Craig Miller, Professor

Closed (1) Genetic analysis of head skeletal evolution

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

A fantastic diversity in organismal form is seen in nature, yet we know little about the genetic basis of evolutionary change. We are using the head skeleton of the threespine stickleback (Gasterosteus aculeatus) as a model system to study the genetic basis of development and evolution. Sticklebacks have undergone one of the most dramatic and recent adaptive radiations on earth. Ancestral marine sticklebacks colonized and rapidly adapted to new freshwater lakes and streams at the end of the last ice age about 10,000 years ago. Major changes to the head skeleton have evolved repeatedly as populations adapt to new diets found in new freshwater environments. Fish with different morphologies can be crossed in the lab, allowing genetic analysis to identify which chromosome regions control the changes to the head skeleton. In a previous detailed genetic analysis, we identified a set of chromosome regions controlling a suite of head skeletal traits. We now want to ask how predictable evolution is, and how general the use of these chromosome regions is in other populations where the same skeletal changes have evolved in parallel. Several F2 genetic crosses have been generated and will be the focus of this project. Molecular biology methods will be used to isolate DNA, and the polymerase chain reaction (PCR) used to amplify genetic markers that can be used to genotype different genomic locations of interest. The skeletons of fish from these genetic crosses will be stained with dyes that label bone, allowing the size and number of various bones to be quantified. These phenotypes will be compared to the genotypes to identify chromosome regions underlying evolutionary change. In other genetic crosses, candidate genes have been knocked out with new genome editing tools.

Please see recent 2014-2015 papers from the lab (see website for references: papers with Ellis, Erickson, Glazer, or Cleves as first authors) for more details. All of these papers have former URAP students as co-authors.

Qualifications: The apprentice should be willing to work 12+ hours/week on average (including about two hours/week meeting to plan research and discuss results, possibly up to two hours/week helping with animal husbandry, and at least eight hours/week doing independent research). No specific skills are required, but the apprentice should be familiar with basic concepts of genetics and molecular biology, and excited to learn about genetics, development and evolution. Ideally, the apprentice is highly-motivated, committed to doing research, pays attention to detail, enjoys working with their hands and looking through a microscope, and is familiar with Macs and PCs. We are especially interested in apprentices with a strong desire to potentially continue the project in future semesters.

Weekly Hours: 12 or more hours

Related website: http://mcb.berkeley.edu/index.php?option=com_mcbfaculty&name=millerc
Related website: http://mcb.berkeley.edu/labs/miller/





Open (4) Developmental biology of tooth regeneration

Open. Apprentices needed for the spring semester. Enter your application on the web beginning January 15th. The deadline to apply is Monday, January 28th at 9 AM.

The general concept, system, methods, and qualifications are similar to Project 1, but this project will specifically focus on studying the molecular and cellular basis of vertebrate organ regeneration, using teeth as a model system. The initial focus will be on assisting with ongoing experiments to identify putative stem cells in adult fish that give rise to regenerating teeth. This project involves cutting histological sections of fish to examine detailed patterns of cell division and gene expression at cellular resolution. We want to identify stem cells that mediate regeneration, as well as the molecular genetic pathways that regulate regeneration. Please see lab’s 2018 PLoS Genetics paper for more background (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007449).

Weekly Hours: 12 or more hours