Life Sciences Commons^™

Fecal Genomics Provides Insights On Connectivity Of Endangered Wildlife In A Human Dominated Landscape, Abhinav Tyagi

Theses and Dissertations

Many mammalian species, facing severe historic range reductions, now inhabit fragmented habitats. Habitat fragmentation involves the reduction of habitat into smaller patches, increasing distances between them, and eventually leading to small isolated populations. Species' responses to habitat alteration may vary based on factors such as body size, dispersal ability, and abundance. Understanding these differences is crucial for effective multispecies conservation planning. Genomic data, within a landscape genetic framework, are increasingly applied to evaluate the effects of habitat fragmentation and understand influential landscape features for connectivity. The quantity of data enhances the power and precision of assessing landscape impacts on gene …

Molecular Therapy And Nucleic Acid Adeno-Associated Virus-Based Gene Therapy Delivering Combinations Of Two Growth-Associated Genes To Mps Iva Mice, Estera Rintz, Betul Celik, Nidhi Fnu, Angélica María Herreño-Pachón, Shaukat Khan, Shunji Tomatsu, Eliana Benincore-Flórez

Department of Medicine Faculty Papers

Mucopolysaccharidosis type IVA (MPS IVA) is caused by a deficiency of the galactosamine (N-acetyl)-6-sulfatase (GALNS) enzyme responsible for the degradation of specific glycosaminoglycans (GAGs). The progressive accumulation of GAGs leads to various skeletal abnormalities (short stature, hypoplasia, tracheal obstruction) and several symptoms in other organs. To date, no treatment is effective for patients with bone abnormalities. To improve bone pathology, we propose a novel combination treatment with the adeno-associated virus (AAV) vectors expressing GALNS enzyme and a natriuretic peptide C (CNP; NPPC gene) as a growth-promoting agent for MPS IVA. In this study, an MPS IVA mouse model was treated …

Effects Of Improved Amino Acid Balance Diet On Lysine Mammary Utilization, Whole Body Protein Turnover And Muscle Protein Breakdown On Lactating Sows, Sai Zhang, Juan C Marini, Vengai Mavangira, Andrew Claude, Julie Moore, Mahmoud A Mohammad, Nathalie L Trottier

Children’s Nutrition Research Center Staff Publications

Background: The study objective was to test the hypothesis that low crude protein (CP) diet with crystalline amino acids (CAA) supplementation improves Lys utilization efficiency for milk production and reduces protein turnover and muscle protein breakdown. Eighteen lactating multiparous Yorkshire sows were allotted to 1 of 2 isocaloric diets (10.80 MJ/kg net energy): control (CON; 19.24% CP) and reduced CP with "optimal" AA profile (OPT; 14.00% CP). Sow body weight and backfat were recorded on d 1 and 21 of lactation and piglets were weighed on d 1, 14, 18, and 21 of lactation. Between d 14 and 18, a …

New York City’S Rising Sea Level And Coastal Erosion: Approaches To Resiliency, Ryder D. Isidro

Student Theses 2015-Present

No abstract provided.

Protein Oxidation In Aging And Alzheimer’S Disease Brain, Rukhsana Sultana, D. Allan Butterfield

Markey Cancer Center Faculty Publications

Proteins are essential molecules that play crucial roles in maintaining cellular homeostasis and carrying out biological functions such as catalyzing biochemical reactions, structural proteins, immune response, etc. However, proteins also are highly susceptible to damage by reactive oxygen species (ROS) and reactive nitrogen species (RNS). In this review, we summarize the role of protein oxidation in normal aging and Alzheimer’s disease (AD). The major emphasis of this review article is on the carbonylation and nitration of proteins in AD and mild cognitive impairment (MCI). The oxidatively modified proteins showed a strong correlation with the reported changes in brain structure, carbohydrate …

Predicting The Pathway Involvement Of Metabolites Based On Combined Metabolite And Pathway Features, Erik D. Huckvale, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

A major limitation of most metabolomics datasets is the sparsity of pathway annotations for detected metabolites. It is common for less than half of the identified metabolites in these datasets to have a known metabolic pathway involvement. Trying to address this limitation, machine learning models have been developed to predict the association of a metabolite with a “pathway category”, as defined by a metabolic knowledge base like KEGG. Past models were implemented as a single binary classifier specific to a single pathway category, requiring a set of binary classifiers for generating the predictions for multiple pathway categories. This past approach …

The Trnaval Half: A Strong Endogenous Toll-Like Receptor 7 Ligand With A 5′-Terminal Universal Sequence Signature, Kamlesh Ganesh Pawar, Takuya Kawamura, Yohei Kirino

Computational Medicine Center Faculty Papers

Toll-like receptors (TLRs) are crucial components of the innate immune system. Endosomal TLR7 recognizes single-stranded RNAs, yet its endogenous ssRNA ligands are not fully understood. We previously showed that extracellular (ex-) 5'-half molecules of tRNA^HisGUG (the 5'-tRNA^HisGUG half) in extracellular vesicles (EVs) of human macrophages activate TLR7 when delivered into endosomes of recipient macrophages. Here, we fully explored immunostimulatory ex-5'-tRNA half molecules and identified the 5'-tRNA^ValCAC/AAC half, the most abundant tRNA-derived RNA in macrophage EVs, as another 5'-tRNA half molecule with strong TLR7 activation capacity. Levels of the ex-5'-tRNA^ValCAC/AAC half were highly up-regulated in macrophage EVs …

Regulation Of Neuronal Cell-Type-Specific Transcription By Non-Cg Methylation And Mecp2, James Russell Moore

Arts & Sciences Graduate Student Theses and Dissertations

Modulation of gene expression is fundamental to the exceptional complexity and diversity of cells in the nervous system. Within that last decade, evidence has emerged that neurons utilize unique forms of DNA methylation to regulate transcriptional programs, with multiple types of neurons displaying high levels of cytosine methylation in a non-CG context compared to non-neural cells. This non-CG methylation primarily occurs at CA dinucleotides (mCA) and is read out by methyl-CpG binding protein 2 (MeCP2). Inactivation of MeCP2 results in Rett Syndrome (RTT), a severe neurodevelopmental disorder, while overexpression of MeCP2 results in MeCP2 duplication syndrome, an autism spectrum disorder. …

Identification And Characterization Of Ube3a Gain Of Function Variants As A Driver Of Neurodevelopmental Disease, Kellan Phoebe Weston

Arts & Sciences Graduate Student Theses and Dissertations

UBE3A is a HECT (homologous to E6AP-Terminus) domain E3 ubiquitin ligase that targets substrate proteins for polyubiquitination and subsequent degradation through the ubiquitin-proteasome pathway. The UBE3A gene is of unique interest for its gene dosage-dependent effect in the developing brain: deletion of the maternal copy of UBE3A causes a severe intellectual disability known as Angelman syndrome; meanwhile, duplication or triplication of the genomic region containing UBE3A is linked to a prevalent syndromic form of autism known as Dup15q syndrome. However, little is known about the effects of missense variants which cause a single amino acid change in the resulting UBE3A …

Creating Sustainable School And Home Gardens: Raised Bed Gardening, Rita Hagevik, Kathy Cabe Trundle

All Current Publications

This fact sheet is part of a series about creating sustainable school and home gardens. It provides information and resources on raised bed gardening, which can help gardeners maximize space and increase food or flower production, all with fewer weeds.

Single Extracellular Vesicle Imaging And Computational Analysis Identifies Inherent Architectural Heterogeneity, Kshipra S Kapoor, Seoyun Kong, Hikaru Sugimoto, Wenhua Guo, Vivek Boominathan, Sibani Lisa Biswal, Kathleen M Mcandrews, Raghu Kalluri

Faculty, Staff and Student Publications

Evaluating the heterogeneity of extracellular vesicles (EVs) is crucial for unraveling their complex actions and biodistribution. Here, we identify consistent architectural heterogeneity of EVs using cryogenic transmission electron microscopy (cryo-TEM), which has an inherent ability to image biological samples without harsh labeling methods while preserving their native conformation. Imaging EVs isolated using different methodologies from distinct sources, such as cancer cells, normal cells, immortalized cells, and body fluids, we identify a structural atlas of their dominantly consistent shapes. We identify EV architectural attributes by utilizing a segmentation neural network model. In total, 7,576 individual EVs were imaged and quantified by …

Histone Demethylase Kdm5 Regulates Cardiomyocyte Maturation By Promoting Fatty Acid Oxidation, Oxidative Phosphorylation, And Myofibrillar Organization, Manisha Deogharia, Leslye Venegas-Zamora, Akanksha Agrawal, Miusi Shi, Abhinav K Jain, Francisco Altamirano, Priyatansh Gurha

Faculty, Staff and Student Publications

Aims: Human pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) provide a platform to identify and characterize factors that regulate the maturation of CMs. The transition from an immature foetal to an adult CM state entails coordinated regulation of the expression of genes involved in myofibril formation and oxidative phosphorylation (OXPHOS) among others. Lysine demethylase 5 (KDM5) specifically demethylates H3K4me1/2/3 and has emerged as potential regulators of expression of genes involved in cardiac development and mitochondrial function. The purpose of this study is to determine the role of KDM5 in iPSC-CM maturation.

Methods and results: KDM5A, B, and C proteins were mainly expressed …

Developing And Validating A Nomogram For Early Predicting The Need For Intestinal Resection In Pediatric Intussusception, Shi-Kun Guo, Zhong-Rong Li, Hui-Ya Huang, Xiao-Zhong Huang

Faculty, Staff and Student Publications

PURPOSE: Develop and validate a nomogram for predicting intestinal resection in pediatric intussusception suspecting intestinal necrosis.

PATIENTS & METHODS: Children with intussusception were retrospectively enrolled after a failed air-enema reduction in the outpatient setting and divided into two groups: the intestinal resection group and the non-intestinal resection group. The enrolled cases were randomly selected for training and validation sets with a split ratio of 3:1. A nomogram for predicting the risk of intestinal resection was visualized using logistic regression analysis with calibration curve, C-index, and decision curve analysis to evaluate the model.

RESULTS: A total of 547 cases were included …

Agreement Of Air Bike And Treadmill Protocols To Assess Maximal Oxygen Uptake: An Exploratory Study, Travis Lipscomb, Megan Sax Van Der Weyden, Ali Boolani, Bryan St. Andrews, Joel Martin

International Journal of Exercise Science

International Journal of Exercise Science 17(4): 633-647, 2024. Maximal oxygen consumption (V̇O_2max) is an important measure of aerobic fitness, with applications in evaluating fitness, designing training programs, and assessing overall health. While treadmill assessments are considered the gold standard, airbikes (ABs) are increasingly popular exercise machines. However, limited research exists on AB-based V̇O2max assessments, particularly regarding agreement with treadmill graded exercise tests. To address this gap, a randomized crossover study was conducted, involving 15 healthy adults (9M, 6F, 7 familiar with AB) aged 30.1 ± 8.6 years. Paired t-tests, intraclass correlation coefficients (ICC), Bland-Altman and Principal component …

The Effects Of A Core Stabilization Training Program On The Performance Of Functional Tasks In Firefighters, Emily G. Maxwell, Sean M. Collins, Jill M. Lucas

International Journal of Exercise Science

International Journal of Exercise Science 17(4): 602-610, 2024. The purpose of this study was to observe if core stabilization training plays a significant role in firefighter time-to-completion during a functional performance test. A within subjects study design was used in which subjects (n = 13, 84.6% male, 33.7 ± 7.4 years of age, 91.06 ± 13.29 kg, 25.79 ± 6.55 percent body fat, 8.96 ± 7.51 years of firefighting experience) completed two performance tests (pre and post core training), comprised of 7 firefighter-specific exercises performed while wearing a 22.68 kg weight vest to mimic typical firefighter equipment. Between testing …

Probing The Paradox: Investigating The Impact Of Affect, Exercise Type, And Cannabis Use On The Alcohol-Exercise Relationship In College Students, Vanessa Stallsmith, Cianna Piercey, Maggie Mataczynski, Hollis Karoly, Noah Emery

International Journal of Exercise Science

International Journal of Exercise Science 17(3): 623-632, 2024. Alcohol has previously shown a paradoxical positive relationship with exercise behaviors. However, the relationship has not been explored according to type of exercise (aerobic vs. anaerobic), nor has the research considered other contextual variables that commonly co-occur with alcohol use, such as cannabis and mood. This study sought to expand upon previous research to understand how the alcohol-exercise relationship may vary based on exercise type. Additionally, this study included cannabis use and mood as moderators of the alcohol-exercise association. Cross-sectional survey data was collected from college students (N = 335). Negative …

Effects Of Ankle Compression Garments On Fatigue And Single-Leg Balance In Collegiate Basketball Players, Lauren Debolt, Jeff Hamon, Justin Hu, Tyler Vickers, You-Jou Hung

International Journal of Exercise Science

International Journal of Exercise Science 17(1): 611-622, 2024. Basketball players are prone to ankle injuries. It is unclear if wearing ankle compression garments (CGs) can enhance balance control and time to fatigue in those athletes. The purpose of this study was to examine the impact of ankle CGs on both time to fatigue and single-leg balance. Sixteen Division II (D2) collegiate basketball players participated in the study. The Cumberland Ankle Instability Tool (CAIT) was used to assess ankle stability. Fatigue was induced through deficit heel raises, and single-leg balance was assessed with the Athletic Single Leg Stability Test (ASLST) of …

Major Axes Of Variation In Tree Demography Across Global Forests, Melina De Souza Leite, Sean M. Mcmahon, Paulo Inácio Prado, Stuart J. Davies, Alexandre Adalardo De Oliveira, Hannes P. De Deurwaerder, Salomón Aguilar, Kristina J. Anderson-Teixeira, Nurfarah Aqilah, Norman A. Bourg, Warren Y. Brockelman, Nicolas Castaño, Chia-Hao Chang-Yang, Yu-Yun Chen, George Chuyong, Keith Clay, Álvaro Duque, Sisira Ediriweera, Corneille E. N. Ewango, Gregory Gilbert, I. A. U. N. Gunatilleke, C. V. S. Gunatilleke, Robert Howe, Walter Huaraca Huasco, Akira Itoh, Daniel J. Johnson, David Kenfack, Kamil Král, Yao Tze Leong, James A. Lutz, Jean-Remy Makana, Yadvinder Malhi, William J. Mcshea, Mohizah Mohamad, Musalmah Nasardin, Anuttara Nathalang, Geoffrey Parker, Renan Parmigiani, Rolando Pérez, Richard P. Phillips, Pavel Šamonil, I-Fang Sun, Sylvester Tan, Duncan Thomas, Jill Thompson, María Uriarte, Amy Wolf, Jess Zimmerman, Daniel Zuleta, Marco D. Visser, Lisa Hülsmann

Wildland Resources Faculty Publications

The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatio-temporal patterns in tree population dynamics. While previous research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach to overcome these limitations is to group mechanisms according to their shared effects on the variability of tree vital rates and quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in …

Open Resources For Biology Education (Orbe): A Resource Collection, Sanah Ahmed, Tiffany Adjei-Opong, Ashley B. Heim, Keenan Noyes, Kelly Schmid, Brian A. Couch, Mackenzie R. Stetzer, Lillian G. Senn, Erin Vinson, Michelle K. Smith, Kira Treibergs

School of Biological Sciences: Faculty Publications

In undergraduate life sciences education, open educational resources (OERs) increase accessibility and retention for students, reduce costs, and save instructors time and effort. Despite increasing awareness and utilization of these resources, OERs are not centrally located, and many undergraduate instructors describe challenges in locating relevant materials for use in their classes. To address this challenge, we have designed a resource collection (referred to as Open Resources for Biology Education, ORBE) with 89 unique resources that are primarily relevant to undergraduate life sciences education. To identify the resources in ORBE, we asked undergraduate life sciences instructors to list what OERs they …

Investigating The Antibacterial And Immunomodulatory Effects Of Resolvin D2 On Monocytes And Macrophages, Cristina Maria Padovani

Theses and Dissertations

In the late phase of sepsis, immunosuppression occurs, where the host is unable to clear the pre-existing infection and is susceptible to secondary infections. It is believed that the ideal treatments for sepsis should attenuate immunosuppression so that the host can get back to homeostasis. Specialized Pro-resolving Mediators (SPMs) are endogenously- produced fatty acids that resolve infectious inflammation without being immunosuppressive. We hypothesize that an SPM – Resolvin D2 (RvD2) – can augment exhausted macrophage function during the immunosuppressive phase of sepsis. We developed a two-hit model to establish macrophage exhaustion in vitro, and found that RvD2 increased NF-κB activity, …

Regulation Of Intracellular Sorting Of The Bruno Protein In Drosophila Flight Muscles, Travis Main

Master's Theses

Understanding mechanisms of intracellular sorting is a fundamental inquiry of cell biology. We used the B-body and protein Bruno (Bru) as a model to study the formation of nuclear domains that are membraneless organelles inside the cell nucleus. Specifically, we sought to identify protein sequences that regulate Bru's affinity to B-bodies and protein aggregation. We generated various Bru mutants and subsequently tested them in vivo using fluorescence microscopy. We found that the protein solubility of Bru is determined through an interplay of RNA recognition motifs (RRMs) and intrinsically disordered regions (IDRs). Using truncation analysis, we identified a 31-amino acid region …

Investigating The Electrostatics Of Mucins As Key Contributors To Mucus Stasis In Cystic Fibrosis, Elex Skylar Rose

All ETDs from UAB

Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a channel responsible for the transport of chloride and bicarbonate ions across the apical cell surface. In the respiratory tract, defective CFTR results in viscous and adherent mucus that becomes static within the airway, which leads to chronic infections, progressive lung damage, and early mortality. Historically, CF mucus stasis has been attributed to significant airway dehydration; however, growing evidence has demonstrated that aberrant electrostatic properties of mucins also contribute to mucus stasis in CF. Mucins are large, polymeric glycoproteins …

Serine Deamination By Human Serine Racemase Synergizes With Antibiotics To Curtail The Replication Of Chlamydia Trachomatis, Patricia D. Mott, Arnold H. Zea, Jamiya Lewis, Oygul Mirzalieva, Ashok A. Aiyar

School of Medicine Faculty Publications

The obligate intracellular bacterium, Chlamydia trachomatis, has evolved to depend on its human host for many metabolites, including most amino acids and three of the four nucleotides. Given this, it is not surprising that depletion of a single amino acid in the host cell growth medium blocks chlamydial replication. Paradoxically, supra-normal levels of some amino acids also block productive replication of Chlamydia. Here, we have determined how elevated serine levels, generated by exogenous supplementation, impede chlamydial inclusion development and reduce the generation of infectious progeny. Our findings reveal that human serine racemase, which is broadly expressed in multiple tissues, potentiates …

Measuring The Effects Of Selenium Exposure On Batrachochytrium Dendrobatidis (Bd) Growth In Vivo In Larval American Bullfrogs (Rana Catesbeiana)., Taylor Morrison

Honors Thesis

Most amphibians in today’s world are exposed to a variety of environmental stressors. This project’s main objective was to determine any effects of selenium on Batrachochytrium dendrobatidis (Bd) and infection levels in South Dakota amphibians. I selected American bullfrogs (Rana catesbeiana) as they are susceptible to Bd and are found throughout eastern South Dakota. The secondary objective of this project was to measure any impact of Bd and selenium, combined, on growth measures of the frogs. The third objective was to see if survival rates were reduced when amphibians were exposed to Bd and selenium. Tadpoles were collected (n=225) from …

Lmpact Of Salmonella Enterica Effector Proteins On Plant Physiology And Immunity, Sara Qader

Honors Theses

Salmonella enterica serovar Typhimurium are primarily recognized as pathogens associated with foodborne illnesses in humans. Salmonella also can colonize plant tissue effectively. The pathogen relies on type III secretion systems (T3SS) to infect mammals and plants successfully and counteract the immune response. Understanding the molecular mechanisms underlying Salmonella’s interactions with plants is essential for developing effective strategies to reduce its impact on human health and agriculture. Effector proteins, known for their role in modulating host-pathogen interactions, have been implicated in the virulence and pathogenicity of Salmonella. However, their specific functions and contributions to Salmonella’s interactions with plants remain largely unknown. …

05.06.2024 Orsp Connect, Liz Williamson

ORED Newsletter

Library Faculty Win NIH Award, Uniform Guidance Updates,

Identifying Key Evolving Residues That Drive Cid/Cal1 Incompatibility In Drosophila Species, Hayden Yuan, Barbara Mellone

Honors Scholar Theses

The centromere, an essential locus on the chromosome critically important for faithful chromosome segregation during cell division, requires the incorporation of centromere protein A (CENP-A/CID) orchestrated by the chaperone CAL1. This thesis investigates the structural requirements governing the interaction between CAL1 and CID, with a focus on two diverged Drosophila species. Using a combination of structural analysis prediction and cellular assays, I explored the compatibility between the N-terminal region of CAL1 and the L1 domain of CID. Previous results demonstrate species specific interactions between CAL1 and CID, with endogenous Drosophila melanogaster (mel) CAL1 efficiently depositing Drosophila melanogaster CID …

Using Chatgpt With Novice Arduino Programmers: Effects On Performance, Interest, Self-Efficacy, And Programming Ability, Donald M. Johnson, Will Doss, Christopher M. Estepp

Journal of Research in Technical Careers

A posttest-only control group experimental design compared novice Arduino programmers who developed their own programs (self-programming group, n =17) with novice Arduino programmers who used ChatGPT 3.5 to write their programs (ChatGPT-programming group, n = 16) on the dependent variables of programming scores, interest in Arduino programming, Arduino programming self-efficacy, Arduino programming posttest scores, and types of programming errors. Students were undergraduates in an introductory agricultural systems technology course in Fall 2023. The results indicated no significant (p < .10) differences between groups for programming rubric scores (p = .50) or interest in Arduino programming (p = .50). There were significant differences for Arduino programming self-efficacy, (p = .03, Cohen’s d = 0.75) and Arduino posttest scores, (p = .03, Cohen’s d = 0.76); students in the self-programming group scored significantly higher on both measures. Analysis of students’ errors indicated the ChatGPT group made significantly (p < .01) more program punctuation errors. These results indicated novice students writing their own programs developed greater Arduino programming self-efficacy and programming ability than novice students using ChatGPT. Nevertheless, ChatGPT may still play an important role in assisting novices to write microcontroller programs.

The Biltmore Forest School And The Establishment Of Forestry Education In America, Dan Barry Croom

Journal of Research in Technical Careers

The Biltmore Forest School, despite its unusual existence within the affluent Biltmore Estate, played a crucial role in the early 20th-century American forestry movement. Founded by Carl A. Schenck and supported by George Vanderbilt II, the school aimed to educate foresters and promote sustainable forest management. However, many aspects of the Biltmore experiment failed due to the new and untested nature of forestry science in America. This experiment exposed a fundamental divide in forestry education, with Gifford Pinchot advocating for conservation-centered teaching while Schenck believed in the economic viability of lumber production. Ultimately, the Biltmore Forest School offered valuable vocational …

Eviction-Driven Infanticide And Sexually Selected Adoption And Infanticide In A Neotropical Parrot, Steven R. Beissinger, Karl S. Berg

School of Integrative Biological & Chemical Sciences Faculty Publications

Significance

Infanticide and adoption are puzzling forms of sexual conflict and cooperation, respectively. However, both may be explained by sexual selection, where an individual later reproduces with the parent whose offspring it killed or adopted. While sexually selected infanticide is well known, evidence for sexually selected adoption is anecdotal. Our long-term study of a parrotlet in Venezuela found infanticide attacks were mostly enacted by nonbreeding pairs attempting to evict parents from their nests to usurp the cavity. Infanticide attacks occurred less often at nests where a parent died, and adoption by stepparents was as common as infanticide. Becoming an adoptive …