IUPUI Research Day

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https://hdl.handle.net/1805/4255

Research Day provides an opportunity for the IUPUI faculty, staff, and students, and their academic, industrial, governmental partners, and the broader community, to come together and learn more about the research enterprise at IUPUI, explore new collaborations, and lay the foundation for new partnerships. IUPUI Research Day is sponsored by the IUPUI Office of the Vice Chancellor for Research.

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1H NMR of Deep Eutectic Solvents
(Office of the Vice Chancellor for Research, 2014-04-11) Wallis, J. Lincoln; Sapir, Liel; Harries, Daniel; Petrache, Horia I.; Ray, Bruce D.
Deep Eutectic Solvents (DESs) form between a variety of quaternary ammonium or phosphonium salts and hydrogen-bond donors. Over the past decade, DESs have been studied as green solvents with potential applications in industrial processes, chemical extractions, and pharmaceuticals. The recent suggestion that many plants produce natural deep eutectic solvents (NADES) from primary metabolites led to investigation of the potential uses of DESs in biophysics research. This study examined the 1H NMR spectra of the choline chloride:urea 1:2, and choline chloride:ethylene glycol 1:3 molar ratio DES. Spectra of the choline chloride:urea 1:2 with various solutes were acquired to see what effect these solutes had on the DESs NMR spectrum. For both DESs tested, the NMR spectra were a superposition of the spectra of the components. DES-solute spectra showed that interaction between components persisted, indicating the solvent properties of the DESs were not lost upon addition of solutes.
3D Assessment of Nasopharyngeal and Craniofacial Phenotypes in Ts65Dn Down Syndrome Mice Treated with a Dyrk1a Inhibitor
(2014-04-11) Starbuck, John M.; Harrington, Emily; Kula, Katherine S.; Ghoneima, Ahmed A.; Roper, Randall J.
Background: Down syndrome (DS) originates from having three copies of chromosome 21 (i.e. Trisomy 21). DS is associated with many detrimental phenotypes including intellectual disabilities, heart defects, abnormal craniofacial development, and obstructive sleep apnea, which develops from restricted nasopharyngeal airways and an underdeveloped mandible. Ts65Dn mice are trisomic for about half of the orthologs on human chromosome 21 and display many phenotypes associated with DS including craniofacial abnormalities. Dyrk1a is found in three copies in Ts65Dn mice and individuals with DS, and thought to be a root cause of the craniofacial phenotypes. Epigallocatechin 3-gallate (EGCG) is a green tea polyphenol and inhibitor of Dyrk1a activity. Purpose: We hypothesize that decreased Dyrk1a activity in Ts65Dn mice will ameliorate craniofacial dysmorphology. Methods: To test our hypothesis we compared Ts65Dn mice with two or three copies of Dyrk1a and compared Ts65Dn mice with and without prenatal EGCG treatment. EGCG treated mothers were fed 200mg/kg EGCG on gestational day 7. Six week old mice were sacrificed and their heads imaged using micro-computed tomography (μCT). From μCT images, we measured nasopharyngeal airway volume and anatomical landmarks (n = 54) from the facial skeleton, cranial vault, cranial base, and mandible. Mean nasopharyngeal airway volumes were graphically compared, and a landmark-based multivariate geometric morphometric approach known as Euclidean Distance Matrix Analysis (EDMA) was carried out to assess local differences in craniofacial morphology between trisomic mouse samples. Results: Our preliminary results indicate that EGCG treatment and reduced Dyrk1a copy number increases mean nasopharyngeal airway volume in Ts65Dn mice. Craniofacial morphometric differences were found among all samples. EGCG treatment increased portions of the mandible and decreased portions of the cranial vault and cranial base. Conclusion: Preliminary analyses suggest that both EGCG treatment and reduced Dyrk1a copy number affect craniofacial morphology.
Ab initio study of anisotropic mechanical properties of LiCoO2 during lithium intercalation and deintercalation process
(Office of the Vice Chancellor for Research, 2016-04-08) Wu, Linmin; Zhang, Jing
The mechanical properties of LixCoO2 under various Li concentrations and associated anisotropy have been systematically studied using the first principles method. During the lithium intercalation process, the Young's modulus, bulk modulus, shear modulus, and ultimate strength increase with increasing lithium concentration. Strong anisotropy of mechanical properties between a-axis and c-axis in LixCoO2 is identified at low lithium concentrations, and the anisotropy decreases with increasing lithium concentration. The observed lithium concentration dependence and anisotropy are explained by analyzing the charge transfer using Bader charge analysis, bond order analysis, and bond strength by investigating partial density of states and charge density difference. With the decrease of Li concentration, the charge depletion in the bonding regions increases, indicating a weaker Co-O bond strength. Additionally, the Young's modulus, bulk modulus, shear modulus, and toughness are obtained by simulating ab initio tensile tests. From the simulated stress-strain curves, LixCoO2 shows the highest toughness, which is in contraction with Pugh criterion prediction based on elastic properties only.
Abstract thinking and its correlates with insight, metacognition and social cognition in the early and prolonged phases of schizophrenia
(Office of the Vice Chancellor for Research, 2016-04-08) Thakkar, Rut; Vohs, Jenifer
Schizophrenia is a severe mental illness that affects approximately one percent of the population worldwide. Symptoms of the illness include abnormal perceptual experiences, social withdrawal and cognitive impairments, with the mechanisms underlying the illness still being ambiguous. Abstract thinking, a core deficit in schizophrenia, is characterized by adaptability, flexibility, and the use of concepts and generalizations. However, its changes along with the different phases of the illness are still obscure. The limited data available suggests that those in the earlier phases of schizophrenia tend to have a higher capacity for abstraction than those in the prolonged phases (Wang et. al, 2013). In addition to the differences across the illness phase, supplemental studies further suggest that abstract thinking could be related to clinical insight, or the awareness of one’s illness (Dickerson, et. al, 1997). Therefore, in this study we examined the differences in abstract thinking between two groups; patients with chronic schizophrenia and patients with early onset schizophrenia. Furthermore, we conducted exploratory analyses of abstraction with clinical insight, metacognition and social cognition, hypothesizing that patients with better abstract thinking would possess better insight and cognition. The results from the 70 patient study indicate that while abstract thinking did not differ across the phases of the illness, it was significantly correlated with insight, metacognition and social cognition. This relationship between abstract thinking and insight and cognition, elucidated by the theory that more fluid and liberal thought patterns would enable patients to contemplate their own illness and its symptoms, could be crucial in developing novel therapeutic approaches for treating psychosis and might lead to better outcomes.
Academic Success of English Language Learners: Are Mainstream Teachers Underprepared?
(Office of the Vice Chancellor for Research, 2015-04-17) Covarrubias, Maritza; Teemant, Annela; Bhathena, Cathy
The population of English Language Learners (ELLs) in Indiana schools has increased over the years and will keep increasing. However, the graduation rates of ELLs and their standardized test scores are not improving. After reading various articles about why this might be occurring and using my personal experience as an ELL, there was one factor that stood out to me: mainstream teachers are underprepared to work with ELLs. The purpose of this research project is to investigate how prepared mainstream teachers feel to work with ELLs and what, if any, are the barriers that keep them from doing so. For this project, I will be using mixed methods research: qualitative and quantitative. Qualitative research will be the primary method and will be collected in the form of teacher interviews. These interviews will include questions about how teachers feel about working with ELLs and the teachers’ observations about how ELLs function in their classrooms. The qualitative research will be supported by quantitative research that will be collected through surveys and classroom observations of teacher pedagogy. The overall goal of this project is to help make classrooms places where ELLs can be academically successful and improve graduations rates and test scores.
Acceptance of a Risk Estimation Tool for Colorectal Cancer Screening
(Office of the Vice Chancellor for Research, 2016-04-08) Luckhurst, Cherie; Imperiale, Tom; Matthias, Marianne S.
Abstract: While colonoscopy is the most prevalent screening test for colorectal cancer (CRC), it is often too expensive, too uncomfortable, or too time-consuming for patients. Non-compliance is common. Recently, fecal immunochemical testing (FIT) has become a guideline-recommended alternative. The FIT is a non-invasive, inexpensive method that requires no uncomfortable preparation by patients. The decision to recommend the colonoscopy or the FIT is based on the patient’s estimated risk for CRC. Several countries have created risk prediction tools to help identify patients at high risk for advanced colorectal neoplasia (the combination of CRC and advanced, precancerous polyps). A U.S.-based prediction tool was recently published1 that uses five easily and reliably measured factors (age, sex, a first degree relative with CRC, waist circumference, and cigarette smoking history) to quantify risk. We aimed to learn the impressions of clinicians and patients to this risk estimation tool. In the first phase of this study, we used a semi-structured format to interview clinicians at a VA medical center and a non-VA hospital. Using a paper prototype of the risk estimation tool, we asked about its usefulness to estimate risk and to aid their selection of a CRC screening tool. Using a grounded theory approach, we analyzed the interview transcripts and identified major themes. We found that clinicians thought the tool was clear and easy to use. However, they are unlikely to use it as a decision aid until FIT is more widely-endorsed as an acceptable alternative screening test. In phase two of the study, we will interview patients to assess their responses to the tool.
Access to Complex Dental Treatment for Patients with an Intellectual/Developmental Disability
(Office of the Vice Chancellor for Research, 2012-04-13) West, Darlene
Third and fourth year dental students obtain clinical experience providing dental care to intellectually and developmentally disabled community members by participating in a clinical elective course offered in the IU School of Dentistry, through a partnership with Goodwill. This partnership enables students to provide dental services in Goodwill locations. Dental students work to provide access to much needed complex dental treatments for patients with intellectual/ developmental disabilities throughout the community.
ACCESS TO SERVICES FOR THE HOMELESS
(Office of the Vice Chancellor for Research, 2012-04-13) Bozzo, Anthony; Wilson, Jeffrey S.
My project is based on research done in the anthropology and geography departments by myself, Dr. Zimmerman and Courtney Singleton pertaining to homeless encampments in Indianapolis. This poster presentation illustrates locations of selected encampments and their access to service providers. Geographic information system (GIS) technologies were used to conduct a network analysis that visually shows access to services and quantifies travel time and network distance to selected service locations. The analysis presented is based on data collected by my colleagues from subjects in one specific camp describing preferred travel routes, distances traveled and services needed- prescription medication for example. I plan to apply this analytical method to other encampments to create a model of hypothetical routes based upon tow paths, walking trails and street networks.
Acetylation of DNA Polymerase Beta Regulates the Choice of the Base Excision Repair Pathway
(Office of the Vice Chancellor for Research, 2016-04-08) Howald, Olivia; Balakrishnan, Lata
Base excision repair (BER) is the main pathway through which base damages are repaired in the cell. Single nucleotide damage can be corrected either through short patch BER (SP-BER), in which the single damaged base is replaced, or long patch BER (LP-BER), in which two or more nucleotides can be replaced. Several proteins are involved in the process including DNA polymerase beta (pol β) and FEN1, both of which are the focus for this study. DNA pol β is a multifunctional protein which contains both polymerase and lyase properties. In LP-BER, pol β displaces the uncleaved 5’dRP moiety into a flap structure which is recognized and cleaved by FEN1 and subsequently ligated by DNA ligase 1. Previous in vitro studies show that pol β acetylation reduces lyase activity, requiring repair to proceed via LP-BER. In this study, we determined the effect of in vitro acetylation on the enzymatic activities of DNA pol β and FEN1. Both unmodified and acetylated forms of pol β were tested for their synthesis and strand displacement activities. Interestingly, acetylated forms of pol β showed much greater activity at all concentrations versus unmodified forms. Interestingly we also found that FEN1 cleavage activity was increased in reactions containing acetylated pol β compared to the unmodified form due to the increased strand displacement activity of the polymerase. Our results suggest that the acetylated form of DNA pol β more actively participates in LP-BER, creating longer strands of corrected, higher fidelity nucleotides.
Acetylation of Replication Protein A (RPA) Improves its DNA Binding Property
(Office of the Vice Chancellor for Research, 2016-04-08) Surendran, Sneha; Ononye, Onyeka; Balakrishnan, Lata
Genome maintenance is critical for cellular survival and growth. Replication Protein A (RPA), a single-strand DNA (ssDNA) binding protein, is vital for various aspects of genome maintenance such as replication, recombination, repair and checkpoint activation. RPA binding to ssDNA protects it from degradation by cellular nucleases, prevents secondary structure formation and from illegitimate recombination. Within the cell, RPA is subject to many post-translational modifications including phosphorylation, SUMOylation and ribosylation. These modifications regulate the activity of RPA with DNA and other binding partners. RPA has been reported to be also modified by acetylation. We found that human RPA (hRPA) can be in vitro acetylated by p300, an acetyl transferase (AT). To study the effect of this modification on its ssDNA binding function, we made use of electro-mobility gel shift assay (EMSA) and bio-layer interferometry (BLI) technology. Using various length oligos, we tested the binding property of unmodified and acetylated RPA. Our results showed that acetylation of RPA increased its binding affinity compared to unmodified RPA. Interestingly, the acetylated form was also able to bind more stably to shorter length oligos compared to the unmodified form. This suggests that the acetylation of RPA improves its ssDNA binding function. This alteration in its enzymatic activity would have significant implications in maintenance of genome fidelity since improved DNA binding function of RPA will protect the genome from both endogenous and exogenous stresses. Additionally, using mass spectrometry analysis we have identified the lysine residues that get modified by the acetyl group both in vitro and in vivo. We are currently studying the factors that trigger this post-translational modification in the cell.

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