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- All Subjects: Genetics
- Genre: Academic theses
- Creators: Pratt, Stephen
- Member of: ASU Electronic Theses and Dissertations
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Description
Synechocystis sp PCC 6803 is a photosynthetic cyanobacterium that can be easily transformed to produce molecules of interest; this has increased Synechocystis’ popularity as a clean energy platform. Synechocystis has been shown to produce and excrete molecules such as fatty acids, isoprene, etc. after appropriate genetic modification. Challenges faced for large–scale growth of modified Synechocystis include abiotic stress, microbial contamination and high processing costs of product and cell material. Research reported in this dissertation contributes to solutions to these challenges. First, abiotic stress was addressed by overexpression of the heat shock protein ClpB1. In contrast to the wild type, the ClpB1 overexpression mutant (Slr1641+) tolerated rapid temperature changes, but no difference was found between the strains when temperature shifts were slower. Combination of ClpB1 overexpression with DnaK2 overexpression (Slr1641+/Sll0170+) further increased thermotolerance. Next, we used a Synechocystis strain that carries an introduced isoprene synthase gene (IspS+) and that therefore produces isoprene. We attempted to increase isoprene yields by overexpression of key enzymes in the methyl erythritol phosphate (MEP) pathway that leads to synthesis of the isoprene precursor. Isoprene production was not increased greatly by MEP pathway induction, likely because of limitations in the affinity of the isoprene synthase for the substrate. Finally, two extraction principles, two–phase liquid extraction (e.g., with an organic and aqueous phase) and solid–liquid extraction (e.g., with a resin) were tested. Two–phase liquid extraction is suitable for separating isoprene but not fatty acids from the culture medium. Fatty acid removal required acidification or surfactant addition, which affected biocompatibility. Therefore, improvements of both the organism and product–harvesting methods can contribute to enhancing the potential of cyanobacteria as solar–powered biocatalysts for the production of petroleum substitutes.
ContributorsGonzalez Esquer, Cesar Raul (Author) / Vermaas, Willem (Thesis advisor) / Chandler, Douglas (Committee member) / Bingham, Scott (Committee member) / Nielsen, David (Committee member) / Arizona State University (Publisher)
Created2013
Description
How a colony regulates the division of labor to forage for nutritional resources while accommodating for changes in colony demography is a fundamental question in the sociobiology of social insects. In honey bee, Apis mellifera, brood composition impacts the division of labor, but it is unknown if colonies adjust the allocation of foragers to carbohydrate and protein resources based on changes in the age demography of larvae and the pheromones they produce. Young and old larvae produce pheromones that differ in composition and volatility. In turn, nurses differentially provision larvae, feeding developing young worker larvae a surplus diet that is more queen-like in protein composition and food availability, while old larvae receive a diet that mimics the sugar composition of the queen larval diet but is restrictively fed instead of provided ad lib. This research investigated how larval age and the larval pheromone e-β ocimene (eβ) impact foraging activity and foraging load. Additional cage studies were conducted to determine if eβ interacts synergistically with queen mandibular pheromone (QMP) to suppress ovary activation and prime worker physiology for nursing behavior. Lastly, the priming effects of larval age and eβ on worker physiology and the transition from in-hive nursing tasks to outside foraging were examined. Results indicate that workers differentially respond to larvae of different ages, likely by detecting changes in the composition of the pheromones they emit. This resulted in adjustments to the foraging division of labor (pollen vs. nectar) to ensure that the nutritional needs of the colony's brood were met. For younger larvae and eβ, this resulted in a bias favoring pollen collection. The cage studies reveal that both eβ and QMP suppressed ovary activation, but the larval pheromone was more effective. Maturing in an environment of young or old larvae primed bees for nursing and impacted important endocrine titers involved in the transition to foraging, so bees maturing in the presence of larvae foraged earlier than control bees reared with no brood.
ContributorsTraynor, Kirsten S. (Author) / Page, Robert E. (Thesis advisor) / Hölldobler, Berthold (Committee member) / Pratt, Stephen (Committee member) / Liebig, Jürgen (Committee member) / Brent, Colin (Committee member) / Baluch, Page (Committee member) / Arizona State University (Publisher)
Created2014
Description
Proper cell growth and differentiation requires the integration of multiple signaling pathways that are maintained by various post-translational modifications. Many proteins in signal transduction pathways are conserved between humans and model organisms. My dissertation characterizes four previously unknown manners of regulation in the Drosophila Decapentaplegic (Dpp) pathway, a pathway within TGF-beta family. First, I present data that the Dpp signal transducer, Mothers Against Dpp (Mad), is phosphorylated by Zeste-white 3 (Zw3), a kinase involved in the Wingless pathway. This phosphorylation event occurs independently of canonical phosphorylation of Mad by the Dpp receptor. Using ectopic expression of different alleles of Mad, I show that Zw3 phosphorylation of Mad occurs during the cell cycle in pro-neuronal cells and the loss of phosphorylation of Mad by Zw3 results in ectopic neuronal cells. Thus, Mad phosphorylation by Zw3 is necessary for cell cycle control in pro-neuronal cells. Second, I have shown that the regulator dSno, which has previously been shown to be a TGF-beta antagonist and agonist, is also a Wingless pathway antagonist. Loss of function flip-out clones and ectopic expression of dSno both resulted in changes of Wingless signaling. Further analysis revealed that dSno acts at or below the level of Armadillo (Arm) to inhibit target gene expression. Third, I have demonstrated that the protein Bonus, which is known to be involved in chromatin modification, is required in dorsal-ventral patterning. Further experiments discovered that the chromatin modifier is not only a necessary Dpp agonist, but it is also necessary for nuclear localization of Dorsal during Toll signaling. Last, I showed that longitudinal lacking-like (lola-like) is also required in dorsal-ventral patterning. The loss of maternally expressed lola-like prevents dpp transcription. This shows that lola-like is integral in the Dpp pathway. The study of these four proteins integrates different signaling pathways, demonstrating that the process of development is a web of connections rather than a linear pathway.
ContributorsQuijano, Janine C (Author) / Newfeld, Stuart J (Thesis advisor) / Goldstein, Elliott (Committee member) / Chandler, Douglas (Committee member) / Capco, David (Committee member) / Arizona State University (Publisher)
Created2014
Description
Gene-centric theories of evolution by natural selection have been popularized and remain generally accepted in both scientific and public paradigms. While gene-centrism is certainly parsimonious, its explanations fall short of describing two patterns of evolutionary and social phenomena: the evolution of sex and the evolution of social altruism. I review and analyze current theories on the evolution of sex. I then introduce the conflict presented to gene-centric evolution by social phenomena such as altruism and caste sterility in eusocial insects. I review gene-centric models of inclusive fitness and kin selection proposed by Hamilton and Maynard Smith. Based their assumptions, that relatedness should be equal between sterile workers and reproductives, I present several empirical examples that conflict with their models. Following that, I introduce a unique system of genetic caste determination (GCD) observed in hybrid populations of two sister-species of seed harvester ants, Pogonomyrmex rugosus and Pogonomyrmex barbatus. I review the evidence for GCD in those species, followed by a critique of the current gene-centric models used to explain it. In chapter two I present my own theoretical model that is both simple and extricable in nature to explain the origin, evolution, and maintenance of GCD in Pogonomyrmex. Furthermore, I use that model to fill in the gaps left behind by the contributing authors of the other GCD models. As both populations in my study system formed from inter-specific hybridization, I review modern discussions of heterosis (also called hybrid vigor) and use those to help explain the ecological competitiveness of GCD. I empirically address the inbreeding depression the lineages of GCD must overcome in order to remain ecologically stable, demonstrating that as a result of their unique system of caste determination, GCD lineages have elevated recombination frequencies. I summarize and conclude with an argument for why GCD evolved under selective mechanisms which cannot be considered gene-centric, providing evidence that natural selection can effectively operate on non-heritable genotypes appearing in groups and other social contexts.
ContributorsJacobson, Neal (Author) / Gadau, Juergen (Thesis advisor) / Laubichler, Manfred (Committee member) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2012
Description
Persistent cooperation between unrelated conspecifics rarely occurs in mature eusocial insect societies. In this dissertation, I present evidence of non-kin cooperation in the Nearctic honey ant Myrmecocystus mendax. Using microsatellite markers, I show that mature colonies in the Sierra Ancha Mountain of central Arizona contain multiple unrelated matrilines, an observation that is consistent with primary polygyny. In contrast, similar analyses suggest that colonies in the Chiricahua Mountains of southeastern Arizona are primarily monogynous. These interpretations are consistent with field and laboratory observations. Whereas cooperative colony founding was observed frequently among groups of Sierra Ancha foundresses, founding in the Chiricahua population was restricted to individual foundresses. Furthermore, Sierra Ancha foundresses successfully established incipient laboratory colonies without undergoing queen culling following emergence of the first workers. Multi-queen laboratory Sierra Ancha colonies also produced more workers and repletes than haplometrotic colonies, and when brood raiding was induced between colonies, queens of those with more workers had a higher survival probability.
Microsatellite analyses of additional locations within the M. mendax range suggest that polygyny is also present in some other populations, especially in central-northern Arizona, albeit at lower frequencies than that in the Sierra Anchas. In addition, analyses of multiple types of genetic data, including microsatellites, the mitochondrial barcoding region, and over 2000 nuclear ultra-conserved elements indicate that M. mendax populations within the southwestern U.S. and northwestern Mexico are geographically structured, with strong support for the existence of two or more divergent clades as well as isolation-by-distance within clades. This structure is further shown to correlate with variation in queen number and hair length, a diagnostic taxonomic feature used to distinguish honey ant species.
Together, these findings suggest that regional ecological pressures (e.g. colony density , climate) may have acted on colony founding and social strategy to select for increasing workforce size and, along with genetic drift, have driven geographically isolated M. mendax populations to differentiate genetically and morphologically. The presence of colony fusion in the laboratory and life history traits in honey ant that are influenced by colony size, including repletism, brood raiding, and tournament, support this evolutionary scenario.
Microsatellite analyses of additional locations within the M. mendax range suggest that polygyny is also present in some other populations, especially in central-northern Arizona, albeit at lower frequencies than that in the Sierra Anchas. In addition, analyses of multiple types of genetic data, including microsatellites, the mitochondrial barcoding region, and over 2000 nuclear ultra-conserved elements indicate that M. mendax populations within the southwestern U.S. and northwestern Mexico are geographically structured, with strong support for the existence of two or more divergent clades as well as isolation-by-distance within clades. This structure is further shown to correlate with variation in queen number and hair length, a diagnostic taxonomic feature used to distinguish honey ant species.
Together, these findings suggest that regional ecological pressures (e.g. colony density , climate) may have acted on colony founding and social strategy to select for increasing workforce size and, along with genetic drift, have driven geographically isolated M. mendax populations to differentiate genetically and morphologically. The presence of colony fusion in the laboratory and life history traits in honey ant that are influenced by colony size, including repletism, brood raiding, and tournament, support this evolutionary scenario.
ContributorsEriksson, Ti (Author) / Gadau, Jürgen (Thesis advisor) / Taylor, Jay (Thesis advisor) / Fewell, Jennifer (Committee member) / Hӧlldobler, Bert (Committee member) / Johnson, Robert (Committee member) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2018
Description
In species with highly heteromorphic sex chromosomes, the degradation of one of the sex chromosomes can result in unequal gene expression between the sexes (e.g., between XX females and XY males) and between the sex chromosomes and the autosomes. Dosage compensation is a process whereby genes on the sex chromosomes achieve equal gene expression which prevents deleterious side effects from having too much or too little expression of genes on sex chromsomes. The green anole is part of a group of species that recently underwent an adaptive radiation. The green anole has XX/XY sex determination, but the content of the X chromosome and its evolution have not been described. Given its status as a model species, better understanding the green anole genome could reveal insights into other species. Genomic analyses are crucial for a comprehensive picture of sex chromosome differentiation and dosage compensation, in addition to understanding speciation.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
In order to address this, multiple comparative genomics and bioinformatics analyses were conducted to elucidate patterns of evolution in the green anole and across multiple anole species. Comparative genomics analyses were used to infer additional X-linked loci in the green anole, RNAseq data from male and female samples were anayzed to quantify patterns of sex-biased gene expression across the genome, and the extent of dosage compensation on the anole X chromosome was characterized, providing evidence that the sex chromosomes in the green anole are dosage compensated.
In addition, X-linked genes have a lower ratio of nonsynonymous to synonymous substitution rates than the autosomes when compared to other Anolis species, and pairwise rates of evolution in genes across the anole genome were analyzed. To conduct this analysis a new pipeline was created for filtering alignments and performing batch calculations for whole genome coding sequences. This pipeline has been made publicly available.
ContributorsRupp, Shawn Michael (Author) / Wilson Sayres, Melissa A (Thesis advisor) / Kusumi, Kenro (Committee member) / DeNardo, Dale (Committee member) / Arizona State University (Publisher)
Created2016