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Item type: Item , The Impact of the atpB and atpE Genes on Metabolic and Viral Replication Cycles in E. coli(2025) Wolkomir, Dana; Watson, Eleanora; Fisher, Emily; Goryachev, Natalie; O'Hara, JessicaBacteriophage has shown to be a promising treatment for bacterial infections as antibiotic resistance becomes more prevalent. The ability of bacteriophage to effectively infect host cells, however, requires the use of the host cell’s metabolic pathways for energy. Previous research has found that certain genetic alterations within these host cell pathways can disrupt bacterial growth and replication efficiency. In our research, we decided to specifically investigate how bacteriophage replication is affected by deletions of the atpB and atpE genes, which code for proton transport proteins involved in E coli’s ATP biosynthesis pathway. To determine the effects of removing these genes, we first performed streak plates and growth curves with our parent and knockout strains of E. coli to evaluate their impact on bacterial growth. We then ran lysis curves with the parent, ΔatpB, and ΔatpE strains of E. coli using T2 and T4 phage. Finally, we completed a series of plaque assays with the parent and ΔatpB strains and a two time point phage titer experiment to quantify how bacteriophage replication was affected by the knockout gene. We discovered that bacteriophage replication and overall growth of the E. coli was hindered by the ΔatpB and ΔatpE knockout genes. The streak plates and growth curves showed that the knockout strain of E. coli grew significantly slower than the parent strain. The lysis curves revealed that the atpB and atpE knockout strains exhibited far less phage-driven lysis than the parent strain. Additionally, the plaque assays and two time point experiments with the knockout strains showed no plaques forming, while the parent strain had plaque formation. While the atpB gene is nonessential for E. coli growth, it greatly affects the efficiency and ability for the bacteria to grow. This information points to the fact that bacteriophage cannot be used as an effective treatment in bacterial infections that have mutations affecting the atp genes. The results from our experiment also point to the need for more research to be done on effectively knocking out the atp genes as a potential treatment for controlling bacterial infections. We concluded that effective phage replication is dependent on sufficient ATP availability in the host cells. This finding could be used to help improve the efficiency of phage therapy.Item type: Item , Colorimetric Detection of miRNA with DNA-Functionalized Gold Nanoparticles(2025) Elassal, Emily; Liao, Mina; Salib, Megan; Scott, Michael; Spirito, CatherineEarly detection of cancer is important for improving patient prognosis. miRNAs are good biomarkers for cancer screening because they are found in peripheral blood and their dysregulation is associated with cancer development. However, current miRNA detection assays, like RT-PCR, require expensive equipment. We are developing an assay that can be heated and quantified in a portable sensor. The assay involves a rolling circle transcription reaction that activates a Cas12a enzyme in the presence of a miRNA target, resulting in the cleavage of DNA-conjugated gold nanoparticles. This produces a colorimetric output that is quantified using a 3D printed portable detector. The presence of miRNA successfully initiates ligation, rolling circle transcription, and the activation of Cas12a. Successful aggregation of AuNPs occurs in the presence of the linker sequence, while absence of a linker prevents aggregation. However, the Cas12a activation assay must be combined with the AuNP complex to ensure proper aggregation when linker is intact, and lack of aggregation when Cas12a cleaves the linker.Item type: Item , Radio Occultation Web Page Development(2025-08-19) Wang, Leo; Ma, Emily Xinran; Zhou, Xinjia; Shao, Xi; Gu, Guojun; Chen, YongThis presentation was shared at the in-person conference of the 2025 CISESS Summer Internship Program held on 19 August 2025. The slides were presented by Leo Wang, an undergraduate student at the University of Maryland, and Emily Xinran Ma, a student at River Hill High School, under the mentorship of Xinjia Zhou (NOAA), Xi Shao (CISESS/UMD), and Guojun Gu (CISESS/UMD), and Yong Chen (NOAA). This presentation showcased the newly added features to the NOAA STAR Global Navigation Satellite System Radio Occultation (GNSS-RO) webpage. This included improvements to Integrated Calibration/Validation System (ICVS) page routing, multi-graph view functionality for ICVS pages, the addition of a monthly mean humidity anomaly page, and compiled product download statistics (such as user location, popular products, and downloads over time). The major feature highlighted was the creation of the Ground Tracker application, a web-based tool for plotting and interacting with large quantities of GNSS-RO profiles. The work done during this internship ensures that the Radio Occultation webpage remains a reliable source for accessing NOAA STAR GNSS-RO datasets and extends the page with new functionality to provide users with better tooling.Item type: Item , Radio Occultation Web Page Development(2025) Wang, Leo; Ma, Emily Xinran; Zhou, Xinjia; Shao, Xi; Gu, Guojun; Chen, YongGlobal Navigation Satellite System Radio Occultation (GNSS-RO) is an important remote sensing technique for weather forecasting, climate monitoring, and ionospheric research. Within this data ecosystem, the NOAA STAR GNSS-RO webpage serves a critical role as the primary provider of up-to-date GNSS-RO data for, but not limited to, the NOAA National Centers for Environmental Prediction (NCEP) Weather Prediction Center, the Joint Center for Satellite Data Assimilation (JCSDA), and the European Centre for Medium-Range Weather Forecasts (ECMWF). The work detailed in this paper thus focuses on reinforcing the continued reliability of the site while also expanding it with new functionality to better serve users. These changes include better routing and a new multi-graph view for the Integrated Calibration/Validation System (ICVS) pages, a new monthly mean humidity anomaly (MMHA) page, tooling to analyze downloaded product statistics, and the implementation of the Ground Tracker application. The primary focus of the paper, the Ground Tracker application, is a web-based tool for plotting and interacting with large quantities of GNSS-RO profiles. Users are able to visualize the position of the profiles on a 2D (equirectangular) and 3D (globe) projection, view profile metadata (such as time, quality, LEO altitude, etc.), and compare profiles based upon GNSS ID, mission name, penetration depth, SNR value, and quality. Profile data is automatically populated from the PlanetiQ, COSMIC-2, and Spire missions and the GPS, GLONASS, GALILEO, and BEIDOU GNSS systems from July 2025 onwards. This work ensures that the Radio Occultation webpage remains a useful and important component of the GNSS-RO data ecosystem.Item type: Item , Language in an ontological register: Embodied speech in the Northwest Amazon of Colombia and Brazil(2018) Chernela, JanetSpeakers of Eastern Tukanoan languages in Brazil and Colombia construe linguistic differences as indices of group identity, intrinsic to a complex ontology in which language is a consubstantial, metaphysical product, a ’substance’ in the development of the person. Through speech, speakers of the same language signal a corporality based in theories of shared ancestry and mutual belonging while speakers of different languages signal difference. For Tukanoans, then, one creates one’s self in the act of speaking. These ontological beliefs underlie speech practices, influencing language maintenance and contributing to one of the most extreme examples of multilingualism reported in the literature.