ScholarWorks@UMassAmherst
We are now able to accept submissions directly in ScholarWorks. For submissions that are not doctoral dissertations or masters theses, please log in with your NetID, click the + (plus) in to the top left corner, and select the Submit Research option.
Graduate students filing for February 2025 degrees: We are now accepting submissions directly to ScholarWorks. Directions for submissions can be found in this guide. Please email scholarworks@library.umass.edu if you have any questions.
Request forms are functional. If you do not receive a reply to a submitted request, please email scholarworks@library.umass.edu.
This site is still under construction, please see our ScholarWorks guide for updates.
Recent Submissions
Publication Investigating the activity of Calcium/Calmodulin protein kinase II (CaMKII) in mouse oocytes using Förster resonance energy transfer (FRET) based biosensors(2025-05)Calcium (Ca2+) is a pivotal and universal second messenger in cells. Changes in the intracellular concentration of Ca2+ are responsible for initiating, progressing, and completing various cellular processes, including fertilization. In mammals, fertilization triggers a series of Ca2+ oscillations inside the egg. The Ca2+ rise activates Ca2+/calmodulin-dependent protein kinase II (CaMKII), a serine/threonine kinase. CaMKII activity is required for cell cycle resumption or exit from the metaphase II (MII) stage of arrested eggs. In mammals, genetic experiments involving the knockout or down-regulation of CaMKII showed that female mice were sterile despite their eggs showing the ability to initiate regular Ca2+ oscillations. A series of well-structured studies unveiled that CaMKII activity corresponded with the early distinct Ca2+ increases within the first hour post-fertilization. Intriguingly, it has been revealed that CaMKII is sensitive to the frequency of Ca2+. Despite these findings, the complete profile, and alterations of CaMKII activity in oocytes remain unexplored. Many of the studies so far have been egg-lysate-based or dependent on in vitro assays. Hence, there is an evident lack of efficient tools to measure CaMKII's real-time activity. To study the CaMKII activity, we have developed a genetically encoded Förster resonance energy transfer (FRET)-based biosensors that provide a powerful approach for monitoring real-time endogenous CaMKII activity. We have characterized the responses of these CaMKII biosensors through various Ca2+ stimuli and have shown that the sensors are efficient, specific, and can monitor CaMKII activity for a long time. Additionally, we have elucidated the role of phosphatases, which are critical for regulating CaMKII activity.Publication Novel Reagents and Approaches for Portable Sample Preparation and Detection of Foodborne Pathogens(2025-05)Significant advances have been made in recent years to develop portable endpoint detection methods for foodborne virus detection, particularly in the form of isothermal nucleic acid amplification methods. However, these methods have significant drawbacks; namely, they can only analyze a very small sample volume, and are vulnerable to matrix-associated amplification inhibitors. If these isothermal amplification methods are to be effective in in-field settings, there is a need for equally portable sample preparation methods. The first step in any diagnostic assay is disinfection. Both intact microbes and residual nucleic acid from previous samples can contaminate nucleic acid-based detection assays, leading to false positive results. However, few surface disinfectants have been validated against free nucleic acid. For this reason, we tested the capacity of several commercial surface disinfectants to degrade three types of nucleic acid (viral ssRNA, eukaryotic DNA, PCR product). Only hypochlorite-based disinfectants were effective (dilute chlorine bleach and a commercial hypochlorite-based disinfectant). However, the bleach must be diluted fresh in distilled water before each use for best results, while the commercial disinfectant gave consistent results over several months without the need for extra preparation steps. Therefore, the commercial hypochlorite-based disinfectant would work better as part of a portable microbial detection kit. The next step is sample preparation, specifically target separation and concentration from the sample matrix. For this purpose, we evaluated a class of capture reagents known as magnetic ionic liquids (MILs) which would be ideal for in-field applications as their use requires minimal electrical equipment and no cold-chain storage. The MIL formulations used had already been evaluated for capture of bacterial pathogens from liquid food matrices, but had not yet been tested with non-enveloped viruses. Therefore, we tested a number of parameters impacting MIL-based capture and recovery of both an intact human norovirus surrogate (bacteriophage MS2) and purified viral ssRNA from aqueous suspension. All MIL formulations were effective for both targets, though they varied some in capture and recovery efficiency, and none appeared to significantly damage the virus capsid. We also determined that maximizing MIL dispersion is critical for ensuring optimal performance, and is determined by both the complexity of the input suspension and the relative volume of MIL used. We also showed that MILs have some capacity to concentrate the target. Most interestingly, they were able to effectively capture and recover free RNA while also appearing to give some protection from degradation in suspension. This raised the possibility that they could play a role in nucleic acid extraction. The last sample preparation step needed for nucleic acid-based detection is genomic extraction. However, though many established methods exist for viral nucleic acid extraction, few are designed with a focus toward in-field applications. Therefore, we explored the use of MILs as a binding substrate similar to the magnetic silica beads in commercial kits, which would enable target separation, concentration, and genomic extraction to occur in a single tube with minimal target loss. We found that some MIL formulations were able to recover target RNA at levels comparable to magnetic silica beads when used with commercial RNA extraction reagents. We also developed our own lysis, wash, and elution buffers that showed comparable performance to the commercial reagents when used with both MILs and magnetic silica beads. Though there is still much to explore, this work constitutes a meaningful step toward development of a complete and portable sample preparation method for foodborne virus detection. When combined with a portable endpoint detection method, this could significantly reduce barriers to in-field pathogen detection, facilitating faster outbreak tracking and more routine testing for foodborne viruses.Publication Relationship-centered engagement bridges the divide between science and management, and enhances climate adaptation(Oxford University Press, 2025)The rapid pace of climate change demands changes in management practices. Despite abundant climate adaptation research, the implementation of climate adaptation can lag in the management space. In the present article, we argue that relationship-centered engagement—establishing and maintaining relationships among researchers and natural resource managers—is critical for bridging the research–management gap. We evaluated researcher–manager partnerships within the US Northeast Climate Adaptation Science Center and identified three cultural shifts that institutions, funders, researchers, and managers could adopt to boost the odds of trans- lating findings into action: acknowledging and supporting the central role of relationships in creating and implementing actionable science, lengthening funding timelines to better support establishing and maintaining relationships, and aligning institutional rewards to support relationship building. A renewed focus on relationships can lead to more diverse and effective partnerships that bridge knowledge to practice and hasten adaptation to climate change.Publication Formate and hydrogen metabolism in the hyperthermophile Thermococcus and their application in waste-to-hydrogen conversion(2025-05)Fossil fuel-driven climate change is worsening at an alarming rate with energy demands expected to keep rising in the coming decades. Hence, novel sustainable energy technologies are needed to curb climate change and meet growing energy needs. Hydrogen (H2) energy is expected to increase and complement renewable electricity as production, storage, and transportation technologies are drastically improving, playing a critical role in decarbonizing the world. Therefore, there is growing interest in biohydrogen (bioH2) – the production of H2 using microorganisms. This dissertation explores H2 metabolism enzymes of organisms in the genus Thermococcus and studies the link between formate and H2 metabolism to optimize bioH2 production using waste as a substrate. Thermococci are hyperthermophilic archaea that are commonly found in hydrothermal vents. They are obligate heterotrophs and perform either sulfur- or proton-based respiration. A literature and genome survey of thirty Thermococcus species found that all species encoded for at least one membrane-bound hydrogenase (mbh) operon and all but one encoded for a soluble sulfhydrogenase (sh). The two operons formed the core hydrogenases of Thermococci. All surveyed species also encoded for a formate dehydrogenase catalytic subunit (fdhA) or fdhA-containing operon in the form of formate hydrogenlyase (fhl) or NAD(P)+-dependent formate dehydrogenase (nfd). Fhl-encoding Thermococci likely produce formate from H2 and CO2 in a reversible reaction when H2 concentrations become inhibitory. Formate production and utilization was only observed in species encoding a formate transporter. Formate concentration in hydrothermal vents is highly dependent on H2 concentration; vent sites with high formate concentrations also contain more H2. While there is a strong link between H2 and formate metabolism in Thermococci and in hydrothermal vents, further studies are needed to fully elucidate their physiological roles. H2 production by Thermococcus paralvinellae using brewery wastewater as a feedstock and the effect of formate on H2 production were examined. Brewery wastewater was identified as a test waste feedstock based on customer discovery through the NSF I-Corps™ program at UMass Amherst. Growth, H2 yield, and activities of hydrogenases and formate hydrogenlyase (Fhl) were determined when T. paralvinellae was grown on maltose only (model brewery wastewater), formate only, maltose plus formate, brewery wastewater only, and brewery wastewater plus formate to identify conditions for optimum H2 production. H2 yield was higher in formate-containing media compared to media without formate. However, activities of hydrogenases and formate hydrogenlyase remained largely consistent showing that formate did not affect relative enzyme abundance in the cell. Formate was identified as an additive to increase H2 production by T. paralvinellae using brewery wastewater as a feedstock. A pilot-scale 2 L bioreactor was operated in batch and chemostatic mode using brewery wastewater with and without the addition of formate. In batch mode, H2 production was higher with formate relative to without formate but dropped to levels comparable to the absence of formate by mid-logarithmic growth phase. High H2 production in the presence of formate was sustained during chemostatic growth. Proof-of concept showing that formate enhances H2 production by T. paralvinellae when grown on brewery wastewater was demonstrated. Further optimization and scale-up in needed to determine the true industrial potential of this waste-to-H2 process.
Communities in ScholarWorks
Select a community to browse its collections.