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School of Chemistry and Biochemistry
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ItemIntegrating Machine Learning Solutions into Untargeted Metabolomics and Xenobiotics Workflows(Georgia Institute of Technology, 2024-05-01) Rainey, Markace AlanUntargeted metabolomics explores the entirety of small molecules within biological samples, providing insights into metabolic alterations associated with various conditions. Standard methodologies like NMR and LC-MS are pivotal in identifying molecular markers but often fall short in fully deciphering the metabolic landscape due to limitations in accurately annotating a vast number of metabolites. This gap in annotation hampers the diagnostic application and biological interpretation of metabolomic data. Ion mobility spectrometry (IMS) offers a solution by providing semi-orthogonal data that enhances metabolite annotation. IMS separates ions based on their collision cross-section (CCS), a property influenced by an ion's mass, shape, charge, and external factors like temperature and pressure. When integrated with mass spectrometry (MS), IMS aids in resolving ions’ of similar or identical mass-to-charge ratio (m/z), offering a refined approach to metabolite characterization. This thesis focuses on employing computational strategies within LC-IM-MS workflows to facilitate rapid metabolite characterization. Chapter 1 outlines the challenges in metabolomics, specifically the limitations of current LC-MS workflows and the concept of the "dark metabolome." This introductory chapter provides the theoretical framework to better understand ion mobility and the use of quantitative-structural activity relationships to predict molecular properties. The chapter also discusses xenobiotics—external compounds impacting health—and their characterization challenges. Chapter 2 introduces Collision Cross Section Predictor 2.0 (CCSP 2.0), a machine learning-based tool for predicting ion mobility-derived CCS values. CCSP 2.0, developed to improve the accuracy and ease of CCS prediction, is evaluated for its efficacy in enhancing annotation accuracy in LC-MS workflows. It utilizes a support-vector regression model and incorporates a comprehensive library of molecular descriptors, demonstrating superior prediction accuracy and utility in reducing false positive annotations. Chapter 3 presents a workflow for automated detection of polyhalogenated xenobiotics in biological samples using LC-IM-MS. This approach combines CCS to m/z ratios, Kendrick mass defect analysis, and CCS prediction to filter isomeric candidates. A case study on the detection of per- and polyfluorinated alkyl substances in human serum exemplifies the workflow's effectiveness. Chapter 4 describes an analytical chemistry experiment for undergraduate students, focusing on laser-induced breakdown spectroscopy (LIBS) and its application in data science education. This chapter emphasizes enhancing students' programming literacy and analytical skills through hands-on experiments and analysis using Jupyter Notebooks. The experiment, adaptable to various curricula, showcases real-world applications of LIBS, including its use in space exploration. Chapter 5 summarizes key findings from the research, discussing the implications of integrating computational methods in metabolomics and the potential advancements in ion-mobility mass spectrometry. Future research directions are proposed to further explore and refine these methodologies. Appendix A explores an on-going project aimed at predicting analyte concentrations without standard calibration curves using machine learning. This approach predicts relative ionization efficiencies of lipids from their structural properties, demonstrating the potential of machine learning in streamlining quantitative analyses in metabolomics. In conclusion, this thesis underscores the importance of computational approaches in enhancing metabolite annotation and characterizing xenobiotics, contributing valuable tools and methodologies to the field of metabolomics.
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ItemAnalytical Method Development and Mission Design Studies to Inform the Search for Biosignatures on Ocean Worlds(Georgia Institute of Technology, 2023-01-25) Seaton, Kenneth MarshallOur search for extraterrestrial life is enabled by both the development and maturation of chemical instruments capable of life detection and the characterization of extraterrestrial analogues on Earth representing the extreme conditions present on other planetary bodies. Yet, despite the extreme physical and chemical conditions present in these extraterrestrial analogues (salinity, acidity, pH, etc.), terrestrial life finds a way to adapt and even thrive. Here, I present an outline of my thesis, the goals of which are twofold. The first portion of my thesis focuses on the development of analytical methods to enable the quantitative compositional analysis of these extraterrestrial analogue environments using capillary electrophoresis with laser-induced fluorescence detection, enabling a better understanding of the relative abundances of amino acids present in extreme environments hosting complex ecosystems. The second part of my thesis explores the development of a New Frontiers class mission concept for the Saturnian moon Enceladus to (1) directly search for life through a combination of in situ chemical compositional analysis and (2) contextualize these measurements through a combination of geophysical and geomorphological investigations to assess the habitability of Enceladus. Reviews of instrumentation for planetary chemical and astrobiological studies are presented, followed by the mission concept study undertaken.
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ItemDistribution, Characterization, & Temporal Study of Biosignatures at the Dyngjusandur, Iceland Mars Analog(Georgia Institute of Technology, 2022-05-03) Sutton, Scot M.From 2016 to 2018, the FELDSPAR team visited the Dyngjusandur, Iceland, Mars analog plains to characterize the importance of spatial separation and abiotic measurements for extraterrestrial sampling protocols and the predictivity of biosignatures. The FELDSPAR team has approached analog sampling with the goal of emulating the protocols and instruments available on board the Mars 2020 Perseverance Rover so as to inform future missions and optimize science return. The Dyngjusandur plains are primarily comprised of fine basaltic tephra, ideal for investigating biological variability at visually homogenous sampling sites. Samples were collected using a schematic of nested triangles established over three years of field campaigns, designed to allow for statistical comparisons between samples at multiple spatial scales. Characteristic factors analyzed for each sample included: ATP, dsDNA, gravimetric moisture content, and grain size composition. Data from 2016-2018 was analyzed to identify shifts in these characteristic factors over time and the dependance of their relationships on spatial groupings and environmental factors. Aeolian action was found to be a primary source of biosignature variability at Dyngjusandur, with biomass content increasing at sampling sites with environmental protection from the wind. Grain size fractions were also influential for bioactivity and biomass with both ATP and dsDNA positively correlating with larger sediment grains. Samples collected with 10 m of separation were most likely to be significantly different, while samples separated by 1 m were found to be statistically similar. Samples collected at 100 m of separation were often significantly different, however more comparisons are necessary to characterize the variability of biosignatures at larger scales. This work provides additional evidence to influence sampling protocols for approaching Martian targets with similar environmental stresses, and the patterns uncovered over three years of study serve as a starting point for deeper characterization of the Icelandic Mars analog.
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ItemAssessment of Mars Analogue Instruments and Biosignatures in Icelandic Mars Analogue Environments: Implications for Astrobiology(Georgia Institute of Technology, 2021-12-13) Tan, George K.To search more efficiently for a record of past life on Mars, it is critical to know where to look and thus maximize the likelihood of success. Large-scale site selection for the Mars 2020 mission has been completed, but small (meter to 10 cm)-scale relationships of microenvironments will not be known until the rover reaches the surface. This thesis aims to study different Icelandic Mars analog environments to simultaneously look at all domains of life interpreted in the context of the underlying mineralogical and geochemical environment. The overarching premise for this work is a comprehensive understanding of the geological and biological characteristics of terrestrial basaltic systems to better develop strategies to help guide the life-detection mission and sampling location selection to ensure best scientific return. This dissertation include 1) a study to describe an analogue mission in low biomass Mars analogue environments comparing the effectiveness, spatial variation, and inter-correlations of life-detection techniques and implications for Mars sampling selection 2) an examination of spatial distributions and levels of biosignatures in Icelandic Mars analogue environments 3) a study exploring the composition of microbial communities at different spatial scales in apparently homogenous environments, 4) final study linking biological indicators to physical characteristics including bulk chemical composition, spectral signatures of mineralogy, and grain size. The last chapter of the thesis will summarize major findings and present several recommendations for continued research.
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ItemPrecipitation Dynamics at the Solution-Solution Interface in Confined Geometries, and the Effects of Organics on Precipitate Evolution(Georgia Institute of Technology, 2021-07-07) Pital, Aaron C.Precipitate produced by the interaction of aqueous reactant solutions in a microchannel is evaluated through instrumental analysis and numerical modeling. Instrumental analysis of analogs of iron sulfide, iron carbonate, and iron phosphate minerals and the effect of modeled ionic strength and mass transport mechanisms are presented. Implications on fluid dynamics due the production of colloids at a solution-solution interface is developed. A phenomenon of electroless reduction in this system transitioning to self-catalyzed electrodeposition is presented in light of the dynamics previously discussed and is used as an example of the convergent effects of coupled physiochemical systems on the microscale. All three of the above results (precipitate analysis, fluid and mass transport dynamics, and coupled physiochemical systems) are leveraged to present results of the interaction of organic species with precipitating iron sulfide material. It is found that the presence of organic species has a strong impact on the morphology of iron sulfide mineral analogs, and that morphology may be diagnostic for the presence of organics during formation even when Raman spectra show no signs of extant organic material. This has profound implications for the use of autonomous rovers in exploring the organic-mineral interactions of ancient aqueous systems such as Mars’s Jezero Crater.
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ItemAnalysis of Adenosine Triphosphate in Spatially Distributed Planetary Analog Field Samples to Inform Biosignature Detection Missions(Georgia Institute of Technology, 2021-05-11) Novak, Carlie MarieNew discoveries of potentially habitable environments elsewhere in our solar system, and at the extremes here on Earth, have reopened the imagination to possibilities for extraterrestrial life. Planetary field analog research enables us to study the impact of similar extreme environmental stressors and the bioactivity of an ecosystem. This thesis research was designed to better understand biosignature detection in extreme environments by exploring distributions and patterns of biosignatures in harsh planetary environments. Adenosine triphosphate (ATP) was used as a proxy of bioactivity due to its ubiquitous role in terrestrial metabolism and can be quantified easily by a bioluminescence assay. Observing variations in concentrations of ATP can provide insight on where bioactivity becomes concentrated, or evenly distributed which is essential in the search for life outside of Earth. A variety of chemical and physical studies of samples from analog locations aids in understanding the limits of life terrestrially, and therefore can help make more informed predictions about the potential habitability on other planetary bodies.
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ItemRAPID-PROTOTYPING OF PDMS-BASED MICROFLUIDIC DEVICES(Georgia Institute of Technology, 2020-07-06) Morbioli, GiorgioMicrofluidics uses the manipulation of fluids in microchannels to accomplish innumerous goals, and is attractive to analytical chemistry because it can reduce the scale of larger analytical processes. The benefits of the use of microfluidic systems, in comparison with conventional processes, include efficient sample and reagent consumption, low power usage and portability. Most microfluidic applications require a development process based on iterative design and testing of multiple prototype microdevices. Typical microfabrication protocols, however, can require over a week of specialist time in high-maintenance cleanroom facilities, making the iterative process resource-intensive and prohibitive in many locations. Rapid prototyping techniques can alleviate these issues, enabling faster development of microfluidic structures at lower costs. Print-and-peel techniques (PAP), including wax printing and xurography, are low-cost fast-prototyping tools used to create master molds for polydimethylsiloxane (PDMS) miniaturized systems. In this work, three different methods were created to improve the rapid-prototyping of PDMS-based microfluidic devices. Using the wax printing method, PDMS microdevices can now be fabricated from design to testing in less than 1 hour, at the cost of $0.01 per mold, being one of the fastest and cheapest methods to date. If extensive fluidic manipulation is required, xurography becomes the method of choice. The xurography technique presented here is the most rapid tool to fabricate PDMS-based microdevices to date, presenting turnaround times as fast as 5 minutes. The first hybrid technique that can be used either as a PAP or a scaffolding method is also presented here, using the same materials and fabrication process. The green, low-cost, user-friendly elastomeric (GLUE) rapid prototyping method to fabricate PDMS-based devices uses white glue as the patterning material, and is capable of fabricating multi-height molds in a single step, improving even further the development of PDMS microfluidic devices. Device fabrication is only one of the steps in the iterative process of designing a fully-functional microfluidic tool. The design of the microdevice itself plays a crucial role in its performance, which directly impacts processes conducted in miniaturized devices. In this work, the influence of hydrodynamic resistance in sample dispersion on a microfluidic multiplexer was studied using paper-based analytical microfluidic devices (µPADs) as the testbed. When microfluidic devices are not rationally designed, and when the influence of fluidic resistance is not taken into account, sample dispersion can be biased. A bias can influence the output of colorimetric enzymatic assays supported on these microstructures, which are the most common applications of µPADs, demonstrating the need for rational design of microdevices. The third essential component of developing microfluidic devices is their effective testing, especially when incorporating active pumping elements on-chip. To overcome issues in the manual operation or coding for operation of microvalves, a program that can automatically generate sequences for fluidic manipulation in microfluidic processors was written in Python, with the only inputs required from the user being reservoir positions, mixing ratio and the desired input and output reservoirs. To further improve testing and avoid the use of fixed mounts, a modular system was created to aid the testing of devices with different designs, another advance in the area. This research enables better design and testing of microfluidic devices in shorter times and at lower costs, enabling improvements in the interfacing between different unit operations on-chip, a challenge in the microfluidics area. More than that, it also makes this area, traditionally confined into expensive cleanroom facilities, available to more research groups worldwide.