Life Sciences Commons^™

Characterization Of Β-2-Microglobulin Pre-Amyloid Oligomers And Their Role In Amyloid Inhibition, Tyler M. Marcinko

Doctoral Dissertations

In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint, bone, and organ function, and eventually causes organ failure. To understand the early stages of the amyloid assembly process, we have employed a series of biophysical tools including chromatography, spectroscopy, and most especially, native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble pre-amyloid oligomeric species. We have also collaborated and integrated computational modeling to help better understand and rationalize the structural basis behind oligomerization. Recently, several small molecules have been identified …

The Catalytic Urease Subunit Urec Is Critical For Bifidobacterium Longum Urea Utilization, Yang Lyu

Doctoral Dissertations

In the first study, we investigated the utilization of a human milk nitrogen source, urea, by Bifidobacterium. Urea accounts for ~15% in human milk, which is an abundant non-protein nitrogen (NPN). Some bifidobacteria are found to harbor urease gene clusters that potentially enable their hydrolysis of the human milk urea. However, the underlying mechanisms are still unclear. To incisively link the urease gene cluster with bifidobacterial urea utilization, chemical mutagenesis (i.e. ethyl methanesulfonate) was performed on the urease-positive Bifidobacterium longum subsp. suis UMA399. Mutants were selected on differential media and genetic lesions were identified using whole genome sequencing. …

Cytochrome P450 Monooxygenase-Mediated Lipid Metabolism In Obesity And Colon Tumorigenesis, Weicang Wang

Doctoral Dissertations

Colon cancer is a major public health issue: it is expected to have 140,250 new cases and 50,630 deaths during 2018, making colon cancer the third most common type of cancer and the second leading cause of cancer death in the United States. Obesity is associated with enhanced colonic inflammation, which is a major risk factor of colorectal cancer. Currently, more than 35% of adults and nearly 17% of children are obese. Considering the obesity and colon cancer epidemic in the United States, there is an urgent need to identify novel therapeutic targets for obesity and colon cancer. Here, using …

Supramolecular Nanoassemblies For The Separation And Mass Spectrometric Analysis Of Peptides And Modified Proteins, Meizhe Wang

Doctoral Dissertations

Protein post-translational modifications (PTMs) play key roles in cellular physiology and disease, and identifying their locations on proteins can be beneficial for understanding more deeply protein chemistry. The methods applied for PTM analysis are most often based on mass spectrometry (MS). In the past few years, considerable progress has been made in developing MS-based proteomics technologies for global PTM analysis. Novel mass spectrometric peptide sequencing and analysis technologies allow for modification site mapping at molecular level. However, detecting PTMs on proteins and peptides by MS is challenging because of their low abundance and heterogeneity. Therefore, separation prior to MS analysis …

Metabolic Cost Of Asymmetrical Walking: Preferred Step Time Asymmetry Optimizes Metabolic Cost Of Walking, Jan Stenum

Doctoral Dissertations

Hemiparetic and amputee walking often has asymmetrical step lengths and step times, and it is metabolically costlier than symmetrical able-bodied walking. Consequently, asymmetry has been suggested to account for the greater energy expenditure, but the metabolic cost of asymmetrical walking is poorly understood. Conversely, even though symmetry is metabolically optimal in able-bodied walking, it is also possible that asymmetrical gait parameters may be selected if they are optimal under imposed constraints. First, to understand the metabolic cost of asymmetry, we performed experiment 1 in which we recruited 10 able-bodied subjects to walk with a range of different combinations of asymmetrical …

Protein Detection And Structural Characterization By Mass Spectrometry Using Supramolecular Assemblies And Small Molecules, Bo Zhao

Doctoral Dissertations

Mass spectrometry (MS) has played an increasingly prominent role in proteomics and structure biology because it shows superior capabilities in identification, quantification and structural characterization of proteins. To realize its full potential in protein analysis, significant progress has been made in developing innovative techniques and reagents that can couple to MS detection. This dissertation demonstrates the use of polymeric supramolecular assemblies for enhanced protein detection in complex biological mixtures by MS. An amphiphilic random co-polymer scaffold is developed to form functional supramolecular assemblies for protein/ peptide enrichment. The influences of charge density and functional group pK_a on host-guest interactions …

Environmental Risk Factors For Inflammatory Bowel Disease: Triclosan And Other Consumer Antimicrobials, Katherine Z. Sanidad

Doctoral Dissertations

Inflammatory bowel disease (IBD) has become a serious health problem since the incidence and prevalence of IBD has dramatically increased throughout the world. There is evidence that environmental factors are primarily responsible for the increase of IBD, therefore, it is important to identify novel environmental risk factors to reduce the risk of IBD and its associated diseases. Antimicrobials used in consumer products might serve as environmental risk factors for IBD and its associated diseases. Triclosan (TCS), triclocarban (TCC), benzalkonium chloride (BAC), benzethonium chloride (BET), and chloroxylenol (PCMX) are widely used antimicrobial ingredients in consumer products and are ubiquitous contaminants in …

Factors Influencing Spartina Alterniflora Productivity In Relationship To Estuary Inlet Opening Ellisville Marsh, Plymouth, Ma, Ellen K. Russell

Doctoral Dissertations

A scientific basis for understanding the health of salt marsh vegetation, primarily Spartina alterniflora, in apposition to dredging of the tidal inlet to Ellisville Marsh in Plymouth, Massachusetts was determined. A three-hectare S. alterniflora loss, and coincident coastal bank erosion occurred; ostensibly due to inlet blockage from sand deposition, prolonged inundation, and meandering of inlet channel into coastal bank. This warranted dredging the tidal inlet, whereby tidal flushing would restore growth or discontinue die-off, and deter coastal bank erosion. A pre- and post dredge study was conducted assessing environmental factors related to plant productivity. Following dredging, an increase in …

Changes In Soil Microbial Communities After Long-Term Warming Exposure, William G. Rodríguez-Reillo

Doctoral Dissertations

Microbial metabolism is a key controller of ecosystem processes (e.g., carbon cycling). However, we are only starting to identify the molecular mechanisms and feedback in response to long-term warming. My dissertation integrates multi-omics techniques to capture changes in soil microbial communities after long-term warming exposure. The research projects leverage three warming sites (i.e., SWaN, Barre Woods, and Prospect Hill) located in Western Massachusetts at Harvard Forest. These sites provided a unique experimental setup to better understand microbes in response to long-term temperature change. For the three research projects, we delved into the (i) microbial biodiversity across all three warming sites, …

Silver Mirror Substrate And Rolling Method For Improved Surface-Enhanced Raman Spesctroscopic Analysis In Food, Yanqi Qu

Doctoral Dissertations

Surface-enhanced Raman spectroscopy, short for SERS, is an emerging technology with great potential in food analysis due to rapid detection, high sensitivity, portable instrumentation, and simple sample preparation. However, it is always a bottleneck to obtain reproducible SERS measurements in real analytical cases due to the complicity of food systems and inhomogeneous aggregation of colloidal nanoparticles. To improve its performance for practical applications in food analysis, efforts have been made in improving the reproducibility, enhancing the selectivity and reducing the matrix interference to the analyte. Herein, a self-assembly silver nanoparticles mirror substrate was fabricated to improve the and the quantitative …

Effects Of Ivermectin And Perfluorobutanesulfonic Acid (Pfbs) On Lipid Metabolism, Weipeng Qi

Doctoral Dissertations

Accumulating evidence has shown a link between environmental contaminants and altered lipid metabolism. There is currently, however, limited knowledge regarding the causal molecular mechanisms. Therefore, we investigated the molecular mechanisms of two environmental contaminants, ivermectin and perfluorobutanesulfonic acid (PFBS), on lipid metabolism in adipocytes and hepatocytes using cell culture models. We first studied the effects of ivermectin, an anti-parasitic agent, on the adipogenesis of 3T3-L1 preadipocytes. Our current results suggest that ivermectin inhibits adipogenesis in 3T3-L1 preadipocytes and the expression of adipogenic genes where these effects were found to be partially via PPARγ-dependent, but not FXR-dependent, pathway. Additionally, ivermectin also …

Drivers And Consequences Of Carbon Use Efficiency - And Its Measurement In Soil, Grace Pold

Doctoral Dissertations

Soils serve as massive carbon sinks, but their ability to continue this ecological service is contingent on how the resident soil microbial community will respond to the ongoing climate crisis. One key dimension of the microbial response to warming is its carbon use efficiency (CUE), or the fraction of carbon taken up by an organism which is allocated to growth rather than respiration. However, the scientific community is still in the early stages of understanding the drivers, consequences - and even accurate measurements of - CUE. In this dissertation, I first quantified the variability of CUE and its responsiveness to …

Engineering Nanomaterials For Imaging And Therapy Of Bacteria And Biofilm-Associated Infections, Akash Gupta

Doctoral Dissertations

Infections caused by multidrug-resistant (MDR) bacteria pose a serious global burden of mortality, causing thousands of deaths each year. The “superbug” risk is further exacerbated by chronic infections generated from antibiotic-resistant biofilms that are highly resistant to available treatments. Synthetic macromolecules such as polymers and nanoparticles have emerged as promising antimicrobials. Moreover, ability to modulate nanomaterial interaction with bacterial cellular systems plays a pivotal role in improving the efficacy of the strategy. In the initial studies on engineering nanoparticle surface chemistry, I investigated the role played by surface ligands in determining the antimicrobial activity of the nanoparticles. In further study, …

Ecology And Conservation Of Immature Sea Turtles Across Multiple Scales, Lucas Griffin

Doctoral Dissertations

Considering many sea turtle populations are a fraction of their historic size and anthropogenic threats within the marine environment are increasing, additional data are imperative to help mitigate anthropogenic disturbances and to build resilience into sea turtle populations. In this dissertation, I present three data chapters focused on immature sea turtle ecology and conservation. These chapters evaluate sea turtle ecology and conservation at varying scales, ranging from mitigating human-wildlife interactions at the individual level, to coastal movements and space use at the ecosystem level, and to large scale climate change impacts at the population level. Ultimately, these chapters provide a …

Rna-Seq And Mechanistic Enzymology Confirm Rna Self-Templated Extension By T7 Rna Polymerase And Suggest Novel Approaches Towards Improved In Vitro Rna Synthesis, Yasaman Gholamalipour

Doctoral Dissertations

Synthetic RNA is widely used in basic science, nanotechnology and therapeutics research. The vast majority of this RNA is synthesized in vitro by T7 RNA polymerase. However, the desired RNA is generally contaminated with products longer and shorter than the DNA-encoded product. To better understand these undesired byproducts and the processes that generate them, we analyzed in vitro transcription reactions using RNA-Seq as a tool. The results unambiguously confirmed that product RNA rebinds to the polymerase and self-primes (in cis) generation of a hairpin duplex, a process that favorably competes with promoter driven synthesis under high yield reaction conditions. …

Dietary Oligosaccharides Are Differentially Metabolized By Commensal Microbiota Within In Vitro Model Systems, Ezgi Özcan

Doctoral Dissertations

Our diet contains indigestible carbohydrates that are available for microbial metabolism within the gastrointestinal tract. These carbohydrate sources are oligosaccharides found in plants and human milk. Oligosaccharide utilization phenotypes are often consistent with the ecological niche that microbes occupy (e.g. adult gut, infant gut, plants). This study represents an in-depth metabolic analysis for utilization of human milk oligosaccharides (HMOs) including lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), and cranberry oligosaccharides (i.e. xyloglucans) within in vitro modeled systems. These model systems include microplate systems for pure cultures as well as an adapted bioreactor system to mimic microbial interactions within the gut. Infant-colonizing Bifidobacterium …

Effects Of Fertilization And Drying Conditions On The Quality Of Selected Chinese Medicinal Plants, Zoe Gardner

Doctoral Dissertations

Demand for Chinese medicinal herbs in the U.S. is increasing and American acupuncturists and farmers are interested in domestic production of these plants. Little is known about the feasibility of production of these species outside of China. Four species of herbs were selected for cultivation trials. The purposes of this research were to evaluate the feasibility of cultivation of these species in the northeastern United States, to develop basic agronomic data for each species, and to determine the effects of nitrogen fertilizer on plant growth, yield, and secondary metabolites. Agastache rugosa, Schizonepeta tenuifolia, Leonurus japonicus, and Leonurus …

Function And Dissipation In Finite State Automata - From Computing To Intelligence And Back, Natesh Ganesh

Doctoral Dissertations

Society has benefited from the technological revolution and the tremendous growth in computing powered by Moore's law. However, we are fast approaching the ultimate physical limits in terms of both device sizes and the associated energy dissipation. It is important to characterize these limits in a physically grounded and implementation-agnostic manner, in order to capture the fundamental energy dissipation costs associated with performing computing operations with classical information in nano-scale quantum systems. It is also necessary to identify and understand the effect of quantum in-distinguishability, noise, and device variability on these dissipation limits. Identifying these parameters is crucial to designing …

Temporal And Spatial Management Tools For Marine Ecosystems: Case Studies From Northern Brazil And Northeastern United States, Beatriz Dos Santos Dias

Doctoral Dissertations

Anthropogenic interventions and actions upon the marine habitat pose threats to a range of species of economic and conservation concern. The dynamic nature of marine ecosystems offers a difficult challenge to incorporate spatial and temporal distributions of different species, and the interactions among species and human activities into a formal management framework. Each country has its own priorities when it comes to management of the marine resources (e.g. conservation, food security, sustainable fisheries, and optimization of revenue). Therefore, a key hurdle is to create tools adequate for use within an Ecosystem Approach to Management (EAM) and Ecosystem-based Management (EBM) framework, …

Improving Chinese Mothers’ Health Literacy: A Wechat Intervention, Qiong Chen

Doctoral Dissertations

The health literacy and eHealth literacy of women during the reproductive age is crucial, as it can affect their health and the health of their children. Promoting health literacy is essential to achieve mothers’ empowerment by improving access to and capacity of using health information effectively. However, functional, interactive, and critical health literacy and eHealth literacy have never been assessed among Chinese women. The first study during this dissertation assessed functional, interactive, and critical health literacy and eHealth literacy among 421 of Chinese mothers with children under 3 years old. The results revealed overall less than optimal level of health …

Engineering Of An Antibody-Conjugated Nanogel Platform For Targeted Drug Delivery To T Lymphocytes, Mine Canakci

Doctoral Dissertations

In an ideal chemotherapy, cytotoxic drugs travel through the bloodstream, reach cells all over the body and preferentially kill abnormal cells. Yet, the hydrophilic or lipophilic property of the small-molecule drugs affects their ability to reach cells from the bloodstream. So, only a small portion of the drug reaches to the diseased tissue. A selective cell killing approach for cancer therapy gained momentum after the realization that cancer cells carry unique set of molecular markers on their cell surface. The development of antibody drug conjugates (ADC) revolutionized the targeted approach for drug delivery. ADCs are composed of cytotoxic agents covalently …

Multi-Level Barriers To Art Adherence Among Hiv-Infected Women In Rural Eswatini: A Mixed Methods Approach, Nozipho Becker

Doctoral Dissertations

Eswatini has the highest global prevalence of HIV despite universal access to free treatment. Lack of compliance continues to be a significant challenge for HIV care and management programs throughout the country. Studies investigating barriers to antiretroviral therapy (ART) adherence, particularly in women, who are the most vulnerable to HIV infections, are limited. The disproportionate impact of HIV on women can be attributed to multiple risk factors at the individual, household, and community/structural levels. Women living in rural settings are particularly at risk as a result of socio-cultural and environmental vulnerabilities such as oppressive traditional practices, intimate partner violence, and …

Mechanisms That Limit Oxidative Phosphorylation During High-Intensity Muscle Contractions In Vivo, Miles F. Bartlett

Doctoral Dissertations

Skeletal muscle oxidative capacity plays a critical role in human health and disease. Although current models of oxidative phosphorylation sufficiently describe skeletal muscle energetics during moderate-intensity contractions, much is still unknown about the mechanisms that control and limit oxidative phosphorylation during high-intensity contractions. In particular, the oxygen cost of force generation is augmented during exercise at workloads above the lactate threshold. Presently, it is unclear whether this augmentation in muscle oxygen consumption is driven by increased rates of oxidative ATP synthesis (ATP_OX) or by decreases in the efficiency of ATP_OX due to mitochondrial uncoupling. To address this …

Game-Assisted Rehabilitation For Post-Stroke Survivors, Hee-Tae Jung

Doctoral Dissertations

Stroke is a leading cause of permanent impairments among its survivors. Although patients need to go through intensive, longitudinal rehabilitation to regain function before the stroke, patients show poor engagement and adherence to rehabilitation therapies which hampers their recovery. As a means to enhance stroke survivors' motivation, engagement, and adherence to intensive and longitudinal rehabilitation, the use of games in stroke rehabilitation has received attention from research and clinical communities. In order to realize this, it is important to take a holistic, end-to-end research approach that encompasses 1) the development of game technologies that are not only entertaining but also …

The Roles Of Morphology And Posture On Gait Mechanics, Russell T. Johnson

Doctoral Dissertations

Humans walk with an upright posture, extended limbs during stance, and a double-peaked vertical ground reaction force. Our closest living relatives, chimpanzees, sometimes walk bipedally but do so with a flexed, abducted hind limb. Previous researchers have studied humans walking with a crouched, chimpanzee-like gait pattern to try to infer how extinct human ancestors walked. However, it is not clear if the way humans perform this crouched posture gait would be similar to the way a species that is adapted to walk with a crouched posture would walk. The purpose of this dissertation was to investigate the impact of morphology …

Ecology Of The Elusive: Genome-Informed Investigation Of Soil Microbial Diversity, Lauren Alteio

Doctoral Dissertations

Soil is considered one of the most diverse ecosystems on Earth, harboring diversity of organisms across the three domains of life. It is spatially and chemically heterogeneous: properties that intertwine in a complex matrix to support organismal diversity and function across different scales. Soil microorganisms both respond to and drive changes in ecosystems through metabolic activities. A single gram of soil is teeming with millions of cells comprised of thousands of species. Much of this diversity remains uncharacterized due to technical and methodological challenges faced by soil ecologists. Due to the complex physicochemical properties of soil and cross-feeding interactions between …

Surface-Enhanced Raman Spectroscopic Imaging Of Bacteria Within Fresh Produce In Situ, Michael Hickey

Doctoral Dissertations

The growth curves for E. coli O157:H7 (#043888) are reported. We make the case that the onset of stationary growth is the optimal point at which a bacteria culture is considered suitable for quantitative Raman analyses. The optimal conditions for 3-mercaptophenylboronic acid coating of bacteria cells is also reported. Fundamental drawbacks of the status-quo approach have been elucidated and overcome, based on measurable improvements to the experimental methodology. This approach is shown to be suitable for the evaluation of bacterial rinse-washing efficacy by means of Raman light-scattering. The data were compared to label-free applications and the measurable differences between each …

Predicting Successful Chaperoning Of Fabry Disease Mutants Via Computation, Priyank Patel

Masters Theses

Fabry disease is an inherited X-linked recessive disorder caused by mutations in the galactosidase alpha (GLA) gene, leading to deficiencies in α-galactosidase A (α-GAL) enzyme production. α-GAL, a lysosomal glycosidase, catalyzes the removal of a terminal α-galactose; however, loss of α-GAL activity leads to accumulation of globotriaosylceramide (an endogenous substrate) and the eventual onset of the disease. Approved treatments for Fabry disease include enzyme replacement therapy and pharmacological chaperone therapy. In the latter treatment, 1-deoxygalactonojirimycin (DGJ), a pharmacological chaperone, is administered to Fabry disease patients, leading to increased enzymatic activity. The DGJ iminosugar acts as a competitive inhibitor …

An Examination Of Tern Diet In A Changing Gulf Of Maine, Keenan Yakola

Masters Theses

The Gulf of Maine is a dynamic ecosystem with rapidly warming sea surface temperatures (SSTs), therefore it is vital to understand how species interactions vary over time and space. In chapter two, I quantify and compare dietary differences among four tern species, across seven islands in the region, over a 32-year period. Multivariate statistical analyses were employed to discern spatial and temporal differences in foraging ecology. Findings suggest there are significant differences between species and islands; however, only three prey species comprise the majority of chick diet for all terns and islands. The reliance on only a few prey items …

Investigating The Role Of Lbh During Early Embryonic Development In Xenopus Laevis, Emma Weir

Masters Theses

LBH is a highly conserved protein whose role during vertebrate development is relatively under-studied. In collaboration with the Albertson lab, our lab has previously shown that it is necessary for cranial neural crest cell migration in the zebrafish and in Xenopus laevis. The molecular mechanisms through which it acts are not well understood.

In Xenopus, LBH is a maternally deposited protein. As such, studying its role in early development has not been feasible through the morpholino-mediated knockdown techniques that prevent translation of target genes. Recently, a technique for degrading endogenous proteins was developed, called Trim-Away. This was developed in mammalian …