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  • ItemOpen Access
    Modeling Nation-Wide U.S. Swine Movement Networks at the Resolution of the Individual Premises
    (Colorado State University. Libraries, 2022) Sellman, Stefan; Beck-Johnson, Lindsay; Hallman, Clayton; Miller, Ryan S.; Owers Bonner, Katharine A.; Portacci, Katie; Webb, Colleen T.; Lindström, Tom
    The spread of transboundary animal diseases (TAD) is a major cause for concern to the worlds agricultural systems. In the dynamics of the spread of TADs between agricultural premises, the movement of livestock between herds plays an important role. Therefore, when constructing mathematical models used for activities such as forecasting epidemic development, evaluating mitigation strategies, or determining important targets for disease surveillance, incorporating a model component describing between-premises shipments is often a necessity. In the cases when up-to-date and comprehensive shipment data is available, this is a relatively simple task; when data is nonexistent or patchy, researchers need to model the shipments in addition to the disease dynamics, a task that can be complex and time consuming. In the United States (U.S.), livestock shipment data is not generally collected, and when it is, it is not easily available and mostly concerned with between-state shipments. To cover this gap in knowledge and provide insight into the complete shipment networks of livestock animals, the U.S. Animal Movement Model (USAMM) was developed. Previously, USAMM has only modeled cattle shipments, but here we present a version for the U.S. swine shipment network. Like previous versions, USAMM for swine is a Bayesian model fit to premises demography data, and county-level livestock industry variables and the available data of between-state swine movements. The model is then used to simulate, nation-wide networks of both within- and between-state shipments at the level of individual premises for the U.S. swine industry. Here we describe the model in detail and demonstrate its usefulness in a rudimentary predictive model of the prevalence of porcine epidemic diarrhea virus (PEDv) across the U.S. Additionally, in order to promote further research on TADs and other topics involving the movements of swine in the U.S., we also make a set of 250 simulated swine shipment networks freely available to the research community as a useful surrogate for the missing data.
  • ItemOpen Access
    Dataset associated with “Using isotope pool dilution to understand how organic carbon additions affect N2O consumption in diverse soils”
    (Colorado State University. Libraries, 2022) Stuchiner, Emily R.; von Fischer, J. C.
    Nitrous oxide (N2O) is a formidable greenhouse gas with warming potential ~300x greater than CO2. However, its emissions to the atmosphere have gone largely unchecked because the microbial and environmental controls governing N2O emissions have proven difficult to manage. The microbial process N2O consumption is the only know biotic pathway to remove N2O from soil pores and therefore reduce N2O emissions. Consequently, manipulating soils to increase N2O consumption by organic carbon (OC) additions has steadily gained interest. However, the response of N2O emissions to different OC additions are inconsistent, and it is unclear if lower N2O emissions are due to increased consumption, decreased production, or both. Simplified and systematic studies are needed to evaluate the efficacy of different OC additions on N2O consumption. We aimed to manipulate N2O consumption by amending soils with OC compounds (succinate, acetate, propionate) more directly available to denitrifiers. We hypothesized that N2O consumption is OC-limited and predicted these denitrifier-targeted additions would lead to enhanced N2O consumption and increased nosZ gene abundance. We incubated diverse soils in the laboratory and performed a 15N2O isotope pool dilution assay to disentangle microbial N2O emissions from consumption using laser-based spectroscopy. We found that amending soils with OC increased gross N2O consumption in six of eight soils tested. Furthermore, three of eight soils showed Increased N2O Consumption and Decreased N2O Emissions (ICDE), a phenomenon we introduce in this study as an N2O management ideal. All three ICDE soils had low soil OC content, suggesting ICDE is a response to relaxed C-limitation wherein C additions promote soil anoxia, consequently stimulating the reduction of N2O via denitrification. We suggest, generally, OC additions to low OC soils will reduce N2O emissions via ICDE. Future studies should prioritize methodical assessment of different, specific, OC-additions to determine which additions show ICDE in different soils.
  • ItemOpen Access
    Data associated with "Modeling U.S. cattle movements until the cows come home: who ships to whom and how many?"
    (Colorado State University. Libraries, 2021) Sellman, Stefan; Beck-Johnson, Lindsay; Hallman, Clayton; Miller, Ryan S.; Owers Bonner, Katharine A.; Portacci, Katie; Webb, Colleen T.; Lindström, Tom
    Livestock movements between agricultural premises is an important pathway for the spread of infectious disease. Data providing details about the origin and destination of shipments, as well as information about the shipment size is an important component of computer models used to formulate mitigation strategies and design surveillance programs. The United States (U.S.) currently lacks a comprehensive database of farm animal shipments, which hinders such efforts. With the U.S. Animal Movement Model (USAMM), earlier work has successfully scaled up from limited data based on interstate certificates of veterinary inspection (CVI) to comprehensive county-level shipment networks at the national scale. In this work, we present three major improvements to earlier versions of USAMM: (1) increased resolution of the model and simulated networks to the level of individual premises; (2) predictions of shipment sizes; (3) taking into account the types and herd sizes of the premises. We fitted parameters in a Bayesian framework to two sets of CVI data consisting of sub-samples of one year's between-state beef and dairy shipments. Through posterior predictive simulation, we then created 1,000 synthetic beef and dairy networks, which we make publicly available to support livestock disease modeling. The simulated networks were validated against summary statistics of the training data as well as out-of-sample CVI data from subsequent years. This new development opens up the possibility of using USAMM in a broader spectrum of applications where information about shipment size and premises identity is necessary and gives novel insights into the U.S. cattle shipment network.
  • ItemOpen Access
    Dataset associated with “What’s in a name? The paradox of citizen science and community science”
    (Colorado State University. Libraries, 2021) Lin Hunter, Danielle; Newman, Gregory; Balgopal, Meena
    Citizen science has expanded ecological and environmental sciences by making possible studies across greater spatial and temporal scales while incorporating local expertise and interests that might otherwise be overlooked. Broadly, citizen science involves the public in the process of science. However, it continues to struggle to engage diverse participants. Citizen science project coordinators are increasingly trying to promote inclusivity by rebranding as “community science” to avoid the term “citizen.” Rebranding efforts, while well-intentioned, are uninformed by research, as we lack an evidenced-based understanding of these terms. We distributed a survey to those who participate in citizen and community science. We found differences in how well known and accepted the terms are, who is perceived as initiating and benefiting from the projects, and associated levels of inclusivity. Our findings have important implications for those involved in citizen and community science seeking to better describe projects in the future.
  • ItemOpen Access
    Dataset associated with “An in-frame deletion mutation in the degron tail of auxin co-receptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale”
    (Colorado State University. Libraries, 2021) de Figueiredo, Marcelo R. A.; Küpper, Anita; Malone, Jenna M.; Petrovic, Tijana; de Figueiredo, Ana Beatriz T. B.; Campagnola, Grace; Peersen, Olve B.; Prasad, Kasavajhala V.S.K.; Patterson, Eric L.; Reddy, Anireddy S. N.; Kubeš, Martin F.; Napier, Richard; Dayan, Franck E.; Preston, Christopher; Gaines, Todd A.
    The natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides such as 2,4-D mimic the effects of IAA by inducing strong auxinic signaling responses in plants. To determine the mechanism of 2,4-D resistance in a Sisymbrium orientale (Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and -susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing 9 amino acids in the degron tail (DT) of the auxin co-receptor Aux/IAA2 (SoIAA2). The deletion allele co-segregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D resistant field populations of this species. Arabidopsis transgenic lines expressing the SoIAA2 mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1 in vitro with both natural and synthetic auxins, causing reduced association and increased dissociation rates. This novel mechanism of synthetic auxin herbicide resistance assigns a new in planta function to the DT region of this Aux/IAA co-receptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin resistant crops using gene editing.
  • ItemOpen Access
    Dataset associated with: "Intentional mentoring should increase inclusivity in ecology"
    (Colorado State University. Libraries, 2021) Stuchiner, Emily; Lin Hunter, Danielle; Neuwald, Jennifer; Webb, Colleen; Balgopal, Meena
    High quality mentoring relationships can be pivotal to recruitment, retention, and long-term persistence in ecology majors and careers. The graduate-undergraduate student mentoring relationship can become uniquely important during activities like ecological fieldwork. However, graduate students often have little experience as research mentors, which can lead to negative research experiences for undergraduate mentees. Given the potential for mentoring relationships to impact people’s decisions on pursuing ecological studies and/or careers, we created and piloted a mentoring professional development program designed around intentional mentoring. Intentional mentoring requires that mentors preemptively identify what skills and knowledge their mentee should develop as well as the practices to help mentees develop these competencies. Our rationale for using intentional mentoring was that it has the potential to increase mentors’ and mentees’ awareness of issues around diversity, equity, inclusion, and social justice (DEIJ) in research experiences, in addition to developing professional competencies. To evaluate our program, we conducted focus group interviews with graduate and undergraduate student participants following a multi-week mentoring training workshop, the primary aspect of the program. Participants described an increased valuation of intentional mentoring and a desire to be more intentional in their mentoring relationships. Graduate student mentors described an increased desire to be more intentional mentors, whereas undergraduate mentees described an increased desire to seek mentors with whom they could develop intentional relationships. Undergraduates also better recognized the importance of academic mentors. Based on our evaluation, we posit that intentional mentoring can increase the retention and persistence of students with diverse identities in ecology by fostering a sense of belonging. We advocate the implementation of mentoring training workshops as a part of academic ecological programs to increase inclusion in our discipline.
  • ItemOpen Access
    Dataset associated with “NSF Noyce Phase II: Empowering Scholars and STEM Teachers” project
    (Colorado State University. Libraries, 2021) Balgopal, Meena; Sample McMeeking, Laura; Weinberg, Andrea; Wright, Diane; Lin Hunter, Danielle
    The CSU Noyce program was supported by the National Science Foundation Noyce Program. Funding supported undergraduate majors in science, technology, engineering, and mathematics majors who were also enrolled in CSU’s licensure program to become public school teachers in STEM disciplines. Noyce Scholars (those receiving financial and professional development support) commited to teaching at least one year in a high-need public school district for every semester they received funding. High-need school districts, defined by the NSF, are those in which one or more schools has high levels of students who receive free or reduced lunch, have high teacher turnover, or significant numbers of teachers who teach outside of their disciplinary expertise. CSU Noyce Scholars could receive up to 2 years of financial support in the form of stipends. They committed to maintaining contact with the CSU PI for up to eight years after graduation, so we could track their professional persistence and ensure that they have fulfilled their teaching obligations. A supplementary award from NSF allowed our team to administer three surveys to Noyce Scholars spread out across 12 other STEM teacher licensure programs that received NSF Noyce funding. The surveys were administered soon after the COVID-19 pandemic prompted school districts to shift their instructional delivery methods. These 12 other programs were spread out across six states listed below.
  • ItemOpen Access
    Dataset associated with “Characterizing the importance of denitrification for N2O production in soils using natural abundance and isotopic labelling techniques”
    (Colorado State University. Libraries, 2021) Stuchiner, Emily
    Nitrous oxide (N2O), a potent greenhouse gas that contributes significantly to climate change, is emitted mostly from soils by a suite of microbial metabolic pathways that are nontrivial to identify, and subsequently, to manage. Using either natural abundance or enriched stable isotope methods has aided in identifying microbial sources of N2O, but each approach has limitations. Here, we conducted a novel pairing of natural abundance and enriched assays on two dissimilar soils, hypothesizing this pairing would better constrain microbial sources of N2O. We incubated paired natural abundance and enriched soils from a corn agroecosystem and a subalpine forest in the laboratory at 10-95% soil saturation for 28 hr. The natural abundance method measured intramolecular site preference (SP) from emitted N2O, whereas the enriched method measured emitted 15N2O from soils amended with 15N-labelled substrate. The isotopic composition of emitted N2O was measured using a laser-based N2O isotopic analyzer, yielding two key findings. First, both methods revealed that denitrification was the primary source of N2O in all soils: isotopic enrichment revealed clear NO3- reduction to N2O, while SP indicated a likely combination of fungal and bacterial denitrification. Second, we quantified, to our knowledge for the first time, persistent (>55%) β-position-specific enrichment in N2O emitted from 15NO3- -amended soils. This counter-intuitive enrichment pattern could be indicative of co-denitrification, an understudied but potentially important contributor to N2O emissions. Our work revealed the ubiquity of denitrification among the soils tested. Future pairings of natural abundance and enriched methods could better characterize diverse denitrification pathways.
  • ItemOpen Access
    Data associated with "The importance of extreme rainfall events and their timing in a semi-arid grassland"
    (Colorado State University. Libraries, 2020) Post, Alison; Knapp, Alan
    Climate change is intensifying the hydrologic cycle globally, increasing both the size and frequency of extreme precipitation events, or deluges. Arid and semi-arid ecosystems are expected to be particularly responsive to this change because their ecological processes are largely driven by distinct soil moisture pulses. However, since soil moisture, air temperature, and plant phenology vary throughout the growing season, deluges will likely have differing impacts on these systems depending on when they occur. We conducted a field experiment to assess how the seasonal timing (early, middle, or late growing season) of a single deluge (70 mm precipitation event) altered key ecological processes in the semi-arid shortgrass steppe of North America. Regardless of timing, a single deluge stimulated most ecosystem processes, but a deluge at mid-season caused the greatest increase in soil respiration, canopy greenness, aboveground net primary production (ANPP), and growth and flowering of the dominant plant species (Bouteloua gracilis). In contrast, belowground net primary production (BNPP) was insensitive to deluge timing, with a consistent BNPP increase in all the deluge treatments that was almost twice as large as the ANPP response. This BNPP response was largely driven by enhanced root production at 10-20 cm, rather than 0-10 cm, soil depths. In a semi-arid ecosystem, a single deluge can have season-long impacts on many ecosystem processes, but responses can be mediated by event timing. Therefore, predicting responses of semi-arid ecosystems to more dynamic precipitation regimes, and subsequent impacts on the global carbon budget, will require knowledge of how deluge magnitude, frequency, and timing are being altered by climate change.
  • ItemOpen Access
    Soil CO2 flux from plots with various fire histories at the Konza Prairie Biological Station
    (Colorado State University. Libraries, 2020) Slette, Ingrid
    There is abundant evidence that ongoing changes to fire regimes are affecting the global carbon cycle. However, uncertainty about how the response to an individual fire may be affected by historical factors such as the time elapsed since the last fire or the long-term fire frequency makes it difficult to predict the effects of changing fire regimes on carbon cycling. We took advantage of a 35-year fire frequency experiment (annual fire, fire every two or four years, and unburned treatments) in a native, mesic grassland to assess how fire history (time since last fire and long-term frequency) affects soil CO2 flux, a key ecosystem carbon output. We found that historic fire frequency altered the magnitude of the response to fire, with greater post-fire soil CO2 flux stimulation in annually burned grassland than in grassland burned every two or four years. Fire-induced flux increases persisted for two years after fire in grassland burned every four years. Though we found that fire also stimulated aboveground net primary productivity (ANPP), a key ecosystem carbon input, this stimulation was not altered by long-term fire frequency and didn't persist into later years, unlike soil CO2 flux. This asymmetry emphasizes the importance of measuring impacts both aboveground and belowground. Our findings demonstrate that fire history modifies a key response to individual fires in this grassland. To understand and predict the dynamics of important global carbon cycle components, it is necessary to consider not only the presence vs. absence of fire, but also the long-term fire regime.
  • ItemOpen Access
    Dataset associated with "mRNA localization is linked to translation regulation in the Caenorhabditis elegans germ lineage"
    (Colorado State University. Libraries, 2020) Parker, Dylan, M.; Winkenbach, Lindsay, P.; Boyson, Samuel, P.; Saxton, Matthew, N.; Daidone, Camryn; Al-Mazaydeh, Zainab, A.; Nishimura, Marc, T.; Mueller, Florian; Osborne Nishimura, Erin
    Caenorhabditis elegans early embryos generate cell-specific transcriptomes despite lacking active transcription. This presents an opportunity to study mechanisms of post-transcriptional regulatory control. In seeking the mechanisms behind this patterning, we discovered that some cell-specific mRNAs accumulate non-homogenously within cells, localizing to membranes, P granules (associated with progenitor germ cells in the P lineage), and P-bodies (associated with RNA processing). Transcripts differed in their dependence on 3'UTRs and RNA Binding Proteins, suggesting diverse regulatory mechanisms. Notably, we found strong but imperfect correlations between low translational status and P granule localization within the progenitor germ lineage. By uncoupling these, we untangled a long-standing question: Are mRNAs directed to P granules for translational repression or do they accumulate there as a downstream step? We found translational repression preceded P granule localization and could occur independent of it. Further, disruption of translation was sufficient to send homogenously distributed mRNAs to P granules. Overall, we show transcripts important for germline development are directed to P granules by translational repression, and this, in turn, directs their accumulation in the progenitor germ lineage where their repression can ultimately be relieved.
  • ItemOpen Access
    Simulated cattle shipment networks from the U.S. animal movement model
    (Colorado State University. Libraries, 2019) Lindstrom, Tom; Grear, Daniel A.; Buhnerkempe, Michael; Webb, Colleen T.; Miller, Ryan S.; Portacci, Katie; Wennergren, Uno
    Networks are rarely completely observed and prediction of unobserved edges is an important problem, especially in disease spread modeling where networks are used to represent the pattern of contacts. We focus on a partially observed cattle movement network in the U.S. and present a method for scaling up to a full network based on Bayesian inference, with the aim of informing epidemic disease spread models in the United States. The observed network is a 10% state stratified sample of Interstate Certificates of Veterinary Inspection that are required for interstate movement; describing approximately 20,000 movements from 47 of the contiguous states, with origins and destinations aggregated at the county level. We address how to scale up the 10% sample and predict unobserved intrastate movements based on observed movement distances. Edge prediction based on a distance kernel is not straightforward because the probability of movement does not always decline monotonically with distance due to underlying industry infrastructure. Hence, we propose a spatially explicit model where the probability of movement depends on distance, number of premises per county and historical imports of animals. Our model performs well in recapturing overall metrics of the observed network at the node level (U.S. counties), including degree centrality and betweenness; and performs better compared to randomized networks. Kernel generated movement networks also recapture observed global network metrics, including network size, transitivity, reciprocity, and assortativity better than randomized networks. In addition, predicted movements are similar to observed when aggregated at the state level (a broader geographic level relevant for policy) and are concentrated around states where key infrastructures, such as feedlots, are common. We conclude that the method generally performs well in predicting both coarse geographical patterns and network structure and is a promising method to generate full networks that incorporate the uncertainty of sampled and unobserved contacts.
  • ItemOpen Access
    Writing matters: increasing undergraduate cell biology literacy through writing-­to-­learn activities-dataset
    (Colorado State University. Libraries, 2015-2016) Balgopal, Meena M.; Casper, Anne Marie A.; Laybourn, Paul J.; Birsch, Ellen; Wallace, Alison M.; Dahlberg, Steven
    Biology educators need instructional strategies to improve student learning and achievement, especially in foundational courses when students are presented with vast amounts of content knowledge. Writing-­to-­learn (WTL) tasks in lecture courses can help biology students improve the quality of their arguments and increase content knowledge. WTL activities can model how scientists use inductive reasoning to design studies and arguments; encourage revision of ideas; support peer review and discussion; and help with writing-­to-­communicate tasks. Our WTL interventions include the use of graphic organizers, iterative writing, peer evaluation, and self-­evaluation. We examined the effects of WTL on content knowledge, performance (grades), and argumentation. WTL is associated with 1) increased use of abstract concepts over the course of the semester in two WTL interventions (intense and moderate); 2) increased performance for some students (first generation, women, and minorities); and dialectical argumentation (persuasive) compared to demonstration arguments (expository).
  • ItemOpen Access
    Supporting information (SI) for Gill et al. 2016 manuscript
    (Colorado State University. Libraries, 2015) Gill, Brian A.; Kondratieff, Boris C.; Casner, Kayce L.; Encalada, Andrea C.; Flecker, Alex S.; Gannon, Dustin; Ghalambor, Cameron K.; Guayasamin, Juan M.; Poff, N. LeRoy; Simmons, Mark P.; Thomas, Steven A.; Zamudio, Kelly R.; Funk, W. Chris