Scholars' Bank :: Browsing by Author "Cresko, William"

Browsing by Author "Cresko, William"

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Open Access
Advancing threespine stickleback fish as an outbred immunogenetics model by pinpointing the onset of adaptive immunity
Niebergall, Emily; Beck, Emily; Cresko, William
T-cell deficiencies cause cell-mediated immunodeficiencies including Severe Combined Immunodeficiency (SCID) and DiGeorge Syndrome. Understanding cell-mediated deficiency is complicated by the invasive nature of prenatal tests and by the large role genetic variation plays in etiologies of immune disease. Development of an outbred immunogenetics model system is therefore needed to understand how genetic variation impacts phenotypic variation of immune disease. Threespine stickleback fish (Gasterosteus aculeatus) provide just such a model, with divergent natural populations harboring high levels of genetic and phenotypic variation. Importantly, external fertilization and transparent development of large numbers of progeny facilitate the study of immune cell development in a less labor intensive manner to mammalian systems. However, the timing of onset of the adaptive immune system is currently unknown in stickleback. To identify onset of adaptive immunity, we will analyze gene expression of early activators of adaptive immunity in genetically divergent lines of stickleback. These include V(D)J recombination activating genes, rag1 and rag2, and T cell receptor progenitor genes, tcr-β and tcr-γ. To analyze when expression of these genes is initiated, we will perform rtPCR and in situ hybridization in a developmental time series. Knowing when adaptive immunity onset occurs advances threespine stickleback as an immunogenetics disease model, allowing manipulative studies of immunological phenotypes in the context of genetic variation.
Open Access
The Cellular Basis of Dermal Bone Evolution and Development in Threespine Stickleback Fish
(University of Oregon, 2015) Sichel, Sophie; Alligood, Kristin; Cresko, William
Embargo
Evolution of a Metamorphic Life Cycle in a Marine Invertebrate: Origin of the Pilidium Larva in the Phylum Nemertea
(University of Oregon, 2015-08-18) Hiebert, Laurel; Cresko, William
The pilidium is a novel larval form that arose within a single clade in the phylum Nemertea - the Pilidiophora. While the sister clade of the Pilidiophora, Hoplonemertea, and the basal nemertean clade develop relatively directly, pilidiophorans have a long- lived feeding larva with a body plan distinctly different from that of the juvenile. Uniquely, the pilidiophoran juvenile develops inside the larva from several discrete rudiments. The purpose of this dissertation is to illuminate how this life cycle evolved, both the developmental-genetic mechanisms and timing with respect to the three nemertean clades. With colleagues I describe development of the hoplonemertean Pantinonemertes californiensis using confocal microscopy. We find that the larva possesses two pairs of epidermal invaginations and a transitory epidermis. We hypothesize that these features are homologous to invaginated rudiments and loss of larval epidermis in pilidial development. We examine the expression of the Hox genes during development of the pilidiophoran Micrura alaskensis. We identify nine Hox genes and one ParaHox gene with transcriptome analysis and molecular cloning and determine their developmental expression patterns. We find that Hox genes are not expressed in the pilidium at any stage. Instead, Hox gene expression is restricted to the juvenile trunk rudiments, suggesting that the larva and juvenile are patterned with somewhat dissociated mechanisms. We examine developmental genes in P. californiensis. We find that Hox genes are expressed in the posterior invaginations. We find Six3/6 expression in both pilidial cephalic discs and the hoplonemertean anterior invaginations. Our results support the homology between the pilidium imaginal discs and hoplonemertean larval invaginations. This finding, which is also supported by cell-proliferation patterns, suggests that invaginated rudiments evolved before the pilidiophorans diverged from the hoplonemerteans. Juvenile growth via invaginated rudiments may have paved the way for the more complete separation between larval and juvenile morphogenesis seen in modern pilidiophorans. These discoveries illuminate how larval and juvenile bodies can become mechanistically and morphogenetically dissociated, allowing for somewhat independent evolution across life stages. This may help explain the evolution of metamorphosis and the evolution of the great diversity of marine invertebrate larval forms. This dissertation includes published and unpublished co-authored material.
Open Access
Exploring Biological Agency and Embodiment to Overcome the Limitations of Gene-Centric Perspectives and Relationalize Biological Inquiry
(University of Oregon, 2023-06) Woods, Micah; Muraca, Barbara; Cresko, William
Much of 20th-century biology has been driven by and proceeded through a finer understanding of biological mechanisms at the level of genes and molecules. These gene-centric approaches have located medical interventions, clarified evolutionary histories, and identified molecular signaling pathways, among other invaluable contributions, by mechanistically decomposing biological systems into genetic parts to examine how their structure and functioning explain the system as a whole. However, biology and philosophy of biology scholarship reveal that studying organisms in terms of their genes is limited because it overemphasizes genetic components’ role in development, inheritance, and evolutionary innovation and, in doing so, reduces organisms to the objects of their genes’ predeterminations. Engaging biological case studies and philosophy of biology, I reveal that gene-centrism’s limitations suggest the need for a complementary approach––biological agency––capable of recognizing organisms as agents of their genes, instead of passive objects of their genes’ expression. Through this exploration, I show that a biological agency perspective realizes the ways in which gene expression is interactively shaped by organisms’ spontaneous engagement with their environments, which is further indicative of organisms’ context sensitivity and relational responsiveness. The biological agency approach overcomes gene-centrism’s limitations because it considers organisms as embedded in many intersecting and co-constitutive relationships––genetic, biological, and environmental––of which the organism responds to and accommodates into itself. Using perspectives from feminist epistemology and science studies, I question further into biological agency’s account of organismal relationality to reveal that relationality does not just apply to the organism being studied, but to scientists as well. Considering this extra dimension of relationality helps soften the boundary between subject and object and illuminates that biological scientific inquiry is performed by embodied researchers, theorizing is situated, and objectivity is subjectivity-dependent. Through this consideration, I hope to convey the viability of biological agency as a complement to gene-centrism and build appreciation for biological inquiry that not only recognizes organismal relationality, but the scientist’s relationality.
Open Access
Fish Out of Water: Understanding the Impacts of Regional Species Pool Variation on Local Community Assembly in a Host-Microbiome Model System
(University of Oregon, 2024-08-07) Evens, Kayla; Cresko, William
The host-microbiome is essential to many aspects of host health and function, and acts as a useful model system in which to investigate broader questions of community assembly. Since the composition of host-microbiomes is, in part, determined by the input of microbes from the surrounding environment, it is integral to understand how variation in the environmental microbiome may influence host-microbiome assembly. For my dissertation research, I used a species pool conceptual framework to investigate drivers of variation in the microbiomes of aquaculture research facilities and the fish they house. Zebrafish (Danio rerio) are used extensively as model organisms in scientific research, especially in studies investigating host-microbiome dynamics. For in-vitro experimentation utilizing model organisms, we rely on the reproducibility of results to make broadly applicable conclusions about the host-microbiome. However, evidence suggests that inter-facility variation may influence zebrafish gut microbiome composition via acquisition of microbes from the environment, potentially leading to phenotypic differences among fish housed at different aquaculture facilities. To investigate the relationship between aquaculture facility water and fish gut microbiomes, I first characterized spatial and temporal variation across multiple aquaculture facilities on the University of Oregon campus. Facility water microbiota not only varied over time, but patterns of spatial variation in each facility were consistent despite differences in host species. I then used this information to guide an expanded, intensive sampling of water and fish across four zebrafish facilities in Oregon and Norway. I observed significant variation in microbiome composition both within and between facility water systems and zebrafish gut samples. Further, there was evidence that variation in the water microbiome was a source of variation in zebrafish gut microbiomes. Finally, as differences in facility management and technical specifications can make directly linking microbiome variation in the water to variation in fish difficult, I attempted to isolate the effects by experimentally manipulating the water microbiome in a laboratory study using germ-free larval fish. My results indicate that microbial inputs from live feed overwhelmed any potential influence of water microbiome variation in early-life microbiome assembly. Overall, this dissertation provides a comprehensive look at the drivers of environmental microbiome variation and how these may mediate aspects of host-associated microbiota. My results have implications for fish microbiome research and suggest that research conducted with zebrafish sourced from a single facility may be heavily influenced by facility-specific effects.
Restricted
Gene, Organism and Environment: Understanding Patterns of Genome Evolution in Bacteria and Bacteriophage
(University of Oregon, 2013-10-03) Perry, Elizabeth; Cresko, William
For my dissertation research, I used a model system of bacteria and bacteriophage to study patterns of genome evolution. I performed whole-genome sequencing of replicate populations to determine the genetic changes responsible for a repeatable pattern of coevolution between bacteria and phage. I found that genetic changes conferring resistance in bacteria negatively impacted other traits such as growth rates and sensitivity to antibiotic. Different resistance mutations varied in the magnitude of their pleiotropic costs, and this resulted in a fixation bias favoring mutations that minimized pleiotropic effects. I manipulated the environment and found that differential pleiotropy between environments drove repeatable evolution at different genetic scales. Finally, I explored theoretically how bacteria, phage, and resource interact through a dynamic system of feedbacks. I used a mathematical model to describe priority effects in evolution, where the expected fate of a beneficial mutation varies depending upon whether it appears before or after a competing mutation.
Open Access
Hox Cluster Evolution in the Highly Derived Pipefish & Seahorse Family
(University of Oregon, 2019-04-30) Fuiten, Allison; Cresko, William
A central question in evolutionary biology is how organisms evolve highly derived and novel morphologies. More specifically, what changes to conserved developmental genes lead to the evolution of divergent morphologies? Here, I investigate the genetic and genomic changes to the developmentally important Hox genes using comparative genomics, gene expression and gene editing approaches. Hox genes code for homeodomain transcription factors that are responsible for determining the body plan of an embryo along the anterior-posterior axis, and changes to these genes have paralleled the rise of morphological diversity in the vertebrate animals. I focus my studies in a group of fish that exhibit a striking departure from the typical fish body plan: the pipefish and seahorse family, Syngnathidae. The evolution of syngnathid fish involved major modifications to their vertebrate body plan, but the developmental genetic basis of those changes is largely unknown. I describe the genomic organization of Hox clusters in a species of syngnathid pipefish—the Gulf pipefish (Syngnathus scovelli). I present an initial investigation on phenotypic consequences to the loss of hox7 genes in teleost fish—a group of Hox genes that are missing in syngnathids—using of the CRISPR/Cas9 system to induce indels in all hox7 genes (hoxa7a, hoxb7a) in the threespine stickleback (Gasterosteus aculeatus). In the second half of my thesis, I investigate noncoding changes in the syngnathid Hox clusters. I use syngnathid representative species and compared their conserved noncoding sequences within the Hox clusters to other teleost fish, non-teleost fish, and non-fish vertebrates. I present a detailed study regarding the nature of the loss of one conserved non-coding element. Results from this research indicate that the divergent syngnathid body plan is not due to rampant change in throughout Hox clusters. Also, these data do not argue for the absence of any role of genetic changes in Hox clusters. Instead, the findings presented here support the intermediate hypothesis that certain key changes to the Hox genes, microRNAs, and regulatory elements have probably contributed to their body plan developmental evolution in this unique family of fish. This work includes published co-authored material.
Open Access
Investigating the Molecular Mechanisms of Evolutionary Novelty
(University of Oregon, 2015-01-14) Anderson, David; Cresko, William
Evolution is the descent with modification from common ancestors. Forms and functions diversify as a result of changes in genomic sequence that result in changing molecular functions performed by biological molecules such as proteins, RNA, or DNA. Not all genetic changes, however, result in a change in molecular function; highly distinct gene sequences may nonetheless produce similar functions. At the same time, there are some genetic changes that have a significant effect on molecular function and sometimes highly similar gene sequences may nonetheless produce distinct functional molecules. In order to identify and understand the subsets of genetic changes that were responsible for novel functions, we must apply the tools of molecular biology within an evolutionary framework in order to specifically characterize the functional differentiation of diversified genotypes and further to understand the molecular mechanisms that mediated their functional effects. This dissertation has sought to contribute to this work in three related ways: first, by analyzing the dominant approach used in molecular evolutionary research and outlining a program of research that would best yield insight into the mechanisms of evolutionary change; second, by examining the genetic, biochemical, and biophysical mechanisms that gave rise to a novel DNA-binding function in the steroid receptor transcription factors; and third, by functionally characterizing the sequence space that separates the ancestral and derived DNA-binding function across that evolutionary transition. This body of work has sought to contribute to our general understanding of the principles that underlie the evolutionary process by characterizing the molecular mechanisms that were responsible for some of the interesting, diverse functions that evolution has produced. In doing so, it points towards some important potential general principles that guide evolutionary processes. This dissertation includes published and unpublished co-authored material.
Open Access
Molecular Physiological Evolution: Steroid Hormone Receptors and Antifreeze Proteins
(University of Oregon, 2015-01-14) Cziko, Paul; Cresko, William
For my dissertation research I explored the diversity and functional evolution of steroid hormone receptors (SRs) in animals and the physiological implications of the evolution of antifreeze proteins in Antarctic notothenioid fishes. For the former, I discovered multiple new SRs from the vast and under-sampled swath of animal diversity known as invertebrates. I used the sequences of these and other newly discovered related receptors in combination with genomic data and molecular phylogenetic techniques to revise the understanding of the evolutionary history of this important gene family. While previous studies have suggested that vertebrate SR diversity arose from a gene duplication in an ancestor of all bilaterian animals, my work presents strong evidence that this duplication occurred much later, at the base of the chordates. Furthermore, to determine the implications of added diversity and a revised phylogeny on inferences of the functional evolution of SRs, I functionally characterized heretofore-unknown SRs from hemichordates, an acoelomate flatworm, and a chaetognath and statistically reconstructed and functionally characterized ancestral SRs. My results expand the known sequence and functional repertoire of SRs in animals while reinforcing the previous inference that all SRs evolved from an estrogen-sensitive ancestral receptor. I also explored the consequences of the evolution of antifreeze proteins in Antarctic notothenioid fishes, a crucial adaptation to their icy, polar environment. These special proteins adsorb to ice crystals that enter a fish's body and prevent further growth, thereby averting death. I discovered that, in addition to their lifesaving growth-inhibiting ability, AFPs also prevent the melting of internal ice crystals at temperatures above the expected equilibrium melting point. Together with a decade-long temperature record of one of the coldest fish habitats on earth, my experimental results show that the evolution and expression of antifreeze proteins is accompanied by a potentially detrimental consequence: the lifelong accumulation of ice inside these fishes' bodies. This dissertation includes previously published co-authored material as well as unpublished co-authored material.
Open Access
The Phenotypic and Genetic Distribution of Threespine Stickleback that Inhabit the Willamette Basin, Oregon, USA
(University of Oregon, 2014-10-17) Currey, Mark; Cresko, William
A key to understanding the origin and maintenance of the diversity of life is to understand how phenotypic and genetic variation is partitioned within and among populations. I characterize the spatial partitioning of phenotypic and genetic variation in an old Willamette Basin freshwater distribution of threespine stickleback (Gasterosteus aculeatus) and compare these results to younger populations. Phenotypic variation was measured using 14 phenotypic traits, and genetic variation was assessed using RADseq and Stacks software to identify tens of thousands of single nucleotide polymorphisms. The major partitioning of phenotypic and genetic variation in Oregon is along a stereotypical transition from oceanic to freshwater that has been seen in younger systems. Phenotypic and genetic variation is significantly partitioned between basin populations, and the genetic variation is geographically structured. This work suggests that parallel divergence between oceanic and freshwater forms originated before the end of the last glacial maximum.
Open Access
The Origins and Maintenance of Genomic Variation in the Threespine Stickleback (Gasterosteus aculeatus)
(University of Oregon, 2017-09-06) Nelson, Thomas; Cresko, William
Genetic variation is the raw material of evolution. The sources of this variation within a population, and its maintenance within a species, have been mysterious since the birth of the field of evolutionary genetics. In this work, I study divergently adapted freshwater and marine populations of the threespine stickleback (Gasterosteus aculeatus) as an evolutionary model to track the origin of adaptive genetic variation and to describe the evolutionary processes maintaining variation across the genome. The stickleback is a small fish with a large geographic range encompassing the northern half of the Northern Hemisphere and composed of coastal marine habitats, freshwater lakes, and river systems. Populations of stickleback adapt rapidly to changes in habitat, and fossil evidence suggests that similar adaptive transitions have been ongoing in this lineage for at least ten million years. In this work, I develop a significant extension of restriction site-associated DNA sequencing (RAD-seq) to generate phased haplotype information to estimate gene tree topologies and divergence times at thousands of loci simultaneously. I find anciently derived clades of variation associated with marine and freshwater habitats in genomic regions involved in recent adaptive divergence; some divergence times extend to over ten million years ago. This history of adaptive divergence has had profound effects on genetic variation elsewhere in the genome: chromosomes harboring freshwater-adaptive variants retain anciently derived variation in linked genomic regions, while marine chromosomes have much more recent ancestry. I present a conceptual model of asymmetric selective and demographic processes to explain this result, which will form a nucleus for future research in this species. Lastly, by incorporating genome-wide recombination rates estimated from multiple genetic maps, I describe a recombination landscape that is favorable to the maintenance of marine-freshwater genomic divergence. Low recombination rates in key chromosomal regions condense widespread divergence of the physical genome, encompassing many megabases, into a small number of Mendelian loci. Combined, my results demonstrate the interconnectedness of evolutionary processes taking place on ecological and geological timescales. The genetic variation available for adaptive evolution today is a product of the long-term evolutionary history of a species.

Browsing by Author "Cresko, William"

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