Digital Commons Network^™

Alternative Splicing In A Coral During Heat Stress Acclimation And Recovery, Nitin Baliga, Kathryn Stanklewicz, Jacob Valenzuela, Serdar Turkarsian, Wei-Ju Wu, Kelly Gomez-Campo, Nicolas Locatelli, Trinity Conn, Veronica Radice, Katherine Parker, Rachel Alderdice, Line Bay, Christian Voolstra, Daniel Barshis, Iliana Baums

Biological Sciences Faculty Publications

Climate change has caused drastic declines in corals. As sessile organisms, corals acclimate to environmental shifts through genome-wide changes in gene expression, epigenetic modifications, and alterations in microbiome composition. However, alternative splicing (AS), a conserved mechanism of stress response in many organisms, has been under-explored in corals. Using short-term acute thermal stress assays, we investigated patterns of AS in the scleractinian coral Acropora cervicornis during response to low (33°C), medium (35°C), and high (37°C) heat stress and subsequent overnight recovery. Our findings demonstrate reproducible dynamic shifts in AS of at least 40 percent of all genes during response to heat …

Selective Nutrient Incorporation May Underestimate Heterotrophy Of A Mixotrophic Reef-Building Coral, Connor R. Love, Marleen Stuhr, Michael D. Fox, Veronica Z. Radice, Maoz Fine, Kelton W. Mcmahon, David L. Valentine

Biological Sciences Faculty Publications

Mixotrophic reef-building corals acquire nutrition via photosynthate translocation from endosymbiotic microalgae and by heterotrophic prey/particle capture. Heterotrophy promotes resistance to, and recovery from, environmental stress, but quantifying coral heterotrophy remains difficult due to complex resource exchanges within the coral holobiont. We interrogated the response of multiple biomarkers to coral heterotrophy using fatty acid profiling and stable isotope analysis of Stylophora pistillata grown along a controlled feeding gradient from pure autotrophy to pure heterotrophy. We found that fatty acids and nitrogen were effectively incorporated into both coral host and symbiont tissues, while carbon, which is the primary target for conventional heterotrophy …

Huchum: The Legacy Of Fire Suppression, Indigenous Land Management, And Media Representation, Carolyn Coyne

Pomona Senior Theses

In my thesis, I examine how various forms of news media from the 1900s to present day in Ohlone territory have framed a particular hegemonic ideology around fire that matches early colonial journal entries – an ideology that is fueled by fear, sensationalism, and exclusion and directly commits violence against the Ohlone people. I investigate this time period because this is when modern news corporations, like The New York Times, rose into prominence. Specifically, I question how media representations of fire inform regulations over controlled burns; what are the similarities in discourse between media framing and policy? What tactics are …

“Nice To See You”: Addressing Plant Awareness Disparity With Locally Specific Ecological And Cultural Plant Education, Cecilia Muecke

Pomona Senior Theses

Plants form the basis of life on Earth. However, due to the phenomenon of plant awareness disparity, a self-perpetuating cycle whereby plants are overlooked on an individual and global level ensues. Lack of plant awareness leads to a lessened emphasis on plants in sustainability and conservation as well as biology education, resulting in negative impacts on biodiversity and food security. The severity of plant awareness disparity is dependent on cultural context, and Indigenous and/or traditional societies are less likely to experience plant awareness disparity because of they are typically more connected to plants for their everyday needs. Native plants are …

Florida Scrub Is Nuts (And Drupes): Fruit Production And Consumption In Florida’S Fire-Prone, Xeric Uplands, Warren G. Abrahamson Ii

Faculty Journal Articles

This is a story about how plant size, fire, and climate affect fruit and nut production (i.e., mast) in Florida’s fire-prone, xeric uplands and the importance of mast as food for wildlife. To set the stage, let’s first explore the primary mast-producing plants of Florida’s xeric uplands: oaks, hickory, and palmettos.

A Decision-Space Model Explains Context-Specific Decision Making, Dirk W. Beck, Cory N. Heaton, Luis D. Davila, Lara I. Rakocevic, Sabrina M. Drammis, Danil Tyulmankov, Atanu Giri, Shreeya Umashankar Beck, Qingyang Zhang, Michael Pokojovy, Kenichiro Negishi, Alexis A. Salcido, Neftali F. Reyes, Andrea Y. Macias, Serina A. Batson, Paulina Vara, Raquel J. Ibáñez Alcalá, Safa B. Hossain, Graham L. Waller, Laura E. O'Dell, Travis M. Moschak, Ki A. Goosens, Alexander Friedman

Mathematics & Statistics Faculty Publications

Optimal decision-making requires consideration of internal and external contexts. Biased decision-making is a transdiagnostic symptom of neuropsychiatric disorders. We created a computational model demonstrating how the striosome compartment of the striatum constructs a context-dependent mathematical space for decision-making computations, and how the matrix compartment uses this space to define action value. The model explains multiple experimental results and unifies other theories like reward prediction error, roles of the direct versus indirect pathways, and roles of the striosome versus matrix, under one framework. We also found, through new analyses, that striosome and matrix neurons increase their synchrony during difficult tasks, caused …

Mobula, Bioinspiration, Filter Feeding, Form And Function, J. B. Teeple, S. R. Kahane-Rapport, K. E. Cohen, L. Hamann, J. A. Strother, E. W.M. Paig-Tran

Biological Sciences Faculty Publications

Mobulas (manta and devil rays) are large-scale ram filter feeders that separate planktonic food particles from large volumes of water with minimal clogging. This contrasts with most human-made filters that can suffer from problematic clogging requiring additional mechanisms for clearing blocked surfaces and maintaining performance. Prior studies have shown that mobulas employ a unique mechanism referred to as ricochet separation to filter feed, whereby captive vortices in filter pores cause particles to bounce off the filter surfaces and away from the filter pores. This mechanism enables the filtration of particles smaller than the pore size and reduced clogging. However, few …

Systematic Review Of Immunohistochemistry Protocols, Arpitha Parthasarathy

Pitzer Senior Theses

Immunohistochemistry (IHC) is an essential technique in biological research that allows for the visualization and localization of proteins within tissue samples. This systematic review analyzes the most effective, efficient and reproducible protocols for IHC. It focuses on three critical steps: freezing, cryosectioning, and staining of skeletal muscle tissues in mice models. A total of 41, 44, and 48 articles on freezing, cryosectioning, and staining techniques, respectively, were analyzed, from reputable sources in biology like PubMed and Web of Science. Results showed the following. For freezing, the use of isopentane combined with liquid nitrogen appeared to be the best method, minimizing …

Crisis In The Current: A Proposed Study On The Impact Of Columbia River Basin Water Quality On Juvenile Chinook Salmon Survival, Olivia Buist-Thuillier

Pitzer Senior Theses

Salmon occupy a vital role in the ecosystem, economy, and indigenous culture of the Pacific Northwest of the United States, specifically within the Columbia River Basin. Of the five species of Pacific Salmon that live in the basin, Chinook salmon (Oncorhynchus tshawytscha) are the most widely commercially fished and are the largest. In recent years, Chinook Salmon populations have heavily declined from human influence. Rising temperatures from anthropogenic climate change, habitat destruction (dams, human presence), runoff from agricultural practices, and overfishing have all contributed to this decline. Because of their role as a keystone species and their cultural significance, there …

Chronic Alcohol Consumption Induces Phenotypic And Functional Alterations Consistent With A Hyper-Inflammatory State In Peripheral Blood Mononuclear Cell-Derived Microglia In A Rhesus Macaque Model, Hami Hemati, Madison B. Blanton, Heather E. True, Jude Koura, Rupak Khadka, Kathleen A. Grant, Ilhem Messaoudi

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Alcohol-induced dysregulation of microglial activity is associated with neuroinflammation, cognitive decline, heightened risk for neurodegenerative diseases, alcohol dependence, and escalation of alcohol drinking. Given the challenge of longitudinally sampling primary microglia, we optimized an in vitro method to differentiate peripheral blood mononuclear cells (PBMC) from rhesus macaque (RM) into induced microglia-like cells (RM-iMGLs). The RM-iMGLs displayed transcriptional profiles distinct from monocyte progenitors and closely resembling primary microglia. Notably, morphological features showed that differentiated RM-iMGLs derived from subjects with chronic alcohol consumption (CAC), while bigger, exhibited a bipolar-like morphology. Additionally, dysregulation in key inflammatory and regulatory markers, along with increased baseline …

Inquiries Into The Mycobacterial Caseinolytic Protease System, Felipe Badke D'Andrea

Student Theses and Dissertations

Despite progress over the last century, Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), remains the leading cause of death from an infectious disease worldwide. The high global burden of Mtb, alongside its protracted treatment regimen and insidious rise of multi-drug resistance, underscores the need for non-canonical drug targets and pathways to improve antitubercular chemotherapy. Mtb's success as a pathogen is linked to its ability to infect and evade clearance by the human immune system despite a wide range of noxious host stressors. Along with transcriptional responses, the maintenance of protein homeostasis is critical to this adaptability and pathogenicity. …

Nurture Is Nature: The Molecular Basis Of Caregiver Genotype Effects On Larval Growth And Caste Development In The Clonal Raider Ant, Patrick Konrad Piekarski

Student Theses and Dissertations

The distinction between nature (genetics) and nurture (environment) is blurry, in part because the environment includes the genes of social partners. This is especially evident for parents and their offspring, where genes expressed in one partner profoundly influence the physiology and behavior of the other. Such indirect genetic effects (IGEs) are mediated through social interactions. Although parental care has evolved in many disparate lineages, in most systems it is challenging to delineate the effects of genetics and environment on the phenotypes of caregivers and offspring. This is because most animals with parental care reproduce sexually, meaning each genotype is represented …

Serine Metabolism Leverages The Integrated Stress Response To Direct Stem Cell Fate During Tissue Regeneration, Jesse Stephen Swyer Novak

Student Theses and Dissertations

Epidermal stem cells constantly rejuvenate the skin's barrier, which excludes harmful microbes and prevents dehydration. While hair follicle stem cells (HFSCs) normally regenerate hair, they must also reconstruct and thereafter maintain the overlying epidermis upon a barrier breach, such as a wound. How these fate choices are balanced to restore physiologic function to damaged tissue remains poorly understood. Here, I uncover the non-essential amino acid serine as a surprising regulator in this process. Utilizing dietary intervention and HFSC-specific loss-of-function studies, I demonstrate that under serine-depleted conditions HFSCs delay hair growth. Upon injury, serine-restricted HFSCs skew their fate towards epidermal re-epithelialization …

Molecular And Cellular Mechanisms Of Lim Protein Mechanotransduction, Donovan Yong Zhi Phua

Student Theses and Dissertations

For tissues to develop and maintain mechanical homeostasis, cells must be able to perceive and respond to mechanical cues in their local environments (mechanosense). While there has been significant progress in understanding the physiological significance of mechanosensation, the mechanisms by which proteins convert mechanical stimuli into biochemical signals (mechanotransduction) are poorly understood. The actin cytoskeleton serves as a nexus for cellular mechanotransduction, generating and transducing forces into intracellular signals that coordinate cell migration, cellular contractility, organelle dynamics, and gene expression. However, our understanding of the molecular mechanisms by which cytoskeletal mechanotransduction is achieved is limited. LIM domain proteins are a …

Quantification Of Auxin-Cytokinin Response During Primary Root And Lateral Root Development In Common Bean, Gurdeep Singh

Electronic Theses and Dissertations

Roots support water and nutrient uptake, anchorage, and soil interactions through continuous growth at the primary root tip (PRT). In common bean (Phaseolus vulgaris), new cells are produced in an open root apical meristem and subsequently elongate in the elongation zone, and together these processes drive root tip progression through the soil. Lateral roots (LRs) arise in the differentiation zone, where pairs of pericycle founder cells dedifferentiate, divide asymmetrically, and form lateral root primordia (LRP) that pass through defined developmental stages before emergence. Auxin and cytokinin (CK) are central regulators of both primary root growth and LR development, yet their …

Programming Carcass Composition Through Gestational Nutrition, Sydni Elise Borders

Electronic Theses and Dissertations

The objective of this study was to evaluate the influence of maternal nutrient restriction during mid-gestation on the performance of the dam, feeding performance, carcass composition, and genetic expression in the offspring. Cows (n = 46) were randomly assigned to one of two treatments based on global nutrient intake: 1) fed to achieve and/or maintain a BCS of 5 or 6 (Positive Energy Status [PES]; n = 24) or 2) fed to lose one BCS during 99 days of mid-gestation (Negative Energy Status [NES]; n = 22). Cows in NES had greater decreases (P < 0.05) in body fat stores and muscle mass, elevated NEFA concentrations, and displayed decreased (P < 0.05) DMI, HP, and GHG emissions. There were no differences in milk components or volume produced between treatments (P > 0.05). There were no differences in …

How Forest Stand Conditions Influence Whitebark Pine And Clark’S Nutcracker: A Systematic Review, Bryan Mathew Cohen

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Whitebark pine (Pinus albicaulis), a keystone species of high-elevation ecosystems of western North America, is threatened with extinction due to disease (Blister rust), pests (Mountain pine beetle), and climate change. Regeneration of the species depends nearly exclusively on the seed-caching behavior of Clark’s nutcracker (Nucifraga columbiana, Family Corvidae). Because of this, conservation of whitebark ecosystems requires restoring stand structures that favor nutcrackers. Although there are increasing numbers of studies on the relationship between nutcrackers and whitebark pine, findings have not yet been synthesized, limiting knowledge for application to management. I did a systematic literature review to answer the following questions: …

Exploring The Role Of Bingocize® Workshops In Enhancing Health And Well-Being In Older Adults, Kaitlyn Gray

Mahurin Honors College Capstone Experience/Thesis Projects

As the population of older adults grows, the need for better health and well-being also grows, making it necessary to implement effective strategies for healthy aging to improve the length and quality of life of older adults (CDC, 2024). This study evaluates the effectiveness of a Bingocize^® Workshop in improving the physical health of older adults. Bingocize^®, a unique program combining bingo with exercise, is designed to increase physical activity. Eleven (11) participants aged 68.55 ± 6.235 attended a ten-week workshop, two times per week focusing on physical exercises tailored to their abilities. The primary objective was …

Investigating The Role Of Fnci-1 In The Development And Function Of The C. Elegans Nervous System, Meagan Collins

Open Access Master's Theses

Fanconi Anemia (FA) is a rare human genetic disease caused by mutation of any of twenty-three genes on the FA pathway, which functions in the repair of DNA damage and the maintenance of genome stability. FA is clinically characterized by congenital abnormalities and a predisposition to aplastic anemia and malignancies. Recently, progressive neurological symptoms and abnormal neurological findings on imaging have been noted in FA patients, including cerebral and cerebellar lesions, calcification, necrosis, gliosis, and associated acute and chronic neurological symptoms; this constellation of symptoms has been termed Fanconi Anemia-Associated Neurological Syndrome (FANS).

To elucidate the molecular etiology of FANS, …

Association Between Vitamin D Status And Cortisol Concentration Among Pregnant Women, Kenneth Addae

Open Access Master's Theses

Objective: Vitamin D deficiency (VDD) and high circulating cortisol during pregnancy have each been linked to adverse maternal and child outcomes such as preterm birth. However, limited research has explored the association between vitamin D status and cortisol concentration during pregnancy. Our objective for this study was to determine the association between vitamin D status and cortisol concentration among pregnant women.

Methods: The Prenatal Health and Nutrition (PHAN) study was a pilot cross-sectional study of 30 healthy pregnant women conducted in targeted areas in Rhode Island. Data was collected on sociodemographic characteristics, substance use, perceived stress scale, household food security, …

Herbivore Kairomones Affect Germination Speed, Seedling Growth, And Herbivory, Brooke Pellegrini

Open Access Master's Theses

Seeds and seedlings are particularly vulnerable to herbivory. Unlike mature plants, which can wait until herbivory is experienced to induce defense, seeds and seedlings face mortality if they wait. Slug mucus functions as a kairomone, a non-attack-related substance emitted by consumers that is detected by a prey species (in this case, plants). While snail mucus has been shown to induce defense in seedlings, it is not widely confirmed whether slugs have the same effect and whether seeds can also detect and react to such herbivore cues. We investigated how exposure to Arion subfuscus mucus affected growth and defense in Brassica …

Field Performance Evaluation Of Selectively Bred Eastern Oyster Lines In New Jersey And Rhode Island, Seraphina Satkowski

Open Access Master's Theses

Eastern oyster aquaculture has increased steadily over the last three decades, but the industry has yet to achieve its full potential. In the Northeast USA, production is limited in part by a lack of high performing stocks suited to the geographically broad and heterogenous growing environments. For this study, hatchery lines from Maine, New York, and New Jersey as well as crosses between each hatchery line and the selectively bred Northeast high survival (NEHÒ) line, were deployed at oyster farms in Rhode Island and New Jersey for performance evaluation. Replicate bags of each line were stocked and maintained according to …

Investigating Regulation And The Regulome Of The Nucleic Acid Binding Protein Spovg Within Borrelia Burgdorferi, Timothy C. Saylor

Theses and Dissertations--Medical Sciences

Prior studies indicated Borrelia burgdorferi SpoVG protein was regulated, SpoVG binds specifically to a number of nucleic acids, and SpoVG binds to the non-variable section of the major virulence factor vlsE. Although a direct transcriptional activator or inhibitor was not elucidated, it is shown that SpoVG is regulated based on cell culture density independent of the growth rate of B. burgdorferi, indicating that SpoVG regulation is outside the scope of the alternative sigma factor RpoS. Using a dCas9 CRISPRi construct to target SpoVG resulted in protein expression trending towards upregulation of the BosR-RpoS regulon, and a marked decrease …

Leveraging Clinical Standards To Improve The Translational Relevance Of Therapies For Experimental Spinal Cord Injury, Aaron L. Silverstein

Theses and Dissertations--Neuroscience

Efforts to improve treatment of spinal cord injury (SCI) often use animals to develop effective therapeutics, intending to improve the survival and the quality of life of persons with SCI. Over half of all SCIs in the United States occur at the cervical level and often cause locomotor deficits and life-threatening breathing dysfunction. Thus, my dissertation is focused on this important patient population.

After beginning with a description of translational research and surveying SCI from a clinical standpoint, I turned to describe experimental models of cervical SCI and more detailed neuroimmunological findings relevant to my work. Then, I conducted a …

Immune Dynamics And B Cell Contributions To Neuroplasticity And Recovery After Stroke, Thomas A. Ujas

Theses and Dissertations--Neuroscience

This dissertation explores the dynamic interplay between the immune system and the brain across stroke and aging using clinical, post-mortem, and pre-clinical models. The immune system plays critical roles in shaping brain function, responding to injury, and mediating recovery. These studies aim to enhance our understanding of neuroimmune dynamics across spatial and temporal dimensions.

In the first part, we conducted longitudinal sampling of aneurysmal subarachnoid hemorrhage (aSAH) patients to track immune cell and cytokine changes at days 3, 5, 7, 10, and 14 post-stroke, with a focus on delayed cerebral ischemia (DCI), a common complication. We observed distinct temporal patterns, …

Cell-Type Specific Apoe4 To Apoe2 ‘Switching’ In Astrocytes And Microglia Alters Alzheimer’S Disease Neuropathology, Lesley R. Golden

Theses and Dissertations--Physiology

Apolipoprotein E (APOE) is the strongest genetic risk factor for late-onset Alzheimer’s disease (LOAD). APOE exists in three common protein isoforms throughout the population: ApoE2 (E2), ApoE3 (E3), and ApoE4 (E4). While APOE allele frequencies and the degree of AD-associated risk vary across different ethnic groups, when compared to the ‘neutral’ and most common E3 allele, the E4 allele confers up to a 33-fold increase in Alzheimer’s Disease (AD) risk. Conversely, the neuroprotective E2 allele decreases AD risk by up to 67%. Here, we aimed to determine the therapeutic potential of cell-type specific APOE allele ‘switching’ and explore …

Dinotefuran Resistance In The German Cockroach (Blattella Germanica L.), Hannah F. Blevins

Theses and Dissertations--Entomology

German cockroaches (Blattella germanica L.) are one of the most prevalent and pervasive indoor pest species in the world. Infestations can lead to many negative impacts on humans, including sensitization to allergens, increase in asthmatic symptoms, mental health declines, and potentially, the spread of diseases. While insecticides remain the most effective and affordable option for German cockroach control, resistance to many commonly used insecticide active ingredients (AIs), such as pyrethroids, has been observed globally at high levels across different populations. Given such resistance to pyrethroids, inclusion of insecticides with alternative modes of action into insecticidal treatments could potentially improve cockroach …

Bed Bugs: Health Risks And Control, Simona Principato

Theses and Dissertations--Entomology

Bed bugs are blood-feeding hemipterans strongly associated with humans. Their detection in indoor environments, such as homes, hotels, trains, and public facilities, has increased gradually over the past 20 years. The exact cause of their resurgence is still unclear, but the increase of international travel and insecticide resistance are thought to have contributed to it.

Although bed bugs are not known to transmit diseases, the EPA, CDC, and USDA have classified them as a pest of significant public health concern, mainly due to the dermatitis that they can cause. Beyond the dermatological burden of the bites, other health implications often …

The Role Of Nutrition In Managing Honey Bee Viral Pathogen, Caroline Wylie Kane

Theses and Dissertations--Entomology

This study evaluated the impact of nutritional supplements on viral infections in honey bee colonies, focusing on Lake Sinai Virus 2 (LSV2), Deformed Wing Virus A (DWVA), and Deformed Wing Virus B (DWVB). I partnered with 32 hobbyist beekeepers across Kentucky, who volunteered 138 colonies for a month-long field study. Half of the colonies received weekly commercial supplements, while the other half served as controls. Viral titers were measured before and after the supplementation period using qPCR. Supplements did not significantly reduce viral titers for any of the three viruses, suggesting that short-term supplementation may not be effective in lowering …

Exportin 1 Is The Central Hub In Antiviral Defensive Mobilization Of Nuclear Factors And The Target Of Counter-Defence By Tombusviruses, Biao Sun Dr.

Theses and Dissertations--Plant Pathology

Positive-strand RNA viruses, such as coronaviruses and flaviviruses, are obligate parasites whose genomic RNAs function as mRNAs. These viruses infect a wide range of hosts-including plants, animals, and humans-resulting in significant economic losses and posing serious threats to public health. Due to the relatively simple structure of the genome of positive-strand RNA viruses, many host factors and physiological processes are co-opted to support virus infection and replication. In our previous studies, we identified numerous host factors and associated physiological processes involved in the replication of tombusviruses, a cytosolic-replicating model that includes tomato bushy stunt virus (TBSV) and carnation Italian ringspot …