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• 1. [Article] Paleosol data from Pennsylvania, New York, Maryland, Ohio, Tennessee, West Virginia, and Quebec.

  Data were collected to establish a paleoclimatic time series for Devonian and Early Carboniferous rocks with evidence of fossils transitional between fish and amphibians. Data was collected in Pennsylvania, ...

  Citation × Citation Citation Abstract Copy Title: Paleosol data from Pennsylvania, New York, Maryland, Ohio, Tennessee, West Virginia, and Quebec. Author: Retallack, Greg J. Year: 2016, 2011 Data were collected to establish a paleoclimatic time series for Devonian and Early Carboniferous rocks with evidence of fossils transitional between fish and amphibians. Data was collected in Pennsylvania, New York, Maryland, Ohio, Tennessee, West Virginia, and Quebec. Title: Paleosol data from Pennsylvania, New York, Maryland, Ohio, Tennessee, West Virginia, and Quebec. Author: Retallack, Greg J. Year: 2016, 2011 Data were collected to establish a paleoclimatic time series for Devonian and Early Carboniferous rocks with evidence of fossils transitional between fish and amphibians. Data was collected in Pennsylvania, New York, Maryland, Ohio, Tennessee, West Virginia, and Quebec. Close

• 2. [Article] CONTEMPORARY GENETIC TOOLS FOR IN VIVO INVESTIGATIONS OF H3K27 DEMETHYLASES IN ZEBRAFISH CARDIOGENESIS

  Dynamic histone modification has emerged as a robust and versatile regulator of gene expression in eukaryotic cells. One such modification, the trimethylation of lysine 27 on histone H3 (H3K27me3) is facilitated ...

  Citation × Citation Citation Abstract Copy Title: CONTEMPORARY GENETIC TOOLS FOR IN VIVO INVESTIGATIONS OF H3K27 DEMETHYLASES IN ZEBRAFISH CARDIOGENESIS Author: Akerberg, Alexander Year: 2016 Dynamic histone modification has emerged as a robust and versatile regulator of gene expression in eukaryotic cells. One such modification, the trimethylation of lysine 27 on histone H3 (H3K27me3) is facilitated by the Polycomb repressive complex 2 (PRC2) and contributes to the localized repression of transcription. Subsequently, lysine specific demethylase Kdm6b (Jmjd3) can relieve the repressive H3K27me3 mark, allowing for transcriptional activation. In vitro studies have suggested a role for Kdm6b during mesodermal and cardiovascular differentiation in mammalian embryonic stem cells; however, this relationship has yet to be characterized in vivo. I utilized the advantages of the zebrafish model to investigate the in vivo roles of Kdm6b-family demethylases during development using a reverse genetic approach. I carried out two independent loss-of-function studies to analyze the role of Kdm6b-family demethylases during embryonic development in zebrafish. By comparing genetic loss-of-function and morpholino-mediated knockdown approaches, I found that morpholino–mediated knockdown of kdm6bb transcript produces off-target effects and does not portray an accurate representation of in vivo function. I then show that, while not required for early cardiogenesis, histone demethylases kdm6ba and kdm6bb function redundantly to promote late stage proliferation during heart ventricle trabeculation. These data reveal a previously unknown functional relationship and support the hypothesis that Kdm6b-family demethylases function primarily during later stages of development. Additionally, my description of morpholino-induced off-target effects supports the need to use extreme caution when interpreting morphant phenotypes. Due to the embryonic lethality exhibited by kdm6b-deficient embryos and the limited tools available for spatiotemporal transgene control in zebrafish, I was unable to investigate demethylase function within adult animals. I attempted to circumvent these limitations by creating an inducible gene expression system that uses tissue-specific transgenes that express the Gal4 transcription factor fused to the estrogen-binding domain of the human estrogen receptor. I showed that these Gal4-ERT driver lines confer rapid, tissue-specific induction of UAS-controlled transgenes following tamoxifen exposure in both embryos and adult fish. I then demonstrated how this technology could be used to define developmental windows of gene function by spatiotemporally controlling expression of constitutively active Notch1 in embryos. This dissertation contains previously published co-authored material. Title: CONTEMPORARY GENETIC TOOLS FOR IN VIVO INVESTIGATIONS OF H3K27 DEMETHYLASES IN ZEBRAFISH CARDIOGENESIS Author: Akerberg, Alexander Year: 2016 Dynamic histone modification has emerged as a robust and versatile regulator of gene expression in eukaryotic cells. One such modification, the trimethylation of lysine 27 on histone H3 (H3K27me3) is facilitated by the Polycomb repressive complex 2 (PRC2) and contributes to the localized repression of transcription. Subsequently, lysine specific demethylase Kdm6b (Jmjd3) can relieve the repressive H3K27me3 mark, allowing for transcriptional activation. In vitro studies have suggested a role for Kdm6b during mesodermal and cardiovascular differentiation in mammalian embryonic stem cells; however, this relationship has yet to be characterized in vivo. I utilized the advantages of the zebrafish model to investigate the in vivo roles of Kdm6b-family demethylases during development using a reverse genetic approach. I carried out two independent loss-of-function studies to analyze the role of Kdm6b-family demethylases during embryonic development in zebrafish. By comparing genetic loss-of-function and morpholino-mediated knockdown approaches, I found that morpholino–mediated knockdown of kdm6bb transcript produces off-target effects and does not portray an accurate representation of in vivo function. I then show that, while not required for early cardiogenesis, histone demethylases kdm6ba and kdm6bb function redundantly to promote late stage proliferation during heart ventricle trabeculation. These data reveal a previously unknown functional relationship and support the hypothesis that Kdm6b-family demethylases function primarily during later stages of development. Additionally, my description of morpholino-induced off-target effects supports the need to use extreme caution when interpreting morphant phenotypes. Due to the embryonic lethality exhibited by kdm6b-deficient embryos and the limited tools available for spatiotemporal transgene control in zebrafish, I was unable to investigate demethylase function within adult animals. I attempted to circumvent these limitations by creating an inducible gene expression system that uses tissue-specific transgenes that express the Gal4 transcription factor fused to the estrogen-binding domain of the human estrogen receptor. I showed that these Gal4-ERT driver lines confer rapid, tissue-specific induction of UAS-controlled transgenes following tamoxifen exposure in both embryos and adult fish. I then demonstrated how this technology could be used to define developmental windows of gene function by spatiotemporally controlling expression of constitutively active Notch1 in embryos. This dissertation contains previously published co-authored material. Close

• 3. [Article] Speaking to Crisis: Intellectuals, Literacy, and Public Discourse

  This dissertation analyzes public-intellectual work that deploys crisis tropes in its treatment of literacy, arguing that such work provides insight into the influence that intellectual engagement might ...

  Citation × Citation Citation Abstract Copy Title: Speaking to Crisis: Intellectuals, Literacy, and Public Discourse Author: Gentile, Francesca Year: 2016 This dissertation analyzes public-intellectual work that deploys crisis tropes in its treatment of literacy, arguing that such work provides insight into the influence that intellectual engagement might exert on discourse in the public sphere. From A.S. Hill’s lament that freshman entering Harvard in 1874 could barely construct a legible sentence to Stanley Fish’s charge that millions of college graduates earning degrees in 2005 did so without learning what a sentence was, the relationship between literacy and the communicative skills required of productive citizens has been a constant source of concern. Between these two historical moments, this relationship has been an undertheorized feature of debates surrounding racial uplift, feminist protest, and America’s role as a world power. When interlocutors in such debates minimize the significance of literacy practices, they encourage rhetorical action driven by a coercive conception of social crisis that limits critical engagement on the part of the public. I argue that the public intellectual’s capacity to facilitate rhetorically literate discursive exchange at the level of the mass public can transform the paralysis of crisis into possibility. I reframe well-known debates between W.E.B. Du Bois and Booker T. Washington, Betty Friedan and Gloria Steinem, and Mortimer Adler and Glenn T. Seaborg in terms of the rhetorical models they offer for responsible public-intellectual work. Title: Speaking to Crisis: Intellectuals, Literacy, and Public Discourse Author: Gentile, Francesca Year: 2016 This dissertation analyzes public-intellectual work that deploys crisis tropes in its treatment of literacy, arguing that such work provides insight into the influence that intellectual engagement might exert on discourse in the public sphere. From A.S. Hill’s lament that freshman entering Harvard in 1874 could barely construct a legible sentence to Stanley Fish’s charge that millions of college graduates earning degrees in 2005 did so without learning what a sentence was, the relationship between literacy and the communicative skills required of productive citizens has been a constant source of concern. Between these two historical moments, this relationship has been an undertheorized feature of debates surrounding racial uplift, feminist protest, and America’s role as a world power. When interlocutors in such debates minimize the significance of literacy practices, they encourage rhetorical action driven by a coercive conception of social crisis that limits critical engagement on the part of the public. I argue that the public intellectual’s capacity to facilitate rhetorically literate discursive exchange at the level of the mass public can transform the paralysis of crisis into possibility. I reframe well-known debates between W.E.B. Du Bois and Booker T. Washington, Betty Friedan and Gloria Steinem, and Mortimer Adler and Glenn T. Seaborg in terms of the rhetorical models they offer for responsible public-intellectual work. Close

• 4. [Article] Modeling Historical Meander Bends Reconnection on the lower Long Tom River in Lane Co. and Benton Co., OR

  Since the damming and channelization of the lower Long Tom River in the 1940s and 1950s, the quality and quantity of habitat for coastal cutthroat trout and spring Chinook salmon in the watershed has dramatically ...

  Citation × Citation Citation Abstract Copy Title: Modeling Historical Meander Bends Reconnection on the lower Long Tom River in Lane Co. and Benton Co., OR Author: Appleby, Christina Year: 2016 Since the damming and channelization of the lower Long Tom River in the 1940s and 1950s, the quality and quantity of habitat for coastal cutthroat trout and spring Chinook salmon in the watershed has dramatically diminished. In order to better understand the potential for stream restoration, this study uses 2D hydraulic modeling to determine the impact of reconnecting historical meander bends to the main stem of the lower Long Tom River on localized flooding, sediment erosion and deposition, and salmonid physical habitat. These models compare the current conditions to two restoration scenarios that allow for fish passage given 1, 2, and 5-year flood events at two study sites. This study reveals important variations in the impact of restoration between the study sites and the reconnection methods. It also suggests that there is the potential for a large increase in the area of accessible habitat with stream restoration. Title: Modeling Historical Meander Bends Reconnection on the lower Long Tom River in Lane Co. and Benton Co., OR Author: Appleby, Christina Year: 2016 Since the damming and channelization of the lower Long Tom River in the 1940s and 1950s, the quality and quantity of habitat for coastal cutthroat trout and spring Chinook salmon in the watershed has dramatically diminished. In order to better understand the potential for stream restoration, this study uses 2D hydraulic modeling to determine the impact of reconnecting historical meander bends to the main stem of the lower Long Tom River on localized flooding, sediment erosion and deposition, and salmonid physical habitat. These models compare the current conditions to two restoration scenarios that allow for fish passage given 1, 2, and 5-year flood events at two study sites. This study reveals important variations in the impact of restoration between the study sites and the reconnection methods. It also suggests that there is the potential for a large increase in the area of accessible habitat with stream restoration. Close

• 5. [Article] Developing Methods Based on Light Sheet Fluorescence Microscopy for Biophysical Investigations of Larval Zebrafish

  Adapting the tools of optical microscopy to the large-scale dynamic systems encountered in the development of multicellular organisms provides a path toward understanding the physical processes necessary ...

  Citation × Citation Citation Abstract Copy Title: Developing Methods Based on Light Sheet Fluorescence Microscopy for Biophysical Investigations of Larval Zebrafish Author: Taormina, Michael Year: 2014 Adapting the tools of optical microscopy to the large-scale dynamic systems encountered in the development of multicellular organisms provides a path toward understanding the physical processes necessary for complex life to form and function. Obtaining quantitatively meaningful results from such systems has been challenging due to difficulty spanning the spatial and temporal scales representative of the whole, while also observing the many individual members from which complex and collective behavior emerges. A three-dimensional imaging technique known as light sheet fluorescence microscopy provides a number of significant benefits for surmounting these challenges and studying developmental systems. A thin plane of fluorescence excitation light is produced such that it coincides with the focal plane of an imaging system, providing rapid acquisition of optically sectioned images that can be used to construct a three-dimensional rendition of a sample. I discuss the implementation of this technique for use in larva of the model vertebrate Danio rerio (zebrafish). The nature of light sheet imaging makes it especially well suited to the study of large systems while maintaining good spatial resolution and minimizing damage to the specimen from excessive exposure to excitation light. I show the results from a comparative study that demonstrates the ability to image certain developmental processes non-destructively, while in contrast confocal microscopy results in abnormal growth due to phototoxicity. I develop the application of light sheet microscopy to the study of a previously inaccessible system: the bacterial colonization of a host organism. Using the technique, we are able to obtain a survey of the intestinal tract of a larval zebrafish and observe the location of microbes as they grow and establish a stable population in an initially germ free fish. Finally, I describe a new technique to measure the fluid viscosity of this intestinal environment in vivo using magnetically driven particles. By imaging such particles as they are oscillated in a frequency chirped field, it is possible to calculate properties such as the viscosity of the material in which they are embedded. Here I provide the first known measurement of intestinal mucus rheology in vivo. This dissertation includes previously published co-authored material. Title: Developing Methods Based on Light Sheet Fluorescence Microscopy for Biophysical Investigations of Larval Zebrafish Author: Taormina, Michael Year: 2014 Adapting the tools of optical microscopy to the large-scale dynamic systems encountered in the development of multicellular organisms provides a path toward understanding the physical processes necessary for complex life to form and function. Obtaining quantitatively meaningful results from such systems has been challenging due to difficulty spanning the spatial and temporal scales representative of the whole, while also observing the many individual members from which complex and collective behavior emerges. A three-dimensional imaging technique known as light sheet fluorescence microscopy provides a number of significant benefits for surmounting these challenges and studying developmental systems. A thin plane of fluorescence excitation light is produced such that it coincides with the focal plane of an imaging system, providing rapid acquisition of optically sectioned images that can be used to construct a three-dimensional rendition of a sample. I discuss the implementation of this technique for use in larva of the model vertebrate Danio rerio (zebrafish). The nature of light sheet imaging makes it especially well suited to the study of large systems while maintaining good spatial resolution and minimizing damage to the specimen from excessive exposure to excitation light. I show the results from a comparative study that demonstrates the ability to image certain developmental processes non-destructively, while in contrast confocal microscopy results in abnormal growth due to phototoxicity. I develop the application of light sheet microscopy to the study of a previously inaccessible system: the bacterial colonization of a host organism. Using the technique, we are able to obtain a survey of the intestinal tract of a larval zebrafish and observe the location of microbes as they grow and establish a stable population in an initially germ free fish. Finally, I describe a new technique to measure the fluid viscosity of this intestinal environment in vivo using magnetically driven particles. By imaging such particles as they are oscillated in a frequency chirped field, it is possible to calculate properties such as the viscosity of the material in which they are embedded. Here I provide the first known measurement of intestinal mucus rheology in vivo. This dissertation includes previously published co-authored material. Close

• 6. [Article] The Taphonomy of Archaeological Fish Remains: Experimental Approaches to Understanding the Effects of Natural and Cultural Processes on the Presence and Identification of Cut Marks

  Despite the fact that fish are a common component of coastal and other aquatic archaeological sites, fish bone taphonomy--including bone surface modifications and the effects of burial--remains woefully ...

  Citation × Citation Citation Abstract Copy Title: The Taphonomy of Archaeological Fish Remains: Experimental Approaches to Understanding the Effects of Natural and Cultural Processes on the Presence and Identification of Cut Marks Author: Willis, Lauren Year: 2014 Despite the fact that fish are a common component of coastal and other aquatic archaeological sites, fish bone taphonomy--including bone surface modifications and the effects of burial--remains woefully understudied. Various ethnographic accounts describe fish butchering techniques for immediate consumption and drying, yet cut marks are rarely reported on archaeological fish remains. To address a significant gap in our understanding of fish taphonomy, I devised an experimental research program aimed at assessing whether butchering fish produces cut marks on fish bones and, if so, what factors might account for the discrepancy between the experimental results and the archaeological record. Chapter I provides an introduction to experimental archaeology, including the criticisms and benefits of this approach. Chapter II presents the results of my initial butchery experiment, which establishes that butchering fish can produce abundant cut marks. Chapter III evaluates the effect of the butcher's skill level on the number and distribution of cut marks produced on fish bone during butchery. The results indicate that professional butchers produce nearly 50 percent fewer cut marks than novice- and intermediate-level butchers. Chapter IV addresses the effect of post-depositional taphonomic processes on the long-term visibility of cut marks. Despite a relatively short burial period (27 months), visible cut marks decreased by up to 75 percent, depending on the species. Chapter V is a re-analysis of the fish bone from column E6 at Daisy Cave (CA-SMI-261). Appling the referential framework I acquired through the experiments, I identified 62 cut marks on bones dating from the Early to Late Holocene. A comprehensive understanding of aquatic resource use has implications for a broad range of archaeological topics, including our understanding of hominid diet and resource use; identifying butchery and processing practices among fishing peoples; distinguishing between human and natural agency in the accumulation of fish remains; and assessing questions of behavioral modernity and social complexity. As we continue to recognize the primacy of coastal adaptations throughout human history, it is increasingly critical to expand the breadth of our knowledge regarding the taphonomy of fish remains at archaeological sites. This dissertation includes previously published and unpublished co-authored material. Title: The Taphonomy of Archaeological Fish Remains: Experimental Approaches to Understanding the Effects of Natural and Cultural Processes on the Presence and Identification of Cut Marks Author: Willis, Lauren Year: 2014 Despite the fact that fish are a common component of coastal and other aquatic archaeological sites, fish bone taphonomy--including bone surface modifications and the effects of burial--remains woefully understudied. Various ethnographic accounts describe fish butchering techniques for immediate consumption and drying, yet cut marks are rarely reported on archaeological fish remains. To address a significant gap in our understanding of fish taphonomy, I devised an experimental research program aimed at assessing whether butchering fish produces cut marks on fish bones and, if so, what factors might account for the discrepancy between the experimental results and the archaeological record. Chapter I provides an introduction to experimental archaeology, including the criticisms and benefits of this approach. Chapter II presents the results of my initial butchery experiment, which establishes that butchering fish can produce abundant cut marks. Chapter III evaluates the effect of the butcher's skill level on the number and distribution of cut marks produced on fish bone during butchery. The results indicate that professional butchers produce nearly 50 percent fewer cut marks than novice- and intermediate-level butchers. Chapter IV addresses the effect of post-depositional taphonomic processes on the long-term visibility of cut marks. Despite a relatively short burial period (27 months), visible cut marks decreased by up to 75 percent, depending on the species. Chapter V is a re-analysis of the fish bone from column E6 at Daisy Cave (CA-SMI-261). Appling the referential framework I acquired through the experiments, I identified 62 cut marks on bones dating from the Early to Late Holocene. A comprehensive understanding of aquatic resource use has implications for a broad range of archaeological topics, including our understanding of hominid diet and resource use; identifying butchery and processing practices among fishing peoples; distinguishing between human and natural agency in the accumulation of fish remains; and assessing questions of behavioral modernity and social complexity. As we continue to recognize the primacy of coastal adaptations throughout human history, it is increasingly critical to expand the breadth of our knowledge regarding the taphonomy of fish remains at archaeological sites. This dissertation includes previously published and unpublished co-authored material. Close

• 7. [Article] The economic impacts of Oregon's south coast restoration industry

  3 pages

  Citation × Citation Citation Abstract Copy Title: The economic impacts of Oregon's south coast restoration industry Author: Sundstrom, Shiloh, Davis, Emily Jane, Moseley, Cassandra Year: 2015, 2011 3 pages Title: The economic impacts of Oregon's south coast restoration industry Author: Sundstrom, Shiloh, Davis, Emily Jane, Moseley, Cassandra Year: 2015, 2011 3 pages Close

• 8. [Article] Local capacity for integrated forest and wildfire management

  28 pages

  Citation × Citation Citation Abstract Copy Title: Local capacity for integrated forest and wildfire management Author: Huber-Stearns, Heidi, Moseley, Cassandra, Goulette, Nick Year: 2016 28 pages Title: Local capacity for integrated forest and wildfire management Author: Huber-Stearns, Heidi, Moseley, Cassandra, Goulette, Nick Year: 2016 28 pages Close

• 9. [Article] SMILODONICHTHYS RASTROSUS A NEW PLIOCENE SALMONID FISH FROM WESTERN UNITED STATES

  52 pages

  Citation × Citation Citation Abstract Copy Title: SMILODONICHTHYS RASTROSUS A NEW PLIOCENE SALMONID FISH FROM WESTERN UNITED STATES Author: CAVENDER, TED M., MILLER, ROBERT RUSH Year: 2016, 1972 52 pages Title: SMILODONICHTHYS RASTROSUS A NEW PLIOCENE SALMONID FISH FROM WESTERN UNITED STATES Author: CAVENDER, TED M., MILLER, ROBERT RUSH Year: 2016, 1972 52 pages Close

• 10. [Article] THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON

  72 pages

  Citation × Citation Citation Abstract Copy Title: THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON Author: GUSTAFSON, ERIC PAUL Year: 2016, 1978 72 pages Title: THE VERTEBRATE FAUNAS OF THE PLIOCENE RINGOLD FORMATION, SOUTH-CENTRAL WASHINGTON Author: GUSTAFSON, ERIC PAUL Year: 2016, 1978 72 pages Close