IUPUI Research Day 2016

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https://hdl.handle.net/1805/9277

A program describing the Research Day 2016 events and posters is available from: http://hdl.handle.net/1805/9288.

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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.
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.
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.
Active Gaming and Energy Expenditure in Healthy Adults
(Office of the Vice Chancellor for Research, 2016-04-08) Carey, Christopher; Naugle, Keith; Ohlman, Tom; Mikesky, Alan; Naugle, Kelly
The rise in sedentary behavior in US society, along with the associated health risks, makes it necessary to find effective solutions to increase physical activity at all levels. Studies on active gaming have shown promising results in the use of active gaming as a viable exercise tool that combines physical activity with entertainment. However, the research is still mixed on whether active games can elicit similar responses as traditional cardiovascular exercise, such as jogging on a treadmill. This study examined whether participants playing active games could reach a moderate intensity level as defined by the American College of Sports Medicine as 3.0 METs while playing with and without specific instructions designed to maximize physical activity. Twenty young adult participants completed one training session and four experimental sessions. During each session, participants played two 15-minute periods of either Kinect tennis, Kinect boxing, Wii tennis, and Wii boxing. In period one, participants played at a self-selected intensity. During period two, participants were given specific instructions on how to play which were designed to maximize movement during play and down time. During game play, participants wore a portable gas (VO2/VCO2) analyzer to measure energy expenditure. Metabolic equivalents (METS) were analyzed with a repeated measures ANOVA. During period 1, Kinect boxing was able to elicit the highest METs, 3.097±0.3, from the participants. METS during period 2 was significantly greater than during period 1 across all games (p<.001). Participants were able to reach higher than 3.0 METs while playing each of the games during period 2. Regardless of the period, Kinect boxing elicited greater METS than Wii boxing and Wii Tennis (P<.001). This shows evidence that active gaming not only can elicit a moderate intensity level of physical activity, but that specialized instructions can enhance the effects of the active games.
Aminolytic Cleavage from Wang Resin. A New Distributed Drug Discovery Laboratory for the Undergraduate Curriculum
(Office of the Vice Chancellor for Research, 2016-04-08) Scott, William L.; Burris, Sarah D.; Hitchens, Jake R.; Samaritoni, J. Geno; O’Donnell, Martin J.
When treated with ammonia or methylamine, unnatural amino acids bound to Wang resin (1) are released as their corresponding amides 2 in good yield and purity. When carried out at room temperature, aminolytic cleavage proceeds slowly with a four-day exposure to ammonia in methanol representing an optimal reaction time. Aminolytic cleavage proceeds well with unhindered primary amines, however, the hindered amine isopropylamine and benzylamines are unacceptably slow to effect cleavage. Use of the secondary amine pyrrolidine led to a complex mixture. Due to the large stoichiometric amine excess required, the scope is currently limited to unhindered, volatile, primary amines. The overall synthesis of 2 from BPI-Gly-Wang resin represents a new Distributed Drug Discovery Laboratory (D3-7) and was rolled out to the spring 2016 Organic II laboratory.
Analysis of Polysaccharide and Biofilm Production of the Emerging Cystic Fibrosis Pathogen Stenotrophomonas maltophilia
(Office of the Vice Chancellor for Research, 2016-04-08) Casiano-Rivera, Félix M.; Anderson, Gregory G.
Stenotrophomonas maltophilia is an emerging Cystic Fibrosis (CF) lung pathogen, which displays high intrinsic resistance to a number of different antibiotics. Additionally, S. maltophilia is thought to increase antibiotic resistance by forming biofilms during infection. Biofilm disruption could promote clearance of the microorganism from CF-infected lungs. However, the genetic, biochemical and immunological mechanisms underlying S. maltophilia biofilm formation are not well understood. Secreted polysaccharides have been proven to form a vital component of the matrix that surrounds and protects biofilm bacteria. Hundreds of S. maltophilia mutants were generated by transposon mutagenesis and screened for strains with reduced polysaccharide secretion.. These strains were screened through the use of agar plates containing the polysaccharide-binding dye, Congo red. Experimental controls included a S. maltophilia wild-type strain (positive control) and a confirmed polysaccharide deficient mutant (negative control). A Congo red liquid binding assay was utilized to identify the amount of Congo red bound in the samples, which confirmed the amount of polysaccharide present in them. A total of 1,728 mutants were screened with 61 mutants showing reduced polysaccharide production. The mutants were further narrowed down to 8 samples showing the most consistent phenotype. Arbitrary-primed polymerase chain reactions (AP-PCR), followed by sequencing, will be performed on the selected samples in an effort to identify the genes mutated in polysaccharide deficient strains. We will also perform immunological assays in an effort to understand underlying immune responses to S. maltophilia. In order to determine the effects of the deletion of gpmA in S. maltophilia, we will be performing an in-vitro co-culture assay using the wild-type strain and the gpmA mutant strain. These studies will yield evidence to the molecular process involved in polysaccharide production, which could lead to mechanisms to disrupt biofilm formation in CF patients.
Application of Social Media Platforms for the Development of College Basketball Attendance
(Office of the Vice Chancellor for Research, 2016-04-08) Fulton, Nathaniel; Devenney, Parker; Morgan, Zachary
The purpose of the current study was to examine why college students do not attend college basketball games. After surveying 116 college students at Indiana University-Purdue University Indianapolis (IUPUI), one of the biggest reasons for poor basketball game attendance was due to an overall lack of awareness of the game information. Students did not realize that basketball games were taking place throughout the week. Current studies showed that a college’s athletic website and social media platforms were the first places students looked at in order to find out game information. The survey found that a majority of students used three of the four major social media platforms, Twitter, Facebook, and Instagram, on a daily basis. With the shortened attention span of Generation Y and Z, social media platforms are the most effective way to capture the attention of those with short attention spans (Gausby, 2015). Comparisons of similar Division I-AAA universities and their athletic websites were used to find what makes a strong athletic website, as spectators visit a universities’ athletic website first for information on upcoming games and events. In addition, the results of the study indicates that winning alone does not necessarily provide a lasting positive impact on attendance. Full utilization of social media with a mix of a strong official athletics website best captures the attention of Generation Y and Z students. Having a strong online presence keeps the awareness of basketball games throughout the season at the forefront of student’s minds. A core of Generation Y and Z fans can be built through a strong online presence, as this is what they use for identification purposes. With this utilization, college basketball games can see an increase in attendance as fan loyalty is built with technology-driven students.
Artsmesh- An Incremental Development in Telematic Art
(Office of the Vice Chancellor for Research, 2016-04-08) Tyson II, Alan B.; Deal, Scott; Fields, Kenneth
Within the past two decades, telematic art has pushed technological boundaries and created opportunities for artists to collaborate in ways that were not once possible. For example, Auksalaq, a telematic opera created by Scott Deal, DMA, in 2011, incorporates both JackTrip Audio and ConferenceXP Video. Some social media platforms such as Skype and Google Hangouts have also integrated audio and video within their interfaces in order to explore these possibilities; however, there are limitations that some practices have failed to address such as compressed (lossy) formats of audio and/or video. Similarly, other barriers such as high latency and minimal navigation control have often made network music performance (NMP) a limited experience and not an equal alternative to traditional, real-time performance. The purpose of this project is to help test a beta prototype of Artsmesh, a protocol that integrates high quality audio and video for live peer-to-peer (P2P) NMP. Artsmesh contains fourteen panels that are customizable to fit a wide range of network setups. It also incorporates Internet Protocol version 6 (IPv6), Open Sound Control (OSC), Jacktrip, ffmpeg, Youtube, along with other features, making it the ideal choice for artists that have focused/professional needs. The ability for Artsmesh to precisely route high quality audio also makes it a preferable option for recording and mixing engineers who participate in telematic collaborations. Artsmesh is a step forward for creating an environment that integrates necessary features for an optimal NMP platform.

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