2005 Rogers Science Program

Faculty Abstracts

Biology

Kellar Autumn, "Contact dynamics of gecko adhesive nanostructures"
Geckos climb using millions of adhesive setae. Our goal is to reveal how natural dry adhesives function, and how the performance of fabricated adhesives and climbing robots can be enhanced. Previously, we discovered that setae stick by van der Waals force and are self-cleaning. This summer we will study friction and adhesion dynamics in natural setae on rough and compliant surfaces, and on biomatierals. Students will have the opportunity to work with Prof. Autumn, Dr. Geisler, and our research technicians with the goal of developing skills and experience, focusing graduate school goals, and producing publishable results.
Prerequisites: Preference for students with coursework in Physics who are grad-school bound and willing to make a year-long commitment to research in our lab group. Solid quantitative skills required.

Greta Binford, "Molecular evolution of the toxic enzyme sphingomyelinase D in venoms of brown spiders (Loxosceles)."
Brown spider (Loxosceles) bites cause dermonecrotic lesions in human tissues. An enzyme in these venoms, sphingomyelinase D (SMD), is central to lesion formation. The genus Loxosceles has 100 species from the Americas, Africa and Mediterranean Europe. We will use molecular markers to estimate relationships among species of brown spiders and their relatives. We will also sequence cDNAs of SMD from a range of species related to the brown recluse and reconstruct patterns of molecular evolution of these proteins. Results will help direct research toward understanding the molecular evolution of the unique enzyme SMD and improving treatment and diagnosis of bites.
Prerequisites: Bio. 390 preferred but not required.

Greg Hermann, "Investigating the biogenesis of lysosomes in a multi-cellular animal."
Lysosomes are membrane bound organelles that function as major degradative sites within cells. While much is known regarding the biochemical activities of lysosomes, the processes involved in their assembly and maintenance remain poorly understood. An understanding of these processes is important since the abnormal release of lysosomal contents is associated with a variety of human diseases including, Alzheimers, arthritis, and cancer. We are characterizing the function of two genes necessary for the assembly and stability of lysosomes in the model organism, Caenorhabditis elegans. Our work will focus on the phenotypic analysis and cloning of these genes.
Prerequisites: Bio 151 or 200; Prefer Bio 311/312 or Bio 361.

Greg Hermann – "Investigating a monoclonal antibody that recognizes late-stage apoptotic cells in Caenorhabditis elegans."
Cancer, AIDS, and many neurodegenerative diseases result from the misregulation of cell suicide (apoptosis). The nematode C. elegans has emerged as a powerful system to investigate this evolutionarily conserved process. While many participants in the initiation of cell death and corpse engulfment have been identified in C. elegans, little is known about the cellular processes controlled by these genes. We are studying a monoclonal antibody that binds to epitope expressed late in the apoptotic program, possibly localized to phagolysosomes. We will carry out experiments to characterize the spatial expression of the epitope and identify the molecule bound by the antibody.
Prerequisites: Bio 200; Prefer Bio 311/312 or Bio 361.

Deborah Lycan, "Ribosome assembly and export "
The eukaryotic ribosome is the largest and most complex RNA:protein machine assembled in higher cells. It is composed of some 80 ribosomal proteins and 3 ribosomal RNAs. Assembly of the ribosome has been analyzed most extensively in the unicellular eukaryote, the yeast S. cerevisiae. Ribosome assembly is a highly complex and coordinated process that occurs mostly in the nucleolus from premade protein components that must be imported from the cytoplasm. The two subunits are assembled independently and exported through nuclear pores at rates that can exceed 40 new ribosomes/sec. Based on the composition of several ribosome precursor complexes, more than170 proteins are predicted to participate in ribosome biogenesis. So far, the majority of the characterized factors have been implicated in rRNA modification and maturation, but recent work has identified some factors with other roles; in assembly or export. Nonetheless, it would be fair to say that we are largely ignorant of the details surrounding eukaryotic ribosome assembly and export. For example, we do not know the order of protein addition or how this is controlled, how accessory factors regulate or facilitate the assembly process, which steps are under regulatory control (ribosome biogenesis is linked to the growth state of the cell and to environmental stress conditions), how subunits are exported and whether export is regulated to ensure that only fully functional subunits leave the nucleus for the cytoplasm.

In my lab we are studying three proteins with roles in the assembly of the small 40S subunit; RpS3, Yor1 and Lov1. RpS3 is a structural component of the mature 40S subunit, and it interacts with both Yor1 and Lov1. Cells lacking either Yor1 or Lov1 are hypersensitive to protein synthesis inhibitors and produce only half the normal number of 40S subunits. These cells are also defective in rRNA processing, which could be the cause or the consequence of other defects in ribosome assembly or export. Students in my lab have shown that Lov1 shuttles between the nucleus and cytoplasm via the exportin protein, Xpo1, and that RpS3 export is reduced in cells lacking Lov1. Our working model is that Lov1 may be the long sought adapter for the export of 40S subunits from the nucleus. Work this summer will be directed towards testing this model. Experiments in my lab involve genetic, biochemical, molecular and cell biological techniques.
Prerequisites: Some experience with cell and colecular techniques will be helpful. Completion of Bio 200, Bio 361 or Bio 321 recommended by not required.

Chemistry

Louis Kuo , "Hydrogenation chemistry with organometallic molybdenum complexes "
This project explores using a class of organometallic complexes called metallocenes (metal=molybdenum) to carry out two types of environmentally-friendly transformations. In one transformation we seek to make various molybdenum metallocenes to hydrolyze phosphate neurotoxins (i.e. pesticides) in aqueous solution. This will be a project that is intensively on synthesis, for most of these target compounds have not been made before. In the second project we will use these metallocenes to carry catalytically hydrogenate carton-nitrogen double bonds. Such a transformation plays a valuable role in the synthesis of various nitrogen-based pharmaceuticals and metallocenes have not been employed for this reaction in a catalytic fashion.
Prerequsites :Chem 220 (full year of Organic chemistry). 

Niko Loening, Project 1: Pulse Sequence Development for Nuclear Magnetic Resonance Spectroscopy
Nuclear magnetic resonance (NMR) spectroscopy is a fundamental instrumental technique that has seen application to a wide range of problems, including chemical analysis, screening drug targets, the determination of protein structures, understanding fluid dynamics, and medicine. In comparison to other spectroscopic techniques, NMR has drawbacks in that it is relatively insensitive and advanced experiments can take a long time to complete. Our research this summer will focus on the development of techniques that can be used to reduce the experiment time and increase the sensitivity of NMR spectroscopy, including the design of new experiments, physical modifications of the instrument, and the study of advanced processing techniques for analyzing NMR data.
Prerequsites: A solid background in quantum mechanics (Chem 320, Phys 321 or equivlaent; Mathematics through Calc I, experience with computer languages (preferably C/C++), basic lab skills.

Niko Loening, Project 2: Identification of the Autofluorescent and Optically Active Material Present Within Caenorhabditis elegans Intestinal Lysosomes
Soil nematodes, including C. elegans, have been known for over a century to contain autofluorescent and optically active intestinal material. Based on these characteristics, past researchers have suggested that the material is composed of tryptophan catabolites, retinol, or lipofuscin/“age pigment”. Although the characteristics of this material indicate the presence of chiral molecules and of delocalized electron bonds, nothing else is known about the specific chemical composition. We will work in collaboration with Dr. Greg Hermann’s group to isolate this material, and then using a variety of chromatographic and spectroscopic techniques to identify the chemical composition of the material.
Prerequsites: Mathematics through Calc I, Instrumental chemistry skills such as those gained in Chem 220, Chem 450, Chem 366 and Chem 365, experience handling biological samples, coursework in biology/biochemistry/molecular biology.

Niko Loening, Project 3: The Development and Characterization of Chemical Shift Thermometers for Nuclear Magnetic Resonance Spectroscopy
The goal of the proposed research is to design improved chemical-shift thermometers (CSTs) for use in solution-state nuclear magnetic resonance (NMR) spectroscopy. Our plan is to use paramagnetic molecules as CSTs, and then to encapsulate them within dendrimers or micelles so that they do not adversely affect the NMR spectrum. The proposed development of better CSTs will allow more accurate quantification of physical parameters by NMR spectroscopy and help solve problems of sample stability.
Prerequsites: Mathematics through Calc I, synthetic chemistry skills, preferably some background in quantum mechanics (Chem 320, Phys 321 or equavalent).

Niko Loening, Project 4: Structural Studies of Gaussia Princeps Luciferase
The goal of this project is to use solution-state NMR spectroscopy to determine the structure of Gaussia Princeps luciferase (Gluc). Gluc is a 185 amino acid (19.9 kD) protein that catalyzes the oxidative decarboxylation of coelenterazine, producing coelenteramide and 470 nm light in the process. Like other luciferases, Gluc is of interest because of its applicability to visualizing biological processes and disease detection, and knowledge about its structure will help in site-directed mutagenesis studies directed towards improving its applicability. The goal of this project is to express doubly-labeled (13C and 15N) GLuc and begin determining the 3D structure.
Prerequsites: Experience generating and working with protein samples, coursework in biochemistry/molecular biology (preferably structual biochemistry, mathematics through Calc II.

Computer Science

Peter Drake, " Life and Death in the Game of Go"
We continue work on a computer program to play the classical Asian game of Go. Creating a strong Go program is considered a "grand challenge" in the field of artificial intelligence. Go involves many problems that arise in other areas of AI, including planning, resource allocation, attention, and reasoning under uncertainty.

Human players often consider each region of the board separately. The fate of some regions can be evaluated locally. This summer's research focuses on these "life and death" situations: whether an isolated group of pieces can be captured or rendered safe.
Prerequisites: Necessary: Must have taken CS 172 and have rudimentary knowledge of the rules of Go. Any knowledge or experience in artificial intelligence or game theory is
also helpful.

Jens Mache, "Computer security and Internet research"
The Internet, computer networks and distributed systems are fascinating topics. Many challenges remain, including security, peer-to-peer algorithms, grid services, sensor networks, distributed storage and streaming media. This summer, we will investigate important performance, scalability and robustness issues. This internship includes studying existing systems, writing software and experimentation with various designs and algorithms.
Prerequisites:: Computer Networks (CS 393), Computer Architecture (CS 377) and Algorithms (CS 383) are desired.

Math Sciences

Yung Pin Chen, "Locating CpG Islands with Statistical Significance"

Analyzing biological sequences has become a very important part in genome research. Based on some preliminary work done in last two summers, we like to continue and focus on the problem of locating CpG islands. CpG islands refer to short DNA stretches that are rich in the CG dinucleotides. CpG islands can be used as markers to identify genes. Are there any methods that can tell whether a short DNA stretch stands out as a CpG island? Can we quantify the statistical significance of the standout? In addition to investigating these questions, we also want to develop statistical methods for identifying haplotype blocks.

Prerequsites: It is essential that participants have strong problem-solving skills. It is preferred to have some backgrounds in genetics (Bio 151), molecular biology (Bio 200 or Bio 311), computer programming (CS 171), and statistics.

Physics

Tom Olsen, "Simulations of Fluid Flow in a Modified Taylor-Vortex System and Characterization of its Chaotic Behavior "
Taylor-Couette Flow is the motion of a fluid between two concentric cylinders. This flow may be smooth (laminar), form patterns of toroidal flows (Taylor Vortices), or become turbulent. In both laminar and turbulent flow we have observed abrupt changes in the patterns of flow (phase slips). These phase slips may be periodic or chaotic (irregular over long time scales). Through experimental and numerical studies, and we have learned to control the chaos (i.e. re-establish periodic flow using small perturbations). We seek to characterize the strength of the chaos in these patterns and to simulate their evolution.
Prerequsites: Mastery of mechanics at the level of Physics 151-2; Mastery of differential equations and linear algebra at the level of Math 235 & 225; Mastery of computing at the level of CS 171; knowledge of Mathematica and C.

Tom Olsen, "Measurement and Interpretation of Light Curves for Short-Period Eclipsing Binary Star Systems"
If the plane of a star pair’s orbit intersects the position of the Earth, the stars will appear to eclipse each other. This group has studied the light incident upon the earth from eclipsing binaries for 40 years. The system 44i-Bootes has been studied in detail. It executes a complete orbit in 8 hours. We seek to continue to measure light curves, plots of light intensity over time, both of 44i and other systems. At the same time, we seek to understand patterns of period change and long period perturbations on the eclipse times of these systems.
Prerequsites: Knowledge of astronomy at the level of Physics 105 or 205; Mastery of calculus at the level of Math 132; Mastery of computing at an elementary level; interfacing at the level of Physics 201 would be of significant value.

Steve Tufte, "High-Velocity Clouds and Their Role in the Evolution of the Milky Way Galaxy"
The interstellar medium of our galaxy consists of very dilute material filling the vast spaces between the stars. It is the material from which stars form and into which they vent their material when they (sometimes violently) expire. The project is to explore a mysterious sub-component of this medium: interstellar clouds moving at high and unexplained velocities. These high-velocity clouds (or HVCs) are mostly made of hydrogen, can be up to 10 million times the mass of the sun and 10,000 light years across, and are moving toward us at several hundred kilometers per second. We will explore these HVCs using a remotely operable observatory called the Wisconsin H-Alpha Mapper (WHAM). We have established a Remote Observing Laboratory at Lewis & Clark from where we can command the WHAM instrument, located on Kitt Peak in Arizona, to make spectroscopic observations. There is recent evidence that these high-velocity clouds may represent primordial material falling onto the galaxy as part of on on-going formation process (see the article “Our Growing, Breathing Galaxy” in the January 2004 issue of Scientific American for more information). The goal is to better understand HVCs and their role in galactic evolution.

Prerequsites: Computer skills desirable.