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Development and Structural Analysis of Peptide-Based Probes for Modulating Quorum Sensing in Streptococcal Bacteria
No full textThe growing challenge of antibiotic resistance has complicated bacterial infection treatment, emphasizing the need for alternative therapies that circumvent selective pressure. Modulating quorum sensing (QS) with peptide analogs is a promising non-bacteriocidal alternative approach to mitigate bacterial pathogenicity and resistance development. In pursuit of novel therapeutics, this study explored peptide-based treatments to understand how peptide signals modulate QS in two distinct streptococcal species, Streptococcus pneumoniae and Streptococcus constellatus. Furthermore, we conducted a structural analysis of these peptides to provide insights into the design of more stable and potent analogs. The second chapter focuses on the structural and functional optimization of cyclic peptide analogs built upon the S. pneumoniae CSP1-E1A scaffold. Using urea bridge chemistry, libraries of peptides with varying ring sizes and bridge positions were synthesized to pinpoint the optimal region for cyclization. This study also examined how different parameters such as ring size and bridge position influence the overall peptide conformation, with a specific focus on α-helicity, and evaluated their biological activity against S. pneumoniae.
In the third chapter, we identified the competence-stimulating peptide (CSP) of S. constellatus and explored how its competence regulon influences two major phenotypic traits: competence and biofilm development. Moreover, through a comprehensive structure-activity relationship analysis, we determined key structural motifs required for effective ComD receptor binding and activation. We also examined the secondary structure of mutated CSP analogs to investigate the correlation between peptide secondary structure and QS activation. Overall, this study advances our understanding of QS in streptococcal species and paves the way for the development of CSP-based modulators, which could lead to the advancement of novel peptide-based therapies for future medical use
Nevada State Climate Office Drought Report January 2025
No full textThis report was created by the Nevada State Climate Office to provide a statewide drought summary for January 2025
Mitigation of Liquefaction-Induced Shallow Foundation Movements using Scaled 1g Shake Table Tests
No full textThe 1964 Niigata earthquake in Japan and the 1990 Luzon earthquake in the Philippines caused extensive structural damage in buildings with shallow foundations due to widespread soil liquefaction. In response, various ground improvement methods have been developed to mitigate the impact of liquefaction, particularly for shallow foundations. This research investigates four mitigation strategies using 1g scaled shake table model tests to evaluate their effectiveness in reducing liquefaction-induced settlement and tilt: (i) full-length (FL) sheet piles, (ii) full-length sheet piles combined with lowering groundwater (SPGW), (iii) partial floating sheet piles (PFS), and (iv) microbially induced calcite precipitation (MICP).A 1/5 scale model replicating a large-scale test conducted by the research group was used. The model featured three sand layers of varying relative densities: a loose liquefiable middle layer (30%), a medium dense top crust (50%), and a dense bottom layer (85%), with a shallow foundation resting on the surface. The first phase of the study focused on optimizing the installation of sheet piles based on a parametric study using an extensive series of shake table tests. Variations in placement distance and embedment depth revealed that settlement increased with greater distance from the foundation but decreased with deeper embedment. The most effective configuration reduced foundation settlement by approximately 75% when sheet piles were placed at 0.625 times the foundation length (L) from the center.
Since sheet piles alone did not entirely eliminate foundation settlement, the second phase evaluated enhanced mitigation through three approaches: (1) pressing sheet piles around the foundation, (2) lowering the groundwater level (GW), and (3) combining both methods (SPGW). A parametric study further examined the impact of ground motion duration. The combined approach yielded the best results, reducing settlement and tilt by over 75% and 98%, respectively, under both short and long shaking durations.
To address cost-related limitations of FL sheet piles, the third phase investigated the effectiveness of PFS. Results showed that when the PFS extended 75–87% into the dense layer, foundation settlement performance was comparable to that of full-length sheet piles, offering a potentially more economical alternative.
The final phase explored MICP as a sustainable ground improvement method. Treated soil blocks of varying dimensions were placed beneath the foundation. The most effective configurations—L×B×1.25B and 1.5L×1.5B×B—resulted in reductions of 80% in settlement and 98% in tilt, demonstrating that MICP can achieve similar performance to physical barriers.
An embodied carbon analysis compared the environmental impact of each method. While SPGW achieved the greatest performance (90% settlement and 98% tilt reduction under short-duration shaking), it also had the highest carbon footprint. In contrast, MICP offered a more environmentally sustainable option, reducing embodied carbon by 81% while still delivering comparable tilt mitigation and only a 10% reduction in settlement effectiveness relative to SPGW. This study offers practical insights for geotechnical engineers, providing a comparative framework to guide the selection of liquefaction mitigation strategies that balance performance with environmental sustainability
The influence of biotic interactions on carbon allocation in a dominant savanna ant-plant
No full textTerrestrial plants are the main source of energy available to most land-dwelling organisms. How plants partition fixed carbon (C) can have impacts ranging from individuals to entire ecosystems. This dissertation explores how biotic interactions influence plant C allocation. Specifically, it addresses how plant competition, herbivory, and mutualism influence C allocation across life stages of a dominant savanna ant-plant, Acacia (Vachellia) drepanolobium.Chapter One focuses on how aboveground plant competition imposes a C limitation in saplings, and how this impacts C allocation to above- and belowground biomass, storage, and defense. We simulated grass shade in a screenhouse and destructively harvested saplings that experienced shade or full sun. We found that shaded saplings increased relative C allocation to belowground biomass and storage and decreased relative allocation to aboveground biomass. Our results are consistent with possible adaptive allocation strategies that buffer impacts of fire and herbivory, highlighting the essential role of belowground reserve for future regrowth.
Chapter Two investigates the viability of an isotope tracer to study C allocation in a tropical ant-plant in situ. Isotope tracer methods may not be conducive to tropical trees because of methodological constraints: heat and humidity inside a labeling chamber may inhibit the uptake of an isotope tracer. In this study, we piloted a 13C pulse-labeling method to test if trees could withstand labeling conditions and assimilate 13CO2. Trees successfully took up 13CO2 and 13C was detected in all sampled C sinks, including ant mutualists. Our results demonstrate that isotope tracer studies can be used to track C allocation in mature tropical trees in situ.
Chapter Three applies 13C labeling methods established in Chapter Two to examine how changes to the biotic environment of a tree influences C allocation patterns. The tropical ant-plant A. drepanolobium is facing two major changes to its biotic environment: megaherbivore decline and the loss of its ant defensive mutualists due to invasion by the ant Pheidole megacephala. Using a factorial combination of invasion and herbivory, we found that trees invaded by P. megacephala rely on older C for stem metabolism and/or growth, and that uninvaded trees protected from herbivores allocate less new photosynthate to ant rewards (nectar) than trees with herbivores present. Our results emphasize the importance of biotic interactions in determining tree C allocation.
In summary, this dissertation builds on our understanding of how biotic interactions influence tree C allocation. Notably, it incorporates an understudied biotic interaction, mutualism, into tree C dynamics. It examines biotic interactions across ontogeny and shows how plant competition, mutualism, and herbivory can shape C allocation patterns in a dominant savanna ant-plant
Drivers of species distribution in woodrats (Neotoma) of the Great Basin Desert
No full textThe drivers that determine species distributions have long been of interest to ecologists and are highly variable across space and time. Interactions between abiotic and biotic variables may differentially shift fitness outcomes between individuals of different species, and in turn move species’ boundaries and alter community assemblies. Understanding a species’ climatic niche and plastic capacity in response to shifting conditions are important in predicting whether or not they can withstand rapid environmental changes. However, a species’ distribution is also influenced by biotic interactions such as competition, the strength of which is dependent upon factors such as climate and resource availability. Additionally, spatial scale and geographic context affect the relative importance of drivers of distribution and may differ from the regional to the local scale or from one location to another. I studied the distribution across space and time of two species of woodrat (Neotoma) that co-occur across the Great Basin of western North America. I built region-wide species distribution models and conducted extensive field surveys across a single elevational gradient, validating these models and locating previously undiscovered areas of sympatry between the two species studied. I then hindcasted their distributions into the mid-Holocene time period to confirm fossil and midden evidence indicating little to no interactions between the two species over time. I found that the factors most important in determining their distributions are highly variable regionally, but that abiotic factors appear more important than biotic factors, notably the presence of a congener in determining their range limits when their distributions come into proximity of one another. I also show a reduced potential for interaction during the mid-Holocene in comparison to today. I then built generalized linear models to test for both biotic and abiotic drivers of relative abundance across a single mountain range and to measure differences in niche breadth across variables and within each species. I found that temperature is a limiting factor for both species, but that for the smaller-bodied species, an interaction between temperature and the presence of a congener most influenced relative abundance. I also show that the factors that most differentiate the niche of these species include their thermal niche and use of rock structure, presumably for thermal buffering. Finally, to understand diet and microbial niche differences between these species and intraspecific diet and microbiome shifts across this mountain range, I sequenced DNA from fecal pellets collected from both species across sites of allopatry and sympatry. I found that at sites of sympatry both species consumed more juniper, a common plant with toxic plant specialized compounds, but that N. lepida consumed more juniper than N. cinerea. I also found a smaller total dietary niche breadth for N. lepida at sites of sympatry versus sites of allopatry, indicating possible effects of interspecific competition in contact zones. Finally, I found the most significant effect on gut microbial diversity was host species identity, aligning with previous studies of mammalian gut microbiomes. I also found small effects of dietary diversity on gut microbial diversity, indicating that as diet becomes more complex, so too does the gut microbiome
Pseudo-acetylation of ACT88F in Drosophila melanogaster impacts flight, locomotion, and mortality
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