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• 11. [Article] Analytical phytoplankton carbon measurements spanning diverse ecosystems

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/deep-sea-rese...

  Citation × Citation Citation Abstract Copy Title: Analytical phytoplankton carbon measurements spanning diverse ecosystems Author: Brown, Matthew B., Behrenfeld, Michael J., van Dongen-Vogels, Virginie, Westberry, Toby K., Milligan, Allen J., Graff, Jason R., Dall'Olmo, Giorgio, Reifel, Kristen M. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/deep-sea-research-part-i-oceanographic-research-papers/ Title: Analytical phytoplankton carbon measurements spanning diverse ecosystems Author: Brown, Matthew B., Behrenfeld, Michael J., van Dongen-Vogels, Virginie, Westberry, Toby K., Milligan, Allen J., Graff, Jason R., Dall'Olmo, Giorgio, Reifel, Kristen M. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Elsevier. The published article can be found at: http://www.journals.elsevier.com/deep-sea-research-part-i-oceanographic-research-papers/ Close

• 12. [Article] Assessment of the vulnerability of Oregon and Washington's natural areas to climate change

  There are currently more than 580 natural areas in Oregon and Washington managed by 20 federal, state, local, and private agencies and organizations. The natural areas network is unparalleled in its representation ...

  Citation × Citation Citation Abstract Copy Title: Assessment of the vulnerability of Oregon and Washington's natural areas to climate change Author: Margaret, Massie H. There are currently more than 580 natural areas in Oregon and Washington managed by 20 federal, state, local, and private agencies and organizations. The natural areas network is unparalleled in its representation of diverse ecosystems found in the region and may be an excellent collection of sites for monitoring long-term ecological responses to climate change. The goal of this research was to build a framework for a climate change monitoring program for the Pacific Northwest based on natural areas. Objectives were to (1) describe strengths of the existing natural areas network for representing effects of climate change by conducting a proportionality assessment and (2) determine which subset of natural areas have the best potential to detect change over the long term. Findings show that natural areas were generally representative and proportional compared to the Pacific Northwest. Subsets of natural areas were prioritized for long-term monitoring efforts through bioclimatic modelling based on the current and projected (2020s, 2050s, 2080s) outputs from 13 future climate models from ClimateWNA and the Random Forest approach. Projection consensus showed a substantial range increase in suitable climate for warmer adapted forest types coupled with a contraction in cooler forest types. The results highlight the potential stress of climate change on ecosystems across the region and the need for management strategies to adapt to this uncertainty. Title: Assessment of the vulnerability of Oregon and Washington's natural areas to climate change Author: Margaret, Massie H. There are currently more than 580 natural areas in Oregon and Washington managed by 20 federal, state, local, and private agencies and organizations. The natural areas network is unparalleled in its representation of diverse ecosystems found in the region and may be an excellent collection of sites for monitoring long-term ecological responses to climate change. The goal of this research was to build a framework for a climate change monitoring program for the Pacific Northwest based on natural areas. Objectives were to (1) describe strengths of the existing natural areas network for representing effects of climate change by conducting a proportionality assessment and (2) determine which subset of natural areas have the best potential to detect change over the long term. Findings show that natural areas were generally representative and proportional compared to the Pacific Northwest. Subsets of natural areas were prioritized for long-term monitoring efforts through bioclimatic modelling based on the current and projected (2020s, 2050s, 2080s) outputs from 13 future climate models from ClimateWNA and the Random Forest approach. Projection consensus showed a substantial range increase in suitable climate for warmer adapted forest types coupled with a contraction in cooler forest types. The results highlight the potential stress of climate change on ecosystems across the region and the need for management strategies to adapt to this uncertainty. Close

• 13. [Article] Investigation of unique marine environments for microbial natural products

  Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural ...

  Citation × Citation Citation Abstract Copy Title: Investigation of unique marine environments for microbial natural products Author: Thornburg, Christopher C. Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural products. Despite numerous advances in culturing, biosynthetic engineering and genomic-based screening efforts to uncover much of this diversity in relatively accessible environments, a high rediscovery rate has resulted in the investigation of unique, relatively unexplored ecosystems harboring phylogenetically diverse communities of marine organisms. The focus of this research was to establish a culture repository of microorganisms collected from the Red Sea and from deep-sea hydrothermal vents, and to assess their biosynthetic potential for the production of new chemical scaffolds. Cultivation of marine cyanobacteria from the Red Sea has led to the identification of five new cyclic depsipeptides, apratoxin H, grassypeptolides D and E, Ibu-epidemethoxylyngbyastin 3 and leptochelin, the latter possessing a unique chemical scaffold capable of binding metals. A collection of deep-sea hydrothermal vent sediment and microbial mat samples led to the isolation of 64 unique bacterial strains, with eight assigned as members of the order Actinomycetales. Importantly, these isolates, along with a collection of deep-vent invertebrates and microbes, have led to the development of methods for the collection, culturing and biological screening of organisms from this extreme environment for future natural products research. Title: Investigation of unique marine environments for microbial natural products Author: Thornburg, Christopher C. Metagenomics has revealed that the marine microbial biosphere is immensely more diverse than originally considered, and is an almost untapped reservoir for the potential discovery of microbial natural products. Despite numerous advances in culturing, biosynthetic engineering and genomic-based screening efforts to uncover much of this diversity in relatively accessible environments, a high rediscovery rate has resulted in the investigation of unique, relatively unexplored ecosystems harboring phylogenetically diverse communities of marine organisms. The focus of this research was to establish a culture repository of microorganisms collected from the Red Sea and from deep-sea hydrothermal vents, and to assess their biosynthetic potential for the production of new chemical scaffolds. Cultivation of marine cyanobacteria from the Red Sea has led to the identification of five new cyclic depsipeptides, apratoxin H, grassypeptolides D and E, Ibu-epidemethoxylyngbyastin 3 and leptochelin, the latter possessing a unique chemical scaffold capable of binding metals. A collection of deep-sea hydrothermal vent sediment and microbial mat samples led to the isolation of 64 unique bacterial strains, with eight assigned as members of the order Actinomycetales. Importantly, these isolates, along with a collection of deep-vent invertebrates and microbes, have led to the development of methods for the collection, culturing and biological screening of organisms from this extreme environment for future natural products research. Close

• 14. [Article] Status and Ecological Effects of the World’s Largest Carnivores

  To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the author's version of the work. It is posted here by permission of the American ...

  Citation × Citation Citation Abstract Copy Title: Status and Ecological Effects of the World’s Largest Carnivores Author: Schmitz, Oswald J., Hebblewhite, Mark, Wilmers, Christopher C., Wallach, Arian D., Smith, Douglas W., Estes, James A., Beschta, Robert L., Nelson, Michael P., Berger, Joel, Ritchie, Euan G., Ripple, William J., Elmhagen, Bodil, Wirsing, Aaron J., Letnic, Mike To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the author's version of the work. It is posted here by permission of the American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in Science, Vol. 343 (2014), doi:10.1126/science.1241484. The published article can be found at: http://www.sciencemag.org/. Title: Status and Ecological Effects of the World’s Largest Carnivores Author: Schmitz, Oswald J., Hebblewhite, Mark, Wilmers, Christopher C., Wallach, Arian D., Smith, Douglas W., Estes, James A., Beschta, Robert L., Nelson, Michael P., Berger, Joel, Ritchie, Euan G., Ripple, William J., Elmhagen, Bodil, Wirsing, Aaron J., Letnic, Mike To the best of our knowledge, one or more authors of this paper were federal employees when contributing to this work. This is the author's version of the work. It is posted here by permission of the American Association for the Advancement of Science for personal use, not for redistribution. The definitive version was published in Science, Vol. 343 (2014), doi:10.1126/science.1241484. The published article can be found at: http://www.sciencemag.org/. Close

• 15. [Article] Nature in chains : the effects of Thomas Jefferson’s rectangular survey on a Pacific Northwest landscape

  Understanding the impact of humans on the environment has long been a topic of scholarly interest and debate. As environmental problems mount, accounts of historic ecological conditions and the factors ...

  Citation × Citation Citation Abstract Copy Title: Nature in chains : the effects of Thomas Jefferson’s rectangular survey on a Pacific Northwest landscape Author: Schweickert, Tina K. Understanding the impact of humans on the environment has long been a topic of scholarly interest and debate. As environmental problems mount, accounts of historic ecological conditions and the factors of change become increasingly useful. This study considers competing schools of interpretation about human impacts on ecological landscapes and develops a case study of one thirty-six square mile township in Oregon’s Waldo Hills. Built on evidence from 1851 surveyor notes, maps, journals, aerial photos, interviews, and contemporary environmental and ecological data, this study demonstrates a transformation from ecologically diverse ecosystems under the management of native peoples to ecologically depressed monoculture landscapes under industrialized agriculture. This thesis argues that the fundamental beliefs of human societies (i.e., worldviews) become expressed in the landscape. The nature-as-community view of the Kalapuya Indians resulted in a complex, curvilinear mosaic of prairie, savanna, and woodland. The individualized and rationalized view of the Euroamericans resulted in a simplified landscape of squared-off fields, channelized streams, and roads aligned to the survey grid. Thomas Jefferson’s rectangular survey, built on the ‘virtuous square’, is examined as a symbolic and tangible instrument of rapid expansion and exploitation across the American West. Understanding that worldviews become expressed in physical conditions may benefit those working to create sustainable futures; i.e., long-term and widespread ecological improvements will likely succeed only if society at large shares a fundamental belief in the value of healthy ecosystems. Title: Nature in chains : the effects of Thomas Jefferson’s rectangular survey on a Pacific Northwest landscape Author: Schweickert, Tina K. Understanding the impact of humans on the environment has long been a topic of scholarly interest and debate. As environmental problems mount, accounts of historic ecological conditions and the factors of change become increasingly useful. This study considers competing schools of interpretation about human impacts on ecological landscapes and develops a case study of one thirty-six square mile township in Oregon’s Waldo Hills. Built on evidence from 1851 surveyor notes, maps, journals, aerial photos, interviews, and contemporary environmental and ecological data, this study demonstrates a transformation from ecologically diverse ecosystems under the management of native peoples to ecologically depressed monoculture landscapes under industrialized agriculture. This thesis argues that the fundamental beliefs of human societies (i.e., worldviews) become expressed in the landscape. The nature-as-community view of the Kalapuya Indians resulted in a complex, curvilinear mosaic of prairie, savanna, and woodland. The individualized and rationalized view of the Euroamericans resulted in a simplified landscape of squared-off fields, channelized streams, and roads aligned to the survey grid. Thomas Jefferson’s rectangular survey, built on the ‘virtuous square’, is examined as a symbolic and tangible instrument of rapid expansion and exploitation across the American West. Understanding that worldviews become expressed in physical conditions may benefit those working to create sustainable futures; i.e., long-term and widespread ecological improvements will likely succeed only if society at large shares a fundamental belief in the value of healthy ecosystems. Close

• 16. [Article] High Performance Computational Chemistry: Bridging Quantum Mechanics, Molecular Dynamics, and Coarse-Grained Models

  The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters ...

  Citation × Citation Citation Abstract Copy Title: High Performance Computational Chemistry: Bridging Quantum Mechanics, Molecular Dynamics, and Coarse-Grained Models Author: Ozog, David Year: 2017 The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters and scalable programming methods in high performance computing (HPC). However, such massively parallel simulations increasingly require more complicated software to achieve good performance across the vastly diverse ecosystem of modern heterogeneous computer systems. Furthermore, advanced “multi-resolution” methods for modeling atoms and molecules continue to evolve, and scientific software developers struggle to keep up with the hardships involved with building, scaling, and maintaining these coupled code systems. This dissertation describes these challenges facing the computational chemistry community in detail, along with recent solutions and techniques that circumvent some primary obstacles. In particular, I describe several projects and classify them by the 3 primary models used to simulate atoms and molecules: quantum mechanics (QM), molecular mechanics (MM), and coarse-grained (CG) models. Initially, the projects investigate methods for scaling simulations to larger and more relevant chemical applications within the same resolution model of either QM, MM, or CG. However, the grand challenge lies in effectively bridging these scales, both spatially and temporally, to study richer chemical models that go beyond single-scale physics and toward hybrid QM/MM/CG models. This dissertation concludes with an analysis of the state of the art in multiscale computational chemistry, with an eye toward improving developer productivity on upcoming computer architectures, in which we require productive software environments, enhanced support for coupled scientific workflows, useful abstractions to aid with data transfer, adaptive runtime systems, and extreme scalability. This dissertation includes previously published and co-authored material, as well as unpublished co-authored material. Title: High Performance Computational Chemistry: Bridging Quantum Mechanics, Molecular Dynamics, and Coarse-Grained Models Author: Ozog, David Year: 2017 The past several decades have witnessed tremendous strides in the capabilities of computational chemistry simulations, driven in large part by the extensive parallelism offered by powerful computer clusters and scalable programming methods in high performance computing (HPC). However, such massively parallel simulations increasingly require more complicated software to achieve good performance across the vastly diverse ecosystem of modern heterogeneous computer systems. Furthermore, advanced “multi-resolution” methods for modeling atoms and molecules continue to evolve, and scientific software developers struggle to keep up with the hardships involved with building, scaling, and maintaining these coupled code systems. This dissertation describes these challenges facing the computational chemistry community in detail, along with recent solutions and techniques that circumvent some primary obstacles. In particular, I describe several projects and classify them by the 3 primary models used to simulate atoms and molecules: quantum mechanics (QM), molecular mechanics (MM), and coarse-grained (CG) models. Initially, the projects investigate methods for scaling simulations to larger and more relevant chemical applications within the same resolution model of either QM, MM, or CG. However, the grand challenge lies in effectively bridging these scales, both spatially and temporally, to study richer chemical models that go beyond single-scale physics and toward hybrid QM/MM/CG models. This dissertation concludes with an analysis of the state of the art in multiscale computational chemistry, with an eye toward improving developer productivity on upcoming computer architectures, in which we require productive software environments, enhanced support for coupled scientific workflows, useful abstractions to aid with data transfer, adaptive runtime systems, and extreme scalability. This dissertation includes previously published and co-authored material, as well as unpublished co-authored material. Close

• 17. [Article] Synecological effects of cattle grazing riparian ecosystems

  In 1978, a ten year project was begun to examine the synecological effects of livestock grazing riparian ecosystems. A multitude of biotic arid physical factors, many which were unique to riparian ecosystems, ...

  Citation × Citation Citation Abstract Copy Title: Synecological effects of cattle grazing riparian ecosystems Author: Kauffman, John Boone In 1978, a ten year project was begun to examine the synecological effects of livestock grazing riparian ecosystems. A multitude of biotic arid physical factors, many which were unique to riparian ecosystems, interacted to form a complex and diverse riparian ecosystem. A total of 256 stands of vegetation representing 60 discrete plant communities were identified. Twenty species of mammals and 81 species of birds were sited utilizing the area from May-October. Approximately one-half of the riparian vegetation bordering Catherine Creek was excluded from livestock grazing. Ten plant communities were intensively sampled in grazed and exclosed areas during three growing seasons to determine some of the impacts a late season grazing scheme has on riparian vegetation. Three plant communities displayed significant species composition and productivity differences. These commmunities were within' the meadow and Doug1az Hawthorne (Crataegus douglasii) vegetation types and were utilized more heavily by livestock than any other communities sampled. In addition succession appeared to be retarded by grazing on gravel bars dominated by black cottonwood (Populus trichocarpa) saplings and willows (Salix spp.). Few differences were recorded in other plant communities sampled. Late season grazing had few short term impacts on avian populations censused from May-October. There was a significant decrease in small mammal populations after grazing in all communities sampled. However, by the following August small mammals had recolonized the grazed plant communities in essentially the same species composition and densities. Grazed areas had significantly greater streambank losses than areas that were not grazed. While overwinter losses accounted for much of the streambank erosion, the erosion and disturbance caused by livestock grazing and trampling was enough to create significantly greater streambank losses in grazed areas compared to ungrazed areas. Positive characteristics of a late season grazing scheme on. the riparian zone included increased late season livestock production, good plant vigor and productivity, minimal soil disturbance, and minimal short term disturbance to wildlife populations dependent on riparian ecosystems. Title: Synecological effects of cattle grazing riparian ecosystems Author: Kauffman, John Boone In 1978, a ten year project was begun to examine the synecological effects of livestock grazing riparian ecosystems. A multitude of biotic arid physical factors, many which were unique to riparian ecosystems, interacted to form a complex and diverse riparian ecosystem. A total of 256 stands of vegetation representing 60 discrete plant communities were identified. Twenty species of mammals and 81 species of birds were sited utilizing the area from May-October. Approximately one-half of the riparian vegetation bordering Catherine Creek was excluded from livestock grazing. Ten plant communities were intensively sampled in grazed and exclosed areas during three growing seasons to determine some of the impacts a late season grazing scheme has on riparian vegetation. Three plant communities displayed significant species composition and productivity differences. These commmunities were within' the meadow and Doug1az Hawthorne (Crataegus douglasii) vegetation types and were utilized more heavily by livestock than any other communities sampled. In addition succession appeared to be retarded by grazing on gravel bars dominated by black cottonwood (Populus trichocarpa) saplings and willows (Salix spp.). Few differences were recorded in other plant communities sampled. Late season grazing had few short term impacts on avian populations censused from May-October. There was a significant decrease in small mammal populations after grazing in all communities sampled. However, by the following August small mammals had recolonized the grazed plant communities in essentially the same species composition and densities. Grazed areas had significantly greater streambank losses than areas that were not grazed. While overwinter losses accounted for much of the streambank erosion, the erosion and disturbance caused by livestock grazing and trampling was enough to create significantly greater streambank losses in grazed areas compared to ungrazed areas. Positive characteristics of a late season grazing scheme on. the riparian zone included increased late season livestock production, good plant vigor and productivity, minimal soil disturbance, and minimal short term disturbance to wildlife populations dependent on riparian ecosystems. Close

• 18. [Article] Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersi...

  Citation × Citation Citation Abstract Copy Title: Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography Author: Crump, Byron C., Adams, Heather E., Kling, George W. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology. Title: Metacommunity dynamics of bacteria in an arctic lake: the impact of species sorting and mass effects on bacterial production and biogeography Author: Crump, Byron C., Adams, Heather E., Kling, George W. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Frontiers Research Foundation. The published article can be found at: http://www.frontiersin.org/Microbiology. Close

• 19. [Article] The genome of Aiptasia, a sea anemone model for coral symbiosis

  Freely available online through the PNAS open access option.

  Citation × Citation Citation Abstract Copy Title: The genome of Aiptasia, a sea anemone model for coral symbiosis Author: Weis, Virginia M., Oates, Matt E., Aranda, Manuel, Voolstra, Christian R., Liew, Yi Jin, Hambleton, Elizabeth A., Pringle, John R., Baumgarten, Sebastian, Esherick, Lisl Y., Gough, Julian, Guse, Annika, Lehnert, Erik M., Michell, Craig T., Simakov, Oleg, Li, Yong Freely available online through the PNAS open access option. Title: The genome of Aiptasia, a sea anemone model for coral symbiosis Author: Weis, Virginia M., Oates, Matt E., Aranda, Manuel, Voolstra, Christian R., Liew, Yi Jin, Hambleton, Elizabeth A., Pringle, John R., Baumgarten, Sebastian, Esherick, Lisl Y., Gough, Julian, Guse, Annika, Lehnert, Erik M., Michell, Craig T., Simakov, Oleg, Li, Yong Freely available online through the PNAS open access option. Close

• 20. [Article] Evaluating taxonomic homogenization of freshwater fish assemblages in Chile

  This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by SpringerOpen. The published article can be found at: http://link.springer.com/journal/40693

  Citation × Citation Citation Abstract Copy Title: Evaluating taxonomic homogenization of freshwater fish assemblages in Chile Author: Arismendi, Ivan, Gomez-Uchida, Daniel, Vargas, Pamela V. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by SpringerOpen. The published article can be found at: http://link.springer.com/journal/40693 Title: Evaluating taxonomic homogenization of freshwater fish assemblages in Chile Author: Arismendi, Ivan, Gomez-Uchida, Daniel, Vargas, Pamela V. This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by SpringerOpen. The published article can be found at: http://link.springer.com/journal/40693 Close