Education Commons^™

Computational Analysis Of O6-Methylated Guanine And Thioguanine Complexes, Kirsten Stinson, Michael Bowman

Lux et Fides: A Journal for Undergraduate Christian Scholars

DNA methylation occurring on the O⁶ position of guanine has been linked to the formation of cancer. DNA complexes with O⁶-methylated guanine have been studied experimentally, yet questions remain concerning the carcinogenic properties of O⁶-methylguanine. This present research explored the interaction between O⁶-methylguanine and its potential nucleobase pairs of cytosine and adenine in hopes of elucidating the mutagenic characteristics of O⁶-methylguanine. A variety of computational methods including Density Functional Theory (DFT), Symmetry Adapted Perturbation Theory (SAPT), Noncovalent Interaction (NCI) analysis, and Natural Bond Orbital (NBO) analysis were employed to comprehensively probe …

Using Artificial (Ai) To Predict A Structure Of Protein Complex, Yiqing Zang

SACAD: John Heinrichs Scholarly and Creative Activity Days

Proteins play pivotal roles in essential life processes and elucidating their three-dimensional (3D) structures is crucial for understanding their functions. AlphaFold2, an advanced artificial intelligence-based method developed by Google DeepMind, has emerged as a promising tool for predicting protein structures. In this study, we evaluated the predictive capabilities of AlphaFold2. Our findings highlight AlphaFold2's efficacy in providing valuable insights into protein structure prediction, albeit with certain limitations. While AlphaFold2 represents a significant advancement in the field, its utility is best realized when integrated with complementary experimental approaches. Consequently, combining the strengths of AlphaFold2 with experimental validation remains essential for achieving …

Design To Data For Mutants Of Β-Glucosidase B From Paenibacillus Polymyxa: E26k, I170y, And V398n, Carter Ahlstedt, Annika Bennett, Daniel Kaluka

Lux et Fides: A Journal for Undergraduate Christian Scholars

Protein modeling aids in developing novel protein configurations that are critical in, for example, the pharmaceutical and environmental industries. However, the predictive capabilities of the protein modeling algorithms are limited due to a lack of experimental data on structure and function. To bridge this gap, Seigel Lab at UC Davis developed the Design to Data (D2D) program to catalog thermal stability and catalytic efficiency data sets on β-glucosidase B (BglB) variants. Over 300 BglB variants have been characterized. However, there are over 8400 possible BglB single-point mutations. We utilized Foldit software to design BglB mutants E26K, I170Y, and V398N. The …

Analysis Of Botulinum Toxin A And Interacting Proteins In Skeletal Muscle Cells: An Investigation Into The Mechanisms Of Botulinum Toxin A As A Treatment For Chronic Exertional Compartment Syndrome, Lauren R. Kee

ELAIA

Background Chronic exertional compartment syndrome (CECS) is a condition in which muscle tissue expands against the surrounding fascia during activity and is compressed along with the nerves and blood vessels within the muscle compartment, leading to abnormally high intracompartmental pressure (ICP) and debilitating pain. Treatment typically includes fasciotomy, which results in significant levels of CECS recurrence; however, botulinum toxin A (BoNT-A) injection has recently been seen to decrease both ICP and pain through an unknown mechanism with little to no recurrence. Methods In this study, PyRosetta was used to model the probability of docking interaction between BoNT-A light or heavy …

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works, Caitlyn Aldersea, Justin Bravo, Sam Allen, Anna Block, Connor Block, Emma Buechler, Maria De Los Angeles Bustillos, Arianna Carlson, William Christensen, Olivia Kachulis, Noah Craver, Kate Dillon, Muskan Fatima, Angel Fernandes, Emma Finch, Colleen Cassidy, Amy Fishman, Andrea Francis, Stacia Fritz, Simran Gill, Emma Gries, Rylie Hansen, Shannon Powers, Jacqueline Martinez, Zachary Harker, Ashley Hasty, Mykaela Tanino-Springsteen, Kathleen Hopps, Adelaide Kerenick, Colin Kleckner, Ci Koehring, Elijah Kruger, Braden Krumholz, Maddie Leake, Lyneé Alves, Seraphina Loukas, Yatzari Lozano Vazquez, Haley Maki, Emily Martinez, Sierra Mckinney, Mykaela Tanino-Springsteen, Audrey Mitchell, Kipling Newman, Audrey Ng, Megan Lucyshyn, Andrew Nguyen, Stevie Ostman, Casandra Pearson, Alexandra Penney, Julia Gielczynski, Tyler Ball, Anna Rini, Christina Rorres, Simon Ruland, Helayna Schafer, Emma Sellers, Sarah Schuller, Claire Shaver, Kevin Summers, Isabella Shaw, Madison Sinar, Claudia Pena, Apshara Siwakoti, Carter Sorensen, Madi Sousa, Anna Sparling, Alexandra Revier, Brandon Thierry, Dylan Tyree, Maggie Williams, Lauren Wols

DU Undergraduate Research Journal Archive

DU Undergraduate Showcase: Research, Scholarship, and Creative Works

Analysis Of Attitudinal Student Learning Benefits From A Course-Based Undergraduate Research Experience (Cure) Adapted For Online Format, Ambika Kapil, Luis C. Gonzalez Isoba, Niraj Pathak, Arthur Sikora, Santanu De

FDLA Journal

Course-based Undergraduate Research Experiences (CUREs) are an increasingly utilized model for exposing students to research. The lack of robust assessments is a major hurdle to wider adoption of CUREs. The Coronavirus Infectious Disease 2019 (COVID-19) pandemic necessitated a drastic shift of in-person courses to the online format. Using the Participant Perception Indicator (PPI) survey, we measured students’ self-reported changes in learning from such a biochemistry course at a large university in south Florida based on the Biochemistry Authentic Scientific Inquiry Lab (BASIL) model. By doing this, we were able to better understand the student-benefits of CUREs and how these benefits …

Du Undergraduate Showcase: Research, Scholarship, And Creative Works: Abstracts, Emma Aggeler, Elena Arroway, Daisy T. Booker, Justin Bravo, Kyle Bucholtz, Megan Burnham, Nicole Choi, Spencer Cockerell, Rosie Contino, Jackson Garske, Kaitlyn Glover, Caroline Hamilton, Haley Hartmann, Madalyne Heiken, Colin Holter, Leah Huzjak, Alyssa Jeng, Cole Jernigan, Chad Kashiwa, Adelaide Kerenick, Emily King, Abigail Langeberg, Maddie Leake, Meredith Lemons, Alec Mackay, Greer Mckinley, Ori Miller, Guy Milliman, Katherine Miromonti, Audrey Mitchell, Lauren Moak, Megan Morrell, Gelella Nebiyu, Zdenek Otruba, Toni V. Panzera, Kassidy Patarino, Sneha Patil, Alexandra Penney, Kevin Persky, Caitlin Pham, Gabriela Recinos, Mary Ringgenberg, Chase Routt, Olivia Schneider, Roman Shrestha, Arlo Simmerman, Alec Smith, Tessa Smith, Nhi-Lac Thai, Kyle Thurmann, Casey Tindall, Amelia Trembath, Maria Trubetskaya, Zachary Vangelisti, Peter Vo, Abby Walker, David Winter, Grayden Wolfe, Leah York

DU Undergraduate Research Journal Archive

Abstracts from the DU Undergraduate Showcase.

Doors Pushed Open: For Devin Gibbs, College Seemed Like A Longshot--Until It Wasn't, Kardelen Koldas

Colby Magazine

Before enrolling, Devin Gibbs ’14 received an invitation from Colby. The letter offered to bring him to campus and provide accommodations so he could get a feel for the school. What it didn’t say was he had, in essence, been admitted. Gibbs, who lived in Waterville just minutes from campus, thought the letter was a scam. “I had never gotten anything for free before,” he said.

Medical Schools Ignore The Nature Of Consciousness At Great Cost, Anoop Kumar

Journal of Wellness

The essential question of the relationship between consciousness and matter is ignored in medical school curricula, leading to a machine-like view of the human being that contributes to physician burnout and intellectual dissatisfaction. The evidence suggesting that the brain may not be the seat of consciousness is generally ignored to preserve the worldview of the primacy of matter. By investigating new frameworks detailing the nature of consciousness at different levels of hierarchy, we can bring intellectual rigor to a once opaque subject that supports a fundamental reality about our experience: We are human beings, not only human bodies.

Investigation Of Fluorescence In Selected Mammals Of Arkansas, C. Renn Tumlison, Terry L. Tumlison

Journal of the Arkansas Academy of Science

The adaptive value of fluorescence among the vertebrates has been studied most in fishes and birds, and only a few observations have been published regarding fluorescence in the pelage of mammals. Recently, reports of fluorescence in some marsupials, the platypus, and in flying squirrels have become available. We report the occurrence of fluorescent properties in some mammals from Arkansas. Most carnivores, bats, and rodents did not exhibit the property when viewed under UV light. However, opossums, rabbits, a weasel, muskrats, and moles showed substantial UV response, and a few other mammals showed minor fluorescence. Colors fluoresced included pink, green, and …

Tactviz: A Vmd Plugin For Tactile Visualization Of Protein Structures, Olivia R. Shaw, Jodi A. Hadden-Perilla

Journal of Science Education for Students with Disabilities

Scientific disciplines spanning biology, biochemistry, and biophysics involve the study of proteins and their functions. Visualization of protein structures represents a barrier to education and research in these disciplines for students who are blind or visually impaired. Here, we present a software plugin for readily producing variable-height tactile graphics of proteins using the free biomolecular visualization software Visual Molecular Dynamics (VMD) and protein structure data that is publicly available through the Protein Data Bank. Our method also supports interactive tactile visualization of proteins with VMD on electronic refreshable tactile display devices. Employing our method in an academic laboratory has enabled …

Faculty Spotlight—Dr. Phil Danielson, Hannah Stanley, William Moody

DU Undergraduate Research Journal Archive

Interview with Dr. Phil Danielson

Faculty Spotlight—Dr. Robert Dores, Anit Tyagi, William Moody

DU Undergraduate Research Journal Archive

Robert Dores Interview

Edited by Will Moody

Full Issue-- Volume 3 Issue 1, 2020, Issue 1 Volume 3

Pursue: Undergraduate Research Journal

PURSUE: Undergraduate Research Journal

Volume 3 Issue 1, 2020

Article 1 - Harvesting Electrical Energy Produced by Electrogenic Bacteria in Microbial Fuel Cells

Article 2 – The Effects of Fertilizer Rate on the Growth of Egyptian Spinach in a Greenhouse

Article 3 – Exploring the Association Between Nutrition and Mental Health in Adolescence: A Systematic Literature Review

Article 4— Biological Pathways Associated with Wild and Domestic Animals

Chemistry & Biochemistry Guest Lecture Series, Desmond Murray

Andrews Agenda: Campus News

No abstract provided.

Aligning Best Practices In Student Success And Career Preparedness: An Exploratory Study To Establish Pathways To Stem Careers For Undergraduate Minority Students, Kimberly D. Kendricks, Anthony A. Arment, K. V. Nedunuri, Cadance A. Lowell

Journal of Research in Technical Careers

Undergraduate minority retention and graduation rates in STEM disciplines is a nationally recognized challenge for workforce growth and diversification. The Benjamin Banneker Scholars Program (BBSP) was a five-year undergraduate study developed to increase minority student retention and graduation rates at an HBCU. The program structure utilized a family model as a vehicle to orient students to the demands of college. Program activities integrated best K-12 practices and workforce skillsets to increase academic preparedness and career readiness. Findings revealed that a familial atmosphere improved academic performance, increased undergraduate research, and generated positive perceptions of faculty mentoring. Retention rates among BBSP participants …

Approaching Undergraduate Research With Students Who Are Deaf And Hard-Of-Hearing, Austin U. Gehret, Jessica W. Trussell, Lea V. Michel

Journal of Science Education for Students with Disabilities

An undergraduate research experience can provide a unique opportunity for students to learn and grow as scientists; when positive, this experience is often transformative and motivates students to pursue science, technology, engineering and mathematics (STEM) graduate degrees or careers. Conversely, negative research experiences can sour a student’s opinion of research, propagate misconceptions of graduate school, and lead to attrition from STEM fields. Negative research experiences can be equally devastating for faculty mentors and may result in reluctance to mentor future research students. Using a mentoring approach that has traditionally translated to positive research experiences for hearing students may not be …

Exploring The Use Of Free Bioinformatics Modules In An Introductory Biochemistry Course, Charlsey Dodgen, Uzezi Uwerosuo, Chulhee Kang, Cathy Lee

Georgia Journal of Science

Although bioinformatics, the use of computational science to study biology, has become imperative in many areas of the biological sciences and related career paths, introductory biochemistry courses may disregard practical knowledge on bioinformatics. For this reason, we merged a hands-on activity module into an undergraduate biochemistry course in two ways. First, we incorporated bioinformatics modules for building phylogenetic trees by aligning the active sites of 10 chosen related α-amylase enzymes using freely available data. Secondly, we chose three of those 10 α-amylase enzymes to compare the 3D structure of their active sites. This module gives the students an opportunity to …

Required Biochem Class Live-Streamed This Summer: Collaboration With Union College Makes Required Credits Easier To Obtain, Chris Mclean-Wheeler

Andrews Agenda: Campus News

No abstract provided.

Broad Vision: The Art & Science Of Looking, Heather Barnett, John R. A. Smith

The STEAM Journal

Undergraduate students and academic staff from diverse disciplines in the arts and sciences investigated questions of mediated vision through a year-long interdisciplinary research project at the University of Westminster, London, United Kingdom. The Broad Vision project explored the perception and interpretation of microscopic worlds, and investigated the benefits and challenges of working across disciplinary divides in a university setting. This article describes the three-phase model for interdisciplinary learning and research developed through the project, providing a valuable case study for inquiry based art/science education.

Seeing The Future: Biology Research Allows Undergraduates New Insight Into Their Own Futures, Merideth Krevosky, Jeffery Bowen

Bridgewater Review

No abstract provided.

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.