Physical Sciences and Mathematics Commons^™

Chemical Synthesis Of Sensitive Dna, Komal Chillar

Dissertations, Master's Theses and Master's Reports

Over the past decades, researchers have tried various chemical methods to synthesize modified oligodeoxynucleotides (ODNs, i.e. short segments of DNAs). Traditional ODN synthesis methods require strong basic, and nucleophilic conditions for the deprotection and cleavage of the ODN from the solid support. However, the sensitive ODNs containing labile functionalities are vulnerable to such harsh conditions. Sensitive ODNs have a wide range of applications in research and pharmaceuticals. To synthesize sensitive ODNs, researchers devised different strategies but no practical methods have been developed. To overcome these challenges, we developed alkyl Dim alkyl Dmoc technology. This innovative technology uses weakly basic and …

Invasive Buckthorn Mapping: A Uav-Based Approach Utilizing Machine Learning, Gis, And Remote Sensing Techniques In The Upper Peninsula Of Michigan, Vikranth Madeppa

Dissertations, Master's Theses and Master's Reports

An Invasive species is a species that is alien or non-native to the ecosystem which causes harm to economic, environmental, or human health (E.O. 13112 of Feb 3, 1999). Invasive species have posed a serious threat to ecosystems across the globe. These invasive species have impacts on the biodiversity and productivity of invaded forests. Remotely sensed data is a valuable resource for understanding and addressing issues related to invasive species. This study presents a novel approach for mapping the distribution of two invasive plant species, Common and Glossy Buckthorn, using unmanned aerial vehicles (UAVs), machine learning algorithms, geographic information systems …

Prediction Of Sumoylation Sites In Proteins From Language Model Representations, Evgenii Sidorov

Dissertations, Master's Theses and Master's Reports

Sumoylation is an essential post-translational modification intimately involved in a diverse range of eukaryotic cellular mechanisms and plays a significant role in DNA repair. Some researchers hypothesize that a high level of SUMOylation events in cancer cells improves cells' chances for survival under stress conditions by regulating tumor-related proteins.

This study belongs to a booming field of harnessing computational power to the domain of life. Prediction of protein structure, its molecular function, and the design of new drugs are just a few examples of the applications within this exciting area of research. By leveraging computational power, researchers can analyze vast …

Multiscale Molecular Modeling Studies Of The Dynamics And Catalytic Mechanisms Of Iron(Ii)- And Zinc(Ii)-Dependent Metalloenzymes, Sodiq O. Waheed

Dissertations, Master's Theses and Master's Reports

Enzymes are biological systems that aid in specific biochemical reactions. They lower the reaction barrier, thus speeding up the reaction rate. A detailed knowledge of enzymes will not be achievable without computational modeling as it offers insight into atomistic details and catalytic species, which are crucial to designing enzyme-specific inhibitors and impossible to gain experimentally. This dissertation employs advanced multiscale computational approaches to study the dynamics and reaction mechanisms of non-heme Fe(II) and 2-oxoglutarate (2OG) dependent oxygenases, including AlkB, AlkBH2, TET2, and KDM4E, involved in DNA and histone demethylation. It also focuses on Zn(II) dependent matrix metalloproteinase-1 (MMP-1), which helps …

Statistical Methods For Gene Selection And Genetic Association Studies, Xuewei Cao

Dissertations, Master's Theses and Master's Reports

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

In Chapter One, we propose a signed bipartite genotype and phenotype network (GPN) by linking phenotypes and genotypes based on the statistical associations. It provides a new insight to investigate the genetic architecture among multiple correlated phenotypes and explore where phenotypes might be related at a higher level of cellular and organismal organization. We show that multiple phenotypes association studies by considering the proposed network are improved by incorporating the genetic information into the phenotype clustering.

In Chapter Two, we first illustrate the proposed GPN …

Machine Learning Methods For Prediction Of Human Infectious Virus And Imputation Of Hla Alleles, Xiaoqing Gao

Dissertations, Master's Theses and Master's Reports

This dissertation contains three Chapters. The following is a concise description of each Chapters.

In Chapter 1, we introduced the Random Forest, a machine learning method, to foresee whether a virus is capable of infecting humans. The Covid pandemic informs us the importance of predicting the ability of a zoonotic virus that can infect humans from its genomic sequence. We used the -mer with and as features of a virus to predict if it can affect humans. We further employed the Boruta algorithm to select the important features, then fed those important features into the Random Forest method to train …

The Photo-Transformation Of Free Methionine In The Presence Of Surrogate And Standard Isolate Dissolved Organic Matter Under Sunlit Irradiation, Benjamin J. Mohrhardt

Dissertations, Master's Theses and Master's Reports

Sulfur (S)-containing amino acids are key sources of carbon, nitrogen, and sulfur involved in protein synthesis, protein function, and providing energy for microbial growth. Dissolved free and combined methionine is one of two S-containing amino acids incorporated into proteins and has been attributed to their stability and function. The oxidation of methionine has received considerable attention given its ubiquitous presence in most biological systems and has been associated with losses in protein function and pathological disorders. In natural waters, methionine is rapidly and selectively taken up by microorganisms to achieve cellular requirements of carbon, nitrogen, and sulfur. The abiotic transformation …

Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi

Dissertations, Master's Theses and Master's Reports

Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter …

Fine Scale Mapping Of Laurentian Mixed Forest Natural Habitat Communities Using Multispectral Naip And Uav Datasets Combined With Machine Learning Methods, Parth P. Bhatt

Dissertations, Master's Theses and Master's Reports

Natural habitat communities are an important element of any forest ecosystem. Mapping and monitoring Laurentian Mixed Forest natural communities using high spatial resolution imagery is vital for management and conservation purposes. This study developed integrated spatial, spectral and Machine Learning (ML) approaches for mapping complex vegetation communities. The study utilized ultra-high and high spatial resolution National Agriculture Imagery Program (NAIP) and Unmanned Aerial Vehicle (UAV) datasets, and Digital Elevation Model (DEM). Complex natural vegetation community habitats in the Laurentian Mixed Forest of the Upper Midwest. A detailed workflow is presented to effectively process UAV imageries in a dense forest environment …

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 …

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 …

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 …

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 …

Exploring Substrate Specificity Of Fructose Transporters En Route To Glut Specific Probes For Biochemical And Biomedical Applications, Vagarshak Vigenovich Begoyan

Dissertations, Master's Theses and Master's Reports

Carbohydrate Transporters (GLUTs) are responsible for the transportation of sugars into the cell and have been of great interest in research for decades. Alterations or mutations that result in overexpression of GLUTs have been linked to a great number of diseases including, obesity, diabetes, and cancer. Differentiation between transporters has been shown to be incredibly difficult due to the highly conserved nature of the transporter structure, and thus specific targeting of transporters has proven a difficult challenge. Additionally, the GLUTs have been shown to high flexibility in their conformations, so it is difficult to determine what can or cannot pass …

Statistical Methods For Joint Analysis Of Multiple Phenotypes And Their Applications For Phewas, Xueling Li

Dissertations, Master's Theses and Master's Reports

Genome-wide association studies (GWAS) have successfully detected tens of thousands of robust SNP-trait associations. Earlier researches have primarily focused on association studies of genetic variants and some well-defined functions or phenotypic traits. Emerging evidence suggests that pleiotropy, the phenomenon of one genetic variant affects multiple phenotypes, is widespread, especially in complex human diseases. Therefore, individual phenotype analyses may lose statistical power to identify the underlying genetic mechanism. Contrasting with single phenotype analyses, joint analysis of multiple phenotypes exploits the correlations between phenotypes and aggregates multiple weak marginal effects and is therefore likely to provide new insights into the functional consequences …

Biogeochemical Response To Vegetation And Hydrologic Change In An Alaskan Boreal Fen Ecosystem, Danielle L. Rupp

Dissertations, Master's Theses and Master's Reports

Boreal peatlands store approximately one third of the earth’s terrestrial carbon, locked away in currently waterlogged and frozen conditions. Peatlands of boreal and arctic ecosystems are affected increasingly by shifting hydrology caused by climate change. The consequences of these relatively rapid ecosystem changes on carbon cycling between the landscape and the atmosphere could provide an amplifying feedback to climate warming. Alternatively, the advancement of terrestrial vegetation into once waterlogged soils could uptake carbon as a sink. Previous work suggests that fens will become an increasingly dominant landscape feature in the boreal. However, studies investigating fens, their response to hydrologic and …

Near-Infrared Fluorescent Probes For Sensitive Determination Of Lysosomal & Mitochondrial Ph In Live Cells, Wafa Mazi

Dissertations, Master's Theses and Master's Reports

Varied intracellular pH levels are critical for various physiological processes such as enzymatic activity, cell proliferation and apoptosis, ion transport, and muscle contraction. Cellular compartments, like lysosomes, must retain an acidic environment (pH ~ 4.5) to activate hydrolytic enzymes necessary for the breakdown of large biomolecules. Another cellular organelle, the mitochondria, provides the cell with energy and must retain an alkalis environment (pH ~ 8.0) for proper function. Substantial lysosomal and mitochondrial pH deviation is associated with cellular dysfunction and disease. Therefore, the precise detection of lysosomal and mitochondrial pH is essential to provide a better understanding of cellular physiological …

The Abiotic Stress Response Of Hydroponic Vetiver Grass (Chrysopogon Zizanioides L.) To Acid Mine Drainage And Its Potential For Environmental Remediation, Jef Kiiskila

Dissertations, Master's Theses and Master's Reports

Mining activities can generate acid mine drainage (AMD), an acidic discharge that contains elevated sulfate (SO₄^2-), soluble metals, and orange-yellow metal-containing particulates. AMD imposes ecological risks from metal toxicity and physical stress, which may physically spread to nearby water sources or biologically through bioaccumulation. Current methods for AMD treatment, such as chemical or passive biological treatments, are often non-sustainable. Chemical treatments can be expensive and create large amounts of secondary waste, whereas biological treatments like anaerobic wetlands require continuous maintenance through input of organic nutrients. The end goal of this research is to develop a cost-efficient and …

Algorithms For Reconstruction Of Gene Regulatory Networks From High -Throughput Gene Expression Data, Wenping Deng

Dissertations, Master's Theses and Master's Reports

Understanding gene interactions in complex living systems is one of the central tasks in system biology. With the availability of microarray and RNA-Seq technologies, a multitude of gene expression datasets has been generated towards novel biological knowledge discovery through statistical analysis and reconstruction of gene regulatory networks (GRN). Reconstruction of GRNs can reveal the interrelationships among genes and identify the hierarchies of genes and hubs in networks. The new algorithms I developed in this dissertation are specifically focused on the reconstruction of GRNs with increased accuracy from microarray and RNA-Seq high-throughput gene expression data sets.

The first algorithm (Chapter 2) …

Using Remote Site Incubators For Re-Introduction Of Arctic Graylng (Thymallus Arcticus) To The Big Manistee Watershed, Sunflower Wilson

Dissertations, Master's Theses and Master's Reports

Remote Site Incubators (RSIs) were developed for the incubation of salmonid eggs directly at a field site to enhance success and imprinting of young. These have been employed in the re-establishment of Arctic Grayling in Montana and are being laboratory tested for possible reintroduction of this species in the Big Manistee River, MI. Arctic Grayling, Rainbow and Brook Trout eggs, obtained from state hatcheries, were reared in a laboratory using flow through lake water to assess egg and fry survival using RSIs. Dead eggs and fry were removed daily and observations of developmental stages recorded. Rainbow Trout eggs were evaluated …

Dynamics Of Wild Red Raspberry (Rubus Idaeus L.) And The Influence On Tree Regeneration Within Silvicultural Openings In A Northern Hardwood Stand, Matthew J. Widen

Dissertations, Master's Theses and Master's Reports

Previous studies have investigated how the abundance of raspberries (Rubus idaeus L.) impacts tree regeneration, but few have linked these impacts to location within canopy openings with a legacy tree. To fill this knowledge gap, we investigated the presence, abundance, and location of raspberries within openings containing legacy trees and the resulting impacts on tree regeneration. During the winter of 2003, 49 openings were created of three sizes: small, medium, large and 20 reference single-tree selection sites in a northern hardwood stand in Ford Forest near Alberta, Michigan. Tree regeneration and vegetative species cover were recorded in 2005 and …

Characterization Of Ecological Water Stress In The U.S. Great Lakes Region Using A Geospatial Modeling Approach, Sara Alian

Dissertations, Master's Theses and Master's Reports

Anthropocentric water resources management affects aquatic habitats by changing streamflow regime. Understanding the impacts of water withdrawal from different sources and consumption by various economic sectors at different spatial and temporal scales is key to characterizing ecologically harmful streamflow disturbances. To this end, we developed a generic, integrative framework to characterize catchment scale water stress at annual and monthly time scales. The framework accounts for spatially cumulative consumptive and non-consumptive use impacts and associated changes in flow due to depletion and return flow along the stream network. Application of the framework to the U.S. Great Lakes Region indicates that a …

The Effects Of Early Pruning On The Near-Ground Branch Density Of Four Live Fencing Species, Aric Devens

Dissertations, Master's Theses and Master's Reports

Crop losses in home gardens greatly impact the wellbeing of rural West African families. Herbivory by migratory or local livestock represents a significant source of crop loss. Live-fencing gardens with thorny hedges is a low-cost and sustainable strategy for reducing losses due to herbivory. However, guidance on the establishment of thorny hedges is inconsistent, poorly publicized, and often anecdotal. Therefore, this study evaluated the effects of three early pruning treatments on near-ground branch density of four thorny species: Vachellia nilotica, Senegalia laeta, Senegalia mellifera, and Prosopis juliflora. Physical measurements and photographic data indicated that after one growing season, V. …

Effect Of Disulfide Bond Scrambling On Protein Stability, Aggregation, And Cytotoxicity, Colina Dutta

Dissertations, Master's Theses and Master's Reports

Proteins are nano-machines that carry out majority of the cellular functions. Thermodynamically they are functional and stable within a very narrow range (1 kcal/mol). External perturbations in the form of pH change, thermal, or oxidative/reducing stress can destabilize the protein resulting in misfolding and aggregation. Prolonged environmental stress can affect the cells adaptive response resulting in loss of ability to refold or recycle proteins. This can lead to accumulation of misfolded or aggregated proteins within the cell. Such accumulation of aggregated proteins have been associated with neurodegenerative disorders such as Amyotrophic Lateral Sclerosis (ALS), Parkinson’s, Huntington’s, and Alzheimer’s disease. There …

Assessing The Impacts Of Climate Change On The Surface Temperature Of Inland Lakes In Michigan, Kaitlin Reinl

Dissertations, Master's Theses and Master's Reports

The aim of this study was to validate and apply a lake model for predicting the susceptibility of small inland lakes in Michigan to changes in thermal regime and increased cyanobacteria growth as a result of future climate conditions. The Freshwater Lake Model was selected, tested for sensitivity to various inputs, and validated through comparison to observed conditions. The sensitivity analysis showed that the lake model was most sensitive to solar radiation, air temperature, and air humidity. Comparison of predicted climate data with observed conditions revealed highly variable climate model error. The lake model validation was conducted using 10 lakes …

Effects Of Wildfire And Post-Fire Salvage Logging On Rill Networks And Sediment Delivery In California Forests, Will Olsen

Dissertations, Master's Theses and Master's Reports

Wildfires can increase soil erosion by orders of magnitude over rates in unburned forests and negatively impact aquatic resources. Rill erosion is a dominant erosion and sediment transport mechanism in burned forests, and hydrologically connected rills can form networks on burned hillslopes. At the swale scale (< 10,000 m²), little is known about how rill networks develop under different burn severities over time, their relationship with sediment yields, and the effect of post-fire salvage logging on rill networks and sediment yields.

The first study assessed rill networks and sediment yields in three burn severities in the inland Coast Range of …

Sorghum Yield And Zai Holes In Goundi, Burkina Faso, Justin Gelb

Dissertations, Master's Theses and Master's Reports - Open

The purpose of this study was to determine if there was a difference in sorghum yield between the Mossi zai hole and the Gourounsi zai hole, specifically examining the effects of manure and soil water conservation. A study field was created with six different treatments: (1) control with traditional management (no zai holes), (2) traditional management with manure, (3) Mossi zai holes with no manure, (4) Mossi zai holes with manure, (5) Gourounsi zai holes with no manure, and (6) Gourounsi zai holes with manure. Soil moisture readings were taken after each rainstorm (about weekly), soil properties were analyzed before …

Understanding Farmers’ Perceptions And The Effects Of Shea Tree Vitellaria Paradoxa Distribution In Agroforestry Parklands Of The Upper West Region, Ghana, Fahimeh Baziari

Dissertations, Master's Theses and Master's Reports - Open

Agroforestry parklands represent a vast majority of the agricultural landscape under subsistent-oriented farming in semi-arid West Africa. Parklands are characterized by the growth of well- maintained trees (e.g., shea) on cultivated fields as a result of both environmental and human influences. Shea (Vitellaria paradoxa) provides a cultural and economic benefit to the local people of Ghana, especially women. Periods between traditional fallow rotation systems have reduced recently due to agricultural development and a demand for higher production. As a result, shea trees, which regenerate during fallow periods, has decreased over the landscape. The aim of this study was …

Biogeochemical Cycling In Lake Superior Tributaries: Seasonality, Quantity And Quality Of Export, Ashley Anne Coble

Dissertations, Master's Theses and Master's Reports - Open

Seasonal and spatial variability in environmental factors may affect dissolved organic matter composition and nutrient transformation and retention in streams. The objective of this research was to quantify and describe seasonality, quantity, and quality of nutrient processing and export of ammonium (NH₄), soluble reactive phosphate (SRP), and dissolved organic carbon (DOC) into Lake Superior through intensive study in a small 1st order watershed coupled with snapshot measurements across 12 tributaries that varied in size, location, and wetland coverage. Our results suggest biodegradable C is exported from a small headwater stream year-round and that DOC mineralization rates can be …