Digital Commons Network^™

New Paradigms In E. Coli Hemolysin Function And Pathogenesis, Hunter Winston Kuhn

Arts & Sciences Graduate Student Theses and Dissertations

Bacterial pore-forming toxins are potent secreted protein effectors that disrupt cellular ion homeostasis by integrating into the plasma membrane. Among them, the RTX toxin alphahemolysin (HlyA) from uropathogenic Escherichia coli (UPEC) has been extensively studied for its hemolytic activity, broad cell tropism, and role in virulence. HlyA was identified as the first type 1 secreted substrate, with β2 integrin CD18/LFA-1 proposed as its receptor. However, its diverse mechanisms of cellular toxicity and impact on outcomes of urinary tract infection (UTI) have remained incompletely defined. During pyelonephritis, renal epithelial cells are at the front line of infection, directly contacting ascending UPEC …

Multiple Stressors Effects On The Physiological Performance Of Mytilus Trossulus, M. Christina Vasquez, Alana J. Borer, Claribel Y. Alcantar, Osiris Guinea Zepeda, Camya A. Brazil, Colin Carr, Emma Guerrini Romano, Alexander J. Provenzano, Min Jeon Roh

Biology Faculty Works

Mytilus galloprovincialis and M. trossulus co-occur and hybridize along set biogeographical ranges of temperature and salinity along the Pacific coast, USA. However, the role of physiological traits in mussel distribution remains poorly understood. We investigated metabolic rate, antioxidant activity (superoxide dismutase, catalase), oxidative damage (malondialdehyde content, MDA), and clearance rate of M. trossulus under multiple stressors: 7 days of hyposalinity (20, 28, 34 ppt), followed by an acute heat shock (17, 20, 25 ◦C). We found a significant effect of temperature on metabolic rate, an interaction effect on antioxidant activity, and MDA, and independent temperature and salinity effects on clearance …

Effects Of Plasma-Activated Water On Wheat: Germination And Seedling Development, Wafaa Abdulrazzaq Abdullah, Hadeel O. Ismael, Duaa A. Uamran, Hammad R. Humud

Karbala International Journal of Modern Science

The food sector must contend with issues such as pathogen resistance to some of the available chemical agents, environmental pollution, and climate change to provide healthy food for livestock and people. The application of atmospheric pressure plasma jets (APPJs) is one potential solution for such problems. Plasma is appropriate for effective surface decontamination regarding food products and seeds, surface decontamination, and achieving improved agricultural production yields. The impact of plasma-activated water (PAW) produced by plasma jet discharge (PJD) system on in vitro-cultivated wheat seeds is examined in this work. For this aim, a plasma jet system was constructed with a …

Ethical Implications Of Being A Holobiont, Scott F. Gilbert

Biology Faculty Works

Developmental plasticity and holobiont theory have undermined the normative concepts of biological individuality. However, such traditional ideas of biological individuality have helped define and support Western ethical views into the 21st century. Guided by some of the ethical formulae of Simone Weil, Hans Jonas, and Alastair MacIntyre, this essay attempts to outline some possible trajectories for an ethics that is bounded by these new biological paradigms of environmental agency. Specifically, the ecological developmental biology concepts of plasticity and holobiont theory permit the “ethics of attention” to focus on the partnerships of living beings. Highlighting environmentally integrated life cycles and their …

Synthesis Of Cancrinite Zeolite From Toraja Natural Bentonite For Heavy Metal Removal From Wastewater, Yuli Astuti, Paulina Taba, Siti Fauziah, Syarifuddin Liong, Yusafir Hala, Nur Umriani Permatasari, Satria Putra Jaya Negara, Fadliah Fadliah

Karbala International Journal of Modern Science

This study explores the production of cancrinite (CAN) zeolite from bentonite found in Toraja (a place in South Sulawesi Province, Indonesia) and its effectiveness in removing Pb²⁺ and Fe³⁺ ions from wastewater. The synthesis was carried out using a hydrothermal method with varying NaOH concentrations, where a single phase of zeolite was formed at 5 M, as confirmed through XRD analysis. FTIR results showed the characteristics of CAN zeolite with typical absorption peaks at 676, 622, and 565 cm^-1, as well as the presence of carbonate groups (CO₃^2-) at 1300-1400 cm^-1. SEM …

Machine Learning Crime Prediction Models And The Gap Between Research And Implementation: A Systematic Review, Ricardo Huamantingo, Miguel Cano-Lengua, Ciro Rodriguez

Karbala International Journal of Modern Science

A crime is an illegal or violent act committed by one individual against another. The increasing crime rate has become a major concern as it negatively affects people's quality of life and generates significant social and economic costs. This study aims to identify the most widely used machine learning (ML) models for crime prediction, determine evaluation metrics for assessing model performance, and analyze key data characteristics to enhance real-world implementation. The study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) methodology. A search string was formulated using the population, intervention, comparison, and outcomes (PICO) framework and applied …

Investigating Molecular Mechanisms Of Meiosis And Mitosis In Cryptosporidium Parvum, Abigail Kimball

Arts & Sciences Graduate Student Theses and Dissertations

The apicomplexan parasite Cryptosporidium parvum (Cp) is a major global contributor to infectious diarrhea in children and poses a serious threat to immunocompromised adults. This dissertation investigates Cp's unique life cycle, which alternates between sexual and asexual reproduction to achieve three critical objectives: producing oocysts capable of transmission, enhancing genetic variation through recombination, and generating sufficient progeny for survival. Sexual reproduction is essential for forming infectious oocysts that facilitate disease transmission. Yet, the process of meiosis in Cp has been historically understudied due to limitations of traditional in vitro culture methods. The newly developed air-liquid interface (ALI) culture system supports …

Neurophysiology And Endocrine Responses To Hunger And Satiety Mechanisms: The Brain-Gut Crosstalk, Nour Shakir Rezaieg, Muthanna M. Awad

Karbala International Journal of Modern Science

Background: Obesity is a main public health problem which substantially increases the risk of many diseases. The complex neural circuitry controls energy homeostasis and food consumption by the incorporation of hormonal and neural signals. Circulating hormones, in specific the gut hormones, have been found to be very important in appetite regulation. These hormones transfer energy situation signs to the brain throughout three principle paths: the circulation system, activation of the vagus nerve, and direct modification of main brain regions such as the hypothalamus and brainstem. The control of food eating is not exclusively dependent on the homeostatic processes, rather it …

A Novel Chaotic Dna-Based Image Cryptosystem Leveraging Euclidean Division, Dynamic Josephus Traversal, And Reservoir Computing, Ahmed Kareem Shibeeb, Salah Albermany, Sadiq A. Mehdi

Karbala International Journal of Modern Science

This study presents a new chaotic DNA-based image cryptosystem that combines Euclidean division, dynamic Josephus traversal (DJT), and reservoir computing to address the weaknesses of current methods. Old chaotic DNA cryptosystems usually have problems such as using the same keys for different messages, simple DNA processes, and being vulnerable to attacks where the attacker can choose the input or try many options. The cryptosystem in this study uses a 7D hyperchaotic system that starts with keys created from SHA-512 hashes to produce changing keystreams based on the plaintext, making it very strong against such attacks. The proposed cryptosystem uses a …

Life Of Moo Deng, The Internet Sensation Pygmy Hippopotamus: An Overview Of The Biology And Conservation Breeding Program In Thailand, Ampika Thongphakdee, Atthapon Nundee, Umaporn Maikeaw, Narongwit Chodchoy, Chainarong Punkong, Kaywalee Chatdarong

The Thai Journal of Veterinary Medicine

The hippopotamus, commonly known as the hippo, is classified into two extant species: the common hippopotamus (Hippopotamus amphibius) and the pygmy hippopotamus (Choeropsis liberiensis). Pygmy hippos are fascinating creatures native to the forests and swamps of West Africa. Their survival is increasingly threatened by habitat loss resulting from agricultural expansion and urban development. As the population declines, zoological institutions play a crucial role in conservation by acting as genetic reservoirs and promoting public awareness of wildlife and environmental protection. “Moo Deng”, a pygmy hippo, whose name in Thai has gained international recognition, represents a notable success …

Human Contributions To Global Soundscapes Are Less Predictable Than The Acoustic Rhythms Of Wildlife, Panu Somervuo, Tomas Roslin, Brian L. Fisher, Bess Hardwick, Deirdre Kerdraon, Dimby Raharinjanahary, Eric Tsiriniaina Rajoelison, Patrik Lauha, Lukas Griem, Petteri Lehikoinen, Pekka Niittynen, Esko Piirainen, Markus Lumme, Ville-Matti Riihikoski, Orlando Acevedo-Charry, Solny A. Adalsteinsson, Maaz Ahmad, Sandra Alcobia, Jón Aldará, Tad Dallas

Faculty Publications

Across the world, human (anthropophonic) sounds add to sounds of biological (biophonic) and geophysical (geophonic) origin, with human contributions including both speech and technophony (sounds of technological devices). To characterize society’s contribution to the global soundscapes, we used passive acoustic recorders at 139 sites across 6 continents, sampling both urban green spaces and nearby pristine sites continuously for 3 years in a paired design. Recordings were characterized by bird species richness and by 14 complementary acoustic indices. By relating each index to seasonal, diurnal, climatic and anthropogenic factors, we show here that latitude, time of day and day of year …

Emergent Collective Reproduction Via Evolving Neuronal Flocks, Nam H. Le, Michael Levin, Richard A. Watson, Josh Bongard, Christopher L. Buckley

Northeast Journal of Complex Systems (NEJCS)

This study advances the understanding of evolutionary transitions in individuality (ETIs) through a novel artificial life framework, VitaNova, which integrates self-organization and natural selection to simulate the emergence of complex, reproductive groups. By dynamically modeling individual agents within an environment shaped by predators and spatial constraints, VitaNova reveals mechanisms by which simple agents evolve into cohesive units exhibiting collective reproduction. The findings highlight the synergy between self-organized behaviors and adaptive evolutionary strategies as fundamental drivers of ETIs. This approach deepens our understanding of higher-order biological individuality and offers a new empirical pathway for investigating ETIs, extending current theoretical frameworks.

Cortical Functional Organization In Early Childhood, Jiaxin Tu

Arts & Sciences Graduate Student Theses and Dissertations

The advent of connectivity-based methods, particularly those utilizing spontaneous BOLD signals, has significantly advanced brain mapping and deepened our understanding of the human brain's functional architecture. While prior research has explored functional organization in early childhood, most studies have focused on coarse, group-level distinctions aligned with adult literature, often within narrow age ranges. This dissertation extends these investigations by examining cortical functional organization in greater detail among healthy infants and toddlers aged 1 to 5 years. Chapter 1 employs spontaneous BOLD signals in sleeping infants and toddlers to derive a group-level functional organization at the resolution of areas and networks. …

Robust Embeddings Of Genetics, Anatomy, And State Decoded From A Neuron’S Activity, Aidan Schneider

Arts & Sciences Graduate Student Theses and Dissertations

Neural spike trains are shaped by both extrinsic inputs and intrinsic structural constraints. While prior work has focused on how spike timing encodes externally driven variables, such as stimuli or behavior, this dissertation explores whether principles that organize neural activity in space and time—such as genetic cell type, anatomical location, and arousal state—are also embedded in the spiking output of individual neurons. I hypothesize that these organizing principles are not quenched as irrelevant variability, but rather multiplexed within the neural code itself. To test this, I attempt to decode these principles from the spike trains of neurons recorded in behaving …

Genetic Gain And Loss In The Evolution Of Amniote T Cell Receptor And Immunoglobulin Genes, Jordan M. Sampson

Biology ETDs

The immune system of most jawed vertebrates consists of three major cell types: αβ T cells, γδ T cells, and B cells. Every species evaluated contains the loci that encode the highly conserved αβ T cells, however, γδ T cells are less conserved and have been lost in squamate reptiles. The loci that encode the B cell receptor have also varied across evolution. Seven immunoglobulin (Ig) heavy chain isotypes have been identified in amniotes: IgM, IgD, IgY, IgG, IgE, IgO, and IgA. Some are found in most species (IgM and IgD) and others only in specific lineages (IgY or IgG). …

​​Site Fidelity Is Associated With The Social Experience Of Forked Fungus Beetles (Bolitotherus Cornutus), Joo Yeon Kim , '22, C. W. Wood, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Consistently returning to or remaining within a specific location, a behavior known as site fidelity, is a useful metric for quantifying animal space use. When multiple individuals display similar site fidelity patterns, they are likely to interact, shaping the degree and quality of their social interactions. However, the link between the expression of site fidelity behavior and an individual’s social experience has not been thoroughly investigated. In this study we examined (1) how intrinsic individual properties (body size and sex) predicted variation in site fidelity and (2) whether site fidelity was linked to the social experience of individuals in wild …

Identification Of Novel Components Of The Retinal Determination Gene Network In Drosophila Cell Lines, Robert Drewell, Jacqueline Dresch

Biology

The retinal determination genetic network controls the development of the visual system in all seeing animals through the molecular regulation of cells to adopt an eye tissue fate. The compound eye of the fruit fly, Drosophila melanogaster, is an excellent model system to study the complex mechanisms within the network that regulate specification of cellular identity during embryogenesis. In Drosophila, the two Pax6 paralogues, eyeless and twin of eyeless, sit at the very pinnacle of the network and their expression early in development activates critical downstream components of the retinal determination pathway. In this study, we investigate the expression of …

Contributions Of Citizen Science Data To Butterflies Of The Lower Rio Grande Valley, Akane Jazmyn Benitez

Theses and Dissertations

Citizen science-provided insect data inherently exhibits variability in accuracy. In the Lower Rio Grande Valley (LRGV), butterfly occurrence reporting is predominantly reliant on citizen science contributions. My research compared fieldwork conducted monthly over a year to occurrence records submitted by visitors at the National Butterfly Center and in Mission, Hidalgo County, Texas. I hypothesized that butterfly occurrences at the Center would be maximized during the fall and minimized during winter and summer months. My research findings revealed that butterfly taxa richness is contingent upon the following factors: 1) the impact of citizen science submitting reports, and 2) monthly butterfly activity …

Teratogenic Effects Of Serotonin Receptor 2b Disruption On The Migration And Cardiac Derivatives Of The Cardiac Neural Crest, Brian K. Wells, Gwyneth K. Garramone, Amira Mahomed, Max Ezin

Biology Faculty Works

Background: Cardiac neural crest cells (cNCCs) are critical for heart development, and their disruption can result in congenital heart defects. Serotonin (5-HT) signaling, specifically via 5-HT2B and 5-HT2C receptors, regulates diverse physiological processes, including neural crest migration. This study investigates how modulation of 5-HT2B and 5-HT2C receptor activity impacts cNCC migration and the development of their derivatives, with relevance to serotonergic drug safety during pregnancy.

Methods

Chicken embryos at HH8 were treated with 50 μL of 20 μM 1-Methylpsilocin (1-MP), an inverse agonist of 5-HT2B and agonist of 5-HT2C, and collected at HH14 to assess cNCC migration. Embryos were pre-treated …

Mammals Of Malheur National Wildlife Refuge And Surrounding Harney County, Oregon, John E. Cornely, Leslie N. Carraway

Monographs of the Western North American Naturalist

Malheur National Wildlife Refuge (NWR), located in southeastern Oregon, is part of the National Wildlife Refuge System (NWRS) of the United States. Currently, NWRS includes more than 568 NWRs, 38 Wetland Management Districts, and 5 Marine National Monuments. Malheur NWR, like a majority of the refuges in the NWRS, was established for the conservation of migratory birds. Many of these NWRs also provide significant habitat for mammals. Malheur NWR, one of the oldest (established 1908) and largest refuges in the system, is one of those with significant habitat for mammals. In addition to the refuge, we have included Harney County, …

Investigating The Immunomodulatory Effects Of Cdk8/19 Inhibitor Senexin631 In A Her2-Positive Breast Cancer Model, Stephen O'Rourke

Theses and Dissertations

HER2-positive (HER2⁺) breast cancer is aggressive and often develops resistance to anti-HER2 therapies. CDK8 and CDK19, transcription-associated cyclin-dependent kinases (tCDKs) in the Mediator complex, are dysregulated in HER2⁺ breast cancer, correlate with poor survival, and support transcriptional escape driving therapeutic resistance. Previous studies Previous studies in immune-deficient models demonstrated that CDK8/19 inhibition (CDK8/19i) reduces pro-tumor macrophages (M2Φs), but its role in immune-competent tumors and innate immune–mediated tumor control remains unclear. Since HER2⁺ tumors are often immunogenic and anti-HER2 therapies rely on innate immune activation, reprogramming immunosuppressive M2Φ toward an M1Φ-like phenotype could enhance antitumor immunity. We hypothesized that CDK8/19i modulates …

Circannual And Kinship Cues Shape Reproduction And Epigenetic Aging In Peromyscus, Kim Tuyen Huynh Dam

Theses and Dissertations

Evolutionary success is defined by the ability of a species to adapt and survive across many generations. This success is not determined by any single attribute but rather includes the entrenched, complex system that could be associated with biological rhythms, reproductive strategies, and regulations of epigenetic and genetic components. By using closed Peromyscus colonies as a model and by coupling mathematical modeling, analyses of breeding records, epigenetic studies, and in vitro and in vivo experiments, this dissertation aims to discover how Peromyscus adjusts to the internal and external pressures to ensure their survival and preserve evolutionary fitness in controlled environments. …

Exploring The Ancestry And Mutational Signatures Of Free-Breeding Dogs From Chernobyl And The Galápagos Islands, Gabriella Jean Spatola

Theses and Dissertations

Two free-breeding dog populations, one in Chernobyl, Ukraine, and the other on the Galápagos Islands, Ecuador, exist on opposite sides of the globe, yet both hold unique scientific potential to further our understanding of free-breeding dog population dynamics and evolutionary processes related to their environments. In the following studies, blood samples from more than 400 individual Chernobyl dogs were collected and their genomes were analyzed alongside over 1500 purebred and 200 global free-breeding dogs, describing genetic relationships and the extent of admixture with purebred migrants. Importantly, the sampled Chernobyl dogs had long-term exposures to ionizing radiation because of the 1986 …

Metabolic And Physiological Regulation In C. Elegans: Insights Into Sperm Activation And Peroxisome-Mediated Longevity, Yash Flora

LSU Doctoral Dissertations

Organelle dynamics lie at the heart of cellular signaling and metabolic regulation, orchestrating physiological processes such as reproduction and aging across the lifespan. In this dissertation, I investigate how organelle-based signaling coordinates sperm activation and modulates organismal aging in the nematode Caenorhabditis elegans. I identify SPIN-4, a previously uncharacterized Spinster family transporter, as a key regulator of spermiogenesis. SPIN-4 is strongly expressed in developing sperm, localizes to the plasma membrane, and promotes sperm activation by facilitating the export of sphingosine-1-phosphate (S1P). Loss of spin-4 results in defective pseudopod formation, reduced motility, and compromised fertility, phenotypes that can be rescued …

Exploring Students’ Perceptions Of Science Laboratory Practices: A Comparative Study Between Rural And Urban Schools, Safrida Dwiningsih, Ina Lestari, Roma Ismi, Sri Wahyu Rahmadina, Masdalena Sinaga, M. Rahmad

Jurnal Pendidikan Sains

This study aims to analyze students' perceptions of the implementation of science laboratory practicums at public middle school 020 Pekanbaru and public middle school 7 Pangkalan Kuras, Riau Province. Using a quantitative survey method, this study involved 75 student respondents. The instrument used was a questionnaire consisting of 26 statements, analyzed descriptively. The results show that students' perceptions of the preparation, implementation, and conclusion stages of the practicum fall into the "good" category, with urban schools having a higher percentage. In conclusion, the implementation of practicums in urban schools is better than in rural schools, bringing attention to the need …

Digital Comic Learning Media (E-Comic) To Increase Student Learning Interest In Reaction Rate Material At High School, Berliana Afsohin Nabila, Achmad Lutfi

Jurnal Pendidikan Sains

This study aims to develop digital comic learning media that is effective in increasing students' interest in learning about reaction rate material, focusing on the media's validity, practicality, and overall effectiveness. This research utilizes the research and development method with the ADDIE model. Research instruments were used, including validity sheets to assess the media's validity, student activity observations, and student response questionnaires to evaluate the media's practicality, as well as student interest questionnaires and learning outcomes to measure the effectiveness of the learning media. The findings show that validity results showed a mode score of 4, indicating a very valid …

The Effort To Improve Students’ Problem-Solving Ability: Physics E-Modules For High School Students, Hidayatullah Hana Putra, Edi Supriana, Nasikhuddin Nasikhuddin, Annisa U. Yana, Suhailee Sohnui

Jurnal Pendidikan Sains

Physics teachers in Indonesia still face obstacles during learning, such as students who are less active and have difficulty in solving physics problems. The physics learning media used are also still not very interesting and are not based on authentic problem solving. Therefore, this study focuses on the development of PBL-based e-modules on work and energy to improve the physics problem-solving abilities of high school students. This research and development used the ADDIE design and was tested on 90 high school students in High School 1 Sumber Pucung Malang in the 2022/2023 academic year. The questionnaire instrument was used in …

Vitamin D3 Toxicity-Induced Hypercalcemia In Staphylococcal Arthritis: A Focus On Il-6, Ali Jabbar Abd Al-Hussain Alkawaz, Maryam Sabah Naser, Ali Jalil Obaid, Zakaria M. Al-Ghazaly

Karbala International Journal of Modern Science

Background: Vitamin D3  over-supplementation can induce toxicity through the development of hypercalcemia and may disturb immune modulation. This study examines the relationship between hypercalcemia  resulting from Vitamin D3 Overdose and serum Interleukin-6 (IL-6) levels in patients diagnosed with staphylococcal arthritis.

Methods: Forty male patients (mean age: 31 years; range: 17–45 years) were enrolled from Dec. 2024 to Feb. 2025. Twenty cases of staphylococcal arthritis were compared with twenty healthy male controls. Serum concentrations of Vitamin D3, calcium, IL-6, and other biochemical markers (urea, creatinine, ESR, WBC, and potassium) were analyzed. Staphylococcus aureus was isolated from synovial fluid and confirmed using …

American Kestrels (Falco Sparverious) In Row Crop Agriculture Of The Lower Mississippi Alluvial Valley Of Northeast Arkansas: Factors Influencing Nest And Roost Box Use, Nest Success, And Effects On Agricultural Pests, Ty Spencer Sharrow

Student Theses and Dissertations

Utilizing birds of prey for pest control is a sustainable, environmentally friendly approach to pest management that can benefit not just the environment and human health but also the birds themselves. The American Kestrel (Falco sparverius; hereafter ‘kestrel’) is one such species that can provide pest management services while benefiting from nest boxes used to attract them in agricultural areas. I examined how box and habitat characteristics influenced kestrel box use for nesting, winter roosting, and nest success in the row crop-dominated landscape of northeast Arkansas’ Lower Mississippi Alluvial Valley. In addition, I assessed kestrel impact on pests by systematically …

The Effects Of Hsa-Mir-26a-5p On Cell Proliferation, Migration, And Pi3k Inhibitor Sensitivity In Metformin-Resistant Triple Negative Breast Cancer Cells, Şahi̇ka Cingir Köker, Senem Noyan, Banu Yalçin, İrem Doğan Turaçli

Turkish Journal of Biology

Background/aim: Metformin is commonly used to manage type 2 diabetes (T2D) and is being investigated for its potential antiproliferative effects in cancer, particularly in patients with both T2D and malignancies. Drug resistance can develop with any therapeutic agent, and metformin is no exception. As we showed in our previous study, metformin-resistant MDA-MB-468 (MET-R) cells exhibited an EMT-like phenotype. Many transcription factors, as well as miRNAs, can contribute to this altered phenotype. Our current study identifies the contribution of hsa-miR-26a-5p expression to the previously observed phenotype. Materials and methods: By utilizing bioinformatic tools, we identified hsa-miR-26a-5p, whose expression was significantly altered …