to work with PhD research mentor as part of a collaborative team. -Student must be willing to have regular meetings with mentor, but there will be some flexibility in where/when computational work may be completed. Day-to-day supervisor for this project: PhD Student, Ana Lyons

Weekly Hours: 9-11 hrs

Related website: cmwilliamslab.com