FURF Handout 2011 Final Draft

8/3/2019 FURF Handout 2011 Final Draft

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College of Science Fall Undergraduate Research Fair 2011

Welcome!

The purpose of this event is to provide science students with an opportunity to get many of their

questions answered about undergraduate research. Not only about how to get more involved inresearch, but also how to get more out of the research experience itself.

Throughout and beyond the College of Science there are many different ways in which studentscan get involved in research. Often its just a question of looking in the right places and being

persistent in the hunt for the right opportunity. However, getting the right opportunity is alsoabout getting as much information as possible from a diversity of sources. This could be as

simple as a fellow student but there are also many organizations, institutes, and centers oncampus that are also more than willing to help a student find and support their research

endeavors. Furthermore, there are many ways for students to get even more out of their researchexperience, through publishing and presenting their research to their peers.

Through a combination of listening to speakers, poster presenters, and representatives fromvarious institutions, students should be able to get some ideas about how best to get started

looking for research opportunities. Also, students should be able to see how they can add valueto their research experience by participating in other related activities. The sooner a student

begins the search, the sooner they will be able to start participating in undergraduate research andgetting the most from that experience!

Schedule and Table of Contents

Page6 - 7 pm Undergraduate Research Opportunities in Chemistry (Jordan 105)

7 - 8 pm Poster Presentations (Jordan Galleria) 4Information Tables 25

Refreshments

8 - 9 pm Undergraduate Research Internships Information Night (Jordan 105) 29


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Research Poster Presentations (Jordan Galleria)

Paul Baranay - Metassembler: Improvingde novo genome assembly

Erik Blackwood - Investigation of the Effects of Hypoxia and Hydrogen Sulfide Concentration and

Production in Vertebrate Blood, Gill Perfusion Method

Maureen Choman - The Effects of a Synbiotic Diet on Bone Density and Bone Composition in Hindlimb

Unloaded Rats

Rachel Cotton - Chemokines modulate chondrocyte homeostasis: implications in osteoarthritis

Michael Franczak - The Importance of The Electronic Medical Record in Delivering HighQuality Health

Care in an Emergency Department Setting

Henry Gens -Rescue of neurodegeneration in Niemann-Pick Type C mice via an induced pluripotent stem

cell therapy

Brendan Heiden -Immunological analysis of a phase I clinical trial: a non-oncolytic fowlpox vaccine

affecting Ig-Like Transcript 2 (ILT2) expression on regulatory and suppressor T cell populations

Patrick Kramer -Lead Poisoning Investigation: Bioavailability of Heavy Metals Following Inhalationand Ingestion

Patrick McIntyre -Applications of Multi-mode Interference in Fibers

Colleen McKenna - Potential Therapeutic Targets for Melanoma

Grace Meikle - Solar Infrastructure in India and Market Analysis of Solar Infrastructure in India

Young Moon - Dissecting glucocorticoid pathways regulating eosinophil viability and activation in

asthma

Rick Morasse - Synthesis, Characterization and Optical Properties of CdSe Nanosheets

Michael Nokes - The Role of Odorant Binding Proteins in Mediating Perception of Taste in D.

melanogasterPatrick OHayerAnalysis of TNF receptor expression within the regenerating zebrafish retina

Kevin Park - The effect of temperature and diet on the growth and mortality ofCamnula pellucida

(Orthoptera: Acrididae)

Antoinette Pusateri -Investigating the Presence of Type B Conformer Complexes in Healthy and Colitis

Models

Roger S. Smith -Predicting Antimalarial Mode of Action from Gene Expression Signatures

Do Trong Thanh - Real roots properties and asymptotic normality of graph Stirling numbers

Cong Charles Xu - The genetic basis of sperm competitiveness in monogamous and promiscuous

Peromyscus mice


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Metassembler: Improvingde novo genome assembly

Paul Baranay

Biological Sciences and Applied Mathematics

College of Science

Advisors: Michael Schatz, Cold Spring Harbor Laboratory andScott Emrich, Dept. of Computer Science and Engineering

Presently, researchers can choose from any of several programs forde novo assembly of genomes using

short-read second-generation sequencing data, such as SOAPdenovo, Velvet, and ALLPATHS-LG.

These new assemblers assemble the genome by constructing, simplifying, and walking a graph of reads;

however, because assemblers can differ substantially in implementation and function, it is frequently the

case that one assembly program can correctly assemble a difficult region of the genome, whereas others

cannot.

To exploit this fact, we have developed a technique we call metassembly, which combines multiple

assemblies to produce a single draft genome that is superior to all its contributing assemblies. Our

implementation of this technique is available as a Python package called Metassembler. Metassembleremploys Nucmer to align assemblies to each other and detect gaps between contigs in one assembly,

which can be closed by patching sequence from the other assembly into the gap. Metassembler can

also detect and correct indels within contigs, or regions of deleted sequence in one assembly compared tothe other, which are often caused by a misassembly around a repetitive region.

We employed Metassembler in our submission to the Assemblathon 2 competition, which challenged

researchers from across the world to use the same set of sequence data to create the best possible de novo

assemblies of three vertebratesa fish, a bird, and a snake. We assembled the fish genome using two

assemblers, SOAPdenovo and ALLPATHS-LG. The ALLPATHS assembly was substantially superior to

the SOAPdenovo assembly but still contained approximately 600 regions where sequence from the

SOAPdenovo assembly was used to improve the overall assembly. Filling in these gaps resulted in a

substantial increase in the quality, connectivity, and coverage of the fish genome compared to eitheroriginal assembly.

While a variation of this technique was previously used to improve several fly genomes, we believe this

work represents the first use of this technique both for vertebrate-sized genomes and for assemblies

created from short-read sequencing. By enabling researchers to perform metassembly in a straightforward

and efficient fashion, we hope to improve the overall quality of assemblies produced by researchers

across the world. In particular we hope to apply Metassembler to theAnopheles mosquito genome and

the human genome in the near future.

More information about the Metassembler package and method is available online at

http://schatzlab.cshl.edu/research/metassembler


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Investigation of the Effects of Hypoxia and Hydrogen Sulfide Concentration and Production in

Vertebrate Blood, Gill Perfusion Method

Erik Blackwood

Science-Business and Philosophy

College of Science

Advisor: Ken Olson, Indiana University School of Medicine, South Bend, and

Dept. of Biological Sciences, University of Notre Dame

The research uses the gills of rainbow trout and the reasons are twofold; first, rainbow trout, a freshwater

fish that possesses the ability to inhabit salt-water environments, is an example of an animal model that

guards against blood volume expansion and hypertension. Their unique characteristic of fresh and salt-

water habitats represent a dehydrating experience similar to the continual loses of fluids experienced by

mammals. Secondly, the gills are specifically isolated because they are the only organs to receive the

entire cardiac output. By extracting the gills and exposing them to varying concentrations of H2S, the rate

of dispersion amongst the gill tissue is measured and quantified using a colorimetric assay. It has been

noted that the gill tissue absorbs hydrogen sulfide to a peak critical level. Additionally, no evidence of

H2S is present flowing through the dorsal aorta and thus supports the claim that H2S is only absorbed bygill tissue.


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The Effects of a Synbiotic Diet on Bone Density and Bone Composition in

Hindlimb Unloaded Rats

Maureen T. Choman

Biological Sciences

College of Science

Advisors: Annette Gabaldn, Dept. of Biological Sciences, Colorado State University Pueblo, CO and

Cynthia Blanton, Dept. of Health and Nutrition Sciences, Idaho State University, Pocatello, ID

The effects of a synbiotic diet and hindlimb unloading on bone density and bone composition in the

humerus, femur, and tibia were studied in 40 adult male rats. Rats were divided into four groups that

received either a synbiotic diet or a control diet and were either loaded, with all four limbs on the ground,

or unloaded, in which rats were suspended by their tails, just relieving the hindlimbs of any weight

bearing pressure. Following unloading for 14 days, rats were allowed 14 days of recovery. Using a

volumetric system and an Archimedes scale apparatus, the density of each whole bone and cortical bone

shaft was measured. Results showed decreased density in the whole bones of the unloaded femur and

tibia, but no diet effect. Bone shafts of the femur showed a decreased density in unloaded rats, but no diet

effect. Using a gravimetric system, the bones were dried, defatted, and ashed to obtain the percent water,fat, organic matter, and mineral. There were no apparent differences among the four groups regarding

percent composition. Overall, results suggest the unloading technique causes bone deterioration, the

synbiotic diet does little to assuage this deterioration, and a recovery period seems to allow for adequate

restoration of mineral content.


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Chemokines modulate chondrocyte homeostasis: implications in osteoarthritis

Rachel Cotton

Biological Sciences

College of Science

M. Farooq Rai, Aihua Liu, Linda J. Sandell,Washington University School of Medicine, St. Louis, MO

Advisor: Linda Sandell, Washington University School of Medicine, St. Louis, MO

Osteoarthritis (OA) is the most common degenerative joint disorder. It is a disease of the whole joint

resulting from an imbalance of catabolic and compensatory anabolic mechanisms. It is commonly

implicated that multiple chemokines alter the expression of key matrix degrading enzymes, but their

specific role in disrupting chondrocyte homeostasis is unknown. Increased expression of several suchchemokine genes has been observed in OA patients. The goal of this study is to evaluate chemokine

involvement in altering expression of other OA-related genes in chondrocyte cell lines, in the context of

OA as a disease of the whole joint. Chondrocyte cell lines T/C-28a2 and hCh-1 were stimulated with

CCL3L1 or CXCL12 in a time- and dose-dependent manner. The mRNA expression of IL-1, MMP-1,MMP-13, ADAMTS-4, ADAMTS-5, Runx2, VEGF, CD-RAP, Col21, and Aggrecan was assessed byquantitative real-time PCR. Preliminary results show that CCL3L1 and CXCL12 differentially upregulate

these OA-related genes in both cell lines over time. We surmise that production of these chemokines by

joint tissues in vivo may have a paracrine affect on the gene expression pattern of chondrocytes in OA

pathobiology.


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The Importance of The Electronic Medical Record in Delivering High

Quality Health Care in an Emergency Department Setting

Michael Franczak

Science Pre-Professional

College of Science

Leighton Mark and Flavius Raslau, Medical College of Wisconsin, Wauwatosa, WI

Advisor: John Ulmer, Medical College of Wisconsin, Wauwatosa, WI

Remote-site telemedicine is a growing phenomenon, providing increased healthcare access to patients

around the world; however, remote-site telemedicine runs the risk of decreasing physician-to-physician

contact, which is critical in delivering high quality care. Although electronic medical records (EMR) have

been shown to optimize physician-to-physician contact, only a minority of institutions have adopted

EMR. As a standard of practice at the Medical College of Wisconsin, the EMR is accessed for all

Radiology examinations to search for indications beyond that entered directly by physicians, prior to

rendering interpretations. This study compares the discrepancies between indications for emergency head

CT scans, entered directly by emergency department (ED) physicians, with actual indications retrievedfrom the EMR, supported when necessary by direct verbal access to ordering physicians. Specifically, we

seek to estimate the positive impact of full EMR access on patient care in the emergency department

setting. This was a prospective expert rater analysis using retrospective data from 2,000 consecutive head

CT scans ordered in the emergency department of this academic Level I Trauma Center. The clinical

indications entered into the electronic order directly by the ED physicians for all head CTs over a 3 month

interval were compared to actual indications retrieved by practicing Radiologists from the EMR,

supported by direct verbal physician-to-physician contacts where necessary. Three practicing

Neuroradiologists independently compared the two sets of clinical indications based on the following

criteria: 1)The discrepancy in medical content between ED physician-directed indications and actual

indications retrieved through direct access to the EMR, and referring physicians where necessary. The

scoring was binary; yes or no that a discrepancy existed. 2)When a discrepancy was present, each

Neuroradiologist determined the likelihood (very likely, possibly, or unlikely) that the discrepancy wouldimpact their interpretation in a way that would adversely influence medical management. A high rate of

discrepancy between the physician-directed and actual EMR retrieved head CT indications was observed.

On average, 49.3% of the indications showed disagreement (see Figure1). Most importantly, an average

of 9.0% of the physician-entered clinical indications were rated as very likely to have an adverse

influence on the interpretation and medical management (see Figure 2). Thus, approximately 180 patients

during the 3-month interval were likely to be adversely affected by the errors in physician entered clinical

indications. Additionally,14.0 to 38.9% were rated as possibly having a clinically significant impact.

Due to the intense clinical demands and unique workflow requirements of ED physicians, the clinical

indications entered directly by ED physicians may sometimes be incomplete or even incorrect. This study

suggests that discrepancies between ED physician-directed and EMR-directed indications are very

likely to have an adverse effect on care in 9% of patients. Effective communication is critical between

the ED physician and the interpreting radiologists, and is best achieved through direct access to the EMR,supported by direct communication between physicians. Remote-site health care organizations should

consider analogous scenarios and the serious implications of inadequate access to the full medical record.


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Rescue of neurodegeneration in Niemann-Pick Type C mice via an

induced pluripotent stem cell therapy

Henry Gens

Biochemistry

College of Science

Cheryl Schaeper, Tresa Fraser, David Yang,Dept. of Biological Sciences, University of Notre Dame

Advisor: Malcolm Fraser, Dept. of Biological Sciences, University of Notre Dame

Neimann-Pick type C (NPC) disease is an autosomal recessive disorder caused by mutations in theNPC1

andNPC2 genes, with an estimated frequency of about 1 in 150,000 live births. NPC disease is a

lysosomal storage disorder, with the loss of function of the NPC1 or NPC2 protein resulting in

accumulation of cholesterol and other lipids within late endosomes/lysosomes (LE/L). This deficiency

causes progressive neurodegeneration and eventual death, with a range of onset from a few months of age

to early adulthood. Currently there are no effective treatments for NPC disease patients. Gene therapy

using induced Pluripotent Stem Cells (iPS) to derive NPC-expressing neuronal stem cells from adipose

tissues, however, provides a compelling potential rescue and treatment of the fatal neurodegeneration in

NPC disease patients. Our goal is to use a piggyBac transposon system to reprogram isolated AdiposeStem Cell (ADSC) cultures to a transgene-free iPS state with an NPC-expressing plasmid and then inject

these cells into the cerebellum of NPC-deficient mice to rescue the effects of neurodegeneration. ADSC

were isolated from dissections using C57/BL6cJ and BALB/c mice, and then expanded in vitro. The

ADSC cultures were then transfected with a plasmid expressing ectopic transcription factors (Oct4, Sox2,

and Nanog) using Fugene HD reagent, and then transferred to a mitotically-inactivated feeder layer.

Alkaline Phosphatase (AP) staining, SSEA-1, and Nanog immunofluoresence were used to detect iPSC in

these cultures. Efficiency of the cellular reprogramming event was negligible, however, and detection

tests were largely inconclusive. We speculate that this lack of expression can be attributed to the viral

CMV promoter in our reprogramming plasmid, which has been demonstrated to be inactive in Embryonic

Stem (ES) cells. We confirmed this by testing the pXLBac-CMV-EGFP-2A-Neo-SV40 plasmid in non-

ES state mammalian cells (hek293 line), and noted that GFP was clearly expressed whereas it had not

been in the ADSC transfection. We are now working on incorporating a cellular promoter (hEF1-) in amicroRNA-expressing (miRNA-302/367 cluster) plasmid system, a more effective reprogramming

method. Once successful iPS generation has been confirmed we will move ahead with the injection and

monitoring of NPC-null mice.


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Immunological analysis of a phase I clinical trial: a non-oncolytic fowlpox vaccine affecting Ig-Like

Transcript 2 (ILT2) expression on regulatory and suppressor T cell populations

Brendan Heiden

Biochemistry

College of Science

Advisors: Howard Kaufman and Carl Ruby, Rush University Cancer Center, Chicago, IL

Immunotherapeutic treatment of metastatic melanoma continues to be a great clinical challenge.

Established melanoma tumors evade immune responses of the body through a variety of mechanisms. In

one such possible mechanism, the melanoma microenvironment may cause local T cell tolerance by

down-regulating co-stimulatory molecules, such as B7.1 (CD80). A clinical trial was performed using

two non-oncolytic fowlpox virus vaccines engineered to express the B7.1 co-stimulatory molecule (rF-

B7.1) or to express three co-stimulatory molecules, B7.1, ICAM-1, and LFA-3 (rF-TRICOM). By

collecting patient blood sera, general analysis and T cell phenotypes were monitored throughout the

duration of treatment. In comparison with a related clinical trial using an oncolytic vaccinia virus vaccine

(rV-B7.1), we observed a decrease in both suppressor T cell (T s) and regulatory T cell (Treg) populations

in responding patients. ELISA assays showed an increase in fowlpox and vaccinia antibodies in bothtrials. Healthy donor blood was treated with rV-B7.1 and differential gene expression was determined.

Among the top down-regulated genes was immunoglobulin-like transcript 2 (ILT2). ILT2 is a member of

a superfamily of membranous signaling proteins that possess immunosuppressive function. In particular,

ILT2 modulates T cell activation and may prevent T cell differentiation. Comparing healthy donor and

melanoma patient blood, we saw that suppressor (CD8+Foxp3+) and regulatory (CD4+Foxp3+) T cell

populations both showed increased expression of ILT2 in melanoma. Furthermore, responding patients in

the rV-B7.1 trial showed a significant decrease in CD4+Foxp3+ILT2+ and CD8+Foxp3+ILT2+ T cell

populations. This data suggests that ILT2 expression drastically inhibits the immune response by

preventing T cell differentiation and by inducing Treg and Ts proliferation.


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Lead Poisoning Investigation:Bioavailability of Heavy Metals Following Inhalation and Ingestion

Patrick Kramer

Chemistry

College of Science

Advisor: Gabriel Filippelli, Dept. of Earth Sciences, Indiana University - Purdue University Indianapolis,Indianapolis, IN

Urban children remain plagued by harmfully elevated blood lead levels (EBLL), despite widespread

remediation efforts including removal of the heavy metal lead (Pb) from gasoline and paint. Hundreds of

thousands of children are still Pb-poisoned, with a significant portion having no obvious source of

exposure. Investigation regarding the inhalation and absorption of fine particulate matter (PM) could lend

significant insight into chronic exposure pathways of Pb poisoning. Using national certified soil

standards, absolute and relative bioavailabilities of Pb were measured after samples were introduced into

modified physiologically based extraction tests (PBET), namely gastric and pulmonary fluid (Gamble)

environments. Concentrations of Pb and other metals were obtained from inductively coupled plasma

optical emission spectroscopy (ICP-OES) analysis. Initial results indicate that Pb had increased

bioavailability in gastric solutions, while results for other metals varied greatly between gastric andpulmonary conditions. As expected, the highly acidic environment of the gastrointestinal solution made

the metal-bearing particles susceptible to acid attack, releasing the metals from organic matter. This is

significant because metals accumulate in blood vessels, thereby increasing BLLs. Future investigations

will specifically focus on the bioavailability of Pb in fine materials in gastric and pulmonary

environments, to better understand the specific reactivity of air particulates that are ingested and inhaled

by humans on a daily basis. Specifically, the ultimate goal of this study is to ascertain the reactivity of the

very finest particulates, as these air particulates are small enough to reach the smallest alveoli of the lungs

and enter the pulmonary blood vessels via dissolution.

Funding provided by the Indiana Clinical and Translational Sciences Institute (CTSI).


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Applications of Multi-mode Interference in Fibers

Patrick McIntyre

Physics and Chemistry

College of Science

Advisors: Axel Schlzgen, The College of Optics and Photonics, University of Central Florida, Orlando,FL, and Peter Hofmann, University of Arizona, Tucson, AZ

In this work we demonstrate and investigate two applications of multi-mode interference in optical fibers.

First, an all-fiber temperature sensor is being designed, fabricated and characterized. The underlying

principle here is a temperature dependent shift of the self-imaging wavelength due to multi-mode

interference in a short section of highly multi-mode fiber spliced between two sections of standard single-

mode fiber. In the second part of this work, the above principle has been used to design and implement a

single-mode fiber laser from a multi-mode active fiber by splicing it between two fiber Bragg gratings

written in single-mode fiber. By accurately controlling the length of the active fiber, the mode-fields of

the two single-mode fibers are imaged onto each other, resulting in a minimized coupling loss between

the multi-mode and single-mode fiber sections. The preliminary results of the fiber temperature sensor

are important for the construction of more sophisticated temperature sensors, and they are useful due totheir small size, precision, and temperature range. The results of the fiber laser investigation are

important to the optimization of the design and construction of similar fiber lasers so that they can be

used in other applications.


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Potential Therapeutic Targets for Melanoma

Colleen McKenna

Biochemistry

College of Science

Advisor: Dr. Eduardo Davila, University of Maryland Medical Center, Baltimore, MD

Toll-like receptors (TLRs) are associated with immune cells, and when they are activated TLRs promote

cell survival and cell division. Recent studies show that TLRs are highly expressed in cancer cells,

especially melanoma cell lines. The high expression in TLRs might be due to the high levels of

phosphorylated IRAK, a molecule in the TLR pathway. When IRAK is phosphorylated it turns on the

signaling pathway, which ultimately results in cell division. IRAK-1/4 inhibitor has shown to induce cell

death in melanoma cell lines. A combination therapy of IRAK-1/4 inhibitor with chemotherapy drugs

might be an effective treatment for melanoma. A375, C32, Malme-3M, & SKMEL melanoma cell lines

were studied in order to determine a therapeutic target for melanoma. A combination of IRAK-1/4

inhibitor with vinblastine greatly increased cell death as compared to a therapy with just IRAK-1/4

inhibitor alone. The results show that this could potentially be an effective treatment, but more studies

must be done in order to determine the exact concentration and the effect in vivo of the treatment.


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Solar Infrastructure in India

Grace Meikle

Physics

College of Science

Advisor: Gundu Sabde, Relyon Solar Pvt Ltd, Pune, India

My research was conducted in order to study individual system components, designs, and installation

sites for optimization of off-grid solar applications at a start-up solar infrastructure company located in

Pune, Maharashtra, India. Data showed that component selection, grid availability, shading characteristics

and electrical design can impact the efficiency of the final system. I concluded that India has enormous

potential for off-grid solar applications and that there are many opportunities for innovation in India's

solar market.

Market Analysis of Solar Infrastructure in India

Grace MeiklePhysics

College of Science

Pratap Kanawade, Electrical Engineer

Vikram Kondguli, Finance Consultant

Amit Parshette, Civil Engineer, Pune University

Sushant Satish, Marketing Specialist

Advisor: Gundu Sabde, founder of RelyOn Solar Pvt. Ltd, Pune, India

I worked as an intern for six weeks from May-July 2011 at a company in Pune, Maharashtra, India called

Relyon Solar Pvt. Ltd., founded by Dr. Gundu Sabde. The company focuses on development andinstallation of efficient solar power systems for off-grid applications in India. The purpose of my study

was to acquire a general understanding of off-grid solar technical and marketing challenges by studying

components, designs and installation sites. I tested lights and charge controllers for solar power systems

and compared efficiencies of different solar panel arrangements. I visited some installation sites and

helped compile data for several of Relyon Solars ongoing projects. As a result of my studies, I can see

that India has enormous potential for off-grid solar applications and that by studying components, system

design and applications needs, there are many opportunities for innovation and optimization in the Indian

market for off-grid solar power systems.


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Dissecting glucocorticoid pathways regulating eosinophil viability and activation in asthma

Young Moon

Biological Sciences

College of Science

Konrad Pazdrak, Christof Straub, Rosario Maroto, Yashoda Hosakote,University of Texas Medical Branch, Galveston, TX

Advisor: Alexander Kurosky, University of Texas Medical Branch, Galveston, TX

Rationale: Glucoccorticoids (GC) effectively treat asthma in many patients, although some patients are

steroid resistant. The mechanism of glucocorticoid-mediated suppression of eosinophils, major effector

cells targeted by antiinflammatory therapy, was studied. Eosinophils usually respond to GC with

suppression of function; e.g. viability, in a manner that parallels the clinical response to GC therapy.

However, the mechanism of eosinophil suppression is not completely understood. Most effects of

glucocorticoids are mediated through the glucocorticoid receptor (GCR), which enhances the transcription

of antiinflammatory genes (transactivation) or suppresses proinflammatory transcription factors

(transrepression). We investigated viability of eosinophils exposed to cytokines overexpressed inasthmatic airways (GM-CSF, IL-2, IL-4) and tested apoptosis with nonselective GC (dexamethasone) or

selective GC (Compound A).

Methods: Calcein AM/ethidium homodimer-1 assay for cell viability and phosphorylation of GCR were

tested on eosinophils isolated by CD16-immunomagnetic negative selection from peripheral blood of

healthy donors.

Results: Viability assays revealed differential proapoptotic effect of dexamethasone and compound A on

eosinophils (dexamethasone>compound A). The proapoptotic effect of dexamethasone was mediated by

GCR since GCR antagonist (RU 486) decreased dexamethasone-induced death. Phosphorylation of GCR

on serine-211 revealed further differences between the selective and nonselective GCs.

Conclusion: Novel GCR-binding compounds with selective transrepression and limited transactivation

may provide beneficial effects in eosinophil-mediated pathologies such as asthma. Our findings of GM-

CSF-induced resistance to GC may also have implications for mechanism of steroid resistance and can beexplored in further studies of aberrant GCR signaling in activated eosinophils.

NIH/NHLBI Proteomics Initiative N01-HV-00245.


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Synthesis, Characterization and Optical Properties of CdSe Nanosheets

Rick Morasse

Chemistry

College of Science

Advisor: Masaru Kuno, Dept. of Chemistry and Biochemistry, University of Notre Dame

The synthesis, characterization, and optical properties of high quality CdSe nanosheets are described. A

solution-based approach is used to synthesize the nanosheets by mixing Cd and Se precursors with an

organic fatty acid and noncoordinating solvent at low temperatures with a subsequent cadmium acetate (in

solvent) injection in order to create a Cd rich environment and induce two dimensional (2D) growth. This

leverages advances in the development of high quality colloidal quantum dots (QDs) with those of

producing 1D nanowires in order to create scale-up synthetic procedures for 2D nanosheets. Resulting

rectangular CdSe nanosheets are approximately 20nm in width and 50nm in length with a size distribution

of approximately 25%. Intrasheet width variations are very small, although sheets exhibit both straight

and curved edges along their widths. High resolution transmission electron microscopy (TEM) images

reveal that the sheets are crystalline. Quantum confinement effects are observed in the UV-visible

absorption spectra of the CdSe nanosheets, with first and second absorbances at 465nm and 435nm inaddition to red shifted absorbances based upon the varying thickness of the nanosheets. Synthetic

approaches used to vary the thickness of CdSe nanobelts have been investigated. Ensemble emission

studies were also performed. This facile synthesis affords more opportunities for further investigations of

the optical and electrical properties of 2D nanomaterials. The decoration of CdSe sheets with gold

particles, for use in photochemical hydrogen generation, will be explored in future experiments. Overall,

this research represents a survey of simple synthetic routes towards the size and shape control of 2D CdSe

nanosheets which have potential uses in photovoltaics, optoelectronics, functional materials, and solar

hydrogen generation.


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The Role of Odorant Binding Proteins in Mediating Perception of Taste in D.melanogasterMichael S. Nokes

Biological Sciences

College of Science

Advisor: Shilpa Swarup, Dept. of Genetics, North Carolina State University, Raleigh, NC

The perception of taste controls the intake of nutrients and the avoidance of toxins, and is essential for

survival. We use the fruit fly,Drosophila melanogaster, as a model system to study perception of

aversive ("bitter") compounds, as it has one of the best-characterized chemosensory systems.

Chemosensation inDrosophila is mediated by large multigene families of chemoreceptors, including

olfactory receptors, gustatory receptors, and odorant binding proteins (OBPs). OBP gene family members

are expressed in chemosensory tissues, such as the antennae, maxillary palps, proboscis, tarsi, and wing

margins. Although the contributions of OBPs to olfaction is well-documented, their role in mediating

taste remains largely unknown. In this study we standardized the "CAFE" (capillary feeder) assay to

quantify the responses of flies to bitter compounds. Eight flies were separated by sex and deprived of

food for 24h. These were placed in a vial and three capillaries, filled with either a sucrose solution

containing a bitter tastant or a 50mM sucrose control solution, were fitted through the foam caps of thevials. The vials were kept in a closed, humidified chamber and the flies were given 24h to feed on the

solution; the amount of solution consumed was then measured. We have used the CAFE assay to measure

taste preference for sucrose (control), denatonium benzoate, berberine chloride, N-phenylthiourea,

papaverine hydrochloride and caffeine in lines in which expression of individual OBPs was reduced by

RNAi. We used a previously validated set of 17 OBP RNAi lines and their co-isogenic control to

systematically characterize the importance of OBPs in mediating perception of taste.


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Analysis of TNF receptor expression within the regenerating zebrafish retina

Patrick OHayer

Biological Sciences

College of Science

Craig Nelson and David Hyde, Dept. of Biological Sciences, University of Notre Dame

Advisor: David Hyde, Dept. of Biological Sciences, University of Notre Dame

Constant intense light induces photoreceptor apoptosis within the adult zebrafish (Danio rerio) retina. In

response to this damage, Mller glial cells divide, giving rise to neuronal progenitor cells that transiently

amplify and migrate to the outer nuclear layer where they differentiate into new photoreceptors. Recent

work has demonstrated that this regeneration process is initiated by Tumor Necrosis Factor Alpha (TNF)signaling. Dying photoreceptors express TNF as a trans-acting signal that is required for the maximalnumber of Mller glia to begin proliferating. It is likely that TNF binds a transmembrane receptor onMller glial cells and activates a JAK/Stat3-mediated pathway. However, there are 7 unique TNFreceptors (TNFRSF members) within the zebrafish genome and it is unknown what receptor(s) functions

within this signaling pathway. It is hypothesized that expression of the relevant TNF receptor will beup-regulated as the TNF signaling pathway is activated. To identify the TNF receptor that initiatesMller glial cell division, gene specific RT-PCR and qRT-PCR were conducted using RNA isolated from

both control retinas and light-damaged retinas. Both TNFRSFa and TNFRSF18 were found to be up-

regulated in light-treated retinal tissue. Also, in response to morpholino-mediated knockdown of TNFprotein, both TNFRSFa and TNFRSF18 decreased in expression, suggesting that these two receptors are

downstream of TNF within the cascade. Immunohistochemical analysis using antisera generated againstthe TNFRSFa receptor revealed that TNFRSFa is expressed by Mller glia at the time when they begin

dividing. This data suggests that TNFRSFa binds TNF and initiates regenerative cell division within thelight-damaged zebrafish retina.


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The effect of temperature and diet on the growth and mortality of

Camnula pellucida (Orthoptera: Acrididae)

Kevin S. Park

Mathematics

College of Science

Advisor: Anthony Joern, Division of Biology, Kansas State University, Manhattan, KS

Temperature and diet are important factors that affect the growth and mortality of grasshoppers

(Orthoptera: Acrididae). Camnulapellucida (Scudder) are commonly found species of grasshoppers and

can cause detrimental damage to agricultural crops. This experiment will examine the contribution of

heat-exposure (8 hours vs. 16 hours of preferred temperatures) and food quality (low nitrogen vs. high

nitrogen) to the growth and mortality ofC. pellucida nymphs from UNDERC-East in Upper Michigan. I

hypothesized that heat and diet would significantly affect growth and mortality, with the highest rates in

high heat - high nitrogen conditions. The results showed that heat had a significant effect on nymph

growth, but dietary nitrogen did not. Temperature and diet are both important factors that affect growth

and mortality when the factors are independent of each other, but when the factors were combined, only

temperature showed significant effects. Another experiment also looked at how heat-exposure affectedthe metabolism of the nymphs by measuring food consumption. I predicted that food consumption would

be the highest in high heat conditions because of increased activity in grasshoppers, and the results

supported this hypothesis.


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21

Investigating the Presence of Type B Conformer Complexes in Healthy and Colitis Models

Antoinette Pusateri

Biological Sciences

College of Science

Advisor: Peter Velazquez, Indiana University School of Medicine, South Bend, andDept. of Biological Sciences, University of Notre Dame

In these experiments, the two types of peptide-Major Histocompatibility Complexes being observed are

known as Type A and Type B based on their conformation (shape), which in turn is dictated by the

manner in which they process antigen and present it on the cell surface for T-Cells to recognize. Type A

conformers process native, whole protein through a deep endosomal compartment and then present the

degraded protein (peptide) up to the cell surface. Type B conformers exogenously exchange peptide on

their cell surface1. There are then two types of T-Cells that recognize these conformers. The first

recognizes both Type A and Type B conformers, while the second type of T-Cell only recognizes Type B

conformers. The problem with this is that the second type of T-Cell evades negative selection in the

thymus and so it is not tolerized for2. This means that if it is presented with self-peptide, it will see it as

foreign and counter with an immune attack. Therefore there is the danger in the presentation of peptide asthe Type B conformer complex to the second type of T-Cell.

In an inflammatory context as found in Crohns and Colitis, self-protein may be degraded and

presented as free peptide. So, there is the possibility that Type B complexes are being formed in the gut,

which may potentiate disease. Thus, we are asking the following in this study: do Type B conformers

form in the gut in both a healthy and inflammatory setting, and if so, does this contribute to IBD?

Using T-Cell hybridomas that model the reactivity of the first and second type of T-Cells

explained above, in vitro protein assays are performed to assess the presence of the Type B conformer

complexes in the gut of a strain of mice that exhibit a trans-gene self-peptide called mHel (Hen Egg-white

Lysozyme) on the membranes of their APCs. The presence of these conformers will be tested for in both

a healthy mouse model and DSS (dextram sodium sulfate salt)-induced colitis mouse model.

Experiments thus far have supported the statement that Type B conformer complexes are not formed

when self-peptide is presented in healthy mouse models.

1Zheng Pu, Scott B. Lovitch, Elizabeth K. Bikoff, and Emil R. Unanue, T Cells Distinguish MHC-

Peptide Complexes Formed in Separate Vesicles and Edited by H2-DM, Immunity, Vol. 20, 467476

(April, 2004, Copyright 2004 by Cell Press)2

Daniel A. Peterson, Richard J. DiPaolo, Osami Kanagawa, and Emil R. Unanue, Quantitative Analysis

of the T Cell Repertoire that Escapes Negative Selection, Immunity, Vol. 11, 453462, (October, 1999,

Copyright 1999 by Cell Press)


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22

Predicting Antimalarial Mode of Action from Gene Expression Signatures

Roger S. Smith

Biological Sciences

College of Science

Geoffrey H. Siwo, Asako Tan, and Michael T. Ferdig, Dept. of Biological Sciences, Eck Institute forGlobal Health, University of Notre Dame

Advisor: Michael T. Ferdig, Dept. of Biological Sciences, University of Notre Dame

Malaria is a mosquito-borne infectious disease caused by a parasite of the genusPlasmodium that is

responsible for approximately one million deaths each year, affecting mostly young children and pregnant

women. The mechanisms of action of antimalarial drugs are largely unknown. Here, we test the idea that

exposure of parasites to drugs results in gene expression changes in several genes, leaving behind a

unique signature that reflects the drug mechanism of action. Comparing the gene expression profile of

drugs targeting a specific pathway with those of other pathways may define relationships between the

drugs. This signature of gene expression would be unique to drugs targeting a given pathway of the

parasite. To test this idea, we exposed malaria parasite cultures to drugs that target different pathwaysand measured gene expression levels using microarrays. For each pair of drugs, we computed the

correlations between the gene expression levels of parasite cultures obtained after perturbations by the

drugs for a period of 2 hours. Consistent with our hypothesis, we found that drugs targeting the same

metabolic pathways do confer similar changes on gene expression. We also applied a network view of

the pairwise relationships between the effects of the drug on gene expression and uncovered complex

effects of some drugs. For instance, the network approach confirmed that the anti-cancer drug

methotrexate has effects on both the folate and DNA damage repair pathways. In addition, the approach

predicted a novel and an unexpected relationship between chloroquine and 5-Fluorouracil. We are

currently extending this idea using more drugs targeting distinct pathways to develop a system that could

aid the discovery of the mechanism of action of current and future anti-malarials.


23/29

23

Real roots properties and asymptotic normality of graph Stirling numbers

Do Trong Thanh

Mathematics

College of Science

Advisor: David Galvin, Dept. of Mathematics, University of Notre Dame

For a graph G and a positive integerk, thegraphical Stirling numberS(G,k) is the number of partitions of

the vertex set ofG into knon-empty independent sets. Equivalently it is the number of proper colourings

ofG that use exactly kcolours, with two colourings identified if they differ only on the names of the

colours. IfG is the empty graph on n vertices then S(G,k) is S(n,k), the Stirling number of the second

kind. In this note we first consider Stirling numbers of forests. We show that if (Fc(n)

n)n 0 is a sequence of

forests withFc(n)

n having n vertices and c(n)=o({n/logn}) components, and ifXc(n)

n is a random variable

that takes value kwith probability proportional to S(Fc(n)

n,k) (that is,Xc(n)

n is the number of partitionclasses in a uniformly chosen partition ofF

c(n)n into non-empty independent sets), thenX

c(n)n is

asymptotically normal, meaning that suitably normalized it tends in distribution to a standard normal.

This generalizes a seminal result of Harper on the ordinary Stirling numbers. Along the way we give

recurrences for calculating the generating function of the sequence (S(Fcn,k))k 0, show that thesefunctions have all real roots, and exhibit a number of different interlacing patterns between the roots of

pairs of consecutive generating functions. We next consider Stirling numbers of cycles. We establish

asymptotic normality for the number of partition classes in a uniformly chosen partition ofCn (the cycle

on n vertices) into non-empty independent sets. We give a recurrence for calculating the generating

function of the sequence (S(Cn,k))k 0, and use this to give a direct proof of a strong log-concavity result

that had previously been proven only in a very indirect way.


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24

The genetic basis of sperm competitiveness in monogamous and promiscuous Peromyscus mice

Cong Charles Xu

Environmental Sciences, Chinese

College of Science

Heidi S. Fisher, Emily Jacobs-Palmer, and Hopi E. Hoekstra,Museum of Comparative Zoology, Harvard University

Advisor: Hopi E. Hoekstra, Museum of Comparative Zoology, Harvard University

Many of the most extraordinary traits in nature are the result of sexual selection, or the competition for

increased fertilization success. To study the genetic basis of traits associated with sperm competition, it is

ideal to use a model that spans this continuum of mating strategies, yet one where divergent groups

remain interfertile. Two closely related species exhibit highly-divergent strategies: the promiscuous deer

mouse (P. maniculatus) and the monogamous oldfield mouse (P. polionotus). A spermatozoons midpiece

contains the array of mitochondria that power its flagellar motion, which largely determines its motility.

As predicted, midpiece length is correlated with speed inPeromyscus, and using Quantitative Trait Locus

(QTL) mapping, members of the Hoekstra lab have identified a genomic region associated with this trait.

Fine-scale mapping through a candidate gene approach identified 7 candidate genes with sequences for 15different introns. Restriction digest assays were developed for 2 of the candidate genes. Besides

increasing flagellar power, rodent sperm cells can form motile aggregations to increase their swimming

speed, often at substantial individual cost. Fisher and Hoekstra showed that in P. polionotus (monogamous and lacking sperm competition), spermatozoa aggregate indiscriminately with sperm from

other males, whereas sperm from the promiscuousP. maniculatus aggregate selectively and discriminate

against unrelated sperm, even when the other sperm belong to a full sibling. A protocol for the laser

capture microdissection of individual sperm clumps was successfully verified using whole genome

amplification, a first step towards identifying the gene responsible for sperm recognition during aggregate

formation.


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25

Information Tables (Jordan Galleria)

Biology Club (www.nd.edu/~bioclub/new/new.htm)

Biology Club aims to encourage an interest in Biology and fellowship among the club's

members. These goals are accomplished by multiple avenues. The club holds meetings anddiscussions among student members throughout the school year, and works to provide special

biology related activities to encourage learning outside the classroom, such as dissection nightduring Geek Week. Furthermore, Biology Club offers educational and entertaining activities for

student members and non-members such as the Faculty Student Research Networking Dinner orscience themed movie watches.

Contact: Michael D'Netto ([email protected]), Academic Commissioner.

The Career Center (careercenter.nd.edu/)

The Career Center offers resources for all students including ideas on searching for an internship

or job, tips on writing your resume and cover letters, and contacting and networking with NotreDame alums and others. Lists of past internships at which science students have participated and

hints on making a successful internship connection are also available. Workshops on theInternship Search for Science Students will be held monthly from October through January, sowatch for details and attend one of these informative sessions.

Contact: Laura Flynn ([email protected]), Science and Engineering Career Counselor.

The Center for Undergraduate Scholarly Engagement (CUSE, cuse.nd.edu)

CUSE has a mission to promote the intellectual engagement of Notre Dame students through

undergraduate research and post-graduate fellowship application. It also promotes engagementthrough student-run initiatives like The Hub, an online, multimedia networking site where

students can exchange ideas and information, and share scholarly and creative work.

Contact: Cecilia Lucero ([email protected]), Assistant Director.

The Four Horseman Society (www.nd.edu/~horsemen/likebox.html)

This is a student-run organization of graduate and undergraduate members meeting to learn moreabout the process of vetting and capitalizing innovations. Since its inception, the club has

continued to gain momentum, with a regular attendance of 50 or more at its events. Starting in

2009, the club welcomed students in the College of Science, greatly adding to our ranks. Recentevents have included those on how to identify ideas with commercializing potential, entering theMcCloskey business plan

Contact Person: Lynette Prezyna ([email protected]), Faculty Advisor.


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26

Hesburgh Library (library.nd.edu)

The Hesburgh Libraries system includes the main Hesburgh Library, as well as the O'Meara

Mathematics Library in Hayes-Healy, the Engineering Library in Fitzpatrick, the Chemistry-Physics Library in Nieuwland, the Architecture Library in Bond Hall, and the Mahaffey Business

Information Center in Mendoza. The Libraries provide critical support for your research,

including access to thousands of online databases, journals, DVDs, books, maps and more.Librarians are prepared to assist you with your research by providing individual researchconsultations, or through a variety of library workshops and in-class instructional sessions.

Theres also the Library's Undergraduate Research Award, http://guides.library.nd.edu/subject-guide/77-2012-Undergraduate-Library-Research-Award. To contact your subject librarian use

www.library.nd.edu/directory/subjects or the Ask-A-Librarian service at asklib.nd.edu/. Registerfor a workshops at www.library.nd.edu/instruction/workshops.shtml

Contacts: Parker Ladwig ([email protected]), Biological Sciences and Mathematics librarian;Thurston Miller [email protected], Chemistry and Physics Librarian; Carol Brach

([email protected]), Engineering Librarian; Cheri Smith ([email protected]),Coordinator for Library Instruction.

Ruth M. Hillebrand Center for Compassionate Care in Medicine

The central mission of the Center for Compassionate Care in Medicine is to provideundergraduate students entering medical school and other health professions with a foundation in

compassionate care and medical interpersonal skills before pursuing graduate medical training.Along with instruction and networking, the Center will also conduct research in Caring Science.

Such research will include an undergraduate research team. This research team will focus onissues related to how physicians and patients perceive caring and compassion in their medical

care. The research team will meet weekly to review recent research on this issue with the goal of

designing and implementing research studies. One project will involve interviewing patients ontheir perceptions of medical care focusing especially on how bad news is discussed with themand how compassionate care is defined as they undergo treatment. A second project will focus

on how clinicians rely on their spirituality and/or philosophy of caring as a way to maintaincaring practice and buffer burnout. Other projects include analyzing qualitative data on

exemplary physicians on the art of medicine and quantitative data on the relation betweenempathy and burnout among physicians and other health care professionals.

Contact: Dominic Vachon ([email protected]), Director

The Hub (thehub.nd.edu)

The Hub is a student-run website sponsored by CUSE with the tagline, "Your academic life

online". This academic networking site provides a space for students to discuss their ideas and toshare their academic work in an online setting. Additionally, the Hub provides resources such as

a virtual poster wall and PDF copies of student publications.

Contacts: Kirsten Adam ([email protected]) and Paul Baranay ([email protected]), Editors.


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The Kellogg Institute (kellogg.nd.edu)

The Kellogg Institute is an international research institute that focuses on democracy and human

development. To engage undergraduate students in its mission, the Institute offers a variety ofprograms including funded internships, research grants, and fellowships. Information regarding

all of these programs can be found at http://kellogg.nd.edu/students/index2.shtml

Contact: Holly Rivers ([email protected]), Assistant Director.

Museum of Biodiversity (science.nd.edu/jordan/about/museum-of-biodiversity.shtml)

The Museum of Biodiversity, located near the northern end of Jordan Hall, showcases theDepartment of Biological Sciences extensive collection of amphibians, fishes, birds, mammals,

and insects that have been collected over the last 150 years. As part of the museum, theherbarium preserves the scientifically important collection of dried and pressed plants of the

Greene-Nieuwland Herbarium. There are many opportunities for undergraduate research projectsincluding identification and organization of specimens contained in museum collections,

development of databases of plants and animals and their distributions, identification of rare,endangered, or invasive species, and development of thematic displays. Projects can be

supported by the Robert E. Gordon Museum of Biodiversity Undergraduate Research SupportFund.

Contacts: Barbara Hellenthal ([email protected]), Curator, and Ron Hellenthal([email protected]), Professor.

National Science Foundation Research Experience for Undergraduates (NSF-REU)

Notre Dame currently has two extant NSF-REU programs in the Depts. of Physics and Biology,which reflect similar programs available across the nation. For many years there was also very

successful program in the Dept. of Mathematics. Programs usually consist of 10 weeks of full-time research, together with a intensive schedule of various enrichment activities, and typically

provide stipend, housing, and travel allowance. Application materials for the BiologicalSciences program can be found at http://nd.edu/~biosreu/, and for the Physics program at

physics.nd.edu/research/reu/. Such REU programs at other institutions funded by NSF can befound at www.nsf.gov/crssprgm/reu/index.jsp.

Contacts: Michelle Whaley ([email protected]), Teaching Professor and Director;Umesh Garg ([email protected]), Professor and Director, Frank Connolly

([email protected]), Professor.

ND Chapter of the American Chemical Society (sites.google.com/a/nd.edu/ndsaacs/ )

The ND Chapter for ACS strives for excellence and unity within their major, providing

assistance through tutoring for underclassmen and mutual support for our peers. We advocatesuccess through teamwork and excellence in Chemistry and Biochemistry.

Contact: [email protected]


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Notre Dame Society of Physics Students (www.nd.edu/~physclub/)

The Notre Dame Society of Physics Students (SPS) is a local branch of the national SPS,committed to preparing students to be contributing members of the professional physics world

through exposure to research, networking opportunities, and undergraduate community building(a.k.a "physics fun"). SPS sponsors trips to FermiLab, tours of ND research facilities, and hosts

various other events including physics movie watches and Coffee with Your Professors.

Contact: Michelle Consiglio ([email protected]).

Scientia (scientia.nd.edu)

Scientia, ND's own student-run Journal of Undergraduate Research, is looking for student editorsand news writers for this year's publication. Editors should have some research experience and

be interested in reading, critiquing, and commenting on student research. News writers can befrom any discipline and must simply want to write about some of the cool things happening in

the College of Science. Interested students should write the editors. Don't have time to work forScientia but still want to be involved? Come to one of our general meetings and "Talk Science"

with student and faculty researchers in an informal setting. Pizza is always provided andeveryone is welcome.

Contacts: Nancy Paul ([email protected]), Paul Baranay ([email protected]), Co-Chief Editors.

University of Notre Dame Environmental Research Center (UNDERC,

www.nd.edu/~underc/)

UNDERC offers two 9 week, 6 credit summer programs: East in the Upper Peninsula of

Michigan and West in western Montana. Each has a set of modules (East: amphibian/reptile,insect, forest, aquatic, and mammal/bird ecology; West: environmental history tour,grassland/wildlife, montane, avian, and Native American ecology), but the focus is an

independent research project for each student mentored by a faculty member or Ph.D. candidate.Admission to East is open to sophomores and above, and West requires attending East. Apply

by early November on the UNDERC webpage and decisions are announced in early December toenroll in the preparatory course (1 cr., Spring semester).

Contact: Gary Belovsky ([email protected]), Professor and Director.

The Writing Center (writingcenter.nd.edu)

The University Writing Center offers free, one-on-one consultations with writers from all

disciplines, at any level of study, at any stage in the composing process--from understanding anassignment, to developing a thesis, to organizing the paper, to revising the first draft, to editing

the final product. To make an appointment, visit the online appointment scheduler at thewebsite.

Contact: Matthew Capdevielle ([email protected]), Director.


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Undergraduate Research Internships Information Night (Jordan 105)

Organizer - Mark Olsen ([email protected])

8:00 - 8:05 Introductions

8:05 - 8:20 Paul Baranay - Metassembler: A tool for improvingde novo genome assembly,Cold Spring Harbor Laboratory, Undergraduate Research Program, NY.

8:20 - 8:30 Mary Gaugler -Relationship between PTEN Pathway Signaling and Autism

Spectrum Disorders, Genomic Medicine Institute at the Cleveland Clinic,Cleveland, OH.

8:30 - 8:40 Jessica Choi -National Science Foundation-funded REU program at theUniversity of Oklahoma, Norman, OK.

8:40 - 8:50 Karen Scheller -Relationship of public knowledge of red tide and fertilizerregulations to assess needs for future public education, Mote Marine Laboratory

Research Experience for Undergraduates program, Sarasota, FL.

8:50-9:00 Questions

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