Digital Commons Network^™

Gene Expression In Relation To Bone Fractures In Throughbred Racehorses, Anna M. Rauber-Ramos

Theses and Dissertations--Veterinary Science

Evidence that fractures in Thoroughbred racehorses are outcomes of chronic bone microdamage has led to extensive research into identifying horses at increased risk of fracture. This includes the use of biomarkers and messenger RNA (mRNA) as a measure of bone turnover. Previous research has found expression differences in horses with fractures compared to controls. Utilizing pre-race whole blood samples collected over an 18-month period from Thoroughbred racehorses in Southern California, RNA-sequencing was conducted on horses with bone fractures and race-matched controls to identify differences in gene expression. Focusing on third metacarpal (MC3) and proximal sesamoid bone (PSB) fractures, differentially expressed …

Avian Response To Legacy Coal Mine Reforestation In The Cumberland Plateau, Kentucky, Madoline J. Varias

Theses and Dissertations--Forestry and Natural Resources

Surface coal mining and reclamation processes alter the ecological characteristics of landscapes, which affects the presence and distribution of native wildlife. The Forestry Reclamation Approach (FRA) is a coal mine reclamation method that aims to establish native forests on surface mines and has been widely implemented across the Central Appalachian region. Avian response the FRA, in particular, is unknown in Kentucky and limited throughout Appalachia. Thus, the goal of this project was to assess the effects of the FRA on avian community occupancy, species richness, and abundance in the Cumberland Plateau of Kentucky. Point count surveys were conducted across three …

Fire And Mammal Herbivory On Arthropods In The Protected Savannas: A Systematic Review, Ludzula Mukwevho, Mduduzi Ndlovu, Frank Chidawanyika

All Peer-Reviewed Publications

Protected areas in the savannas are key global reserves for biological diversity, including arthropods. Fire and mammal herbivory disrupts the diversity of biological organisms that alternately affects the functioning of the ecosystem. The study presents a global synthesis review of arthropod responses to varying intensities of fires and mammal herbivory in the protected savannas. We hypothesise that the intensity of predetermined fires and mammal herbivory has cascading impacts on abundance, species richness and diversity of terrestrial arthropods in the protected savannas. A minimum selection criteria was used to collate relevant literature from electronic databases of previous studies performed in the …

The Comparative Effects Of A Thermal Gradient On The Age And Growth Characteristics Of Largemouth Bass (Micropterus Nigricans), And Atlantic Cod (Gadus Morhua), Whitney Hall

Theses and Dissertations

Thermal gradients impact fishes differently, due to variations in ecological niches and physiological adaptations. I assessed the effects of temperature on Largemouth Bass (Micropterus nigricans) and Atlantic Cod (Gadus morhua) using data from peer-reviewed journals, state records, and fisheries agencies. For Largemouth Bass, I analyzed the relationships between air temperature (MAT_min°C, MAT24hr°C, and MAT_max°C), and growth parameters including maximum length and weight, growth rate (K), longevity, and total length-at-ages 3, 5, and 8 years (TLAge_3,5,8), using least squares regression. Significant correlations were found between all temperature and growth metrics. Positive correlations were found between …

A Comprehensive Uhplc-Ms/Ms And Extraction Method Reveals Flavonoid Profile And Concentration Are Diverse In Spinach (Spinacia Oleracea L), Michael P Dzakovich, Elaine A Le, Alvin L Tak, Shaji K Chacko

Children’s Nutrition Research Center Staff Publications

INTRODUCTION: Spinach produces an array of unique flavonoids not commonly found in other fruits and vegetables. These molecules likely serve as defense agents against biotic and abiotic stress and may have health beneficial properties for humans. Current methods to analyze spinach flavonoids are incomplete and only capture a portion of this uncharacterized pathway. A comprehensive analysis method is needed to determine how genetics, environmental conditions, and other factors influence spinach flavonoid biosynthesis.

METHODS: We developed and validated a high-throughput extraction and ultra high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) method to separate and quantify 39 spinach flavonoid species in 11.5 …

New Genetic Tools To Define The Pathophysiology Of Inborn Errors Of Cobalamin Metabolism Impacting Mammalian Development, Tiffany Chern, Xuefei Tong, William G Bauer, David J Quispe-Parra, Xia Gao, Kamryn N Gerner-Mauro, Ross A Poché

Children’s Nutrition Research Center Staff Publications

The congenital, autosomal recessive disorder combined methylmalonic acidemia and homocystinuria - cblC type, is the most common inborn error of cobalamin (vitamin B12) metabolism. In its early onset form, cblC profoundly impacts fetal development of the central nervous system, hematopoietic system, and other tissues. Previously, mutations in the MMACHC gene, which encodes a protein required for the intracellular trafficking and enzymatic processing of free cobalamin into active coenzyme forms, were found to cause cblC. These coenzymes are required in two metabolic pathways which produce either succinyl-CoA in the mitochondria or methionine in the cytosol. However, due to a lack of …

Comparing Microct Staining And Scanning Methodology For Brain Studies In Various Sizes Of Spiders, Vanessa Penna-Gonçalves, Nikolas J. Willmott, Michael B.J. Kelly, Jay R. Black, Elizabeth C. Lowe, Marie E. Herberstein

Research outputs 2022 to 2026

Recent advances in microCT are facilitating the investigation of microstructures in spiders and insects leading to an increased number of studies investigating their neuroanatomy. Although microCT is a powerful tool, its effectiveness depends on appropriate tissue preparation and scan settings, particularly for soft, non-sclerotized tissues, such as muscles, organs, and neural tissues. As the application of microCT in spiders is only in its infancy, published protocols are often difficult to implement due to substantial size variation of the specimens. The present study was initiated to determine how to account for this variation. Our work builds on previous methods using microCT …

Non-Stereotypy (To Species) In Mysticete Downsweeps, Paul Nguyen Hong Duc, Christine Erbe, Shyam Madhusudhana, Daniel Wilkes, Lachlan Gill, Cristina Tollefsen, Narissa De Bruin, Aiyana Erbeking, Curt Jenner, Micheline Jenner, Angela Recalde-Salas, Chandra P. Salgado Kent, Kautilya Srivastava, Chong Wei, Robert Mccauley

Research outputs 2022 to 2026

The Australian EEZ provides habitat for ten species of mysticete whales seasonally supporting critical life functions ranging from feeding to breeding. All of these species produce downsweeping calls, which may confound passive acoustic monitoring efforts. In an attempt to optimize a detector for Eastern Indian Ocean pygmy blue whale (EIOPBW) downsweeps, we tried a spectrogram correlator based on confirmed templates and a neural network trained on general blue whale D-calls followed by clustering algorithms. Outputs were manually validated by bioacousticians. We found that downsweeps exhibit significant variability and form a graded continuum of acoustic features, as opposed to clusters. Comparative …

The Impact Of Solvent Extraction And Enzyme-Assisted Extraction On The Yield And Quality Of Black Soldier Fly Larvae (Hermetia Illucens) Oil, Achini Madushani Mannawa Arachchige, Mark Williams, W. M.A.D.Binosha Fernando, Weeraya Karnpanit, Jane Lumanlan, Vijay Jayasena

Research outputs 2022 to 2026

The increased interest in black soldier fly larvae (BSFL) oil is driven by its beneficial fatty acid composition, leading to the development of effective extraction methods. This study evaluated the impact of solvent extraction (SE) and enzyme-assisted extraction (EAE) on the yield and quality of BSFL oil. SE using hexane, petroleum ether, isopropanol, and ethanol after 6 hr of extraction resulted in higher yields compared to EAE using alcalase, papain, and trypsin after 24 hr, with the highest yield recorded for petroleum ether (33%), followed by isopropanol (30%). Isopropanol extraction demonstrated the highest antioxidant activity (77%). The results indicated a …

The Dirt Underneath My Fingernails: The American Pastoral And 21st-Century Food System Reform, Annabella Isaacson

Scripps Senior Theses

The following is an amalgamation of my experiences personally and vested interests academically, and is meant to be read as just that. As a thesis that combines Environmental Analysis and Writing & Rhetoric degrees, this project challenges traditional academic forms by integrating creative nonfiction and poetry with academic writing and analysis. This thesis attempts to fuse the academic and personal essay into one cohesive piece. The inconclusive nature of the narratives and explorations that follow are intended to represent my process in grappling with the histories and significance of American pastoral literature through the ways in which this genre has …

Assessing The Effects Of Wildfire Season Pm2.5 Exposure And Environmental Variables On Breeding Season Avian Body Condition, Cira Seyer-Ochi

Scripps Senior Theses

The increasing frequency and intensity of wildfires pose growing threats to wildlife, yet the indirect effects of wildfire smoke on avian populations remain largely unstudied. This exploratory study provides an initial assessment of how particulate matter 2.5 (PM2.5) associated with smoke pollution from the 2017 California wildfire season, in conjunction with precipitation and habitat type, influences the body condition of four resident bird species during the 2018 breeding season. Using bird banding data from 29 Monitoring Avian Productivity and Survivorship (MAPS) stations, I assessed the potential interactions between PM2.5 concentrations, precipitation, and habitat type with body condition for Song Sparrows …

Behavioral Observations And Analysis Of Twix: The Cape Porcupine At The Lake Superior Zoo, Erin Davidson

Scripps Senior Theses

The three main goals of zoos are outlined as: education, conservation, and research. In our modern world, the focus of zoos has shifted away from simply housing animals, and towards how we can best promote proper animal welfare for individuals in human care. Animal welfare can be defined as the “mental health” of non-human species of fauna, and is greatly influenced by the stressors within the environment, as well as the option of choosing how to interact with and respond to the environment. Animals housed in zoos are presented with unique stressors that they often do not choose to experience, …

Characterization Of Dietary And Hormonal Influences On Renal Sodium Transporters And Channels In Rodent Models, Evelyn Chan

Scripps Senior Theses

Within kidneys, a diverse array of renal epithelial cells works to maintain electrolyte and water balance to regulate blood pressure and pH. These cells contain varying types of sodium transporters that adjust sodium reabsorption according to the body’s needs. Previous studies have observed sex-specific differences in renal sodium transporter regulation, which are thought to optimize reproduction in females. In this study, we performed high resolution microscopy and detailed characterization of cell type-specific expression and localization of major sodium transporters and channels in rodents in response to dietary and hormonal influences. Specifically, we examined the impact of dietary salt intake and …

If You Give A Tadpole A Chemosensory Stimulus: Detection Of Invasive Predatory Cues And Signs Of Conspecific Communication In Pseudacris Sierra Tadpoles, Faben Tesfazion

Scripps Senior Theses

Amphibians are at disproportionately higher risks of extinction than all other vertebrate classes, and a major causing factor is invasive predation. The American bullfrog (Lithobates catesbeianus), native to Eastern North America, is a notorious invasive species which preys on native Sierran treefrogs (Pseudacris sierra) in Northern and Central California. These treefrogs have yet to be placed on any Special Animals List, suggesting the presence of adopted behaviors against predation. Past studies have documented the importance of chemical sensing in anuran tadpoles as predator detection tools. This study tests if Sierran treefrog tadpoles can recognize invasive chemical …

El Maíz Del Abuelo: Fidel Márquez Sanchez’S Legacy And Mexico’S Historical Maize Agriculture, Lucia Marquez-Uppman

Scripps Senior Theses

The Green Revolution was an era of scientific development in productive agricultural methods and technologies in the mid-twentieth century. High-yielding seed varieties, artificial fertilizers, irrigation infrastructure, pesticides, and herbicides all developed from this period. Texcoco, Mexico was the center of much of the Green Revolution's education and research from the 1940s onward at the Autonomous University of Chapingo, a prestigious agricultural school, with funding from the US-based philanthropic Rockefeller Foundation. Powerful consequences in the globe's agriculture emerged from the Green Revolution, including the production of maize, a staple crop in Mexico, especially for Indigenous and campesino populations. My abuelo, Fidel …

Commentary: Impact Of Resistance Training Intensity On Body Composition And Nutritional Intake Among College Women With Overweight And Obesity: A Cluster Randomized Controlled Trial, Joshua L Keller, Sarah E Deemer, Gian Luca Di Tanna, Sherri L Pals, Kevin R Fontaine, David B Allison

Children’s Nutrition Research Center Staff Publications

No abstract provided.

The Human Spinothalamic Tract: Lessons From Cordotomy, Anthony K Allam, Michael Benjamin Larkin, Ishan A Patel, Mohammed Hasen, David Mears, Patrick Dougherty, Ashwin Viswanathan

Faculty, Staff and Student Publications

The spinothalamic tract has long been known as a primary conductor of nociceptive information, with its anatomical and physiological understanding evolving over centuries of research. This comprehensive review traces the history of the spinothalamic tract beginning with Brown-Sequard’s 1860 report of contralateral analgesia following a hemisection of the spinal cord. As clinical and surgical interventions, such as cordotomies have advanced, so did our understanding of the spinothalamic tract’s function and anatomy. The spinothalamic tract’s role as a crossed pathway conducting pain and temperature sensations was solidified by the mid-20th century. However, intricate details of its somatotopic arrangement, anatomical distributions and …

Bat Genomes Illuminate Adaptations To Viral Tolerance And Disease Resistance, Ariadna E. Morales, Yue Dong, Thomas Brown, Kaushal Baid, Dimitrios Georgios Kontopoulos, Victoria Gonzalez, Zixia Huang, Alexis Walid Ahmed, Arkadeb Bhuinya, Leon Hilgers, Sylke Winkler, Graham Hughes, Xiaomeng Li, Ping Lu, Yixin Yang, Bogdan M. Kirilenko, Paolo Devanna, Tanya M. Lama, Yomiran Nissan, Martin Pippel, Liliana M. Dávalos, Sonja C. Vernes, Sebastien J. Puechmaille, Stephen J. Rossiter, Yossi Yovel, Joseph B. Prescott, Andreas Kurth, David A. Ray, Burton K. Lim, Eugene Myers, Emma C. Teeling, Arinjay Banerjee

Biological Sciences: Faculty Publications

Zoonoses are infectious diseases transmitted from animals to humans. Bats have been suggested to harbour more zoonotic viruses than any other mammalian order1. Infections in bats are largely asymptomatic2,3, indicating limited tissue-damaging inflammation and immunopathology. To investigate the genomic basis of disease resistance, the Bat1K project generated reference-quality genomes of ten bat species, including potential viral reservoirs. Here we describe a systematic analysis covering 115 mammalian genomes that revealed that signatures of selection in immune genes are more prevalent in bats than in other mammalian orders. We found an excess of immune gene adaptations in the ancestral chiropteran branch and …

A Transferable Approach For Quantifying Benthic Fish Sizes And Densities In Annotated Underwater Images, Peter C. Esselman, Shadi Moradi, Joseph K. Geisz, Christopher Roussi

Michigan Tech Publications

Benthic fishes are a common target of scientific monitoring but are difficult to quantify because of their close association to bottom habitats that are hard to access. Advances in image-acquisition technologies, machine vision and deep learning have made capturing and quantifying fishes with cameras increasingly feasible. We present a method and open-source software called ‘FishScale’ to estimate benthic fish lengths, numeric abundance and biomass density in underwater environments assessed with down-looking monocular images. ‘FishScale’ estimates fish abundances and size frequencies from near-nadir monocular images where fish have already been semantically segmented. The software accounts for lens distortion, underwater magnification effects …

Impact Of Obesity On The Gut Microbiome And Inflammatory Markers During Siv Infection And Antiretroviral Therapy, Casey M. Mcguire, Isaac R. Cinco, Diana Takahashi, Kristin A. Sauter, Melissa Kirigiti, Ilhem Messaoudi, Jonah B. Sacha, Charles T. Roberts, Paul Kievit

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Dysbiosis and impaired gut barrier integrity contribute to chronic immune activation associated with both obesity and HIV infection. Given the increased incidence of obesity in people living with HIV, we explored the impact of obesity on the gut microbiome and microbial translocation (MT) biomarkers during HIV infection and antiretroviral therapy (ART). Lean and obese rhesus macaques were infected with simian immunodeficiency virus (SIV) and subsequently treated with ART. Obese animals exhibited higher initial MT and inflammation biomarkers that remained constant throughout the study, while lean animals exhibited significant increases in these biomarkers that approached levels observed in obese animals. Lean …

‘Who’S Your Daddy?’: Ddradseq Parentage In Broodstock-Offspring Pairs Of Diadema Antillarum In A Population Restoration Initiative, Bianca R. Rosendahl

Undergraduate Scholarship and Creative Works

In the early 1980s Diadema antillarum, or the long-spined urchin, was hit by a catastrophic mass mortality event across the western Atlantic and Gulf of Mexico, inclusive of the Florida Keys. The cause of this die-off event was likely triggered by a pathogen or environmental stressor that decimated native populations by up to 98%. The species has not yet fully recovered and is struggling with recruitment success which is why it may benefit from an ex-situ recovery program. In this study, I used single nucleotide polymorphisms (SNPs) to identify genetic variation and analyze parentage in a captive population of …

An Understanding Of The Feeding Ecology Of Teleoceras Fossiger And Teleoceras Aepysoma Using Dental Microwear And Mesowear Analysis, Gabriel S. Goncalves

Master's Theses or Doctor of Nursing Practice

Teleoceras is a genus of rhinocerotids that belongs to the Tribe Teleoceratines and was widespread across North America from the late Early Miocene into the Early Pliocene. This genus was very successful, spreading across the continental United States from Florida and Tennessee to California and Washington state down to central Mexico and Honduras. Teleoceras is characterized by having a large, rounded chest cavity and short limbs with relatively high crowned teeth and lower incisors modified into tusk-like teeth. Initial ecological comparisons were made to the modern hippopotamus based on proportions of the chest cavity and its hypsodont dentition. Stable carbon …

Impact Of Minimally Processed Red Meat On Biomarkers Of Cognitive Decline, Saba Vaezi

Electronic Theses and Dissertations

No abstract provided.

Evaluation Of High-Moisture Ear Corn As A Roughage Source In Finishing Diets Fed To Beef Steers, Riley J. Leeson

Electronic Theses and Dissertations

The objective of this study was to evaluate the feedlot performance, rumination activity, and carcass characteristics of high moisture ear corn (HMEC) as a roughage source in finishing diets fed to beef steers. Backgrounded steers (n = 191; initial shrunk weight [4% BW] = 449 kg  23.9 kg) were assigned randomly to 1 of 24 pens (8 steers/pen) with pens randomly assigned to one of four dietary treatments (6 pens/treatment): control diet with hay fed at 10% roughage equivalency (RE; HAY10), or HMEC at either 14% (EAR14), 10% (EAR10), or 6% (EAR6) RE. High-moisture ear corn was assumed to …

Finishing Location And Forage Diversity Influences Carcass Characteristics, Meat Quality Attributes, Terroir, And Color Stability Of Grass-Finished Bison Bulls, Garrett Tyler Weldy

Electronic Theses and Dissertations

The overall objective of this thesis is to determine the influence of finishing location and forage diversity on carcass characteristics, meat quality, terroir, and color stability of grass-finished bison bulls. The specific objectives were 1) Determine the effect of finishing location on carcass characteristics, meat quality attributes, and terroir of grass-finished bison bulls, 2) Investigate the effect of forage diversity on the carcass characteristics, meat quality attributes, and terroir of grass-finished bison bulls, and 3) Determine the effect of finishing location on the meat color stability of grass-finished bison bulls. Overall, results indicate that finishing location influenced carcass characteristics, objective …

The Influence Of Bottom-Up And Top-Down Effects On The Density And Distribution Of Common Leopards In The Eastern Himalayas, Karma Choki

Electronic Theses and Dissertations

Leopards (Panthera pardus fusca) are widely distributed across Asia, yet their conservation is overshadowed by the conservation status of other flagship predators like tigers (Panthera tigris), in the Eastern Himalayas. Despite their ability to coexist with other large carnivores, leopard populations are shaped by intricate ecological interactions and increasing human pressures. This thesis investigates the abundance and density, habitat use, and drivers of persistence of leopards across Bhutan to inform multi-species carnivore conservation planning. My first chapter provides an overview of the ecological roles of large carnivores and how they persist on the landscape. I review the mechanisms that facilitate …

Comparative Evaluation Of Fungal Strains For The Bioprocessing Of Soybean Hulls Using Cheese Whey As Fermentation Medium, Ruchita Bhattarai

Electronic Theses and Dissertations

Globally, soybean is the most widely cultivated oilseed crops, and serve as the primary source of cooking oil, contributing to around 50% of global oilseed production. During the industrial processing of soybean oil, a significant amount of soybean hull (SH) is produced, which makes up about 8% of the grain yield, resulting in approximately 18–20 million tons of hulls, one of the largest by-products in the soybean industry. The hulls have limited commercial value and are primarily used as fiber additives in dairy cattle feed, but a large portion is still discarded as agricultural waste. Similarly, cheese whey (CW), a …

Quantifying Landscape Variability Of Dynamic Soil Properties In The James River Valley, Eastern South Dakota, Sage Reuter-Schmitt

Electronic Theses and Dissertations

Dynamic soil properties (DSP) are a great tool for monitoring land-use change, and they are frequently used as soil health metrics. The NRCS and other soil researchers often use repeating, single-point or nested-point DSP studies to monitor and better understand the effects of land management decisions. While these studies capture the temporal variability of DSPs, they overlook the field-scale spatial variability of DSPs. Soil organic carbon (SOC) provides critical services to the ecosystem and other environments. These traits, as well as its susceptibility to management decisions, make SOC an important soil health indicator and DSP. Measuring SOC is often time …

Impacts Of Early/Mid-Gestation Shearing On Umbilical Blood Flow And Lamb Birth Weight, Mara Johnson

Electronic Theses and Dissertations

Studies outside the USA have reported that shearing pregnant ewes during mid to late gestation increases lamb birth weight. Our hypothesis was that shearing pregnant ewes on day 50 of gestation would increase umbilical blood flow (UBF), fetal size, lambing and placental weights. Twenty-eight Polypay ewes were randomly assigned to two treatments: shorn (S) and sham-shorn (Control, CON) and divided in singleton (S: n=4; CON: n=4), twins (S: n=5; CON: n=5) and triplets (S: n=5; CON: n=5). Umbilical BF and fetal and placental measurements were obtained via ultrasonography every 10 days from day 50 to 110 of gestation. Lamb birth …

Isolation And Characterization Of Rhizobia Bacteria From Midwest Soils, Jr Loya

Electronic Theses and Dissertations

Symbiotic bacteria, known as rhizobia, can colonize the roots of legume plants and then convert atmospheric nitrogen into a usable form by the host through the process called biological nitrogen fixation (BNF). Many of these bacteria produce other plant-growth-promoting benefits, such as nutrient acquisition, phytohormone production, and the modification of plant stress responses. Agricultural inoculants made from these bacteria have helped reduce the need for man-made nitrogenous fertilizers, known causes of pollution and eutrophication. There are additional benefits in developing bacteria inoculants local to regional soils. The ability to survive and compete in Midwest soil and climates present an opportunity …