Digital Commons Network^™

What A Waste: Nitrogen Runoff And Rates In The Maumee River (Ohio, Usa), Ryanne Antonette Cimatu

Browse all Theses and Dissertations

Excess anthropogenic nitrogen (N), primarily from agricultural field fertilization, causes nutrient runoff that stimulates harmful algal blooms (HABs) in western Lake Erie. As a critical tributary to Lake Erie, nutrient loading from the Maumee River drives the intensity of the annual summer HABs in the western basin. Knowledge gaps around rates of N transformations in the Maumee River currently hinder the calibration of in-river parameters in Soil and Water Assessment Tool (SWAT) models for the Maumee watershed. To address these gaps, this research quantified rates of ammonium uptake, ammonium remineralization, nitrification, and bacterial respiration alongside physicochemical parameters of the river. …

Investigating Calcium Levels During Excitation-Contraction Coupling In Model Huntington's Disease Skeletal Muscle, Pooneh Hajmirza Mohammadi Kamalabadi

Browse all Theses and Dissertations

One of the less studied aspects of Huntington’s disease (HD) is its impact on skeletal muscle function. Recent studies have suggested that HD patients exhibit altered muscle function and reduced muscle strength, which may be related to defects in Ca2+ handling during excitation-contraction coupling (ECC). However, the underlying mechanisms of these alterations remain poorly understood. This study aims to determine if the myoplasmic Ca2+ during ECC is reduced in late-stage R6/2 (mouse model of HD) muscle fibers compared to age-matched controls during twitch or tetanic stimulation. Such a decrease would help explain weakness or fatigue in the model HD muscle. …

Investigating The Effects Of Human Astroviruses On Aquaporins And Tight Junction Proteins In Vitro, Makalia T. Robinson

Browse all Theses and Dissertations

Human Astroviruses (HAstV) are positive sense non-enveloped single stranded RNA viruses. HAstV is divided into classical (serotype 1-8) and non-classical (HAstVMLB 1-3 and HAstV-VA1-5) astroviruses. Classical HAstV is known to cause diarrhea in children, elderly, and immunocompromised patients. Additionally, the etiology of nonclassical HAstV remains unknown. However, recent studies have implicated non-classical HAstV closely associated with immunocompromised patients diagnosed neurological diseases like acute encephalitis. The mechanisms by which HAstV cause diarrhea is currently unknown. Aquaporins (AQPs) are integral membrane proteins that regulate the movement of water and small uncharged molecules across the cell membrane in response to osmotic gradients. Tight …

Softening And Cross-Susceptibility: Exposure To Heat And Desiccation Reduces Future Stress Tolerance In An Insect, Lauren Harter

University of the Pacific Theses and Dissertations

The frequency and duration of environmental stressors, such as heat waves and drought, will continue to grow due to ongoing climate change, thereby increasing the likelihood that organisms will experience stressors consecutively. Exposure to one stressor can improve or impair future tolerance to the same stressor (i.e., hardening or softening, respectively), or enhance or reduce future tolerance to a different stressor (i.e., cross-protection or cross-susceptibility, respectively). Understanding whether stress improves or impairs animals’ abilities to withstand future stressors is critical for determining the physiological sensitivity of animals to ongoing climate change. Here, I evaluated the responses to consecutive heat and …

Asynchronous Movement Patterns Between Breeding And Stopover Locations In A Long-Distance Migratory Songbird, Theodore Zenzal, Andrea Contina, Hannah Vander Zanden, Leanne Kuwahara, Daniel Allen, Kristen Covino

Faculty Publications

The species-specific migratory patterns and strategies of many songbirds remain unknown or understudied, as research in animal ecology is biased toward the breeding period, with the fewest studies on the migratory period across taxa. Identifying large-scale spatiotemporal migratory patterns is challenging, as individuals within a species may vary in their migratory behavior and strategies. The Yellow Warbler (Setophaga petechia) is a Nearctic-Neotropical migrant that is relatively well studied during the breeding season, but its species-wide migratory patterns remain understudied. Our aim in studying Yellow Warbler movement ecology was to characterize temporal migration patterns during fall migration. We sought to determine …

Effects Of Glyphosate-Based Herbicide Exposure On Life History, Stress Tolerance, And Microbiome—From Plasticity To Evolution, Jacob R. Whitlock

University of the Pacific Theses and Dissertations

Glyphosate (GLY) is the most used pesticide worldwide, and GLY-based herbicides (GBHs) can affect animals’ microbiomes and, in turn, their physiology and morphology. Environmental stressors can be mitigated by flexibility in life-history strategies, which can also dictate animal physiology and morphology. However, we lack an understanding of how GBH influences life-history strategies and stress tolerance, in addition to its effects across generations. Thus, I exposed the variable field cricket, Gryllus lineaticeps, to GBH within- and across-generations to examine the role of GBH in developmental plasticity and evolution. Specifically, I measured its effects on life-history traits (e.g., developmental duration and a …

Effects Of Fetal Bovine Serum On The Proteome And Secretome Of Pichia Pastoris, Kenneth L. Nguyen

University of the Pacific Theses and Dissertations

Komagataella pastoris, formerly known as Pichia pastoris, and hereafter referred to as Pichia, is a methylotrophic yeast widely employed as a recombinant protein factory for biotechnical and industrial purposes. P. pastoris boasts the ability to thrive at high cell densities, executes numerous post-translational modifications, and exhibits minimal secretion of endogenous proteins, thus greatly facilitating the expression and purification of recombinant proteins. Despite these advantages, Pichia still presents certain challenges as an expression system. Occasionally, recombinant proteins are retained within the cell and subject to degradation. Furthermore, Pichia falls short in matching the production capabilities of more widely used systems like …

The Role Of The Unfolded Protein Response In Fatty Liver Disease, Anusha L. Murshed

University of the Pacific Theses and Dissertations

The unfolded protein response (UPR) is composed of three highly conserved pathways (ATF6, IRE1, PERK). Cellular stressors induce protein misfolding and aggregation in the endoplasmic reticulum (ER). This signaling pathway maintains protein homeostasis when there is stress in the ER. When the UPR is activated, the eukaryotic initiation factor 2 alpha (eIF2α) becomes phosphorylated, which inhibits global mRNA translation. If ER stress remains chronically unmitigated, the UPR induces apoptosis. GADD34 and CReP shift in expression when the UPR is activated and work as phosphatases and dephosphorylate eIF2α in a feedback loop, allowing protein synthesis to resume. Several human diseases, including …

Insight Into A Sexually Dimorphic Ostracod Crustacean By Mass Spectrometry And Microtomography, Cindy D. Davis

University of the Pacific Theses and Dissertations

The importance of the central nervous system cannot be understated. An array ofmolecules associated with the brain regulate basic behaviors as well as sex specific behaviors. Describing the molecular background is not the only way that I can learn more of the central nervous system. Describing the anatomy of the central nervous system can be crucial in understanding what regions of the brain is particularly key to the animal. Euphilomedes carcharodonta is a small marine crustacean native to the subtidal zone of the California coast. This ostracod makes for a compelling candidate to explore these research interests as this organism …

Plasticity In Response To Temperature Magnitude And Variation---From Life History To Thermal Tolerance And Coloration, Austin Rex Hoffman

University of the Pacific Theses and Dissertations

Warming associated with climate change has many direct and downstream effects on animals. For example, warmer developmental temperatures can improve heat tolerance and reduce insect melanization, which is related to coloration, thermoregulation, immunity, desiccation resistance, and potentially life-history traits, such as investment into reproduction and dispersal. Increased temperature variation is also a feature of climate change, and it may have a larger impact on animals than warming. However, I lack insight into the combined effects of temperature magnitude and variability on important traits of life history, thermal tolerance, and coloration. Thus, I integrated temperature variation into thermal performance using a …

Transgenerational Effects Of Stress On The Plasma Proteome Of A Marine Mammal, Emily Voelkner

University of the Pacific Theses and Dissertations

The physiological stress response enables animals to respond to changes in their environment, and is mediated by the hypothalamic-pituitary-adrenal (HPA) axis in mammals. Increased activation of the HPA axis by repeated stress during critical life stages like reproduction could affect fitness. Information about a stressor can be communicated to offspring via hormone signals prenatally, or postnatally via milk, and affect offspring development and stress reactivity. Experimentally activating the HPA axis by adrenocorticotropic hormone (ACTH) administration results in the synthesis of the major glucocorticoid hormone cortisol, which has well-studied far-reaching effects on growth, metabolism, and immunity. Beyond cortisol levels alone, biomarkers …

How Does A Global Climate Cycle Affect The Reproductive Output Of A Neotropical Migratory Bird?, Abby K. Bressette, Emma Cummings, Daniel Albrecht-Mallinger, Lesley Bulluck

UROP Posters

El-Niño Southern Oscillation (ENSO) causes regional changes in climate and has been found to have varying effects on the survival, fecundity, and recruitment of migratory songbirds. This study seeks to better understand the effect of ENSO on the fecundity of Virginia-breeding Prothonotary warbler (Protonotaria citrea; PROW), a neotropical migratory songbird. PROW breed in the Eastern United States and spend the non-breeding season primarily in Panama and Colombia. Ongoing research in Virginia has found a positive relationship between spring precipitation and predicted number of PROW fledgelings during La Niña, but the opposite during El Niño. To better understand this relationship, we …

Carry-Over Effects Of Climate On Prothonotary Warbler (Protonotaria Citrea) Feather Quality, Alyssa N. Spasic, Dan Albrecht-Mallinger, Lesley Bulluck

UROP Posters

Avian species have inspired numerous studies on ornamentation, exploring its role in intra- and intersexual selection as a marker for individual quality. Male birds have been the focus of most of these studies while females, which can also display ornamentation, have been studied less. Coloration achieved through molt, particularly carotenoid-based pigments, requires energy derived from food resources. As climate affects insect abundance, there may be a link between climate conditions during molt and feather quality the following season. We assessed the relationship between temperature and precipitation during molt and female Prothonotary Warbler (Protonotaria citrea) breast and crown feather reflectance metrics …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Effects Of Doxorubicin On Extracellular Matrix Regulation In Primary Cardiac Fibroblasts From Mice, Cameron Skaggs, Steve Nick, Conner Patricelli, Laura Bond, Kali Woods, Luke Woodbury, Julia Thom Oxford, Xinzhu Pu

Biomedical Research Institute Publications and Presentations

Objective Doxorubicin (DOX) is a highly effective chemotherapeutic used to treat many adult and pediatric cancers. However, its use is limited due to a dose-dependent cardiotoxicity, which can lead to lethal cardiomyopathy. In contrast to the extensive research efforts on toxic effects of DOX in cardiomyocytes, its effects and mechanisms on cardiac extracellular matrix (ECM) homeostasis and remodeling are poorly understood. In this study, we examined the potential effects of DOX on cardiac ECM to further our mechanistic understanding of DOX-induced cardiotoxicity.

Results DOX-induced significant down-regulation of several ECM related genes in primary cardiac fibroblasts, including Adamts1, Adamts5, Col4a1, Col4a2, …

Development And Application Of Sem/Eds In Biological, Biomedical & Nanotechnological Research, Aniruddha Acharya

Faculty Publications - Biological Sciences

This comprehensive review discusses the development of scanning electron microscopy and the application of this technology in different fields such as biology, nanobiotechnology and biomedical science. Besides being a tool for high resolution imaging of surface or topography, the technology is coupled with analytical techniques such as energy dispersive spectroscopy for elemental mapping. Since the commercialization of the technology, it has developed manifold and currently very high-resolution nano scale imaging is possible by this technology. The development of FIB-SEM has allowed three-dimensional imaging of materials while the development of cryostage allows imaging of hydrated biological samples. Though variable pressure or …

The Role Of Dietary Fats In Driving Atherosclerosis, Zenan Wang

Yale Graduate School of Arts and Sciences Dissertations

Cardiovascular diseases (CVDs) are the number one killer of people worldwide, of which coronary heart disease, which is mainly due to atherosclerosis, is the main contributor to death. Nonetheless, the etiology of atherosclerosis remains poorly understood. It is universally accepted that dietary fat influences atherosclerosis, however, the role of specific fats is not well-understood. Despite the widely-held perception that saturated fats drive atherosclerotic CVDs while monounsaturated fats are protective, there have been numerous studies from human and mice that do not fit with this prevailing narrative. Thus, despite the importance of dietary fats in CVDs, the exact effects remain controversial …

Social And Biological Perspectives To Investigate And Address Illegal Shooting Of Raptors, Eve Thomason, Kenneth Wallen, Todd Katzner

Raptor Research Center Publications and Presentations

Humans have shot raptors for centuries. However, in many countries these actions have been illegal since the mid-twentieth century. Despite this history, there is not a comprehensive understanding of the characteristics of this activity, its frequency, and why it occurs. We used literature review and principles drawn from ecology, sociology, and criminology to understand this problem. First, we review literature on raptor shooting globally to explore documented motivations for shooting and we describe the history of raptor shooting in the United States of America (USA). Then, to illustrate the contemporary frequency and geographic breadth of the shooting of raptors, we …

Pollinators Of Gonzaga University, Sophie O'Shei, Gary Chang

Biology Student Scholarship

This data is from a public science project conducted by Sophie O'Shei (Gonzaga '24) investigating pollinator diversity in and around Gonzaga's campus. Photos of plants and pollinators were submitted using iNaturalist, an online platform and app that allows users to upload photos of animals, plants, insects, etc. and identifies their species using AI. It also tracks where photos were taken. Users were then able to go through uploaded images and suggest what species they identify in the photo, which can confirm or correct the AI's identification.

The project started during Earth Week 2023, giving students, staff, and other members …

Biology (Nucleo)Tidings- Fall 2023, Biology Department Staff

Biology (Nucleo)tidings

News from the Biology Department at Northeastern Illinois University

Lifelines Fall 2023, Southern Adventist University

Lifelines - Biology Department Newsletter

The Fall 2023 issue of Lifelines contains articles on student research, service, and information on this summer's BIOS program.

Using Multiple Modes Of Learning In A High School Genetic Engineering Lesson, Hannah Stuart

Inclusive Strategies for Teaching Secondary Mathematics and Science

The goal of this article is to discuss a genetic engineering lesson presented to high school biology students to obtain mastery of the Biology Standard of Learning (BIO.5e) associated with genetic engineering products and practices. The lesson described in this article follows the 5E lesson plan model. Therefore, the article will describe the 5Es used in the creation and implementation of this lesson: engage, explore, explain, elaborate, and evaluate. This article focuses on the use of resources and activities that appeal to students with varying learning styles and looks at the effectiveness of individualized teacher-student attention during individual practice time. …

Microscope Investigations: An Inquiry-Based Cell Lab, Joshua Whittaker, R. Whitlow

Inclusive Strategies for Teaching Secondary Mathematics and Science

This lesson is a collaborative effort between a student teacher and a cooperating senior teacher to design and implement an engaging and exploratory microscope lab for 7th-grade students. The goal of this lesson is to cultivate excitement, interest, and exploration in students who are new to using microscopes, aligning with the Virginia 7th Grade Life Science Standards of Learning on cells and cell theory. This lab incorporates two microscope stations—one focusing on fundamental skills and the other on inquiry-based exploration. By employing the 5E model of instruction, this paper details how students progress through engagement, exploration, explanation, elaboration, and evaluation …

Renal Cell Carcinoma Of Variant Histology: Biology And Therapies, Pavlos Msaouel, Giannicola Genovese, Nizar M Tannir

Faculty, Staff and Student Publications

The term variant histology renal cell carcinomas (vhRCCs), also known as non-clear cell RCCs, refers to a diverse group of malignancies with distinct biologic and therapeutic considerations. The management of vhRCC subtypes is often based on extrapolating results from the more common clear cell RCC studies or basket trials that are not specific to each histology. The unique management of each vhRCC subtype necessitates accurate pathologic diagnosis and dedicated research efforts. Herein, we discuss tailored recommendations for each vhRCC histology informed by ongoing research and clinical experience.

Structural Biology Of Mcr-1-Mediated Resistance To Polymyxin Antibiotics, Isabel Cristina Materon, Timothy Palzkill

Faculty, Staff and Students Publications

Polymyxins, a last resort antibiotic, target the outer membrane of pathogens and are used to address the increasing prevalence of multidrug-resistant Gram-negative bacteria. The plasmid-encoded enzyme MCR-1 confers polymyxin resistance to bacteria by modifying the outer membrane. Transferable resistance to polymyxins is a major concern; therefore, MCR-1 is an important drug target. In this review, we discuss recent structural and mechanistic aspects of MCR-1 function, its variants and homologs, and how they are relevant to polymyxin resistance. Specifically, we discuss work on polymyxin-mediated disruption of the outer and inner membranes, computational studies on the catalytic mechanism of MCR-1, mutagenesis and …

Leafy Sea Dragon, Phycodurus Sp., Kennedi X. Light

PANDION: The Osprey Journal of Research and Ideas

Artist Statement

Leafy sea dragons, Phycodurus sp. are part of the Syngnathidae family. Syngnathidae is a genus made up of seahorses, pipefishes, and sea dragons. All three of the species are known to have beautiful patterning. However, leafy sea dragons got their name from their leafy appendages like their fins and limbs. The reason I chose to draw a leafy sea dragon is due to my own interest in astrobiology. Astrobiology is the study of life in the universe and astrobiologists look for signs of life within the universe. I would like to be an astrobiologist one day and focus …

Beyond The Symptom: The Biology Of Fatigue, David M Raizen, Janet Mullington, Christelle Anaclet, Gerard Clarke, Hugo Critchley, Robert Dantzer, Ronald Davis, Kelly L Drew, Josh Fessel, Patrick M Fuller, Erin M Gibson, Mary Harrington, W Ian Lipkin, Elizabeth B Klerman, Nancy Klimas, Anthony L Komaroff, Walter Koroshetz, Lauren Krupp, Anna Kuppuswamy, Julie Lasselin, Laura D Lewis, Pierre J Magistretti, Heidi Y Matos, Christine Miaskowski, Andrew H Miller, Avindra Nath, Maiken Nedergaard, Mark R Opp, Marylyn D Ritchie, Dragana Rogulja, Asya Rolls, John D Salamone, Clifford Saper, Vicky Whittemore, Glenn Wylie, Jarred Younger, Phyllis C Zee, H Craig Heller

Faculty, Staff and Student Publications

A workshop titled "Beyond the Symptom: The Biology of Fatigue" was held virtually September 27-28, 2021. It was jointly organized by the Sleep Research Society and the Neurobiology of Fatigue Working Group of the NIH Blueprint Neuroscience Research Program. For access to the presentations and video recordings, see: https://neuroscienceblueprint.nih.gov/about/event/beyond-symptom-biology-fatigue. The goals of this workshop were to bring together clinicians and scientists who use a variety of research approaches to understand fatigue in multiple conditions and to identify key gaps in our understanding of the biology of fatigue. This workshop summary distills key issues discussed in this workshop and provides a …

Connecting Underrepresented Scientists To The Biology Core Curriculum, Volume 1, Aaron Schirmer, Lisa C. Wallis, Sumaiya Ahmed, Carla M. Amaya, Sara Crow, Dallia Husameddin, Nahid (Nina) Irani, Sadia Khanam, Dahlia Lou, Ivan Morales, Eduardo Vaca, Brittany Zaruszak

Open Educational Resources

Northeastern Illinois University and its Department of Biology have been working to center diversity and amplify the voices of underrepresented scholars. To help with this, we (the editors) developed an assignment where undergraduate and graduate students identified underrepresented scientists and researched their personal story and their contributions to science. This assignment culminated in a final paper based on the students’ research. In the Spring of 2023, this assignment was instituted in our Senior Seminar and Biological Literature courses for upper-level undergraduates and graduate students, respectively. From the completed assignments ten were chosen for inclusion in this publication. These ten scientists …

Biol 484-H01: Evolution Of Animal Behavior Laboratory, Caroline Devan

Biology Syllabi

No abstract provided.

Biol 475-H01: Ecological Field Methods, Maria Stanko

Biology Syllabi

No abstract provided.