Research Projects Available at HMC 2013-2014

NOTE: Prof. Bush will be on leave during 2013-14 and will not be accepting senior research students

Matrix Models of Lizard Populations

Advisor: Prof. Adolph

Many field studies have determined how survival and reproductive rates of lizards vary with age. These data can be used to construct matrix models of population dynamics, which in turn can be used to explore interesting ecological, conservation and evolutionary questions.  This project will involve building and analyzing computer models of lizard populations using published life history data.

Evolution of Trade-Offs

Advisor: Prof. Adolph

A central concept in evolutionary ecology and physiology is that there are inevitable trade-offs between certain kinds of traits.  This computer modeling project will simulate the evolution of traits to determine the conditions under which trade-offs evolve.

Lizard Foraging Ecology

Advisor:  Prof. Adolph

Western fence lizards are ambush predators that feed on a variety of insects and spiders.  This field project will study foraging behavior of lizards at the Bernard Field Station.   We will examine how food availability, temperature and other ecological factors affect foraging behavior and success.  This project could also include some mathematical modeling of optimal foraging behavior.

Lizard Locomotion

Advisor: Prof. Adolph

Lizards experience a variety of temperatures and habitat structures in their natural environments.  This laboratory project will measure lizard locomotor performance across different conditions (e.g., temperature, slope).

The Role of the Global Regulatory Protein RpoS in Shaping the Transcriptome

Advisor: Prof. Stoebel

Bacteria regulate the transcription of their genome in response to to their external environment. Global regulatory proteins shape these patterns of transcription, regulating hundreds or thousands of genes. Of particular interest to my lab is the protein RpoS, which regulates over 10% of the genes in the E. coli genome in response to stresses like starvation, low temperature, or high osmolarity. Different sets of genes are regulated by RpoS under these conditions. How can one protein regulate different sets of genes under different conditions?

One clue comes from the observation that the amount of RpoS that cells produce varies from stress to stress. We aim to test the hypothesis that genes respond differently to the concentration of RpoS in the cell.

Projects are available that test this hypothesis using a variety of approaches. Depending on your interests and skills, you might analyze existing RNA-seq data (and potentially generate more) to define the entire RpoS regulon; build and use a system to measure how individual promoters respond to variation in the amount of RpoS produced by cells; and create synthetic promoters and specific mutants to understand rules for why some promoters are more sensitive than others to levels of RpoS. Other approaches and projects may be available for students with specific interests. If this sounds like fun, come talk!

Therapeutic Small RNA Delivery and Processing

Advisor: Prof. Haushalter

Students in the Haushalter lab design, construct, and evaluate vectors for delivering therapeutic small RNA molecules.  A theme of recent projects has been building chimeric RNA molecules that combine one or more therapeutic modalities onto a tRNA template.  For example, short hairpin RNAs targeted against HIV have be inserted into the 3′ trailing sequence of a pre-tRNA expressing construct and tested for their ability to knockdown target genes important for HIV replication.  Interested students should contact Prof. Haushalter for additional information.

Discovering Genetic Loci That Influence Food Preference Behavior

Advisor: Prof. Glater

A central question in neuroscience is understanding the mechanisms by which genes influence behavior.  In humans, differences in genes can cause or modify susceptibility to neurological disorders.  However, many common inherited diseases have an unknown and likely complex genetic basis.
We study how genes influence the food choice behavior of the free-living nematode,Caenorhabditis elegans.  The free-living soil nematode Caenorhabditis elegans uses olfaction to discriminate among pure volatile chemicals and among different kinds of bacteria, which are its major food source.  Several wild strains of C. elegans isolated from various geographic regions exhibit different bacterial preference behavior.  We will study the genetic basis of these differences in innate bacterial preferences.  We will address questions such as how many genetic loci are likely involved and whether there are interactions between these loci.  This project will involve using molecular biology, genetics, and behavioral assays.

The Neuronal Basis of Food Choice Behavior

Advisor: Prof. Glater

How does the nervous system drive behavior? We know little about how C. elegansrecognizes and discriminates among complex, volatile odors, such as those released by its food, bacteria.  This project is to determine the sensory neurons involved in discriminating among several different species of bacteria that are likely to be found in the natural habitat of C. elegans.  To do this, we will use genetic tools to inhibit the function of specific sensory neurons and then determine the effects of these manipulations on bacterial preference.  In addition, we will measure the response of neurons to different species of bacteria using the genetically-encoded fluorescent calcium indicator (G-CaMP).  G-CaMP measures changes in cellular calcium levels that correlate with neuronal activity.  This project will involve using molecular biology, genetics, microscopy and behavioral assays.

Molecular and Bioinformatic Analyses of the Mitochondrial mutS DNA Repair Mechanism in Octocorals

Advisor: Prof. McFadden

Unlike almost all other metazoan animals, the mitochondrial genomes of octocorals (soft corals and sea fans) evolve at rates that are slower than those of the nuclear genome. One hypothesis for this difference is the presence in the octocoral mt genome of mtMutS, a gene that codes for a DNA mismatch repair protein.  This gene, believed to have been acquired by horizontal gene transfer from a giant virus, evolves rapidly by a process that includes many insertions and deletions of amino acids; as a result, the mtMutS genes of different octocoral genera and families differ greatly in sequence and presumably also in function and efficiency.  Two projects are available for 2013-14 to explore the relationship between mtMutS and evolutionary rate in octocorals.  These include: (1) Obtaining complete sequences of mtMutS for octocorals in families with different apparent rates of mt gene evolution to (a) identify conservative vs. variable regions of the gene and (b) infer bioinformatically those regions of the gene most important for its repair function. (2) Obtaining partial or complete mitochondrial genome sequences for one or more of the species we suspect lack a functional mtMutS protein to determine the influence of mtMutS on mitochondrial gene order.

Using Computational Genomics to Document Hybridization Among Species of Soft Corals

Advisor: Prof. McFadden

For many decades, hybridization has been known to play an important role in the evolution of plants.  More recently, it has been suggested that hybridization may also be common among corals, but this hypothesis has been difficult to confirm experimentally or genetically.  Alcyonium digitatum and Alcyonium sp. A are two closely related species of soft coral that co-occur in Britain.  Although these two species reproduce by very different mechanisms, some morphological and genetic evidence suggests that they may occasionally hybridize under natural conditions.  In collaboration with researchers at U. Hawaii, we are using next-generation sequencing protocols to obtain genomic data for A. digitatumA. sp. A, and a number of putative hybrid individuals.  This project will involve computational analysis of the genomic data, primarily screening loci across the genome for single-nucleotide polymorphisms (SNPs) that distinguish parental species, and subsequently determining if putative hybrids share alleles with both parents.  Adaptation of existing computational pipelines or development of novel pipelines will be required.

Neural Control and Biomechanics of Human Walking:  Toe- vs Heel-Runners

Advisor: Prof. Ahn

Humans use two motor control patterns in their lower limb muscles during walking.  Half the population (MG-biased) walks while activating their medial calf muscle (MG) much more strongly than their lateral calf muscle (LG).  The other half of the population walks while activating both calf muscle equally (unbiased).  An MG-biased motor control pattern always correlates with MG muscles.  In sedentary walkers, an MG-biased motor control pattern correlates with shorter muscle moment arms (heel length) and increased variability in plantar pressures on the medial side of the foot.  In recreational runners, however, an MG-biased motor control pattern correlates with longer muscle moment arms.  The senior research student will examine whether toe-runners and heel-runners show similar muscle activity and biomechanics or whether the different styles of running correlates with differing neural control and biomechanics during the seemingly simple behavior of walking.

Neural Control of Tarantula Locomotion

Advisor: Prof. Ahn

Tarantulas locomote using an elaborate hydraulic system. Not only do they lack extensor muscles in 2 joints in each of their 8 legs, but they also they maintain very high internal pressures.  By compressing their body segments, they push hemolymph into their limbs, which further increases the internal pressure and extends the jointed limb segments. Despite the seemingly coarse hydraulic system, tarantula behaviors can range from incredibly fine motor during web-weaving to sprinting, pouncing on, and capturing prey.  This project will measure and quantify the recruitment patterns of the muscles controlling hydraulic extension mechanism of their legs while running at different speeds.