Expansion of Armatimonadetes through marine sediment sequencing reveals three classes with unique ecological roles

Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. With the advent of improved sampling techniques, recent scientific studies have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here we add to our understanding of understudied microbes by obtaining 77 metagenome-assembled genomes from the bacterial phylum Armatimonadetes in the Guaymas Basin, Gulf of California, and the Bohai Sea, coastal China. Seven of these MAGs are not classified at the class level. Thus, we propose to name these organisms Zipacnadia. Searches of public databases revealed that the 77 Armatimonadetes described in this study (including Zipacnadia) are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of the GB metagenomic raw reads). The Armatimonadetes described here also have unique metabolic capabilities for this phylum. They have pathways to reduce CO₂ to acetate via the Wood-Ljungdahl pathway (WLP) and generate energy through the oxidative branch of the Embden-Meyerhof-Parnas pathway using CO2 as an electron sink, maintaining the redox balance via WLP. Some of these organisms may also have an autotrophic lifestyle not previously identified in Armatimonadetes. Furthermore, these Armatimonadetes may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. The description of the Armatimonadetes identified in this study enhances our understanding of the diversity and metabolic potential of anoxic habitats worldwide.Marine Scienc

Microdroplet assay development for metabolic engineering and synthetic biology applications

Sustainable, efficient production of societally relevant chemicals in microorganisms is the epicenter of the field of metabolic engineering. Modern developments in DNA synthesis and sequencing have enabled high-information gene perturbation and protein engineering libraries that require reliable, reproducible, high throughput screening assays. Detailed herein are examples of utilizing growth-based assays and microfluidic screening to extract pertinent information from different gene perturbation libraries, microbial consortia, and engineered proteins. The first study details an approach to regulate gene expression in S. cerevisiae through utilization of a single-guide RNA library paired with dCas9 fused to either Mxi1 or VPR. Through these fusions and targets of guide RNAs, genes are either up or down regulated at increasing degrees. Using this library it was possible to identify target genes for moderate up and down regulation to improve growth on alternative carbon sources, namely glycerol and galactose. Final analysis of enriched guides via next generation sequencing identified moderate down regulation of essential genes, novel perturbations that would not have been isolated in traditional gene knock-out approaches. The studies detailed in chapters 3 and 4 delve into technical applications of microfluidics to screen for improved small molecule production. In chapter 2, the library detailed above is utilized to screen for gene targets that improve small molecule production in S. cerevisiae. This study also results in the development of a pico-injection microdroplet approach that utilizes cell-based biosensors to transduce small molecule production into a fluorescent signal. The study in chapter three characterizes this application further, ultimately leading identifying gene perturbations that improve early productivity or higher overall production, based on the time at which they were screened. In the fourth study, a previously developed CuAAC probe for extracellular electron transfer (EET) is ported into droplets to analyze an environmental microbial consortium. This study centers on the development of an oxygen-limited platform for anaerobic microbe cultivation in microdroplets, ultimately enriching environmental microorganisms previously uncharacterized for EET. This work expands the range of microorganisms compatible with this microdroplet system. In the final study, the microorganism array is expanded further through the development of a cytotoxicity assay for Sf9 insect cells is developed for use in microdroplets. This work lays a foundation for future applications to identify novel insecticidal toxins from engineered protein libraries. Collectively, these studies establish generalizable assays for high throughput screening of a wide array of organisms related to the field of synthetic biology.Biochemistr

Factors associated with food delivery app use in young adults

Food delivery apps are highly popular among young adults and are often used to purchase calorie-dense foods, which are associated with a variety of health issues such as increased risk for obesity. Limited research exists on the use of food delivery apps and the research that has been conducted, focused on adults, suggests that food delivery app use differs by sociodemographic factors. Thus, the purpose of this study is 1) to describe food delivery app use among young adults, and 2) to examine the association between young adult food delivery app use and factors including age, race, ethnicity, sex, SES, food insecurity, living arrangement, financial responsibility, and full-time student status. Data are from the Promoting Young Adult Health Survey, a cross-sectional online survey with 1,038 young adults online from the Qualtrics panel January-February 2022. Poisson regression was used to examine the relationship between food delivery app use and the sociodemographic variables. Our results suggest that participants who reported being non-Hispanic Black and Hispanic had greater food delivery app use frequency as compared to participants who reported being white. Having higher perceived subjective social status, being food insecure, being financially responsible, and being a full-time student were all significantly associated with greater food delivery app use frequency. Living with someone else was significantly associated with lower food delivery app use frequency. Age, sex, and ‘Other’ Race/ethnicity were not associated with food delivery app use frequency. Overall, young adults use food delivery apps approximately twice a week with vulnerable groups such as Black and Hispanic young adults and young adults reporting food insecurity having greater frequency of use. This study provides a first step in understanding the characteristics of young adults who use food delivery apps more frequently. Given that this new technology can both increase access to unhealthy food options as well as healthy food options, future research is needed to better understand the types of food purchased through food delivery apps and the differences by the sociodemographic factors explored in this study.Kinesiology and Health Educatio

Open Source GIS: From QGIS to Python

This workshop will guide attendees through open source GIS workflows using QGIS's approachable user interface and demonstrate how to replicate those processes programmatically in Python for enhanced reproducibility and efficiency. GIS beginners can expect a well rounded introduction to geospatial data and software, while seasoned users will benefit from techniques for automating their workflows with Python.UT Librarie

Examining physical activity among US college students following COVID-19 outbreaks and lockdowns : the role of race/ethnicity and acculturation

Objective: This study examined physical activity among US college students in the context following COVID-19 outbreaks and lockdowns, with a focus on racial/ethnic and cultural determinants. Sample: This study used cross-sectional data of the COVID-19 University Research on Education and Sustainability (CURES) project. Participants were college students from 7 public universities in the US (N = 1210; 75% female; 33.5% White, 9.1% Black, 47.6% Hispanic, and 7.1% Asian; Mage = 21.06; 85.6% born in the US, 51.6% had mother born in the US, and 49% had father born in the US). Method: The International Physical Activity Questionnaire - short form (IPAQ-SF) was used to assess physical activity and the Vancouver Index of Acculturation (VIA) – the American version was used to assess levels of heritage and US acculturation. Results: White students reported statistically significant higher physical activity than Hispanic (p < .05, Cohen’s d = .19) and Asian (p < .05, Cohen’s d = .36). In sedentary level, White students reported statistically significant lower levels than Asian (p < .05, Cohen’s d = -.45). Asian reported lowest physical activity, highest sedentary level, and highest prevalence of not meeting physical activity recommendation. Small negative correlation was found between heritage cultural level and total weekly physical activity among Hispanic students (r = - .09, p < .05). Conclusion: Race/ethnicity and cultural perception and practices could play a role in determine physical activity and sedentary behaviors among college students. The study calls for more qualitative research, and racial/ethnic and cultural-specific interventions to improve physical activity among Hispanic/Latin and Asian student populations.Kinesiology and Health Educatio

Controls on carbonate precipitation in subsurface environments using microfluidics

Research on carbonate resevior is critical for advancing both enhanced oil recovery (EOR) and geologic gas storage, offering significant benefits in energy security and environmental sustainability. Carbonate formations, such as limestone and dolomite, make up over half of the world's petroleum reserves. These formations, hoIver, present challenges due to their complex and heterogeneous structures, which include variations in porosity and permeability. Advances in EOR techniques, such as CO₂ injection and low-salinity water flooding, help to overcome these challenges through enhancing the mobility of oil within these rock structures. Moreover, carbonate reservoirs hold enormous capacity for CO₂ storage, but are encumbered by their reactivity with CO₂ which raises questions on the long-term security of injected CO₂. Research in this field allows for the development of optimized EOR strategies that improve oil extraction in challenging carbonate settings and enables safe, long-term CO₂ storage, contributing to a balanced pathway toward a low-carbon future. First, I use a micromodel with pore geometry and geochemistry representative of geologic media to promote deep microbially-induced carbonate precipitation (MICP) penetration into subsurface formations as a natural approach to secure the geologic storage of gases (e.g., CO₂, H₂, CH₄). Cracks in embrittled Illbore cement, for example, provide a pathway for atmospheric gas leakage, while permeability heterogeneities in the storage reservoir leads to fingering effects that diminish the storage capacity. The design of MICP processes, hoIver, remains a challenge due to limited understanding of the coupled nonlinear reaction kinetics and multiphase transport involved. Specifically, previous attempts at MICP through porous media have been encumbered by carbonate precipitation localized to the first 1-3 cm of the bulk injection surface. I use a micromodel to image direct pore- and pore-ensemble-level mineral, fluid, and microbial distributions. An approach to adsorb microbes uniformly across the micromodel, rather than local accumulation near the inlet, is developed that enables deep MICP penetration into the porous medium. A sensitivity analysis was performed to investigate the impact of injection conditions (e.g., rates, concentrations) required to maximize CaCO₃ precipitation away from the injection site. With multiple cycles of MICP, a 78% reduction in permeability was achieved with ~ 8% carbonate pore volume occupation. Second, I present a novel improved oil recovery approach whereby MICP reduces the local permeability of water-saturated preferential flow paths to improve the overall sIep of the reservoir. Mobility contrasts betIen oil and water, along with permeability heterogeneity, lead to fingering instabilities that impede the recovery of hydrocarbons from the subsurface. With MICP, local pore geometry in preferential pathways are altered to divert successive injection fluids to oil-saturated pores. I demonstrate the feasibility of the approach using a silicon microfluidic device with etched geometries representative of real rock pores, where a ~ 5 % reduction in the porosity of preferential flow paths increased overall oil recovery by ~ 28 % original oil in place (OOIP). I performed a sensitivity analysis on the injection conditions required to maximize oil recovery and bacterial growth. Overall, I show that calcium carbonate grains grown using MICP can provide a secure and stable method to control fluid flow in situ and recover additional hydrocarbons to provide an avenue for cost-effective and environmentally-benign hydrocarbon extraction. Third, I functionalized a micromodel with dolomite to study the confinement integrity of formation during carbon dioxide storage and sequestration. Calcite was selectively precipitated along the edges of silicon grains, and dolomitized hydrothermally using a magnesium-rich fluid. Mineral dissolution and re-precipitation Ire observed through the microfluidic platform, and mineral composition evolution was characterized by using X-ray crystallography (XRD) and energy-dispersive spectroscopy (EDS). After dolomitization, the carbonate volume decreased by 14.5%, sligh higher than the 11%-14% reduction reported in previous studies. Insights into the dissolution and precipitation of the dolomite rind enhance our understanding of the diagenetic history of carbonate reservoirs, influencing interpretations of hydrocarbon potential and informing reservoir management strategies.Petroleum and Geosystems Engineerin

No-reference image and video quality assessment for user-generated media

User-generated content (UGC) constitutes a significant portion of global internet traffic, with billions of videos and images shared daily on social media and streaming platforms. Despite its ubiquity, UGC often suffers from diverse and complex perceptual quality issues due to distortions introduced during capture, processing, and sharing. Addressing these challenges is critical for improving user experience, enabling better content optimization, and providing tools for inclusive content creation. This dissertation focuses on three critical problems in no-reference (NR) perceptual quality assessment for UGC: video quality prediction, image quality enhancement for visually impaired users, and the quality assessment of text embedded in multimedia content. First, we tackle the challenging and unsolved problem of NR video quality assessment (VQA) for UGC. Traditional VQA models struggle to generalize to the diverse and “in-the-wild” nature of UGC. To address this gap, we developed the largest subjective video quality dataset to date, containing 38,811 real-world distorted videos, 116,433 space-time localized video patches, and 5.5 million human perceptual quality annotations. Using this dataset, we proposed two novel NR-VQA models: (a) Pathc-VQ (PVQ), a region-based architecture that captures local-to-global quality relationships, achieving state-of-the-art performance on three benchmark UGC datasets, and (b) PVQ Mapper, the first space-time video quality mapping tool that visualizes and localizes perceptual distortions. These models advance the state of the art in VQA, offering robust predictions and actionable insights into the quality of real-world UGC videos. Second, we address the unique challenges faced by visually impaired users in capturing high-quality images. This demographic often produces content exhibiting severe distortions, including blur, noise, and poor exposure, which pose significant barriers to quality assessment and actionable feedback. To address these issues, we created the LIVE-Meta VI-UGC Database, the largest dataset of its kind, comprising 40,000 distorted images, 40,000 patches, and 2.7 million human perceptual quality and distortion labels. Leveraging this dataset, we developed a blind image quality predictor that models local-to-global spatial relationships, achieving state-of-the-art prediction accuracy on VI-UGC data. Furthermore, we designed a prototype feedback system based on a multi-task learning framework, empowering visually impaired users with actionable insights to improve their photography and confidently share higher-quality content on social media. Third, we investigate the underexplored problem of assessing the quality and legibility of text embedded in UGC, particularly in short-form videos. The quality of embedded text significantly affects user comprehension and the overall perception of multimedia content, as well as applications like visual search and recognition. To advance this domain, we created two novel datasets: the LIVE-COCO Text Legibility Database, featuring 74,440 text patches with subjective legibility annotations, and the LIVE-YouTube Text-in-Video Quality Database, containing approximately 19,000 subjective quality ratings on 405 videos and 641 text patches. Using these datasets, we developed models capable of predicting both text quality and legibility. We further introduced a multi-task model that simultaneously predicts overall video quality and local text quality, addressing the interplay between text legibility and multimedia quality in UGC. Overall, this dissertation presents a comprehensive approach to improving the perceptual quality of UGC through the development of advanced datasets, innovative quality prediction models, and user-centric tools. By addressing the diverse challenges of video, image, and text quality in UGC, this work provides solutions that enhance user experience, optimize content, and support accessibility. The outcomes of this dissertation are expected to benefit applications such as quality monitoring, content creation tools, accessibility enhancements, and user guidance, ultimately improving the global experience of social media and streaming platforms.Electrical and Computer Engineerin

Beyond the personal income tax : direct taxation without representation in colonial Africa

Recent work has emphasized the rise of direct taxation after World War I as a phenomenon of Western Europe and the United States, mostly due to the establishment of the personal income tax. However, other forms of direct taxation have been more prevalent throughout history. I analyze the example of sub-Saharan African colonies during the early twentieth century. Colonial rule in Africa reached its peak in the interwar period, consolidating dramatically after World War I. I explain this consolidation through the rise of direct taxes. I develop a theory on the shift to direct taxation, mostly in the form of head and hut taxes, as a result of increasing revenue pressures due to World War I. The theory is informed by qualitative historical evidence from British and Portuguese colonies documenting the choice by colonial administrators to increase and establish new direct taxes. A synthetic control method expands the analysis. I propose that in the colonial context, a shift to direct taxation need not be redistributive at all.Governmen

On the Doppelperfekt in German dialects

This paper examines the periphrastic tense formation known as Doppelperfekt (DPF), used in various non-standard German dialects. The DPF, also referred to as doppelte Perfektformen, gesteigertes Perfekt, Perfekt II, and Ultraperfekt, involves adding an additional Partizip II of the auxiliary verb to a Perfekt construction. Examples include "Ich habe dem Kunden den Brief geschickt gehabt!" and "Er ist mit dem Zug angekommen gewesen." Historically marginalized in grammar books, the DPF's usage has often been overlooked. This study emphasizes the importance of non-standard tenses like the DPF for understanding language history and usage evolution. It explores the DPF's attributes, usage, history, and theorized origins, aiming to position the DPF within the German tense system both historically and in contemporary language.Germanic Studie

Does Cobalt Hexamine induce DNA-DNA Attraction? Investigations to Understand Nucleic Acid Compaction in the Cell

Nucleic acid compaction is a fundamental process in all living systems, exemplified by the tight packaging of DNA into chromatin in eukaryotic nuclei, as well as nucleic acid compaction in the viral capsid. The strong negative charge on the DNA backbone must be mitigated by positively charged species, including polyvalent ions and proteins, to achieve the necessary close packing. To dissect the electrostatic interactions driving DNA compaction, the xHEED (X-linking of Helices to measure Electrostatic Effects at Distance) method, previously developed in the Russell Lab, was used to measure distant-dependent interhelical encounter frequencies, and the atomic forces that mitigate these mechanisms as previous poisson-boltzmann models did a poor job of it. Rate constants were measured that reflect the equilibrium constant for transient DNA-DNA encounters under varying ionic conditions. Using the xHEED method, DNA-DNA crosslinking interactions were compared to DNA-Aldrithiol, a neutral molecule, to understand the effect of positive ions mitigating negative charge repulsion from the DNA Backbones. Previous work indicated that the maximal DNA-Aldrithiol neutral rate constant was 1.3 x 104 M-1s-1. This work indicated that crosslinking at moderate millimolar concentrations of Co(NH₃)₆³⁺ not only fully screen interhelical repulsion but also induce net attractions at higher concentrations, eventually reaching a plateau at 3.5 x 104 M-1s-1, faster than the neutral reaction, where further increases in Co(NH₃)₆³⁺ concentration have no additional effect. However, new work conducted in the lab indicates that the neutral rate constant at lower concentrations of Co(NH₃)₆³⁺ is lower than the maximal rate constant, indicating that there is still net attraction induced by Co(NH₃)₆³⁺ at lower concentrations, removing support for the net-neutral screening regime. Future side-by-side comparisons between cross-linked DNA and aldrithiol-mediated reactions at the same concentration of Co(NH₃)₆³⁺ are needed to fully clarify the impact of Co(NH₃)₆³⁺ on electrostatic interactions and the potential existence of an attractive regime. Measuring DNA-DNA crosslinking and comparing it to DNA-Aldrithiol at lower concentrations of Co(NH₃)₆³⁺ will clarify if Co(NH₃)₆³⁺ can induce attraction at lower concentrations of trivalent ions. This will refine understanding of in vivo DNA Compaction and provide further understanding on the role of multivalent compounds that naturally exist in the nucleus, such as spermine and spermidine.Biochemistr