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Description
The discovery and development of novel antibacterial agents is essential to address the rising health concern over antibiotic resistant bacteria. This research investigated the antibacterial activity of a natural clay deposit near Crater Lake, Oregon, that is effective at killing antibiotic resistant human pathogens. The primary rock types in the deposit are andesitic pyroclastic materials, which have been hydrothermally altered into argillic clay zones. High-sulfidation (acidic) alteration produced clay zones with elevated pyrite (18%), illite-smectite (I-S) (70% illite), elemental sulfur, kaolinite and carbonates. Low-sulfidation alteration at neutral pH generated clay zones with lower pyrite concentrations pyrite (4-6%), the mixed-layered I-S clay rectorite (R1, I-S) and quartz.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
Antibacterial susceptibility testing reveals that hydrated clays containing pyrite and I-S are effective at killing (100%) of the model pathogens tested (E. coli and S. epidermidis) when pH (< 4.2) and Eh (> 450 mV) promote pyrite oxidation and mineral dissolution, releasing > 1 mM concentrations of Fe2+, Fe3+ and Al3+. However, certain oxidized clay zones containing no pyrite still inhibited bacterial growth. These clays buffered solutions to low pH (< 4.7) and oxidizing Eh (> 400 mV) conditions, releasing lower amounts (< 1 mM) of Fe and Al. The presence of carbonate in the clays eliminated antibacterial activity due to increases in pH, which lower pyrite oxidation and mineral dissolution rates.
The antibacterial mechanism of these natural clays was explored using metal toxicity and genetic assays, along with advanced bioimaging techniques. Antibacterial clays provide a continuous reservoir of Fe2+, Fe3+ and Al3+ that synergistically attack pathogens while generating hydrogen peroxide (H2O¬2). Results show that dissolved Fe2+ and Al3+ are adsorbed to bacterial envelopes, causing protein misfolding and oxidation in the outer membrane. Only Fe2+ is taken up by the cells, generating oxidative stress that damages DNA and proteins. Excess Fe2+ oxidizes inside the cell and precipitates Fe3+-oxides, marking the sites of hydroxyl radical (•OH) generation. Recognition of this novel geochemical antibacterial process should inform designs of new mineral based antibacterial agents and could provide a new economic industry for such clays.
ContributorsMorrison, Keith D (Author) / Williams, Lynda B (Thesis advisor) / Williams, Stanley N (Thesis advisor) / Misra, Rajeev (Committee member) / Shock, Everett (Committee member) / Anbar, Ariel (Committee member) / Arizona State University (Publisher)
Created2015
Description
Amorphous phases are detected over large regions of the Martian surface from orbit and in more localized deposits by rovers on the surface. Amorphous silicates can be primary or secondary in origin, both having formed through very different processes, so the unambiguous identification of these phases is important for understanding the geologic history of Mars. Secondary amorphous silicates are poorly understood and underrepresented in spectral libraries because they lack the long-range structural order that makes their crystalline counterparts identifiable in most analytical techniques. Fortunately, even amorphous materials have some degree of short-range order so that distinctions can be made with careful characterization.
Two sets of laboratory experiments were used to produce and characterize amorphous weathering products under probable conditions for the Martian surface, and one global spectral analysis using thermal-infrared (TIR) data from the Thermal Emission Spectrometer (TES) instrument was used to constrain variations in amorphous silicates across the Martian surface. The first set of experiments altered crystalline and glassy basalt samples in an open system under strong (pH 1) and moderate (pH 3) acidic conditions. The second set of experiments simulated a current-day Martian weathering scenario involving transient liquid water where basalt glass weathering solutions, formed in circumneutral (pH ~5.5 and 7) conditions, were rapidly evaporated, precipitating amorphous silicates. The samples were characterized using visible and near-infrared (VNIR) spectroscopy, TIR spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD).
All experiments formed amorphous silicate phases that are new to spectral libraries. Moderately acidic alteration experiments produced no visible or spectral evidence of alteration products, whereas exposure of basalt glass to strongly acidic fluids produced silica-rich alteration layers that are spectrally consistent with VNIR and TIR spectra from the circum-polar region of Mars, indicating this region has undergone acidic weathering. Circum-netural pH basalt weathering solution precipitates are consistent with amorphous materials measured by rovers in soil and rock surface samples in Gale and Gusev Craters, suggesting transient water interactions over the last 3 billion years. Global spectral analyses determine that alteration conditions have varied across the Martian surface, and that alteration has been long lasting.
Two sets of laboratory experiments were used to produce and characterize amorphous weathering products under probable conditions for the Martian surface, and one global spectral analysis using thermal-infrared (TIR) data from the Thermal Emission Spectrometer (TES) instrument was used to constrain variations in amorphous silicates across the Martian surface. The first set of experiments altered crystalline and glassy basalt samples in an open system under strong (pH 1) and moderate (pH 3) acidic conditions. The second set of experiments simulated a current-day Martian weathering scenario involving transient liquid water where basalt glass weathering solutions, formed in circumneutral (pH ~5.5 and 7) conditions, were rapidly evaporated, precipitating amorphous silicates. The samples were characterized using visible and near-infrared (VNIR) spectroscopy, TIR spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), and X-ray diffraction (XRD).
All experiments formed amorphous silicate phases that are new to spectral libraries. Moderately acidic alteration experiments produced no visible or spectral evidence of alteration products, whereas exposure of basalt glass to strongly acidic fluids produced silica-rich alteration layers that are spectrally consistent with VNIR and TIR spectra from the circum-polar region of Mars, indicating this region has undergone acidic weathering. Circum-netural pH basalt weathering solution precipitates are consistent with amorphous materials measured by rovers in soil and rock surface samples in Gale and Gusev Craters, suggesting transient water interactions over the last 3 billion years. Global spectral analyses determine that alteration conditions have varied across the Martian surface, and that alteration has been long lasting.
ContributorsSmith, Rebecca (Author) / Christensen, Philip R. (Philip Russel) (Thesis advisor) / Shock, Everett (Committee member) / Hartnett, Hilairy (Committee member) / Shim, Sang-Heon (Committee member) / Sharp, Thomas (Committee member) / Arizona State University (Publisher)
Created2016
Polycyclic aromatic hydrocarbon (PAH) redistribution in extreme dust storms and processing in clouds
Description
Dust storms known as 'haboobs' occur in the City of Tempe, AZ during the North American monsoon season. A haboob classification method based on meteorological and air quality measurements is described. There were from 3 to 20 haboob events per year over the period from 2005 to 2014. The calculated annual TSP (total suspended particulate) dry deposition during haboobs is estimated to contribute 74% of the total particulate mass deposited in Tempe, AZ.
Dry deposition is compared with the aqueous chemistry of Tempe Town Lake. Water management and other factors may have a stronger impact on Tempe Town Lake chemistry than haboob dry-deposition. Haboobs alter the Polycyclic Aromatic Hydrocarbon (PAH) concentrations and distributions in Tempe, AZ. PAH isomer ratios suggest PM2.5 (particulate matter with aerodynamic diameters less than or equal to 2.5 μm) sources consistent with approximate thunderstorm outflow paths.
The importance of the atmospheric aqueous phase, fogs and clouds, for the processing and removal of PAHs is not well known. A multiphase model was developed to determine the fate and lifetime of PAHs in fogs and clouds. The model employed literature values that describe the partitioning between three phases (aqueous, liquid organic, and gas), in situ PAH measurements, and experimental and estimated (photo)oxidation rates. At 25 °C, PAHs with two, three and four rings were predicted to be primarily gas phase (fraction in the gas phase xg > 90 %) while five- and six-ring PAHs partitioned significantly into droplets (xg < 60 %) with aqueous phase fractions of 1 to 6 % and liquid organic phase fractions of 31 to 91 %. The predicted atmospheric lifetimes of PAHs in the presence of fog or cloud droplets (< 5 hours) were significantly shorter than literature predictions of PAH wet and dry deposition lifetimes (1 to 14 days and 5 to 15 months respectively) and shorter than or equal to predicted PAH gas phase / particle phase atmospheric lifetimes (1 to 300 hours). The aqueous phase cannot be neglected as a PAH sink due to the large aqueous volume (vs. organic volume) and the relatively fast aqueous reactions.
Dry deposition is compared with the aqueous chemistry of Tempe Town Lake. Water management and other factors may have a stronger impact on Tempe Town Lake chemistry than haboob dry-deposition. Haboobs alter the Polycyclic Aromatic Hydrocarbon (PAH) concentrations and distributions in Tempe, AZ. PAH isomer ratios suggest PM2.5 (particulate matter with aerodynamic diameters less than or equal to 2.5 μm) sources consistent with approximate thunderstorm outflow paths.
The importance of the atmospheric aqueous phase, fogs and clouds, for the processing and removal of PAHs is not well known. A multiphase model was developed to determine the fate and lifetime of PAHs in fogs and clouds. The model employed literature values that describe the partitioning between three phases (aqueous, liquid organic, and gas), in situ PAH measurements, and experimental and estimated (photo)oxidation rates. At 25 °C, PAHs with two, three and four rings were predicted to be primarily gas phase (fraction in the gas phase xg > 90 %) while five- and six-ring PAHs partitioned significantly into droplets (xg < 60 %) with aqueous phase fractions of 1 to 6 % and liquid organic phase fractions of 31 to 91 %. The predicted atmospheric lifetimes of PAHs in the presence of fog or cloud droplets (< 5 hours) were significantly shorter than literature predictions of PAH wet and dry deposition lifetimes (1 to 14 days and 5 to 15 months respectively) and shorter than or equal to predicted PAH gas phase / particle phase atmospheric lifetimes (1 to 300 hours). The aqueous phase cannot be neglected as a PAH sink due to the large aqueous volume (vs. organic volume) and the relatively fast aqueous reactions.
ContributorsEagar, Jershon (Author) / Herckes, Pierre (Thesis advisor) / Hayes, Mark (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2016
Description
N-Nitrosodimethylamine (NDMA), a probable human carcinogen, has been found in clouds and fogs at concentration up to 500 ng/L and in drinking water as disinfection by-product. NDMA exposure to the general public is not well understood because of knowledge gaps in terms of occurrence, formation and fate both in air and water. The goal of this dissertation was to contribute to closing these knowledge gaps on potential human NDMA exposure through contributions to atmospheric measurements and fate as well as aqueous formation processes.
Novel, sensitive methods of measuring NDMA in air were developed based on Solid Phase Extraction (SPE) and Solid Phase Microextraction (SPME) coupled to Gas Chromatography-Mass Spectrometry (GC-MS). The two measuring techniques were evaluated in laboratory experiments. SPE-GC-MS was applicable in ambient air sampling and NDMA in ambient air was found in the 0.1-13.0 ng/m3 range.
NDMA photolysis, the main degradation atmospheric pathway, was studied in the atmospheric aqueous phase. Water soluble organic carbon (WSOC) was found to have more impact than inorganic species on NDMA photolysis by competing with NDMA for photons and therefore could substantially increase the NDMA lifetime in the atmosphere. The optical properties of atmospheric WSOC were investigated in aerosol, fog and cloud samples and showed WSOC from atmospheric aerosols has a higher mass absorption efficiency (MAE) than organic matter in fog and cloud water, resulting from a different composition, especially in regards of volatile species, that are not very absorbing but abundant in fogs and clouds.
NDMA formation kinetics during chloramination were studied in aqueous samples including wastewater, surface water and ground water, at two monochloramine concentrations. A simple second order NDMA formation model was developed using measured NDMA and monochloramine concentrations at select reaction times. The model fitted the NDMA formation well (R2 >0.88) in all water matrices. The proposed model was then optimized and applied to fit the data of NDMA formation from natural organic matter (NOM) and model precursors in previously studies. By determining the rate constants, the model was able to describe the effect of water conditions such as DOC and pH on NDMA formation.
Novel, sensitive methods of measuring NDMA in air were developed based on Solid Phase Extraction (SPE) and Solid Phase Microextraction (SPME) coupled to Gas Chromatography-Mass Spectrometry (GC-MS). The two measuring techniques were evaluated in laboratory experiments. SPE-GC-MS was applicable in ambient air sampling and NDMA in ambient air was found in the 0.1-13.0 ng/m3 range.
NDMA photolysis, the main degradation atmospheric pathway, was studied in the atmospheric aqueous phase. Water soluble organic carbon (WSOC) was found to have more impact than inorganic species on NDMA photolysis by competing with NDMA for photons and therefore could substantially increase the NDMA lifetime in the atmosphere. The optical properties of atmospheric WSOC were investigated in aerosol, fog and cloud samples and showed WSOC from atmospheric aerosols has a higher mass absorption efficiency (MAE) than organic matter in fog and cloud water, resulting from a different composition, especially in regards of volatile species, that are not very absorbing but abundant in fogs and clouds.
NDMA formation kinetics during chloramination were studied in aqueous samples including wastewater, surface water and ground water, at two monochloramine concentrations. A simple second order NDMA formation model was developed using measured NDMA and monochloramine concentrations at select reaction times. The model fitted the NDMA formation well (R2 >0.88) in all water matrices. The proposed model was then optimized and applied to fit the data of NDMA formation from natural organic matter (NOM) and model precursors in previously studies. By determining the rate constants, the model was able to describe the effect of water conditions such as DOC and pH on NDMA formation.
ContributorsZhang, Jinwei (Author) / Herckes, Pierre (Thesis advisor) / Westerhoff, Paul (Thesis advisor) / Fraser, Matthew (Committee member) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation is presented in two sections. First, I explore two methods of using stable isotope analysis to trace environmental and biogeochemical processes. Second, I present two related studies investigating student understanding of the biogeochemical concepts that underlie part one. Fe and Hg are each biogeochemically important elements in their own way. Fe is a critical nutrient for phytoplankton, while Hg is detrimental to nearly all forms of life. Fe is often a limiting factor in marine phytoplankton growth. The largest source, by mass, of Fe to the open ocean is windblown mineral dust, but other more soluble sources are more bioavailable. To look for evidence of these non-soil dust sources of Fe to the open ocean, I measured the isotopic composition of aerosol samples collected on Bermuda. I found clear evidence in the fine size fraction of a non-soil dust Fe source, which I conclude is most likely from biomass burning. Widespread adoption of compact fluorescent lamps (CFL) has increased their importance as a source of environmental Hg. Isotope analysis would be a useful tool in quantifying this impact if the isotopic composition of Hg from CFL were known. My measurements show that CFL-Hg is isotopically fractionated, in a unique pattern, during normal operation. This fractionation is large and has a distinctive, mass-independent signature, such that CFL Hg can be uniquely identified from other sources. Misconceptions research in geology has been a very active area of research, but student thinking regarding the related field of biogeochemistry has not yet been studied in detail. From interviews with 40 undergraduates, I identified over 150 specific misconceptions. I also designed a multiple-choice survey (concept inventory) to measure understanding of these same biogeochemistry concepts. I present statistical evidence, based on the Rasch model, for the reliability and validity of this instrument. This instrument will allow teachers and researchers to easily quantify learning outcomes in biogeochemistry and will complement existing concept inventories in geology, chemistry, and biology.
ContributorsMead, Chris (Author) / Anbar, Ariel (Thesis advisor) / Semken, Steven (Committee member) / Shock, Everett (Committee member) / Herckes, Pierre (Committee member) / Hartnett, Hilairy (Committee member) / Arizona State University (Publisher)
Created2014
Description
Flavivirus infections are emerging as significant threats to human health around the globe. Among them West Nile(WNV) and Dengue Virus (DV) are the most prevalent in causing human disease with WNV outbreaks occurring in all areas around the world and DV epidemics in more than 100 countries. WNV is a neurotropic virus capable of causing meningitis and encephalitis in humans. Currently, there are no therapeutic treatments or vaccines available. The expanding epidemic of WNV demands studies that develop efficacious therapeutics and vaccines and produce them rapidly and inexpensively. In response, our lab developed a plant-derived monoclonal antibody (mAb) (pHu-E16) against DIII (WNV antigen) that is able to neutralize and prevent mice from lethal infection. However, this drug has a short window of efficacy due to pHu-E16's inability to cross the Blood Brain Barrier (BBB) and enter the brain. Here, we constructed a bifunctional diabody, which couples the neutralizing activity of E16 and BBB penetrating activity of 8D3 mAb. We also produced a plant-derived E16 scFv-CH1-3 variant with equivalent specific binding as the full pHu-E16 mAb, but only requiring one gene construct for production. Furthermore, a WNV vaccine based on plant-derived DIII was developed showing proper folding and potentially protective immune response in mice. DV causes severe hemorrhaging diseases especially in people exposed to secondary DV infection from a heterotypic strain. It is hypothesized that sub-neutralizing cross-reactive antibodies from the first exposure aid the second infection in a process called antibody-dependent enhancement (ADE). ADE depends on the ability of mAb to bind Fc receptors (FcγRs), and has become a major roadblock for developing mAb-based therapeutics against DV. We aim to produce an anti-Dengue mAb (E60) in different glycoengineered plant lines that exhibit reduced/differential binding to FcγRs, therefore, reducing or eliminating ADE. We have successfully cloned the molecular constructs of E60, and expressed it in two plant lines with different glycosylation patterns. We demonstrated that both plant-derived E60 mAb glycoforms retained specific recognition and neutralization activity against DV. Overall, our study demonstrates great strives to develop efficacious therapeutics and potent vaccine candidates against Flaviviruses in plant expression systems.
ContributorsHurtado, Jonathan (Author) / Chen, Qiang (Thesis advisor) / Huffman, Holly A (Committee member) / Steele, Kelly P (Committee member) / Arizona State University (Publisher)
Created2014
Description
In enzyme induced carbonate precipitation (EICP), calcium carbonate (CaCO3) precipitation is catalyzed by plant-derived urease enzyme. In EICP, urea hydrolyzes into ammonia and inorganic carbon, altering geochemical conditions in a manner that promotes carbonate mineral precipitation. The calcium source in this process comes from calcium chloride (CaCl2) in aqueous solution. Research work conducted for this dissertation has demonstrated that EICP can be employed for a variety of geotechnical purposes, including mass soil stabilization, columnar soil stabilization, and stabilization of erodible surficial soils. The research presented herein also shows that the optimal ratio of urea to CaCl2 at ionic strengths of less than 1 molar is approximately 1.75:1. EICP solutions of very high initial ionic strength (i.e. 6 M) as well as high urea concentrations (> 2 M) resulted in enzyme precipitation (salting-out) which hindered carbonate precipitation. In addition, the production of NH4+ may also result in enzyme precipitation. However, enzyme precipitation appeared to be reversible to some extent. Mass soil stabilization was demonstrated via percolation and mix-and-compact methods using coarse silica sand (Ottawa 20-30) and medium-fine silica sand (F-60) to produce cemented soil specimens whose strength improvement correlated with CaCO3 content, independent of the method employed to prepare the specimen. Columnar stabilization, i.e. creating columns of soil cemented by carbonate precipitation, using Ottawa 20-30, F-60, and native AZ soil was demonstrated at several scales beginning with small columns (102-mm diameter) and culminating in a 1-m3 soil-filled box. Wind tunnel tests demonstrated that surficial soil stabilization equivalent to that provided by thoroughly wetting the soil can be achieved through a topically-applied solution of CaCl2, urea, and the urease enzyme. The topically applied solution was shown to form an erosion-resistant CaCO3 crust on fine sand and silty soils. Cementation of erodible surficial soils was also achieved via EICP by including a biodegradable hydrogel in the stabilization solution. A dilute hydrogel solution extended the time frame over which the precipitation reaction could occur and provided improved spatial control of the EICP solution.
ContributorsHamdan, Nasser M (Author) / Kavazanjian Jr., Edward (Thesis advisor) / Rittmann, Bruce (Thesis advisor) / Shock, Everett (Committee member) / Arizona State University (Publisher)
Created2015
Description
The taxonomic and metabolic profile of the microbial community inhabiting a natural system is largely determined by the physical and geochemical properties of the system. However, the influences of parameters beyond temperature, pH and salinity have been poorly analyzed with few studies incorporating the comprehensive suite of physical and geochemical measurements required to fully investigate the complex interactions known to exist between biology and the environment. Further, the techniques used to classify the taxonomic and functional composition of a microbial community are fragmented and unwieldy, resulting in unnecessarily complex and often non-consilient results.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
This dissertation integrates environmental metagenomes with extensive geochemical metadata for the development and application of multidimensional biogeochemical metrics. Analysis techniques including a Markov cluster-based evolutionary distance between whole communities, oligonucleotide signature-based taxonomic binning and principal component analysis of geochemical parameters allow for the determination of correlations between microbial community dynamics and environmental parameters. Together, these techniques allow for the taxonomic classification and functional analysis of the evolution of hot spring communities. Further, these techniques provide insight into specific geochemistry-biology interactions which enable targeted analyses of community taxonomic and functional diversity. Finally, analysis of synonymous substitution rates among physically separated microbial communities provides insights into microbial dispersion patterns and the roles of environmental geochemistry and community metabolism on DNA transfer among hot spring communities.
The data presented here confirms temperature and pH as the primary factors shaping the evolutionary trajectories of microbial communities. However, the integration of extensive geochemical metadata reveals new links between geochemical parameters and the distribution and functional diversification of communities. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial community functional composition and inter-community DNA transfer rates. Finally, the taxonomic classification and clustering techniques developed within this dissertation will facilitate future genomic and metagenomic studies through enhanced community profiling obtainable via Markov clustering, longer oligonucleotide signatures and insight into PCR primer biases.
ContributorsAlsop, Eric Bennie (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Farmer, Jack (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2014
Description
One goal of geobiochemistry is to follow geochemical energy supplies from the external environment to the inside of microbial cells. This can be accomplished by combining thermodynamic calculations of energy supplies from geochemical processes and energy demands for biochemical processes. Progress towards this goal is summarized here. A critique of all thermodynamic data for biochemical compounds involved in the citric acid cycle (CAC) and the formulation of metabolite properties allows predictions of the energy involved in each step of the cycle as well as the full forward and reverse cycles over wide ranges of temperature and pressure. These results allow evaluation of energy demands at the center of many microbial metabolic systems. Field work, sampling, and lab analyses from two low-temperature systems, a serpentinizing system, and a subglacial setting, provide the data used in these thermodynamic analyses of energy supplies. An extensive literature summary of microbial and molecular data from serpentinizing systems found is used to guide the evaluation and ranking of energy supplies used by chemolithoautotrophic microbes. These results constrain models of the distribution of microbial metabolisms throughout the low-temperature serpentinization systems in the Samail ophiolite in Oman (including locales of primary and subsequent alteration processes). Data collected from Robertson Glacier in Alberta, Canada, together with literature data from Lake Vida in Antarctica and bottom seawater, allowed thermodynamic analyses of low-temperature energy supplies in a glacial system. Results for 1460 inorganic redox reactions are used to fully inventory the geochemical energy sources that support the globally extensive cold biosphere.
ContributorsCanovas, Peter Anthony (Author) / Shock, Everett (Thesis advisor) / Hartnett, Hilairy (Committee member) / Sharp, Thomas (Committee member) / Tyburczy, James (Committee member) / Heimsath, Arjun (Committee member) / Arizona State University (Publisher)
Created2016
Description
The greatest barrier to understanding how life interacts with its environment is the complexity in which biology operates. In this work, I present experimental designs, analysis methods, and visualization techniques to overcome the challenges of deciphering complex biological datasets. First, I examine an iron limitation transcriptome of Synechocystis sp. PCC 6803 using a new methodology. Until now, iron limitation in experiments of Synechocystis sp. PCC 6803 gene expression has been achieved through media chelation. Notably, chelation also reduces the bioavailability of other metals, whereas naturally occurring low iron settings likely result from a lack of iron influx and not as a result of chelation. The overall metabolic trends of previous studies are well-characterized but within those trends is significant variability in single gene expression responses. I compare previous transcriptomics analyses with our protocol that limits the addition of bioavailable iron to growth media to identify consistent gene expression signals resulting from iron limitation. Second, I describe a novel method of improving the reliability of centroid-linkage clustering results. The size and complexity of modern sequencing datasets often prohibit constructing distance matrices, which prevents the use of many common clustering algorithms. Centroid-linkage circumvents the need for a distance matrix, but has the adverse effect of producing input-order dependent results. In this chapter, I describe a method of cluster edge counting across iterated centroid-linkage results and reconstructing aggregate clusters from a ranked edge list without a distance matrix and input-order dependence. Finally, I introduce dendritic heat maps, a new figure type that visualizes heat map responses through expanding and contracting sequence clustering specificities. Heat maps are useful for comparing data across a range of possible states. However, data binning is sensitive to clustering cutoffs which are often arbitrarily introduced by researchers and can substantially change the heat map response of any single data point. With an understanding of how the architectural elements of dendrograms and heat maps affect data visualization, I have integrated their salient features to create a figure type aimed at viewing multiple levels of clustering cutoffs, allowing researchers to better understand the effects of environment on metabolism or phylogenetic lineages.
ContributorsKellom, Matthew (Author) / Raymond, Jason (Thesis advisor) / Anbar, Ariel (Committee member) / Elser, James (Committee member) / Shock, Everett (Committee member) / Walker, Sarah (Committee member) / Arizona State University (Publisher)
Created2017