Life Sciences Commons^™

Effects Of Increasing Temperature And Acidification On The Growth And Competitive Success Of Alexandrium Catenella From The Gulf Of Maine, Drajad Seto

Electronic Theses and Dissertations

The increases in ocean temperature and pCO2 due to climate change are projected to affect the growth and future prevalence of Harmful Algal Blooms (HABs) in nearshore waters, but systematic studies on the effects these climate drivers have on harmful algal species are lacking. In particular, little is known about how future climate scenarios will affect the growth of the toxic dinoflagellate Alexandrium catenella, which produces the toxins responsible for paralytic shellfish poisoning (PSP) that threaten the health and economy of coastal communities in the Gulf of Maine. I examined growth responses of A. catenella and two other naturally co-occurring …

Climatic Range Filling Of North American Trees, Benjamin Seliger

Electronic Theses and Dissertations

Understanding the degree to which species distributions are controlled by climate is crucial for forecasting biodiversity responses to climate change. Climatic equilibrium, when species are found in all places which are climatically suitable, is a fundamental assumption of species distribution models, but there is evidence in support of climate disequilibria in species ranges. Long-lived, sessile organisms such as trees may be especially vulnerable to being outpaced by climate change, and thus prone to disequilibrium. In this dissertation, I tested the degree to which North American trees are in equilibrium with their potential climatic ranges using the ‘range filling’ metric, which …

The Effects Of Seasonal Variations In Chemistry And Hydrology On The Microbial Community And Its Sulfide Oxidation Potential In A Naturally Acidic Maine Stream, Raymond C. Kahler Iii

Electronic Theses and Dissertations

Sulfide minerals oxidize through interaction with water and oxygen, releasing hydrogen ions. The process often occurs naturally near metal sulfide deposits, and can be accelerated through mining. Microorganisms accelerate the rate of sulfide oxidation. Acidified streams typically contain high metal concentrations (e.g. aluminum) and microbes in these systems may develop resistances to metal toxicity. Stream flow can affect sulfide oxidation and microbial community structure. Baseflow can influence stream chemistry from interactions with the surrounding bedrock, while stormflow affects stream chemistry and the local microbial community through dilution and addition of microbes transported by runoff. Microbial community composition is affected by …

Nitrogen Cycling During A Period Of Environmental Change, Kaizad Patel

Electronic Theses and Dissertations

Natural and anthropogenic disturbances have altered the N cycle on the regional to global scale. Although numerous studies have examined the effects of chronic atmospheric N deposition on ecosystem processes, less is known about intra-annual variability of these processes, or how these responses might be altered under conditions of changing climate. The work described in this dissertation focuses on the effects of a changing chemical and physical climate, particularly terrestrial N processes (a) during Maine’s changing winters, and (b) in response to chronic elevated N additions.

Subnivean winter soil processes were examined at the Dwight B. DeMerritt Forest (DBDF) and …

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation. This …

Bayesian Analytical Approaches For Metabolomics : A Novel Method For Molecular Structure-Informed Metabolite Interaction Modeling, A Novel Diagnostic Model For Differentiating Myocardial Infarction Type, And Approaches For Compound Identification Given Mass Spectrometry Data., Patrick J. Trainor

Electronic Theses and Dissertations

Metabolomics, the study of small molecules in biological systems, has enjoyed great success in enabling researchers to examine disease-associated metabolic dysregulation and has been utilized for the discovery biomarkers of disease and phenotypic states. In spite of recent technological advances in the analytical platforms utilized in metabolomics and the proliferation of tools for the analysis of metabolomics data, significant challenges in metabolomics data analyses remain. In this dissertation, we present three of these challenges and Bayesian methodological solutions for each. In the first part we develop a new methodology to serve a basis for making higher order inferences in metabolomics, …

Evaluation Of Drug-Loaded Gold Nanoparticle Cytotoxicity As A Function Of Tumor Tissue Heterogeneity., Hunter Allan Miller

Electronic Theses and Dissertations

The inherent heterogeneity of tumor tissue presents a major challenge to nanoparticle-medicated drug delivery. This heterogeneity spans from the molecular to the cellular (cell types) and to the tissue (vasculature, extra-cellular matrix) scales. Here we employ computational modeling to evaluate therapeutic response as a function of vascular-induced tumor tissue heterogeneity. Using data with three-layered gold nanoparticles loaded with cisplatin, nanotherapy is simulated with different levels of tissue heterogeneity, and the treatment response is measured in terms of tumor regression. The results show that tumor vascular density non-trivially influences the nanoparticle uptake and washout, and the associated tissue response. The drug …

Hydrodynamic Drivers Of Dissolved Oxygen Variability Within A Highly Developed Tidal Creek In Myrtle Beach, South Carolina, Douglas Matthew Pastore

Electronic Theses and Dissertations

Erosion and water quality degradation have been observed in Singleton Swash in Myrtle Beach, SC, and have been hypothesized to be related to migration of the beach-face channel. Dredging this channel temporarily fixes erosional threats to nearby infrastructure but the effects on water quality are not well understood. It is hypothesized that variations in dissolved oxygen (DO) concentration (used here as a proxy for water quality) within the water column are related to changes in vertical mixing and transport due to oceanic tidal forcing. This study utilizes current meters, pressure sensors, and optical DO probes to measure and study the …

Extraction And Purification Of (E)-Resveratrol From The Bark Of Maine's Native Spruces, Panduka S. Piyaratne

Electronic Theses and Dissertations

Resveratrol is a plant secondary metabolite which protects plants from pathogenic invasions and acts as a remedial agent against injury, stress, and tissue damage by UV radiation. With its characteristic stilbene structure, resveratrol adopts (E) and (Z) isomeric forms. However, the (E) isomer is the most biologically active and abundant form of resveratrol in nature.

(E)- Resveratrol confers a variety of benefits to human health and well-being. Besides its antioxidant activity, the role of (E)-resveratrol as an anti-inflammatory, anti-aging, cardioprotection, and anticancer agent has been a widely explored research interest. …

Spatio-Temporal Dynamics Of Atlantic Cod Bycatch In The Maine Lobster Fishery And Its Impacts On Stock Assessment, Robert E. Boenish

Electronic Theses and Dissertations

Of the most iconic fish species in the world, the Atlantic cod (Gadus morhua, hereafter, cod) has been a mainstay in the North Atlantic for centuries. While many global fish stocks have received increased pressure with the advent of new, more efficient fishing technology in the mid-20^th century, exceptional pressure has been placed on this prized gadoid. Bycatch, or the unintended catch of organisms, is one of the biggest global fisheries issues. Directly resulting from the failed recovery of cod in the GoM, attention has been placed as to possible sources of unaccounted catch. Among the most …

New Approaches To Mapping Forest Conditions And Landscape Change From Moderate Resolution Remote Sensing Data Across The Species-Rich And Structurally Diverse Atlantic Northern Forest Of Northeastern North America, Kasey R. Legaard

Electronic Theses and Dissertations

The sustainable management of forest landscapes requires an understanding of the functional relationships between management practices, changes in landscape conditions, and ecological response. This presents a substantial need of spatial information in support of both applied research and adaptive management. Satellite remote sensing has the potential to address much of this need, but forest conditions and patterns of change remain difficult to synthesize over large areas and long time periods. Compounding this problem is error in forest attribute maps and consequent uncertainty in subsequent analyses. The research described in this document is directed at these long-standing problems.

Chapter 1 demonstrates …

Developing A Risk Assessment Protocol To Quantify Distribution And Uptake Of Persistent Organic Pollutants In Glacial Outflows, Kimberley Rain Miner

Electronic Theses and Dissertations

Pollutants released by industrialized nations between 1960 and 2004 have been transported northward through atmospheric processes and deposited into glaciated alpine ecosystems. Many of these chemicals retain their original structure and are absorbed into the biota thousands of miles away from where they were originally utilized. With a warming climate increasing the melt of alpine glaciers, these glaciers may be introducing growing amounts of toxins into the watershed. While studies have demonstrated the existence of resident pollutants within glaciated ecosystems, no one has developed a risk assessment to identify sources and quantity of risk posed by these compounds when released …

Polyp To Population: A Tale Of Two Corals, Christopher T. Fountain

Electronic Theses and Dissertations

Deep-sea corals are of conservation concern in the North Atlantic due to prolonged disturbances associated with the exploitation of natural resources and a changing environment. As a result, the recovery rates of deep-sea coral communities are of heightened interest. These recovery rates are suggested to be on the order of decades to millennia, based on slow growth rates and longevity, of various deep-sea coral species. In 2014 and 2017 two research cruises in the Gulf of Maine, collected samples of two locally dominant species, Primnoa resedaeformis and Paramuricea placomus. These specimen collections were coupled with video surveys, conducted by …

Immersed In Fire: The Use Of Virtual Reality As An Attitude Assessor And Boundary Object In Wildland Fire Management, Casey Olechnowicz

Electronic Theses and Dissertations

Interest in using prescribed burning as a forest management tool to promote forest health and regeneration is growing in Maine. The goal for this research was to better understand the way that the public perceives prescribed burning practices in wildland-urban interfaces, with an emphasis placed on how immersive imagery, closely related to virtual reality (VR), compares to traditional communication methods. We specifically focus on the social acceptability of prescribed burning and analyze how the level of immersive imagery is related to that acceptability (Ahn, 2015; Bricken, 1990; Fogg, Cuellar, and Danielson, 2009; Smith 2015; Wiederhold, Davis, and Wiederhold, 1998). The …

Self-Organized Structures: Modeling Polistes Dominula Nest Construction With Simple Rules, Matthew Harrison

Electronic Theses and Dissertations

The self-organized nest construction behaviors of European paper wasps (Polistes dominula) show potential for adoption in artificial intelligence and robotic systems where centralized control proves challenging. However, P. dominula nest construction mechanisms are not fully understood. This research investigated how nest structures stimulate P. dominula worker action at different stages of nest construction. A novel stochastic site selection model, weighted by simple rules for cell age, height, and wall count, was implemented in a three-dimensional, step-by-step nest construction simulation. The simulation was built on top of a hexagonal coordinate system to improve precision and performance. Real and idealized …

Photonic Tools For Advanced Sensing And Imaging At The Nanoscale., Jafar Hamed Ghithan

Electronic Theses and Dissertations

This dissertation reports a novel bio-sensing strategy based on single-mode, electro-active, integrated optical waveguide (SM-EA-IOW) platforms. It also reports the development of a super-resolved far-field optical imaging tool to enable optical, electronic, and spectroelectrochemical investigations at the nanoscale. SM-EA-IOW platforms with its outstanding sensitivity for spectroelectrochemical interrogation was combined with a sandwich bioassay for the development of a novel immunosensing based strategy for label-free detection of infectious pathogens. The strategy begins with the functionalization of the electroactive waveguide surface with a capturing antibody aimed at a specific target analyte. Once the target analyte is bound to the photonic interface, it …

Reducing Tillage In Small-Scale Permanent Bed Organic Vegetable Production Systems, Jeremiah D. Vallotton

Electronic Theses and Dissertations

The response of field-grown vegetable crops to reduced tillage and mulching in permanent beds was evaluated through measuring crop yields, weed pressure, earthworm counts, and soil basal respiration. Two vegetable crops (“Bush Delicata” squash and “Farao” cabbage) were started in April and May of 2016 and 2017 respectively, transplanted in late June, and harvested on 15-Sep-2016 and 25-Aug-2017. Fruit number and weight of squash, and head weight and feeding damage of cabbage were measured. These results suggest that intensive tillage (8” rototill every year) can be successfully reduced to alternating years of shallow (2”) rototilling and a less intensive form …

Detrital Protein Contributes To Oyster Nutrition And Growth In The Damariscotta Estuary, Maine, Usa, Cheyenne M. Adams

Electronic Theses and Dissertations

Oyster aquaculture is an expanding industry that relies on identifying and utilizing natural estuarine conditions for the economically viable production of a filter-feeding crop. The eastern oyster, Crassostrea virginica, is the principal species currently cultured in Maine. In addition to preferentially consumed phytoplankton, various detrital complexes (non-algal and/or non-living organic matter) may provide some nutrition to C. virginica between times of phytoplankton abundance. Here I investigated the importance of detrital proteins in supporting the growth of oysters cultured in the upper Damariscotta Estuary. Oyster aquaculture in this area is highly successful and previous reports indicate that labile detrital protein …

Region Based Gene Expression Via Reanalysis Of Publicly Available Microarray Data Sets., Ernur Saka

Electronic Theses and Dissertations

A DNA microarray is a high-throughput technology used to identify relative gene expression. One of the most widely used platforms is the Affymetrix® GeneChip® technology which detects gene expression levels based on probe sets composed of a set of twenty-five nucleotide probes designed to hybridize with specific gene targets. Given a particular Affymetrix® GeneChip® platform, the design of the probes is fixed. However, the method of analysis is dynamic in nature due to the ability to annotate and group probes into uniquely defined groupings. This is particularly important since publicly available repositories of microarray datasets, such as ArrayExpress and NCBI’s …

Longitudinal Tracking Of Physiological State With Electromyographic Signals., Robert Warren Stallard

Electronic Theses and Dissertations

Electrophysiological measurements have been used in recent history to classify instantaneous physiological configurations, e.g., hand gestures. This work investigates the feasibility of working with changes in physiological configurations over time (i.e., longitudinally) using a variety of algorithms from the machine learning domain. We demonstrate a high degree of classification accuracy for a binary classification problem derived from electromyography measurements before and after a 35-day bedrest. The problem difficulty is increased with a more dynamic experiment testing for changes in astronaut sensorimotor performance by taking electromyography and force plate measurements before, during, and after a jump from a small platform. A …

An Examination Of Beta Diversity Indices And Their Predictors In Two Large-Scale Systems, Philip Schroeder

Electronic Theses and Dissertations

Biodiversity is what conservation biology was developed to conserve. It is the physical manifestation of life as a concept and, be it for practical or idealistic reasons, all conservationists seek to protect or, in some cases, enhance it. Because of its monolithic importance to the field, much effort has been expended trying to better measure and understand it. Recently, greater attention has been paid to the partition of diversity; the observation that the total diversity of a system (γ) can be broken down into within-site diversity (α) and between-site diversity (β). In particular, it has been noticed that the β …

Improving The Detection Limit Of Tau Aggregates For Use With Biological Samples, Emily Rickman Hager

Electronic Theses and Dissertations

The protein Tau is found in neurofibrillary tangles in Alzheimer's disease and over 20 other neurodegenerative diseases. An assay has been developed to detect minute amounts of fibrils from human brain tissue. This assay subjects brain tissue extract and recombinant Tau to several rounds of sonication and incubation. Incubation allows recombinant Tau to add itself to the ends of the existing fibrils in brain tissue extract. Sonication breaks the existing fibrils in the brain tissue extract offering more ends for Tau to add onto. Cycles of sonication and incubation have been shown to allow for amplification of Tau fibrils from …

The Investigation Of Lactoferrin Nitration: Quantification, Function, And Inhibition, Amani Yahya Alhalwani

Electronic Theses and Dissertations

Lactoferrin (LF) is an iron-binding glycoprotein of molecular mass ca. 80 kDa that is predominantly found in mammalian body fluids. Lactoferrin is a multifunctional protein that has a wide range of properties such as antibacterial, antiviral, anti-inflammatory, and anti-allergic functions. Tyrosine residues in the protein play a part in many lactoferrin functions. Protein tyrosine nitration modification represents an oxidative and nitrosative stress process which can be caused by the exposure of proteins to oxidants from air pollution or disease. Understanding the way nitrated lactoferrin interacts with the biochemical environment of the body is thus important to the broader goal of …

Learning From Disorder And Noise In Physical Biology, Taylor Emil Firman

Electronic Theses and Dissertations

Stochasticity, disorder, and noise play crucial roles in the functioning of many biological systems over many different length scales. On the molecular scale, most proteins are envisioned as pristinely folded structures, but intrinsically disordered proteins (IDPs) have no such folded state and still serve distinct purposes within the cell. At the scale of gene regulation, realistic in vivo conditions produce stochastic fluctuations in gene expression that can lead to advantageous bet-hedging strategies, but can be difficult to characterize using a deterministic framework. Even at the organismal scale, germband extension (GBE) in Drosophila melanogaster embryos systematically elongates the epithelial tissue using …

The Ecology Of Land Managers In Riparian Restoration, Lisa Buie Clark

Electronic Theses and Dissertations

While previous studies in restoration ecology have focused on the efficacy of direct management actions, the driving forces on management decisions (e.g., managers' characteristics or attitudes, environmental conditions) and the indirect impacts on restoration outcomes from management decisions (such as whether to collaborate) are quantified here for the first time. As a case study, I used data from 244 sites across the riparian Southwest US where the invasive shrubby tree Tamarix sp. was removed using various different methods. I surveyed and interviewed the 45 land managers who were responsible for the removal projects to determine their characteristics, attitudes, and …

Brønsted Acid Catalyzed Carbon-Carbon Bond Forming Reactions, Jiangyue Miao

Electronic Theses and Dissertations

The focus of this research project lies in the development of new methodology in the field of Brønsted acid catalysis enabling rapid synthesis of medicinally relevant compounds. It is foreseen that small molecule sulfonic acids evaluated in this research project will unveil new asymmetric carbon carbon bond forming reactions between substrates hitherto unexplored with Brønsted acid catalysis. It has been established that strong Brønsted acids, such as phosphoric acids, are capable of mediating highly selective transformations operating through unique mechanistic manifolds.

Specific focus for the sulfonic acid catalysts was geared towards asymmetric coupling reactions with synthetically useful precursors such as …

Evolution And Distribution Of Phenotypic Diversity In The Venom Of Mojave Rattlesnakes (Crotalus Scutulatus), Jason Strickland

Electronic Theses and Dissertations

Intraspecific phenotype diversity allows for local adaption and the ability for species to respond to changing environmental conditions, enhancing survivability. Phenotypic variation could be stochastic, genetically based, and/or the result of different environmental conditions. Mojave Rattlesnakes, Crotalus scutulatus, are known to have high intraspecific venom variation, but the geographic extent of the variation and factors influencing venom evolution are poorly understood. Three primary venom types have been described in this species based on the presence (Type A) or absence (Type B) of a neurotoxic phospholipase A2 called Mojave toxin and an inverse relationship with the presence of snake venom metalloproteinases …

Impacts Of Diverse Crop Rotations And Integrated Crop-Livestock System On Soil Quality In South Dakota, Atilla Polat

Electronic Theses and Dissertations

Crop diversification can be beneficial in improving soil quality parameters. Diverse crop rotations and integrated crop-livestock systems (ICLS), are two examples of crop diversification used in this study to assess soil quality. The objectives of this study were to: (i) assess the impacts of diverse rotations on soil quality parameters, and (ii) assess the impacts of low and high stocking density on soil quality parameters. Both of the studies were conducted separately and are presented as two different chapters. To accomplish objective (i), a long-term experiment was selected which was established near Brookings, South Dakota, USA at USDA-ARS lab in …

A Comprehensive Analysis Of Aromatic-Proton Mediated Hydrogen Bonds, Mona S. Alshamrani

Electronic Theses and Dissertations

Hydrogen bonds play critical role in folding, structure and recognition of biological macromolecules (e.g., proteins, RNA, DNA). In addition to classical hydrogen bonds (e.g., ─OH---O=, ─OH---O─, ─NH---O─ etc.), structural analysis of protein and nucleic acids, almost a decade ago, showed that hydrogen bonds (e.g., CH---O) with hydrogen atoms on aliphatic carbon atoms (hereafter, aliphatic-protons) also play very important role in the structure and function of biomolecules. Even though, protons of aromatic ring systems (hereafter, aromatic-protons) are more polar than the aliphatic-protons, systematic analysis of hydrogen bonds of aromatic-protons have not been carried out. Therefore, I carried out a systematic analysis …

Aspects Of White-Tailed Deer Ecology And Management: Effects Of Imidacloprid And An Evaluation Of Management At Great Swamp National Wildlife Refuge, Elise Hughes Berheim

Electronic Theses and Dissertations

White-tail deer (Odocoileus virginianus) are an economically and recreationally important species throughout their range, and understanding their ecology to implement beneficial management techniques is invaluable. This thesis focused on two studies 1) the effect of Imidacloprid on adult female and fawn physiology and 2) an evaluation of techniques to monitor white-tailed deer at Great Swamp National Wildlife Refuge (GSNWR). Imidacloprid, a widely-used pesticide, has been linked to lethal and sub-lethal effects in insects and small vertebrates, however, no research has been conducted on white-tailed deer. Twenty captive pregnant adult female and subsequent fawns housed at the South Dakota …