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Rogers Science Research

2007 Abstracts for Rogers Science Program

April 02, 2007

Faculty Abstacts

Biology

Paulette Bierzychudek: Feeding performance of Oregon silverspot butterfly larvae on host plants from different populations

The Oregon silverspot butterfly (OSB) population at Cascade Head, OR (CH) is threatened with extinction. OSB larvae feed on Viola adunca leaves, which are declining. We plan to supplement violet numbers at CH by transplanting adult plants. What source material should we use? If the CH population has low genetic variability, it may be beneficial to introduce new genotypes. Sasha Stortz ’07’s thesis will determine genetic relatedness between the CH population and others. But might OSB larvae discriminate between plants from different populations, or grow at different rates? Feeding experiments using OSB larvae will answer this question.

Prerequisites: Student should be patient, conscientious, should be comfortable working alone, should have good manual dexterity, and some experience gardening/growing plants. Some experience performing statistical analyses/graphing data highly desirable.

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 200 required, Biol 311/312, Biol 390 and 408 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 genes necessary for the assembly and stability of lysosomes in the model organism, Caenorhabditis elegans. Our work will focus on investigating the cellular pathways controlled by these genes.

Prerequisites: Bio 151 or Bio 200. Prefer if have also taken Bio 311/312, Bio 361, or Bio 412.

Deborah Lycan: Nuclear export: How are ribosomal subunits exported through nuclear pores?

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, S. cerevisiae. Ribosome assembly is a highly complex and coordinated process that occurs mostly in the nucleus from premade protein components that are imported from the cytoplasm. The two subunits are assembled independently and exported through nuclear pores at rates that can exceed 40 subunits/sec in exponentially growing cells. More than150 accessory proteins are required for the proper assembly and export of ribosomes in yeast. Many of these proteins have been implicated in rRNA modification and cleavage, but recently proteins with other roles in assembly and export have been identified. 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, which steps are under regulatory control (ribosome biogenesis is linked to the growth state of the cell), how subunits are exported and whether export is subject to quality control 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, Yar1 and Ltv1. RpS3 is a structural component of the mature 40S subunit, and it interacts with both Yar1 and Ltv1. Cells lacking either Yar1 or Ltv1 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 Ltv1 shuttles between the nucleus and cytoplasm via the exportin protein, Xpo1, and that RpS3 export is reduced in cells lacking Ltv1. Our working model is that Ltv1 may be the long-sought adapter for 40S subunit export, linking the pre40S subunit to the XpoI exportin. Work this summer will be directed towards testing this model. Experiments in my lab involve genetic, biochemical, molecular and cell biological techniques.

Prerequisites: Molecular Biology 311/312 or Cell Biology 360

Gary Reiness: Characterization of a Secretory Signal for Chicken Ciliary Neurotrophic Factor

We study the mechanisms of non-classical protein secretion. Most secreted proteins use a “classical” pathway to exit cells; they move sequentially through the endoplasmic reticulum, Golgi apparatus, and secretory vesicles before being released. Some secreted proteins, including, ciliary neurotrophic factor (CNTF), which we study, do not use this classical pathway. CNTF acts in cell-to -cell communication to direct proper formation of the nervous system. Thus investigating “nonclassical” secretory pathways will aid understanding of intercellular communication and nervous system development. A variety of projects in cell and molecular biology are available, depending on student interests and skills.

Prerequisites: Biology 200 is required. Experience with molecular biology, cell biology or biochemistry in 300-level courses is desirable (e.g., Biology 311/312 or 361; chemistry 330 or 335/335).

Chemistry

Barbara Balko: Investigation of the Enhanced Reactivity of Smectite Clays in Contact with Iron Metal

Reductants are often used to remediate organic contaminants in groundwater. The interaction of clay and iron metal creates a reductant, presumably sorbed Fe(II), that is stronger than either the iron metal or the clay. The primary goal of our research is to characterize these sites in terms of location, regeneration time, and reactivity. Our secondary goal is to explore the unique capabilities of the iron-clay system. Specifically, we will investigate how manipulation of the clay environment changes the reactivity of the system. We will use iron electrodes coated with a clay film in our proposed experiments to allow us to electrochemically control the interaction between the clay and iron metal.

Prerequisites: none

James Duncan: A Search for Pseudopericyclic Allenyl Cope Rearrangement Pathways, Employing CASSCF Ab Initio Molecular Orbital Calculations

The prototypical allenyl Cope rearrangement (ACR) of 1,2,6-heptatiene (1) has been shown to involve competitive concerted and non-concerted pathways, proceeding through transition structures TSa(pericyclic) and TSc, respectively.1 High-level (CASSCF) computations on the ACR¡¦s of 2 and 3, however, show they rearrange exclusively through pathways involving, respectively, TSd and TSa.2 No ACR has been shown to proceed through TSb a pseudopericyclic process. Through computational studies of additional ACR’s, we propose to test the hypothesis that the factors affecting the mechanistic course of ACR’s are: (1) ring strain in potential intermediates; (2) early vs. late TS’s; (3) strength of σ-bond cleaved; and (4) approach geometry of allenyl (C=C=C) and vinyl (C=C) components. In the process, we hope to discover the first example of a pseudopericyclic ACR.

from Professor James Duncan

Prerequisites: Completion of Chemistry 210 and 220, Organic Chemistry I and II.

Louis Kuo: Project 1 - Hydrolysis of Phosphate Triester Neurotoxins with Organometallic Complexes

This project explores using organometallic complexes called metallocenes (metal = molybdenum) to carry out the degradation of a class of phosphate neurotoxins. Phosphino-thioates are the functional core of neurotoxins, some of which have been used as pesticides. Besides having inert and strong P-C and P=O bonds, the core consists of P-S and P-O linkages wherein the preferable mode of degradation involves cleavage of the P-S bond; scission of the P-O bond yields a complex just as toxic as the parent neurotoxin. We have recently found that molybdenum metallocenes yields this preferable bond scission on a model phosphinothioate in aqueous solution. This project will synthesize new molybdenum complexes with the objective of determining structure-activity relationships on how metallocenes affect the degradation/hydrolysis of phosphinothioates.

Prerequisites: Chem 220 (Full year of Organic chemistry), Chem 366 preferred (Inorganic chemistry laboratory)

Louis Kuo: Project 2 - Isolation and Purification of Diterpenoid Metabolites Used in Herbivory Deterrence from Marine Algae

Organic molecules that deter herbivore activity have applications towards pest control and anti-cancer studies. On coral reefs, where herbivore activity by fish play a significant ecological role, several classes of compounds have been isolated from marine algae, including a class of metabolites that contain carbon double bonds. These diterpenoids deter herbivory and concentrations appear to vary during the reproductive ecology of algae in the genus Halimeda. The first portion of the project entails isolation of these diterpenoids from marine algae to the point where they can be quantified in ecological studies and chemically labeled for cellular investigations in algae.

Prerequisites: Chem 220 (Full year of Organic chemistry), Chem 366 and Chem 365 Preferred (Inorganic Physical chemistry laboratory), Bio 141 or 151 (Biology core courses), Bio 200 Preferred (Biology core course)

Janis Lochner (with Greta Binford): Evolutionary patterns of neurotoxin expression in spider venoms

Venoms of spiders in the genus Loxosceles and Sicarious induce severe dermonecrosis in bite victims. The constituents of these venoms have not been systematically characterized with respect to neurotoxic activities. We propose to begin this characterization by looking for calcium channel active toxins within venom derived from spiders in the Loxosceles phylogeny. The ability of venom to inhibit synaptic release of secretory proteins in response to membrane depolarization will form the basis of our assay to identify neurotoxins that inhibit voltage gated calcium channels.

Prerequisites: Chemistry 220 and Bio 200 required

Janis Lochner: Synaptic secretion of neuromodulators implicated in long-term memory formation

Long-term memory formation is accompanied by enduring changes in synaptic organization. The structural and functional changes that underlie these changes in synaptic efficacy are triggered by the release of neuromodulators. Brain-derived neurotrophic factor (BDNF) and tissue plasminogen activator (tPA), are two neuromodulators that are highly expressed in the hippocampus and are implicated in modifying synaptic efficacy during learning and memory. To better understand the molecular determinants of synaptic plasticity, we will characterize the properties and cellular mechanisms of secretion of tPA and proBDNF from cultured hippocampal neurons.

Prerequisites: Chemistry 220 required, Chem 336 and Bio 312 preferred but not required.

Mathematics/Statistics/Computer Science

Yung-Pin Chen: Detecting statistical signal in genetic linkage and association studies

Linkage disequilibrium refers to the fact that alleles at different loci co-occur on the same haplotype more often than expected by chance. Many studies have found haplotype block structure exhibited by alleles at nearby loci. Haplotype blocks can be useful in understanding the association between certain genomic markers and traits. This project will examine the genetic variations known as single nucleotide polymorphisms (SNPs). In particular, we will look at statistical measures that can be used to quantify pairs or multiple-locus linkage disequilibrium in SNPs. We will employ those measures to investigate possible approaches to detecting the block structure of the SNPs haplotype

Prerequisites: basic probability theory and statistics or equivalent; molecular biology (Bio 200) some experiences in a programming language

Jens Mache: Sensor Networks and Grid Computing

Wireless sensor networks and grid computing are both considered “Emerging Technologies That Will Change the World” according to MIT Technology Review. (Grid computing uses the Internet to allow sharing of computational and data resources among geographically distributed users. Wireless sensor networks are systems that combine potentially thousands of low-powered, remotely-deployed mini-computers, embedded in the physical world.)

New applications as well as security issues are rising. In order to achieve performance, scalability and robustness, many resource management problems have to be solved. This internship includes studying existing systems, writing software and experimentation with various designs and algorithms.

Prerequisites: Computer Architecture CS 277 and Computer Networks CS 393

Liz Stanhope: Listening to Orbifolds and Orbigraphs

There is a beautiful pairing of theorems between the smooth world of geometric shapes and the discrete world of graph theory. For example, geometers proved that you can hear the volume of a smooth object. Using natural definitions of the volume and ‘sound’ of a graph, graph theorists obtained the analogous result. This summer we ask ‘What happens to this pairing if the geometric objects have sharp corners?’ These pointy shapes are called orbifolds. Our challenge is to define what an orbigraph should be, and then see if geometric facts about orbifolds correspond to graph theoretic facts about orbigraphs.

Prerequisites: Math 215: Discrete Math and Math 225: Linear Algebra

Physics

Steve Tufte: Investigating the Kinematics and Physical Conditions of Interstellar Matter in Face-on Spiral Galaxies

The universe is organized into a vast number of galaxies, each one a gravitationally bound collection of stars and interstellar material. Stars form within interstellar clouds, and once formed they affect their interstellar environment through intense star light, stellar winds, and sometimes by generating giant explosions called supernovae. When they die, they return some of their material to the interstellar medium where it is eventually incorporated into the next generation of stars. Understanding galaxies and how they evolve requires an understanding of this complex cyclic process.

We will investigate 39 spiral galaxies viewed face-on with data from the WIYN 3.5 telescope on Kitt Peak in Arizona. A new observational technique was used that allows the simultaneous measurement of high-resolution spectra for each location on the galactic image. The research students will help analyze these spectra probing the heating, excitation, and motion of interstellar gas in the vicinity of star forming regions with the goal of better understanding the interplay of stars and interstellar material in galaxies.

Prerequisites: Computer skills and an interest in observational astronomy are desirable.

Thomas Olsen – Project 1: “Light Curves and Spectra of Eclipsing Binary Star Systems”

Most stars are members of groups of two or more stars. Some binary pairs, viewed along their orbital plane, are seen to eclipse each other. We have measured the light curves, plots of light intensity versus time, for a variety of these systems. In one, we have determined the rate at which this orbit is slowing. Together with other measurements of these systems, we have modeled the internal motions of these systems. We will measure light spectra to test these models. We will continue to measure light curves to learn the evolution of these systems.

Prerequisites: 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.

Thomas Olsen – Project 2: “Modified Taylor-Couette Flow: Models to predict the onset of Spatio-Temporal Chaos and Algorithms to achieve Control of Chaos”

Taylor-Couette Flow is the motion of a fluid layer between two concentric cylinders, at least one of which is moving. Our system of interest is modified in that the inner cylinder is hourglass shaped. For a certain rotation rate of the inner cylinder, vortices form. We study the chaotic nature of this vortex formation and the effectiveness of potential algorithms to control the system (return it to periodic vortex formation). We also seek to model the onset of chaos and especially to learn for what shaping of the inner cylinder the vortex formation with distribute itself chaotically in space.

Prerequisites: 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.

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