Life Sciences Commons^™

Auxin-Induced Degradation Of Dream Proteins, Lin-9 And Lin-54, In Caenorhabditis Elegans, Karli E. Chosa

Dissertations, Master's Theses and Master's Reports

The Dp, Retinoblastoma, E2F, And MuvB (DREAM) complex mediates transcriptional repression and is highly conserved throughout a number of species, including vertebrates, Drosophila melanogaster, and Caenorhabditis elegans. Differing from mammalian DREAM, C.elegans DRM, appears to act solely in a repressive role, with the MuvB subcomplex (LIN-9, LIN-37, LIN-52, LIN-53, and LIN-54) playing a key role in the repression of genes. In this study, we use the auxin-inducible degron (AID) system, an effective, fast-acting, tool used in the degradation of degron-tagged proteins to individually deplete two key proteins of the MuvB subcomplex, LIN-9 and LIN-54, in C. elegans. The …

Short-Term Fasting And Autonomic Control, Joshua Gonzalez

Dissertations, Master's Theses and Master's Reports

Obesity is a chronic metabolic disorder associated with increased risk of cardiovascular disease. Evidence suggests that chronic intermittent fasting improves cardiometabolic health and reduces arterial blood pressure. However, the mechanisms underlying the reductions in blood pressure and improved cardiovascular health observed from chronic fasting studies remain unclear. The autonomic nervous system has a central role in the regulation of blood pressure and is essential for cardiovascular homeostasis. We conducted a study to investigate how acute fasting influences autonomic control of blood pressure at rest and during stress. Twenty-five young, healthy, normal weight, normotensive participants were tested twice, once in the …

Hydrocarbon Biodegradation And Microbial Community Composition In Freshwater Systems And Enrichment Cultures, Emma Byrne

Dissertations, Master's Theses and Master's Reports

In this study, we investigated if significant differences existed seasonally in the microbial response to oil in the Straits of Mackinac, and if crude (Bakken) and refined (non-highway diesel) oil exposure had impacts on microbial community composition and hydrocarbon biodegradation across seasons using a microcosm-level experiment. Ambient microbial communities differed between seasons, with significantly enriched microbial groups present between all sample types except for between fall 23 ℃ and fall 4 ℃ microcosms. We found significantly different microbial communities between control samples and oil-amended samples in every season, but no significant community differences between either oil type. We found Amplicon …

Development Of A Propagation Program For Beech Bark Disease-Resistant American Beech (Fagus Grandifolia) And An Applied Restoration Plan For Mitigation Of Beech Bark Disease, Ande Myers

Dissertations, Master's Theses and Master's Reports

This dissertation describes the work accomplished towards mitigation of beech bark disease (BBD) through a joint venture by Michigan Technological University and the National Park Service. American beech is an ecologically important species that is threatened throughout its range by beech bark disease and other newer, emergent pressures such as climate change and beech leaf disease. A literature review is included to synthesize recent advances in American beech (Fagus grandifolia Ehrh.) propagation and their application in mitigation of BBD (Chapter 2). These concepts are examined in an applied restoration framework to outline the importance of understanding ecological and technological …

Controls On Autotrophic Respiration, Heterotrophic Respiration, And Decomposition In Northern Forested Rivers, Renn Schipper

Dissertations, Master's Theses and Master's Reports

Autotrophic respiration (AR), heterotrophic respiration (HR), and decomposition are important contributors to the carbon cycle in streams. It is important to understand how different environmental factors, such as canopy cover and dissolved organic carbon (DOC), influence these processes. DOC concentrations in northern forested streams are increasing, which may affect light and carbon availability. To examine the effects of DOC and canopy cover on these processes we measured gross primary production, ecosystem respiration and decomposition at 8 sites in 4 streams in the Upper Peninsula of Michigan and used quantile regression to estimate AR and HR. Among sites, AR and decomposition …

Construction And Analysis Of Genetic Regulatory Networks With Rna-Seq Data From Arabidopsis Thaliana, Tessa Kriz

Dissertations, Master's Theses and Master's Reports

Reconstruction of gene regulatory networks (GRNs) is a fundamental aspect of genetic engineering and provides a deeper understanding of the biological processes of an organism. Two methods were implemented to reconstruct the gene regulatory networks of Arabidopsis thaliana under two treatments: methyl jasmonate (MeJa) and salicylic acid (SA). The Joint Reconstruction of multiple Gene Regulatory Networks (JRmGRN) method was utilized to construct a joint network for identifying hub genes common to both conditions in addition to networks specific to each condition. The Differential Network Analysis with False Discover Rate Control method constructed a network of connections unique to only one …

Understory Dynamics Across 62-Years Of A Northern Hardwood Management Gradient Study, Heidi Harmala

Dissertations, Master's Theses and Master's Reports

Northern hardwood selection silviculture relies on the perpetuation of natural regeneration. However, many researchers and forest managers have concerns about deficiencies in regeneration and the associated ingrowth and recruitment of advance regeneration under single-tree selection. Given the differences of management application in the Great Lakes region, long-term studies and datasets are critical to understanding of how these systems function and change. Using the Cutting Methods Study, in the Western Upper Peninsula of Michigan, these concerns were investigated with a multi-decadal dataset, for understory tree species composition and density, diversity, recruitment, and age-diameter relationships across management methods. In response to the …

Evaluating Long-Term Growth And Yield In Upper Great Lakes Region Northern Hardwoods Cutting Trials, Maeve Draper

Dissertations, Master's Theses and Master's Reports

Common partial cutting management methods in Lake States hardwoods include both selection management and diameter-limit cuttings. Single-tree selection in particular is a widely prescribed silvicultural system in northern hardwoods and has an established history of use throughout the entire range of the forest type. Using data from two historic silvicultural studies, long-term comparison of single-tree selection methods and other partial cutting practices in northern hardwoods reveals that single-tree selection to higher residual basal areas, as widely applied in Great Lakes northern hardwood forests, is inferior using financial and volume yield criteria. Alternatives that remove more of the larger trees appear …

The Effect Of Nutrition On Longevity And Fertility In Diverse Drosophila: A Tor-Mediated Process, Tessa E. Steenwinkel

Dissertations, Master's Theses and Master's Reports

Nutrition and growth are strongly linked, but not much is known about how nutrition leads to growth. To understand the connection between nutrition through diet, growth and/or proliferation, we need to study the phenotypes resulting from the activation and inhibition of central metabolic pathways. Here I use the model organism Drosophila melanogaster (D. mel.) and three non-model Drosophila species with different dietary needs, Drosophila guttifera (D. gut.), Drosophila deflecta (D. def.), and Drosophila tripunctata (D. tri.), to study the effects of dietary amino acid availability in these diverse flies on fecundity and …

Regeneration Patterns In Silvicultural Openings Of Western Great Lakes Northern Hardwood Forests 15-24 Years Post-Harvest, Matthew S. Vandermolen

Dissertations, Master's Theses and Master's Reports

In managed northern hardwood forests, successful forest regeneration can depend on the application of silvicultural methods tailored to stand-specific recruitment limitations. The objective of this research is to develop a deeper understanding of the factors that interfere with tree regeneration at three long-term, well-replicated experimental canopy gap studies in the upper Great Lakes region, USA. Chapter 2 examines regeneration at a hemlock canopy gap study 18 years post-harvest that included deer exclosures and a gradient of gap sizes. Chapter 3 investigates the spatial patterns of low-density regeneration along gradients of gap size and different levels of legacy-tree retention at two …

Functional Genetic Approaches To Provide Evidence For The Role Of Toolkit Genes In The Evolution Of Complex Color Patterns In Drosophila Guttifera, Mujeeb Olushola Shittu

Dissertations, Master's Theses and Master's Reports

Toolkit genes are set of genes that orchestrate the development of basic body plan of animals, and they are highly conserved in all animals. The co-option of the toolkit genes into the pigmentation pathway has led to the evolution of novel species. This study focuses on understanding how the complex color patterns in animals develop by using the Drosophila species in the quinaria group as models. We developed an mRNA in situ hybridization (ISH) protocol, which allowed us to study gene expression patterns in the abdomen of developing pupae of non-model Drosophila species (Chapter 2). Through ISH, we found that …

Impact Of Hemodynamic Vortex Spatial And Temporal Characteristics On Analysis Of Intracranial Aneurysms, Kevin W. Sunderland

Dissertations, Master's Theses and Master's Reports

Subarachnoid hemorrhage is a potentially devastating pathological condition in which bleeding occurs into the space surrounding the brain. One of the prominent sources of subarachnoid hemorrhage are intracranial aneurysms (IA): degenerative, irregular expansions of area(s) of the cerebral vasculature. In the event of IA rupture, the resultant subarachnoid hemorrhage ends in patient mortality occurring in ~50% of cases, with survivors enduring significant neurological damage with physical or cognitive impairment. The seriousness of IA rupture drives a degree of clinical interest in understanding these conditions that promote both the development and possible rupture of the vascular malformations. Current metrics for the …

Impacts Of Forest Tax Programs On Property Tax Rates In Michigan's Upper Peninsula And Northern Wisconsin, Elsa Schwartz

Dissertations, Master's Theses and Master's Reports

Forest tax programs offer reduced property taxes to private forest owners as incentive to sustainably manage their forests and to encourage the provision of ecosystem services. They also protect forests from conversion to other land uses and ensure the viable supply of timber for forest products industries. Despite the benefits that these programs provide, they can negatively impact local municipalities by reducing the property tax base, which can then cause local governments to increase tax rates for non-preferential properties in order to maintain revenue needed to run their services. This shifts the tax burden from participating properties to nonparticipating properties. …

Applications Of Machine Learning In Microbial Forensics, Ryan B. Ghannam

Dissertations, Master's Theses and Master's Reports

Microbial ecosystems are complex, with hundreds of members interacting with each other and the environment. The intricate and hidden behaviors underlying these interactions make research questions challenging – but can be better understood through machine learning. However, most machine learning that is used in microbiome work is a black box form of investigation, where accurate predictions can be made, but the inner logic behind what is driving prediction is hidden behind nontransparent layers of complexity.

Accordingly, the goal of this dissertation is to provide an interpretable and in-depth machine learning approach to investigate microbial biogeography and to use micro-organisms as …

Metagenomic Identification And Classification Of The Mercury-Methylating Gene Hgca In Response To Water Table And Plant Functional Group Manipulations In Peat Soil, Madeline Peterson

Dissertations, Master's Theses and Master's Reports

Methyl-mercury (MeHg) is a potent neurotoxin that threatens the health of humans and wildlife alike. Climate warming threatens to shift regional precipitation and climate regimes in peatland environments, which could destabilize northern peatlands and accelerate both Hg release from soil and MeHg production. Peatlands are among the leading hotspots for MeHg, yet little is known about the community composition or functional relationship of mercury-methylating microbes in response to varying environmental conditions. The recognized mercury-methylating genes responsible for this activity are the obligatory gene pair hgcA and hgcB. Metagenomic data from the full-factorial peatland mesocosm experiment PEATcosm was obtained to …

Statistical Methods In Genetic Studies, Cheng Gao

Dissertations, Master's Theses and Master's Reports

This dissertation includes three Chapters. A brief description of each chapter is organized as follows.

In Chapter 1, we proposed a new method, called MF-TOWmuT, for genome-wide association studies with multiple genetic variants and multiple phenotypes using family samples. MF-TOWmuT uses kinship matrix to account for sample relatedness. It is worth mentioning that in simulations, we considered hidden polygenic effects and varied the proportion of variance contributed by it to generate phenotypes. Simulation studies show that MF-TOWmuT can preserve the type I error rates and is more powerful than several existing methods in different simulation scenarios, MFTOWmuT is also quite …

Spatial And Temporal Comparison Of Persistent Organic Pollutants In The Boardman River, Collin Diedrich

Dissertations, Master's Theses and Master's Reports

Dam removal is a critical part of river and stream remediation projects around the world. Frequently dams are associated with impoundment ponds containing sediments that can act as a sink of various persistent organic pollutants (POPs) that can pose risks for human and aquatic wildlife. In this study, we deployed semi-permeable membrane devices (SPMDs) at multiple locations along a 25-mile stretch of the Boardman River in Traverse City Michigan to passively sample POP concentrations in this area that has recently undergone dam and impoundment pond sediment removal. Concentrations of polychlorinated biphenyl (PCB), di-chloro-diphenyl-trichloroethane (DDT) and cyclodiene compounds were in the …

Utilization Of Paenibacillus Polymyxa In The Recovery Of Lithium Bearing Minerals, Diana Bullen

Dissertations, Master's Theses and Master's Reports

In the global transition to green energy in the transportation and power production sectors, lithium has emerged as a viable solution, and crucial component, for the effective storage of renewable resources. To avoid further degradation of the land due to mining for virgin material, methods focused on recovering lithium must be developed. This research project seeks to explore a new way to recover lithium by using the bacterium Paenibacillus polymyxa. The bacteria were grown and then applied to the lithium bearing mineral spodumene. Settling velocity profiles were constructed for different treatments of spodumene. It was found that the spodumene …

Regional Impacts Of Invasive Species And Climate Change On Black Ash Wetlands, Joseph Shannon

Dissertations, Master's Theses and Master's Reports

For more than a decade intensive research on the ecohydrology of black ash wetland ecosystems has been performed to understand these systems before they are drastically altered by the invasive species, emerald ash borer (EAB). In that time there has been little research aimed at the scale and persistence of the alterations. Three distinct but related research articles will be presented to demonstrate a method for moderate resolution mapping of black ash across its entire range, understand the relative impacts of EAB and climate change on probable future wetland conditions, and develop an experimental and modeling approach to quantify and …

Denitrification And Nitrogen Fixation Commonly Co-Occur But Rates Vary Throughout The Year And In Different Environments, Kevin Nevorski

Dissertations, Master's Theses and Master's Reports

Denitrification and nitrogen fixation are nitrogen cycling processes that can occur simultaneously in streams but are rarely studied together. The overarching goal of this dissertation was to quantify temporal and spatial variation of these processes in streams across the USA, characterize the environmental drivers of that variation, and determine the role that denitrification plays in the carbon cycle. To characterize temporal variation in these processes, a 2-year study in the Pilgrim River in Michigan’s Upper Peninsula found no difference in rates among seasons but high day-to-day variation in rates of both processes (maximum daily change 4,390 μg N/m²/hr …