Summer 2012

The Harvey Mudd Biology Department has a number of summer research positions available.  Most of these are funded by our grant from the Howard Hughes Medical Institute (HHMI).  Applications for these summer positions are due February 24.  (See link below to download the application.)

All Biology Summer Research Students are expected to work full-time for 10 weeks during the summer. The exact starting and ending dates are stipulated by the faculty advisor. Depending on the source of funding, students may also be required to participate in other activities, such as weekly seminars by guest speakers. Stipends for 2012 HMC summer research students are expected to be approximately $4,400 for rising sophomores, $4,500 for rising juniors and $4,600 for rising seniors.

Available Projects
Available projects for Summer 2012 are listed below.

Application Process

1. Pick up a summer research application from Molly in the Biology office, or download the PDF.

2. Look at the list of available projects and mentors, and talk to the relevant faculty mentor(s) about the project(s) that interest you.

3. Turn in your research application to the Biology office by Friday, February 24, 2012. We will try to notify students about positions by Friday, March 9th.

Financial Support for Summer Research
Summer research students in the Biology Department are supported by funds from a variety of sources. The Harvey Mudd Biology Department has been the fortunate recipient of funds to endow three summer research fellowships:

• The Emily H. Mudd Summer Research Fellowship—established with a bequest from Emily Mudd—supports an Emily Mudd Research Fellow each summer
• The Munzer Summer Research Fellowship—established with a generous donation from Mr. and Mrs. Rudolph J. Munzer—supports a Munzer Summer Research Fellow approximately every two out of three summers
• The William K. Purves Summer Research Fellowship—established with a lead gift and additional donations from many HMC faculty and biology alumni to honor Dr. Bill Purves, the founding member of the HMC Biology Department, on his retirement—supports a Purves Summer Research Fellow approximately one out of three summers.

In addition, several grants and awards to Harvey Mudd College can support summer research students in the Biology Department. Funding is currently available from grants to HMC from the Howard Hughes Medical Institute and the Merck/AAAS Undergraduate Science Research Program. Students and faculty interested in Environmental Biology may also apply for funding from the HMC Center for Environmental Studies.

Please contact Prof. Drewell at drewell@hmc.edu if you have additional questions.

Projects available for Summer 2012:

Effect of the Neural Control on the Biomechanics of Human Walking
Advisor: Prof. Ahn (Biology)

How variable is the neural control and biomechanics of walking between individuals?  In previous work, we showed humans use two motor recruitment strategies while walking.  About half the people examined recruit their two major calf muscles equally ('unbiased').  The other half of those examined recruit their medial gastrocnemius (inner calf) muscles much more strongly than their outer calf muscles ('MG-biased').  Using a foot pressure measurement system, we will test the hypothesis that MG-biased individuals pronate their feet during walkiing much more strongly than unbiased undividuals.  This project will involve using a high-speed motion-capture system, electromyography, a foot pressure system, and ultrasonography on human subjects.

Number of positions: 3

Computational studies of evolution 
Advisor:  Prof. Bush (Biology)

I'm looking for one or two students interested in working in one of several areas. Brief descriptions are included below.  Those interested should talk more with me.

- The evolution of allosteric cooperativity. This project involves building models of enzymes, metabolism and how they evolve.

- Analysis of methylation data in the bee. This is a collaboration with Prof. Drewell which involves analyzing high throughput bisulfate sequencing data.

- Identification of horizontal transfer events in E coli. This is a collaboration with Prof. Stoebel, and involves comparing the genomes of 88 strains of E. coli to find horizontal transfer events.

Number of positions:  2

Elucidating the function of an F-Box Protein in food choice behavior of Caenorhabditis elegans
Advisor: Prof. Glater (Biology)

A central question in neuroscience is understanding the mechanisms by which genes influence behavior.  We study the genetic basis of the innate olfactory preferences of the free-living nematode, Caenorhabditis elegans.  In previous work we identified a gene that modifies the innate preferences of C. elegans for different species of bacteria, its major food source.  

The gene, f-box-c protein 5 (fbxc-5), is a member of a recently evolved F-box protein family, but its function is unknown.  F-box proteins are components of the ubiquitin-proteasome system (UPS), a pathway that mediates the degradation of proteins.  Dysfunction of the UPS has been strongly implicated in a number of neurological disorders, including Alzheimer’s disease, Parkinson’s disease and autism, but little is known about how the UPS affects neuronal function.  

One focus of our research is to understand how fbxc-5, a component of the UPS, affects neuronal function in C. elegans.  This summer we will test the hypothesis that the FBXC-5 protein changes bacterial preference behavior by modifying the function of sensory neurons.  This project will involve using molecular biology, microscopy, and behavioral assays.

Number of positions: 2

Investigating gene regulatory networks during animal development
Advisor: Prof. Drewell (Biology)

The animal embryo is a mass of uniform cells that becomes a complex, segmented and highly organized structure of differentiated cells through the process of development. This vital process is controlled by networks of developmental genes interacting with each other on the molecular level.  In this project we will utilize a combination of computational, genetic and molecular approaches to examine the function of DNA sequences within evolutionarily conserved regulatory modules. These findings have important implications for our understanding of transcription, cell signaling and epigenetic regulation during development and across diverse animal species ranging from insects to humans.

Number of positions: Up to 6

Effects of variation in levels of RpoS, a global regulatory protein in E. coli
Advisor: Prof. Stoebel (Biology)

Bacteria respond to their changeable environments by modifying levels of gene expression. For example, E. coli responds to changes in temperature, osmolarity, or nutrient availability by the up-regulation of a distinct set of genes. The master regulator of this program is the alternative sigma factor RpoS, which recruits RNA polymerase to transcribe a distinct set of genes. E. coli produces different levels of RpoS in response to different stresses.  Very little is known about how this quantitative variation in protein abundance affects programs of gene expression and consequently physiology, growth and survival. We have developed a system that allows us to vary the amount of RpoS that is produced in a single environment, and we are now ready to use it to test hypotheses about the effect of this variation on transcription.

Research projects in the lab may involve creating knock-outs and performing other genetic manipulations in E. coli, improving our Western-blot based assay for RpoS levels, measuring effects of changes in RpoS concentration on transcription with reporter gene assays and QPCR, and exploring transcriptome-wide effects using microarrays.

Number of positions: Up to 4

The evolution and expression of frz, a horizontally acquired operon in E. coli
Advisors: Prof. Stoebel (Biology)

Horizontal transfer, the movement of DNA from one strain/species to another, is an important process in bacterial evolution. It is responsible for the evolution of new pathogens, the spread of antibiotic resistance, and the creations of important agricultural symbionts. We have begun studying the frz operon, a set of metabolic genes that have been horizontally acquired in some strains of E. coli. We know that the acquisition of these genes increase fitness in some environments. We would like to know if this is true of all strains of E. coli, or if only some strains are able to benefit from the gain of this operon. In addition, we would like to understand how variation in how different strains transcribe frz influences the fitness benefit of gaining the operon.

This project may involve measuring bacterial fitness, molecular cloning and transfer of frz, and the construction and use of a reporter gene assay to frz.

Number of positions:  Up to 4

Optimizing the sequence of tRNA-shRNA chimeras for anti-HIV gene therapy
Advisor: Prof. Haushalter (Chemistry & Biology)

The long-range goal of this project is to develop a gene therapy approach to treating HIV-AIDS.  As an intermediate goal, students in the Haushalter lab will synthesize and characterize variants of a tRNA-shRNA chimera molecule that can be introduced into target cells and has been designed to downregulate CCR5 expression.  By performing site-directed mutagenesis of the acceptor stem of the tRNA portion of the molecule, students will investigate the effect of perturbations in the structure of the tRNA acceptor stem on the processing and downstream activity of the short-hairpin RNA, as measured by dual-luciferase functional assays.

Background: Bio111 (or equivalent) is desirable, but not required.

Number of positions:  2

Effects of energy intake on reproduction in desert night lizards
Advisor: Prof. Adolph

The reproductive success of desert night lizards in the field is highly correlated with winter rainfall.  This is probably due to the effect of rainfall on insect abundance, but this has not been demonstrated.  In this project, we will test this connection in the laboratory, by giving female night lizards different amounts of food and then measuring the number and size of their offspring.

Background: Bio 108 preferred; interest in animal ecology.

Number of positions:  1

Biophysics of water uptake in lizard eggs
Advisor: Prof. Adolph (collaboration with Prof Orwin in Engineering)

Lizard eggs take up water during incubation in the soil.  In this ongoing project, we are measuring the properties of eggs that influence water uptake, and using this information to construct a mathematical model of water uptake.

Background: Interest in animal physiology; previous experience with lizard egg research preferred.

Number of positions:  1-2

The Effect of Stretching on Drug Transport Across Human Skin
Advisor: Prof. Lape (Engineering)

Human skin provides a two-way barrier that prevents potentially harmful chemicals or diseases from entering the body while slowing water as it exits the body. These barrier effects are mainly due to the brick-and-mortar structure of the outer-most layer of skin, the stratum corneum (SC). The SC is composed of many corneocyte “bricks” linked together by corneodesmosomes in a lipid bilayer continuum “mortar.” In order to reach the bloodstream, any molecule on the surface of the skin must pass through the SC. The ability to understand and modify transport across the SC is therefore crucial for developing new transdermal drug delivery methods and setting dermal exposure limits for toxins. While there is evidence for some transcellular transport across the corneocytes, the majority of the transport across skin is thought to occur intercellularly (i.e. in the lipid bilayer continuum that surrounds the corneocytes). Because the dimensions and nature of the lipid bilayer dictate drug and toxin transport and water loss across skin, a change in the lipid bilayer size and structure would greatly affect this transport. We believe that just such a change must occur upon uniaxial extension of the skin, a viscoelastic tissue: as evidenced by the significantly higher Young’s modulus (a measure of stiffness) of the corneocytes alone (~450 MPa) as compared to intact SC (~ 3-210 MPa), it is likely that extension of the SC results in a major alteration in lipid bilayer dimensions. To examine these effects, we are undertaking in vivo (human subjects) testing of drug transport across stretched and non-stretched (control) sites of skin. We are also using finite element modeling to determine what proportion of changes in transdermal transport is due to geometry only versus geometry and changes to lipid bilayer structure.

Number of positions: 2

Controlling the Cell Phenotype in a Tissue-Engineered Corneal Model
Advisor: Prof. Orwin (Engineering)

Corneal keratocytes alter their expressed phenotype in response to wound healing. It has been shown that these phenotypic changes have an effect on the transparency of the tissue. Cells expressing α smooth muscle actin are present during wound healing when the cornea is hazy, while normal keratocytes in the cornea express high levels of two soluble proteins: transketolase (TKT) and aldehyde dehydrogenase 1 (ALDH 1). RT-PCR, Western blots and immunohistology are being used to assess levels of these three proteins in cells grown in co-culture with endothelial cells in two dimensional and three-dimensional culture environments.

Effect of Bioreactor Culture on Cell Phenotype in a Tissue-Engineered Corneal Model
Advisor: Prof. Orwin (Engineering)

Corneal keratocytes alter their expressed phenotype in response to wound healing. It has been shown that these phenotypic changes have an effect on the transparency of the tissue. Cells expressing α smooth muscle actin are present during wound healing while the cornea is hazy, while normal keratocytes in the cornea express high levels of two soluble proteins: transketolase (TKT) and aldehyde dehydrogenase 1 (ALDH 1). RT-PCR, Western blots and immunohistology will be used to assess levels of these three proteins in cells grown under applied stress in our corneal bioreactor.  In addition, finite element modeling and strain characterization of the bioreactor system will be performed in order to optimize the design.

Recreating the Microstructure of the Corneal Stroma
Advisor: Prof. Orwin (Engineering)

Our lab has been using type I collagen sponges as the scaffold for our tissue-engineered cornea. We have shown these sponges to be a good substrate for the growth of all three corneal cell types. The structure of these sponges can be visualized in the SEM and OCM and large collagen sheets can be observed. These structures could be contributing to light scatter in the samples. We have recently used electrospinning as a method for creating highly aligned, small diameter type I collagen fibers, which would more accurately reflect in vivo corneal microstructure.   This project will involve assessing cell response to aligned collagen fibers as well as incorporating other collagen types and proteoglycans into the aligned mats to more closely mimic the native cornea.

Cell Delivery System for Traumatic Brain Injury
Advisor: Prof. Orwin (Engineering)

Our overall project focuses on a cell delivery system to treat traumatic brain injury using novel scaffold materials and human adult stem cell populations. Our approach is novel in that we propose to differentiate human adult stem cell populations in three-dimensional culture in a scaffold specifically designed to recreate the natural microenvironment of neural cells.  The cells will be delivered in high density attached to scaffolds optimized for cellular growth and differentiation.  One potential summer research project involves culturing adult stem cell populations in two dimensional and three dimensional culture environments with a variety of growth factors to determine optimal differentiation of the cells along neural pathways.  Differentiation is assessed via immunofluorescence and Western blotting.  We hope to incorporate gene chip analysis into this project in the near future.  A second potential research project involves designing new composite collagen/chitosan matrices by gellation or electrospinning and testing them for use in our projects.  We are in the process of developing numerous testing strategies, including: cell viability, antibacterial properties, diffusion studies, degradation studies, and mechanical properties.

Computational Biology:  The Cophylogeny Reconstruction Problem
Advisor:  Prof. Libeskind-Hadas (Computer Science)

This research addresses the problem of determining the similarity or difference between pairs of phylogenetic trees.  For example, the trees might be those of a host and a parasite species and we wish to study likely scenarios for the coevolution of these species.  Alternatively, one tree could be a species tree and the other a gene tree and we wish to explore the duplication, loss, and transfer events that allow us to best reconcile the gene tree with the species tree.  This problem is computationally hard (NP-complete), but we have developed algorithms that find good solutions and have implemented these algorithms in our Jane software system.  The objectives of this project are to develop and implement new algorithms that allow us to capture more complex scenarios.

Number of positions: 2

Mathematical and Experimental Characterization of Collective Behavior
Advisor: Prof. Bernoff (Mathematics)

Many biological organisms aggregate, including fish, birds, mammals, insects, zooplankton, and bacteria. These groups (swarms, flocks, schools, herds, etc.) often arise as social phenomena, without direction from a leader or external cues such as food. Cohesive group structure emerges from evolutionarily-programmed rules, e.g. visual, auditory or olfactory attraction to members of the same species, which confer benefits such as protection and mate choice.  Prof. Bernoff and Prof. Chad Topaz at Macalester College have an ongoing undergraduate research group studying these swarming behaviors. There are two opportunities to work in our group this summer:

1) Mathematical Modeling of Heterogeneous Swarms.  Most swarm models assume that all individuals are identical and interchangeable but in nature individuals are heterogeneous. For example, if one assumes that visual attraction to larger individuals is stronger in a popular model of fish schools, larger individuals drift to the swarms periphery and smaller individuals drift to the interior. This behavior is observed in nature and biologically can be interpreted as protection of juveniles.  This project will be a combination of biological modeling, numerical simulation, and mathematical analysis of models of swarm heterogeneity.

2) Motion Tracking of Aphids. The Topaz Lab has the ability to motion track aphids and has begun collecting data on individual aphid movements and aphid interactions; our hope is to both improve the experimental apparatus and to expand our aphid motion database. Our goal is to then use this data to refine and validate a model of aphid motion and interaction. This project will be a combination of data collection, data analysis, model building, and statistical validation.

This project will be conducted at Macalester College in Minnesota. 

Number of positions: 2 

Dynamics of bacterial aggregates

Advisor: Prof. Byrne (Mathematics)

A biofilm is an aggregate of microorganisms that adheres to a surface.  Aggregates can shed from biofilm to become suspended in the surrounding fluid. Prof. Byrne's research models bacterial aggregates commonly found in hospitals that can infect the bloodstream of critically-ill patients. This summer, 1 or 2 students majoring in mathematics, biology, Math/Bio, or Math/CS will be hired to work on these problems. Computation, mathematical modeling, or experiments are all possible aspects of this project.  For more information, contact Prof. Byrne.