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Research Projects Available for Students for Academic Year 2007-2008 in the Harvey Mudd Biology Department
Submit your Thesis Preferences Form to Prof. McFadden by Wed, 18 Apr 2007!
NOTE: Profs. Ahn and Orwin are on sabbatical during 2007-08 and will not be accepting senior research students.
Locomotion and thermal biology in lizards
Advisor: Prof. Adolph (Biology)My laboratory studies various aspects of thermal biology and locomotion in lizards. A variety of projects are possible, including the thermal sensitivity of sprint speed; whether there are consistent individual differences in running endurance; how exercise and feeding affect temperature preferences.
Lizard predator-prey relationships
Advisor: Prof. Adolph (Biology)Surprisingly little is known about predator-prey relationships of lizards in their natural environment. This project will involve investigating relationships between the predatory western fence lizard (Sceloporus occidentalis) and its arthropod prey species (e.g, spiders, beetles, and ants). The research will include lab studies and field work at the Bernard Field Station, and will address various questions, such as: locations of lizard perch sites vs. spatial distributions and abundance of prey; temporal patterns of prey activity vs. lizard activity; seasonal variation in prey abundance vs. predator satiation; and the relationship between prey size, predator size, and prey capture success (measured in the laboratory).
Evolution of regulatory elements at a homeotic gene complex in Drosophila
Advisor: Prof. Drewell (Biology)The homeotic genes program the basic body plan during development of the embryo and are important in the evolution of animal morphology. The bithorax complex (BX-C) in Drosophila contains three homeotic genes, which are regulated in the embryo by cis-regulatory elements (CREs), including enhancers and insulators. How the CREs functionally evolve is not clear. The recent publication of the genomic sequences of a number of different Drosophila species has allowed us to examine the underlying evolutionary conservation of the CREs. We will apply bioinformatic and computational approaches to perform cross-species analysis of the CREs. We will also test the functional activity of the CREs using molecular genetic approaches in embryonic transgenic assays.
Morphometric analysis of soft coral sclerites
Advisors: Prof. McFadden (Biology)Species of soft coral are distinguished from one another by the size and shape of their sclerites, microscopic crystals of calcium carbonate that are embedded in their tissues. Sclerites vary greatly in form-like snowflakes, no two sclerites are exactly alike, although they can typically be separated into general shape categories (e.g., clubs, spindles, needles, ovals). Because sclerite shapes vary greatly both within and between individuals of the same species, distinguishing intraspecific from interspecific differences is often difficult. For instance, although genetic markers suggest that the widespread tropical soft coral Sarcophyton glaucum is actually a complex of six distinct species, we have been unable so far to identify differences in sclerite form that reliably distinguish them. This project will involve the development of Fourier-based shape metrics to allow us to quantify and statistically analyze differences in sclerite form among the different genetic groups of S. glaucum. Exploration of available morphometric analytical methods and software will be required.
Molecular systematics of octocorals
Advisor: Prof. McFadden (Biology)Our lab uses molecular tools (primarily DNA sequencing) to study the evolutionary relationships among octocorals, a poorly known group of marine invertebrates that includes 2000+ species of soft corals, sea fans and sea pens. A variety of projects are available for 2007-2008 in conjunction with our NSF-funded Cnidarian Tree of Life grant. Projects may include (1) using ribosomal DNA and mitochondrial gene sequences to construct a phylogeny of all described genera of the morphologically heterogeneous soft coral family Alcyoniidae; (2) using one or more newly-identified single-copy nuclear genes to explore the relationships of all families within the sub-class Octocorallia; or (3) using the rapidly-evolving multicopy ITS rDNA genes or the nuclear SRP54 intron to identify species boundaries in several genera in which species cannot reliably be distinguished morphologically.
Cellular, molecular, biochemical and genetic analysis of phosphoinositide signaling in Arabidopsis
Advisor: Prof. Williams (Biology); see research websitePhosphoinositides are membrane-associated phospholipids that play key regulatory roles in eukaryotic cells, primarily through serving as binding sites for proteins. In plants, the phosphoinositide PtdIns(4,5)P2 transiently accumulates in response to osmotic stress. We use a multifaceted approach to understand the functions of PtdIns(4,5)P2 in plant cells. Mutations in the SAC9 gene in Arabidopsis leads to a constitutive accumulation of PtdIns(4,5)P2 and a constitutive osmotic stress response. One project involves using confocal microscopy to visualize cellular morphologies and responses in wild-type, sac9 mutants and SAC9 overexpressing plants in control and stressed conditions. Another project examines the structure and function of the SAC9 protein in vivo and in vitro , and involves molecular cloning, transgenic plant production and protein purification methods. A final project uses genetics to unravel the regulatory network involved in phosphoinositide signaling and responses.
Asailum Projects
Advisor: Prof. Asai (Biology)Overview. Molecular motors are proteins that are constructed to directly transduce the free energy obtained from the hydrolysis of ATP into work. Dynein is one of the important molecular motors, transporting cellular cargoes along microtubule tracks. In situ, dynein is a complex of one, two, or three heavy chains and several other smaller subunits, including light, light-intermediate, and intermediate chains. The heavy chains contain the motor activity; the smaller subunits are thought to be important for tethering the dynein to the appropriate intracellular location and for the regulation of the dynein activity. Our laboratory studies the structure and function of dynein. Our experimental system is the ciliated protozoan Tetrahymena thermophila because of its superior cell biology and genetics. Experimental approaches include bioinformatics investigation of the Tetrahymena sequenced genome, molecular biology, and fluorescence microscopy. Here are projects that may be senior thesis projects:
25 dynein heavy chains. Until a year ago, the best evidence indicated that Tetrahymena expresses 14 dynein heavy chain genes. The 14 are highly conserved with the dynein heavy chains found in other organisms, and there is good evidence that the 14 heavy chain isoforms are functionally specialized (see Asai and Wilkes, 2004, J. Euk. Micro. 51: 23-29). This view dramatically changed when we searched the recently sequenced Tetrahymena genome; we found 11 new dynein heavy chain (DYH) genes (D.E. Wilkes, H. Watson, and D.J. Asai, in preparation). Quantitative real-time PCR indicated that all 25 (14 "old" and 11 "new") heavy chain genes are expressed and that the 11 new DYH genes encode ciliary dyneins. If dynein heavy chains are functionally specialized, then what are these (too many) heavy chains doing in this simple organism? One approach will be to epitope tag a few of the DYH genes in order to visualize the locations of the heavy chain proteins. Are different dyneins located in different cilia? Or in different places along the cilium?
LC4A and LC4B. The dynein light chain LC4 is intriguing. In Chlamydomonas , LC4 may regulate the calcium sensitivity of the flagellar waveform (Stephen King and co-workers); this hypothesis is based on indirect evidence and has not been directly tested in any system. Tetrahymena expresses two LC4 genes, LC4A and LC4B (Alice Wiedeman, senior thesis, 2005; Erin Heyer, senior thesis, 2007). Does one or the other or both LC4 proteins regulate calcium sensitivity of ciliary activity, manifested as a ciliary reversal in Tetrahymena ? We can approach this problem by making single and double knockdowns of the LC4A and LC4B genes and then testing the cells for swimming behavior in the presence and absence of cations.
DYH2. In Tetrahymena, the depletion of the dynein heavy chain Dyh2 results in cells that are mis-shapened and mis-sized but that retain cilia (Lee et al., 1999, Mol. Biol. Cell 10: 771-784). However, in other systems, Dyh2 is thought to be responsible for retrograde intraflagellar transport, and its knockdown results in cells with short stumpy flagella. Where is Dyh2 in the Tetrahymena cell? We think we can approach this question by expressing an epitope-tagged version of the Dyh2 heavy chain proteins and then subsequently locating the dynein-2 by fluorescence microscopy.
D2LIC. In In other organisms, dynein-2 is responsible for retrograde intraflagellar transport, IFT (see J. Rosenbaum et al.). In Chlamydomonas, disruption of the DYH2 gene results in cells with no or stumpy flagella (see G. Pazour et al., 1999; M. Porter et al., 1999). The dynein-2 complex is simple, comprising only the Dyh2 heavy chain and one accessory protein, dynein-2 light-intermediate chain, D2LIC. The D2LIC subunit is thought to be responsible for linking the Dyh2 motor to the IFT cargo. When the D2LIC gene is knocked out in Tetrahymena , the cells still have cilia, but the cilia are fewer and functionally compromised (V. Rajagopalan, D.E. Wilkes, and D.J. Asai, in preparation). A different approach is to over-express D2LIC or fragments of D2LIC in the hope that the over-expressed protein will act as a "dominant negative" mutation (Nicole Bennardo, senior thesis, 2006; Jon Hetzel, senior thesis, 2007). The project will continue this work and also over-express epitope-tagged versions of D2LIC in order to locate the protein in cells.
LC1. Dynein light chain-1 is unique in that it appears to bind to the motor domain of one of the dynein heavy chains, instead of the tail domain where the other light chains bind. By virtue of its location, LC1 may regulate dynein motor activity. We can approach this question by (i) disrupting the LC1 gene and assessing the effect of the loss of the LC1 on ciliary motility, and (ii) epitope-tagging LC1 in order to locate it in cells and in isolated dynein.
DNA repair in chromatin
Advisor: Prof. Haushalter (Chemistry & Biology)Researchers in my lab use biochemical techniques to study the mechanism employed by DNA glycosylases, a class of DNA repair enzymes that recognize and excise damaged bases from the genome. DNA glycosylases employ a "base-flipping" mechanism in which the Watson-Crick structure is locally distorted and the damaged base is inserted into an extrahelical pocket in the DNA glycosylase active site. While the base-flipping mechanism for DNA glycosylases acting on naked DNA has been well established, it is not known how the need to base-flip the DNA is reconciled with the structure of DNA assembled into nucleosomes, the fundamental repeating unit of chromatin. Kinetic and structural studies of DNA glycosylases acting on chromatin substrates will increase our understanding of how the structure of the nucleosome modulates DNA repair.
Rapidly evolving elements in the lineage leading to anthropoid primates
Advisor: Prof. Bush (Biology)Humans possess numerous behaviors absent in other animals. Such behavioral specializations reflect anatomical, physiological and ultimately genetic modifications which occurred during the course of primate evolution. We are using a likelihood ratio test approach to identify noncoding elements which have undergone positive selection during primate evolution. We scan whole genome multiple alignments looking for regions where a large number of substitutions have occurred in a particular lineage. In previous work we focused on the terminal human lineage, and the stem lineage leading to primates. With the newly available 2X galago genome we can look for elements which evolved rapidly in one of the internal branches of the primate tree. The interest here is to find regions which were involved in the evolution of anthropoid primates (that is new world monkeys, old world monkeys, and apes). This is a computational project, and would be best for someone who is enthusiastic about programming. Please email Prof. Bush (bush@uchicago.edu) with any questions.
Evolution of genomic word composition
Advisor: Prof. Bush (Biology)The field of molecular evolution provides many examples of the principle that molecular differences between species contain information about evolutionary history. One case can be found in the frequency of short words in DNA: more closely related species have more similar word compositions. Of particular interest to us is the rate at which word frequencies change over evolutionary time. Slow changes reflect the presence of purifying selection and functional constraints in the genome. In previous work, we examined word frequency changes in a number of animal genomes, focusing on particular word sizes while statistically removing the effects of smaller constituent words. One puzzling result was the following. In the many millions of years since the pufferfish and the zebrafish diverged, it appears that 8 bp words have been under greater constraint in pufferfish, while 4 bp words have been under greater constraint in zebrafish. This difference likely reflects some underlying functional differences in their genomes. We would like to figure out what those are. The project will involve scanning available animal genomes for similar cases. These can then be studied in detail by restricting the analysis to particular categories of sequence or particular genomic regions. For selected species we will also examine multiple alignments in order characterize the rates at which one word converts to another. This is a computational project, and would be best for someone who is enthusiastic about programming. Please email Prof. Bush (bush@uchicago.edu) with any questions.
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