Theses and Dissertations
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Item Open Access Breaking the MF curse: the regulatory role of the Methyl farnesoate – MEKRE93 pathway in crustacean molting(Colorado State University. Libraries, 2025) Bentley, Vanessa Leah, author; Mykles, Donald L., advisor; Garrity, Deborah M., committee member; Montgomery, Taiowa, committee member; Reist, Noreen, committee memberEcdysis, or the active shedding of the exoskeleton, is critical for arthropod growth, development, and/or regeneration of lost or damaged appendages. The antagonistic interaction between the steroid hormone 20-hydroxyecdysone (20-E) and the sesquiterpenoid juvenile hormone (JH) control insect molting and development, respectively. On the other hand, crustacean molting is primarily regulated through the endocrine crosstalk between 20-E and the neuropeptide molt-inhibiting hormone (MIH). MIH secretion by the X-organ, sinus gland complex (XO) inhibits Y-organ (YO) synthesis of 20-E. Molting is initiated by the decrease in MIH titers thereby allowing increasing 20-E concentrations in the hemolymph. The molting process is divided into different stages where the YO exhibits different phenotypic states: intermolt (IM)– basal, early premolt (EP)– activated, mid premolt (MP)– committed, late premolt (LP)– committed/repressed, ecdysis (E)– repressed, and postmolt (PM)– repressed/basal. The mechanistic target of rapamycin (mTOR) and transforming growth factor beta (TGF-β) signaling leads to YO activation and commitment, respectively. However, the YO transition to- and from- the repressed state is unknown. Methyl farnesoate (MF), commonly referred to as the crustacean JH, is produced by the mandibular organ (MO) and is suppressed by the mandibular organ-inhibiting hormone (MOIH). MF regulates several physiological processes in crustaceans including metamorphosis, development, reproduction, morphogenesis, and molting; however, the underlying mechanism remains unknown and thereby is considered to be "cursed". The differential effects MF has on molting and ecdysteroidogenesis is hypothesized to be regulated through the Methoprene tolerant– Krüppel homolog 1– E93 (MEKRE93) transcriptional cascade. Using bioinformatic approaches, the components of the MF signaling pathway were identified in the European green shore crab (Carcinus maenas) and the blackback land crab (Gecarcinus lateralis) YO transcriptomes, including the MF/JH receptor Methoprene tolerant (Met), the zinc finger transcription factor Krüppel homolog 1 (Kr-h1), Ecdysone response gene 93 (E93), Steroid receptor coactivator (Src), and transcription comediators CREB–binding protein (CBP) and C-terminal–binding protein (CtBP). Additionally, genes encoding for the MF synthetic pathway enzymes were also identified in the YO transcriptomes including 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR), farnesoic acid O-methyltransferase (FAMeT), and FAMeT2. Additionally, a FAMeT2 transcript was also identified in the YO and contains an unconventional domain organization compared to annotated FAMeT. Nonetheless, phylogenetic analysis of each gene was overall highly conserved across pancrustaceans (and occaisionally panarthropodans). Furthermore, in vitro assays showed that C. maenas and G. lateralis YOs were responsive to JH-mimics (e.g. pyriproxyfen, fenoxycarb, methoprene, and hydroprene), but not to MF. Taken altogether, these data suggest that the YO can respond to MF and may have its own MF-innate system serving as an autocrine factor to regulate the YO by acting through a MEKRE93 transcriptional network that can be mediated by coregulators.Item Embargo Integrating genomics and telomere dynamics to understand climate adaptation in a migratory songbird(Colorado State University. Libraries, 2025) Rodriguez, Marina D., author; Ruegg, Kristen C., advisor; Bailey, Susan F., committee member; Bay, Rachael A., committee member; Hoke, Kim L., committee memberDeclines in avian species have become widespread due to numerous threats, including anthropogenic climate change. Migratory birds, which occupy multiple environments throughout their annual cycle, are particularly vulnerable. Understanding and predicting the response of migratory bird species to climate change is critical for targeted conservation efforts and the mitigation of further declines. A key factor in species resilience lies in their ability to genetically adapt to changing environments. Recent advances in conservation genomics have improved our ability to detect local adaptation and predict maladaptation to climate change in non-model species. In my dissertation, I test the overall hypothesis that integrating telomere dynamics and conservation genomics will allow for the identification and validation of fitness-related traits in studies of local adaptation. With this hypothesis, I aim to uncover potential mechanisms of local adaptation and assess the impacts of climate change on the yellow warbler (Setophaga petechia). In my first chapter, I link genetic, phenotypic, and environmental data with telomere length measurements to enhance our understanding of local adaptation and the effects of climate change in this species. In the second chapter, I combine models of genomic offsets with telomere data to validate the prediction that yellow warblers inhabiting regions with high genomic offset experience elevated physiological stress due to climate change. Finally, in my third chapter, I investigate local adaptation to the non-breeding grounds and test whether climate tracking reflects local adaptation across the annual cycle in this migratory species. Taken together, my doctoral research highlights the importance of understanding local adaptation to inform population responses to the changing climate. Importantly, this work represents the first demonstration of how integrating methodologies from modern genomics and assessment of biological measures of stress like telomeres can advance our knowledge of wild species' responses to environmental change and enhance conservation efforts.Item Embargo Function of cGMP-dependent protein kinases that regulate molting in two decapod crustaceans, Gecarcinus lateralis and Carcinus maenas(Colorado State University. Libraries, 2025) Head, Talia, author; Mykles, Donald L., advisor; Sloan, Dan, committee member; Peers, Graham, committee member; Tjalkens, Ron, committee memberPhysiological regulation of molting in decapods is predominantly coordinated by two hormones, the neuropeptide molt-inhibiting hormone (MIH), and steroid molting hormones termed ecdysteroids. MIH is produced and secreted by the X-organ/sinus gland complex located in the eyestalk ganglia and negatively regulates the production of ecdysteroids in the molting gland (Y-organ, YO). MIH signaling begins with a cAMP-dependent triggering phase followed by a cGMP-dependent summation phase which ultimately leads to inhibition of mTORC1-dependent ecdysteroid synthesis. The involvement of cGMP in MIH signaling implicates the activity of cGMP-dependent protein kinase (PKG), although the downstream effects of PKG remain unknown. The goal of this work was to phylogenetically characterize PKGs in crustaceans, characterize the physiological effects of PKG-inhibition on YO ecdysteroid synthesis, and identify potential substrates and downstream effects of MIH-dependent PKG activity in the YO. Two genes encoding PKG, pkg1 and pkg2, were identified in crustaceans and are conserved across metazoans. Alternative splicing of the PKG1 N-terminal region yields three PKG1α and one PKG1β isoform in crustaceans. PKG1 sequences with a 14- to 17- amino acid insertion within the kinase domain were identified in ten decapods and one stomatopod, and may indicate that alternative splicing occurs outside of the N-terminal region. In vitro assays of paired YOs incubated with MIH and PKG inhibitors were used to assess the effects of PKG activity on YO ecdysteroidogenesis in the European green shore crab, Carcinus maenas, and the blackback land crab, Gecarcinus lateralis. In the presence of MIH, inhibition of both PKG1 and PKG2 increased ecdysteroid synthesis relative to MIH alone, whereas PKG2 inhibition enhanced the effects of MIH. These data indicate that the two PKG isoforms have opposing roles in modulating ecdysteroidogenesis via MIH signaling in YOs. Specifically, PKG1 plays a dominant role in MIH signaling by inhibiting ecdysteroid synthesis, while PKG2 counters that inhibition and maintains basal ecdysteroidogenesis in the intermolt YO. Transcriptomic analysis of the PKG isoforms expressed in the YO in both G. lateralis and C. maenas suggest that PKG1α2 may be the dominant isoform expressed in the YO. Transcriptomic expression of PKG2 is dramatically reduced at each point in the molt cycle relative to PKG1 expression. Differential expression of the two kinases may explain how MIH signaling balances ecdysteroid inhibition while maintaining the basal secretion needed for peripheral metabolism during intermolt. Liquid chromatography/tandem mass spectrometry analysis of phosphopeptides enriched from PKG-inhibited YOs from C. maenas and G. lateralis revealed several novel potential substrates of PKG in the YO. Phosphopeptides were identified from proteins that regulate cytoskeletal organization, regulators of transcription and translation, and signaling pathways associated with growth factors and inhibition of the mechanistic target of rapamycin complex 1 (mTORC1). Together, these data indicate that PKG signaling in the YO is isoform-dependent, and may regulate ecdysteroidogenesis by interacting with multiple signaling pathways.Item Open Access Selection and fluorescence based screening of algal strains for temperature tolerance and increased productivity for industrial scale cultivation(Colorado State University. Libraries, 2025) Bertucci, Conor, author; Peers, Graham, advisor; Khakhar, Arjun, committee member; Peebles, Christie, committee member; Reddy, Anireddy, committee memberMicroalgae are emerging as a viable source of sustainable energy and bioproducts due to their rapid growth and capacity to produce valuable products. Their ability to grow in diverse, non-arable environments while minimizing resource use makes them a promising alternative to traditional crops for biofuel, feedstock, and other value-added products. Industrial-scale outdoor cultivation of microalgae subjects cells to dynamic environmental conditions such as fluctuating temperatures that can influence growth and biomass accumulation. This makes selecting a strain that can maintain high productivity crucial for industrial-scale cultivation. The first aim of this thesis was to compare the growth and biomass accumulation of ten strains that were known for their high productivities in temperatures ranging from 18°C to 30°C. Of the ten selected strains, Scenedesmus rubescens NREL 46B-D3 and Monoraphidium minutum 26B-AM were determined to have the best overall growth performance in both temperatures and the highest biomass accumulation when grown at 30°C. S. rubescens and M. minutum exhibited an 88.5% and 22.6% higher average total organic carbon accumulation compared to the next highest performing strain tested. The second aim of this thesis was to utilize gamma irradiation mutagenesis to generate mutants with improved biomass accumulation. Optimal LD90% dosages of 300 Gy and 75 Gy were determined for S. rubescens and M. minutum respectively. 3135 and 3356 putative mutants were characterized for S. rubescens and M. minutum, respectively. A fluorescence-based screening approach was used to screen for putative mutants with altered photophysiology traits correlated with photosynthetic efficiency. A total of 37 S. rubescens putative mutants and 14 putative M. minutum mutants demonstrated repeated photophysiological alterations and were selected for growth comparisons between their wild type counterparts. Only one putative M. minutum mutant, MRM J-325, demonstrated improvements in specific growth rate compared to wild type. This assumed mutant will be scaled up for biomass accumulation experiments at large scale.Item Open Access Uncovering mechanisms driving variation in mutation rates in organellar and nuclear genomes(Colorado State University. Libraries, 2024) Waneka, Gus, author; Sloan, Daniel B., advisor; Lockridge Mueller, Rachel, committee member; Argueso, Juan Lucas, committee member; Stenglein, Mark, committee memberMutations are changes to DNA sequences which drive evolution by supplying raw genetic variation for natural selection to act upon. At the same time, mutations tend to have negative fitness consequences and are the source of genetic diseases. Such costs and benefits of mutation create opposing forces of selection on mutation rate modifiers, which are alleles (typically in DNA repair genes) responsible for increases or decreases to mutation rates. Essentially all eukaryotes possess at least two genomes: the nuclear genome (nucDNA) and the endosymbiotically derived mitochondrial genome (mtDNA). Photosynthetic plants and algae additionally possess endosymbiotically derived plastid genomes (cpDNAs). Together, the mtDNA and cpDNA are referred to as organellar genomes. Chapter 1 of this dissertation provides a framework for understanding how DNA repair machinery and mutation rates have evolved in complex eukaryotic cells. Chapters 2 and 3 focus on specific repair pathways active in organellar genomes. Finally, Chapter 4 shifts focus to understand how environmental perturbations in expression level impact mutation in plant nuclear genomes. Repair of organellar genomes is conducted by nuclear-encoded genes that are translated in the cytosol and targeted to the organelles. In terms of evolutionary history, organellar repair machinery is a mosaic network of bacterial-like repair genes, which came into the cell with the organelles, and nuclear repair genes that have been co-opted for organellar function. In some cases, repair proteins are targeted to both the nucDNA and mtDNA (and/or cpDNA in plants) to perform similar functions. This is the case as for many base excision repair (BER) proteins, which identify and remove of chemically damaged bases. In contrast, organellar repair arsenals are thought to lack canonical mismatch-repair (MMR) and nucleotide excision repair (NER), which are both important repair pathways in nuclear genomes. Instead, the diverse eukaryotic lineages have adopted unique strategies for organellar genome maintenance. As a result, there is a tremendous diversity in mtDNA mutation rates, which show over a 4000-fold variation across eukaryotes. Interestingly, much of this variation is driven by the extremely low point mutation rates plant mtDNAs. In addition, plant organellar genomes are more recombinationally active and plant mtDNAs are structurally unstable compared to the mtDNAs of other eukaryotes. Chapter 2 of this dissertation explores the mechanistic basis of low point mutation rates and recombination-mediated repair in plant organellar genomes. We performed high-fidelity Duplex Sequencing on a panel of Arabidopsis thaliana lines lacking specific organellar genome repair genes. We report large point mutation increases in mutant lines lacking MSH1, a mutS homolog that has been proposed to induce double-stranded breaks at the site of DNA mismatches, effectively shuttling such lesions into homologous recombination (HR) pathways that play important roles in plant organellar genome replication and repair. We see smaller point mutation increases in other mutant lines lacking RADA, RECA1 and RECA3. In addition, we generated long-read Oxford Nanopore sequencing to characterize repeat-mediated recombination in several of the mutants in the panel. Our findings provide valuable insights into the mechanisms driving the fascinating patterns of organellar genome evolution in land plants. The aforementioned lack of NER in organellar genomes is surprising given the importance of NER as a 'catchall' for repair of a variety of bulky DNA lesions in nuclear genomes. Chapter 3 focuses in on the fate of photodamage (an important type of bulky DNA damage) in organellar DNA. To do so, we leverage publicly available XR-seq datasets, which were generated to quantify and map active NER excision products in nuclear genomes following UV exposure. The taxonomic scope of chapter is expanded from plants to also include fungi (the brewer's yeast Saccharomyces cerevisiae) and animals (the model fruit fly Drosophila melanogaster). We find that mtDNA-derived XR-seq reads in A. thaliana and S. cerevisiae have distinct and repeatable patterns in terms of length and internal positioning of pyrimidine dimers (known targets of photodamage formation). These data mirror established patterns of NER-derived reads originating from the nuclear genomes, raising the exciting possibility that NER-like repair pathways may exist in for repair of photodamage in organellar genomes. The focus of chapter 4 shifts to understanding how environmental changes impact mutation in plant nuclear genomes. The textbook view of mutation and adaptation is that mutations occur randomly with respect to their environment-specific fitness consequences. However, this view of random mutation is challenged as evidence increasingly establishes a correlation between increased expression and decreased mutation via the coordination of transcription and DNA repair machinery at the molecular level. As a result of this correlation, intragenomic mutation rates likely vary with changing environments given that expression levels are environmentally labile. Therefore, certain genes may be predisposed to higher or lower mutation rates depending on the environment, though the magnitude and importance of this effect remains largely untested. A technical challenge in addressing these questions is that large scale plant mutation datasets are time and resource intensive to generate. A recent plant study relied on low frequency somatic calls from Illumina based shotgun libraries to generate a large number of mutations, but others report that most of these inferred mutations are sequencing errors. To overcome these challenges, we took a novel approach to measuring somatic mutations by using Duplex Sequencing to quantify mutations in targeted regions of the A. thaliana nucDNA. We identified a set of differentially expressed genes in plants grown at different temperatures, which we then targeted for mutation detection using hybrid capture. In addition to wild type (WT) lines, we also studied mutant lines deficient in BER and MMR to test if either of these pathways are responsible for the correlation between expression and mutation in plants. We found large point mutation increases in the MMR mutants compared to WT plants, which displayed surprisingly few mutations at either temperature. Though the small number of WT mutations precluded a meaningful comparison of expression and mutation in a WT background, this result if nonetheless valuable for establishing that the true frequency of somatic mutations in plants is indeed very low suggesting that previous estimates likely conflated Illumina based sequencing artifacts with mutations. Mutation rates vary by over three orders of magnitude across the tree of life. Much of this variation is captured in mitochondrial mutation rates. The chapters of this dissertation provide valuable insights into the molecular processes that drive mutation rate variation in eukaryotic genomes. Such mechanistic understandings are critical for advancing the broader field of mutation rate evolution.Item Open Access The role of CpNifS in selenium and sulfur plant metabolism: implications for phytoremediation and photosynthesis(Colorado State University. Libraries, 2008) Van Hoewyk, Doug, author; Pilon, Marinus, advisor; Pilon-Smits, Elizabeth, advisorNifS-like proteins are a conserved group of proteins that can cleave the sulfur-containing amino acid cysteine in alanine and elemental sulfur (S), and selenocysteine alanine and selenium (Se). In yeast and bacteria, NifS-like proteins are essential for survival because they provide the S for iron(Fe)-S clusters, a prosthetic group that is inserted into various FeS proteins that have a role in electron transfer. Furthermore, NifS-proteins are an essential part of Se metabolism in organisms that require this trace element. The goal of this research was to characterize the function of a chloroplastic NifS-like protein in Arabidopsis thaliana, designated AtCpNifS. As described in this dissertation, overexpression of CpNifS increases plant tolerance to selenate and accumulation of Se. Increased levels of CpNifS prevents toxic incorporation of selenocysteine into proteins, and thus enhances Se tolerance. This may benefit phytoremediation-the use of plants to naturally clean polluted soils and groundwater. In an effort to further the field of phytoremediation, a transcriptome experiment was performed in order to identify other genes and pathways that are involved in responding to Se stress. However, as divulged, plants likely do not require Se for essential metabolism, and the true function of CpNifS is more likely in the maturation of FeS clusters. The knockdown of CpNifS proteins in Arabidopsis using an inducible RNAi approach revealed that chloroplast function and structure became impaired, and that levels of all tested FeS proteins decreased. Consequently, the rate of photosynthetic electron transport, which is dependent on FeS proteins, diminished, and plants became chlorotic and eventually died. Therefore, CpNifS is required for FeS proteins, and is essential for proper photosynthesis and plant growth.Item Open Access Colorado cytospora canker complex on Populus tremuloides Michx.(Colorado State University. Libraries, 2009) Kepley, Jeff B., author; Reeves, F. Brent, advisorCytospora canker is a serious fungal disease affecting aspen in natural and commercial forests as well as urban sites. In Colorado the causal organism responsible for this canker disease is typically reported to be Cytospora chrysosperma (Pers.) Fr. However, a thorough understanding of the species of Cytospora attacking aspen in Colorado is lacking. Fungal identification has been based upon morphological characteristics of fruiting/vegetative structures despite the plasticity known to occur in such diagnostic features. Examinations of cankers on aspen stems in Colorado revealed a morphologically distinct Cytospora-like fungus that frequently co-occurs with C. chrysosperma. This fungus is a new species and is closely associated with and superficially resembles C. chrysosperma. Based on these findings Cytospora canker on aspen in Colorado is a complex of fungi, contrary to what is typically reported in the literature. Isoenzyme analysis was employed as an initial step to determine the genetic/biochemical differences that occur among and between C. chrysosperma and the new non-C. chrysosperma isolates. Of the twelve enzyme systems initially screened only three, viz., alpha esterase, amylase, and glucose-6-phosphate dehydrogenase, provided good resolution for all isolates. Following cluster analysis, two major clades well-delineated the two taxa. Phylogenetic analyses of ITS1-5.8S-ITS2 rDNA and EF-1α sequences produced phylogenetic trees in which non- C. chrysosperma isolates formed a monophyletic clade (with strong bootstrap support and high posterior probability) within a Cytospora spp. phylogeny. Based on these results the non-C. chrysosperma isolates from aspen in Colorado are considered a new Cytospora species. External morphological features of the ascostromata and conidiomata (natural specimens) as well as histological sections of the new Cytospora sp. reveal conceptacles and conceptacle-like tissues which gives fruit bodies a unique target-like appearance. Cultures are darkly pigmented and display robust (large diameter) bead-like hyphae; many hyphal tips from young cultures lyse. Pycnidia produced in vitro do not enclose a multi-lobed locular structure; rather they have indentations/pockets with conidiophores lining these invaginations as well as pycnidial surfaces. In addition to the Cytospora anamorph a Phialocephala-like synanamorph is produced by some isolates. Descriptions of the new Cytospora species and C. chrysosperma, occurring on aspen in Colorado, are provided.Item Open Access Regulation of copper transport into and within Arabidopsis thaliana chloroplasts: a focus on copper transport proteins(Colorado State University. Libraries, 2007) Gogolin, Kathryn Amy, author; Pilon, Marinus, advisorCopper is an essential micronutrient that is required for the biological processes of photosynthesis and respiration. Nutrients, such as copper, must travel long distances through several organs and across many membranes before they are incorporated into target enzymes. Plastocyanin is a small, copper containing protein that is located within the thylakoid lumen and is vital for photosynthetic activity in higher plants. In addition chloroplasts contain a second target for copper, the superoxide dismutase enzyme CSD2. Although copper is essential it can also be toxic to the cell, therefore there is tight regulation of ion transport. The objective of the research conducted here is to develop a better understanding of copper homeostasis in plant cells. By focusing on the proteins that are involved in the transport of copper new insight can be gained on the delivery pathways of this metal. In this dissertation, I further characterize P-type ATPase of Arabidopsis 1 (PAA1) and P-type ATPase of Arabidopsis 2 (PAA2). An Arabidopsis Copper Chaperone for Cu,Zn Superoxide dimustase (CCS) is identified as a functional homolog of the yeast copper chaperone for Cu,Zn superoxide dimustase (Ccs1/Lys7). I study the effects of altered CCS expression on copper homeostasis in a plant system and I determine that the Heavy Metal Associated 1 transporter functions to transport a metal other than Cu(I) across the chloroplast envelope which affects photosynthetic activity. Finally, I completed a comprehensive analysis of copper transport protein-protein interactions in Arabidopsis studied by the yeast two-hybrid system. With the data gathered here, I propose several new models for copper homeostasis in Arabidopsis. I suggest that there is regulation of Fe Superoxide Dismutase (FeSOD), CCS, and CSD2 in the chloroplast which is controlled by metal cofactor availability, specifically copper. By utilizing the yeast two-hybrid technique, I have identified two new possible delivery pathways for copper. I believe that CCS can deliver copper to Heavy Metal Associated 5 to aid in cell detoxification or possible long distance transport of the ion. Additionally, I propose that copper is transported directly from PAA1 to PAA2 in the chloroplast for delivery to plastocyanin.Item Open Access Pathogen persistence in wildlife populations: case studies of plague in prairie dogs and rabies in bats(Colorado State University. Libraries, 2009) George, Dylan, author; Webb, Colleen, advisorDisease ecology focuses, in part, on how pathogens persist within host wildlife populations For my dissertation my colleagues and I investigated pathogen persistence mechanisms in two host-pathogen systems: Yersinia pestis (plague) in prairie dogs and rabies virus in bats. Plague, caused by the bacterium Yersinia pestis, recently spread into the range of black-tailed prairie dogs (Cynomys ludovicianus) in North America, and has caused drastic and rapid reduction in local prairie dog populations which have generated a metapopulation dynamic for prairie dogs. We developed a stochastic patch occupancy model to determine if prairie dog populations could persist long-term given the effects of plague. Our model demonstrates that metapopulation dynamics can allow prairie dog persistence. Town extinction in this system is caused by plague. Thus, town extinction and plague colonization are two sides of the same coin, which allows to us to interpret plague dynamics implicit within the prairie dog metapopulation. Long-term metapopulation dynamics indicate plague persists within the system and does not require the involvement of additional reservoir hosts (i.e., other resistant rodent species). Bats are a natural reservoir for rabies, and an increasing number of emerging zoonotic viruses. Little is known about mechanisms that generate unique seasonal patterns and allow enzootic pathogen persistence in bat populations. We propose that life history characteristics unique to many bat species coupled with viral adaptations allow for rabies persistence. First, we developed a statistical model to investigate seasonal patterns of rabies cases in bats. Second, we used data from a five-year study of rabies in big brown bats (Eptesicus fuscus) to parameterize a dynamic disease model that elucidates pathogen persistence mechanisms. We show rabies persists in two distinct ways, (1) through effects on bat population viability, and (2) through effects on viral persistence within a viable bat population. Mortality rates vary across seasons, and low rates during hibernation allow long-term bat population viability. Within a viable bat population, viral persistence occurs because of a lengthy incubation period, enhanced by the metabolic effects of host torpor. The mechanisms we identify may be operating in a similar manner for other bat-borne diseases.Item Open Access New roles for calcium channel beta subunits in early zebrafish development(Colorado State University. Libraries, 2008) Ebert, Alicia Marie, author; Garrity, Deborah, advisorVoltage-gated calcium channels are present on pre-synaptic terminals and at neuromuscular junctions in the adult. In embryos, the channel is primarily expressed in the developing heart. The auxiliary β subunit is responsible for trafficking the pore-forming α subunit to the membrane, and regulating the calcium channel kinetics. In non-canonical roles, the β subunit regulates gene silencing, vesicle docking, and calcium release from pancreatic cells. We report here the cloning and expression of two zebrafish β2 genes and two β4 genes. Morpholino inhibition of the β4 subunit slowed or blocked the morphogenetic movements of gastrulation, causing the blastoderm to retract and the embryos to assume dorsalized phenotypes. The nuclei of the extra-embryonic yolk syncytial layer (YSL) contained extra centrosomes, which led to formation of abnormal mitotic spindle. Microtubule arrays in the yolk were disrupted or absent. In 48 hpf embryos, the axis of the embryo was expanded mediolaterally and shorter anteroposteriorly. Gastrulation defects were present as early as shield formation. These data combined support the hypothesis for a novel role of the β4 subunit in early zebrafish development.Item Open Access Regulation of copper homeostasis in plants: a focus on chloroplastic superoxide dismutases and copper delivery mechanisms(Colorado State University. Libraries, 2009) Cohu, Christopher Michael, author; Pilon, Marinus, advisorCopper (Cu) is an essential micronutrient for higher plant growth and is found in proteins that are important in photosynthesis and respiration. As a cofactor, this trace element is associated with many proteins including plastocyanin, Cu/Zn superoxide dismutase (Cu/ZnSOD), and mitochondrial cytochrome- c oxidase. Due to its redox-active role, Cu is essential for plant life, yet Cu is also dangerous as a free cellular ion and even toxic if in excess. Therefore, delivery and sequestration of Cu must be tightly regulated. The research of this dissertation indicates that sensory mechanisms and signaling pathways exist to coordinate Cu transport and target protein expression based on Cu status. For Arabidopsis and crop species, chloroplastic Cu/ZnSOD is down-regulated during limited Cu availability while at the same time FeSOD is up-regulated. During Cu-limited growth, when Cu/ZnSOD is down-regulated, plastocyanin levels do not change. We suggest that this reduction in Cu/ZnSOD allows for preferential Cu delivery to plastocyanin, which is essential for photosynthesis, while also maintaining chloroplast SOD activity. Cu delivery to Cu/ZnSOD is accomplished by the Cu Chaperone for SOD (CCS). When a CCS loss of function mutant was grown on Cu supplemented soil Cu/ZnSOD and FeSOD activity was not detected. Chloroplast did not exhibit an observable phenotype or photosynthetic deficiencies, even after high light stress treatments. Recent studies have shown that Cu/ZnSODs in the cytosol and chloroplast, along with other Cu proteins, are regulated by Cu via microRNA directed cleavage of Cu protein mRNA. It has also been determined that during Cu-limited growth the SPL7 transcription factor plays a central role in activating Cu-microRNAs and possibly Cu transporters. The research of this dissertation indicates that CCS is also regulated by Cu, mediated by microRNA398, which was not previously predicted by bioinformatic algorithms. Furthermore, data is presented to suggest that SPL7 likely regulates the promoter of FeSOD by activating transcription during limited Cu availability.Item Open Access Population ecology of black-footed ferrets (Mustela nigripes) in relation to sylvatic plague(Colorado State University. Libraries, 2023) Livieri, Travis M., author; Angeloni, Lisa, advisor; Antolin, Michael, committee member; Biggins, Dean, committee member; Crooks, Kevin, committee memberInfectious diseases can have significant impacts, both direct and indirect, on the conservation of endangered species. A full understanding of these impacts is hindered by the difficulty of teasing apart disease effects from other factors that led to endangerment, the scarcity of population data from before and after disease detection, and the inherent challenge of studying rare species, which are often difficult to detect. Ideally, a disease and population monitoring strategy will detect outbreaks so effective management and mitigation strategies can be implemented. Disease mitigation strategies, such as vaccination or removal of infected individuals, can be effective but costly to implement and rigorous evaluations of such efforts are rare. Here we present a case study and evaluation of a multi-faceted effort to manage multiple impacts of sylvatic plague (plague hereafter), an invasive disease, in a reintroduced population of endangered black-footed ferrets (Mustela nigripes) and their prey, black-tailed prairie dogs (Cynomys ludovicianus), in Conata Basin/Badlands National Park, South Dakota. Since reintroduction in 1994-1999, this is the largest free-ranging ferret population. Chapter One provides a broad introduction to black-footed ferret natural history, ecology, and conservation efforts. We briefly described the life history of black-footed ferrets, their reliance upon prairie dogs (Cynomys spp.) as prey and habitat engineers, and the conflicts between prairie dogs and agricultural interests that motivated human efforts to eradicate prairie dogs and inadvertently drove ferrets towards extinction. Ensuing captive breeding and reintroduction efforts averted extinction of the species, but plague, caused by Yersinia pestis bacteria, led to high mortality in both black-footed ferrets and prairie dogs, was a second factor in ferret decline, and continues to threaten reintroduced populations. Plague management, through flea vector control and vaccination, is a high priority for the black-footed ferret recovery program, along with maintaining genetic diversity and securing habitat. We concluded that black-footed ferret recovery to date has been partially successful, but challenges remain, and plague represents the largest biological threat. In Chapter Two, we evaluated the efforts to manage plague for black-footed ferrets and prairie dogs at Conata Basin/Badlands National Park. We effectively monitored plague using carnivore serology, prairie dog testing, and visual surveys to detect the invasion of plague and inform our mitigation efforts. Both prairie dog colonies and black-footed ferret populations declined precipitously with the plague epizootic. We applied deltamethrin dust into prairie dog burrows to kill fleas and vaccinated black-footed ferrets against plague during annual monitoring efforts. Our results suggested that dusting was effective in maintaining prairie dog colonies compared to non-dusted colonies and significantly increasing survival of black-footed ferrets. Additionally, our vaccination of black-footed ferrets added incremental gains in ferret survival. These combined efforts of plague surveillance, dusting prairie dog burrows, and vaccinating black-footed ferrets likely prevented extirpation of this population. In Chapter Three, we used stable isotope analysis to understand the effects of plague on the proportion of prairie dogs in black-footed ferret diets. Previous studies on black-footed ferrets found up to one-third of ferret diet is comprised of non-prairie dog rodents. Plague causes high mortality in prairie dogs and other small mammals found on prairie dog colonies, potentially increasing variability in prey available for black-footed ferrets. We sampled black-footed ferrets and two prey items, prairie dogs and deer mice (Peromyscus sonoriensis), before and during a plague epizootic and used stable isotope analysis to estimate the diet proportions in relation to plague and dusting. We found that prior to plague black-footed ferret diets in Conata Basin/Badlands National Park were similar to previous studies, but during a plague epizootic ferrets shifted their diet almost completely to prairie dogs. Dusting prairie dog burrows prior to the invasion of plague had a similar effect in shifting black-footed ferret diets. We concluded that despite observed foraging plasticity, black-footed ferrets can be considered prairie dog colony specialists, and any diet effects following deltamethrin dust treatment are likely less severe than the impacts of plague on unprotected ferret populations.Item Open Access Expanding on expansion: genome gigantism and its effects on DNA methylation, RNA splicing and organellar scaling(Colorado State University. Libraries, 2023) Adams, Alexander Nichols, author; Mueller, Rachel, advisor; Hanson, Jeffrey, committee member; Hoke, Kim, committee member; Sloan, Dan, committee memberAcross the tree of life, the correlated traits of genome size and cell size both vary by orders of magnitude, with the increase in genome size being largely attributable to an increase in transposable elements (TEs) throughout the genome. This accumulation of TEs affects many facets of the cell including DNA regulation, organellar scaling, and RNA transcription. This dissertation will explore all 3 of these facets through the lens of genome gigantism and address how these facets differ in large cells in comparison to cells that are more typical in size. The first chapter will discuss methylation of cytosines at genomic CpG dinucleotide sites that silence TEs. TE abundance drives differences in genome size, but TE silencing variation across genomes of different sizes remains largely unexplored. Salamanders include most of the largest C-values — 9 to 120 Gb. We measured CpG methylation levels in salamanders with genomes ranging from 2N = ~58 Gb to 4N = ~116 Gb. We compared these levels to results from endo- and ectothermic vertebrates with more typical genomes. Salamander methylation levels are ~90%, higher than all endotherms. However, salamander methylation does not differ from the other ectotherms, despite a ~100-fold difference in nuclear DNA content. Because methylation affects the nucleotide compositional landscape through 5-methylcytosine deamination to thymine, we quantified salamander CpG dinucleotide levels and compared them to other vertebrates. Salamanders have comparable CpG levels to other ectotherms, and ectotherm levels are higher than endotherms. These data show no shift in global methylation at the base of salamanders, despite a dramatic increase in TE load and genome size. This result is reconcilable with previous studies by considering endothermy and ectothermy, which may be more important drivers of methylation in vertebrates than genome size. The next chapter will look at how an increase in cell size affects organellar structure and abundance. Depending on their shape, organelles can scale in larger cells by increasing volume, length, or number. Scaling may also reflect demands placed on organelles by increased cell size. The 8,653 species of amphibians exhibit diverse cell sizes, providing a powerful system to investigate organellar scaling. Using transmission electron microscopy and stereology, we analyzed three frog and salamander species whose enterocyte cell volumes range from 228 to 10,593 μm3. We show that the nucleus increases in radius (i.e. spherical volume) while the mitochondria increase in total network length; the endoplasmic reticulum and Golgi apparatus, with their complex shapes, are intermediate. Notably, all four organelles increase in volume proportionate to cell volume. This pattern suggests that protein concentrations are the same across amphibian species that differ 50-fold in cell size, and that organellar building blocks are incorporated into more or larger organelles following the same "rules" across cell sizes, despite variation in metabolic and transport demands. This conclusion contradicts results from experimental cell size increases, which produce severe proteome dilution. We hypothesize that salamanders have evolved the biosynthetic capacity to maintain a functional proteome despite a huge cell volume. Finally, the last chapter will be discussing differences in intronic splicing, an important step that pre-mRNA transcripts undergo during processing in the nucleus to become mature mRNAs. Although long thought to occur exclusively in a single step, some introns are now also known to be removed in multiple steps through a process called recursive splicing. This non-canonical form of splicing is hypothesized to aid with intron splicing fidelity, particularly in longer introns. Using West African lungfish (Protopterus annectens; genome size ~40Gb) as a model, we use total RNA-seq data to test the hypothesis that gigantic genomes, which have relatively long introns, have increased levels of recursive splicing compared to genomes of more typical size. Our results reveal levels of recursive splicing at conserved sites similar to those seen in humans, suggesting that genome-wide intronic expansion accompanying evolutionary increase in genome size is not associated with the evolution of high levels of recursive splicing. However, in addition to these results, we also observed patterns of decreasing RNA-seq read depths across entire intron lengths and note that both canonical co-transcriptional splicing and stochastic recursive splicing using many random splice sites could produce this pattern. Thus, we infer canonical co-transcriptional splicing and/or stochastic recursive splicing — but not widespread recursive splicing at conserved sites — manage the removal of long introns.Item Open Access Advancing conservation genomics of migratory species toward a full annual cycle approach(Colorado State University. Libraries, 2023) DeSaix, Matthew G., author; Ruegg, Kristen C., advisor; Funk, W. Chris, committee member; Koons, David N., committee member; Marra, Peter M., committee memberGlobal biodiversity loss is one of the foremost concerns of conservation efforts in the 21st century. The maintenance of genetic diversity within species is a critical factor in a species' persistence and adaptive potential in the face of changing environmental conditions. Migratory species make up more than 12% of the global vertebrate biodiversity and pose distinct challenges to conservation efforts due to inhabiting different geographical regions at different times of the year. The field of conservation genomics provides a valuable toolkit to addressing and understanding global biodiversity loss but requires additional methodological developments to better address the conservation challenges posed by migratory species. In my dissertation, I demonstrate advancements in conservation genomics aimed toward better understanding migratory species. In my first study, I addressed the question of ecological and genomic vulnerability to climate change in the Brown-capped Rosy-Finch (Leucosticte australis), an elevational migratory songbird of conservation concern. Second, I addressed a methodological gap in population genomics and developed statistical genetics models for using genotype likelihood data from low-coverage whole genome sequencing data to implement population assignment. In my last study, I demonstrate the utility of low-coverage whole genome sequencing for population assignment with detailing migratory connectivity in the American Redstart (Setophaga ruticilla). Altogether, my doctoral research demonstrates how genomic tools can help unravel the complexities of migratory species conservation. Furthermore, the species-specific results are tied to knowledge gaps identified by wildlife managers and provide valuable information tied to conservation and management applications.Item Open Access The evolution of plasticity in the transcriptome of the Trinidadian guppy(Colorado State University. Libraries, 2023) Whedbee, Miles, author; Hoke, Kim, advisor; Sloan, Dan, committee member; Montgomery, Taiowa, committee member; Ben-Hur, Asa, committee memberPhenotypic plasticity is a ubiquitous feature of all living systems, and there is much interest in how plasticity influences long term evolutionary trajectories. One of the major complications with modeling evolutionary trajectories is that plasticity itself is known to evolve. The evolution of plasticity has mainly been focused on at the level of the whole organism, and it is unclear if plasticity at all levels of biological organization evolve. Models that assume no generational change in plasticity may be overly simplistic; a more nuanced approach could incorporate the evolution of plasticity into the modeling. A first step towards this end is to determine what levels of biological organization plasticity evolves, and then to determine if there are predictable patterns of evolved plasticity. RNA is an intermediate to DNA and protein, that can undergo changes in response to environmental conditions, thereby modifying the genetic information passed on to non-coding RNAs, functional RNAs, and proteins. Responses to environment include both changes in abundance of RNAs, as well as changes to the composition of the molecules. This dissertation focuses on the evolution of plasticity within the transcriptome of Poecilia reticulata (Trinidadian guppy). One of the major known regulators of transcript abundance are small RNAs (sRNAs). Micro RNAs (miRNAs), are a specific type of sRNA that bind transcripts, typically leading to translational silencing. We investigated two forms of plasticity, an abundance measure of plasticity (miRNA differential expression), and a compositional measure of plasticity (A-to-I RNA editing). A-to-I RNA editing is the chemical nucleotide change from adenosine to inosine, catalyzed by the enzyme ADAR. We first produced a set of miRNAs in guppies, and confirmed the presence of key biogenesis pathway components, i.e. argonaute proteins in the genome. Tissue-specific miRNA expression patterns were identified for three tissues in Poecilia reticulata (Trinidadian guppy), brain, ovary and testis. We found most discovered miRNAs were located in intergenic regions of the genome. Some miRNAs matched known miRBase sequences, while others were considered novel guppy miRNAs. We observed miRNAs expressed from tandem clusters and analyzed piRNA distribution in ovary samples. This study provides important insights into guppy small RNA expression, laying the groundwork for future investigations into their regulatory roles. The 3rd chapter of this dissertation revealed many miRNAs with differential expression (DE), including population main effects, rearing condition, and their interactions. Population DE miRNAs showed a wide range of expression levels. Rearing condition main effects were (slightly) less common. We identified miRNAs with evolved expression plasticity, distributed across four categories: reversed, evolved plastic, assimilated, and accommodated. Both populations showed similar numbers of miRNAs exhibiting plasticity. In the final chapter of this dissertation we characterized the "editome" of guppies. The majority of the edits were consistent with A-to-I editing, with a smaller proportion of C-to-U edits. The intragenic edits were distributed among a number of genes. However, there were no significant differences in editing between populations, rearing conditions, or their interaction. This dissertation revealed significant miRNA expression differences and provided insights into A-to-I editing patterns in guppies.Item Open Access Slow and noisy: developmental time and gene expression kinetics in big cells(Colorado State University. Libraries, 2023) Taylor, Alexandra, author; Mueller, Rachel, advisor; Prasad, Ashok, advisor; Hoke, Kim, committee member; Krapf, Diego, committee memberEvolutionary increases in genome size, cell volume, and nuclear volume have been observed across the tree of life, with positive correlations documented between all three traits. It is well documented that developmental tempo slows as genomes, nuclei, and cells increase in size, yet the driving mechanisms are poorly understood. Meanwhile, the dramatic increases in cell volume seen across the tree of life pose interesting questions about a potential relationship between cell volume and stochastic noise at the single cell level, but this remains an underexplored area of research. To bridge these knowledge gaps, we use a mix of deterministic and stochastic, as well as species-specific and more general, models of the somitogenesis clock. In doing so, we explore the impact of changing intra-cellular gene expression kinetics induced by increasing genome size, nuclear volume, and cell volume on developmental tempo and gene expression noise. Results suggest that longer transcriptional and nuclear export times act to slow cell and developmental processes down as genome size and cell volume increase, and that "search processes" undergone by gene products within a cell become noisier with increasing volume. Analyses of stochastic model simulations and existing empirical data bring into question whether or not cell-autonomous oscillations can truly exist in the absence of cell-to-cell signaling.Item Open Access Enrichment as a conservation tool to enhance behavior, morphology, gene expression, and survival in Arkansas darters(Colorado State University. Libraries, 2023) Kopack, Christopher J., author; Angeloni, Lisa, advisor; Fetherman, Eric, advisor; Ghalambor, Cameron, committee member; Kanno, Yoichiro, committee memberConservation practitioners often rely on captive breeding programs to supplement wild populations at risk of extinction. While population augmentation has been successful for some taxa, the use of hatchery fish to supplement wild populations can be severely impacted by predation. Elevated predation on hatchery fish may arise because hatchery environments often differ starkly from wild environments, constraining the ability of hatchery fish to phenotypically match the environments in which they are targeted for release. Phenotypic mismatch caused by differences between hatchery and wild environments can limit efforts to conserve fish species at risk of extinction when hatchery-reared fish are used to augment wild populations. Phenotypes adapted to or induced by hatchery environments are thought to be maladapted for life in the wild. Thus, enriching the hatchery environment (abiotically and biotically) to make it more similar to the wild may induce phenotypes, including behavior, morphology, and gene expression profiles, that are better suited to the environments fish will experience after release. Chapter One explores how hatchery-reared fish respond to novel predators and whether those responses can be enhanced to improve survival. Identifying the presence of innate predator recognition and the capacity for learning to recognize predators can inform conservation management practices. We assessed antipredator behavior (time spent moving and distance from a predator) and the efficacy of predator training for three populations of a species of conservation concern, the Arkansas darter (Etheostoma cragini), which is vulnerable to predation by esocid predators like the introduced northern pike (Esox lucius). Arkansas darters demonstrated an innate ability to recognize and respond to a novel esocid predator. Their behavior also changed in response to predator cues (training), though the direction of response to cues was opposite our prediction. Populations differed in their response to the predator treatment, highlighting the potential value of managing populations separately. Our results suggest that antipredator behavior is innate and that exposure to predator cues does affect behavior. This study demonstrates the importance of evaluating enrichment practices and incorporating behavioral observations into conservation programs to guide population-specific management decisions. In Chapter Two, we used a factorial approach to assess whether abiotic enrichment and biotic enrichment (predator recognition training) increase survival of Arkansas darters during encounters with a novel predator. We also assessed the effects of abiotic enrichment on the expression of behavioral and morphological phenotypes across three populations. Morphology and behavior differed among populations and between abiotic treatments, and populations responded differently to the abiotic treatments. Furthermore, we found that in combination with predator training, abiotic enrichment increased the probability of surviving a first encounter with a predator. We therefore recommend conservation practitioners incorporate abiotic enrichment and predator recognition training in the hatchery, as any increase in survival is expected to benefit efforts to conserve this species. In Chapter Three, we took a molecular approach (TagSeq) to elucidate how abiotic enrichment and biotic enrichment impacts the whole-brain gene expression of Arkansas darters, comparing the effects in two hatchery populations to a wild reference population. Although, we found no effect of biotic enrichment on gene expression, we did find that abiotic enrichment has the potential to reduce phenotypic mismatch between hatchery and wild fish, indicating that enrichment may aid current conservation efforts. Overall, these studies suggest a potential role for enrichment in the conservation of imperiled fish, and they highlight the value of a phenotypic approach to managing populations.Item Open Access Genetic background and experience affect courtship behavior in male Trinidadian guppies (Poecilia reticulata)(Colorado State University. Libraries, 2023) Phipps, Nathan M., author; Hoke, Kim, advisor; Angeloni, Lisa, committee member; Kanno, Yoichiro, committee memberAn animal's behavior may be shaped by its genetics and life experience, but the extent to which each of these factors contributes to determining behavioral phenotypes is an outstanding question in biology. Mating behaviors are of particular interest due to their importance in determining fitness. We sought to investigate the genetic architecture of mating behaviors and their plasticity in response to mating experience. Trinidadian guppies (Poecilia reticulata) occur in streams with either high or low predation rates. This genetic background has shaped the evolution of many behavioral phenotypes, including those involved in male courtship strategy. We observed male guppies from high predation, low predation, and intercross populations in their first encounter with a female, then later repeated the encounter to observe how experience affects mating behaviors. We recorded occurrences of three behaviors – sigmoids, forced copulation attempts, and gonopodial swings – to determine how they are affected by sexual experience and genetic background. We found that the frequencies of sigmoids and gonopodial swings vary depending on genetic background and experience. Our findings support existing literature demonstrating that mating behaviors respond plastically to experience. We also found that intercross guppies matched the gonopodial swing and sigmoid frequency phenotypes of the QH genetic line, suggesting that these behaviors may be controlled by loci that are dominant in the high-predation population.Item Open Access Evolutionary increase in genome size drives changes in cell biology and organ structure(Colorado State University. Libraries, 2022) Itgen, Michael Walter, author; Mueller, Rachel Lockridge, advisor; Sloan, Daniel B., committee member; Hoke, Kim L., committee member; Zhou, Wen, committee memberThe evolution of large genome size has been associated with patterns of phenotypic change in cell and organismal biology. The most fundamental of these is between genome size and cell size, which share a strong positive and deterministic relationship. As a result, increases in cell size alter the structure and function of the cell. Genome and cell size, together, are hypothesized to produce emergent consequences on development and physiology at the cellular and organismal level. My dissertation aims to better understand these patterns and identify potential mechanisms underlying these phenotypic changes. I test for the effects of genome and cell size on cell function, cellular physiology, and organ morphology by leveraging the natural variation in genome size found in salamanders (Genus: Plethodon). First, I show that transcriptomic data supports the predictions that large genome and cell size has functional consequences on cell biology. I also reject the hypothesis that large cell size is functionally linked to lower metabolic rate at the cellular level, but I provide transcriptomic evidence that cell size alters the metabolic state of cells. Finally, I show that genome and cell size drives morphological change in organ-specific ways in the heart and liver. I conclude that large cell size does not lower metabolic rate in salamanders. As an alternative, I propose that the evolution of low metabolic rate lifts the constraint of cell size, thus permitting the evolution of genome gigantism.Item Open Access Selenium accumulation in plants and implications for human health: a survey of molecular, biochemical, and ecological cues(Colorado State University. Libraries, 2022) Lima, Leonardo Warzea, author; Pilon-Smits, Elizabeth, advisor; Schiavon, Michela, committee member; Pilon, Marinus, committee member; Antunes, Mauricio, committee member; Paschke, Mark, committee memberTo view the abstract, please see the full text of the document.