19468 research outputs found
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Hijackers: Identifying Putative Satellite Phage in Metagenomic Data
No full textSatellite phages, mobile genetic elements that parasitize other phages, harbor extensive and unique molecular machinery that could offer immense applications for research in synthetic biology. As ubiquitous as they are in the environment - 3.2 x 1026 for marine phage satellites alone - their diversity and function remain largely unexplored and understudied. This project aims to identify and assemble genome sequences of suspected satellite phages from metagenomic data. To this day, there has yet to be a comprehensive search for satellites within metagenomic data. To uncover these elements, paired-end shotgun metagenomic sequencing data were retrieved from the NCBI Sequence Read Archive. The raw sequencing reads were assembled into contiguous sequences (contigs) and then analyzed with a novel protein clustering algorithm, developed by a collaborator, to identify families of suspected satellite phages. Through this process, satellite phages were identified across five distinct satellite phage families. Their open reading frames (ORFs) were further analyzed to detect patterns in hypothetical protein similarity and genomic organization, revealing potential functional relationships and conserved elements within and across families. These findings offer new insights into the genetic landscape of satellite phages, shedding light on their roles in microbial ecosystems and their evolutionary relationships with both viruses and bacteria. Understanding these elements may also have applications in synthetic biology and virology, contributing to broader research on employing synthetic biology systems into real world environments.Computational & Applied Mathematics & StatisticsBachelors of Science (BS
Tuning into Friendships: Promoting Supportive Emotion Socialization and Friendship Quality in Early Adolescence Through a Modified TINT Program
No full textAdolescence constitutes a critical developmental window for the refinement of emotion regulation skills and the learning of adaptive emotion socialization (ES) practices. Despite extensive evidence underscoring the importance of peer relationships in adolescent socioemotional development, few interventions have directly targeted adolescents’ ES practices to foster adolescent friendships. The present study evaluated the effectiveness of a modified Tuning in to Teens (TINT) program, adapted for direct adolescent delivery, in promoting supportive ES practices and enhancing friendship quality among a community sample of 52 early adolescents (Mage = 11.76; 60% girls; 78.8% White). Youth participated in a 6-week in-person group intervention that aimed to improve emotion competencies and friend ES practices. Adolescents completed the You and Your Friends Questionnaire (Klimes-Dougan et al., 2014) and the Friendship Quality Questionnaire (Parker & Asher, 1989) at baseline (T1), post-intervention (T2), and at the one-month follow-up (T3). Repeated-measures ANOVAs revealed significant increases in adolescents’ validation of their friends’ emotions, particularly sadness and worry. Although there were no reported reductions in neglect of friends’ emotions, a significant decrease in the punishment of sadness displays was found. Additionally, adolescents reported significant improvements in overall friendship quality, particularly in companionship and intimate exchange domains. These findings provide preliminary evidence that the modified TINT intervention may be a promising approach for fostering supportive friend ES practices and strengthening friendship quality during early adolescence, with broader implications for socioemotional adjustment.PsychologyBachelors of Science (BS
Petrogenesis and Metamorphic History of Kyanite-Bearing Rocks in the Virginia Chopawamsic-Milton Terrane during Appalachian Orogenesis
No full textThe Virginia Piedmont is largely comprised of terranes accreted onto Laurentia during three Paleozoic orogenies that built the Appalachian Mountains (Bailey & Owens, 2012). Key aspects of these terranes’ metamorphic history remain poorly understood, yet they provide valuable information about the architecture of the Appalachians and the processes involved in continental growth during Appalachian orogenesis (Fig. 1). The Chopawamsic terrane, an Ordovician volcanic island-arc metamorphosed to amphibolite facies conditions, contains kyanite quartzites with an unusual assemblage of nearly entirely quartz and kyanite (Owens & Pasek, 2007; Taber 1913). Detailed work on the P-T conditions recorded by these kyanite quartzites, from terrane to outcrop scale, is lacking, due in part to the challenging mineralogy of these samples for application of conventional geothermobarometry methods. In this study I investigate kyanite-crystallization textures using cathodoluminescence (CL) imaging, and petrogenesis of kyanite quartzites by analyzing the trace element abundances in kyanite and rutile. Furthermore, I constrain pressure-temperature (P-T) conditions recorded across the terrane using Ti-in-quartz and Zr-in-rutile trace element thermobarometry to spatially resolve metamorphic conditions recorded by these rocks. Two distinct types of kyanite quartzites are found in the Chopawamsic terrane: blue-green kyanite and white to light grey-blue kyanite-bearing quartzites. CL imaging of kyanite reveals (1) core-rim zoning patterns with either patchy zoning or CL-dark cores, and CL-bright oscillatory zoning of kyanite rims, observed in both types of kyanite quartzites, and (2) kyanite with no core-rim structure. Kyanite CL-zoning is not correlated with optically identifiable features of kyanite such as kinking and twinning. It is likely that different kyanite CL domains (cores vs. rims) reflect differential availability of trace elements present during different stages of kyanite crystallization during metamorphism. Trace element analysis of kyanite grains reveals a strong correlation between CL zoning and the concentration of Cr and V, potentially recording a prograde P-T pathway. Trace element analysis of rutile and kyanite grains supports the interpretation of Owens & Dickerson (2001) that quartzites with blue-green kyanite had mafic (likely volcanic) protoliths, while those with white-grey kyanite had intermediate or felsic protoliths. Finally, Zr-in-Rt geothermometry records amphibolite facies P-T conditions, with rutile inclusions in kyanite recording lower temperatures than rutile inclusions in quartz. Thermobarometry using the crossed-isopleth method of Thomas et al. (2010) yields metamorphic conditions in the middle amphibolite facies, higher by 2-4 kbar and 0-50ºC compared to previous P-T estimated from schists adjacent to the kyanite quartzites (~6.5 kbar, ~600ºC, Cochrane, 1986). A trend of increasing equilibration temperature to the southwest is recorded. Ti-in-Qtz geothermometry records systematically lower temperatures, due to either partial equilibration of the rutile-quartz system, or depletion of Ti due to the activity of fluoride-bearing hydrothermal fluids.GeologyBachelors of Science (BS
“Levers a Dansh” [Get Up and Dance]: Monastic Dance in Sixteenth-Century England as Revealed by The Gresley Dance Manuscript
No full textMy thesis investigates dance in early modern Europe, with specific focus on a document retrospectively entitled the Gresley Dance Manuscript. This handwritten twenty-six page document was probably created between 1480-1520, antedating previously discovered written records of English dance. Little is known about the Gresley Dance Manuscript and the text has gone largely unexamined by historians. My study of the manuscript begins by considering the dances themselves through reconstruction of the dance choreographies recorded in the manuscript. Reconstruction of the movements of dance within space contributes to the understanding of early modern English dance choreographies and is essential to the analysis of the dances themselves. I argue that the dances recorded in the Gresley Dance Manuscript are an early example of English dance choreographies which share similarities with European dance forms; similarities which are not identifiable in later English dance choreographies. The Gresley dances share with European dance forms the choreographic elements associated with courtship in continental dance styles. Study of the Gresley Dance Manuscript may also further the subfield of research concerning the relationship of the Catholic Church with dance; I argue that the Gresley dances may have been recorded in the Gresley Priory, suggesting the presence of complex dance forms which feature choreographic markers of courtship in a monastic setting. Due to its rarity as a manuscript recording early English dance, the Gresley Dance Manuscript should receive further scholarly attention and should be considered a valuable primary source for both dance scholars concerned with European and English dance practices and scholars of religious history concerned with monastic performance and dance.HistoryBachelors of Arts (BA
From the Iapetus to the Atlantic: Geology, Geochronology, and Petrology of the eastern Blue Ridge cover sequence, central Virginia
No full textIn central Virginia, the eastern Blue Ridge includes a cover sequence of low-grade meta-igneous and meta-sedimentary rocks that record the opening of the Iapetus Ocean at the end of the Neoproterozoic. We combine new geological mapping, stratigraphic analysis, petrology, and geochronology to better understand the tectonic setting and temporal history of the eastern Blue Ridge. The Catoctin Formation forms a thick sequence of primarily thoellitic meta-basalt, but also includes meta-arkose and phyllite near its top. Pillow lavas are common in the upper Catoctin Formation and evidence for marine effusion of lavas. The Catoctin Formation is overlain by a thick package of phyllite, meta-sandstone, meta-graywacke, tuffaceous meta-sandstone, and marble. Collectively, we correlate these strata with the Evington Group to the south and interpret the sequence to be marine. Locally, previous workers mapped both dacitic meta-volcanic rocks and quartz diorite porphyries in this sequence. Our petrographic analysis indicates that the dacitic meta-volcanic rocks are fine-grained mica-rich meta-sandstones with quartz clasts. LA-ICP-MS U-Pb detrital zircon geochronology reveals a dominate, but broad, age population between 1.0 to 1.2 Ga with a few older grains back to 1.8 Ga. We interpret these rocks to have a Laurentian provenance. The porphyritic rocks occur in narrow NE-striking dikes that obliquely cross-cut older meta-sedimentary units. Chemically, these rocks are phonolites (~53% SiO2, ~15% alkalis) and contain broken phenocrysts of alkali feldspars in a hornblende/biotite-rich matrix. LA-ICP-MS U-Pb apatite dating of two samples of porphyritic phonolite yield late Jurassic ages (155 to 160 Ma). We infer these dikes to represent off-axis rift margin magmatism related to the nascent opening of the Atlantic Ocean.GeologyBachelors of Science (BS
Where the crawdads sing: Modeling crayfish abundance in relation to abiotic and biotic factors in eastern-deciduous forest streams
No full textCrayfish (infraorder Astacidea) are a keystone species in their freshwater habitats, influencing ecological functioning. While habitat degradation and non-native crayfish invasions become an increasing threat to crayfish populations in the southeastern United States, researchers have yet to fully understand crayfish life history, behaviors, and ecosystem roles. Effective conservation will require a better understanding of crayfish ecology, and current knowledge gaps are the primary barrier to successful efforts. In our study, we address the lack of biological information about crayfish populations by investigating the physical, spatial, and organismal drivers of their abundance. Our study focuses on eight small, forested streams, each sampled along four 5-m transects (transects), in the Virginia Coastal Plain, including sites in Williamsburg and James City County. We related crayfish abundance to predictors on the basis of Generalized Linear Mixed Modeling (GLMM). Crayfish presence was detected at 30 of the 32 transects, with an abundance ranging from 1 to 27. Crayfish abundance had a positive association with summer months, water volume, and water temperature, and a trend for a negative association with phosphate concentration, but not percent oxygen, nitrate + nitrite, and leaf litter. Our study increases the understanding of the ecology and habitat use of crayfish to better inform conservation efforts.BiologyBachelors of Science (BS
STARS: Scope Temperature Auto-Regulation System
No full textThis thesis puts forward the design for a device called STARS (Scope Temperature Auto-Regulation System), which is an advanced yet affordable solution to the problem of moisture condensation on small telescope lenses. A design is achieved which can precisely control the temperature of a resistive heating band by driving power transistors with a pulse-width modulated signal generated by a Raspberry Pi Pico microcontroller. The device is capable of switching between user-operated and automatic control modes and integrates multiple temperature and humidity sensors to provide a smart solution to a problem that is almost exclusively addressed by the current market using purely analog devices which feature poor feedback and user control.PhysicsBachelors of Science (BS
The Probability Distribution of the Kaplan-Meier Product-Limit Estimator and its Application to Bias and Interval Estimation
No full textKaplan and Meier’s 1958 paper developed a nonparametric estimator of the survivor function from a right-censored data set. We devise two algorithms for determining the support values and calculating the support size for the Kaplan–Meier Product–Limit Estimator (KMPLE). We also derived a generalized formula to calculate the associated probability mass function for all sample sizes. The probability mass function is then applied to confirm the bias in the KMPLE as well as calculating the actual coverage functions for different confidence intervals. Finally, we investigated the concept of competing risks in a right-censored data set.MathematicsBachelors of Science (BS
Synthesis of Novel Triynes and Investigation of Their Antibiotic Activity
No full textAntibiotic resistance is a threat to future human health, especially as the incidence of infections rises and biofilm formation remains a possibility in the hospital setting. Antibiotics with new methods of action are needed to combat this threat, especially regarding biofilms, which are already resistant to many current antibiotics. Polyynes (polyacetylenes) are a class of natural products that contain more than one conjugated carbon-carbon triple bond. They display a wide variety of biological effects such as antifungal, antibacterial, and anti-cancer, and they are a promising class of molecules to investigate for novel antibiotics. Previously, several diynes have been identified by the Hinkle and Young labs that have potent biological activity against E. coli, P. fluorescens, and biofilm cultures. This thesis focuses on the synthesis and biological testing of triyne libraries based on the most biologically active diynes. A series based around 2-propyn-1-ol was synthesized and showed less potent antibacterial activity than the related diynes, showing that a third conjugated triple bond does not increase biological activity. Another series based around 1-heptyn-4-ol was synthesized and showed less potent antibacterial activity than the related diynes against planktonic bacteria. Some compounds in this triyne series, however, had potent biofilm-enhancing properties. Overall, diynols are far more potent antibacterials and anti-biofilm molecules than their triyne counterparts and hold promise as future antibiotics.ChemistryBachelors of Science (BS
Metal Antipyrine Complexes for Hydrogen Evolution and Oxygen Reduction
No full textThe usage of fossil fuels for energetic purposes has resulted in global climate change and a host of environmental issues. In order to combat these issues, alternative energy sources must be explored and improved. Among the potential alternative sources, two chemical reactions are of great interest: the hydrogen evolution reaction, which splits water to form hydrogen gas that can be used for energetic and industrial purposes, and the oxygen reduction reaction, which reduces oxygen to water and is used in hydrogen fuel cells. Here we report two metal complexes with antipyrine type ligands relevant to the hydrogen evolution reaction, an iron complex which shows promise as a potential photocatalyst for hydrogen evolution and a zinc complex used to elucidate the mechanism of hydrogen evolution in this iron complex. Additionally, we report a copper antipyrine complex which acts as a catalyst for the oxygen reduction reaction. In our studies, it has shown activity for the two-electron reduction of oxygen to hydrogen peroxide, and further studies are underway to determine its activity for the four-electron reduction of oxygen to water.ChemistryBachelors of Science (BS