Digital Commons Network^™

Benthic Macroinvertebrate Pre-Assessment Of A Proposed Restoration In The Grand River, Grand Rapids, Mi, Usa, Matthew L. Bain

Masters Theses

River restoration is the dominant field of applied water resources management in the United States. Ecological improvement should be the goal of all river restorations, though many restoration projects fail to produce positive results due to limited scope or inadequate assessment methodologies. Pre-restoration, biotic data is essential for such projects as it can be paired with post-restoration data to gauge ecological outcomes. A major restoration effort is now underway in Michigan's longest river, the Grand River, where it flows through downtown Grand Rapids. The primary restoration measures will occur in-stream at local scale. We conducted a pre- restoration survey for …

Rumen Biogeographical Regions And Their Impact On Microbial And Metabolome Variation, Macey P. Soltis

Masters Theses

The rumen microbiome is a complex microbial network critical to the health and nutrition of its host, due to their inherent ability to convert low-quality feedstuffs into energy. In rumen microbiome studies, the ventral sac is sampled from due to ease of access and repeatability. However, anatomical musculature demarcates the rumen into five sacs which may support distinct microbial communities. The distinction among the microbes may generate functional variation among the rumen microbiome, thus, specialized tasks within different sacs. The objective of this study was to determine the rumen liquid metabolome and epimural, planktonic, and fiber-adherent bacterial communities among each …

Predicting Immunization Status At Arrival In Tennessee Stocker Calves, Claire E. Hunkler

Masters Theses

Bovine respiratory disease is a multifaceted disease with agent, host, and environmental factors. Stocker calves are at high risk of contracting the disease through many stressors like weaning, transportation, commingling, etc. The purpose of this project was to test if externally observed physical characteristics of calves on arrival at a stocker facility can be used to predict calfhood vaccination status determined based on antibody titer levels. Knowledge of highly correlated characteristics could allow stocker operators to reduce the occurrence of BRD through targeted management strategies, thus lowering morbidity, mortality, and treatment costs. Ear notches, blood, and visual characteristics were collected …

Systematic Evaluation Of Database Builds In Metaproteomics For The Advancement Of Microbiome Research, Katherine E. Ostrouchov

Masters Theses

The microscopic life that inhabits a human shares a unique bond with its host. Microbes perform many functions that are vital to the survival of the human species and have long been shown to regulate the absorption of nutrients and to promote immune function. A lack of exposure to certain microbes early in life, excessive antibiotic usage, and improper diet can perturb human microbiomes and lead to disease. Since the emergence of omic sequencing technologies, it has now become possible to measure and monitor the genes and proteins made by these microorganisms to better understand how they contribute to host …

Encapsulation Of Antimicrobial Peptides In Bicontinuous Microemulsions For Topical Delivery To Surgical Site Infections And Chronic Wounds, Madison A. Oehler

Masters Theses

Surgical site infections and chronic wounds, especially those caused by antibiotic-resistant microorganisms, result in hospitalization and fatalities each year. Methods to prevent these infections, such as cleaning and preparing medical tools, have had minimal success in preventing infections. Further, antibiotic treatments have become less successful in treating infections and wounds because of antibiotic-resistant bacteria. Antimicrobial peptides (AMP) are a possible treatment solution for wound infections. AMPs are oligopeptides that occur in nature or can be synthesized in vitro which possess a broad spectrum of antimicrobial activity against bacteria and other harmful microorganisms. AMPs operate by disrupting the packing arrangements of …

Staphylococcal Surface Proteins As Vaccine Candidates For The Control Of Staphylococcal Mastitis In Dairy Cows, Jessica Jean Vidlund

Masters Theses

Bovine mastitis, an inflammation of the mammary gland, is the single most costly disease of dairy cattle. Staphylococci, a major bacteria that cause bovine mastitis, are commonly divided into two major groups: Staphylococcus aureus and non-aureus staphylococci (NAS), previously known as coagulase-negative Staphylococcus species (CNS). Current mastitis control programs are not fully effective against staphylococcal mastitis and antibiotics are not sustainable due to limited success and the emergence of antimicrobial resistant bacteria. Non-antibiotic sustainable control tools, such as effective vaccines, are critically needed. Our lab developed and evaluated Staphylococcus aureus surface associated protein (SASP) and Staphylococcus chromogenes surface associated protein …

The Effects Of Deleting Lrb E3 Ligase Region 2 On Red Light Responses In Arabidopsis Thaliana, Sabina Liskey

Masters Theses

The ability of plants to absorb light through photoreceptors is essential for successful plant development. Phytochromes are important plant photoreceptors that detect and absorb red and far-red light and must function properly for plant survival. The Light Response BTB proteins (LRB) play an important role in a plant’s response to red light by degrading phytochrome B (PhyB) via the ubiquitin proteasome system (UPS). Although there has been a successful investigation into understanding the function of the LRBs, the function of a few regions within LRB proteins remains unknown, including a portion located on the N-terminal end of the protein, termed …

Comparison Of The Humoral Immune Response Following Both Bacterial Challenge And Rnai Of Major Factors On Proliferation Of Bartonella Quintana In The Human Louse, Jake Zina

Masters Theses

Human body lice, Pediculus humanus humanus, and head lice, Pediculus humanus capitis, have been hematophagous ectoparasites of humans for thousands of years. Despite being ecotypes, only body lice are known to transmit bacterial diseases to humans, and it appears that lower humoral and cellular immune responses allow body lice to possess a higher vector competence. We previously observed that the transcription level of the defensin 1 gene was up-regulated only in head lice following oral challenge of Bartonella quintana, a causative agent of trench fever, and also that body lice excreted more viable B. quintana in their …

Changes In Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping To Fac-Sorted Bacteria, Christopher A. Colvin

Masters Theses

Soil microbiomes play pivotal roles to the health of the environment by maintaining metabolic cycles. One question is how will climate change affect soil bacteria over time and what could the repercussions be. To answer these questions, the Harvard Forest Long-Term Warming Experiment was established to mimic predicted climate change by warming plots of land 5℃ above ambient conditions. In 2017, 14 soil core samples were collected from Barre Woods warming experiment to mark 15 years since the establishment of the soil warming in that location. These samples underwent traditional metatranscriptomics to generate an mRNA library as well as a …

The Mouse Mammary Gland: A Tool To Evaluate The Environmental Chemical Butyl Benzyl Phthalate, And Approaches To Improve Regulatory Testing, Jessica Daum

Masters Theses

In the first part of this thesis, we utilize the mouse model to evaluate the environmental chemical Butyl Benzyl Phthalate. Due to lack of research on female exposure to BBP, this thesis focuses on quantifying the effects of gestational exposure on the female mammary gland Here male and female parental mice were exposed before mating and through pregnancy and lactation to one of three doses of BBP or the control via oral ingestion. After weaning, offspring were sacrificed at puberty or early adulthood and evaluated for altered mammary gland morphology or hormonal receptor expression. Results indicate a persistent statistically significant …

Characterization Of The Poly (Adp-Ribose) Polymerase Family In The Fusarium Oxysporum Species Complex, Daniel Norment

Masters Theses

Fusarium oxysporum is a filamentous fungus that is known to invade over a hundred different hosts and poses a major threat to the economy and food supply world-wide. Poly (Adenosine diphosphate-Ribose) Polymerase (PARP) is a family of regulatory proteins that affect change in the cell through transfer of ADP-Ribose moieties onto target molecules. The most well-studied PARP protein is the human PARP1, a PARylating nuclear protein that serves as our model PARP protein. F. oxysporum was found to contain a large expansion of PARP catalytic-domain-containing proteins compared to other filamentous fungi. We utilized in silico multiple sequence alignments and domain …

Assessing Warm-Season Annual Grasses To Increase Forage Inventory, Andrea Marroquin

Masters Theses

Summers are expected to continue to increase in heat/dryness in the Northeast, causing issues pertaining to forage production during the summer to worsen. Many pastures grow cool season grasses, even during the summer. These grasses enter a dormant period and slowdown in production during the months of July and August, leading to what is referred to as “summer slump”. Some farms grow corn silage during the summer, and while corn silage is a valuable crop, its cultivation often does not support soil biology. This research addresses solutions for both summer slump foraging and more sustainable silage. Summer annuals grow more …

Evaluation Of Semiochemicals For Attractiveness To Multiple Tortricid (Lepidoptera) Pests In Apple Orchards, Ajay P. Giri

Masters Theses

Tortricid moths (Lepidoptera) are known for their outstanding olfaction capabilities that allow them to detect, process, and respond to chemical information emitted by host or non-host plants. Such an ability to filter out odors from the complex mixture to locate their host has allowed researchers and integrated pest management (IPM) practitioners to develop and implement semiochemically-based pest control strategies. The major goal of this study was to evaluate, under field conditions, the response of male and female oriental fruit moth (OFM), codling moth (CM), redbanded leafroller (RBLR) and three lined leafroller (TLLR) to experimental kairomone lures in commercial apple orchards …

Chemosensory Receptors In Berghia Stephanieae: Bioinformatics And Localization, Kelsi L. Watkins

Masters Theses

Chemosensation is achieved through the binding of chemical signals to chemoreceptor proteins embedded in the membranes of sensory neurons. The molecular identity of these receptors, as well as the downstream processing of chemosensory signals, has been well studied in arthropods and vertebrates. However, very little is known about molluscan chemosensation. The identity of chemoreceptor proteins in the nudibranch mollusc Berghia stephanieae are unknown. Data from other protostome and molluscan studies suggest Berghia may use ionotropic receptors for some forms of chemoreception. This study used a bioinformatics approach to identify potential chemosensory ionotropic receptors in the transcriptome of Berghia. A …

Incorporating Excess Post-Exercise Oxygen Consumption Into Accelerometer Energy Expenditure Estimation Algorithms, Nicholas Remillard

Masters Theses

Accelerometers are objective monitors of physical activity (PA) that can be used to estimate energy expenditure (EE). Most accelerometer EE estimation equations are based on steady-state data and do not consider excess post-exercise oxygen consumption (EPOC) after exercise. PURPOSE: To quantify the error in accelerometer EE estimates due to EPOC after varying durations of high-intensity treadmill running. METHODS: Nine young, healthy, recreationally active males participated in three study visits. Visit 1 included a treadmill VO₂ peak test to determine the treadmill speed correlating to 80% VO₂ peak for visits 2 and 3. Visit 2 included a seated 20-min …

Developmental Exposures To Pfas Mixtures Impair Elongation Of The Exocrine Pancreas In Zebrafish (Danio Rerio), Emily M. Formato

Masters Theses

Poly- and perfluoroalkyl substances (PFAS) are a class of bioaccumulative toxicants used in numerous industrial and commercial products. Perfluorooctanesulfonic acid (PFOS) alters pancreatic organogenesis during development, and perfluorohexanesulfonic acid (PFHxS) has been suggested as a replacement for PFOS due to its shorter carbon chain, but they are often found together in surfactants, such as legacy aqueous film-forming foam. This study investigates how developmental exposures to a PFAS mixture (PFHxS + PFOS) impact the developing exocrine pancreas. Zebrafish embryos (Tg(ptf1a:GFP)) were exposed to 0.01% DMSO, or 8, 16, 32 μM PFHxS alone, 16 μM PFOS alone, and 8, 16, and 32 …

Using Plot Photographs To Estimate Tundra Vegetation Cover In Northern Alaska, Hana Christoffersen

Masters Theses

Plot photography can provide a quick, robust method to measure vegetation, especially in polar environments where logistics can be expensive and challenging. The success and widespread adoption of plot photography in the Arctic hinges on the accuracy of image analysis and data product interpretation. The relative cover of eight vegetation classes was estimated using a point frame and digital camera across thirty, 1-m² plots at Utqiaġvik, Alaska from 2012 to 2021. Geographic object-based image analysis (GEOBIA) was applied to generate objects and classify the three band (red, green, blue) images. Machine learning classifiers (random forest, gradient boosted model, classification …

Evaluating Current And Future Potential Distribution Of Epiphytic Orchids In The Congo Basin With Ecological Niche Models, Michael L. Ngoh

Masters Theses

The Congo Basin Forest harbors a rich diversity of epiphytic communities, with the Orchidaceae alone making up more than 50% of all epiphytes in the region. Despite the huge diversity of epiphytes, many species, including epiphytic orchids, are at risk to a diverse array of threats. Climate change for instance poses severe threats to epiphytic orchids due to elevated temperatures, prolonged periods of droughts, as well as reduced rainfall across the Congo Basin Forest. In this study, we used ecological niche modeling and GIS techniques to identify spatial patterns of species richness, potential future climate refugia, and novel climatic suitability …

Optimal Stocker Production Strategies For Spring And Fall Calving Cow Herds, Cora Beth Key

Masters Theses

This thesis consists of two chapters discussing the economics of raising stocker beef cattle in the southeast United States. The objective of the first chapter is to estimate supplemental feed cost for spring-calving cows, spring-born stockers, cows calving in the fall, and fall-born stockers, while considering the seasonality of forage production and nutritional needs. The chapter explores ways producers can lower their feed costs and demonstrates the importance of managing hay expenses for cattle producers to control cost. The objective of chapter two is to determine the profit-maximizing stocker period in an integrated cow-calf and stocker operation with both fall- …

Switching Palmitoyl And Oleoyl Positions In Sn-2 And Sn-3 Of A Triacylglycerol Led To Differential Body Weight Gain Rates And Hepatic Gene Expressions In Mice Fed A High-Fat Diet, Xinge Hu

Masters Theses

Alterations of triacylglycerol (TAG) are associated with metabolic diseases such as obesity and diabetes. The fatty acyl groups in a TAG molecule determine its characteristics from melting temperature to digestion and absorption. We hypothesize that the TAG fatty acyl position affects the body weight (BW) gain and lipid metabolism in mice fed a high-fat diet (HFD, 36 % w/w diet). Six-week-old male C57BL/6J mice were randomly assigned to 3 dietary groups, 1,2-dipalmitoyl-3-oleoylglycerol (PPO), 1,3-dipalmitoyl-2-oleoylglycerol (POP), and chow control. The food intake and BW were measured daily during 6 weeks of treatment. The PPO group had significantly higher food intake, caloric …

Efficacy Of Sequential Estrus Synchronization And Timed Artificial Insemination In Beef Cattle Beginning 19 Days After An Initial Timed Artificial Insemination, Courtnie Carter Bridges

Masters Theses

A breeding program utilizing single fixed-timed artificial insemination (AI) was compared to a resynchronization program for a second fixed-timed AI. Angus and Angus cross primiparous and multiparous cows were randomly assigned to one of two treatment regimens; either single TAI (CON; n=468) or two sequential TAI (RS; n=473). The main objectives were assessing pregnancy rates and analyzing fetal age to estimate calving distribution rates between the two treatment groups. The 7-day CO-synch + CIDR protocol was utilized in both treatment groups to synchronize estrus for TAI-1 at 60h - 66h post- Prostaglandin injection (PGf2α). Animals in the RS treatment groups …

Computational Analysis Of Transcriptional And Post-Transcriptional Feedback Loops In Development And Cell Differentiation, Benjamin Rigel Nordick

Masters Theses

Regulation of gene expression is critical to organism development and health. Positive and negative feedback in networks of gene regulatory interactions are associated with the maintenance of distinct cell states/types or oscillations, respectively. Recent computational studies identified two structures of positive feedback relevant to establishment of cell type: interconnected transcriptional “high-feedback” loops and a purely post-transcriptional feedback loop arising from multiple microRNA molecules cooperatively regulating one mRNA. The goals of this work were to develop methods for analyzing often-unintuitive high-feedback loops in large networks, generalize the two new regulatory structures to consider oscillation, and further explore the ability of post-transcriptional …

Exploring Urban Forestry Non-Governmental Organizations In The Temperate Forest Region Of The United States, Alexander J. Elton

Masters Theses

The environmental and human health benefits of urban forests have been well documented. In the United States, volunteers conduct 5% of municipal tree care-related activities in urban forests. A literature review related to urban forestry volunteers in the United States was conducted and it was concluded that urban forestry volunteers are often organized via a committee or non-governmental organization (NGO) and that there is limited understanding around many of these entities. Following Dillman’s methods, an electronic qualitative survey with a primary objective of better understanding their characteristics was disseminated to urban forestry NGOs throughout the temperate forest region of the …

Foaming Properties Of Dilute Pea Protein Solutions, Jiani Bao

Masters Theses

Plant-derived protein such as pea protein is a promising replacement for animal protein and is becoming popular in recent years because of its high nutritional value and potential reduction of environmental footprint. However, the increasing demand for plant-derived proteins is accompanied by the increase of wastes during protein processing such as wastewater containing dilute protein content, which may raise the cost for the downstream processing. Therefore, there is an emerging need to develop novel processing strategies to reduce waste while valorizing useful ingredients. Several researchers suggest that foam fractionation technology can be a viable approach to extract and concentrate protein …

Fertilizer Waste Mistreatment Facilities: Investigating The Barrier That Keep Waste In And Attention Out At Central Florida's Phosphogypsum Stacks., Harsha Devaraj

Masters Theses

This project investigates the physical and narrative barriers constructed by the phosphate mining and processing industry to dissuade public engagement with its phosphogypsum sites in Central Florida, USA. The barriers around PG utilize decades of misinformation, racial geographies, and misrepresentations of scale, origin, and risk to create powerful narratives about how we should imagine and relate to these materials. These barriers hinder sustained public attention to their sites, enabling extractive industries to expand while avoiding oversight and responsibility. Attention to how these barriers around phosphogypsum are constructed allows us to recognize these strategies at work in how we see and …

The Spatial Ecology And Habitat Selection Of A Spotted Turtle (Clemmys Guttata) Population In Southwest Michigan, Michela Coury

Masters Theses

Turtles are arguably the most threatened group of vertebrates on the planet. Anthropogenic influences such as habitat loss and fragmentation, road mortality, subsidized predators, climate change, and illegal collection have contributed to their global decline. Understanding which isolated populations of turtles are viable despite these synergistic threats is crucial for making conservation and management decisions. In Michigan, the spotted turtle (Clemmys guttata) is a threatened species subjected to many negative anthropogenic influences that accelerate its rapid population decline. In order to properly sustain their populations, the goal of my research was to investigate relevant factors that help us …

Microbial Experience Increases Cytotoxicity Of Tumor-Infiltrating Cd8+ T Cells And Controls Tumor Growth, Nicholas Aaron Bunda

Masters Theses

Cancer immunotherapy research is traditionally conducted with specific pathogen-free (SPF) mice, which most accurately mimic the immune system of a human newborn. This makes translational research challenging, as this mouse model is not an accurate reflection of the adult patients who ultimately receive newly developed treatments. It is necessary to further develop a mouse model that bridges this gap and increases translatability of current cancer immunotherapy research.

By cohousing specific pathogen-free mice with regular pet store (PS) mice, we have generated a cohoused (CoH) mouse that reflects the microbial experience of an adult human immune system. We investigated antigen experience, …

The Influence Of Cover Crop Termination Strategies And Supplemental Nitrogen On Sweet Corn Yield And Nitrogen Use Efficiency, Sachina Sunuwar

Masters Theses

Cover crops are instrumental in nutrient management and soil health. A field experiment was conducted from fall 2020 to summer 2021 to evaluate the efficiency of different cover crop termination techniques and supplemental nitrogen on sweet corn yield, ear quality and nitrogen use efficiency. The four termination types are herbicide and disk tillage (HDT), herbicide no-till (HNT), cultivation disk till (CDT), and roller crimped no-till (RCNT). These termination types were each divided into four different nitrogen treatment: 0%, 33%, 67% and 100% of the recommended doses (145 kg haˉ¹). Sweet corn yield was highest and % unfilled tip was lowest …

Diterpene Synthases Of The Rice Blast Fungus: Phylogenetic Analysis And Biochemical Characterization, Ayousha Shahi

Masters Theses

Plant-pathogenic fungi harbor various specialized metabolites including diterpenoids that function as hormones and virulence factors. The fungus Magnaporthe oryzae is the causal agent of rice blast disease and can infect over 50 grass species. We demonstrate that the rice blast fungus encodes two diterpene synthases that produce normal pimara-8,15-diene and manoyl oxide scaffolds. Phylogenetic analysis of diterpene synthases among rice blast pathotypes showed functional conservation of the two core diterpene synthases amongst all pathotypes and suggests further expansion in select grass species. These insights into the blast fungal terpenome may inform efforts to counteract deleterious phytopathogens in crucial food crops.

Genetic Structure Of Urban White-Tailed Deer In West Michigan, Jacob David Brand

Masters Theses

In urban areas, green spaces are used by humans and wildlife. The proximity between them can lead to both positive and negative interactions, which can make managing urban wildlife difficult. Managers are challenged due to conflicts between wildlife population sizes that can be naturally supported versus those that are socially tolerable. White-tailed deer (Odocoileus virginianus) thrive in urban environments because their habitat requirements are met within green spaces and backyard vegetation. Matrilineal groups of urban white-tailed deer live within the same areas, at times forming high densities that can lead to the spread of diseases or environmental pests, including hemlock …