Matching Items (127)
Description
Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.
ContributorsNogly, Przemyslaw (Author) / Panneels, Valerie (Author) / Nelson, Garrett (Author) / Gati, Cornelius (Author) / Kimura, Tetsunari (Author) / Milne, Christopher (Author) / Milathianaki, Despina (Author) / Kubo, Minoru (Author) / Wu, Wenting (Author) / Conrad, Chelsie (Author) / Coe, Jesse (Author) / Bean, Richard (Author) / Zhao, Yun (Author) / Bath, Petra (Author) / Dods, Robert (Author) / Harimoorthy, Rajiv (Author) / Beyerlein, Kenneth R. (Author) / Rheinberger, Jan (Author) / James, Daniel (Author) / Deponte, Daniel (Author) / Li, Chufeng (Author) / Sala, Leonardo (Author) / Williams, Garth J. (Author) / Hunter, Mark S. (Author) / Koglin, Jason E. (Author) / Berntsen, Peter (Author) / Nango, Eriko (Author) / Iwata, So (Author) / Chapman, Henry N. (Author) / Fromme, Petra (Author) / Frank, Matthias (Author) / Abela, Rafael (Author) / Boutet, Sebastien (Author) / Barty, Anton (Author) / White, Thomas A. (Author) / Weierstall, Uwe (Author) / Spence, John (Author) / Neutze, Richard (Author) / Schertler, Gebhard (Author) / Standfuss, Jorg (Author) / College of Liberal Arts and Sciences (Contributor) / Department of Physics (Contributor) / Department of Chemistry and Biochemistry (Contributor) / Biodesign Institute (Contributor) / Applied Structural Discovery (Contributor) / School of Molecular Sciences (Contributor)
Created2016-08-22
Description
The experiments conducted in this report supported previous evidence (Bethany et al., 2019) that a newly identified predatory bacterium causes a higher rate of mortality in the biological soil crust cyanobacterium M. vaginatus when in hot soils than in cold soils. I predicted that the extracellular propagules of this predatory bacterium were inactivated at seasonally low temperatures, rendering them non-viable when introduced to M. vaginatus at room temperature. However, I found that the predatory bacterium became only transiently inactive at low temperatures, recovering its pathogenicity when later exposed to warmer temperatures. By contrast, inactivation of infectivity was complete by exposure in both liquid and dry conditions for five days at 40 °C. I also expected that its infectivity towards M. vaginatus was temperature dependent. Indeed, infection was hampered and did not cause high mortality when predator and prey were incubated at or below 10 °C, which could have been due to slowed metabolisms of M. vaginatus or to an inability of the predatory bacterium to attack in cold conditions. Above 10 °C, when M. vaginatus grew faster, time to full death of predator/prey incubations correlated with the rate of growth of healthy cultures.
The experiments in this study observed a correlation between the growth rate of uninfected cultures and the decay rate of infected cultures, meaning that temperatures that cultures that displayed a higher growth rate for uninfected M. vaginatus would die faster when infected with the predatory bacterium. Infected cultures that were incubated at temperatures 4 and 10 °C did not display death and this could have been due to lower activity of M. vaginatus at lower temperatures or the inability for the predatory bacterium to attack at lower temperatures.
The experiments in this study observed a correlation between the growth rate of uninfected cultures and the decay rate of infected cultures, meaning that temperatures that cultures that displayed a higher growth rate for uninfected M. vaginatus would die faster when infected with the predatory bacterium. Infected cultures that were incubated at temperatures 4 and 10 °C did not display death and this could have been due to lower activity of M. vaginatus at lower temperatures or the inability for the predatory bacterium to attack at lower temperatures.
ContributorsAhamed, Anisa Nour (Author) / Garcia-Pichel, Ferran (Thesis director) / Giraldo Silva, Ana Maria (Committee member) / Bethany Rakes, Julie (Committee member) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Magnetic resonance imaging (MRI) data of metastatic brain cancer patients at the Barrow Neurological Institute sparked interest in the radiology department due to the possibility that tumor size distributions might mimic a power law or an exponential distribution. In order to consider the question regarding the growth trends of metastatic brain tumors, this thesis analyzes the volume measurements of the tumor sizes from the BNI data and attempts to explain such size distributions through mathematical models. More specifically, a basic stochastic cellular automaton model is used and has three-dimensional results that show similar size distributions of those of the BNI data. Results of the models are investigated using the likelihood ratio test suggesting that, when the tumor volumes are measured based on assuming tumor sphericity, the tumor size distributions significantly mimic the power law over an exponential distribution.
ContributorsFreed, Rebecca (Co-author) / Snopko, Morgan (Co-author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / WPC Graduate Programs (Contributor) / School of Accountancy (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2018-12
Description
Prostate cancer is the second most common kind of cancer in men. Fortunately, it has a 99% survival rate. To achieve such a survival rate, a variety of aggressive therapies are used to treat prostate cancers that are caught early. Androgen deprivation therapy (ADT) is a therapy that is given in cycles to patients. This study attempted to analyze what factors in a group of 79 patients caused them to stick with or discontinue the treatment. This was done using naïve Bayes classification, a machine-learning algorithm. The usage of this algorithm identified high testosterone as an indicator of a patient persevering with the treatment, but failed to produce statistically significant high rates of prediction.
ContributorsMillea, Timothy Michael (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Glioblastoma multiforme (GBM) is a malignant, aggressive and infiltrative cancer of the central nervous system with a median survival of 14.6 months with standard care. Diagnosis of GBM is made using medical imaging such as magnetic resonance imaging (MRI) or computed tomography (CT). Treatment is informed by medical images and includes chemotherapy, radiation therapy, and surgical removal if the tumor is surgically accessible. Treatment seldom results in a significant increase in longevity, partly due to the lack of precise information regarding tumor size and location. This lack of information arises from the physical limitations of MR and CT imaging coupled with the diffusive nature of glioblastoma tumors. GBM tumor cells can migrate far beyond the visible boundaries of the tumor and will result in a recurring tumor if not killed or removed. Since medical images are the only readily available information about the tumor, we aim to improve mathematical models of tumor growth to better estimate the missing information. Particularly, we investigate the effect of random variation in tumor cell behavior (anisotropy) using stochastic parameterizations of an established proliferation-diffusion model of tumor growth. To evaluate the performance of our mathematical model, we use MR images from an animal model consisting of Murine GL261 tumors implanted in immunocompetent mice, which provides consistency in tumor initiation and location, immune response, genetic variation, and treatment. Compared to non-stochastic simulations, stochastic simulations showed improved volume accuracy when proliferation variability was high, but diffusion variability was found to only marginally affect tumor volume estimates. Neither proliferation nor diffusion variability significantly affected the spatial distribution accuracy of the simulations. While certain cases of stochastic parameterizations improved volume accuracy, they failed to significantly improve simulation accuracy overall. Both the non-stochastic and stochastic simulations failed to achieve over 75% spatial distribution accuracy, suggesting that the underlying structure of the model fails to capture one or more biological processes that affect tumor growth. Two biological features that are candidates for further investigation are angiogenesis and anisotropy resulting from differences between white and gray matter. Time-dependent proliferation and diffusion terms could be introduced to model angiogenesis, and diffusion weighed imaging (DTI) could be used to differentiate between white and gray matter, which might allow for improved estimates brain anisotropy.
ContributorsAnderies, Barrett James (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Stepien, Tracy (Committee member) / Harrington Bioengineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
The oceanic biological carbon pump is a key component of the global carbon cycle in which dissolved carbon dioxide is taken up by phytoplankton during photosynthesis, a fraction of which then sinks to depth and contributes to oceanic carbon storage. The small-celled phytoplankton (<5 µm) that dominate the phytoplankton community in oligotrophic oceans have traditionally been viewed as contributing little to export production due to their small size. However, recent studies have shown that the picocyanobacterium Synechococcus produces transparent exopolymer particles (TEP), the sticky matrix of marine aggregates, and forms abundant microaggregates (5-60 µm), which is enhanced under nutrient limited growth conditions. Whether other small phytoplankton species exude TEP and form microaggregates, and if these are enhanced under growth-limiting conditions remains to be investigated. This study aims to analyze how nutrient limitation affects TEP production and microaggregate formation of species that are found to be associated with sinking particles in the Sargasso Sea. The pico-cyanobacterium Prochlorococcus marinus (0.8 µm), the nano-diatom Minutocellus polymorphus (2 µm), and the pico-prasinophyte Ostreococcus lucimarinus (0.6 µm) were grown in axenic batch culture experiments under nutrient replete and limited conditions. It was hypothesized that phytoplankton subject to nutrient limitation will aggregate more than those under replete conditions due to an increased exudation of TEP and that Minutocellus would produce the most TEP and microaggregates while Prochlorococcus would produce the least TEP and microaggregates of the three phytoplankton groups. As hypothesized, nutrient limitation increased TEP concentration in all three species, however they were only significant in nitrogen-limited treatments of Prochlorococcus as well as nitrogen- and phosphorus-limited treatments of Minutocellus. Formation of microaggregates was significantly enhanced in Minutocellus and Ostreococcus cultures in distinct microaggregate size ranges. Minutocellus produced the most TEP per cell and aggregated at higher volume concentrations compared to Prochlorococcus and Ostreococcus. Surprisingly, Ostreococcus produced more TEP than Prochlorococcus and Minutocellus per unit cell volume. These findings show for the first time how nutrient limited conditions enhance TEP production and microaggregation of Prochlorococcus, Minutocellus, and Ostreococcus, providing a mechanism for their incorporation into larger, sinking particles and contribution to export production in oligotrophic oceans.
ContributorsShurtleff, Catrina (Author) / Neuer, Susanne (Thesis advisor) / Lomas, Michael W. (Committee member) / Garcia-Pichel, Ferran (Committee member) / Arizona State University (Publisher)
Created2022
Description
Under current climate conditions northern peatlands mostly act as C sinks; however, changes in climate and environmental conditions, can change the soil carbon decomposition cascade, thus altering the sink status. Here I studied one of the most abundant northern peatland types, poor fen, situated along a climate gradient from tundra (Daring Lake, Canada) to boreal forest (Lutose, Canada) to temperate broadleaf and mixed forest (Bog Lake, MN and Chicago Bog, NY) biomes to assess patterns of microbial abundance across the climate gradient. Principal component regression analysis of the microbial community and environmental variables determined that mean annual temperature (MAT) (r2=0.85), mean annual precipitation (MAP) (r2=0.88), and soil temperature (r2=0.77), were the top significant drivers of microbial community composition (p < 0.001). Niche breadth analysis revealed the relative abundance of Intrasporangiaceae, Methanobacteriaceae and Candidatus Methanoflorentaceae fam. nov. to increase when MAT and MAP decrease. The same analysis showed Spirochaetaceae, Methanosaetaceae and Methanoregulaceae to increase in relative abundance when MAP, soil temperature and MAT increased, respectively. These findings indicated that climate variables were the strongest predictors of microbial community composition and that certain taxa, especially methanogenic families demonstrate distinct patterns across the climate gradient. To evaluate microbial production of methanogenic substrates, I carried out High Resolution-DNA-Stable Isotope Probing (HR-DNA-SIP) to evaluate the active portion of the community’s intermediary ecosystem metabolic processes. HR-DNA-SIP revealed several challenges in efficiency of labelling and statistical identification of responders, however families like Veillonellaceae, Magnetospirillaceae, Acidobacteriaceae 1, were found ubiquitously active in glucose amended incubations. Differences in metabolic byproducts from glucose amendments show distinct patterns in acetate and propionate accumulation across sites. Families like Spirochaetaceae and Sphingomonadaceae were only found to be active in select sites of propionate amended incubations. By-product analysis from propionate incubations indicate that the northernmost sites were acetate-accumulating communities.
These results indicate that microbial communities found in poor fen northern peatlands are strongly influenced by climate variables predicted to change under current climate scenarios. I have identified patterns of relative abundance and activity of select microbial taxa, indicating the potential for climate variables to influence the metabolic pathway in which carbon moves through peatland systems.
ContributorsSarno, Analissa Flores (Author) / Cadillo-Quiroz, Hinsby (Thesis advisor) / Garcia-Pichel, Ferran (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Childers, Daniel (Committee member) / Arizona State University (Publisher)
Created2022
Description
The ability to find evidence of life on early Earth and other planets is constrained by the current understanding of biosignatures and our ability to differentiate fossils from abiotic mimics. When organisms transition from the living realm to the fossil record, their morphological and chemical characteristics are modified, usually resulting in the loss of information. These modifications can happen during early and late diagenesis and differ depending on local geochemical properties. These post-depositional modifications need to be understood to better interpret the fossil record. Siliceous hot spring deposits (sinters) are of particular interest for biosignature research as they are early Earth analog environments and targets for investigating the presence of fossil life on Mars. As silica-supersaturated fluids flow from the vent to the distal apron, they precipitate non-crystalline opal-A that fossilizes microbial communities at a range in scales (μm-cm). Therefore, many studies have documented the ties between the active microbial communities and the morphological and chemical biosignatures in hot springs. However, far less attention has been placed on understanding preservation in systems with complex mineralogy or how post-depositional alteration affects the retention of biosignatures. Without this context, it can be challenging to recognize biosignatures in ancient rocks. This dissertation research aims to refine our current understanding of biosignature preservation and retention in sinters. Biosignatures of interest include organic matter, microfossils, and biofabrics. The complex nature of hot springs requires a comprehensive understanding of biosignature preservation that is representative of variable chemistries and post-depositional alterations. For this reason, this dissertation research chapters are field site-based. Chapter 2 investigates biosignature preservation in an unusual spring with mixed opal-A-calcite mineralogy at Lýsuhóll, Iceland. Chapter 3 tracks how silica diagenesis modifies microfossil morphology and associated organic matter at Puchuldiza, Chile. Chapter 4 studies the effects of acid fumarolic overprinting on biosignatures in Gunnuhver, Iceland. To accomplish this, traditional geologic methods (mapping, petrography, X-ray diffraction, bulk elemental analyses) were combined with high-spatial-resolution elemental mapping to better understand diagenetic effects in these systems. Preservation models were developed to predict the types and styles of biosignatures that can be present depending on the depositional and geochemical context. Recommendations are also made for the types of deposits that are most likely to preserve biosignatures.
ContributorsJuarez Rivera, Marisol (Author) / Farmer, Jack D (Thesis advisor) / Hartnett, Hilairy E (Committee member) / Shock, Everett (Committee member) / Garcia-Pichel, Ferran (Committee member) / Trembath-Reichert, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2021
Description
Predatory bacteria are a guild of heterotrophs that feed directly on other living bacteria. They belong to several bacterial lineages that evolved this mode of life independently and occur in many microbiomes and environments. Current knowledge of predatory bacteria is based on culture studies and simple detection in natural systems. The ecological consequences of their activity, unlike those of other populational loss factors like viral infection or grazing by protists, are yet to be assessed. During large-scale cultivation of biological soil crusts intended for arid soil rehabilitation, episodes of catastrophic failure were observed in cyanobacterial growth that could be ascribed to the action of an unknown predatory bacterium using bioassays. This predatory bacterium was also present in natural biocrust communities, where it formed clearings (plaques) up to 9 cm in diameter that were visible to the naked eye. Enrichment cultivation and purification by cell-sorting were used to obtain co-cultures of the predator with its cyanobacterial prey, as well as to identify and characterize it genomically, physiologically and ultrastructurally. A Bacteroidetes bacterium, unrelated to any known isolate at the family level, it is endobiotic, non-motile, obligately predatory, displays a complex life cycle and very unusual ultrastructure. Extracellular propagules are small (0.8-1.0 µm) Gram-negative cocci with internal two-membrane-bound compartmentalization. These gain entry to the prey likely using a suite of hydrolytic enzymes, localizing to the cyanobacterial cytoplasm, where growth begins into non-compartmentalized pseudofilaments that undergo secretion of vesicles and simultaneous multiple division to yield new propagules. I formally describe it as Candidatus Cyanoraptor togatus, hereafter Cyanoraptor. Its prey range is restricted to biocrust-forming, filamentous, non-heterocystous, gliding, bundle-making cyanobacteria. Molecular meta-analyses showed its worldwide distribution in biocrusts. Biogeochemical analyses of Cyanoraptor plaques revealed that it causes a complete loss of primary productivity, and significant decreases in other biocrusts properties such as water-retention and dust-trapping capacity. Extensive field surveys in the US Southwest revealed its ubiquity and its dispersal-limited, aggregated spatial distribution and incidence. Overall, its activity reduces biocrust productivity by 10% at the ecosystem scale. My research points to predatory bacteria as a significant, but overlooked, ecological force in shaping soil microbiomes.
ContributorsBethany Rakes, Julie Ann (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Gile, Gillian (Committee member) / Cao, Huansheng (Committee member) / Jacobs, Bertram (Committee member) / Arizona State University (Publisher)
Created2022
Description
Climate change is one of the most pressing issues affecting the world today. One of the impacts of climate change is on the transmission of mosquito-borne diseases (MBDs), such as West Nile Virus (WNV). Climate is known to influence vector and host demography as well as MBD transmission. This dissertation addresses the questions of how vector and host demography impact WNV dynamics, and how expected and likely climate change scenarios will affect demographic and epidemiological processes of WNV transmission. First, a data fusion method is developed that connects non-autonomous logistic model parameters to mosquito time series data. This method captures the inter-annual and intra-seasonal variation of mosquito populations within a geographical location. Next, a three-population WNV model between mosquito vectors, bird hosts, and human hosts with infection-age structure for the vector and bird host populations is introduced. A sensitivity analysis uncovers which parameters have the most influence on WNV outbreaks. Finally, the WNV model is extended to include the non-autonomous population model and temperature-dependent processes. Model parameterization using historical temperature and human WNV case data from the Greater Toronto Area (GTA) is conducted. Parameter fitting results are then used to analyze possible future WNV dynamics under two climate change scenarios. These results suggest that WNV risk for the GTA will substantially increase as temperature increases from climate change, even under the most conservative assumptions. This demonstrates the importance of ensuring that the warming of the planet is limited as much as possible.
ContributorsMancuso, Marina (Author) / Milner, Fabio A (Thesis advisor) / Kuang, Yang (Committee member) / Kostelich, Eric (Committee member) / Eikenberry, Steffen (Committee member) / Manore, Carrie (Committee member) / Arizona State University (Publisher)
Created2023