Life Sciences Commons^™

Calmodulin Like 38 Is Required For Autophagy Of Hypoxia-Induced Cytoplasmic Rna Granules In Arabidopsis Thaliana, Sterling Field

Doctoral Dissertations

In response to the energy crisis resulting from submergence stress and hypoxia, the model plant Arabidopsis thaliana limits non-essential mRNA translation, and accumulates cytosolic stress granules. Stress granules are phase-separated mRNA-protein particles that partition transcripts for various fates: storage, degradation, or return to translation after stress alleviation. Another response by the plant cell to low oxygen stress is the induction of the turnover pathway autophagy. Stress granule regulation by autophagy occurs by a ‘granulophagy’ pathway in yeast and mammalian systems through which parts or whole stress granules are degraded. Whether this occurs in plants has not been investigated.

A connection …

A Systematic And Biogeographic Study Of Trillium (Melanthiaceae), Jayne A. Lampley

Doctoral Dissertations

Trillium (Melanthiaceae, Parideae) has a disjunct distribution occurring in eastern and western North America, and eastern Asia. Past studies have examined the phylogeny and historical biogeography of Melanthiaceae and Parideae, however these studies either did not fully examine these aspects within Trillium or did not employ sufficiently broad taxonomic or character sampling to clarify relationships among taxa. The first phylogenetic analysis presented in this study provides a resolved phylogeny for Trillium s.l. and Paris s.l. by using a dataset of 70 plastid coding genes and by sampling broadly from Trillium s.s., Pseudotrillium, Trillidium, Paris s.s., Daiswa, and Kinugasa. The results …

Porous Food Microparticles As Carriers Of Lipophilic Bioactive Compounds To Improve Functionalities, Inseob Choi

Doctoral Dissertations

Lipophilic bioactive compounds (LBCs) have been gaining attention due to their antioxidation and health-promotion properties. Although many delivery systems have been studied to encapsulate LBCs to increase stability and bioaccessibility of the LBCs, most of delivery systems lack of practicality for application in the food industry due to energy-extensive encapsulation processes and high-cost carrier materials used. Additionally, while a variety of encapsulating systems exist in nanoscale to achieve efficient encapsulation of LBCs, nanoscale systems with encapsulated LBCs may be subjected to reassessment of toxicity. In this dissertation, freeze-dried potato microparticles (FDPMs) and freeze-dried mushroom microparticles (FDMMs) were studied as carrier …

The Studies Of Effects Of Vitamin A Status On Type 2 Diabetes In Zucker Diabetic Fatty Rats And Retinoic Acid On Glucose Transporter 4 Expression In L6 Cells, Tiannan Wang

Doctoral Dissertations

The epidemic of metabolic diseases such as diabetes has become a public health concern. Previous research data from our lab have shown that vitamin A (VA) status and retinoic acid (RA), a metabolite of VA, contribute to the glucose and lipid metabolism in the body and cells. As the skeletal muscle contributes to metabolic homeostasis, the effects of VA signaling system on its glucose metabolism are worth to be investigated. Here in this dissertation, the following two projects were carried out to study the VA’s role in the control of metabolism. (1) The effects of VA status on the development …

Effects Of N-3 Pufa-Derived Epoxides Combined With Seh Inhibition On Brown Adipose Tissue And Brown Adipocytes In Obesity, Yang Yang

Doctoral Dissertations

Brown adipose tissue (BAT) has become a promising target for obesity treatment and prevention. However, effective dietary factors to promote BAT mass and function have not been identified. 17,18-epoxyeicosatetraenoic acid (17,18-EEQ) and 19,20-epoxydocosapentaenoic acid (19,20-EDP) are two prominent epoxy fatty acids (EpFAs) produced from n-3 polyunsaturated fatty acid eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), respectively. EpFAs are quickly metabolized to less active diols by soluble epoxide hydrolase (sEH). In this dissertation, the effects of an sEH inhibitor (t-TUCB) (which stabilizes EpFAs) alone or combined with n-3 EpFAs on thermogenic activity in the BAT and brown adipocytes in …

Erecta Family Genes Regulate The Shoot Apical Meristem And Organ Formation, Daniel A. Degennaro

Doctoral Dissertations

Plants are sessile and must adjust their organ growth to their environments. A reservoir of stem cells in the shoot apical meristem (SAM) supplies cells for differentiation into organs. The SAM must balance organ production with stem cell maintenance. The ERECTA family (ERfs) encodes the leucine-rich repeat receptor-like kinases ERECTA (ER), ERECTA-LIKE 1 (ERL1), and ERL2. ERf signaling regulates organ initiation and stem cell maintenance. Results presented in this work include the following:

1) WUSCHEL (WUS) and CLAVATA3 (CLV3) make up a negative feedback loop to maintain SAM size. WUS and CLV3 expression localization is critical for …

Response Of Soil Viral And Microbial Functional Diversity To Long-Term Agricultural Management In Jackson, West Tennessee, Ning Duan

Doctoral Dissertations

Soil microbial communities are a critical component for ecosystem stability and function. Viruses, as an important biotic controller, have the potential to regulate the abundance and diversity of bacterial communities through infection. Soil is known to harbor abundant and diverse viral assemblages but their ecological role and influence on microbial processes has not been fully elucidated. Microbes can be influenced by viruses not only from infection but though biogeochemical feedbacks of the “microbial (bacterium–phage–DOC) loop” or “viral shunt”. However, we know relatively little about the microbial community and function under the regulation of viruses in soil and how they respond …

Geographic Patterns Of Genetic Diversity Under Climate Change: Linking Genes And Ecosystems, Shannon L. Bayliss

Doctoral Dissertations

Climate change is having profound effects on species distributions. However, much less is understood about how climate change may alter the distribution of genetic variation within species across landscapes. Maintaining genetic diversity within populations is essential for the survival of species in the face of rapid climatic changes, but importantly, losses of genetic variation will also have significant consequences on entire ecosystems. The objective of this dissertation is to understand how genetic variation in a riparian cottonwood species, Populus angustifolia, affects mass and energy exchange between the land and atmosphere across ~1700 km of latitude of the western United …

Microbial Community Dynamics Of A Microcystis Bloom, Helena Pound

Doctoral Dissertations

Harmful algal bloom events are notoriously associated with massive economic and environmental consequences, causing wildlife and human health risks. As these blooms increase in occurrence, duration, and severity around the world, it is essential to understand conditions leading to bloom formation and why they persist. Abiotic factors such as nutrients are commonly considered in bloom dynamics, but biotic interactions with co-occurring microbial species and viruses must also be taken into account. Harmful algal blooms dominated by the cyanobacterial genus Microcystis occur in bodies of water around the world and provide an ideal system in which to study top-down controls on …

Determining The Ecological And Physiological Factors Contributing To The Competitive Success Of Prochlorococcus In The Oligotrophic Ocean, Benjamin C. Calfee

Doctoral Dissertations

Prochlorococcus is a genus of extremely successful marine cyanobacteria. This success is realized through its pervasive biogeographical range and presence in almost all open ocean environments where it usually it the dominant phytoplankton. Limited capabilities of culturing and genetic manipulation of this organism have resulted in assumptions about this success overwhelmingly based on field observations. These studies have assumed adaptations for resource uptake and utilization in nutrient limited environments to cause dominance of Prochlorococcus over other photosynthetic microbes. In an attempt to definitively explain this through laboratory culture, we developed a culturing system to assay questions of nutrient limitation effects …

Perturbing Fatty Acid Metabolism In Enterococcus Faecalis Disrupts Responses To Exogenous Fatty Acids And The Antibiotic Daptomycin, Rachel D. Johnston

Doctoral Dissertations

Enterococcus faecalis is an opportunistic pathogen. In the host, it is exposed to fatty acids which impact cellular physiology and induce tolerance to the antibiotic daptomycin. To determine the requirements for induction of daptomycin tolerance, I examined the impacts of blocking de novo fatty acid synthesis or protein synthesis and removing cell wall. I observed that removal of the cell wall induced daptomycin tolerance, indicating that peptidoglycan is necessary for daptomycin to function. As specific exogenous fatty acids induce protection against daptomycin in E. faecalis, I also opted to examine whether incorporation of these free fatty acids was necessary …

High Arctic Permafrost Microbial Characterizations: Siberian And Svalbard Microbiology Of Ancient And Active Layer Permafrost, Katie Sipes

Doctoral Dissertations

Permafrost is soil that has remained frozen for at least two years. The active layer is a surface portion above the permafrost that experiences seasonal thaw and refreezing. The environmental characteristics of permafrost and active layer are different but are directly related to each other. As the climate continues to warm, the active layer will expand into the permafrost and the continuously frozen soil will be subjected to seasonal thawing. The organisms that inhabit both the active layer and the permafrost soil will respond differently to the climate based on where in the soil they are present and the soil …

Analytical Considerations And Methods For Comprehensive Analysis Of Bacterial Phospholipidomics Using Hilic-Ms/Ms, David Thomas Reeves

Doctoral Dissertations

Omics technologies have rapidly evolved over the last half century through vast improvements in efficient extraction methodologies, advances in instrumentation for data collection, and a wide assortment of informatics tools to help deconvolute sample data sets. However, there are still untapped pools of molecules that warrant further analytical attention. As the frontline defense of the cell against exterior influences, the phospholipid membrane is key in structure, defense, and signaling, but current omics studies are only just now catching up to the potential hidden within cellular lipid profiles. Examination of shifts in phospholipid speciation and character could provide researchers with a …

Functional Morphology, Biomechanics, And Evolution Of Ruminant Mammals, Abby Vander Linden

Doctoral Dissertations

Ruminant mammals, including the families Bovidae, Cervidae, Tragulidae, Moschidae, Antilocapridae, and Giraffidae, display incredible past and present diversity in morphology, ecology, and behavior. They inhabit an impressive range of environments across North and South America, Europe, Asia, and Africa, and compel the fascination of naturalists and researchers alike with their charismatic social behavior and conspicuous cranial appendages. I explore the drivers and consequences of this spectacular diversity through a comparative morphological framework, biomechanical modeling approaches, and semi-parametric and likelihood-based methods for estimating state-dependent diversification rates across the ruminant phylogeny. Together, these investigations provide evidence for adaptation via correlated evolution of …

The Effect Of Disturbance And Invasion On Fungal And Plant Communities Over An Elevational Gradient, Adam N. Trautwig

Doctoral Dissertations

High-elevation ecosystems are at risk of disruption from the future effects of climate change. Sub-alpine meadows are a source of unique plant populations, intraspecific variation of elevationally extreme populations, and vital sources of fresh water resources. We evaluated the whole fungal communities, arbuscular mycorrhizal fungal (AMF) communities, plant communities, and edaphic variables of sub-alpine meadows in undisturbed, disturbed, and disturbed with a non-native member of the Brassicaceae (Thlaspi arvense) plots. In conjunction with measuring the effects of disturbance on native communities we conducted potting experiments on a dominant grass of sub-alpine meadows (Festuca thurberi). We also …

Understanding How Camkii Holoenzyme Dynamics Facilities Activation-Triggered Subunit Exchange, Ana P. Torres-Ocampo

Doctoral Dissertations

Long-term memory and learning are still poorly understood from a molecular and cellular standpoint. Ca²⁺/calmodulin-dependent protein kinase II (CaMKII) is an oligomeric kinase that is involved in this remarkable process. However, the molecular details of its specific roles in these processes remains elusive. CaMKII activation-triggered subunit exchange presents a novel possible mechanism involved in long-term memory and learning by exchanging active subunits with other CaMKIIs. CaMKII subunit exchange also shows that exchanged CaMKIIs spread their phosphorylation state to newly synthesized CaMKIIs. This provides a long-lasting signal that might possibly be involved in long-term memory by escaping a cell’s …

Mechanistic Insights Into Diverse Protease Adaptor Functions, Nathan J. Kuhlmann

Doctoral Dissertations

Protein degradation is an essential cellular process that helps maintain proper homeostasis. The ClpXP protease broadly regulates bacterial development and quality control during the cell cycle. The range and order of substrates that ClpXP degrades during the cell cycle is dictated by 3 accessory proteins, which are known as adaptors. This thesis will elaborate on how dimerization tightly regulates the stability and activity of the adaptor protein at the center of this hierarchy, RcdA, and show how this affects normal cellular processes in Caulobacter crescentus. I will discuss the mechanism by which dimerization limits RcdA activity and how the dimerization …

Attitudes And Interactions Of Indigenous And Non-Indigenous People With Wildlife In The Northern Talamanca Mountains Of Costa Rica, Carolina Saenz-Bolaños

Doctoral Dissertations

In this study I investigated wildlife and human use of landscapes in the northern Talamanca Mountains of Costa Rica (Pacuare-Barbilla sector), including three contiguous protected areas (a national park, a forest reserve, and an indigenous territory), as well as surrounding unprotected areas. I describe and compare perceptions of wildlife by different social actors in the Pacuare-Barbilla sector, collecting information with a questionnaire as an instrument. I also inventoried and monitored the abundance and distribution of a variety of wildlife species occurring throughout the area using camera traps. The species with greater abundance or only occurrence in the national park were …

Antibiotic Sensitivity Testing Of Foodborne Bacteria Using Surface-Enhanced Raman Spectroscopy, Joshua Gukowsky

Doctoral Dissertations

The spread of antibiotic resistant bacteria around the world has become a major public health issue, and it is essential that effective detection methods exist for identifying these organisms and preventing them from spreading throughout our food systems and into the environment. The goal of this research is to develop a novel analytical procedure that is capable of easily identifying antibiotic resistance in bacterial samples, and also provides more information about the biochemical characteristics of the bacteria and their responses to antibiotic exposure. Surface-enhanced Raman Spectroscopy (SERS), an analytical technique that uses light scattering to produce a spectrum based on …

Investigating The Developmental Impacts Of 3,3’-Dichlorobiphenyl (Pcb-11) In Zebrafish (Danio Rerio), Monika A. Roy

Doctoral Dissertations

The environmental pollutant 3,3’-dichlorobiphenyl (PCB-11) is a lower-chlorinated polychlorinated biphenyl (PCB) congener present in air and water samples. Both PCB-11 and its metabolite, 4-PCB-11-Sulfate, are detected in humans, including in pregnant women. The work conducted for this dissertation takes a developmental toxicology approach and uses zebrafish (Danio rerio) to investigate PCB-11’s potential impacts to the liver and pancreas. Chapter 1 introduces PCBs and the current knowledge gaps. Chapter 2 investigates PCB-11 interactions in short-term 4-day exposures with the Aryl hydrocarbon receptor (Ahr) pathway in both 0-20 mM individual and mixture exposures with other Ahr agonists. In Chapter 3, …

Data Access, Distribution Models, And Stable Isotopes: Merging Approaches To Improve Bear Distribution Estimates And Bear Carnivory For Conservation, Nereyda Falconi

Doctoral Dissertations

My dissertation aims to contribute to the knowledge of Andean bears in Peru. The Andean bear (Tremarctos ornatus) is the sole bear species in south America. The lack of knowledge on different aspects of Andean bear ecology, biogeography, and abundance patterns hinders current conservation efforts for the species. I compiled Andean bear occurrence records in Peru with collaboration from many colleagues and created an open-access database at the GBIF data repository. Next, I modeled the distribution of Andean bear within Peru and compared estimates including and excluding unpublished records. I found that models combining published and unpublished records …

On Spatiotemporal Connectivity Dynamics: Perspectives From A Naturally Fragmented Metapopulation, Joseph Drake

Doctoral Dissertations

Connectivity has quickly become a central tenet of ecological research, frequently evoked for conservation research and management activities. However, the concept of connectivity has proliferated into many forms for many different perspectives. Generally said, population distributions, demography, landscape, and dispersal all contribute to connectivity in a meaningful way. While great progress has been made in increasing realism in connectivity, one component seemed to stand out as being underappreciated: the role of population dynamics in the application of landscape connectivity. I began to acquire an appreciation for how common modeling approaches make assumptions about these core components of connectivity. In Chapter …

Monitoring Mammals At Multiple Scales: Case Studies From Carnivore Communities, Kadambari Devarajan

Doctoral Dissertations

Carnivores are distributed widely and threatened by habitat loss, poaching, climate change, and disease. They are considered integral to ecosystem function through their direct and indirect interactions with species at different trophic levels. Given the importance of carnivores, it is of high conservation priority to understand the processes driving carnivore assemblages in different systems. It is thus essential to determine the abiotic and biotic drivers of carnivore community composition at different spatial scales and address the following questions: (i) What factors influence carnivore community composition and diversity? (ii) How do the factors influencing carnivore communities vary across spatial and temporal …

Role Of The Prefrontal Cortex In Reward Seeking Behaviors, Jessica Caballero-Feliciano

Doctoral Dissertations

Disorders associated with compulsive seeking of rewards, like binge-eating, are associated with abnormalities of the prefrontal cortex in humans, which is analogous to the prelimbic (PL) and infralimbic (IL) subregions of the medial prefrontal cortex (mPFC) in rodents. Although studies have examined the role of the mPFC in drug seeking behaviors, studies examining natural reward seeking behaviors (i.e. food and sucrose) are often unclear and contradictory. This dissertation aims to characterize the role of the PL and IL mPFC in operant sucrose seeking behaviors. We used pharmacological and chemogenetic tools to selectively inactivate the PL, IL and PL-nucleus accumbens (NAc) …

Diversity And Evolution Of Human Eccrine Sweat Gland Density, Andrew W. Best

Doctoral Dissertations

Human eccrine density is highly derived. However, little is known about contemporary variation in this trait, what shapes it, and how it influences heat dissipation. This project explores 3 questions: 1) Is variation in functional eccrine density (FED) explained by childhood climate? 2) Is this variation patterned by geographic ancestry? 3) Is variation in FED associated with differences in heat dissipation capacity? We measured FED and sweat production in 6 body areas via pharmacological stimulation and impressions of sweating skin in 72 participants. Childhood climate variables were taken from the WorldClim database and geographic ancestry was estimated with 23andMe tests. …

The Characterization Of Traits Associated With Freezing Tolerance In Perennial Ryegrass, Rachael Preston Bernstein

Doctoral Dissertations

Plants are constantly subjected to adverse environmental conditions that alter their growth and productivity, with an estimation that approximately 50% of annual average crop yields are reduced due to abiotic stresses. Freezing stress causes desiccation and ice damage in plants and is becoming more important as temperatures and unpredictable weather patterns increase. Normally, plants acclimate to cold temperatures as winter approaches and deacclimate as temperatures warm in the spring. Cold acclimation in fall is required for plants to build up their cellular defenses against desiccation and intracellular ice formation, while deacclimation is the process in which plants metabolize protective compounds …

Discovering Mechanisms Driving Adaptive Evolution In The Cross-Kingdom Fungal Pathogen Fusarium Oxysporum, Dilay Hazal Ayhan

Doctoral Dissertations

Fusarium oxysporum is a cross-kingdom pathogenic fungus that can cause vascular wilt disease in many economically important plants and local or disseminated infections in humans. Although it lacks a sexual stage in its life cycle, F. oxysporum can adapt to a wide range of hosts because of accessory chromosomes (ACs) which are enriched in host-specific genes and repeat content. This dissertation investigates the mechanisms that drive the adaptive evolution in the cross-kingdom pathogen F. oxysporum using comparative genomics and an experimental evolution approach. The first chapter compares phenotypes and genomes of a plant pathogenic isolate F. oxysporum f. sp. lycopersici …

Mechanisms Of Mitotic Checkpoint Silencing By The Disordered Kinetochore Protein Spc105, Margaux Audett

Doctoral Dissertations

The kinetochore protein Spc105R (DmSpc105R) is a large intrinsically disordered protein (IDP) that recruits spindle assembly checkpoint (SAC) proteins and is required for SAC signaling in a conserved manner. Chromosome biorientation satisfies the SAC and while it has been proposed that SAC satisfaction may require the establishment of stable kinetochore-MT (KT-MT) attachments and tension generation, the question of whether tension directly regulates SAC signaling is unresolved and controversial. Here we present data in support of Spc105R as a tension-sensing IDP that directly regulates checkpoint protein localization and signaling independent of the establishment of stable KT-MT attachments. The N-terminus of DmSpc105R …

Amyloidogenesis Of Β-2-Microglobulin Studied By Mass Spectrometry And Covalent Labeling, Blaise G. Arden

Doctoral Dissertations

Amyloid-forming proteins are implicated in a number of debilitating diseases. While many amyloid-forming proteins are well studied, the early stages of amyloidosis are still not well understood on a molecular level. Covalent labeling, combined with mass spectrometry (CL-MS), is uniquely well suited to provide molecular-level insight into the factors governing the early stages of amyloidosis. This dissertation leverages CL-MS techniques to examine the early stages of β-2-microglobulin (β2m) amyloidosis. β2m is the protein that forms amyloids in the condition known as dialysis-related amyloidosis. An automated CL-MS technique that uses dimethyl(2-hydroxy-5-nitrobenzyl) sulfonium bromide as a labeling reagent was developed and used …

Primary Kinetic Isotope Effect For Substrate Hydroxylation And Iron Binding Regulation In Factor Inhibiting Hif-1, Michael A. Mingroni

Doctoral Dissertations

The hypoxic response is a vast and complex system, delicately designed through evolution to allow our tissues to rapidly adapt and survive fluctuations in pO2. HIF1α, the master regulator of oxygen, is tightly controlled through oxygen-dependent, post-translational hydroxylation via PHD2 and FIH1.The aberrant stabilization of HIF1α is an adverse consequence of disease states, but can also occur under normoxia in the presence of ROS or in iron depletion. The extensive transcriptional network regulated by HIF1α makes the HIF pathway an attractive therapeutic target, particularly through the inhibition of the hydroxylases, PHD2 and FIH, however the active site chemistry is mechanistically …