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Watch Salif Doubere '12 Discuss His Research

Regulation of MARK2 by KSR1: Insights into Alzheimer's and other diseases

Vivian Chou ('13); Paula Klutho*; Mentor: Robert E. Lewis*
*University of Nebraska Medical Center, Omaha, NE

Abstract: The KSR1-MARK2 interaction is potentially implicated in cancer, Alzheimer’s Disease, and diabetes. MARK family proteins phosphorylate the Tau protein, thus promoting neurofibrillary tangles associated with neurodegenerative disease. MARK2 also phosphorylates the molecular scaffold KSR1. pTau levels in the murine brain indicate that in some systems, KSR1 acts upstream of and negatively regulates MARK2. Phosphorylation of MARK2 on T208 positively regulates its activity, while phosphorylation on S400 negatively regulates MARK2. To determine if KSR1 regulates MARK2 activity via phosphorylation, the phospho-status of MARK2 in the presence or absence of KSR1 was screened. Cerebral and transfected cell lysates were prepared, and Western blotting was performed with antibodies specific to phosphorylated T208 and S400 on MARK2. Surprisingly, pT208 was mildly decreased and pS400 was increased in the absence of KSR1, suggesting that KSR1 is a positive regulator of MARK2 activity. Thus, KSR1 may affect Tau phosphorylation via mechanisms distinct from MARK2 regulation.
Funding Provided by: UNMC

Nox1 Trafficking in Vascular Smooth Muscle Cells

Katharine Brieger ('11); Bojana Stanic*; Kate Brieger†; Jennifer Streeter‡; Francis Miller‡*$
*Internal Medicine Dept (UI); †Summer Undergraduate MSTP Research Program (UI); ‡Anatomy and Cell Biology Dept (UI); !Free Radical Radiation Biology Program (UI), University of Iowa, Iowa City, IA

Interdisciplinary: Internal Medicine

Abstract: NADPH oxidases (Nox) are membranebound proteins that are a major source of oxidative stress. A thorough understanding of Nox function is essential for the development of therapeutics. Our lab has demonstrated that TNF-a induces vascular smooth muscle cells (SMCs) to generate reactive oxygen species in a process that is Nox1- dependent and dynamin-dependent. Since dynamin is necessary for endocytosis, we believe that endocytosis is an important regulatory step for Nox1 activation. In studies using cultured A7r5 rat aortic SMCs utilizing a biotinylation technique, we found that 5% of Nox1 resides at the plasma membrane under basal conditions. We found that stimulation with TNF-a does not cause trafficking of intracellular Nox1 to the plasma membrane. We found that 48% of plasma membrane Nox1 is endocytosed in a 15-minute time period under basal conditions. These findings provide novel insights into the trafficking of Nox1 and could contribute to the development of cardiovascular therapeutics.
Funding Provided by: Veterans Affairs, University of Iowa Summer MSTP Program, University of Iowa

WorldTeach Namibia

Salif Doubare ('12); Mentor: Ami Radunskaya

Interdisciplinary: Teaching

Abstract: This project describes the WorldTeach Namibia Summer volunteer program in which the twenty year old developing country’s Ministry of Education deploys their nationwide Information and Communication Technology (ICT) initiative. We describe the computer literacy training agenda for Etalaleko Senior Secondary School’s twelfth graders and teachers in the northern town of Okahao. Providing an introduction to the technological world of computers became a task of introducing a language. Therefore, the teaching of this new techno-lingo required learning Oshiwambo, the native tongue. With a slight understanding of this Bantu language and its structure, it was possible to translate basic computer commands essential to operating a CPU. Teachers participated in training sessions after school in order to gain their International Computer Driving Lesson (ICDL); successful completion of the ICDL was rewarded by a governmental laptop. The lack of technology is a universal challenge to progress – we are pleased to be allowed a part.
Funding Provided by: The Fletcher Jones Foundation, Posse Foundation Summer Leadership Award

Hydraulic Features of Engineered Log Jams and their Influence on Salmonid Behavior

David Fetter ('11); Virginia Somerville ('11 Lehigh Univ.); Will Rice*; Desiree Tullos†; Matt Cox†
*University of North Carolina, Charlotte, NC; †Oregon State University, Corvallis, OR

Interdisciplinary: Environmental Engineering

Abstract: Stream restoration using natural materials is becoming a common practice, yet questions remain regarding the effectiveness of these Engineered Log Jams, due to lack of observations of hydraulics and fish use around these structures. Four such structures were studied on two different streams in western Oregon. The structures and near-structure stream environments were surveyed for bathymetry, instrumented with an Acoustic Doppler Stream Profiler to understand flow dynamics, and then snorkeled to observe salmonid behavior. Complex structures with more components created a more varied bottom profile, while simpler structures were more likely to create pools. Flow features proved difficult to analyze, however all jams created flow patterns with distinct areas of high and low velocity. In terms of fish behavior, size of fish correlated with flow velocities, with larger fish more abundant in faster flows. Our results demonstrate the influence of engineered structures on the diversity and versatility of fish habitat.
Funding Provided by: National Science Foundation

Tracking The Angular Momentum Evolution of Young Stars Through a Stellar Variability Study

William Gamber ('13); John Bremseth ('12 HMC); Mentor: Phillip Choi

Interdisciplinary: Physics, Astronomy

Abstract: Astrophysicists have sought to understand the formation of young stars for nearly 30 years. We know that young stars form when massive spinning molecular clouds collapse. The mechanism driving their formation is fairly well understood; however some of the details, such as the interplay between the star's magnetic field an its circumstellar disk as well as the angular momentum evolution angular momentum are still not completely understood. Empirical research has focused on observing large numbers of young stars at different stages of formation to create a timeline of this mechanism. Our project is part of an ongoing, multi-epoch monitoring program to build such a timeline. We observed the Berkeley 87 cluster, and developed a data pipeline to find the angular velocities of the variable stars in the field. Finally, we further analyzed the existing data to find the periods of previously ignored stars.

A GST-Pulldown to Identify Novel Protein Interactors of Drosophila Syndecan

Nicholas Kramer ('11); Mentor: Karl Johnson

Interdisciplinary: Biology, Molecular Biology, Neuroscience

Abstract: Syndecan is a transmembrane heparan sulfate proteoglycan (HSPG) that regulates synaptogenesis in Drosophila. Previous experiments have demonstrated that at the neuromuscular junction, Syndecan’s heparan sulfate (HS) sidechains are required for the interaction of Syndecan and the receptor protein tyrosine phosphatase, LAR, to promote synapse growth. Recently, a body of evidence has emerged that may suggest core protein specificity among HSPGs. Syndecan’s cytoplasmic domain contains two highly conserved amino acid sequences, including a PDZ binding sequence. We proposed a functional role for Syndecan’s cytoplasmic domain at the developing synapse and sought to identify novel protein interactors of this conserved domain. Our lab recently conducted a yeast twohybrid screen that detected five potential binding partners of Syndecan’s cytoplasmic domain; however, now a biochemical binding assay is necessary to confirm these interactions in vitro. A GST-pulldown assay will be used to confirm these novel protein interactors of Syndecan’s cytoplasmic domain.
Funding Provided by: Howard Hughes Medical Institute (NK), National Science Foundation ARRA #IOS-0841551 (KJ)

Building Constructs for Drosophila Syndecan to Elucidate Functional Domains

Jereen Kwong ('12); Margaret Nguyen ('10); Mentor: Karl Johnson

Interdisciplinary: Molecular Biology, Neuroscience

Abstract: Heparan Sulfate Proteoglycans (HSPGs) are important for axon guidance and synapse formation at the midline and neuromuscular junction (NMJ) respectively. There are two hypotheses for HSPG function: (1) they are carriers of HS chain on cell surfaces or (2) their core protein contributes to their specific functions. To test these hypotheses, two structurally different HSPGs, transmembrane Syndecan (Sdc) and GPI-linked Dallylike (Dlp) were examined in Drosophila. At the midline, Dlp significantly rescued sdc mutants but was unable to do so at the NMJ, suggesting that the core protein is important for HSPG function at the NMJ. To identify core protein domains required for function, we would build Sdc constructs that lack specific domains and test if rescue of the sdc mutant is achievable at the NMJ. Each construct is tagged and will be inserted into a pUASTattB vector to control expression levels in vivo using the GAL4-UAS system.
Funding Provided by: NIH Grant (KJ)

Challenges of migrant patient care in emergency facilities: How Berlin's health care system has responded

Janet Ma ('11); Hansjoerg Dilger

Interdisciplinary: Religious Studies, Biology

Abstract: Of the few German studies conducted so far, most show a disproportionately high use of emergency facilities by patients of migrant background compared to those with German background. Based on these initial findings, my goal was to find out the perspective of hospital emergency room personnel on this phenomenon, and what challenges they felt resulted from it. I conducted semi-structured, non-standardized interviews with emergency care staff, and did participant observation at an emergency department in Berlin for six weeks. My results indicate that emergency care staff face a variety of challenges that are either directly or indirectly related to migrant background. The greatest of these is language barrier, which along with perceived cultural differences of pain expression and general misunderstanding about the function of an emergency department, is very time-costly and may negatively impact doctor-patient relationship. The results thus indicate that a more systematic approach is needed to ensure equally
Funding Provided by: The Faucett Family Foundation, Free University Summer Independent Research Project

Heavy metal contamination at the Pomona College Organic Farm

Kellyann Murphy ('12); Kelly Park ('12); Teija Mortvedt ('11 SCR); Katie Purvis-Roberts (JSD); Mentor: Charles Taylor

Interdisciplinary: Chemistry, Environmental Analysis

Abstract: The Pomona College Organic Farm has potential heavy metal contamination due to its history as both a citrus grove and a waste disposal staging area. Soil analyses by X-ray fluorescence (XRF) and atomic absorption (AA) spectroscopy determined the following levels of lead, chromium, and arsenic in the farm: lead XRF measurements were 20.3 – 76.0 ppm, averaging at 39.8 ppm, while AA measurements were 2.4 – 11.7 ppm, averaging at 5.2 ppm; chromium XRF measurements were 155.7 – 726.6 ppm, averaging at 281.6 ppm; arsenic AA measurements were 2.3 – 5.4 ppm, averaging at 4.1 ppm. None of these levels exceed EPA regulations and should not pose a health risk to those using the farm.
Funding Provided by: Rose Hills Foundation (KP), The Andrew W. Mellon Foundation (KM)

Lead and halogen contamination from aviation fuel additives at Brackett Airfield

Kelly Park ('12); Kellyann Murphy ('12); Teija Mortvedt ('11 SCR); Katie Purvis-Roberts (JSD); Mentor: Charles Taylor

Interdisciplinary: Chemistry, Environmental Analysis

Abstract: Compounds containing lead, chlorine, and bromine are used as anti-knock fuel additives in aviation gasoline. Their presence in elevated amounts indicates fuel runoff or particle settlement from combusted fuel. This study aims to measure the concentration of these elements in the soil around Brackett Airfield in LaVerne, California. X-ray fluorescence measurements reveal lead content at 22.13 – 152.2 ppm with an average of 47.99 ppm; bromine at 2.10 – 42.57 ppm, averaging at 10.05 ppm; and chlorine at 315.5 – 2567 ppm, averaging at 605.2 ppm. Atomic absorption spectroscopy measured lead at 5.89 – 94.97 ppm, averaging at 20.25 ppm. None of the results obtained exceed allowable EPA standards and therefore should not pose a health risk to surrounding communities. Further studies are recommended on soils collected within the airport fence line—contamination is likely higher due to closer proximity to the runway, fueling stations, and airplane hangars.
Funding Provided by: Rose Hills Foundation (KP), The Andrew W. Mellon Fellowship (KM)


Smoke & Dust

Jacob Scruggs ('11); Bassam Frangieh (CMC); Mentor: Valorie Thomas

Interdisciplinary: English, Arabic

Abstract: A man asked me why I had come to Egypt. I told him because Egypt is "The Mother of the World." The men who were listening to my answer nodded their heads in approval (many Arabs, especially Egyptians, call Egypt “The Mother of the World” and consider it as such). The questioner knew I was American, so he then asked, “Then what is America?” I replied with a huge smile, “The Father of the World.” All the men listening laughed loudly at my joke, while the man who had questioned me wagged his finger and tsked with disapproval at my reply. I traveled alone throughout this country for a month trying to find moments like this one along the Nile and throughout the Western Desert. I traveled as a student of the Arabic language and an English major. I am in the process of writing a collection of poems.
Funding Provided by: Pomona College SURP

Learning vibrissal sensory representations for texture discrimination

Sophia Yang ('11); Andrew Y. Ng*; Andrew L. Maas*; Mentors: Richard Lewis, Sara Sood
*Computer Science Dept, Stanford University, Stanford, CA

Interdisciplinary: Computer Science, Neuroscience

Abstract: Properties of cortical sensory areas reflect optimal encoding of natural stimuli. We automatically construct a sensory representation based upon this principle on natural and artificial vibrissal data. We demonstrate that the learned sensory representations yield superior performance to baseline representations in a texture discrimination task.
Funding Provided by: 5-C Neuroscience Fellowship

Mechanistic Implications of Phe161 in NADHdependent Persulfide Reductase from Shewanella loihica PV-4

Emily Brotman ('13); Kyu Hyun Lee ('11); Scott Humbarger ('12); Megan Warner ('10); Matthew Sazinsky; Mentor: Edward J. Crane

Interdisciplinary: Chemistry, Biochemistry

Abstract: NADH-dependent persulfide reductase (Npsr) from Shewanella loihica PV-4 may be involved in sulfur-based respiration by catalyzing the following reaction: R-S-SH + NADH + H+ ! H2S + R-S2- + NAD+. Phe161, whose bulk is conserved in Npsr homologues within the glutathione reductase flavoprotein family, is crucial in the enzyme's interaction with the pyridine nucleotide. To better characterize the reductive half reaction of Npsr (NADH + E -> NAD+ + EH2), the Npsr F161A mutant was constructed. The crystal structures of the oxidized wild-type Npsr and Npsr F161A (2.0 and 2.7Å, respectively) show that Phe161 undergoes a significant conformational change upon NADH binding and the removal of steric hindrance allows NADH easier access to its binding site on Npsr. Steady state kinetic analysis shows that the mutation also decreases kcat by approximately threefold but leads to a lower Km, suggesting a tighter NADH binding. Primary kinetic isotope effect (PKIE) pre-steady state
Funding Provided by: The Fletcher Jones Foundation (EB), Howard Hughes Medical Institute (KHL)

Research at Pomona