Life Sciences Commons^™

Deciphering The Source Of Escherichia Coli In Urinary Tract Infections: A Comparative Metagenomic Analysis Of The Female Urogenital Microbiome, Alexis Annabel Avalos

Dissertations

In 2019, there was a 140.19% increase in deaths due to urinary tract infections (UTIs) compared to 1990, worldwide. One of the common uropathogens known to associate with UTIs in females is Escherichia coli. The prevailing belief is that E. coli in the bladder originates in the rectum, passing its way from the perineal, to the vagina, and finally into the bladder. Known as the Fecal-Perineal-Urethral (FPU) hypothesis, this “origin story” has been supported by several studies that have relied on genotyping or serotyping isolates collected from the bladder and rectum. Most notably, culturing isolates from samples has been central …

Selecting For Lysis In A Temperate Phage Population, Haley Atkins

Dissertations

The ongoing evolutionary arms race between bacteria and bacteriophages (phages) is a prime example of Red Queen hypothesis, where continuous adaptation drives survival. This study focuses on Escherichia coli-infecting temperate phages, which dominate natural environments and contribute to bacterial resistance mechanisms. Despite their prevalence, temperate phages are less suited for phage therapy due to their lysogenic life cycle, where they integrate into bacterial genomes instead of lysing the host. In contrast, obligately lytic phages, which directly lyse bacterial cells, are ideal for therapeutic use but occur less frequently in nature. This research aims to select for lytic behavior in temperate …

Refining Cross-Population Polygenic Risk Scores Across Diverse Populations, Mansi Patel

Dissertations

Large biobanks containing whole genome sequences connected to the deidentified electronic health records of hundreds of thousands of individuals are increasingly available to researchers. This has facilitated the development of polygenic risk scores (PRS), which use machine learning to predict risk of disease and other phenotypes from millions of genetic variants. Due to Eurocentricity of available genetic data, PRS have primarily been trained in populations of European descent. Differences in allele frequencies, effect sizes, and linkage disequilibrium patterns between populations can limit the transferability of PRS across different populations. Given that most data are from European genetic ancestry populations, we …

The Impact Of Lactobacillus Supplementation On Gut Microbiome Composition And Phage Induction In Mice, Kimia Boreiri

Dissertations

The mammalian gastrointestinal (GI) tract harbors a dense and dynamic community of microbes known as the gut microbiota, which plays vital roles in digestion, immunity, and overall health. Among these, probiotic bacteria such as Lactobacillus strains have garnered attention for their ability to influence microbial community structure and host physiology. This study investigated the effects of five Lactobacillus strains, Lactobacillus casei R1A482, Lactobacillus casei O3, Lactobacillus rhamnosus GG, Lactobacillus gasseri ATCC 33323, and Lactobacillus paragasseri UMB1065, on the gut microbiome of Swiss Webster mice over a six-week feeding period. To reduce stress, mice were fed Lactobacillus strains using gelatin pellets …

Decoding The Origins Of Infection: A Machine Learning Framework, Nirupama G. Shanbhag

Dissertations

Many infections can be attributed to a specific microorganism. For example, while there can be many causes of urinary tract infections (UTIs), such as the bacterial species Klebsiella pneumoniae or Enterococcus sp., the most widespread cause for UTIs is uropathogenic Escherichia coli. Generally, diseases or infections that are the result of a single pathogenic organism are more easily understood. Other diseases, such as irritable bowel disease (IBD), cannot be attributed to one member in the community; rather, it is a result of dysbiosis of the microbial community (microbiota) of the gastrointestinal tract, a combination of an overgrowth of problematic members …

Role Of Coronavirus Envelope Protein On Infectivity, Garrett E. Zaagman

Dissertations

Coronaviruses infect a wide range of hosts and have caused recent human pandemics. While much has been learned, gaps remain in understanding viral assembly and egress, particularly the role of the envelope (E) protein in specific infectivity. To study this, recombinant MHV viruses were created with E gene deletions and HiBiT-tagged spike (S) proteins to monitor virion release. In mouse cells, MHV∆E S-HiBiT secreted less spike and fewer infectious particles, indicating reduced specific infectivity. Comparisons between human HeLa-CEACAM and mouse DBT cells showed species-specific support for virus production. TMED10, a host membrane protein, was tested as a potential E-interacting partner …

Investigating Whether Txnrd2 Is A Therapeutic Target Against Triple Negative Breast Cancer Using African American-Derived Models, Keacha Chang

Dissertations

Despite similar breast cancer incidence rates, African American (AA) women experience a 40% higher mortality rate compared to Caucasian American (CA) women. This disparity is multifactorial and particularly pronounced in the Chicago area. AA women are twice as likely to be diagnosed with triple-negative breast cancer (TNBC), often at a younger age and with more aggressive disease. TNBC is a heterogeneous subtype lacking targeted therapies and is associated with the poorest prognosis among breast cancer types. Therefore, there is an urgent need for novel therapeutic strategies for TNBC, especially those tailored to AA patients. The thioredoxin pathway is essential for …

Evaluation Of Bacteriophage Infection Of Enterococcus Faecalis In A Monolayer, Alexandria Osborn

Dissertations

Enterococcus faecalis is one of the first colonizers of the human gastrointestinal tract, and it plays a role in the intestinal immune development at the very early stages of life. However, it is also an opportunistic pathogen, capable of translocating across the mucosal barrier to cause systemic infections. E. faecalis is also linked to infections including endocarditis, recurrent urinary tract infections (rUTIs), bacteremia, wound infections, meningitis, root canal infections, intra-abdominal and pelvic infections, and septicemia. Persistent enterococcal opportunistic infections have been associated with the production of virulence factors and sharing of antibiotic resistance genes, thus making E. faecalis difficult to …

Effects Of Nitrogen, Phosphorus And The Fungicide Azoxystrobin Additions On Larval And Post-Metamorphic Fitness Of American Toads (Anaxyrus Americanus), Michael Vosburgh

Dissertations

Since European settlement, vast areas of U.S. land have been modified by humans. In the Midwest, an estimated 99% of native grasslands have been replaced by agriculture and urban development. Such alternations have replaced native habitat, redefined hydrology and introduced a wide array of chemicals into aquatic ecosystems. Modern agricultural practices utilize fertilizers and pesticides to maximize crop production. These chemicals frequently runoff into surrounding waters, potentially effecting aquatic organisms. One group of organism thought to be susceptible to agricultural contaminants are amphibians. Amphibians are vulnerable to pollution due, in part, to their permeable skin and biphasic life history. Global …

Urban Coyotes As A Source Of Conflict With Humans: An Evaluation Of Common Management Practices, Paul D. Curtis, David L. Bergman, Angeline Barker, Daniel Bogan, Mary Ann Bonnell, Pierre Canac-Marquis, David Drake, Dave Kay, Brian F. Wakeling, H. Bryant White

Human–Wildlife Interactions Monographs

Wildlife often serves as a catalyst for conflict among stakeholders. Management actions that are intended to address sources of disagreement may initiate additional conflict. The Association of Fish and Wildlife Agencies Human–Wildlife Conflict Working Group initiated an effort to identify management actions commonly used to address unwanted coyote (Canis latrans) interactions within urban environments and identify the benefits and challenges associated with each action. Challenges with coyotes in urban environments include aggressive behavior toward humans and pets, attacks, disease exposure, and domestic livestock damage. Although elimination of all attractants would prove preventative in most instances, in practice this …

Cultivating Community-University Partnerships Within The Chicago Region Food System, Hanan Abdillahi, Vivian Cossey, Tania Schusler, Kevin Erickson, Karen Schauwecker, Sarah Ku, Ray Dybzinski

School of Environmental Sustainability: Faculty Publications and Other Works

We interviewed 22 organizations in the Chicago Regional Food System to gain insights on their current initiatives, assets, challenges, future visions, and perceived roles of universities in advancing their work. We analyzed themes to report on strong consensus or varied perspectives related to this work. This report aims to advise Loyola’s School of Environmental Sustainability's future work and collaboration activities with Chicago Food System organizations.

Suas Agricultural Aerial Application Operational Field Test, David Thirtyacre, Joseph Cerreta, Scott S. Burgess

International Journal of Aviation, Aeronautics, and Aerospace

One of the most promising uses of aerial applications by a sUAS is on small farms where traditional crewed aerial applicators were not practical due to the limited size of the operations. This controlled field test aimed to assess the feasibility and cost-effectiveness of using a sUAS spreading system compared to the traditional manual application of weed killer and fertilizer on cranberry bogs in Western Washington that were less than 10 acres. The aerial application took place over two separate days as scheduled by the farmer for maximum product efficiency. A total of sixty-three flights were necessary to apply the …

Investigation Of Multiple Factors Influencing The Vector-Borne Transmission Of Salmonella Typhimurium Via Blattella Germanica, Landen Sean Van Hulzen

Dissertations and Theses

The German cockroach (Blattella germanica) is a common urban pest that lives ubiquitously in human structures around the world. German cockroaches are a severe public health threat as they are known carriers and vectors of human pathogens including Salmonella enterica, Escherichia coli, Shigella spp, and more. German cockroach infestations have been associated with Salmonellosis outbreaks. While mechanical transmission by the German cockroach vector is well known, new research suggests that more nuanced biological transmission has a role in maintaining and transmitting Salmonella enterica serovar Typhimurium (S. Typhimurium). Despite this recent finding, many biological variables influencing vector-borne transmission of S. Typhimurium …

Convergence In Cancer: Integrative Multi-Modal Modeling For Pan-Cancer Drug Response Prediction, Jessica Zylla

Dissertations and Theses

Heterogeneity and rarity can make cancer difficult to study and treat. Cancer's heterogeneity, evident in tumor locations, tumor cell types, subtypes, and microbiota within the tumor microenvironment, complicates diagnosis, prognosis, and treatment. Research into the tumor microenvironment and its microbiota is an evolving area of oncology that may advance cancer drug-patient response. Cancer-omics signatures are crucial to drug response, yet there is no tool that physicians use as a gold standard. Research indicates that microbial presence can alter drug metabolism and immune response, affecting cancer-drug efficacy on a patient-specific basis. This work highlights the need for training readiness in transdisciplinary …

Food Finding Ability Does Not Predict Annual Survival In Winter Resident Birds, Aidan Hand

Honors Program: Senior Projects (Public)

Small non-migratory birds in temperate locations face many challenges to survive the winter. They must be able to find enough food, which is in decreased supply, to fuel the energetic demands of staying warm. Prior work has demonstrated that birds show individual variation in their foraging behaviors that could contribute to the discovery of new foraging patches, such as novel environment exploration. A better ability to discover new food sources could increase a bird’s chance of surviving the winter by increasing its access to new food patches. To test this hypothesis, we used radio frequency identification (RFID)-enabled bird feeders to …

Pregnant Adults' Interest In Physical And Mental Health Behavior Change Interventions Using Mobile Technology, Natalie M. Yarish, Cassidy M. Sandoval, Alicia Moulder, Meredith I. Turner, Danielle Symons Downs, Kristin E. Heron

Psychology Faculty Publications

Improving the health and well-being of pregnant adults is an important public health priority in the USA, and mobile health (mHealth) interventions may provide a scalable strategy to disseminate behavior change programs to pregnant adults. This study assessed pregnant people’s use of mobile technology, interest in making health behavior changes during and after pregnancy, and their willingness to use mHealth interventions. Participants were 133 pregnant adults (M_age = 27.86; 81% White) living across the USA recruited from social media to complete an online survey. Measures assessed mobile technology use and beliefs about improving mental/physical health in pregnancy and postpartum …

Impact Of Geography On Institutions In Agricultural And Nomadic Societies, Haiwen Zhou

Economics Faculty Publications

How geography affects the choice of institutions is studied in a theoretical model. In this model, nations are located around a circle. Rulers compete through choosing tax rates, the level of military spending, and the degree of formality of institutions. Geographic condition is captured by population density. It is shown that societies with higher population densities choose lower tax rates, establish more formal institutions, and give government officials lower levels of autonomies than those with lower population densities do. A higher level of external threats induces a ruler to choose a higher level of autonomy for officials. The model is …

Restored Wetlands Show Rapid Vegetation Recovery And Substantial Surface-Water Expansion, Thilina D. Surasinghe, Yin-Hsuen Chen, Kunwar K. Singh

Center for Geospatial Science, Education & Analytics Faculty Publications

Ecological restoration is essential for improving the ecological integrity of degraded ecosystems to enhance ecosystem services and biodiversity. In this study, we assessed the effectiveness of wetland restoration on retired cranberry farms by analyzing vegetation recovery and surface-water dynamics using the enhanced vegetation index (EVI) and normalized difference water index (NDWI) derived from Sentinel-2 satellite imagery. To quantify temporal dynamics of both vegetation recovery and surface-water cover, we identified the spectral distinctions among restored wetland plant communities. Our results indicated the emergence of distinct plant communities upon restoration. Restored wetlands in general showed significant and progressive vegetation recovery and expanding …

Theology Of Creation In The Bulgarian Theology Of The 20th Century, Svetoslav Ribolov

Occasional Papers on Religion in Eastern Europe

Theology of Creation in 20th-century Bulgaria emerged within the broader debate about the role of religious education in state schools and the tension between the prevailing influence of evolutionary theory and a scientific approach to the Orthodox Church’s traditional spiritual heritage. Before World War 2, the primary social and intellectual motivation behind the Theology of Creation in Bulgaria was rooted in an apologetic struggle against secular ideas, which were embraced by a significant portion of Bulgarian society at the time. In the second half of the 20th century, however, this discourse gradually evolved to incorporate more denominationally oriented theological perspectives, …

Understanding How Hearing Works, Cecilia Zoutewelle

A. The Science of Sound

A 7-page introductory overview of the anatomical and neurological processes of hearing, with illustrations and bullet-point summaries. 

A Network-Based Discovery Of Prognostic Markers In Recurrent Idh Wild-Type Gliomas, Yang Liu, Jason Huse, Kasthuri Kannan

Faculty, Staff and Student Publications

Background: Isocitrate dehydrogenase wild-type (IDH wild-type) gliomas represents the most aggressive subtype of diffuse gliomas, characterized by therapeutic resistance and dismal prognosis. Despite advances in molecular classification, reliable prognostic biomarkers for these tumors remain limited, particularly for recurrent disease. This study aims to identify gene expression signatures associated with survival outcomes in recurrent IDH wild-type gliomas, with the goal of improving patient stratification and potential therapeutic targeting.

Methods: We analyzed gene expression data from 180 recurrent IDH wild-type glioma samples from the Glioma Longitudinal AnalySiS (GLASS) Consortium. Using multiple computational approaches including a novel network-based method (netSurvival) and various survival …

Electrochemical Detection Of Prostate Cancer—Associated Mirna-141 Using A Low-Cost Disposable Biosensor, Alexander Hunt, Gymama Slaughter

Center for Bioelectronics Publications

Prostate cancer is the second leading cause of cancer-related deaths among men in the United States. The early detection of aggressive forms is critical. Current diagnostic methods, including PSA testing and biopsies, are invasive and often yield false results. MicroRNA-141 (miRNA-141) has emerged as a promising non-invasive biomarker due to its elevated levels in the urine of patients with metastatic prostate cancer. Here, a low-cost, paper-based electrochemical biosensor for the sensitive detection of miRNA-141 in synthetic urine is reported. The device employs inkjet-printed gold electrodes on photopaper, functionalized with thiolated single-stranded DNA-141 capture probes for specific target recognition. The biosensor …

The Bioremediation Of Nutrients And Heavy Metals In Watersheds: The Role Of Floating Treatment Wetlands, Nirmal Kumar, Bhupinder Singh, Yuanze Chen, Abishek Kafle, Ram L. Ray, Sandeep Kumar, Xiaonan Shan, Venkatesh Balan

Civil & Environmental Engineering Faculty Publications

Floating treatment wetlands (FTWs) are engineered systems that utilize floating platforms planted with aquatic vegetation to treat polluted water such as stormwater, agricultural runoff, and wastewater. FTWs have emerged as promising and environmentally sustainable solutions for water purification. This review synthesizes the current knowledge on FTW design, plant selection, and performance evaluation. It highlights key factors influencing nutrient and heavy metal removal, including the hydraulic retention time, mat thickness, and types of plant species. Recent findings on the roles of root architecture, microbial interactions, and seasonal variability in treatment efficiency are also discussed. Additionally, the review explores advanced analytical methods …

Genome-Wide Snp Analyses Reveal High Gene Flow Of Endemic Smallscale Croaker (Boesemania Microlepsis) In The Lower Mekong Basin, Quyen Dang Ha Vu, Christopher E. Bird, Oanh Thi Truong, Sang Quang Tran, Ellen E. Biesack, Amanda S. Ackiss, Kent E. Carpenter, Binh Truy Dang

Biological Sciences Faculty Publications

The Smallscale Croaker, Boesemania microlepis, is a valuable fishery resource in the Mekong River basin that lacks clear biological data to understand its basic ecology and conservation management priorities. This species is common in the southernmost floodplain of the Mekong which extends from Tonlé Sap in Cambodia to the Mekong Delta in Vietnam. This floodplain is of particular biodiversity conservation concern because of the many upstream dams that restrict water flow in an ecology that relies heavily on a flood-pulse cycle. The literature regarding the biology B. microlepis in this region contains conflicting ideas that populations are both highly …

Intraspecific Variation In Plant–Fungal Interactions Across Tidal Elevation In A Salt Marsh, Torrie Hanley, Catherine Gehring, Ron Deckert, Behzad Mortazavi, Christina Richards, A. Randall Hughes

Biology Faculty Publications

Interspecific interactions vary depending on environmental and genetic factors, with intraspecific variation potentially altering these relationships. Specifically, intraspecific variation within host plants and their endosymbionts may affect above- and belowground interactions depending on environmental conditions. We examined how intraspecific variation within the salt marsh foundation species Spartina alterniflora and a common fungal root endosymbiont (Lulworthia sp.) affected their interactions. We conducted a glasshouse experiment comparing interactions between Spartina growth forms (tall-form from low marsh and short-form from high marsh) and Lulworthia isolates from different marsh locations, and a laboratory experiment exposing Lulworthia isolates from both endpoints of a tidal elevation …

Comparing The Development And Viability Of Horseshoe Crab Eggs Laid In Beach And Salt Marsh Habitats, Daniel A. Sasson, Christopher C. Chabot, Jo-Marie Kasinak, Jennifer Mattei Ph.D., Elizabeth U. Scott, Fletcher K. Hall, Michael R. Kendrick

Biology Faculty Publications

The horseshoe crab, Limulus polyphemus, has recently been found to spawn regularly in salt marshes, despite the long-held assumption that salt marsh sediments are not conducive for embryonic development. Here, we tested the prediction that eggs laid in the salt marsh would develop more slowly and be less viable than eggs laid on beaches. We flagged the nests of spawning horseshoe crabs in the marshes and beaches of three states—South Carolina, Connecticut, and New Hampshire—and then excavated those nests one or three weeks later. We staged the excavated embryos to compare developmental progress between marshes and beaches. We found …

Contemporary Normative Values For Five Common Static Standing Tasks On Firm And Compliant Floor Surfaces In Children Two To Thirteen Years, Nancy Darr

Funded Scholarship

Background/Objectives: Static upright tasks, including standing unsupported (SU), eyes closed (SEC), feet together (SFT), tandem (TS), and single limb (SLS), are routinely examined in children and are included in many norm-referenced measures. Existing normative values for these standing tasks may not apply to contemporary children and have not been established across wide age ranges. The primary purpose of this study was to investigate developmental trajectories of and relationships between four static standing positions (SPs [SU, SFT, TS, SLS]) in children aged 2 through 13 years who are developing typically. The effects of altered sensory input, including floor surface (firm and …

Repositioning Antimalarial Drugs As Anticancer Agents: Focus On Tafenoquine, Chris Barton

Funded Scholarship

Due to the expensive and lengthy process of drug design and approval, drug repurposing (or repositioning) has become another option for identifying preexisting molecules that may be used for alternative purposes. Recently, some antimalarial compounds have been shown to display efficacy against cancer cell proliferation. In this study, we provide evidence to suggest that multiple preexisting antimalarial drugs can reduce the viability of human cancer cells in culture. Furthermore, we provide the first evidence that one antimalarial, Tafenoquine (LD50 = 9.6 μM in HCT116 cells), is capable of decreasing viability with an efficacy comparable to Etoposide (LD50 = 15.2 μM …

Forgoing Nuclear: Nuclear Power Plant Closures And Carbon Emissions In The United States, Luke Petach

Funded Scholarship

This paper examines the effect of nuclear power plant decommissioning on electricity generation and carbon emissions in the United States. Using data on nuclear reactor closures in the United States between 1993 and 2022 and data on state-level carbon emissions and electricity generation from the Energy Information Administration (EIA), this paper adopts a difference-in differences (DiD) approach to estimate the effect of nuclear decommissioning. Two-way fixed-effects (TWFE) DiD estimates suggest a nuclear plant closure increases annual state-level per capita carbon emissions between 6% and 8%. The increase in state-level carbon emissions is driven by a substitution toward fossil fuel electricity—particularly …

Spectral Divergence Prioritizes Key Classes, Genes, And Pathways Shared Between Substance Use Disorders And Cardiovascular Disease, Everest Castaneda, Elissa Chesler, Erich J. Baker

Funded Scholarship

Substance use disorders (SUDs) are heterogeneous diseases with 

overlapping biological mechanisms and often present with co-occurring disease, 

such as cardiovascular disease (CVD). Gene networks associated with SUDs 

also implicate additional biological pathways and may be used to stratify 

disease subtypes. Node and edge arrangements within gene networks impact 

comparisons between classes of disease, and connectivity metrics, such as 

those focused on degrees, betweenness, and centrality, do not yield sufficient 

discernment of disease network classification. Comparatively, the graph 

spectrum’s use of comprehensive information facilitates hypothesis testing 

and inter-disease clustering by using a larger range of graph characteristics. 

By adding a connectivity-based …