IU Indianapolis ScholarWorks :: Browsing by Author "Marrs, Kathleen A."

Browsing by Author "Marrs, Kathleen A."

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Central Indiana STEM Talent Expansion Program: Student and Faculty Interventions
(IEEE, 2015-08) Hundley, Stephen P.; Feldhaus, Charles R.; Watt, Jeffrey X.; Marrs, Kathleen A.; Gavrin, Andy; Mzumara, Howard; Department of Technology and Leadership Communication, School of Engineering and Technology
Funded by 5-year, $2M grant from the National Science Foundation, the Central Indiana STEM Talent Expansion Program (CI-STEP) at Indiana University-Purdue University Indianapolis (IUPUI) is creating a pipeline of students and a campus culture change to increase the number of undergraduates obtaining Science, Technology, Engineering, and Mathematics (STEM) degrees. CI-STEP addresses initiatives needed for transforming the undergraduate STEM experience by propagating, expanding, and creating new evidence-based educational innovations in undergraduate STEM education at IUPUI.
Effect of Curcuminoids in Turmeric on Developing Zebrafish Treated with Ethanol
(Office of the Vice Chancellor for Research, 2016-04-08) Connors, Craig; Mohammed, Arooj; Muralidharan, Pooja; Sarmah, Swapnalee; Marrs, James; Marrs, Kathleen A.; Chism, Grady
This experiment was designed with the intention of determining whether turmeric could act as a rescue agent to prevent or mitigate the extent of Fetal Alcohol Spectrum Disorder (FASD) caused by early ethanol exposure using zebrafish as a model system. A range of turmeric concentrations were made from a stock solution of turmeric dissolved in ethanol (1mg turmeric in 5mL ethanol). The active agents in turmeric are the curcuminoids: Curcumin, Desmethoxycurcumin, and Bisdemethoxycurcumin. The curcuminoids concentration was estimated using liquid chromatography. These agents were present in the turmeric stock solution at the following concentrations: Bisdemethoxycurcumin: 36.6 +/- 0.1 ug/mL, Desmethoxycurcumin: 43.4 +/- 0.1 ug/mL, and Curcumin: 124.1 +/- 0.2 ug/mL. Untreated zebrafish embryos were placed in embryo medium, ethanol treated embryos in 100mM ethanol containing embryo medium, and turmeric co-supplemented medium with differing concentrations of turmeric. Since the turmeric stock solution was dissolved in ethanol, the concentration of ethanol was kept at a constant 100mM ethanol and the amount of turmeric solution added. The concentrations of the test plates were then based on this solution and made to be 100 mM ethanol and 1.16 uM curcuminoids, 100 mM ethanol and 1.74 uM curcuminoids, and 100 mM ethanol and 2.32 uM curcuminoids. The developing embryos were treated with the turmeric solution and/or ethanol during 2-24 hours post fertilization (hpf). These embryos were imaged at 72 hpf and their body length and eye diameter were measured. The embryos supplemented with curcuminoids showed a significant rescue effect on the body length and eye diameter compared to ethanol treated embryos. This indicates that the curcuminoids acted as a rescue agent to reduce the effects that are typical of FASD in developing zebrafish.
Introducing Biology Undergraduates to Authentic Research through Grand Challenges in Global Health: Examining Environmental Factors that Influence the Development of Zebrafish Embryos
(Office of the Vice Chancellor for Research, 2014-04-11) Sarmah, Swapnalee; Chism, Grady; Vaughan, Martin; Marrs, James A.; Marrs, Kathleen A.
To increase student excitement and engagement in science, a course-based undergraduate research experience (CURE) has been introduced in the curriculum at IUPUI. In Fall 2013, original research projects investigating prenatal alcohol, nicotine and caffeine exposure effects on development of zebrafish embryos was introduced into the Introductory Biology K102 course. This research project was also a part of a new Themed Learning Community (TLC) at IUPUI called “From Molecules to Medicines” that examined grand challenges in global health. In documenting the developmental effects on zebrafish embryos, and designing new protocols to address student research questions, students gained experience with authentic research methods, laboratory techniques, microscopy, image analyses, statistical analyses, scientific writing and presentation skills. This project, especially in a freshman undergraduate lab setting, requires a new way of problem-solving, but greatly facilitates student excitement and engagement in science through the use of research-based high-impact practices for student success and persistence. To continue an inquiry-based lab on global health issues and to keep IUPUI biology curricula current with the rapid rise of bioinformatics, concepts of bioinformatics were introduced into the Cell Biology Laboratory K325 course in Spring, 2014. Students were allowed to work on their own investigatory projects to analyzed zebrafish microarray data to find genes affected after ethanol exposure. Students used NCBI/ Ensembl databases to retrieve the gene/protein sequences, and various freely available tools (GeneBank, Protein Data Bank, BLAST, ClustalW, ExPasy, Phylogenetic Tree) to investigate the evolutionary conservation of genes/proteins affected after ethanol exposure. Student learnt 3D-protein structure construction and observed how 3D-protein structure could change with single amino acid changes. Preliminary assessment indicates that students are gaining an understanding the web-based databases and tools and enjoying the investigatory nature of the lab exercises.
NSF GK-12 Urban Educators Program
(Office of the Vice Chancellor for Research, 2013-04-05) Judd, Mariah; Marrs, Kathleen A.
The IUPUI NSF GK-12 Urban Educators program partners STEM graduate students with the K-12 community to bring science into the classroom. Our main goal and conceptual focus is to create an urban partnership between STEM graduate fellows, IPS STEM teachers, and IUPUI School of Science and IU School of Medicine faculty that centers on early exposure to field and laboratory research in biomedical and environmental science education, appropriate for grades 6-12. The largest activity of this project involves GK-12 Fellows working with STEM teachers to bring inquiry-based research projects, linked to classroom needs, and the Indiana Academic Standards, into classrooms. Fellows work under two multidisciplinary research themes: Medicine and Human Health and Discovering the Science of the Environment (DSE). The activities developed provide middle school and high school students with opportunities to learn science by engaging in on-going experimentation and fieldwork. This poster will present a series of posters from specific Fellow-Teacher teams, highlighting their accomplishments in bringing graduate level research into the K-12 classroom. Both Fellows and Teachers will be presenting their work and available to share their experiences and lessons learned.
PONDWATER, BIOFILMS, AND CYSTIC FIBROSIS: INTRODUCING CUTTING EDGE RESEARCH INTO THE HIGH SCHOOL CLASSROOM
(Office of the Vice Chancellor for Research, 2011-04-08) Redelman, Carly V.; Hawkins, Misty A. W.; Anderson, Gregory G.; Marrs, Kathleen A.
A retrospective analysis of comorbid traits affecting feeding in infants with Down syndrome
(2012-07-03) Duvall, Nichole L.; Roper, Randall J.; Marrs, Kathleen A.; Chernoff, Ellen
Down syndrome (DS) is the most common aneuploidy to affect humans and occurs in approximately 1 of 750 live births. Individuals with DS present with a wide range of clinical phenotypes. Common craniofacial phenotypic expressions include a small mandible, protruding tongue, and a flattened nasal bridge. These traits may affect the feeding, breathing, and swallowing of individuals with DS. Because some complications may go unnoticed for longer periods of time, we hypothesize that significant cardiac and GI defects may be indicative of feeding and airway difficulties. In order to better understand the secondary phenotypes resulting from DS, we have implemented a retrospective chart review of 137 infants between zero and six months of age who were evaluated through the Down Syndrome Program at Riley Hospital for Children from August 2005 to August 2008. Data regarding cardiac, gastrointestinal, endocrine, airway, auditory, and feeding abnormalities have been collected and incedences and comorbidites of these traits has been examined. Comprehensive results indicate cardiac abnormalities occur in 80% of infants, 60% experience gastrointestinal complications, feeding difficulties occur in 46%, and airway complications occur in 38% of infants. Infants with DS were found to be breastfed less over time, with an increase in tube feeds. Notably, we have found all infants with videofluoroscopic evaluations had some type of dysphagia. The presence of gastrointestinal abnormalities closely correlate with the need for tube feeds, and the comorbidity between GI anomalies and muscle tone appear to indicate the likelihood of feeding difficulties and need for altered feeding strategies. Comorbidities between feeding difficulties were nearly significant with cardiac defects and significant with GI abnormalities. Identification of such associations will help healthcare providers determine the best course of treatment and recommended feeding methodology for infants with DS. In order to utilize an in vitro model to study the craniofacial dysmorphologies seen in individuals with DS, cranial neural crest cells (NC) have been cultured. With these, we have begun to investigate the mechanisms behind a smaller trisomic mandibular precursor as compared to the euploid. With this in vitro model, we will be able to test proliferation, migration, and senescence of NC in a culture system.
Successful Integration of Distributed Drug Discovery (D3) Components: Computational, Synthetic, and Biological Evaluation of Phenylalanine Derivatives as Potential Biofilm Inhibitors
(Office of the Vice Chancellor for Research, 2013-04-05) Abraham, Milata M.; LaCombe, Jonathan M.; Carnahan, Jon M.; O'Donnell, Martin J. O.; Scott, William L.; Denton, Ryan E.; Samaritoni, J. Geno; Harper, Richard; Anderson, Gregory G.; Marrs, Kathleen A.; Coffey, Barbara M.
Distributed Drug Discovery (D3) is a multidisciplinary approach to identifying molecules that exhibit activity in the treatment of neglected diseases such as malaria, leishmaniasis, and tuberculosis as well as recalcitrant cystic fibrosis (CF) airway infections. D3 seeks to accomplish this task by combining computational chemistry, synthetic chemistry, and biological screening all within an educational framework. Recent reports suggest that D-amino acids are effective in the disassembly and inhibition of bacterial biofilms, which are important for a number of bacterial infections, including those in the CF lung. Utilizing chemical drawing software, we constructed (enumerated) target phenylalanine derivatives from commercially available benzyl halides by substitution at the α position of an amino acid scaffold. A subset of these enumerated molecules was computationally selected for synthesis based on chemical properties. These compounds were synthesized using simple, solid-phase techniques in an undergraduate organic chemistry laboratory class. The resulting racemic unnatural amino acid derivatives were then screened for activity in a biofilm assay. The results show biofilm inhibition with synthesized phenylalanine derivatives. Analysis of the results reveals a trend between lipophilicity and the degree of biofilm inhibition. These new molecules may lead to an avenue for therapy for those CF individuals suffering with bacterial lung infection. As a part of the undergraduate curriculum, this work provides the first example of D3-linked undergraduate student computational analysis, synthesis, and biological evaluation.
Turmeric Extract Rescues Ethanol‐Induced Developmental Defect in the Zebrafish Model for Fetal Alcohol Spectrum Disorder (FASD)
(Wiley, 2017) Muralidharan, Pooja; Connors, Craig; Mohammed, Arooj S.; Sarmah, Swapnalee; Marrs, Kathleen A.; Marrs, James A.; Chism, Grady W.; Biology, School of Science
Prenatal ethanol exposure causes the most frequent preventable birth disorder, fetal alcohol spectrum disorder (FASD). The effect of turmeric extracts in rescuing an ethanol‐induced developmental defect using zebrafish as a model was determined. Ethanol‐induced oxidative stress is one of the major mechanisms underlying FASD. We hypothesize that antioxidant inducing properties of turmeric may alleviate ethanol‐induced defects. Curcuminoid content of the turmeric powder extract (5 mg/mL turmeric in ethanol) was determined by UPLC and found to contain Curcumin (124.1 ± 0.2 μg/mL), Desmethoxycurcumin (43.4 ± 0.1 μg/mL), and Bisdemethoxycurcumin (36.6 ± 0.1 μg/mL). Zebrafish embryos were treated with 100 mM (0.6% v/v) ethanol during gastrulation through organogenesis (2 to 48 h postfertilization (hpf)) and supplemented with turmeric extract to obtain total curcuminoid concentrations of 0, 1.16, 1.72, or 2.32 μM. Turmeric supplementation showed significant rescue of the body length at 72 hpf compared to ethanol‐treated embryos. The mechanism underlying the rescue remains to be determined.
Understanding the Relationship Between HERC2 and OCA2 Variants and Iris Pigmentation Genetics
(2021-08) Wallpe, Clarissa; Walsh, Susan; Picard, Christine J.; Marrs, Kathleen A.
Externally visible characteristics (EVCs) predicted from an unknown sample of DNA are particularly useful in forensics as they can provide information beyond that of an STR profile. Current EVCs which are highly studied and well-predicted include iris, hair, and skin color. Notably, models predicting iris color, such as IrisPlex, are the most accurate with up to ~95% accuracy; however, some inaccurate predictions occur, as is evidenced by the ~5%. Often, these are due to green or hazel eyes, which are frequently viewed as intermediate. Though, some of the inaccurate predictions are due to true-blue being predicted as brown and vice versa. Previous research has theorized the possibility of two SNPs, rs12913832 and rs1800407, acting as a functional haplotype affecting iris color. rs12913832 is recognized as the most predictive SNP for iris color and highly significant in other pigmentation phenotypes; presently, rs1800407 is the second-ranked SNP in the IrisPlex 6-SNP system. Both SNPs are highly variable in Europe, where the majority of variation in iris color originates. In the present study, we explore the SNP variation present in the genetic regions of OCA2-HERC2 as well as possible haplotypes. Our research centers around the functional haplotype and the addition of SNPs to the functional haplotype. In addition, three different ways of classifying the phenotype are assessed simultaneously. First, using a 4-point categorical phenotype—blue/blue grey, blue/green yellow, hazel/light brown, and dark brown. Second, calculating a continuous scale from a quantitative phenotype in which the percentage of each categorical color has been measured. Third, using the IrisPlex 6-SNP system to predict eye color and identify individuals which have been inaccurately predicted. Exploration of the SNP and haplotype variation resulted in two SNPs for both the categorical and quantitative phenotypes which were significantly correlated with hazel/light brown—rs1448484 and rs61335644, both as independent SNPs and when assessed in a haplotype with rs1800407-rs12913832. SNP rs1448484 has been associated with skin pigmentation previously and is located in a possible transcription factor binding site. SNP rs61335644 is not presently associated with pigmentation but is in complete LD with two SNPs in and around regulatory regions present in HERC2. Finally, the addition of rs1448484 and rs61335644 into the current IrisPlex 6-SNP system slightly improved each of the tested performance metrics for hazel/light brown and dark brown. Within the inaccurately predicted phenotypes, rs1800407 is confirmed to affect both inaccurately predicted groups and is the most significant SNP. Additionally, rs121918166, a missense variant in OCA2, is the second most significant SNP in true blue predicted as brown. Both SNPs were also the two most significant haplotypes with at least one allele being derived. Therefore, the next steps should include the addition of the functional haplotype and rs121918166 into the current IrisPlex model, and further testing of rs1448484 and rs61335644 on a molecular level. Consequently, the current IrisPlex model should also be reassessed on an independent test set using the 4-point categorical scale rather than the present 3-point scale.
Using Amino Acid Derivatives to Inhibit Pseudomonas aeruginosa Biofilm Formation on Cystic Fibrosis Bronchial Epithelia Cells
(Office of the Vice Chancellor for Research, 2014-04-11) LaCombe, Jonathan M.; Anderson, Gregory G.; Marrs, Kathleen A.
Cystic Fibrosis is a genetic disease caused by a mutation which inhibits the proper transport of sodium and chloride ions across epithelium. Improper ion transport results in the accumulation of thick mucus in critical organs such as the lungs, pancreas, liver, and intestines. The genetic mutation is incurable, but treating the symptoms can vastly increase life expectancy. CF patients are often afflicted with bacterial infections which colonize the excess mucus within the lungs. The most prevalent pathogen associated with CF lung infection is Pseudomonas aeruginosa, a Gram-negative bacterium found in soil and water. Pseudomonas aeruginosa exists in two forms: planktonic (free-swimming) and sessile (immobile within a biofilm community). The planktonic form is about 1,000x more susceptible to antibiotics and immune cells than the sessile form. Biofilm communities of sessile bacteria are protected by an exopolysaccharide layer outside of the cell wall. Small molecules which inhibit biofilm formation or initiate biofilm disassembly can dramatically increase the effectiveness of drugs and the immune system. In order to identify novel biofilm-inhibitory molecules, we assessed the activity of a library of small molecules in biofilm assays. Active compounds were then screened for activity on living Cystic Fibrosis bronchial epithelial cells infected with Pseudomonas aeruginosa. Compounds which successfully inhibit biofilm formation without affecting the Cystic Fibrosis bronchial epithelium cells can potentially be a new drug for treating Cystic Fibrosis infections.

Browsing by Author "Marrs, Kathleen A."

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