71 results on '"Jonathan D. Coop"'
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2. Biogeographic patterns of daily wildfire spread and extremes across North America
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Jared A. Balik, Jonathan D. Coop, Meg A. Krawchuk, Cameron E. Naficy, Marc-André Parisien, Sean A. Parks, Camille S. Stevens-Rumann, and Ellen Whitman
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wildfire ,extreme events ,daily fire progression ,fire spread ,fire growth ,fire duration ,Forestry ,SD1-669.5 ,Environmental sciences ,GE1-350 - Abstract
IntroductionClimate change is predicted to increase the frequency of extreme single-day fire spread events, with major ecological and social implications. In contrast with well-documented spatio-temporal patterns of wildfire ignitions and perimeters, daily progression remains poorly understood across continental spatial scales, particularly for extreme single-day events (“blow ups”). Here, we characterize daily wildfire spread across North America, including occurrence of extreme single-day events, duration and seasonality of fire and extremes, and ecoregional climatic niches of fire in terms of Actual Evapotranspiration (AET) and Climatic Water Deficit (CWD) annual climate normals.MethodsRemotely sensed daily progression of 9,636 wildfires ≥400 ha was used to characterize ecoregional patterns of fire growth, extreme single-day events, duration, and seasonality. To explore occurrence, extent, and impacts of single-day extremes among ecoregions, we considered complementary ecoregional and continental extreme thresholds (Ecoregional or Continental Mean Daily Area Burned + 2SD). Ecoregional spread rates were regressed against AET and CWD to explore climatic influence on spread.ResultsWe found three-fold differences in mean Daily Area Burned among 10 North American ecoregions, ranging from 260 ha day−1 in the Marine West Coast Forests to 751 ha day−1 in Mediterranean California. Ecoregional extreme thresholds ranged from 3,829 ha day−1 to 16,626 ha day−1, relative to a continental threshold of 7,173 ha day−1. The ~3% of events classified as extreme cumulatively account for 16–55% of total area burned among ecoregions. We observed four-fold differences in mean fire duration, ranging from 2.7 days in the Great Plains to 10.5 days in Northwestern Forested Mountains. Regions with shorter fire durations also had greater daily area burned, suggesting a paradigm of fast-growing short-duration fires in some regions and slow-growing long-duration fires elsewhere. CWD had a weak positive relationship with spread rate and extreme thresholds, and there was no pattern for AET.DiscussionRegions with shorter fire durations had greater daily area burned, suggesting a paradigm of fast-growing short-duration fires in some regions and slow-growing long-duration fires elsewhere. Although climatic conditions can set the stage for ignition and influence vegetation and fuels, finer-scale mechanisms likely drive variation in daily spread. Daily fire progression offers valuable insights into the regional and seasonal distributions of extreme single-day spread events, and how these events shape net fire effects.
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- 2024
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3. Historical fire regimes and contemporary fire effects within sagebrush habitats of Gunnison Sage‐grouse
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Petar Z. Simic, Jonathan D. Coop, Ellis Q. Margolis, Jessica R. Young, and Manuel K. Lopez
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Artemisia tridentata ,Bromus tectorum ,fire regimes ,fire scar ,Gunnison Sage‐grouse ,ponderosa pine ,Ecology ,QH540-549.5 - Abstract
Abstract The historical role of fire in sagebrush (Artemisia tridentata) landscapes remains poorly understood, yet is important to inform management and conservation of obligate species such as the threatened Gunnison Sage‐grouse (GUSG; Centrocercus minimus). We reconstructed fire histories from tree‐ring fire scars at sagebrush–forest ecotones (10 sites, 111 trees) to better understand the role of fire in sagebrush landscapes of the Upper Gunnison Basin (UGB), Colorado, and how fire may have changed following Euro‐American settlement. We assessed likely influences of historical fire by surveying plant composition and structure at 100 sagebrush sites with and without recent (2001–2020) fires. Tree‐ring fire scars revealed a history of repeated low‐severity fire at sagebrush–forest ecotones until 1892, followed by over a century without fire. Between 1684 and 1892, the mean fire interval (MFI) among sites averaged 49.6 years (ranging from 18.2 to 119 years). Fire over this period occurred synchronously at two or more sites on average every 23.6 years, potentially indicative of spread between sites. Most (70%) of the historical fires burned in the early growing season, consistent with times of strong wind. Recent burns exhibited reductions in sagebrush cover (5% vs. 25% in unburned sites) and concomitant increases in herbaceous cover (55% vs. 40%). These differences declined over time but persisted for at least two decades. Burned sites were dominated by native perennial grasses, forbs, and resprouting shrub species. Historically, such openings may have served as seasonal GUSG habitat. Our results indicate that parts of the UGB sagebrush landscapes were characterized historically by frequent fire and dynamic vegetation mosaics that included open, grassy patches. These findings support the use of prescribed fire to restore and maintain this ecological process and vegetation heterogeneity. However, the contemporary context for fire has changed and now includes substantially reduced, Endangered Species Act (ESA)‐listed GUSG populations, increased risk of non‐native plant invasion, and climate warming. These circumstances highlight new risks, information needs, and opportunities for key knowledge co‐production via management–research partnerships.
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- 2023
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4. The North American tree‐ring fire‐scar network
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Ellis Q. Margolis, Christopher H. Guiterman, Raphaël D. Chavardès, Jonathan D. Coop, Kelsey Copes‐Gerbitz, Denyse A. Dawe, Donald A. Falk, James D. Johnston, Evan Larson, Hang Li, Joseph M. Marschall, Cameron E. Naficy, Adam T. Naito, Marc‐André Parisien, Sean A. Parks, Jeanne Portier, Helen M. Poulos, Kevin M. Robertson, James H. Speer, Michael Stambaugh, Thomas W. Swetnam, Alan J. Tepley, Ichchha Thapa, Craig D. Allen, Yves Bergeron, Lori D. Daniels, Peter Z. Fulé, David Gervais, Martin P. Girardin, Grant L. Harley, Jill E. Harvey, Kira M. Hoffman, Jean M. Huffman, Matthew D. Hurteau, Lane B. Johnson, Charles W. Lafon, Manuel K. Lopez, R. Stockton Maxwell, Jed Meunier, Malcolm North, Monica T. Rother, Micah R. Schmidt, Rosemary L. Sherriff, Lauren A. Stachowiak, Alan Taylor, Erana J. Taylor, Valerie Trouet, Miguel L. Villarreal, Larissa L. Yocom, Karen B. Arabas, Alexis H. Arizpe, Dominique Arseneault, Alicia Azpeleta Tarancón, Christopher Baisan, Erica Bigio, Franco Biondi, Gabriel D. Cahalan, Anthony Caprio, Julián Cerano‐Paredes, Brandon M. Collins, Daniel C. Dey, Igor Drobyshev, Calvin Farris, M. Adele Fenwick, William Flatley, M. Lisa Floyd, Ze'ev Gedalof, Andres Holz, Lauren F. Howard, David W. Huffman, Jose Iniguez, Kurt F. Kipfmueller, Stanley G. Kitchen, Keith Lombardo, Donald McKenzie, Andrew G. Merschel, Kerry L. Metlen, Jesse Minor, Christopher D. O'Connor, Laura Platt, William J. Platt, Thomas Saladyga, Amanda B. Stan, Scott Stephens, Colleen Sutheimer, Ramzi Touchan, and Peter J. Weisberg
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climate ,dendrochronology ,fire regime ,fire scar ,humans ,pyrogeography ,Ecology ,QH540-549.5 - Abstract
Abstract Fire regimes in North American forests are diverse and modern fire records are often too short to capture important patterns, trends, feedbacks, and drivers of variability. Tree‐ring fire scars provide valuable perspectives on fire regimes, including centuries‐long records of fire year, season, frequency, severity, and size. Here, we introduce the newly compiled North American tree‐ring fire‐scar network (NAFSN), which contains 2562 sites, >37,000 fire‐scarred trees, and covers large parts of North America. We investigate the NAFSN in terms of geography, sample depth, vegetation, topography, climate, and human land use. Fire scars are found in most ecoregions, from boreal forests in northern Alaska and Canada to subtropical forests in southern Florida and Mexico. The network includes 91 tree species, but is dominated by gymnosperms in the genus Pinus. Fire scars are found from sea level to >4000‐m elevation and across a range of topographic settings that vary by ecoregion. Multiple regions are densely sampled (e.g., >1000 fire‐scarred trees), enabling new spatial analyses such as reconstructions of area burned. To demonstrate the potential of the network, we compared the climate space of the NAFSN to those of modern fires and forests; the NAFSN spans a climate space largely representative of the forested areas in North America, with notable gaps in warmer tropical climates. Modern fires are burning in similar climate spaces as historical fires, but disproportionately in warmer regions compared to the historical record, possibly related to under‐sampling of warm subtropical forests or supporting observations of changing fire regimes. The historical influence of Indigenous and non‐Indigenous human land use on fire regimes varies in space and time. A 20th century fire deficit associated with human activities is evident in many regions, yet fire regimes characterized by frequent surface fires are still active in some areas (e.g., Mexico and the southeastern United States). These analyses provide a foundation and framework for future studies using the hundreds of thousands of annually‐ to sub‐annually‐resolved tree‐ring records of fire spanning centuries, which will further advance our understanding of the interactions among fire, climate, topography, vegetation, and humans across North America.
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- 2022
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5. Contributions of fire refugia to resilient ponderosa pine and dry mixed‐conifer forest landscapes
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Jonathan D. Coop, Timothy J. DeLory, William M. Downing, Sandra L. Haire, Meg A. Krawchuk, Carol Miller, Marc‐André Parisien, and Ryan B. Walker
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burn severity ,dispersal ,fire refuge ,landscape memory ,landscape simulation models ,refugia ,Ecology ,QH540-549.5 - Abstract
Abstract Altered fire regimes can drive major and enduring compositional shifts or losses of forest ecosystems. In western North America, ponderosa pine and dry mixed‐conifer forest types appear increasingly vulnerable to uncharacteristically extensive, high‐severity wildfire. However, unburned or only lightly impacted forest stands that persist within burn mosaics—termed fire refugia—may serve as tree seed sources and promote landscape recovery. We sampled tree regeneration along gradients of fire refugia proximity and density at 686 sites within the perimeters of 12 large wildfires that occurred between 2000 and 2005 in the interior western United States. We used generalized linear mixed‐effects models to elucidate statistical relationships between tree regeneration and refugia pattern, including a new metric that incorporates patch proximity and proportional abundance. These relationships were then used to develop a spatially explicit landscape simulation model. We found that regeneration by ponderosa pine and obligate‐seeding mixed‐conifer tree species assemblages was strongly and positively predicted by refugia proximity and density. Simulation models revealed that for any given proportion of the landscape occupied by refugia, small patches produced greater landscape recovery than large patches. These results highlight the disproportionate importance of small, isolated islands of surviving trees, which may not be detectable with coarse‐scale satellite imagery. Findings also illustrate the interplay between patch‐scale resistance and landscape‐scale resilience: Disturbance‐resistant settings (fire refugia) can entrain resilience (forest regeneration) across the burn matrix. Implications and applications for land managers and conservation practitioners include strategies for the promotion and maintenance of fire refugia as components of resilient forest landscapes.
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- 2019
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6. Fire regimes approaching historic norms reduce wildfire‐facilitated conversion from forest to non‐forest
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Ryan B. Walker, Jonathan D. Coop, Sean A. Parks, and Laura Trader
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ecological restoration ,fuel treatment ,Pinus ponderosa ,reburning ,resilience ,resource objective wildfire ,Ecology ,QH540-549.5 - Abstract
Abstract Extensive high‐severity wildfires have driven major losses of ponderosa pine and mixed‐conifer forests in the southwestern United States, in some settings catalyzing enduring conversions to non‐forested vegetation types. Management interventions to reduce the probability of stand‐replacing wildfire have included mechanical fuel treatments, prescribed fire, and wildfire managed for resource benefit. In 2011, the Las Conchas fire in northern New Mexico burned forested areas not exposed to fire for >100 yr, but also reburned numerous prescribed fire units and/or areas previously burned by wildfire. At some sites, the combination of recent prescribed fire and wildfire approximated known pre‐settlement fire frequency, with two or three exposures to fire between 1977 and 2007. We analyzed gridded remotely sensed burn severity data (differenced normalized burn ratio), pre‐ and post‐fire field vegetation samples, and pre‐ and post‐fire measures of surface fuels to assess relationships and interactions between prescribed fire, prior wildfire, fuels, subsequent burn severity, and patterns of post‐fire forest retention vs. conversion to non‐forest. We found that Las Conchas burn severity was lowest, and tree survival was highest, in sites that had experienced both prescribed fire and prior wildfire. Sites that had experienced only prescribed or prior wildfire exhibited moderate burn severity and intermediate levels of forest retention. Sites lacking any recent prior fire burned at the highest severity and were overwhelmingly converted to non‐forested vegetation including grassland, oak scrub, and weedy, herbaceous‐dominated types. Burn severity in the Las Conchas fire was closely linked to surface woody fuel loads, which were reduced by prior wildfire and prescribed fire. Our results support the restoration of fire regimes via prescribed fire and resource benefit wildfire to promote the resiliency of forest types vulnerable to fire‐mediated type conversion. The application of prescribed fire to reduce surface fuels following wildfire may reduce forest loss during subsequent fire under more extreme conditions. These findings are especially relevant given likely increases in vulnerability associated with climate change impacts to wildfire and forest dynamics.
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- 2018
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7. Characterizing Spatial Neighborhoods of Refugia Following Large Fires in Northern New Mexico USA
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Sandra L. Haire, Jonathan D. Coop, and Carol Miller
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refugial gradient ,Gaussian kernel ,species ordination ,generalized additive models ,terrain ,spatial climate ,disturbance interactions ,rear edge populations ,Pinus ponderosa ,burn severity ,Las Conchas ,Agriculture - Abstract
The spatial patterns resulting from large fires include refugial habitats that support surviving legacies and promote ecosystem recovery. To better understand the diverse ecological functions of refugia on burn mosaics, we used remotely sensed data to quantify neighborhood patterns of areas relatively unchanged following the 2011 Las Conchas fire. Spatial patterns of refugia measured within 10-ha moving windows varied across a gradient from areas of high density, clustered in space, to sparsely populated neighborhoods that occurred in the background matrix. The scaling of these patterns was related to the underlying structure of topography measured by slope, aspect and potential soil wetness, and spatially varying climate. Using a nonmetric multidimensional scaling analysis of species cover data collected post-Las Conchas, we found that trees and forest associates were present across the refugial gradient, but communities also exhibited a range of species compositions and potential functions. Spatial patterns of refugia quantified for three previous burns (La Mesa 1977, Dome 1996, Cerro Grande 2000) were dynamic between fire events, but most refugia persisted through at least two fires. Efforts to maintain burn heterogeneity and its ecological functions can begin with identifying where refugia are likely to occur, using terrain-based microclimate models, burn severity models and available field data.
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- 2017
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8. Rocky Mountain forests are poised to recover following bark beetle outbreaks but with altered composition
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Kyle C. Rodman, Robert A. Andrus, Amanda R. Carlson, Trevor A. Carter, Teresa B. Chapman, Jonathan D. Coop, Paula J. Fornwalt, Nathan S. Gill, Brian J. Harvey, Ashley E. Hoffman, Katharine C. Kelsey, Dominik Kulakowski, Daniel C. Laughlin, Jenna E. Morris, José F. Negrón, Katherine M. Nigro, Gregory S. Pappas, Miranda D. Redmond, Charles C. Rhoades, Monique E. Rocca, Zoe H. Schapira, Jason S. Sibold, Camille S. Stevens‐Rumann, Thomas T. Veblen, Jianmin Wang, Xiaoyang Zhang, and Sarah J. Hart
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Ecology ,Plant Science ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
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9. Cellular trafficking and fate mapping of cells within the nervous system after in utero hematopoietic cell transplantation
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Matthew T. Grant, Hemanth Ramesh Nelvagal, Maria Tecos, Amal Hamed, Kerry Swanson, Jonathan D. Cooper, and Jesse D. Vrecenak
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Biology (General) ,QH301-705.5 - Abstract
Abstract In utero hematopoietic cell transplantation (IUHCT) utilizes fetal immune tolerance to achieve durable chimerism without conditioning or immunosuppression during a unique window in fetal development. Though donor cells have been observed within the nervous system following in utero injection, the timeline and distribution of cellular trafficking across the blood-brain barrier following IUHCT is not well understood. We injected 20 × 106 adult bone marrow mononuclear cells intravenously at gestational age (GA) 12–17 days and found that donor cells were maximally concentrated in the brain with treatment between GA 13–14. Donor cell engraftment persisted within the brain at every timepoint analyzed and concentrated within the hindbrain with significantly more grafted cells than in the forebrain. Additionally, transplanted cells terminally differentiated into various nervous system cellular morphologies and also populated the enteric nervous system. This study is the first to document the timeline and distribution of donor cell trafficking into the immune-protected nervous system and serves as a foundation for the application of IUHCT to treat neurogenetic diseases.
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- 2024
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10. Extreme fire spread events and area burned under recent and future climate in the western USA
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Jonathan D. Coop, Sean A. Parks, Camille S. Stevens‐Rumann, Scott M. Ritter, Chad M. Hoffman, and J. Morgan Varner
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Global and Planetary Change ,Ecology ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
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11. Reduced fire severity offers near-term buffer to climate-driven declines in conifer resilience across the western United States
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Kimberley T. Davis, Marcos D. Robles, Kerry B. Kemp, Philip E. Higuera, Teresa Chapman, Kerry L. Metlen, Jamie L. Peeler, Kyle C. Rodman, Travis Woolley, Robert N. Addington, Brian J. Buma, C. Alina Cansler, Michael J. Case, Brandon M. Collins, Jonathan D. Coop, Solomon Z. Dobrowski, Nathan S. Gill, Collin Haffey, Lucas B. Harris, Brian J. Harvey, Ryan D. Haugo, Matthew D. Hurteau, Dominik Kulakowski, Caitlin E. Littlefield, Lisa A. McCauley, Nicholas Povak, Kristen L. Shive, Edward Smith, Jens T. Stevens, Camille S. Stevens-Rumann, Alan H. Taylor, Alan J. Tepley, Derek J. N. Young, Robert A. Andrus, Mike A. Battaglia, Julia K. Berkey, Sebastian U. Busby, Amanda R. Carlson, Marin E. Chambers, Erich Kyle Dodson, Daniel C. Donato, William M. Downing, Paula J. Fornwalt, Joshua S. Halofsky, Ashley Hoffman, Andrés Holz, Jose M. Iniguez, Meg A. Krawchuk, Mark R. Kreider, Andrew J. Larson, Garrett W. Meigs, John Paul Roccaforte, Monica T. Rother, Hugh Safford, Michael Schaedel, Jason S. Sibold, Megan P. Singleton, Monica G. Turner, Alexandra K. Urza, Kyra D. Clark-Wolf, Larissa Yocom, Joseph B. Fontaine, and John L. Campbell
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Multidisciplinary - Abstract
Increasing fire severity and warmer, drier postfire conditions are making forests in the western United States (West) vulnerable to ecological transformation. Yet, the relative importance of and interactions between these drivers of forest change remain unresolved, particularly over upcoming decades. Here, we assess how the interactive impacts of changing climate and wildfire activity influenced conifer regeneration after 334 wildfires, using a dataset of postfire conifer regeneration from 10,230 field plots. Our findings highlight declining regeneration capacity across the West over the past four decades for the eight dominant conifer species studied. Postfire regeneration is sensitive to high-severity fire, which limits seed availability, and postfire climate, which influences seedling establishment. In the near-term, projected differences in recruitment probability between low- and high-severity fire scenarios were larger than projected climate change impacts for most species, suggesting that reductions in fire severity, and resultant impacts on seed availability, could partially offset expected climate-driven declines in postfire regeneration. Across 40 to 42% of the study area, we project postfire conifer regeneration to be likely following low-severity but not high-severity fire under future climate scenarios (2031 to 2050). However, increasingly warm, dry climate conditions are projected to eventually outweigh the influence of fire severity and seed availability. The percent of the study area considered unlikely to experience conifer regeneration, regardless of fire severity, increased from 5% in 1981 to 2000 to 26 to 31% by mid-century, highlighting a limited time window over which management actions that reduce fire severity may effectively support postfire conifer regeneration.
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- 2023
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12. Reimagine fire science for the anthropocene
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Jacquelyn K Shuman, Jennifer K Balch, Rebecca T Barnes, Philip E Higuera, Christopher I Roos, Dylan W Schwilk, E Natasha Stavros, Tirtha Banerjee, Megan M Bela, Jacob Bendix, Sandro Bertolino, Solomon Bililign, Kevin D Bladon, Paulo Brando, Robert E Breidenthal, Brian Buma, Donna Calhoun, Leila M V Carvalho, Megan E Cattau, Kaelin M Cawley, Sudeep Chandra, Melissa L Chipman, Jeanette Cobian-Iñiguez, Erin Conlisk, Jonathan D Coop, Alison Cullen, Kimberley T Davis, Archana Dayalu, Fernando De Sales, Megan Dolman, Lisa M Ellsworth, Scott Franklin, Christopher H Guiterman, Matthew Hamilton, Erin J Hanan, Winslow D Hansen, Stijn Hantson, Brian J Harvey, Andrés Holz, Tao Huang, Matthew D Hurteau, Nayani T Ilangakoon, Megan Jennings, Charles Jones, Anna Klimaszewski-Patterson, Leda N Kobziar, John Kominoski, Branko Kosovic, Meg A Krawchuk, Paul Laris, Jackson Leonard, S Marcela Loria-Salazar, Melissa Lucash, Hussam Mahmoud, Ellis Margolis, Toby Maxwell, Jessica L McCarty, David B McWethy, Rachel S Meyer, Jessica R Miesel, W Keith Moser, R Chelsea Nagy, Dev Niyogi, Hannah M Palmer, Adam Pellegrini, Benjamin Poulter, Kevin Robertson, Adrian V Rocha, Mojtaba Sadegh, Fernanda Santos, Facundo Scordo, Joseph O Sexton, A Surjalal Sharma, Alistair M S Smith, Amber J Soja, Christopher Still, Tyson Swetnam, Alexandra D Syphard, Morgan W Tingley, Ali Tohidi, Anna T Trugman, Merritt Turetsky, J Morgan Varner, Yuhang Wang, Thea Whitman, Stephanie Yelenik, Xuan Zhang, and Nelson, Karen E
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climate change ,social–ecological systems ,wildland–urban interface ,resilience ,wildfire - Abstract
Fire is an integral component of ecosystems globally and a tool that humans have harnessed for millennia. Altered fire regimes are a fundamental cause and consequence of global change, impacting people and the biophysical systems on which they depend. As part of the newly emerging Anthropocene, marked by human-caused climate change and radical changes to ecosystems, fire danger is increasing, and fires are having increasingly devastating impacts on human health, infrastructure, and ecosystem services. Increasing fire danger is a vexing problem that requires deep transdisciplinary, trans-sector, and inclusive partnerships to address. Here, we outline barriers and opportunities in the next generation of fire science and provide guidance for investment in future research. We synthesize insights needed to better address the long-standing challenges of innovation across disciplines to (i) promote coordinated research efforts; (ii) embrace different ways of knowing and knowledge generation; (iii) promote exploration of fundamental science; (iv) capitalize on the “firehose” of data for societal benefit; and (v) integrate human and natural systems into models across multiple scales. Fire science is thus at a critical transitional moment. We need to shift from observation and modeled representations of varying components of climate, people, vegetation, and fire to more integrative and predictive approaches that support pathways toward mitigating and adapting to our increasingly flammable world, including the utilization of fire for human safety and benefit. Only through overcoming institutional silos and accessing knowledge across diverse communities can we effectively undertake research that improves outcomes in our more fiery future.
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- 2022
13. Vegetation type conversion in the US Southwest: frontline observations and management responses
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Christopher H. Guiterman, Rachel M. Gregg, Laura A. E. Marshall, Jill J. Beckmann, Phillip J. van Mantgem, Donald A. Falk, Jon E. Keeley, Anthony C. Caprio, Jonathan D. Coop, Paula J. Fornwalt, Collin Haffey, R. Keala Hagmann, Stephen T. Jackson, Ann M. Lynch, Ellis Q. Margolis, Christopher Marks, Marc D. Meyer, Hugh Safford, Alexandra Dunya Syphard, Alan Taylor, Craig Wilcox, Dennis Carril, Carolyn A. F. Enquist, David Huffman, Jose Iniguez, Nicole A. Molinari, Christina Restaino, and Jens T. Stevens
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Forestry ,Environmental Science (miscellaneous) ,Ecology, Evolution, Behavior and Systematics - Abstract
Background Forest and nonforest ecosystems of the western United States are experiencing major transformations in response to land-use change, climate warming, and their interactive effects with wildland fire. Some ecosystems are transitioning to persistent alternative types, hereafter called “vegetation type conversion” (VTC). VTC is one of the most pressing management issues in the southwestern US, yet current strategies to intervene and address change often use trial-and-error approaches devised after the fact. To better understand how to manage VTC, we gathered managers, scientists, and practitioners from across the southwestern US to collect their experiences with VTC challenges, management responses, and outcomes. Results Participants in two workshops provided 11 descriptive case studies and 61 examples of VTC from their own field observations. These experiences demonstrate the extent and complexity of ecological reorganization across the region. High-severity fire was the predominant driver of VTC in semi-arid coniferous forests. By a large margin, these forests converted to shrubland, with fewer conversions to native or non-native herbaceous communities. Chaparral and sagebrush areas nearly always converted to non-native grasses through interactions among land use, climate, and fire. Management interventions in VTC areas most often attempted to reverse changes, although we found that these efforts cover only a small portion of high-severity burn areas undergoing VTC. Some areas incurred long (>10 years) observational periods prior to initiating interventions. Efforts to facilitate VTC were rare, but could cover large spatial areas. Conclusions Our findings underscore that type conversion is a common outcome of high-severity wildland fire in the southwestern US. Ecosystem managers are frontline observers of these far-reaching and potentially persistent changes, making their experiences valuable in further developing intervention strategies and research agendas. As its drivers increase with climate change, VTC appears increasingly likely in many ecological contexts and may require management paradigms to transition as well. Approaches to VTC potentially include developing new models of desired conditions, the use of experimentation by managers, and broader implementation of adaptive management strategies. Continuing to support and develop science-manager partnerships and peer learning groups will help to shape our response to ongoing rapid ecological transformations.
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- 2022
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14. Forest and woodland replacement patterns following drought-related mortality
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Juan Carlos Linares, Yamila Sasal, Abdallah Bentouati, Miranda D. Redmond, C. John Burk, Joseph L. Ganey, Thomas T. Veblen, Francesco Ripullone, Christof Bigler, Lucía Galiano, Suzanne B. Marchetti, William R. L. Anderegg, Caroline Vincke, Ermias Aynekulu, J. Julio Camarero, Jeffrey M. Kane, Maria Laura Suarez, Andreas Rigling, Anna L. Jacobsen, Tuomas Aakala, Michael Michaelian, Enric Batllori, Francisco Lloret, R. B. Pratt, Roderick Fensham, Gabriel Sangüesa-Barreda, M. Lisa Floyd, Thomas Kitzberger, Albert Vilà-Cabrera, Rafael M. Navarro-Cerrillo, Sandra Saura-Mas, Devin P. Bendixsen, Ben J. Zeeman, George Matusick, Michele Colangelo, Patrick Gonzalez, Jonathan D. Coop, UCL - SST/ELI/ELIE - Environmental Sciences, Department of Forest Sciences, Boreal forest dynamics and biodiversity research group, and Forest Ecology and Management
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DYNAMICS ,0106 biological sciences ,010504 meteorology & atmospheric sciences ,Biome ,ved/biology.organism_classification_rank.species ,Ecological succession ,Woodland ,Forests ,FIRE ,01 natural sciences ,Shrub ,Forest dynamics ,Trees ,Ecosystem services ,Drought-induced mortality ,global tree mortality ,Global tree mortality ,RESEARCH FRONTIERS ,Climate change ,MAXIMUM-LIKELIHOOD ,4112 Forestry ,Multidisciplinary ,Ecology ,food and beverages ,Biodiversity ,Biological Sciences ,Droughts ,Geography ,Forest resilience ,forest dynamics ,Climate Change ,drought-unduced motality ,010603 evolutionary biology ,INDUCED TREE ,Species Specificity ,REGRESSION ,MANAGEMENT ,Dominance (ecology) ,VEGETATION SHIFTS ,Ecosystem ,forest resilience ,0105 earth and related environmental sciences ,ved/biology ,RESILIENCE ,15. Life on land ,13. Climate action ,drought-induced mortality - Abstract
Significance Forests are experiencing growing risks of drought-induced mortality in a warming world. Yet, ecosystem dynamics following drought mortality remain unknown, representing a major limitation to our understanding of the ecological consequences of climate change. We provide an emerging picture of postdrought ecological trajectories based on field indicators of forest dynamics. Replacement patterns following mortality indicate limited short-term persistence of predrought dominant tree species, highlighting the potential for major ecosystem reorganization in the coming decades. The great variability of the observed dynamics within and among species reinforces the primary influence of drought characteristics and ecosystem legacies, modulated by land use, management, and past disturbances, on ongoing drought-related species turnover and their potential implications for future forest biodiversity and ecosystem services., Forest vulnerability to drought is expected to increase under anthropogenic climate change, and drought-induced mortality and community dynamics following drought have major ecological and societal impacts. Here, we show that tree mortality concomitant with drought has led to short-term (mean 5 y, range 1 to 23 y after mortality) vegetation-type conversion in multiple biomes across the world (131 sites). Self-replacement of the dominant tree species was only prevalent in 21% of the examined cases and forests and woodlands shifted to nonwoody vegetation in 10% of them. The ultimate temporal persistence of such changes remains unknown but, given the key role of biological legacies in long-term ecological succession, this emerging picture of postdrought ecological trajectories highlights the potential for major ecosystem reorganization in the coming decades. Community changes were less pronounced under wetter postmortality conditions. Replacement was also influenced by management intensity, and postdrought shrub dominance was higher when pathogens acted as codrivers of tree mortality. Early change in community composition indicates that forests dominated by mesic species generally shifted toward more xeric communities, with replacing tree and shrub species exhibiting drier bioclimatic optima and distribution ranges. However, shifts toward more mesic communities also occurred and multiple pathways of forest replacement were observed for some species. Drought characteristics, species-specific environmental preferences, plant traits, and ecosystem legacies govern postdrought species turnover and subsequent ecological trajectories, with potential far-reaching implications for forest biodiversity and ecosystem services.
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- 2020
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15. Wildfire-Driven Forest Conversion in Western North American Landscapes
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Solomon Z. Dobrowski, Paula J. Fornwalt, Malcolm P. North, Kyle C. Rodman, Sean A. Parks, Brandon M. Collins, Ellis Q. Margolis, Kimberley T. Davis, Marc-André Parisien, Caitlin E. Littlefield, Van R. Kane, Jonathan D. Coop, Ellen Whitman, Shelley D. Crausbay, Peter Z. Fulé, Matthew D. Hurteau, Donald A. Falk, Brian J. Harvey, Susan J. Prichard, Camille S. Stevens-Rumann, Timothy J. Assal, Alan J. Tepley, and Philip E. Higuera
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stand-replacing fire ,AcademicSubjects/SCI00010 ,ecological transformation ,vegetation type conversion ,Agroforestry ,media_common.quotation_subject ,Vulnerability ,tree seedlings ,Climate change ,Poison control ,Vegetation ,wildfire ,Overview Articles ,Ecosystem services ,climate change ,high-severity fire ,Geography ,Disturbance (ecology) ,Forest ecology ,AcademicSubjects/SOC02100 ,tree regeneration ,Psychological resilience ,General Agricultural and Biological Sciences ,media_common - Abstract
Changing disturbance regimes and climate can overcome forest ecosystem resilience. Following high-severity fire, forest recovery may be compromised by lack of tree seed sources, warmer and drier postfire climate, or short-interval reburning. A potential outcome of the loss of resilience is the conversion of the prefire forest to a different forest type or nonforest vegetation. Conversion implies major, extensive, and enduring changes in dominant species, life forms, or functions, with impacts on ecosystem services. In the present article, we synthesize a growing body of evidence of fire-driven conversion and our understanding of its causes across western North America. We assess our capacity to predict conversion and highlight important uncertainties. Increasing forest vulnerability to changing fire activity and climate compels shifts in management approaches, and we propose key themes for applied research coproduced by scientists and managers to support decision-making in an era when the prefire forest may not return.
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- 2020
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16. Influence of fire refugia spatial pattern on post-fire forest recovery in Oregon’s Blue Mountains
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Jonathan D. Coop, Garrett W. Meigs, Ellen Whitman, Sandra L. Haire, William M. Downing, Geneva W. Chong, Carol Miller, Meg A. Krawchuk, and Ryan B. Walker
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0106 biological sciences ,geography.geographical_feature_category ,Ecology ,biology ,Fire regime ,010604 marine biology & hydrobiology ,Geography, Planning and Development ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Shrubland ,Geography ,Propagule ,Seedling ,Spatial ecology ,Common spatial pattern ,Landscape ecology ,Regeneration (ecology) ,Nature and Landscape Conservation - Abstract
Fire regimes in many dry forests of western North America are substantially different from historical conditions, and there is concern about the ability of these forests to recover following severe wildfire. Fire refugia, unburned or low-severity burned patches where trees survived fire, may serve as essential propagule sources that enable forest regeneration. To quantify the influence of fire refugia spatial pattern and other biophysical factors on the process of post-fire tree regeneration; in particular examining both the proximity and density of surrounding refugia to characterize the landscape of refugial seed sources. We surveyed regeneration at 135 sites in stand-replacement patches across a gradient of fire refugia density in eastern Oregon, USA. We characterized the influence of refugial seed source pattern and other environmental factors on the abundance of regenerating seedlings, and examined the relationship between post-fire climate and the temporal pattern of ponderosa pine seedling establishment. Tree seedlings were present in 83% of plots 12–17 years post-fire, and densities varied substantially (0–67800 stems ha−1, median = 1100). Variation in seedling abundance was driven by the spatial patterns of refugial seed sources. Despite widespread post-fire shrub cover, high-severity burned forests have not undergone a persistent type conversion to shrublands. Ponderosa pine seedling establishment peaked 5–11 years after fire and was not closely associated with post-fire climate. Fire refugia and the seed sources they contain fostered tree regeneration in severely burned patches. Management practices that reduce refugia within post-fire landscapes may negatively influence essential forest recovery processes.
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- 2019
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17. Disturbance refugia within mosaics of forest fire, drought, and insect outbreaks
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Jonathan D. Coop, Arjan J. H. Meddens, Andrés Holz, Garrett W. Meigs, Meg A. Krawchuk, Crystal A. Kolden, Jennifer M. Cartwright, and Raymond J. Davis
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0106 biological sciences ,Geography ,Disturbance (geology) ,010504 meteorology & atmospheric sciences ,Insect outbreak ,Ecology ,Life on Land ,15. Life on land ,010603 evolutionary biology ,01 natural sciences ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
Author(s): Krawchuk, Meg A; Meigs, Garrett W; Cartwright, Jennifer M; Coop, Jonathan D; Davis, Raymond; Holz, Andres; Kolden, Crystal; Meddens, Arjan JH
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- 2020
18. Tamm Review: Postfire landscape management in frequent-fire conifer forests of the southwestern United States
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Jonathan D. Coop, Teresa B. Chapman, Dennis Carril, Larissa L. Yocom, Owen T. Burney, Ellis Q. Margolis, Jens T. Stevens, Matthew D. Hurteau, Sandra L. Haire, Kyle C. Rodman, Andrea E. Thode, Anne Bradley, Paula J. Fornwalt, Craig D. Allen, Collin Haffey, Camille S. Stevens-Rumann, Laura A.E. Marshall, Jose M. Iniguez, Jessica J. Walker, Christopher Marks, and Marin E. Chambers
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Agroforestry ,media_common.quotation_subject ,Forest management ,Reforestation ,Forestry ,Vegetation ,Management, Monitoring, Policy and Law ,Decision points ,Geography ,Ecosystem ,Psychological resilience ,Regeneration (ecology) ,Spatial planning ,Nature and Landscape Conservation ,media_common - Abstract
The increasing incidence of wildfires across the southwestern United States (US) is altering the contemporary forest management template within historically frequent-fire conifer forests. An increasing fraction of southwestern conifer forests have recently burned, and many of these burned landscapes contain complex mosaics of surviving forest and severely burned patches without surviving conifer trees. These heterogeneous burned landscapes present unique social and ecological challenges. Severely burned patches can present numerous barriers to successful conifer regeneration, and often contain heavy downed fuels which have cascading effects on future fire behavior and conifer regeneration. Conversely, surviving forest patches are increasingly recognized for their value in postfire reforestation but often are overlooked from a management perspective. Here we present a decision-making framework for landscape-scale management of complex postfire landscapes that allows for adaptation to a warming climate and future fire. We focus specifically on historically frequent-fire forests of the southwestern US but make connections to other forest types and other regions. Our framework depends on a spatially-explicit assessment of the mosaic of conifer forest and severely burned patches in the postfire landscape, evaluates likely vegetation trajectories, and identifies critical decision points to direct vegetation change via manipulations of fuels and live vegetation. This framework includes detailed considerations for postfire fuels management (e.g., edge hardening within live forest patches and repeat burning) and for reforestation (e.g., balancing tradeoffs between intensive and extensive planting strategies, establishing patches of seed trees, spatial planning to optimize reforestation success, and improving nursery capacity). In a future of increasing fire activity in forests where repeated low- to moderate-severity fire is essential to ecosystem resilience, the decision-making framework developed here can easily be integrated with existing postfire management strategies to optimize allocation of limited resources and more actively manage burned landscapes.
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- 2021
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19. How Much Forest Persists Through Fire? High-Resolution Mapping of Tree Cover to Characterize the Abundance and Spatial Pattern of Fire Refugia Across Mosaics of Burn Severity
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Ryan B. Walker, Garrett W. Meigs, Jonathan D. Coop, Meg A. Krawchuk, Sparkle L. Malone, and William M. Downing
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,High resolution ,010603 evolutionary biology ,01 natural sciences ,scale ,remote sensing ,refugia ,Abundance (ecology) ,Pinus ponderosa ,Forest ecology ,Satellite imagery ,resilience ,0105 earth and related environmental sciences ,dry mixed-conifer ,Reforestation ,Forestry ,lcsh:QK900-989 ,burn severity ,patch size ,lcsh:Plant ecology ,Environmental science ,Common spatial pattern ,Tree cover ,Physical geography ,Scale (map) - Abstract
Wildfires in forest ecosystems produce landscape mosaics that include relatively unaffected areas, termed fire refugia. These patches of persistent forest cover can support fire-sensitive species and the biotic legacies important for post-fire forest recovery, yet little is known about their abundance and distribution within fire perimeters. Readily accessible 30-m resolution satellite imagery and derived burn severity products are commonly employed to characterize post-fire landscapes, however, coarse image resolution, generalized burn severity thresholds, and other limitations can constrain accurate representation of fire refugia. This study quantifies the abundance and pattern of fire refugia within 10 fires occurring in ponderosa pine and dry mixed-conifer forests between 2000 and 2003. We developed high-resolution maps of post-fire landscapes using semi-automated, object-based classification of 1-m aerial imagery, conducted imagery- and field-based accuracy assessments, and contrasted these with Landsat-derived burn severity metrics. Fire refugia area within burn perimeters ranged from 20% to 57%. Refugia proportion generally decreased with increasing Landsat-derived burn severity, but still accounted for 3&ndash, 12% of areas classified as high severity. Patch size ranged from 1-m2 isolated trees to nearly 8000 ha, and median patch size was 0.01 ha&mdash, substantially smaller than a 30-m Landsat pixel. Patch size was negatively related to burn severity, distance to fire refugia from open areas was positively related to burn severity. Finally, optimized thresholds of 30-m post-fire normalized burn ratio (NBR) and relative differenced normalized burn ratio (RdNBR) delineated fire refugia with an accuracy of 77% when validated against the 1-m resolution maps. Estimations of fire refugia abundance based on Landsat-derived burn severity metrics are unlikely to detect small, isolated fire refugia patches. Finer-resolution maps can improve understanding of the distribution of forest legacies and inform post-fire management activities including reforestation and treatments.
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- 2019
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20. Contributions of fire refugia to resilient ponderosa pine and dry mixed‐conifer forest landscapes
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William M. Downing, Sandra L. Haire, Carol Miller, Meg A. Krawchuk, Marc-André Parisien, Timothy DeLory, Jonathan D. Coop, Ryan B. Walker, and Ecological Society of America
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0106 biological sciences ,spatial resilience ,010603 evolutionary biology ,01 natural sciences ,scale ,refugia ,Abundance (ecology) ,lcsh:QH540-549.5 ,Forest ecology ,landscape simulation models ,Satellite imagery ,Regeneration (ecology) ,dispersal ,Biology ,Ecology, Evolution, Behavior and Systematics ,Ecology ,Resistance (ecology) ,Fire regime ,010604 marine biology & hydrobiology ,Simulation modeling ,burn severity ,landscape memory ,Geography ,fire refuge ,Biological dispersal ,lcsh:Ecology - Abstract
Altered fire regimes can drive major and enduring compositional shifts or losses of forest ecosystems. In western North America, ponderosa pine and dry mixed‐conifer forest types appear increasingly vulnerable to uncharacteristically extensive, high‐severity wildfire. However, unburned or only lightly impacted forest stands that persist within burn mosaics—termed fire refugia—may serve as tree seed sources and promote landscape recovery. We sampled tree regeneration along gradients of fire refugia proximity and density at 686 sites within the perimeters of 12 large wildfires that occurred between 2000 and 2005 in the interior western United States. We used generalized linear mixed‐effects models to elucidate statistical relationships between tree regeneration and refugia pattern, including a new metric that incorporates patch proximity and proportional abundance. These relationships were then used to develop a spatially explicit landscape simulation model. We found that regeneration by ponderosa pine and obligate‐seeding mixed‐conifer tree species assemblages was strongly and positively predicted by refugia proximity and density. Simulation models revealed that for any given proportion of the landscape occupied by refugia, small patches produced greater landscape recovery than large patches. These results highlight the disproportionate importance of small, isolated islands of surviving trees, which may not be detectable with coarse‐scale satellite imagery. Findings also illustrate the interplay between patch‐scale resistance and landscape‐scale resilience: Disturbance‐resistant settings (fire refugia) can entrain resilience (forest regeneration) across the burn matrix. Implications and applications for land managers and conservation practitioners include strategies for the promotion and maintenance of fire refugia as components of resilient forest landscapes.
- Published
- 2019
21. Thinning alters avian occupancy in piñon–juniper woodlands
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Jonathan D. Coop, Jacob S. Ivan, and Patrick A. Magee
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0106 biological sciences ,biology ,Occupancy ,Sitta carolinensis ,Ecology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Basal area ,010601 ecology ,Geography ,Poecile ,Animal Science and Zoology ,Gymnorhinus cyanocephalus ,Juniper ,Ecology, Evolution, Behavior and Systematics ,Nuthatch ,Chondestes grammacus - Abstract
Natural resource managers are increasingly applying tree reduction treatments to piñon–juniper woodlands to meet a range of ecological, social, and economic goals. However, treatment effects on woodland-obligate bird species are not well understood. We measured multiscale avian occupancy on 29 paired (control/treatment) sites in piñon–juniper woodlands in central Colorado, USA. We conducted point counts at 232 stations, 3 times each season in 2014 and 2015. We used hierarchical multiscale modeling to obtain unbiased estimates of landscape and local occupancy (i.e. probability of use) in treated and untreated sites for 31 species. Treatments reduced the occupancy of conifer obligates, including Mountain Chickadee (Poecile gambeli), Clark’s Nutcracker (Nucifraga columbiana), and White-breasted Nuthatch (Sitta carolinensis), and increased occupancy of Lark Sparrow (Chondestes grammacus) and Mountain Bluebird (Sialia currucoides). Occupancy of Virginia’s Warbler (Oreothylpis virginiae) and Gray Flycatcher (Empidonax wrightii), two piñon–juniper specialists, decreased at the landscape scale in treated sites, and Pinyon Jay (Gymnorhinus cyanocephalus) occupancy decreased at the local scale. Tree reduction treatments in piñon–juniper woodlands have the potential to reduce habitat quality for a suite of bird species of conservation concern. We suggest that treatments designed to retain higher tree density and basal area will benefit conifer-obligate and piñon–juniper specialist bird species.
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- 2019
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22. Fire regimes approaching historic norms reduce wildfire‐facilitated conversion from forest to non‐forest
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Jonathan D. Coop, Ryan B. Walker, Laura Trader, and Sean A. Parks
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,ecological restoration ,Climate change ,010603 evolutionary biology ,01 natural sciences ,Grassland ,resource objective wildfire ,lcsh:QH540-549.5 ,Fire ecology ,fuel treatment ,resilience ,Restoration ecology ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,geography ,geography.geographical_feature_category ,Ecology ,Fire regime ,Forest dynamics ,Forestry ,Vegetation ,Pinus ponderosa ,reburning ,Environmental science ,lcsh:Ecology ,Woody plant - Abstract
Extensive high‐severity wildfires have driven major losses of ponderosa pine and mixed‐conifer forests in the southwestern United States, in some settings catalyzing enduring conversions to non‐forested vegetation types. Management interventions to reduce the probability of stand‐replacing wildfire have included mechanical fuel treatments, prescribed fire, and wildfire managed for resource benefit. In 2011, the Las Conchas fire in northern New Mexico burned forested areas not exposed to fire for >100 yr, but also reburned numerous prescribed fire units and/or areas previously burned by wildfire. At some sites, the combination of recent prescribed fire and wildfire approximated known pre‐settlement fire frequency, with two or three exposures to fire between 1977 and 2007. We analyzed gridded remotely sensed burn severity data (differenced normalized burn ratio), pre‐ and post‐fire field vegetation samples, and pre‐ and post‐fire measures of surface fuels to assess relationships and interactions between prescribed fire, prior wildfire, fuels, subsequent burn severity, and patterns of post‐fire forest retention vs. conversion to non‐forest. We found that Las Conchas burn severity was lowest, and tree survival was highest, in sites that had experienced both prescribed fire and prior wildfire. Sites that had experienced only prescribed or prior wildfire exhibited moderate burn severity and intermediate levels of forest retention. Sites lacking any recent prior fire burned at the highest severity and were overwhelmingly converted to non‐forested vegetation including grassland, oak scrub, and weedy, herbaceous‐dominated types. Burn severity in the Las Conchas fire was closely linked to surface woody fuel loads, which were reduced by prior wildfire and prescribed fire. Our results support the restoration of fire regimes via prescribed fire and resource benefit wildfire to promote the resiliency of forest types vulnerable to fire‐mediated type conversion. The application of prescribed fire to reduce surface fuels following wildfire may reduce forest loss during subsequent fire under more extreme conditions. These findings are especially relevant given likely increases in vulnerability associated with climate change impacts to wildfire and forest dynamics.
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- 2018
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23. The future of subalpine forests in the Southern Rocky Mountains: Trajectories for Pinus aristata genetic lineages
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Sparkle L. Malone, Jonathan D. Coop, and Anna W. Schoettle
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0106 biological sciences ,Atmospheric Science ,010504 meteorology & atmospheric sciences ,Range (biology) ,Lineage (evolution) ,lcsh:Medicine ,Forests ,01 natural sciences ,Ecosystem services ,Trees ,Wildfires ,lcsh:Science ,Climatology ,Multidisciplinary ,biology ,Ecology ,Geography ,Altitude ,Eukaryota ,Bristlecone Pine ,Plants ,Terrestrial Environments ,Phylogeography ,Biogeography ,Research Article ,Climate Change ,Climate change ,010603 evolutionary biology ,Ecosystems ,Genetics ,0105 earth and related environmental sciences ,Subalpine forest ,Evolutionary Biology ,Fire regime ,Population Biology ,lcsh:R ,Ecology and Environmental Sciences ,Organisms ,Biology and Life Sciences ,Genetic Variation ,biology.organism_classification ,Pinus ,Earth Sciences ,lcsh:Q ,Rocky Mountains ,Pines ,Geographic areas ,Population Genetics - Abstract
Like many other high elevation alpine tree species, Rocky Mountain bristlecone pine (Pinus aristata Engelm.) may be particularly vulnerable to climate change. To evaluate its potential vulnerability to shifts in climate, we defined the suitable climate space for each of four genetic lineages of bristlecone pine and for other subalpine tree species in close proximity to bristlecone pine forests. Measuring changes in the suitable climate space for lineage groups is an important step beyond models that assume species are genetically homogenous. The suitable climate space for bristlecone pine in the year 2090 is projected to decline by 74% and the proportional distribution of suitable climate space for genetic lineages shifts toward those associated with warmer and wetter conditions. The 2090 climate space for bristlecone pine exhibits a bimodal distribution along an elevation gradient, presumably due to the persistence of the climate space in the Southern Rocky Mountains and exclusion at mid-elevations by conditions that favor the climate space of other species. These shifts have implications for changes in fire regimes, vulnerability to pest and pathogens, and altered carbon dynamics across the southern Rockies, which may reduce the likelihood of bristlecone pine trees achieving exceptional longevity in the future. The persistence and expansion of climate space for southern bristlecone pine genetic lineage groups in 2090 suggests that these sources may be the least vulnerable in the future. While these lineages may be more likely to persist and therefore present opportunities for proactive management (e.g., assisted migration) to maintain subalpine forest ecosystem services in a warmer world, our findings also imply heighted conservation concern for vulnerable northern lineages facing range contractions.
- Published
- 2018
24. Severe central nervous system demyelination in Sanfilippo disease
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Mahsa Taherzadeh, Erjun Zhang, Irene Londono, Benjamin De Leener, Sophie Wang, Jonathan D. Cooper, Timothy E. Kennedy, Carlos R. Morales, Zesheng Chen, Gregory A. Lodygensky, and Alexey V. Pshezhetsky
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mucopolysaccharidosis ,oligodendrocyte ,myelination ,lysosomal storage ,GM3 ganglioside ,diffusion basis spectrum imaging ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
IntroductionChronic progressive neuroinflammation is a hallmark of neurological lysosomal storage diseases, including mucopolysaccharidosis III (MPS III or Sanfilippo disease). Since neuroinflammation is linked to white matter tract pathology, we analyzed axonal myelination and white matter density in the mouse model of MPS IIIC HgsnatP304L and post-mortem brain samples of MPS III patients.MethodsBrain and spinal cord tissues of human MPS III patients, 6-month-old HgsnatP304L mice and age- and sex-matching wild type mice were analyzed by immunofluorescence to assess levels of myelin-associated proteins, primary and secondary storage materials, and levels of microgliosis. Corpus callosum (CC) region was studied by transmission electron microscopy to analyze axon myelination and morphology of oligodendrocytes and microglia. Mouse brains were analyzed ex vivo by high-filed MRI using Diffusion Basis Spectrum Imaging in Python-Diffusion tensor imaging algorithms.ResultsAnalyses of CC and spinal cord tissues by immunohistochemistry revealed substantially reduced levels of myelin-associated proteins including Myelin Basic Protein, Myelin Associated Glycoprotein, and Myelin Oligodendrocyte Glycoprotein. Furthermore, ultrastructural analyses revealed disruption of myelin sheath organization and reduced myelin thickness in the brains of MPS IIIC mice and human MPS IIIC patients compared to healthy controls. Oligodendrocytes (OLs) in the CC of MPS IIIC mice were scarce, while examination of the remaining cells revealed numerous enlarged lysosomes containing heparan sulfate, GM3 ganglioside or “zebra bodies” consistent with accumulation of lipids and myelin fragments. In addition, OLs contained swollen mitochondria with largely dissolved cristae, resembling those previously identified in the dysfunctional neurons of MPS IIIC mice. Ex vivo Diffusion Basis Spectrum Imaging revealed compelling signs of demyelination (26% increase in radial diffusivity) and tissue loss (76% increase in hindered diffusivity) in CC of MPS IIIC mice.DiscussionOur findings demonstrate an important role for white matter injury in the pathophysiology of MPS III. This study also defines specific parameters and brain regions for MRI analysis and suggests that it may become a crucial non-invasive method to evaluate disease progression and therapeutic response.
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- 2023
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25. Characterizing Spatial Neighborhoods of Refugia Following Large Fires in Northern New Mexico USA
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Carol Miller, Jonathan D. Coop, and Sandra L. Haire
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0106 biological sciences ,disturbance interactions ,spatial climate ,010504 meteorology & atmospheric sciences ,Range (biology) ,refugial gradient ,Gaussian kernel ,species ordination ,generalized additive models ,terrain ,rear edge populations ,Pinus ponderosa ,burn severity ,Las Conchas ,Microclimate ,Terrain ,010603 evolutionary biology ,01 natural sciences ,lcsh:Agriculture ,Ecosystem ,0105 earth and related environmental sciences ,Nature and Landscape Conservation ,Global and Planetary Change ,Ecology ,Generalized additive model ,lcsh:S ,Soil wetness ,Geography ,Habitat ,Spatial ecology - Abstract
The spatial patterns resulting from large fires include refugial habitats that support surviving legacies and promote ecosystem recovery. To better understand the diverse ecological functions of refugia on burn mosaics, we used remotely sensed data to quantify neighborhood patterns of areas relatively unchanged following the 2011 Las Conchas fire. Spatial patterns of refugia measured within 10-ha moving windows varied across a gradient from areas of high density, clustered in space, to sparsely populated neighborhoods that occurred in the background matrix. The scaling of these patterns was related to the underlying structure of topography measured by slope, aspect and potential soil wetness, and spatially varying climate. Using a nonmetric multidimensional scaling analysis of species cover data collected post-Las Conchas, we found that trees and forest associates were present across the refugial gradient, but communities also exhibited a range of species compositions and potential functions. Spatial patterns of refugia quantified for three previous burns (La Mesa 1977, Dome 1996, Cerro Grande 2000) were dynamic between fire events, but most refugia persisted through at least two fires. Efforts to maintain burn heterogeneity and its ecological functions can begin with identifying where refugia are likely to occur, using terrain-based microclimate models, burn severity models and available field data.
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- 2017
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26. Ground-Dwelling Arthropod Community Responses to Recent and Repeated Wildfires in Conifer Forests of Northern New Mexico, USA
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Scott Ferrenberg, Philipp Wickey, and Jonathan D. Coop
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0106 biological sciences ,Metacommunity ,010504 meteorology & atmospheric sciences ,ground-dwelling community ,Biodiversity ,arthropods ,010603 evolutionary biology ,01 natural sciences ,Basal area ,litter ,reburn ,duff ,jemez mountains ,0105 earth and related environmental sciences ,Ecology ,las conchas fire ,Community structure ,Forestry ,lcsh:QK900-989 ,Understory ,cerro grande fire ,understory vegetation ,Geography ,bandelier national monument ,Disturbance (ecology) ,lcsh:Plant ecology ,Biological dispersal ,Coarse woody debris - Abstract
The increasing frequency and severity of wildfires in semi-arid conifer forests as a result of global change pressures has raised concern over potential impacts on biodiversity. Ground-dwelling arthropod communities represent a substantial portion of diversity in conifer forests, and could be particularly impacted by wildfires. In addition to direct mortality, wildfires can affect ground-dwelling arthropods by altering understory characteristics and associated deterministic community assembly processes (e.g., environmental sorting). Alternatively, disturbances have been reported to increase the importance of stochastic community assembly processes (e.g., probabilistic dispersal and colonization rates). Utilizing pitfall traps to capture ground-dwelling arthropods within forest stands that were burned by one or two wildfires since 1996 in the Jemez Mountains of northern New Mexico, United States (USA), we examined the potential influences of deterministic versus stochastic processes on the assembly of these diverse understory communities. Based on family-level and genera-level arthropod identifications, we found that the multivariate community structures differed among the four fire groups surveyed, and were significantly influenced by the quantities of duff, litter, and coarse woody debris, in addition to tree basal area and graminoid cover. Taxon diversity was positively related to duff quantities, while taxon turnover was positively linked to exposed-rock cover and the number of logs on the ground. Despite the significant effects of these understory properties on the arthropod community structure, a combination of null modeling and metacommunity analysis revealed that both deterministic and stochastic processes shape the ground-dwelling arthropod communities in this system. However, the relative influence of these processes as a function of time since the wildfires or the number of recent wildfires was not generalizable across the fire groups. Given that different assembly processes shaped arthropod communities among locations that had experienced similar disturbances over time, increased efforts to understand the processes governing arthropod community assembly following disturbance is required in this wildfire-prone landscape.
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- 2019
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27. Brain transplantation of genetically corrected Sanfilippo type B neural stem cells induces partial cross-correction of the disease
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Yewande Pearse, Don Clarke, Shih-hsin Kan, Steven Q. Le, Valentina Sanghez, Anna Luzzi, Ivy Pham, Lina R. Nih, Jonathan D. Cooper, Patricia I. Dickson, and Michelina Iacovino
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Sanfilippo type B ,MPS ,LSD ,neural progenitor cells ,cell therapy ,Genetics ,QH426-470 ,Cytology ,QH573-671 - Abstract
Sanfilippo syndrome type B (mucopolysaccharidosis type IIIB) is a recessive genetic disorder that severely affects the brain due to a deficiency in the enzyme α-N-acetylglucosaminidase (NAGLU), leading to intra-lysosomal accumulation of partially degraded heparan sulfate. There are no effective treatments for this disorder. In this project, we carried out an ex vivo correction of neural stem cells derived from Naglu−/− mice (iNSCs) induced pluripotent stem cells (iPSC) using a modified enzyme in which human NAGLU is fused to an insulin-like growth factor II receptor binding peptide in order to improve enzyme uptake. After brain transplantation of corrected iNSCs into Naglu−/− mice and long-term evaluation of their impact, we successfully detected NAGLU-IGFII activity in all transplanted animals. We found decreased lysosomal accumulation and reduced astrocytosis and microglial activation throughout transplanted brains. We also identified a novel neuropathological phenotype in untreated Naglu−/− brains with decreased levels of the neuronal marker Map2 and accumulation of synaptophysin-positive aggregates. Upon transplantation, we restored levels of Map2 expression and significantly reduced formation of synaptophysin-positive aggregates. Our findings suggest that genetically engineered iNSCs can be used to effectively deliver the missing enzyme to the brain and treat Sanfilippo type B-associated neuropathology.
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- 2022
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28. Influences of prior wildfires on vegetation response to subsequent fire in a reburned Southwestern landscape
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Sean A. Parks, Sarah R. McClernan, Jonathan D. Coop, and Lisa M. Holsinger
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,New Mexico ,Conservation of Energy Resources ,Plant Development ,Forests ,010603 evolutionary biology ,01 natural sciences ,Grassland ,Fires ,Trees ,Extreme weather ,Southwestern United States ,Ruderal species ,Ecosystem ,Fire ecology ,0105 earth and related environmental sciences ,geography ,geography.geographical_feature_category ,Ecology ,Resistance (ecology) ,Plant community ,Vegetation ,Plants ,Environmental science - Abstract
Large and severe wildfires have raised concerns about the future of forested landscapes in the southwestern United States, especially under repeated burning. In 2011, under extreme weather and drought conditions, the Las Conchas fire burned over several previous burns as well as forests not recently exposed to fire. Our purpose was to examine the influences of prior wildfires on plant community composition and structure, subsequent burn severity, and vegetation response. To assess these relationships, we used satellite-derived measures of burn severity and a nonmetric multidimensional scaling of pre- and post- Las Conchas field samples. Earlier burns were associated with shifts from forested sites to open savannas and meadows, oak scrub, and ruderal communities. These non-forested vegetation types exhibited both resistance to subsequent fire, measured by reduced burn severity, and resilience to reburning, measured by vegetation recovery relative to forests not exposed to recent prior fire. Previous shifts toward non-forested states were strongly reinforced by reburning. Ongoing losses of forests and their ecological values confirm the need for restoration interventions. However, given future wildfire and climate projections, there may also be opportunities presented by transformations toward fire-resistant and resilient vegetation types within portions of the landscape.
- Published
- 2016
29. Subalpine vegetation pattern three decades after stand-replacing fire: effects of landscape context and topography on plant community composition, tree regeneration, and diversity
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Jonathan D. Coop, Anna W. Schoettle, and Robert Massatti
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Geography ,Ecology ,Habitat ,Forb ,Species diversity ,Plant community ,Introduced species ,Context (language use) ,Plant Science ,Vegetation ,Species richness - Abstract
Objective: Our purpose was to characterize vegetation compositional patterns, tree regeneration, and plant diversity, and their relationships to landscape context, topography, and light availability across the margins of four stand-replacing subalpine burns. Location: Four 1977 to 1978 burns east of the Continental Divide in Colorado: the Ouzel burn, a burn near Kenosha Pass, the Badger Mountain burn, and the Maes Creek burn. Methods: Vegetation and environmental factors were sampled in 200 0.01-ha plots on transects crossing burn edges, and stratified by elevation. We utilized dissimilarity indices, mixed-effects models, and randomization tests to assess relationships between vegetation and environment. Results: Three decades after wildfire, plant communities exhibited pronounced compositional shifts across burn edges. Tree regeneration decreased with increasing elevation and distance into burn interiors; concomitant increases in forbs and graminoids were linked to greater light availability. Richness was roughly doubled in high-severity burn interiors due to the persistence of a suite of native species occurring primarily in this habitat. Richness rose with distance into burns, but declined with increasing elevation. Only three of 188 plant species were non-native; these were widespread, naturalized species that comprised o1% total cover. Conclusions: These subalpine wildfires generated considerable, persistent increases in plant species richness at local and landscape scales, and a diversity of plant communities. The findings suggest that fire suppression in such systems must lead to reduced diversity. Concerns about post-fire invasion by exotic plants appear unwarranted in high-elevation wilderness settings.
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- 2010
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30. CONSTRAINTS ON TREE SEEDLING ESTABLISHMENT IN MONTANE GRASSLANDS OF THE VALLES CALDERA, NEW MEXICO
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Jonathan D. Coop and Thomas J. Givnish
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Chlorophyll ,geography ,Herbivore ,Time Factors ,geography.geographical_feature_category ,biology ,Soil texture ,Ecology ,New Mexico ,Spermophilus lateralis ,Ecotone ,Poaceae ,biology.organism_classification ,Grassland ,Trees ,Seedlings ,Seedling ,Soil water ,medicine ,Environmental science ,Seasons ,medicine.vector_of_disease ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Tree line - Abstract
Montane and subalpine grasslands are prominent, but poorly understood, features of the Rocky Mountains. These communities frequently occur below reversed tree lines on valley floors, where nightly cold air accumulation is spatially coupled with fine soil texture. We used field experiments to assess the roles of minimum temperature, soil texture, grass competition, and ungulate browsing on the growth, photosynthetic performance, and survival of transplanted ponderosa pine (Pinus ponderosa) seedlings at 32 sites straddling such reversed tree lines in the Valles Caldera National Preserve (VCNP) of the Jemez Mountains, New Mexico (USA). Seedling growth increased most strongly with increasing nighttime minimum temperatures away from the valley bottoms; seedlings experiencing the coldest temperatures on the caldera floor exhibited stunted needles and often no measurable height growth. Based on the chlorophyll fluorescence ratios PhiPSII and Fv/Fm, we found that low minimum temperatures, low soil moisture, and fine soil texture all contributed to photoinhibition. Neighboring herbs had only minor negative effects on seedlings. We found no effect of ungulates, but golden-mantled ground squirrels (Spermophilus lateralis) caused substantial seedling mortality. Second-year seedling survival was highest on sandy soils, and third-year survival was highest at sites with higher minimum temperatures. We conclude that differential tree seedling establishment driven by low minimum temperatures in the valley bottoms is the primary factor maintaining montane grasslands of the VCNP, although this process probably operated historically in combination with frequent surface fire to set the position of the tree line ecotone. As at alpine tree lines, reversed tree lines bordering montane and subalpine grasslands can represent temperature-sensitive boundaries of the tree life form.
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- 2008
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31. Gene therapy ameliorates spontaneous seizures associated with cortical neuron loss in a Cln2R207X mouse model
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Keigo Takahashi, Elizabeth M. Eultgen, Sophie H. Wang, Nicholas R. Rensing, Hemanth R. Nelvagal, Joshua T. Dearborn, Olivier Danos, Nicholas Buss, Mark S. Sands, Michael Wong, and Jonathan D. Cooper
- Subjects
Neuroscience ,Therapeutics ,Medicine - Abstract
Although a disease-modifying therapy for classic late infantile neuronal ceroid lipofuscinosis (CLN2 disease) exists, poor understanding of cellular pathophysiology has hampered the development of more effective and persistent therapies. Here, we investigated the nature and progression of neurological and underlying neuropathological changes in Cln2R207X mice, which carry one of the most common pathogenic mutations in human patients but are yet to be fully characterized. Long-term electroencephalography recordings revealed progressive epileptiform abnormalities, including spontaneous seizures, providing a robust, quantifiable, and clinically relevant phenotype. These seizures were accompanied by the loss of multiple cortical neuron populations, including those stained for interneuron markers. Further histological analysis revealed early localized microglial activation months before neuron loss started in the thalamocortical system and spinal cord, which was accompanied by astrogliosis. This pathology was more pronounced and occurred in the cortex before the thalamus or spinal cord and differed markedly from the staging seen in mouse models of other forms of neuronal ceroid lipofuscinosis. Neonatal administration of adeno-associated virus serotype 9–mediated gene therapy ameliorated the seizure and gait phenotypes and prolonged the life span of Cln2R207X mice, attenuating most pathological changes. Our findings highlight the importance of clinically relevant outcome measures for judging preclinical efficacy of therapeutic interventions for CLN2 disease.
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- 2023
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32. Spatial and temporal patterns of recent forest encroachment in montane grasslands of the Valles Caldera, New Mexico, USA
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Thomas J. Givnish and Jonathan D. Coop
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geography ,geography.geographical_feature_category ,Ecology ,Ecotone ,Grassland ,Altitude ,Dendrochronology ,Afforestation ,Caldera ,Spatial variability ,Ecology, Evolution, Behavior and Systematics ,Tree line ,Geology - Abstract
Aim Recent forest encroachment into montane and subalpine grasslands has occurred in the Rocky Mountains and many other mountain ranges globally. The timing, rate, and extent of tree invasion can depend on interactions among topography, positive spatial feedbacks, and temporally variable factors (especially climate, grazing, and fire). Here we examine spatial and temporal patterns of tree invasion in the Valles Caldera of the Jemez Mountains. Location This study was conducted in the Valles Caldera (35°50′–36°00′ N; 106°24′–106°37′ W), a 24-km-wide volcanic basin in northern New Mexico, USA. Grasslands in this otherwise forested region occur in broad valley bottoms of the caldera floor between 2575 and 2700 m, and on south-facing slopes and mountain tops up to 3300 m. Methods We used a GIS analysis of orthorectified aerial photos taken in 1935 and 1996, covering a 40,000-ha study area, to quantify the extent of tree invasion and to assess its relationship to spatial factors. We obtained dates of establishment from 299 increment cores and basal disks from 50 sites in the Valles Caldera National Preserve (VCNP) to reconstruct temporal patterns of tree invasion. Results The area of grasslands in our study area declined from 11,747 to 9336 ha (nearly 18%) between 1935 and 1996. Tree invasion increased with slope, elevation, and proximity to the previous tree line, but showed no relationship to aspect. Tree invasion was more rapid and continuous on upper mountain slopes, while the invasion of valley-bottom grasslands below reversed tree lines was more episodic, and appeared to track mean summer minimum temperatures. Main conclusions The rapid and continuous invasion of steep, high-elevation slopes suggests that frequent fire was the single most important factor in maintaining grassy communities in these sites. The slower, episodic invasion of valley-bottom grasslands, and the apparent relationship between increased invasion and years of higher summer minimum temperatures are consistent with the hypothesis that these grasslands have been maintained by low temperatures or frosts damaging to tree seedlings. We encourage prescribed fire to restore and maintain grasslands in the VCNP, especially small patches on steep, high-elevation slopes.
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- 2007
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33. Gradient analysis of reversed treelines and grasslands of the Valles Caldera, New Mexico
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Jonathan D. Coop and Thomas J. Givnish
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Ecology ,Plant Science - Published
- 2007
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34. Effects of chronic cannabidiol in a mouse model of naturally occurring neuroinflammation, neurodegeneration, and spontaneous seizures
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Joshua T. Dearborn, Hemanth R. Nelvagal, Nicholas R. Rensing, Keigo Takahashi, Stephanie M. Hughes, Thomas M. Wishart, Jonathan D. Cooper, Michael Wong, and Mark S. Sands
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Medicine ,Science - Abstract
Abstract Cannabidiol (CBD) has gained attention as a therapeutic agent and is purported to have immunomodulatory, neuroprotective, and anti-seizure effects. Here, we determined the effects of chronic CBD administration in a mouse model of CLN1 disease (Cln1 −/−) that simultaneously exhibits neuroinflammation, neurodegeneration, and spontaneous seizures. Proteomic analysis showed that putative CBD receptors are expressed at similar levels in the brains of Cln1 −/− mice compared to normal animals. Cln1 −/− mice received an oral dose (100 mg/kg/day) of CBD for six months and were evaluated for changes in pathological markers of disease and seizures. Chronic cannabidiol administration was well-tolerated, high levels of CBD were detected in the brain, and markers of astrocytosis and microgliosis were reduced. However, CBD had no apparent effect on seizure frequency or neuron survival. These data are consistent with CBD having immunomodulatory effects. It is possible that a higher dose of CBD could also reduce neurodegeneration and seizure frequency.
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- 2022
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35. BLACK BEARS FORAGE ON ARMY CUTWORM MOTH AGGREGATIONS IN THE JEMEZ MOUNTAINS, NEW MEXICO
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Jonathan D. Coop, Charles D. Hibner, Aaron J. Miller, and Gregory H. Clark
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Forage (honey bee) ,Army cutworm ,biology ,Ecology ,Grizzly Bears ,Foraging ,organization ,biology.organism_classification ,organization.mascot ,Lepidoptera genitalia ,Geography ,Noctuidae ,Ursus ,Euxoa ,Ecology, Evolution, Behavior and Systematics - Abstract
We observed black bears (Ursus americanus) foraging on aggregations of army cutworm moths (Euxoa auxiliaris) (Lepidoptera: Noctuidae) in subalpine felsenmeers (block fields) in the Jemez Mountains of New Mexico. Moth aggregations serve as food for grizzly bears (Ursus arctos horribilis) in the northern Rocky Mountains of Wyoming and Montana. However, black bears have not been reported to use these aggregations, nor have such aggregations been documented to occur this far south in the Rocky Mountains.
- Published
- 2005
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36. Carex wootonii
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Jonathan D. Coop, Jonathan D. Coop, Jonathan D. Coop, and Jonathan D. Coop
- Abstract
Angiosperms, http://name.umdl.umich.edu/IC-HERB00IC-X-1382862%5DMICH-V-1382862, https://quod.lib.umich.edu/cgi/i/image/api/thumb/herb00ic/1382862/MICH-V-1382862/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. Some materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Herbarium professional staff: herb-dlps-help@umich.edu. If you have concerns about the inclusion of an item in this collection, please contact Library Information Technology: libraryit-info@umich.edu., https://www.lib.umich.edu/about-us/policies/copyright-policy
- Published
- 2002
37. Carex macloviana
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Jonathan D. Coop, Jonathan D. Coop, Jonathan D. Coop, and Jonathan D. Coop
- Abstract
Angiosperms, http://name.umdl.umich.edu/IC-HERB00IC-X-1378031%5DMICH-V-1378031, https://quod.lib.umich.edu/cgi/i/image/api/thumb/herb00ic/1378031/MICH-V-1378031/!250,250, The University of Michigan Library provides access to these materials for educational and research purposes. Some materials may be protected by copyright. If you decide to use any of these materials, you are responsible for making your own legal assessment and securing any necessary permission. If you have questions about the collection, please contact the Herbarium professional staff: herb-dlps-help@umich.edu. If you have concerns about the inclusion of an item in this collection, please contact Library Information Technology: libraryit-info@umich.edu., https://www.lib.umich.edu/about-us/policies/copyright-policy
- Published
- 2002
38. Top-down and bottom-up propagation of disease in the neuronal ceroid lipofuscinoses
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John R. Ostergaard, Hemanth R. Nelvagal, and Jonathan D. Cooper
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neuronal ceroid lipofuscinoses ,CLN1 ,CLN3 ,connectome ,disease propagation ,neurodegeneration ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
BackgroundThe Neuronal Ceroid Lipofuscinoses (NCLs) may be considered distinct neurodegenerative disorders with separate underlying molecular causes resulting from monogenetic mutations. An alternative hypothesis is to consider the NCLs as related diseases that share lipofuscin pathobiology as the common core feature, but otherwise distinguished by different a) initial anatomic location, and b) disease propagation.MethodsWe have tested this hypothesis by comparing known differences in symptomatology and pathology of the CLN1 phenotype caused by complete loss of PPT1 function (i.e., the classical infantile form) and of the classical juvenile CLN3 phenotype. These two forms of NCL represent early onset and rapidly progressing vs. late onset and slowly progressing disease modalities respectively.ResultsDespite displaying similar pathological endpoints, the clinical phenotypes and the evidence of imaging and postmortem studies reveal strikingly different time courses and distributions of disease propagation. Data from CLN1 disease are indicative of disease propagation from the body, with early effects within the spinal cord and subsequently within the brainstem, the cerebral hemispheres, cerebellum and retina. In contrast, the retina appears to be the most vulnerable organ in CLN3, and the site where pathology is first present. Pathology subsequently is present in the occipital connectome of the CLN3 brain, followed by a top-down propagation in which cerebral and cerebellar atrophy in early adolescence is followed by involvement of the peripheral nerves in later adolescence/early twenties, with the extrapyramidal system also affected during this time course.DiscussionThe propagation of disease in these two NCLs therefore has much in common with the “Brain-first” vs. “Body-first” models of alpha-synuclein propagation in Parkinson's disease. CLN1 disease represents a “Body-first” or bottom-up disease propagation and CLN3 disease having a “Brain-first” and top-down propagation. It is noteworthy that the varied phenotypes of CLN1 disease, whether it starts in infancy (infantile form) or later in childhood (juvenile form), still fit with our proposed hypothesis of a bottom-up disease propagation in CLN1. Likewise, in protracted CLN3 disease, where both cognitive and motor declines are delayed, the initial manifestations of disease are also seen in the outer retinal layers, i.e., identical to classical Juvenile NCL disease.
- Published
- 2022
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39. Cross-species efficacy of enzyme replacement therapy for CLN1 disease in mice and sheep
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Hemanth R. Nelvagal, Samantha L. Eaton, Sophie H. Wang, Elizabeth M. Eultgen, Keigo Takahashi, Steven Q. Le, Rachel Nesbitt, Joshua T. Dearborn, Nicholas Siano, Ana C. Puhl, Patricia I. Dickson, Gerard Thompson, Fraser Murdoch, Paul M. Brennan, Mark Gray, Stephen N. Greenhalgh, Peter Tennant, Rachael Gregson, Eddie Clutton, James Nixon, Chris Proudfoot, Stefano Guido, Simon G. Lillico, C. Bruce A. Whitelaw, Jui-Yun Lu, Sandra L. Hofmann, Sean Ekins, Mark S. Sands, Thomas M. Wishart, and Jonathan D. Cooper
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Neuroscience ,Therapeutics ,Medicine - Abstract
CLN1 disease, also called infantile neuronal ceroid lipofuscinosis (NCL) or infantile Batten disease, is a fatal neurodegenerative lysosomal storage disorder resulting from mutations in the CLN1 gene encoding the soluble lysosomal enzyme palmitoyl-protein thioesterase 1 (PPT1). Therapies for CLN1 disease have proven challenging because of the aggressive disease course and the need to treat widespread areas of the brain and spinal cord. Indeed, gene therapy has proven less effective for CLN1 disease than for other similar lysosomal enzyme deficiencies. We therefore tested the efficacy of enzyme replacement therapy (ERT) by administering monthly infusions of recombinant human PPT1 (rhPPT1) to PPT1-deficient mice (Cln1–/–) and CLN1R151X sheep to assess how to potentially scale up for translation. In Cln1–/– mice, intracerebrovascular (i.c.v.) rhPPT1 delivery was the most effective route of administration, resulting in therapeutically relevant CNS levels of PPT1 activity. rhPPT1-treated mice had improved motor function, reduced disease-associated pathology, and diminished neuronal loss. In CLN1R151X sheep, i.c.v. infusions resulted in widespread rhPPT1 distribution and positive treatment effects measured by quantitative structural MRI and neuropathology. This study demonstrates the feasibility and therapeutic efficacy of i.c.v. rhPPT1 ERT. These findings represent a key step toward clinical testing of ERT in children with CLN1 disease and highlight the importance of a cross-species approach to developing a successful treatment strategy.
- Published
- 2022
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40. Intracranial delivery of AAV9 gene therapy partially prevents retinal degeneration and visual deficits in CLN6-Batten disease mice
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Katherine A. White, Hemanth R. Nelvagal, Timothy A. Poole, Bin Lu, Tyler B. Johnson, Samantha Davis, Melissa A. Pratt, Jon Brudvig, Ana B. Assis, Shibi Likhite, Kathrin Meyer, Brian K. Kaspar, Jonathan D. Cooper, Shaomei Wang, and Jill M. Weimer
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CLN6 ,Batten disease ,AAV9 ,NCL ,Gene therapy ,retina ,Genetics ,QH426-470 ,Cytology ,QH573-671 - Abstract
Batten disease is a family of rare, fatal, neuropediatric diseases presenting with memory/learning decline, blindness, and loss of motor function. Recently, we reported the use of an AAV9-mediated gene therapy that prevents disease progression in a mouse model of CLN6-Batten disease (Cln6nclf), restoring lifespans in treated animals. Despite the success of our viral-mediated gene therapy, the dosing strategy was optimized for delivery to the brain parenchyma and may limit the therapeutic potential to other disease-relevant tissues, such as the eye. Here, we examine whether cerebrospinal fluid (CSF) delivery of scAAV9.CB.CLN6 is sufficient to ameliorate visual deficits in Cln6nclf mice. We show that intracerebroventricular (i.c.v.) delivery of scAAV9.CB.CLN6 completely prevents hallmark Batten disease pathology in the visual processing centers of the brain, preserving neurons of the superior colliculus, thalamus, and cerebral cortex. Importantly, i.c.v.-delivered scAAV9.CB.CLN6 also expresses in many cells throughout the central retina, preserving many photoreceptors typically lost in Cln6nclf mice. Lastly, scAAV9.CB.CLN6 treatment partially preserved visual acuity in Cln6nclf mice as measured by optokinetic response. Taken together, we report the first instance of CSF-delivered viral gene reaching and rescuing pathology in both the brain parenchyma and retinal neurons, thereby partially slowing visual deterioration.
- Published
- 2021
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41. Central nervous system pathology in preclinical MPS IIIB dogs reveals progressive changes in clinically relevant brain regions
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Martin T. Egeland, Marta M. Tarczyluk-Wells, Melissa M. Asmar, Evan G. Adintori, Roger Lawrence, Elizabeth M. Snella, Jackie K. Jens, Brett E. Crawford, Jill C. M. Wait, Emma McCullagh, Jason Pinkstaff, Jonathan D. Cooper, and N. Matthew Ellinwood
- Subjects
Medicine ,Science - Abstract
Abstract Mucopolysaccharidosis type IIIB (MPS IIIB; Sanfilippo syndrome B) is an autosomal recessive lysosomal storage disorder caused by the deficiency of alpha-N-acetylglucosaminidase activity, leading to increased levels of nondegraded heparan sulfate (HS). A mouse model has been useful to evaluate novel treatments for MPS IIIB, but has limitations. In this study, we evaluated the naturally occurring canine model of MPS IIIB for the onset and progression of biochemical and neuropathological changes during the preclinical stages (onset approximately 24–30 months of age) of canine MPS IIIB disease. Even by 1 month of age, MPS IIIB dogs had elevated HS levels in brain and cerebrospinal fluid. Analysis of histopathology of several disease-relevant regions of the forebrain demonstrated progressive lysosomal storage and microglial activation despite a lack of cerebrocortical atrophy in the oldest animals studied. More pronounced histopathology changes were detected in the cerebellum, where progressive lysosomal storage, astrocytosis and microglial activation were observed. Microglial activation was particularly prominent in cerebellar white matter and within the deep cerebellar nuclei, where neuron loss also occurred. The findings in this study will form the basis of future assessments of therapeutic efficacy in this large animal disease model.
- Published
- 2020
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42. Glial Dysfunction and Its Contribution to the Pathogenesis of the Neuronal Ceroid Lipofuscinoses
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Keigo Takahashi, Hemanth R. Nelvagal, Jenny Lange, and Jonathan D. Cooper
- Subjects
Batten disease ,neuronal ceroid lipofuscinosis ,astrocyte ,microglia ,oligodendrocyte ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
While significant efforts have been made in developing pre-clinical treatments for the neuronal ceroid lipofuscinoses (NCLs), many challenges still remain to bring children with NCLs a cure. Devising effective therapeutic strategies for the NCLs will require a better understanding of pathophysiology, but little is known about the mechanisms by which loss of lysosomal proteins causes such devastating neurodegeneration. Research into glial cells including astrocytes, microglia, and oligodendrocytes have revealed many of their critical functions in brain homeostasis and potential contributions to neurodegenerative diseases. Genetically modified mouse models have served as a useful platform to define the disease progression in the central nervous system across NCL subtypes, revealing a wide range of glial responses to disease. The emerging evidence of glial dysfunction questions the traditional “neuron-centric” view of NCLs, and would suggest that directly targeting glia in addition to neurons could lead to better therapeutic outcomes. This review summarizes the most up-to-date understanding of glial pathologies and their contribution to the pathogenesis of NCLs, and highlights some of the associated challenges that require further research.
- Published
- 2022
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43. Modelling Neurological Diseases in Large Animals: Criteria for Model Selection and Clinical Assessment
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Samantha L. Eaton, Fraser Murdoch, Nina M. Rzechorzek, Gerard Thompson, Claudia Hartley, Benjamin Thomas Blacklock, Chris Proudfoot, Simon G. Lillico, Peter Tennant, Adrian Ritchie, James Nixon, Paul M. Brennan, Stefano Guido, Nadia L. Mitchell, David N. Palmer, C. Bruce A. Whitelaw, Jonathan D. Cooper, and Thomas M. Wishart
- Subjects
neurological disease ,large animal model ,clinical assessment ,model selection criteria ,Cytology ,QH573-671 - Abstract
Issue: The impact of neurological disorders is recognised globally, with one in six people affected in their lifetime and few treatments to slow or halt disease progression. This is due in part to the increasing ageing population, and is confounded by the high failure rate of translation from rodent-derived therapeutics to clinically effective human neurological interventions. Improved translation is demonstrated using higher order mammals with more complex/comparable neuroanatomy. These animals effectually span this translational disparity and increase confidence in factors including routes of administration/dosing and ability to scale, such that potential therapeutics will have successful outcomes when moving to patients. Coupled with advancements in genetic engineering to produce genetically tailored models, livestock are increasingly being used to bridge this translational gap. Approach: In order to aid in standardising characterisation of such models, we provide comprehensive neurological assessment protocols designed to inform on neuroanatomical dysfunction and/or lesion(s) for large animal species. We also describe the applicability of these exams in different large animals to help provide a better understanding of the practicalities of cross species neurological disease modelling. Recommendation: We would encourage the use of these assessments as a reference framework to help standardise neurological clinical scoring of large animal models.
- Published
- 2022
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44. Genetically Corrected iPSC-Derived Neural Stem Cell Grafts Deliver Enzyme Replacement to Affect CNS Disease in Sanfilippo B Mice
- Author
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Don Clarke, Yewande Pearse, Shih-hsin Kan, Steven Q. Le, Valentina Sanghez, Jonathan D. Cooper, Patricia I. Dickson, and Michelina Iacovino
- Subjects
Genetics ,QH426-470 ,Cytology ,QH573-671 - Abstract
Sanfilippo syndrome type B (mucopolysaccharidosis type IIIB [MPS IIIB]) is a lysosomal storage disorder primarily affecting the brain that is caused by a deficiency in the enzyme α-N-acetylglucosaminidase (NAGLU), leading to intralysosomal accumulation of heparan sulfate. There are currently no treatments for this disorder. Here we report that, ex vivo, lentiviral correction of Naglu−/− neural stem cells derived from Naglu−/− mice (iNSCs) corrected their lysosomal pathology and allowed them to secrete a functional NAGLU enzyme that could be taken up by deficient cells. Following long-term transplantation of these corrected iNSCs into Naglu−/− mice, we detected NAGLU activity in the majority of engrafted animals. Successfully transplanted Naglu−/− mice showed a significant decrease in storage material, a reduction in astrocyte activation, and complete prevention of microglial activation within the area of engrafted cells and neighboring regions, with beneficial effects extending partway along the rostrocaudal axis of the brain. Our results demonstrate long-term engraftment of iNSCs in the brain that are capable of cross-correcting pathology in Naglu−/− mice. Our findings suggest that genetically engineered iNSCs could potentially be used to deliver enzymes and treat MPS IIIB. Keywords: MPS IIIB, lysosomal storage disorder, stem cell therapy
- Published
- 2018
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45. Compromised astrocyte function and survival negatively impact neurons in infantile neuronal ceroid lipofuscinosis
- Author
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Jenny Lange, Luke J. Haslett, Emyr Lloyd-Evans, Jennifer M. Pocock, Mark S. Sands, Brenda P. Williams, and Jonathan D. Cooper
- Subjects
Infantile batten disease, CLN1 disease, neuronal ceroid lipofuscinosis ,Neuron-glial interactions ,Astrocyte and microglial dysfunction ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract The neuronal ceroid lipofuscinoses (NCLs) are the most common cause of childhood dementia and are invariably fatal. Early localized glial activation occurs in these disorders, and accurately predicts where neuronal loss is most pronounced. Recent evidence suggests that glial dysfunction may contribute to neuron loss, and we have now explored this possibility in infantile NCL (INCL, CLN1 disease). We grew primary cultures of astrocytes, microglia, and neurons derived from Ppt1 deficient mice (Ppt1 −/− ) and assessed their properties compared to wildtype (WT) cultures, before co-culturing them in different combinations (astrocytes with microglia, astrocytes or microglia with neurons, all three cell types together). These studies revealed that both Ppt1 −/− astrocytes and microglia exhibit a more activated phenotype under basal unstimulated conditions, as well as alterations to their protein expression profile following pharmacological stimulation. Ppt1 - /− astrocytes also displayed abnormal calcium signalling and an elevated cytoplasmic Ca2+ level, and a profound defect in their survival. Ppt1 −/− neurons displayed decreased neurite outgrowth, altered complexity, a reduction in cell body size, and impaired neuron survival with prolonged time in culture. In co-cultures, the presence of both astrocytes and microglia from Ppt1 −/− mice further impaired the morphology of both wild type and Ppt1 −/− neurons. This negative influence was more pronounced for Ppt1 −/− microglia, which appeared to trigger increased Ppt1 −/− neuronal death. In contrast, wild type glial cells, especially astrocytes, ameliorated some of the morphological defects observed in Ppt1 −/− neurons. These findings suggest that both Ppt1 −/− microglia and astrocytes are dysfunctional and may contribute to the neurodegeneration observed in CLN1 disease. However, the dysfunctional phenotypes of Ppt1 −/− glia are different from those present in CLN3 disease, suggesting that the pathogenic role of glia may differ between NCLs.
- Published
- 2018
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46. A Humoral Immune Response Alters the Distribution of Enzyme Replacement Therapy in Murine Mucopolysaccharidosis Type I
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Steven Q. Le, Shih-hsin Kan, Don Clarke, Valentina Sanghez, Martin Egeland, Kristen N. Vondrak, Terence M. Doherty, Moin U. Vera, Michelina Iacovino, Jonathan D. Cooper, Mark S. Sands, and Patricia I. Dickson
- Subjects
lysosomal disease ,alpha-l-iduronidase ,Hurler ,Scheie ,glycosaminoglycan ,Genetics ,QH426-470 ,Cytology ,QH573-671 - Abstract
Antibodies against recombinant proteins can significantly reduce their effectiveness in unanticipated ways. We evaluated the humoral response of mice with the lysosomal storage disease mucopolysaccharidosis type I treated with weekly intravenous recombinant human alpha-l-iduronidase (rhIDU). Unlike patients, the majority of whom develop antibodies to recombinant human alpha-l-iduronidase, only approximately half of the treated mice developed antibodies against recombinant human alpha-l-iduronidase and levels were low. Serum from antibody-positive mice inhibited uptake of recombinant human alpha-l-iduronidase into human fibroblasts by partial inhibition compared to control serum. Tissue and cellular distributions of rhIDU were altered in antibody-positive mice compared to either antibody-negative or naive mice, with significantly less recombinant human alpha-l-iduronidase activity in the heart and kidney in antibody-positive mice. In the liver, recombinant human alpha-l-iduronidase was preferentially found in sinusoidal cells rather than in hepatocytes in antibody-positive mice. Antibodies against recombinant human alpha-l-iduronidase enhanced uptake of recombinant human alpha-l-iduronidase into macrophages obtained from MPS I mice. Collectively, these results imply that a humoral immune response against a therapeutic protein can shift its distribution preferentially into macrophage-lineage cells, causing decreased availability of the protein to the cells that are its therapeutic targets.
- Published
- 2018
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47. Glial cells are functionally impaired in juvenile neuronal ceroid lipofuscinosis and detrimental to neurons
- Author
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Lotta Parviainen, Sybille Dihanich, Greg W. Anderson, Andrew M. Wong, Helen R. Brooks, Rosella Abeti, Payam Rezaie, Giovanna Lalli, Simon Pope, Simon J. Heales, Hannah M. Mitchison, Brenda P. Williams, and Jonathan D. Cooper
- Subjects
Juvenile batten disease ,CLN3 disease ,Neuronal ceroid lipofuscinosis ,Neuron-glial interactions ,Astrocyte and microglial dysfunction ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract The neuronal ceroid lipofuscinoses (NCLs or Batten disease) are a group of inherited, fatal neurodegenerative disorders of childhood. In these disorders, glial (microglial and astrocyte) activation typically occurs early in disease progression and predicts where neuron loss subsequently occurs. We have found that in the most common juvenile form of NCL (CLN3 disease or JNCL) this glial response is less pronounced in both mouse models and human autopsy material, with the morphological transformation of both astrocytes and microglia severely attenuated or delayed. To investigate their properties, we isolated glia and neurons from Cln3-deficient mice and studied their basic biology in culture. Upon stimulation, both Cln3-deficient astrocytes and microglia also showed an attenuated ability to transform morphologically, and an altered protein secretion profile. These defects were more pronounced in astrocytes, including the reduced secretion of a range of neuroprotective factors, mitogens, chemokines and cytokines, in addition to impaired calcium signalling and glutamate clearance. Cln3-deficient neurons also displayed an abnormal organization of their neurites. Most importantly, using a co-culture system, Cln3-deficient astrocytes and microglia had a negative impact on the survival and morphology of both Cln3-deficient and wildtype neurons, but these effects were largely reversed by growing mutant neurons with healthy glia. These data provide evidence that CLN3 disease astrocytes are functionally compromised. Together with microglia, they may play an active role in neuron loss in this disorder and can be considered as potential targets for therapeutic interventions.
- Published
- 2017
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48. mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases
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Michela Palmieri, Rituraj Pal, Hemanth R. Nelvagal, Parisa Lotfi, Gary R. Stinnett, Michelle L. Seymour, Arindam Chaudhury, Lakshya Bajaj, Vitaliy V. Bondar, Laura Bremner, Usama Saleem, Dennis Y. Tse, Deepthi Sanagasetti, Samuel M. Wu, Joel R. Neilson, Fred A. Pereira, Robia G. Pautler, George G. Rodney, Jonathan D. Cooper, and Marco Sardiello
- Subjects
Science - Abstract
The transcription factor EB (TFEB) is a master regulator of lysosomal biogenesis. Here authors show that trehalose, an mTOR-independent autophagy inducer, alleviates the pathological phenotypes in a mouse model of neurodegenerative disease. Trehalose acts by inhibiting Akt, which normally suppresses TFEB via an mTORC1-independent mechanism.
- Published
- 2017
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49. Combined Anti-inflammatory and Neuroprotective Treatments Have the Potential to Impact Disease Phenotypes in Cln3−/− Mice
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Marta A. Tarczyluk-Wells, Christoph Salzlechner, Allison R. Najafi, Ming J. Lim, David Smith, Frances M. Platt, Brenda P. Williams, and Jonathan D. Cooper
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Batten disease ,CLN3 disease ,inflammation ,ibuprofen ,lamotrigine ,glial activation ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Batten disease, or juvenile NCL, is a fatal neurodegenerative disorder that occurs due to mutations in the CLN3 gene. Because the function of CLN3 remains unclear, experimental therapies for JNCL have largely concentrated upon the targeting of downstream pathomechanisms. Neuron loss is preceded by localized glial activation, and in this proof-of-concept study we have investigated whether targeting this innate immune response with ibuprofen in combination with the neuroprotective agent lamotrigine improves the previously documented beneficial effects of immunosuppressants alone. Drugs were administered daily to symptomatic Cln3−/− mice over a 3 month period, starting at 6 months of age, and their impact was assessed using both behavioral and neuropathological outcome measures. During the treatment period, the combination of ibuprofen and lamotrigine significantly improved the performance of Cln3−/− mice on the vertical pole test, slowing the disease-associated decline, but had less of an impact upon their rotarod performance. There were also moderate and regionally dependent effects upon astrocyte activation that were most pronounced for ibuprofen alone, but there was no overt effect upon microglial activation. Administering such treatments for longer periods will enable testing for any impact upon the neuron loss that occurs later in disease progression. Given the partial efficacy of these treatments, it will be important to test further drugs of this type in order to find more effective combinations.
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- 2019
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50. Correction: Corrigendum: mTORC1-independent TFEB activation via Akt inhibition promotes cellular clearance in neurodegenerative storage diseases
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Michela Palmieri, Rituraj Pal, Hemanth R. Nelvagal, Parisa Lotfi, Gary R. Stinnett, Michelle L. Seymour, Arindam Chaudhury, Lakshya Bajaj, Vitaliy V. Bondar, Laura Bremner, Usama Saleem, Dennis Y. Tse, Deepthi Sanagasetti, Samuel M. Wu, Joel R. Neilson, Fred A. Pereira, Robia G. Pautler, George G. Rodney, Jonathan D. Cooper, and Marco Sardiello
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Science - Abstract
Nature Communications 8: Article number: 14338 (2017); Published: 6 February 2017; Updated: 13 June 2017 This Article contains errors in Figs 2 and 3, for which we apologize. In Fig. 2c, the four images were inadvertently duplicated from the images in Fig. 2b. In Fig. 3g, the image at the upper right corner, corresponding to the condition UT_ Cln3Δex7-8 was inadvertently duplicated from the image in the lower right corner of Fig.
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- 2017
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