50107 research outputs found
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A Sediment and Blue Carbon Budget for Boston Harbor, MA
No full textCoastal beaches, wetlands, marshes, and estuaries are intertidal ecosystems which provide services to neighboring communities as carbon sinks, barriers against storms, and recreational spaces appreciated for their beauty. Recent concerns suggest that human activities are starving coastal habitats of the sediment inputs they need to build elevation against sea level rise, which increases their susceptibility to degradation and drowning. In order to assess the resilience of the estuaries in Boston, MA to the impacts of climate change, we compiled reports and geospatial calculations to create a sediment budget for Boston Harbor. We considered bluff erosion and rivers as the main imports, and dredging as the main export. Some dredged material is re-imported to the system via beach nourishment. We found that exports exceed imports by 340%, resulting in a net sediment deficit of ~5.6 x 105 Mg/yr. We also quantified blue carbon storage for salt marshes and marine muds using carbon density concentrations and areal calculations. Boston Harbor’s subtidal muds store 1.4 x 106 MgC, which is 7x the amount of carbon stored in adjacent salt marshes, and 20% of that stored in salt marshes across the entire state. The results enhance our understanding of sediment dynamics and blue carbon storage in
Boston Harbor, and the ways in which human activities are impacting the transport of material to intertidal ecosystems that need it. These findings have implications for how marine sediment is managed after dredging and assessed for carbon stocks.N
3D Shape Variation of the Cichlid Gill Arch: Genetic Architecture and Evolutionary Implications
No full textVertebrate craniofacial development is a highly dynamic process with many of the mechanisms regulating more subtle variations in morphology poorly understood. Cichlid fishes exhibit a diverse array of craniofacial morphologies well suited to study these more subtle variations. A conserved feature of vertebrate craniofacial development is the formation of embryonic pharyngeal pouches, which are the basis of serially homologous bones (i.e., the pharyngeal skeleton). Of these structures the bones that make up the gill arch skeleton, primarily the epibranchial (EB) dorsally and ceratobranchial (CB) ventrally, have received little attention in the context of development and evolution despite the multifaceted demands of the arch in respiration and feeding. Here, we sought to characterize morphological variation of the cichlid gill arch, assess the degree to which it is associated with foraging ecological, and uncover its genetic basis. Our quantification of gill arch shape was twofold with a 3D geometric morphometric analysis of CB1 and a ratio of CB1 to EB1 length as a proxy of arch curvature. These methods were employed in two main populations: a natural population consisting of 85 species of cichlid and a F5 hybrid population consisting of 402 hybrids, derived from crossing two species with divergent pharyngeal skeletal shape, Labeotropheus fuelleborni (LF) and Tropheops sp. “red cheek” (TRC). Our findings suggest that gill arch curvature exhibits market variation among species and differs between species with different foraging modes. In the hybrid population we saw a recapitulation of the variations in shape observed between species. Next, we used quantitative trait locus (QTL) analysis to identify 5 regions of the genome associated with gill arch shape. Modes of inheritance ranged from additive to dominant to overdominant, suggesting a complex genetic basis. Of those 5 regions, the QTL on chromosome 6 provided as a candidate for fine mapping to increase our genotypic-phenotypic resolution within that interval. Through fine mapping we were able to identify a total of 7 candidate genes that may be responsible for regulating CB1 shape, including fgf20a, a known bone remodeler. Overall, our findings suggest that the ecological consequences of and genetic basis for gill arch shape is worthy of further study.Master of Science (M.S.
EVALUATING THE MICROBIAL QUALITY AND SAFETY RISKS ASSOCIATED WITH USING MODIFIED WASHING MACHINES FOR DRYING FRESH PRODUCE
No full textIntroduction: This study addresses the microbial risks associated with using modified washing machines (MWM) for drying fresh produce in small-scale farming operations. The Centers for Disease Control (CDC) highlights contaminated equipment as a significant contributor to foodborne illnesses in food establishments, with smaller-scale farmers often opting for modified washing machines as a cost-effective alternative to commercial green spinners. However, the potential microbial risks of these modified units remain understudied.
Purpose: The objective of this research is twofold: first, to compare the microbial quality and safety risks of modified washing machines (Speed Queen TC5000 and Whirlpool
WTW5000DW) in small-scale operations, and second, to evaluate the cleaning and sanitizing efficiency of modified washing machines.
Methods: The study involved modifying washing machines following the Washing Machine/Greens Spinner Conversion Guide with support from the UVM Extension Ag
Engineering team. Listeria innocua was used as a microbial indicator at concentrations of 106107 CFU/ml, and experiments assessed microbial loads before and after various treatments, including postharvest washing and different cleaning and sanitizing methods.
Results and Conclusion: Results indicate microbial spread on contact surfaces and spinach within the drying units. However, when comparing both the machines there were no significant differences observed in microbial transfer from inoculated MWMs to uninoculated spinach, suggesting that contamination can occur similarly in both units. Frequent cleaning with detergent and sanitizer (peroxyacetic acid PAA and chlorine based) effectively reduced microbial contamination above 6 log CFU/ml. Additionally, shelf-life studies from days 0–10 were conducted to compare the overall quality of the spinach post spin drying against the different drying units. The Whirlpool washing machine decreased the shelf life of baby spinach by 2 days compared to the Speed Queen washing machine.
Significance: This study emphasizes the importance of regular cleaning and sanitizing practices to mitigate microbial risks in drying units, irrespective of the type. The results contribute insight for small-scale farmers seeking cost-effective alternatives while ensuring the safety of fresh produce.This work was fiscally supported by Specialty Block Crop Grant (SCBGP FY19) administered through the Massachusetts Department of Agricultural Resources, MA, the Capital Area Food
Protection Association, Washington, D.C, Kikkoman Biochemifa Company, Tokyo, Japan, the National Institute of Food and Agriculture, U.S. Department of Agriculture, the Center for
Agriculture, Food and the Environment, and the Food Science Department at University of Massachusetts Amherst, under project number MAS-00529. The contents are solely the authors' responsibility and do not necessarily represent the USDA's or NIFA's official views. This research was also done with the help of the University of Vermont Agricultural Engineering Extension team.Master of Science (M.S.)2026-02-0
A STUDY OF INTERACTIONS BETWEEN AMINO ACIDS AND PEGDA HYDROGEL
No full textHydrogels, three-dimensional crosslinked polymers formed from hydrophilic monomers, can absorb and retain up to 90% of their weight in water. Among different hydrogel chemistries, PEGylated hydrogels are widely studied as biomaterials for drug delivery and bioimplant applications due to their high biocompatibility and mechanical flexibility. Therefore, predictive modeling of the protein-hydrogel interactions is vital to understanding their behavior in biological environments and to the rational design of hydrogels with improved properties. Proteins consist of peptide chains of amino acids. Their interactions with hydrogels are determined both by the constituent amino acids and the three-dimensional complex structures proteins form in their native environments. In this work, we employed molecular dynamics simulations with atomistic forcefields to investigate the structures and interactions of PEGDA hydrogels. Three distinct hydrogel architectures were constructed with varying degrees of branching. We examined the structural and mechanical properties of the PEGDA hydrogels at different solvation levels and the interactions with water and individual amino acids of different types.Master of Science (M.S.
Abca4, mutated in Stargardt disease, is required for structural integrity of cone outer segments
No full textStargardt disease (STGD), the leading cause of inherited childhood blindness, is primarily caused by mutations in the ABCA4 gene; yet, the underlying mechanisms of photoreceptor degeneration remain elusive, partly due to limitations in existing animal disease models. To expand our understanding, we mutated the human ABCA4 paralogues abca4a and abca4b in zebrafish, which has a cone-rich retina. Our study unveiled striking dysmorphology and elongation of cone outer segments (COS) in abca4a;abca4b double mutants, alongside reduced phagocytosis by the retinal pigmented epithelium (RPE). We report that zebrafish Abca4 protein forms a distinctive stripe along the length of COS, suggesting a potential structural role. We further show that, in wild-type zebrafish, outer segments of cone cells constitutively present externalized phosphatidylserine, an apoptotic ‘eat-me’ signal, and that this pattern is disrupted in abca4a;abca4b double mutants, potentially contributing to reduced RPE phagocytic activity. More broadly, constitutive presentation of the ‘eat-me’ signal by COS − if conserved in humans – might have important implications for other retinal degenerative diseases, including age-related macular degeneration. Our zebrafish model provides novel insights into cone dysfunction and presents a promising platform for unraveling the mechanisms of STGD pathogenesis and advancing therapeutic interventions
What Drives The H I Content Of Central Galaxies—a Comparison Between Hydrodynamic Simulations And Observations Using Random Forest
No full textWe investigate the driving mechanisms for the H i gas content in star-forming central galaxies at low redshift, by examining the H i-to-stellar mass ratio (MH i/M*) in both the state-of-the-art hydrodynamic simulations, IllustrisTNG (TNG) and EAGLE, and the xGASS sample. We quantify the correlations of MH i/M* with a variety of galaxy properties using the Random Forest regression technique, and we make comparisons between the two simulations, as well as between the simulations and xGASS. Gas-phase metallicity is found to be most important in both simulations, but is ranked mildly for xGASS, suggesting that metals and gas driven by feedback effects in real galaxies is not as tightly coupled as in the simulations. Beyond that, the accretion rate of supermassive black holes is the most important feature in TNG, while specific star formation rate is the top ranked in EAGLE. This result can be understood from the fact that the H i gas is regulated mainly by thermal-mode AGN feedback in TNG and by stellar feedback in EAGLE. Although neither simulation can fully reproduce the feature importance obtained for real galaxies in the xGASS, EAGLE performs better than TNG in the sense that the observationally top-ranked property, u − r, is also highly ranked in EAGLE. This result implies that stellar feedback plays a more dominant role than AGN feedback in driving the H i gas content of low-redshift galaxies
Towards Understanding Performance Limitations of Superconducting Qubit Systems
No full textSuperconducting qubits have provided a strong path towards viable quantum computation. As qubit systems scale up in size and complexity, the performance of single qubits and multi-qubit logical operations become an important limiting factor. While a great deal of progress has been made, the existing superconducting qubit technology still faces several hurdles and limitations. There remains room to improve and understand the limitations of coherence in different types of superconducting qubits, as well as in two-qubit gate fidelities and efficient qubit readout. This thesis will explore the time-dependent fluctuations of qubit coherence times, including non-Markovian effects, and discuss the implications for future device performance. In addition, I use two-qubit randomized benchmarking to characterize a two-qubit fluxonium gate with 99.49% fidelity, which is a promising tool for a future quantum processor. Finally, I will use readout fidelity measurements to characterize a first-of-its-kind cryogenic integrated circuit capable of doing qubit readout with 99% fidelity and show that this can replace much of the standard readout architecture.Doctor of Philosophy (Ph.D.
Unveiling Contemporary Discrimination: Insights from Racially and Ethnically Minoritized Adolescents in Diverse Contexts
No full textUnderstanding the diverse stressors faced by adolescents of color is critical for addressing the unique challenges they encounter, particularly in a rapidly changing social and cultural landscape. This qualitative research investigates the variability in stressors faced by a diverse group of adolescents of color in New England. Study 1 examines the specific stressors adolescents encounter across various contexts (home, community, social media, school) and their coping strategies. Study 2 builds on this by focusing on contexts where discrimination-related stress is most pervasive (school, neighborhood, online, socio-structural) and identifying context-specific coping strategies used to counteract these stressors. In Study 1, qualitative data from adolescents (N=85) was used to identify key stressors and explore the significance of discriminatory experiences as a source of stress. Focus groups were conducted to address treatment in different contexts and general coping mechanisms. Results revealed 11 context-specific stressors and 4 universal stressors that occur across contexts. Findings also underscored the prevalence of racial/ethnic discrimination and identified primary and secondary control coping strategies. Study 2 utilized semi-structured interviews with adolescents of color (N =22) to explore the variability in discrimination experiences and coping strategies. The findings highlighted differences in discrimination based on context, perpetrators, target, forms of discrimination, and systematic inequalities. Adolescents reported interpersonal and vicarious discrimination within schools perpetrated by teachers, peers, and at the institutional level, neighborhood discrimination perpetrated by store employees, neighbors, and police, and online (i.e. social media), where it significantly impacted their socio-emotional well-being. At the socio-structural level, adolescents discussed challenges related to societal inequities, stereotypes, intersectionality, phenotypic characteristics, and living in a mono-racial society. The study found that responses to discrimination and coping are context-dependent, varying based on identity, situational factors, and individual perceptions. This research advances our understanding of how discrimination and stressors shape the developmental trajectory of adolescents of color, and how context-specific coping strategies can mitigate these impacts. It provides a comprehensive framework for future interventions to reduce the consequences of discrimination and promote protective and adaptive mechanisms among marginalized youth.Doctor of Philosophy (Ph.D.)2026-02-0
Identifying Regulatory Mechanisms That Activate the CheA Kinase for Bacterial Chemotaxis
No full textMotile bacteria have a chemotaxis system that enables them to sense their environment and direct their swimming toward favorable conditions. Chemotaxis involves a signaling process in which ligand binding to the extracellular domain of the chemoreceptor alters the activity of the histidine kinase, CheA, bound ~300 Å away to the distal cytoplasmic tip of the receptor, to initiate a phosphorylation cascade that controls flagellar rotation. The cytoplasmic domain of the receptor is thought to propagate this signal via changes in dynamics and/or stability, but it is unclear how these changes modulate the kinase activity of CheA. The major objective of this study is to address this question by employing hydrogen deuterium exchange mass spectrometry to probe the structure and dynamics of CheA within functional signaling complexes of the Escherichia coli aspartate receptor cytoplasmic fragment, CheA, and CheW. Our results reveal that stabilization of the P4 catalytic domain of CheA correlates with kinase activation. Furthermore, differences in activation of the kinase that occur during sensory adaptation depend on receptor destabilization of the P3 dimerization domain of CheA. Our HDX-MS results of CheA in complexes led us to initiate two new directions to provide additional insights into kinase regulation of CheA. Since P1-P4 interactions at a non-productive and/or productive site may be influenced by P1 dimerization, we have designed single molecule FRET (smFRET) experiments based on our HDX-MS results to inveistigate these P1 interactions. These complementary experiments have the potential to provide details into P1 conformation and positioning that remain elusive to date. Lastly, we explored whether the mechanism of CheA P4 stabilization that was identified in this study is conserved between bacterial species. HDX-MS comparison between thermophilic T. maritima and E.coli CheA in solution reveals that stabilization may not be a requirement for T.maritima CheA activation. Therefore, it is unlikely that these CheAs work similarly as generalized within the chemotaxis field. In all, these studies have yielded novel approaches for investigating protein complexes, insights into long-range membrane signal transduction, and evidence for divergent mechanisms of related enzymes.Doctor of Philosophy (Ph.D.