Biology Commons^™

An Investigation Into Dietary Fibre Intake, Bowel Function And Mood Among A Sample Of Irish Adults, Sophie Mulligan, Ellen Lynch, Suzanne Doyle

SURE Journal: Science Undergraduate Research Experience Journal

Background

Previous studies have examined the relationship between dietary fibre intake and mood and bowel function separately, however, no cross-sectional study has yet explored the relationship between all three variables. This study examines the association between dietary fibre intake, bowel function and mood in a cohort of Irish adults at a university campus.

Methods

A cross-sectional study was conducted. An online questionnaire was distributed to staff and students of TU Dublin through email and publicised using posters. Three validated surveys were used in the design of the questionnaire, to assess dietary fibre intake, mood and bowel function. All staff and …

The Potential Of Stem Cell Therapy In Multiple Sclerosis Treatment: A Review, Sorina Amarculesei, Ava O'Meara Cushen, Cathy Brougham

SURE Journal: Science Undergraduate Research Experience Journal

Multiple Sclerosis is an autoimmune and neurodegenerative disease of the central nervous system. There are currently 2.8 million people living with Multiple Sclerosis worldwide, including 9000 people in Ireland, with a prevalence of 193 per 100,000 people. Symptoms of Multiple Sclerosis include sensory loss, fatigue, cognitive dysfunction, spasticity, depression, optic neuritis, gait ataxia, diplopia, and loss of bladder control. Currently, there is no standardised treatment or cure for Multiple Sclerosis with many strategies focusing on symptoms. Stem cells have emerged as promising approaches for Multiple Sclerosis therapeutics. Clinical trials primarily focus on mesenchymal stem cell-based therapies for Multiple Sclerosis. Furthermore, …

Ungrading: Reflections Through A Feminist Pedagogical Lens, Erin M. Eggleston, Shelby Kimmel

Feminist Pedagogy

Ungrading is a pedagogical approach in which no grades are given on any assignments. Instead, students are provided with many opportunities to submit work and gain feedback. The goal is to shift student focus from achieving a grade to growth as a learner and a person. As instructors, our ungrading approach utilized personalized learning plans, checkpoint reflections, and student-professor learning conferences to put agency in the hands of our students. We employed this method in upper-level biology and computer science courses and provide critical reflections here regarding our experiences and the connections between this approach and feminist STEM pedagogy tenets. …

Feminist Biology: Towards Gender Equity In The Biology Curriculum, Nicole Danos, Carla Y. Bonilla, Sofia Leung

Feminist Pedagogy

The current curriculum in STEM is a product of historically unequal representation of genders in the science community. As a result, most attention has been given to male biology, creating a knowledge gap that has affected our social and political perspectives, such as an underinvestment in women’s health research. Feminist biology seeks to provide equal time and weight to the impact of sex as a biological factor, using inclusive definitions of biological sex that go beyond the male/female binary. Feminist pedagogy is a method of teaching that involves engaged learning and reflection in order to create a community of learners …

Regulation Of Mrna And Circrna As A Cause And Consequence Of Aging In Caenorhabditis Elegans, Rebekah Napier-Jameson

Biological Sciences Theses and Dissertations

A role for RNA binding proteins in regulating lifespan has emerged. We identified a pair of neuronal RBPs, exc-7 and mbl-1, which display synthetic lifespan defects. Such a strong synthetic phenotype represented an opportunity to use transcriptomics to search for potential causative targets that are synthetically regulated. We identified a small handful of genes synthetically dysregulated in double mutants and systematically tested each candidate gene for functional contribution to the exc-7; mbl-1 lifespan phenotype. We identified one such gene, the ion transporter nhx-6, which is highly upregulated in double mutants. Overexpression of nhx-6 causes reduced lifespan, and deletion …

Characterizing The Ecology Of Plains (Spilogale Interrupta) And Eastern (Spilogale Putorius) Spotted Skunks: A Systematic Literature Review And Population Assessment In Kansas, Jenell De La Peña

Electronic Theses & Dissertations

The plains spotted skunk (Spilogale interrupta) has recently been recognized as a distinct species from the eastern spotted skunk (Spilogale putorius). While once abundant across the central and eastern United States, both species have experienced population declines, resulting in their review for listing under the Endangered Species Act (1973). In Kansas, the plains spotted skunk has suffered a particularly dramatic decline, the last detection in the state having occurred in 2020. Additionally, due to the recent taxonomic split, many past studies reporting on S. putorius ecology actually describe findings of two species, potentially complicating our understanding …

Isolation And Characterization Of Bacteriophages From Fish Tank Samples, Oluwaseyi Oluwagbeminiyi Oladele-Ajose

Electronic Theses and Dissertations

Bacteriophages (phages) are viral obligate intracellular parasites that infect bacteria. Research has been carried out on alternative treatment plans for bacterial infections due to the increase in antibiotic resistance. Phages have been proposed as an alternative to antibiotics. This research focused on the isolation and characterization of bacteria from small aquariums. A total of 42 bacterial isolates were isolated from seven different fish tank water samples and were tested to determine if they possessed phages. Spot plaque assay revealed presence of lytic phage for only one of the isolated bacterial strains, which was determined to belong to Enterobacteriaceae family based …

Quantifying The Influences Of Abiotic And Biotic Factors On Post-Fire Vegetation In The Southwestern Us, Joseph Lafayette Crockett

Biology ETDs

The ongoing warming associated with climate change is increasing the flammability of southwestern US dry forests. As larger fractions of the landscape are impacted by high-severity fire, the potential exists for forests to convert to non-forest. Given that the forested area in the southwestern US is an important contributor of ecosystem services, quantifying limitations to vegetation establishment is critical to informing post-fire recovery efforts and understanding how ongoing climate change will limit seedling establishment in the future. To that end, this dissertation focuses on post-fire vegetation recovery of southwestern forests. First, I report on the influence of precipitation and topography …

Monitoring Time Domain Characteristics Of Parkinson's Disease Using 3d Memristive Neuromorphic System, Md Abu Bakr Siddique, Yan Zhang, Hongyu An

Michigan Tech Publications

INTRODUCTION: Parkinson's disease (PD) is a neurodegenerative disorder affecting millions of patients. Closed-Loop Deep Brain Stimulation (CL-DBS) is a therapy that can alleviate the symptoms of PD. The CL-DBS system consists of an electrode sending electrical stimulation signals to a specific region of the brain and a battery-powered stimulator implanted in the chest. The electrical stimuli in CL-DBS systems need to be adjusted in real-time in accordance with the state of PD symptoms. Therefore, fast and precise monitoring of PD symptoms is a critical function for CL-DBS systems. However, the current CL-DBS techniques suffer from high computational demands for real-time …

A Scoping Review Of Wrist-Worn Wearables In Education, Noah L. Schroeder, William L. Romine, Sidney E. Kemp

Biological Sciences Faculty Publications

Within the past ten years, the public's use of wearables, such as smartwatches and fitness trackers, has greatly increased. Recently, researchers have published systematic reviews to examine how wearables are used in educational settings. However, not all wearables are alike. Head-mounted wearables and exoskeletons may be viewed as invasive, whereas smartwatches and wristbands are commonly worn by the public. In this scoping review, we systematically review the literature around wrist-worn wearables (WWs) in educational settings. Our systematic search revealed 1,932 unique research items, of which 46 met the inclusion criteria and were analyzed. Our findings reveal the trends in the …

Habitat And Demography Of The Ozark Chinquapin (Castanea Ozarkensis) At Roaring River State Park In Barry County, Missouri, Danielle Evilsizor

Electronic Theses & Dissertations

The Ozark chinquapin, Castanea ozarkensis Ashe, is a chestnut tree with a range concentrated in the Interior Highlands of North America. Like other North American members of Castanea, it was reduced from an overstory tree to an understory shrub by the invasive chestnut blight fungus (Cryphonectria parasitica [Murrill] M.E. Barr) during the early 20^th century. However, relatively little is known about the habitat of this species or its health and reproductive capability post chestnut blight. Chapter one of this study analyzed the habitat of this species through a random forest species distribution model (SDM) to predict where …

Protocol To Build A Drug-Testing Pipeline Using Large Populations Of Drosophila Melanogaster, Jay Deloriea, Cassandra Millet-Boureima, Chiara Gamberi

Biology

As a small animal that recapitulates many fundamental aspects of human disease, Drosophila lends itself to probing the biological activity of molecules and drug candidates. Here, we present a protocol to build a drug-testing pipeline in Drosophila. We describe steps for generating synchronous populations of Bicaudal C mutants by genetic crossing and wild-type fly culturing for controlled compound administration and exemplary phenotypic assays. For complete details on the use and execution of this protocol, please refer to Millet-Boureima et al.,¹ Millet-Boureima et al.,² and Gamberi et al.³

Characterization Of Trafficking And Metabolic Functions Of The Endocytic Regulator Ehd1 In Ewing Sarcoma, Sukanya Chakraborty

Theses & Dissertations

Ewing sarcoma (EWS) is the second most common bone malignancy in children and adolescents. Despite improvement in survival due to advances in multimodality treatment strategies, patients with metastatic or recurrent disease have very poor outcomes. Overexpression of the EPS15 Homology Domain containing 1 (EHD1) protein has been linked to tumorigenesis but whether its core function as a regulator of intracellular traffic of cell surface receptors plays a role in oncogenesis remains unknown.

Studies presented in this dissertation establish that EHD1 overexpression is a feature of nearly 90% EWS patient tumors with high EHD1 expression specifying shorter patient survival. ShRNA-knockdown and …

Protocol For An Agent-Based Model Of Recombination In Bacteria Playing A Public Goods Game, Isaiah Paolo A. Lee, Omar T. Eldakar, J. Peter Gogarten, Cheryl P. Andam

Biology Faculty Articles

Agent-based models are composed of individual agents coded for traits, such as cooperation and cheating, that interact in a virtual world based on defined rules. Here, we describe the use of an agent-based model of homologous recombination in bacteria playing a public goods game. We describe steps for software installation, setting model parameters, running and testing models, and visualization and statistical analysis. This protocol is useful in analyses of horizontal gene transfer, bacterial sociobiology, and game theory.

For complete details on the use and execution of this protocol, please refer to Lee et al.¹

Advances In Diagnostic Tools And Therapeutic Approaches For Gliomas: A Comprehensive Review, Gayathree Thenuwara Nanolab Research Centre, James Curtin, Furong Tian Nanolab Research Centre

Articles

Gliomas, a prevalent category of primary malignant brain tumors, pose formidable clinical challenges due to their invasive nature and limited treatment options. The current therapeutic landscape for gliomas is constrained by a “one-size-fits-all” paradigm, significantly restricting treatment efficacy. Despite the implementation of multimodal therapeutic strategies, survival rates remain disheartening. The conventional treatment approach, involving surgical resection, radiation, and chemotherapy, grapples with substantial limitations, particularly in addressing the invasive nature of gliomas. Conventional diagnostic tools, including computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET), play pivotal roles in outlining tumor characteristics. However, they face limitations, such as …

Salamander Modeling: Bridging The Gaps In Environmental Science Accessibility, Grace Leopold

Honors Program Theses and Projects

In the realm of science education, ensuring inclusivity and accessibility for all students, especially those with Individualized Education Programs (IEPs), is an imperative goal. IEPs are customized plans designed to support students with diverse learning needs, which can encompass a broad spectrum of disabilities and learning differences (Shaw, 2021). Providing learners with an IEP is an integral part of Special Education, however, there are a host of overarching challenges faced by students with IEPs in science education, especially in environmental science classes. In this thesis, the development and application of clay salamander models are evaluated for their potential to provide …

Tropicalization Fact Sheet, Linda Walters, Carla Perscky

CEELAB Outreach Materials

The goal of this 2-sided fact sheet is to introduce the topic of tropicalization along our coastlines to young audiences and their families. Tropicalization is defined as, "the transformation of ecosystems by tropical organisms that migrate towards the poles in response to warming minimum winter temperatures."

Understanding And Combating The Spread Of Antibiotic-Resistant Organisms, Bejan Mahmud

Arts & Sciences Graduate Student Theses and Dissertations

The introduction of antibiotics in the 20th century stands as one of our greatest scientific achievements, profoundly transforming human health and global well-being. Over the past century, antibiotics have ensured that infectious diseases are no longer the most common causes of death worldwide. In further enabling a vast array of invasive medical procedures (e.g., surgeries, organ transplants), antibiotics have effectively added decades to the average human lifespan. In agriculture, antibiotics have been heavily relied upon to meet the nutritional demands of the growing human population. Thus, ever since the introduction of penicillin, antibiotics have been the “miracle drugs” they were …

Investigating The Role Of Bhlhe40 In Host Responses To Mycobacterium Tuberculosis Infection And Myeloid Cell Development, Skyler Hendrix

Arts & Sciences Graduate Student Theses and Dissertations

Infections with Mycobacterium tuberculosis (Mtb), the causative agent of the disease tuberculosis (TB), remain a prominent global health threat that affects millions of people annually. While antibiotic treatments for Mtb infections are available, the increased prevalence of drug-resistant Mtb cases has highlighted the urgent need to develop additional therapeutic options such as host-directed therapies. Development of host-directed therapies, however, first requires a better understanding of the protective immune responses required to control Mtb infection. Such responses must strike a precise balance between pro-inflammatory and anti-inflammatory responses that promote bacterial clearance while also minimizing tissue damage. Here we show that the …

Construction Of A Human Pangenome Reference To Improve Structural Variation Detection, Wen-Wei Liao

Arts & Sciences Graduate Student Theses and Dissertations

Structural variants (SVs) significantly contribute to genetic diversity among individuals and impact gene regulation, disease, and evolution. The predominant approach to profiling these genetic variants in large-scale population studies is through short-read whole-genome sequencing (WGS). This approach involves sequencing millions of short reads, aligning them to a linear reference genome, and subsequently identifying variants relative to this reference. However, its capability to detect SVs, especially long insertions and complex rearrangements, is limited. The primary limitation arises from the insufficient representation of structural diversity across human populations in the linear reference genome. As a result, short reads derived from non-reference SVs …

Single-Nuclei Resolution Kidney Profiling In Physiological And Disease Settings, Ruiyang Liu

Arts & Sciences Graduate Student Theses and Dissertations

The kidney is a critical organ responsible for the maintenance of fluid, electrolyte and metabolites in the body. Recent advancements in kidney research, including the use of single-nuclei RNA Sequencing (snRNA-Seq), have uncovered a complex landscape that encompasses both physiological and pathological conditions. The scope of my thesis covers two important aspects: (1) the exploration of kidney sexual dimorphism, (2) a detailed investigation of polycystic kidney disease (PKD). To obtain a comprehensive understanding of the molecular regulation of kidney sexual dimorphism, we integrated single nucleus RNA and ATAC sequencing (snRNA-Seq and snATAC-Seq) and Visium spatial transcriptomics (ST) data to build …

Nutrient And Microbiome-Mediated Plant–Soil Feedback In Domesticated And Wild Andropogoneae: Implications For Agroecosystems, Amanda Quattrone, Yuguo Yang, Pooja Yadav, Karrie A. Weber, Sabrina E. Russo

School of Biological Sciences: Faculty Publications

Plants influence the abiotic and biotic environment of the rhizosphere, affecting plant performance through plant–soil feedback (PSF). We compared the strength of nutrient and microbemediated PSF and its implications for plant performance in domesticated and wild grasses with a fully crossed greenhouse PSF experiment using four inbred maize genotypes (Zea mays ssp. mays b58, B73- wt, B73-rth3, and HP301), teosinte (Z. mays ssp. parviglumis), and two wild prairie grasses (Andropogon gerardii and Tripsacum dactyloides) to condition soils for three feedback species (maize B73-wt, teosinte, Andropogon gerardii). We found evidence of negative …

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Investigating Telomere Lengths In Chestnut-Crowned Babblers, Gabriella Rose Beberg

Honors Thesis

Telomeres are chromosomal elements that protect and maintain genes as DNA replicates in many organisms. As individuals age and DNA replicates, telomeres often shorten; thus, telomere length often corresponds with an individual’s lifespan, and early-life decreases in telomere length can be predictive of longevity. Here, I investigated the relationship between telomere length and developmental environment in a cooperatively breeding species, the chestnut-crowned babbler (Pomatostomus ruficeps; CCB). Cooperative species are unique, as some individuals give up their own breeding opportunities to help rear the offspring of others; further, cooperative breeding systems generate considerably more variation in adult carers, which …

Acid Attack: How Escherichia Coli Strains Resist Acid Stress, Lindsey Miller

Honors Theses

The systems used by Escherichia coli to combat heightened levels of acidity within their environment are varied and complex. Four distinct systems used by E. coli to resist acid-induced stress were identified in 2004 by Foster (1), though six now are known today. These systems include the glucose-repressed, glutamate-dependent, arginine-dependent, lysine-dependent, ornithine-dependent, and serine-dependent acid resistance systems. Each system is also known by its corresponding abbreviation, AR1-AR6. What is known about each system varies due to identification date, complexity of the pathway, and amount of research completed. Within this paper, each system will be identified and the pathway defined, combining …

Embracing Digital Mindsets To Ensure A Sustainable Future, Chengjun Li, Riqing Yu, Wenjing Ning, Huan Zhong, Christian Sonne

Biology Faculty Publications and Presentations

The 19th Asian Games astounded global audiences with an opening spectacle that showcased stunning digital fireworks (International Olympic Committee, 2021; Zhe, 2023). The groundbreaking display was brought to life through virtual reality (VR) and augmented reality (AR) technologies. It sets a pioneering example to replace conventional fireworks in major international events as well as in other large-scale entertainment activities, marking a historic milestone in the pursuit of a sustainable and healthy future.

The Potential Of Endophytic Bacteria As The Biocontrol Agents Of Fusarium Proliferatum, Rima Ernia, Nisa Rachmania Mubarik, Lisdar Idwan Sudirman

Makara Journal of Science

Fusarium proliferatum decreases the productivity of shallot (Allium cepa L.). Endophytic bacteria are potential biocontrol agents in controlling the growth of F. proliferatum. This study aimed to select and characterize endophytic bacteria producing bioactive compounds that inhibit the growth of F. proliferatum. The endophytic bacteria used were isolated from the roots, stems, leaves, and soil of shallot plants from healthy and diseased shallot farming fields. The endophytic bacteria were selected using the dual culture method and extracted using ethyl acetate solvent. The results of the 16S rRNA identification suggested that isolate ABP5.2 is similar to Pseudomonas …

Catfish Neurocranium 3-D Scan, Pamela Gonzalez, Jarod Johnson, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

No abstract provided.

Oliver Agee Catfish Neurocranium, Charlotte R. Oliver, Kristina Agee, David Kerstetter

All Scans: Kerstetter Fisheries and Avian Ecology 3D Scan Series

Neurocranium from 10.7 cm total length, [Catfish], collected by [Kerstetter].

Pathogenicity Of Acinetobacter Calcoaceticus, Kaitlan A. Sullivan

MUSC Theses and Dissertations

Acinetobacter is a genus of gram-negative bacteria that have been appearing frequently in hospitals contributing to infections in the blood, lungs, urinary tract, and other parts of the body. It infects patients with weakened immune systems that are placed on ventilators, after the use of catheters, or have any other open wounds produced by prolonged hospital stays. This genus of bacteria is problematic due to its high probability of becoming resistant to multiple classes of antibiotics. Thus, we are determining the pathogenicity of clinical isolates of Acinetobacter calcoaceticus using the organism Caenorhabditis elegans as a model.

We are testing …