Matching Items (33)
Description
Synthetic biology is constantly evolving as new ideas are incorporated into this increasingly flexible field. It incorporates the engineering of life with standard genetic parts and methods; new organisms with new genomes; expansion of life to include new components, capabilities, and chemistries; and even completely synthetic organisms that mimic life while being composed of non-living matter. We have introduced a new paradigm of synthetic biology that melds the methods of in vitro evolution with the goals and philosophy of synthetic biology. The Family B proteins represent the first de novo evolved natively folded proteins to be developed with increasingly powerful tools of molecular evolution. These proteins are folded and functional, composed of the 20 canonical amino acids, and in many ways resemble natural proteins. However, their evolutionary history is quite different from natural proteins, as it did not involve a cellular environment. In this study, we examine the properties of DX, one of the Family B proteins that have been evolutionarily optimized for folding stability. Described in chapter 2 is an investigation into the primitive catalytic properties of DX, which seems to have evolved a serendipitous ATPase activity in addition to its selected ATP binding activity. In chapters 3 and 4 we express the DX gene in E. coli cells and observe massive changes in cell morphology, biochemistry, and life cycle. Exposure to DX activates several defense systems in E. coli, including filamentation, cytoplasmic segregation, and reversion to a viable but non-culturable state. We examined these phenotypes in detail and present a model that accounts for how DX causes such a rearrangement of the cell.
ContributorsStomel, Joshua (Author) / Chaput, John C (Thesis advisor) / Korch, Shaleen (Committee member) / Roberson, Robert (Committee member) / Ghirlanda, Gionvanna (Committee member) / Arizona State University (Publisher)
Created2011
Description
The cyanobacterium Synechocystis sp. PCC 6803 performs oxygenic photosynthesis. Light energy conversion in photosynthesis takes place in photosystem I (PSI) and photosystem II (PSII) that contain chlorophyll, which absorbs light energy that is utilized as a driving force for photosynthesis. However, excess light energy may lead to formation of reactive oxygen species that cause damage to photosynthetic complexes, which subsequently need repair or replacement. To gain insight in the degradation/biogenesis dynamics of the photosystems, the lifetimes of photosynthetic proteins and chlorophyll were determined by a combined stable-isotope (15N) and mass spectrometry method. The lifetimes of PSII and PSI proteins ranged from 1-33 and 30-75 hours, respectively. Interestingly, chlorophyll had longer lifetimes than the chlorophyll-binding proteins in these photosystems. Therefore, photosynthetic proteins turn over and are replaced independently from each other, and chlorophyll is recycled from the damaged chlorophyll-binding proteins. In Synechocystis, there are five small Cab-like proteins (SCPs: ScpA-E) that share chlorophyll a/b-binding motifs with LHC proteins in plants. SCPs appear to transiently bind chlorophyll and to regulate chlorophyll biosynthesis. In this study, the association of ScpB, ScpC, and ScpD with damaged and repaired PSII was demonstrated. Moreover, in a mutant lacking SCPs, most PSII protein lifetimes were unaffected but the lifetime of chlorophyll was decreased, and one of the nascent PSII complexes was missing. SCPs appear to bind PSII chlorophyll while PSII is repaired, and SCPs stabilize nascent PSII complexes. Furthermore, aminolevulinic acid biosynthesis, an early step of chlorophyll biosynthesis, was impaired in the absence of SCPs, so that the amount of chlorophyll in the cells was reduced. Finally, a deletion mutation was introduced into the sll1906 gene, encoding a member of the putative bacteriochlorophyll delivery (BCD) protein family. The Sll1906 sequence contains possible chlorophyll-binding sites, and its homolog in purple bacteria functions in proper assembly of light-harvesting complexes. However, the sll1906 deletion did not affect chlorophyll degradation/biosynthesis and photosystem assembly. Other (parallel) pathways may exist that may fully compensate for the lack of Sll1906. This study has highlighted the dynamics of photosynthetic complexes in their biogenesis and turnover and the coordination between synthesis of chlorophyll and photosynthetic proteins.
ContributorsYao, Cheng I Daniel (Author) / Vermaas, Wim (Thesis advisor) / Fromme, Petra (Committee member) / Roberson, Robert (Committee member) / Webber, Andrew (Committee member) / Arizona State University (Publisher)
Created2011
Description
An issue with the utilization of swimming pools is that pumps are operated an excessive number of hours to keep the pool free of debris and algae. Case in point, according to the pool industry, a pump should operate one hour for every ten degrees of ambient temperature. A dynamic model and a control strategy have been developed using Matlab/Simulink that uses environmental conditions together with chemicals that hinder or aid algae growth in order to determine algae population. This model suggests ways to function the pump on shorter time intervals to reduce energy consumption, while simultaneously maintaining algae populations at acceptable levels. Other factors included in the model are pool thermal dynamics and pool pump/filter performance characteristics, since they also have an effect algae growth. This thesis presents the first step for an alternative way of operating a swimming pool by minimizing operating costs while eliminating algae.
ContributorsBallard, Roderick (Author) / Macia, Narciso (Thesis advisor) / Narveson, Brentt (Committee member) / Mchenry, Albert (Committee member) / Dempster, Thomas (Committee member) / Arizona State University (Publisher)
Created2012
Description
Photosynthesis is a critical process that fixes the carbon utilized in cellular respiration. In higher plants, the immutans gene codes for a protein that is both involved in carotenoid biosynthesis and plastoquinol oxidation (Carol et al 1999, Josse et al 2003). This plastoquinol terminal oxidase (PTOX) is of great interest in understanding electron flow in the plastoquinol pool. In order to characterize this PTOX, polyclonal antibodies were developed. Expression of Synechococcus WH8102 PTOX in E. coli provided a useful means to harvest the protein required for antibody production. Once developed, the antibody was tested for limit of concentration, effectiveness in whole cell lysate, and overall specificity. The antibody raised against PTOX was able to detect as low as 10 pg of PTOX in SDS-PAGE, and could detect PTOX extracted from lysed Synechococcus WH8102. The production of this antibody could determine the localization of the PTOX in Synechococcus.
ContributorsKhan, Mohammad Iqbal (Author) / Moore, Thomas (Thesis director) / Redding, Kevin (Committee member) / Roberson, Robert (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
Transmission electron microscopy has been used to identify poly-3-hydroxybutyrate (PHB) granules in cyanobacteria for over 40 years. Electron-transparent (sometimes containing a slightly electron-dense area in the inclusions) or slightly electron-dense spherical inclusions found in transmission electron micrographs of cyanobacteria are often assumed to be PHB granules. The aim of this study was to test this assumption in Synechocystis sp. PCC 6803, and to determine whether all inclusions of this kind are indeed PHB granules. Based on the results gathered, it is concluded that not all of the slightly electron-dense spherical inclusions are PHB granules in Synechocystis sp. PCC 6803. This result is potentially applicable to other cyanobacteria.
ContributorsTsang, Tin Ki (Author) / Vermaas, Willem F. J. (Thesis director) / Nielsen, David (Committee member) / Roberson, Robert (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2013-05
Description
There is a wide intersection where animal and human lives interact or mimic each other behaviorally or biologically. A lot of the products that are part of our day-to-day were first validated by animals, and eventually found their way to us. From food to beauty products to scientific developments, animals deal with a lot behind the scenes. Some humans are cognizant of what is happening backstage, while others only see the final presentation. Either way, all of us have our opinions in support or against animal treatment. The project is heavily inspired from my experience in a neurorehabilitation lab, so the foundation is similar to the structure and function of neurons. Through this project, I am focusing on one aspect of this debate, which is animal testing in the scietific setting. The goal of the project is not to force the viewer to choose one side, but to understand the big picture and the reasoning of the opposing side.
ContributorsSharma, Bhavya (Author) / Beiner, Susan (Thesis director) / Roberson, Robert (Committee member) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description
Amphibians around the world are suffering the effects of the chytrid fungus, Batrachochytrium dendrobatidis (Bd). Whenever amphibians are housed in captivity, they must go through a decontamination protocol to ensure they are not infected with diseases such as Bd. Itraconazole is the most commonly used fungicide used in these protocols. This study set out to determine if Bd could develop resistance or tolerance to itraconazole. Two 24 well plates were prepared with different concentrations of itraconazole with Bd zoospores added. Plate 1 had concentrations similar to what animals are currently being treated with in decontamination protocols. Plate 2 had concentrations at and below the published minimum inhibitory concentration values (MIC). Plate 1 displayed the ability of itraconazole to kill Bd sporangia with higher concentrations and Plate 2 showed that even under published MIC values, Bd still struggled to complete its reproductive cycle. I find the evolution of a resistant/tolerant strain of Bd unlikely given the efficacy of this drug, the sensitivity of Bd to itraconazole, and the lack of evidence of the completion of Bd’s reproductive cycle under the conditions used in this study.
ContributorsSommer, Bradley Dean (Author) / Collins, James (Thesis director) / Roberson, Robert (Committee member) / Brus, Evan (Committee member) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05
Description
Batrachochytrium dendrobatidis (Bd), the amphibian chytrid fungus causing chytridiomycosis, is the cause of massive amphibian die-offs. As with any host-pathogen relationship, it is paramount to understand the growth and reproduction of the pathogen that causes an infectious disease outbreak. The life-cycle of the pathogen, Bd, is strongly influenced by temperature; however, previous research has focused on Bd isolated from limited geographic ranges, and may not be representative of Bd on a global scale. My research examines the relationship between Bd and temperature on the global level to determine the actual thermal maximum of Bd. Six isolates of Bd, from three continents, were incubated at a temperature within the thermal range (21°C) and a temperature higher than the optimal thermal range (27°C). Temperature affected the growth and zoosporangium size of all six isolates of Bd. All six isolates had proliferative growth at 21°C, but at 27°C the amount and quality of growth varied per isolate. My results demonstrate that each Bd isolate has a different response to temperature, and the thermal maximum for growth varies with each isolate. Further understanding of the difference in isolate response to temperature can lead to a better understanding of Bd pathogen dynamics, as well as allow us the ability to identify susceptible hosts and environments before an outbreak.
ContributorsWoodland, Laura Elizabeth (Author) / Collins, James (Thesis director) / Davidson, Elizabeth (Committee member) / Roberson, Robert (Committee member) / School of Politics and Global Studies (Contributor) / School of Molecular Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has captured human attention because it is a pathogen that has contributed to global amphibian declines. Despite increased research, much is still unknown about how it develops. For example, the fact that Bd exhibits phenotypic plasticity during development was only recently identified. In this thesis, the causes of phenotypic plasticity in Bd are tested by exposing the fungus to different substrates, including powdered frog skin and keratin, which seems to play an important role in the fungus's colonization of amphibian epidermis. A novel swelling structure emerging from Bd germlings developed when exposed to keratin and frog skin. This swelling has not been observed in Bd grown in laboratory cultures before, and it is possible that it is analogous to the germ tube Bd develops in vivo. Growth of the swelling suggests that keratin plays a role in the phenotypic plasticity expressed by Bd.
ContributorsBabb-Biernacki, Spenser Jordan (Author) / Collins, James P. (Thesis director) / Roberson, Robert (Committee member) / Brus, Evan (Committee member) / School of Film, Dance and Theatre (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05
Description
Microscopic algae have been investigated extensively by researchers for decades for their ability to bioremediate wastewater and flue gas while producing valuable biomass for use as feed, fuel, fertilizer, nutraceutical, and other specialty products. Reports of the exciting commercial potential of this diverse group of organisms started appearing in the literature as early as the 1940’s. However, nearly 80 years later, relatively few successful commercial microalgae installations exist and algae have not yet reached agricultural commodity status. This dissertation examines three major bottlenecks to commercial microalgae production including lack of an efficient and economical cultivation strategy, poor management of volatile waste nutrients, and costly harvesting and post processing strategies. A chapter is devoted to each of these three areas to gain a better understanding of each bottleneck as well as strategies for overcoming them.
The first chapter demonstrates the capability of two strains of Scenedesmus acutus to grow in ultra-high-density (>10 g L-1 dry weight biomass) cultures in flat panel photobioreactors for year-round production in the desert Southwest with record volumetric biomass productivity. The advantages and efficiency of high-density cultivation are discussed. The second chapter focuses on uptake and utilization of the volatile components of wastewater: ammonia and carbon dioxide. Scenedesmus acutus was cultured on wastewater from both municipal and agricultural origin and was shown to perform significantly better on flue gas as compared to commercial grade CO2 and just as well on waste nutrients as the commonly used BG-11 laboratory culture media, all while producing up to 50% lipids of the dry weight biomass suitable for use in biodiesel. The third chapter evaluates the feasibility of using gravity sedimentation for the harvesting of the difficult-to-separate Scenedesmus acutus green algae biomass followed by microfluidization to disrupt the cells. Lipid-extracted biomass was then studied as a fertilizer for plants and shown to have similar performance to a commercially available 4-6-6 fertilizer. Based on the work from these three chapters, a summary of modifications are suggested to help current and future microalgae companies be more competitive in the marketplace with traditional agricultural commodities.
The first chapter demonstrates the capability of two strains of Scenedesmus acutus to grow in ultra-high-density (>10 g L-1 dry weight biomass) cultures in flat panel photobioreactors for year-round production in the desert Southwest with record volumetric biomass productivity. The advantages and efficiency of high-density cultivation are discussed. The second chapter focuses on uptake and utilization of the volatile components of wastewater: ammonia and carbon dioxide. Scenedesmus acutus was cultured on wastewater from both municipal and agricultural origin and was shown to perform significantly better on flue gas as compared to commercial grade CO2 and just as well on waste nutrients as the commonly used BG-11 laboratory culture media, all while producing up to 50% lipids of the dry weight biomass suitable for use in biodiesel. The third chapter evaluates the feasibility of using gravity sedimentation for the harvesting of the difficult-to-separate Scenedesmus acutus green algae biomass followed by microfluidization to disrupt the cells. Lipid-extracted biomass was then studied as a fertilizer for plants and shown to have similar performance to a commercially available 4-6-6 fertilizer. Based on the work from these three chapters, a summary of modifications are suggested to help current and future microalgae companies be more competitive in the marketplace with traditional agricultural commodities.
ContributorsWray, Joshua (Author) / Dempster, Thomas (Thesis advisor) / Roberson, Robert (Thesis advisor) / Bingham, Scott (Committee member) / Neuer, Susanne (Committee member) / Arizona State University (Publisher)
Created2019