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Use Of Unoccupied Aerial Vehicle (Drones) Based Remote Sensing To Model Platform Topography And Identify Human-Made Earthen Barriers In Salt Marshes, Joshua J. Ward

Masters Theses

Elevation is a foundational driver of salt marsh morphology. Elevation governs inundation and hydrological patterns, vegetation distribution, and soil health. Anthropogenic impacts at grand scales (e.g., rising sea levels) and local scales (e.g., infrastructure) have altered the elevation of the salt marsh surface, changing the topography and morphology of these ecosystems. This study establishes and assesses means to document and analyze these impacts using Unoccupied Aerial Vehicle (UAV) based remote sensing to model platform topography. This thesis’s first and primary study presents and compares methods of producing high-resolution digital terrain models (DTMs) with UAV-based Digital Aerial Photogrammetry (DAP) and Light …

An Antiviral Response Unleashed: Deciphering The Relationship Between Shiftless And Rna Granules During Kshv Infection, David C. Hatfield

Masters Theses

Herpesviruses persist as a parasitic actor among many species. These viral agents can rapidly seize control over host cells by influencing global gene expression. Through a process known as host shutoff, herpesviruses cause a widespread degradation event of host transcripts within the cytoplasm. Specifically, Kaposi Sarcoma associated herpesvirus (KSHV) encodes for an endoribonuclease, termed SOX, that orchestrates this manipulation of gene expression. We and others have discovered certain transcripts that escape this fate; we suggest that this is an active escape, where transcripts have 3’ UTR elements that disallow SOX cleavage. One of the escapees that has been found is …

Multi-Scale Simulations Of Dynamic Protein Structures And Interactions, Yumeng Zhang

Doctoral Dissertations

Intrinsically disordered proteins (IDPs) are functional proteins that lack stable tertiary structures in the unbound state. They frequently remain dynamic even within specific complexes and assemblies. IDPs are major components of cellular regulatory networks and have been associated with cancers, diabetes, neurodegenerative diseases, and other human diseases. Computer simulations are essential for deriving a molecular description of the disordered protein ensembles and dynamic interactions for mechanistic understanding of IDPs in biology, diseases, and therapeutics. However, accurate simulation of the heterogeneous ensembles and dynamic interactions of IDPs is extremely challenging because of both the prohibitive computational cost and demanding force field …

The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson

Doctoral Dissertations

This research focuses on a specific example of replicated evolution: the grass awn. Awns are typically extensions of the lemma, but may also appear on glumes or paleas. The lemma is a leaf-like organ on the exterior of the grass flower, the glumes are a pair of bracts subtending the basic unit of grass inflorescences, the spikelet, and the palea is the floral organ opposite the lemma. Awns are often described as "hair-" or "bristle-" like, but appear in many different shapes. Many awns are “twisted & geniculate", in which the awn has two sections, a lower twisted column, and …

Investigating The Escape Mechanism Of Sre Bearing Mrna Transcripts During Viral Host Shutoff, Daniel Macveigh-Fierro

Doctoral Dissertations

During viral infection, the virus and host clash for control over gene expression in an evolutionarily arms race that has raged for thousands of years. During lytic replication, Kaposi’s sarcoma associated herpesvirus (KSHV) triggers a massive RNA decay event known as host shut off. This causes over 70% of all RNA to be degraded suppressing the host antiviral response while freeing resources for viral replication. Our lab focuses on a subset of transcripts that escape from this viral degradation event using a cis acting 3’ UTR element known as a “SOX resistant element” or SRE. Although we have identified a …

Associations Between Early Childhood Sleep, Memory Function, And Brain Development Across The Nap Transition, Sanna Lokhandwala

Doctoral Dissertations

Preschool-age children often distribute their sleep across a midday nap and overnight sleep. Skipping the nap is suggested to increase the duration and depth of deep sleep (i.e., slow wave activity; SWA). Moreover, missing the midday nap has been shown to impair learning processes. This may be because children’s brains at this point in development are immature, necessitating the intervening nap period to strengthen memories before they are forgotten. Nonetheless, at some point during the preschool years, many children begin transitioning naturally out of napping. It is unclear whether the memory benefits of overnight SWA after a skipped nap depend …

Analysis Of Micro(Nano)Plastics In Food Using Raman Microscopy, Xin Guo

Doctoral Dissertations

Microplastic pollution has emerged as a global concern in both aquatic and terrestrial environments. The presence of microplastics in the food chain poses a potential threat to human health. To accurately assess the risks associated with microplastics, it is crucial to have a reliable analytical technique capable of detecting, quantifying, and identifying microplastics of varying materials, sizes, and shapes in environmental, agricultural, and food samples. Spectroscopic techniques, specifically vibrational spectroscopy (Raman and Infrared), are extensively utilized in microplastic analysis. These techniques enable rapid and high-throughput identification, while also providing size and shape information. However, there are certain gaps in the …

High Resolution Mass Spectrometry As A Platform For The Analysis Of Polyoxometalates, Their Solution Phase Dynamics, And Their Biological Interactions., Daniel T. Favre

Doctoral Dissertations

Polyoxometalates (POMs) are a class of inorganic molecule of increasing interest to the inorganic, bioinorganic and catalytic communities among many others. While their prevalence in research has increased, tools and methodologies for the analysis of their fundamental characteristics still need further development. Decavanadate (V10) specifically has been postulated to have several unique properties that have not been confirmed independently. Mass spectrometry (MS) and its ability to determine the composition of solution phase species by both mass and charge is uniquely well suited to the analysis of POMs. In this work we utilized high-resolution mass spectrometry to characterize V10 in aqueous …

A Ground-Based L-Band Radar System For Monitoring Forest Temporal Dynamics, Xingjian Chen

Doctoral Dissertations

L-band FMCW radar is implemented for monitoring forest dynamics. It took short-term and long-term measurements with an internal calibration system that guarantees stability and precision. The radar data is compared to in-situ measurement, which infers causal relationships between radar backscatter signal and forest physiology index such as tree dielectric. This paper explains the relationship between radar signals and environmental components such as precipitation based on the measurement. The radar demonstrates some interesting observations, for example, trees' daily activity and freeze-thaw process.

The Impacts Of Environment And Host Evolutionary Relationships On Lemur Microbiota, Rachel B. Burten

Doctoral Dissertations

Recent studies have shown that the mammal microbiome is modified by environmental conditions, and that reduced microbiome functionality is associated with host health issues. Microbiome data in wild and captive primate populations can therefore be used to assess their health as they encounter a variety of environments. Comparative studies of the microbiome can also inform disease ecology, conservation, and captive management strategies tailored to different primate species. Therefore, this study examines how the hair, oral, and gut microbiota of nine wild and captive lemur species are determined by host phylogenetic relationships and host environment. I found that host species identity …

The Wild Tomato Clade Offers Insights Into Fleshy Fruit Trait Evolution At The Phenotypic And Molecular Levels, Jacob R. Barnett

Doctoral Dissertations

Biologists have long been fascinated by the diversity of fleshy fruits, yet questions remain as to how this variety has evolved. According to the dispersal syndrome hypothesis, flowering plants improved their reproductive success by producing fleshy fruits with appealing combinations of traits that attract animal dispersers. However, animal preferences may not be the only selective pressure driving fruit trait diversity—conflicting forces include damage-inflicting seed predators and pathogens, abiotic habitat conditions, or constraints stemming from non-adaptive mechanical, developmental, or phylogenetic limitations. Few studies have examined the early stages of fleshy fruit evolution across an entire clade of recently diverged plant species. …

The Impact Of A Non-Ionic Adjuvant To The Persistence Of Pesticides On Produce Surfaces, Daniel Barnes

Masters Theses

Adjuvants can enhance the performance of the pesticide active ingredients in many ways including decreasing surface tension and reducing evaporation. Understanding how adjuvants effect pesticide behavior (e.g., surface persistence) is crucial for developing effective pesticide formulations, as well as facilitating the development of effective approaches to reduce pesticide residues from the surface of fresh produce post-harvest. The objective of this study is to investigate the effect of a non-ionic surfactant, Surf-Ac 910, on the persistence of two model pesticides, thiabendazole and phosmet on apple surfaces. The result shows that the addition of Surf-Ac 910 increased both the maximum wetted area …

Influences Of High-Fat Diet And Antrodia Camphorata In Early Life On Intestinal Tumorigensis Later In Life, Ting-Chun Lin

Doctoral Dissertations

Young-onset colorectal cancer (CRC) is a growing public health concern globally due to the increasing prevalence of westernized lifestyles during childhood and adolescence. Meanwhile, there have been reports of health-promoting effects, such as anti-inflammatory and anti-cancer properties, associated with Antrodia camphorata (AC), a unique fungus native to Taiwan. This study aimed to investigate the impact of early-life high-fat diet (HF) and AC supplementation on intestinal tumorigenesis in young adulthood, using APC^1638N mice. Additionally, the study aimed to determine the role of Turicibacter, a probiotic negatively associated with diet-induced obesity, in colorectal tumorigenesis, and to explore the anti-cancer mechanism …

Detection And Control Of Environmentally Transmissible Viruses, Anand R. Soorneedi

Doctoral Dissertations

Viruses, owing to their ubiquitous nature and ability to infect almost every other species, have long been a subject of interest for scientists. Some of the virus species can be very deadly to humans and animals alike and can impose a huge economic and health burden across the world. The recent CoVID-19 pandemic underscores the importance of timely detection for developing effective intervention strategies. Unfortunately, some of the virus species that cause significant health and economic impacts do not have robust and reliable detection methods due to several reasons. In some cases, despite having gold standard methods for detection of …

Reactive Chemistries For Protein Labeling, Degradation, And Stimuli Responsive Delivery, Myrat Kurbanov

Doctoral Dissertations

Reactive chemistries for protein chemical modification play an instrumental role in chemical biology, proteomics, and therapeutics. Depending on the application, the selectivity of these modifications can range from precise modification of an amino acid sequence by genetic manipulation of protein expression machinery to a stochastic modification of lysine residues on the protein surface. Ligand-Directed (LD) chemistry is one of the few methods for targeted modification of endogenous proteins without genetic engineering. However, current LD strategies are limited by stringent amino acid selectivity. To bridge this gap, this thesis focuses on the development of highly reactive LD Triggerable Michael Acceptors (LD-TMAcs) …

Understanding And Developing Safer Sanitation Agents And Strategies In Food Production Environments, Pragathi Kamarasu

Doctoral Dissertations

Food is a primary resource for survival of human beings, and it is also one of the primary resources for spread of infectious diseases. When both these factors come together it does not only cause ill effects on our health but also causes a burden on the food and agricultural industry. Through the help of science, us researchers and scientists have always tried to reduce this burden. And I hope like a drop of water in the ocean in some way my research contributes towards this. According to WHO currently in 2023 there are about 1 in 10 people falling …

Chemical Modification And Evaluation Of Cells Towards Use As Delivery Tools, Bishnu Prasad Joshi

Doctoral Dissertations

CHEMICAL MODIFICATION AND EVALUATION OF CELLS TOWARDS USE AS DELIVERY TOOLS SEPTEMBER 2023 BISHNU PRASAD JOSHI M.S., SRI SATHYA SAI INSTITUTE OF HIGHER LEARNING Ph.D., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Michelle E. Farkas Endogenous cells are being studied for use in various applications, such as next generation therapeutics and drug delivery vehicles. This is on account of their biocompatibility, amenable distribution profiles, and in many instances, recruitment to and localization of diseased tissues. Multiple cell types have been employed, including macrophages, stem cells, red blood cells, and T cells. Most examples of cell-based delivery utilize phagocytosed entities as …

Investigating Brainstem Mechanisms Underlying Prepulse Inhibition Of Startle Impaired In Schizophrenia, Wanyun Huang

Doctoral Dissertations

Sensorimotor gating is a fundamental pre-attentive process, which can be operationally measured through prepulse inhibition (PPI) of the startle response. PPI describes the suppression of the startle response when a non-startling stimulus (“prepulse”) precedes the startling stimulus (“pulse”). As a hallmark of schizophrenia, PPI deficits are also found in other neuropsychiatric disorders and are associated with cognitive overload and attention impairments (Braff et al., 2001). However, currently-used dopaminergic antipsychotics exhibit inconsistent effects on PPI in affected individuals (Geyer et al., 2001; Frau et al., 2014; Lally et al., 2016). Therefore, it’s critical to investigate the precise cellular and synaptic mechanisms …

An Investigation Of The Role Of Amygdalar Circuits In The Production Of Social Behavior, Joseph Fd Dwyer

Doctoral Dissertations

Adaptive social behaviors allow animals to survive, thrive, and successfully reproduce. These behaviors, including mating, parenting, affiliation, and aggression, can be stereotyped in response to specific stimuli but often display sex-specific, and interoceptive-dependent variations in their execution. A conserved set of brain regions collectively known as the social behavior network (SBN) interprets sensory information about social cues and generates an appropriate behavioral response. In this dissertation I present 5 chapters. Chapter 1 introduces historical research focusing on the neural circuits that drive social behavior and the potential impact of environmental factors on the activity of these circuits. Chapter 2 describes …

A Biochemical Approach To Characterize A Divergent Trypanosoma Brucei Mitochondrial Dna Polymerase, Polib, Stephanie B. Delzell

Doctoral Dissertations

Trypanosoma brucei is a single-celled parasitic protist that causes African sleeping sickness in people and nagana in cattle in sub-Saharan Africa. T. brucei and related trypanosomatid parasites contain an unusual catenated mitochondrial genome known as kinetoplast DNA (kDNA) composed of dozens of 23 kb maxicircles and thousands of 1 kb minicircles. The kDNA structure and replication mechanism are divergent from other eukaryotes and essential for parasite survival. POLIB is one of three Family A DNA polymerases that are independently essential to maintain the kDNA network, and has been implicated in minicircle replication. However, the division of labor among the paralogs, …

Protein Trafficking In The Endoplasmic Reticulum Mediated By A Tpr-Containing Adapter Protein, Nathan P. Canniff

Doctoral Dissertations

The endoplasmic reticulum (ER) is a large, multifunctional organelle that acts as the entrance into the secretory pathway, which accounts for the folding and maturation of approximately one third of the human proteome. It is the largest organelle in most cell types and is comprised of a single lumen and a contiguous membrane. The ER is responsible for a multitude of roles including protein translocation, folding, maturation, quality control, and glycosylation to name a few. These processes are buoyed by a large collection of chaperones and cochaperones, the largest subfamily of which is characterized by the presence of tetratricopeptide repeat …

Analysis Of Antioxidant Synergism And Its Mechanisms In Different Food Systems, Ipek Bayram

Doctoral Dissertations

Lipid oxidation results in off-flavors, toxic aldehydes, and co-oxidation of proteins and color compounds. Combining antioxidants to achieve synergistic interactions has been practiced for decades to improve oxidative stability. Nevertheless, synergism mechanisms have been poorly understood and rarely studied. This dissertation examines the mechanisms of antioxidant synergism in a model system with α-tocopherol (α-TOC) and myricetin (MYR). The interactions between α-tocopherol and taxifolin (TAX) were also tested because it has structural similarities to myricetin but has a higher redox potential. The first part of this research focused on the antioxidant interactions between α-tocopherol and myricetin in stripped soybean oil-in-water emulsions …

Osmoregulation And Appetite Regulation In A Basal Vertebrate, The Sea Lamprey (Petromyzon Marinus), Jessica Norstog

Doctoral Dissertations

Lamprey (Petromyontiformes) are the oldest extant family in the vertebrate lineage, providing a unique phylogenetic position for studies on vertebrate evolution. As a basal vertebrate, sea lamprey (Petromyzon marinus) is an important species to understand evolution and comparative physiological mechanisms, including osmoregulation and appetite regulation. Sea lamprey has anadromous (native to the Atlantic Ocean) and landlocked (invasive in the Laurentian Great Lakes in North America) populations. In both populations of sea lamprey, the blind filter-feeding freshwater (FW) larvae burrow in stream sediments for until undergoing a hormonal-driven metamorphosis. During this phase, sea lamprey do not feed as major …

Production And Characterization Of Monoclonal Antibodies To Xenopus Proteins, Brett A. Horr

Masters Theses

Monoclonal antibodies are powerful and versatile tools that enable the study of proteins in diverse contexts. They are often utilized to assist with identification of subcellular localization and characterization of the function of target proteins of interest. However, because there can be considerable sequence diversity between orthologous proteins in Xenopus and mammals, antibodies produced against mouse or human proteins often do not recognize Xenopus counterparts. To address this issue, we refined existing mouse monoclonal antibody production protocols to generate antibodies against Xenopus proteins of interest. Here, we describe several approaches for the generation of useful mouse anti-Xenopus antibodies to multiple …

Evaluating The Potential Of Ozone Microbubbles For Inactivation Of Tulane Virus, A Human Norovirus Surrogate, Bozhong Guan

Masters Theses

Microbubbles are small gas-filled bubbles with diameters ranging from 50 to 1 μm, and less than 200 nm are called nanobubbles. Their small sizes and large specific surface area result in a high gas dissolution rate and long lifetime in liquid. Ozone is a strong oxidant that destroys microorganisms and only produces oxygen as the final by-product in fresh water. However, due to the poor stability of aqueous ozone, critical gas waste happens during treatments which leads to a high economic loss. Microbubbles have shown promising enhancement of ozone treatment. In previous studies, ozone microbubbles exhibited excellent efficacy in the …

Head Stabilization And Cortical Activation In Contact Sport Athletes During Walking Under Different Visual Task Constraints, Sam Zeff

Doctoral Dissertations

Contact sport participation exposes athletes to repetitive sub-concussive head impacts, which have been shown to elicit cortical neurophysiologic, cognitive, and motor performance alterations that have the potential to disrupt visual perception. Despite the growing concern regarding sub-concussive impacts, our understanding of their implications on motor performance and risk for further injury is limited. A stable head provides a consistent perceptual platform for the visual and vestibular sensory systems, but the effects of contact sport participation on head stability and visual perception remain poorly understood. The goal of this dissertation was to understand whether contact sport participation modifies athletes’ ability to …

Impact Of Fermented And Non-Fermented Plant-Based Foods Supplementation On Gut Microbiota And Metabolites In C57bl/6j Mice, Priya Darshan Gandhi

Masters Theses

Plant-based proteins have gained popularity because of their high nutritional value and more sustainable alternative to animal-based proteins. Soybean and chickpea are two widely consumed plant-based proteins, whereas tempeh is a popular plant-based fermented whole food product that is rich in protein. With the increase in the development of plant-based food products, there is little research into how plant proteins affect gut microbiota characteristics and metabolites. Therefore, there is a need to understand the underlying mechanisms surrounding the consumption of these foods. The purpose of this study was to investigate the health benefits of soybean, chickpea, and their tempeh counterparts’ …

Incorporating Biodiversity-Ecosystem Function Relationships Into Models And Conservation Planning, Sarah R. Weiskopf

Doctoral Dissertations

Unsustainable use of nature and climate change are leading to unprecedented biodiversity declines. These declines have cascading impacts on ecosystem function and ecosystem services, and ultimately on human well-being. International agreements have been adopted that aim to address both crises. The Paris Agreement, adopted in 2015, set global emission reductions targets. In 2022, most countries agreed to the Kunming-Montreal Global Biodiversity Framework (GBF). The GBF sets 23 ambitious targets for 2030 ranging from reducing threats to biodiversity, meeting people’s needs through sustainable use and benefit sharing, and solutions for implementation. Although adopting global goals and targets is an important first …

The Discovery Of A Novel Bacteria From A Large Co-Assembly Of Metagenomes, Matthew Finkelberg

Masters Theses

In the summer of 2022, a co-assembly of metagenome was created using the microbes found at Barres Woods in Harvard Forest. 14 samples were taken, and sample was split into the organic and mineral layer, which totals 28 Bulk MAGs. Within this Co-assembly, 4 different genomes were found which were designated with the phylum of FCPU426. Three of which were considered medium quality and one being assigned high quality. The novel phyla first appeared in NCBI and GTDB databases in June 2018. The name FCPU426 dates to 2010 and was named based on the 16s amplicon sequencing.

The novel phylum …

Effect Of Metabolic Rate On Mitochondrial Efficiency During Exercise In Human Skeletal Muscle In Vivo, Muhammet Enes Erol

Masters Theses

Introduction: Recent evidence in isolated mitochondria and permeabilized muscle fibers in ex vivo using simultaneous measurements of O₂ consumption and ATP production suggest that mitochondrial efficiency provides an additional mechanism to fine-tune oxidative phosphorylation rate to ATP demand in skeletal muscle. However, in the absence of a direct measurement of both VO₂ and ATP synthesis from the same region of the contracting muscle, whether this mechanism plays a role in the skeletal muscle in vivo is still unknown. Purpose: Using a noninvasive approach combining phosphorus and proton magnetic resonance spectroscopy (³¹P/¹H-MRS), the present study …