Open Access Research and Scholarship Fund (OARS)

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Since 2013, the Colorado State University Libraries, under the guidance of the CSU Faculty Council Committee on Libraries, has allocated funds to support the Open Access Research and Scholarship (OARS) Fund. The fund is open to CSU tenured/tenure track faculty and full-time research scientists. This digital collection contains articles that received OARS funding between 2011 and 2020.

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Open Access
Electrothermal performance of heaters based on laser-induced graphene on aramid fabric
(Colorado State University. Libraries, 2022) Naseri, Iman, author; Ziaee, Morteza, author; Nilsson, Zach N., author; Lustig, Danielle R., author; Yourdkhani, Mostafa, author; American Chemical Society, publisher
Nanostructured heaters based on laser-induced graphene (LIG) are promising for heat generation and temperature control in a variety of applications due to their high efficiency as well as a fast, facile, and highly scalable fabrication process. While recent studies have shown that LIG can be written on a wide range of precursors, the reports on LIG-based heaters are mainly limited to polyimide film substrates. Here, we develop and characterize nanostructured heaters by direct writing of laser-induced graphene on nonuniform and structurally porous aramid woven fabric. The synthesis and writing of graphene on aramid fabric is conducted using a 10.6 μm CO2 laser. The quality of laser-induced graphene and electrical properties of the heater fabric is tuned by controlling the lasing process parameters. Produced heaters exhibit good electrothermal efficiency with steady-state temperatures up to 170 °C when subjected to an input power density of 1.5 W cm–2. In addition, the permeable texture of LIG–aramid fabric heaters allows for easy impregnation with thermosetting resins. We demonstrate the encapsulation of fabric heaters with two different types of thermosetting resins to develop both flexible and stiff composites. A flexible heater is produced by the impregnation of LIG–aramid fabric by silicone rubber. While the flexible composite heater exhibits inferior electrothermal performance compared to neat LIG–aramid fabric, it shows consistent electrothermal performance under various electrical and mechanical loading conditions. A multifunctional fiber-reinforced composite panel with integrated de-icing functionality is also manufactured using one ply of LIG–aramid fabric heater as part of the composite layup. The results of de-icing experiments show excellent de-icing capability, where a 5 mm thick piece of ice is completely melted away within 2 min using an input power of 12.8 W.
Open Access
Evaluating the consistency of subjective activity assessments and their relation to cognition in older adults
(Colorado State University. Libraries, 2021-07-28) Hatt, Cassandra R., author; Brydges, Christopher R., author; Mogle, Jacqueline A., author; Sliwinski, Martin J., author; Bielak, Allison A. M., author; MDPI, publisher
(1) Background: Research examining whether activity engagement is related to cognitive functioning in older adults has been limited to using retrospective reports of activity which may be affected by biases. This study compared two measurements (estimated weekly versus reported daily), and whether these activity assessments were related to cognition in older adults; (2) Methods: Participants from US (n = 199) and Australian (n = 170) samples completed a weekly estimate of activity, followed by 7 consecutive days of daily reporting. Differences between weekly estimates and daily reports were found, such that estimations at the weekly level were lower than self-reported daily information. Multivariate multiple regression was used to determine whether total activity, activity domains and the discrepancy between assessment types (i.e., weekly/daily) predicted cognitive performance across three cognitive domains (fluid, verbal, memory); (3) Results: When activity assessments were totaled, neither predicted cognition; however, when activity was grouped by domain (cognitive, social, physical), different domains predicted different cognitive outcomes. Daily reported cognitive activity significantly predicted verbal performance (β = 1.63, p = 0.005), while weekly estimated social activity predicted memory performance (β = –1.81, p = 0.050). Further, while the magnitude of discrepancy in total activity did not significantly predict cognitive performance, domain specific differences did. Differences in physical activity reported across assessments predicted fluid performance (β = –1.16, p = 0.033); (4) Conclusions: The significant discrepancy between the measurement types shows that it is important to recognize potential biases in responding when conducting activity and cognition research.
Open Access
The tempo and mode of angiosperm mitochondrial genome divergence inferred from intraspecific variation in Arabidopsis thaliana
(Colorado State University. Libraries, 2020-01-21) Wu, Zhiqiang, author; Waneka, Gus, author; Sloan, Daniel B., author; Genetics Society of America, publisher
The mechanisms of sequence divergence in angiosperm mitochondrial genomes have long been enigmatic. In particular, it is difficult to reconcile the rapid divergence of intergenic regions that can make non-coding sequences almost unrecognizable even among close relatives with the unusually high levels of sequence conservation found in genic regions. It has been hypothesized that different mutation/repair mechanisms act on genic and intergenic sequences or alternatively that mutational input is relatively constant but that selection has strikingly different effects on these respective regions. To test these alternative possibilities, we analyzed mtDNA divergence within Arabidopsis thaliana, including variants from the 1001 Genomes Project and changes accrued in published mutation accumulation (MA) lines. We found that base-substitution frequencies are relatively similar for intergenic regions and synonymous sites in coding regions, whereas indel and nonsynonymous substitutions rates are greatly depressed in coding regions, supporting a conventional model in which mutation/repair mechanisms are consistent throughout the genome but differentially filtered by selection. Most types of sequence and structural changes were undetectable in 10-generation MA lines, but we found significant shifts in relative copy number across mtDNA regions for lines grown under stressed vs. benign conditions. We confirmed quantitative variation in copy number across the A. thaliana mitogenome using both whole-genome sequencing and droplet digital PCR, further undermining the classic but oversimplified model of a circular angiosperm mtDNA structure. Our results suggest that copy number variation is one of the most fluid features of angiosperm mitochondrial genomes.
Open Access
Millennial consumers' responses to cause-related marketing in support of LGBTQ homeless youth
(Colorado State University. Libraries, 2019-08-14) Hensley, Cammie, author; Diddi, Sonali, author; Hyllegard, Karen, author; MDPI, publisher
This study explored Millennial consumers' responses to a cause-related marketing (CRM) initiative for a sensitive social cause—lesbian, gay, bisexual, transgender and queer (LGBTQ) homeless youth. Qualitative and quantitative research methods were employed to examine the effctiveness of CRM in generating financial support for LGBTQ homeless youth. Findings revealed that self-cause congruence may be an important factor in determining Millennial consumers' responses to a CRM initiative for LGBTQ homeless youth; whereas, message frame/appeal may be less important for generating response to such an initiative. Findings also indicated that gender, information processing, guilt, and skepticism influenced Millennial consumers' attitudes toward brand, attitudes toward cause, and behavioral intentions toward the CRM initiative. These findings offer implications for brands/companies that may wish to engage in CRM initiative in support of sensitive social causes. By addressing a sensitive social cause-LGBTQ homeless youth-findings provide an original contribution to the CRM literature. Findings reveal that self-cause congruence is an important predictor of behavioral intention toward the LGBTQ social cause. This provides an implication for marketers who want to target their relationship-building efforts toward individuals who have demonstrated prior engagement with a social cause. Findings also have implications for brands/companies that wish to develop CRM initiatives for controversial causes.
Open Access
The mmpL3 interactome reveals a complex crosstalk between cell envelope biosynthesis and cell elongation and division in mycobacteria
(Colorado State University. Libraries, 2019-07-24) Belardinelli, Juan Manuel, author; Stevens, Casey M., author; Li, Wei, author; Tan, Yong Zi, author; Jones, Victoria, author; Mancia, Filippo, author; Zgurskaya, Helen I., author; Jackson, Mary, author; Springer Nature Publishing, publisher
Integral membrane transporters of the Mycobacterial Membrane Protein Large (MmpL) family and their interactome play important roles in the synthesis and export of mycobacterial outer membrane lipids. Despite the current interest in the mycolic acid transporter, MmpL3, from the perspective of drug discovery, the nature and biological significance of its interactome remain largely unknown. We here report on a genome-wide screening by two-hybrid system for MmpL3 binding partners. While a surprisingly low number of proteins involved in mycolic acid biosynthesis was found to interact with MmpL3, numerous enzymes and transporters participating in the biogenesis of peptidoglycan, arabinogalactan and lipoglycans, and the cell division regulatory protein, CrgA, were identified among the hits. Surface plasmon resonance and co-immunoprecipitation independently confirmed physical interactions for three proteins in vitro and/or in vivo. Results are in line with the focal localization of MmpL3 at the poles and septum of actively-growing bacilli where the synthesis of all major constituents of the cell wall core are known to occur, and are further suggestive of a role for MmpL3 in the coordination of new cell wall deposition during cell septation and elongation. This novel aspect of the physiology of MmpL3 may contribute to the extreme vulnerability and high therapeutic potential of this transporter.
Open Access
BIM use by architecture, engineering, and construction (AEC) industry in educational facility projects
(Colorado State University. Libraries, 2019-07-03) Moreno, Cristina, author; Olbina, Svetlana, author; Issa, Raja R., author; Hindawi, publisher
In recent years, many public and private sector owners have started to require a building information modeling (BIM) component in new construction projects. Although there has been a significant increase in industry-wide acceptance of BIM, it is still not a standard practice in the educational facility sector. This research aimed at exploring the use of BIM in educational facility projects by the architecture, engineering, and construction (AEC) disciplines. A survey that investigated BIM adoption at the company level, BIM implementation in projects, benefits of using BIM, and obstacles to using BIM was distributed to architects, site engineers, structural engineers, mechanical engineers, and contractors across the United States. The survey results showed that a majority of the respondents from all five disciplines used BIM. BIM was most commonly used for 3D visualization, automation of documentation, and clash detection. The most important benefits of BIM included better marketing and clearer understanding of projects which is crucial for clients such as school students, teachers, and principals. Lack of expertise and need for training seemed to be main obstacles to BIM use. The research contributes to the body of knowledge by showing prevalence of BIM use on educational facility projects and indicating how BIM could help improve collaborative knowledge sharing among designers, contractors, and clients, resulting in better quality educational buildings. These research findings can be used to assist AEC companies that are interested in implementing BIM in the educational facility projects.
Open Access
Collaborative concession in food movement networks: the uneven relations of resource mobilization
(Colorado State University. Libraries, 2019-05-21) Sbicca, Joshua, author; Luxton, India, author; Hale, James, author; Roeser, Kassandra, author; MDPI AG, Basel, Switzerland, publisher
How do food movements prioritize and work to accomplish their varied and often conflicting social change goals at the city scale? Our study investigates the Denver food movement with a mixed methods social network analysis to understand how organizations navigate differences in power and influence vis-à-vis resource exchange. We refer to this uneven process with the analytical concept of "collaborative concession". The strategic resource mobilization of money, land, and labor operates through certain collaborative niches, which constitute the priorities of the movement. Among these are poverty alleviation and local food production, which are facilitated by powerful development, education, and health organizations. Therefore, food movement networks do not offer organizations equal opportunity to carry out their priorities. Concession suggests that organizations need to lose something to gain something. Paradoxically, collaboration can produce a resource gain. Our findings provide new insights into the uneven process by which food movement organizations-and city-wide food movements overall-mobilize.
Open Access
Confounding factors in algal phosphorus limitation experiments
(Colorado State University. Libraries, 2018-10-18) Beck, Whitney S., author; Hall, Ed K., author; PLOS ONE, publisher
Assessing algal nutrient limitation is critical for understanding the interaction of primary production and nutrient cycling in streams, and nutrient diffusing substrate (NDS) experiments are often used to determine limiting nutrients such as nitrogen (N) and phosphorus (P). Unexpectedly, many experiments have also shown decreased algal biomass on NDS P treatments compared to controls. To address whether inhibition of algal growth results from direct P toxicity, NDS preparation artifacts, or environmental covariates, we first quantified the frequency of nutrient inhibition in published experiments. We also conducted a meta-analysis to determine whether heterotrophic microbial competition or selective grazing could explain decreases in algal biomass with P additions. We then deployed field experiments to determine whether P-inhibition of algal growth could be explained by P toxicity, differences in phosphate cation (K vs. Na), differences in phosphate form (monobasic vs. dibasic), or production of H2O2 during NDS preparation. We found significant inhibition of algal growth in 12.9% of published NDS P experiments as compared to 4.7% and 3.6% of N and NP experiments. The meta-analysis linear models did not show enhanced heterotrophy on NDS P treatments or selective grazing of P-rich algae. Our field experiments did not show inhibition of autotrophic growth with P additions, but we found significantly lower gross primary productivity (GPP) and biomass-specific GPP of benthic algae on monobasic phosphate salts as compared to dibasic phosphate salts, likely because of reduced pH levels. Additionally, we note that past field experiments and meta-analyses support the plausibility of direct P toxicity or phosphate form (monobasic vs. dibasic) leading to inhibition of algal growth, particularly when other resources such as N or light are limiting. Given that multiple mechanisms may be acting simultaneously, we recommend practical, cost-effective steps to minimize the potential for P- inhibition of algal growth as an artifact of NDS experimental design.
Open Access
Building a multi-institutional and interdisciplinary team to develop a zoonotic tuberculosis roadmap
(Colorado State University. Libraries, 2018-06-12) Olea-Popelka, Francisco, author; Fujiwara, Paula I., author; Frontiers in Public Health, publisher
Tuberculosis (TB), as the major infectious disease in the world, has devastating consequences for not only humans, but also cattle and several wildlife species. This disease presents additional challenges to human and veterinary health authorities given the zoonotic nature of the pathogens responsible for the disease across species. One of the main public health challenges regarding zoonotic TB (ZTB) caused by Mycobacterium bovis is that the true incidence of this type of TB in humans is not known and is likely to be underestimated. To effectively address challenges posed by ZTB, an integrated One Health approach is needed. In this manuscript, we describe the rationale, major steps, timeline, stakeholders, and important events that led to the assembling of a true integrated multi-institutional and interdisciplinary team that accomplished the ambitious goal of developing a ZTB roadmap, published in October, 2017. It outlines key activities to address the global challenges regarding the prevention, surveillance, diagnosis, and treatment of ZTB. We discuss and emphasize the importance of integrated approaches to be able to accomplish the short (year 2020) and medium term (year 2025) goals outlined in the ZTB roadmap.
Open Access
Evidence of zoonotic leprosy in Pará, Brazilian Amazon, and risks associated with human contact or consumption of armadillos
(Colorado State University. Libraries, 2018-06-28) da Silva, Moises B., author; Portela, Juliana M., author; Li, Wei, author; Jackson, Mary, author; Gonzalez-Juarrero, Mercedes, author; Hidalgo, Andrea Sánchez, author; Belisle, John T., author; Bouth, Raquel C., author; Gobbo, Angélica R., author; Barreto, Josafá G., author; Minervino, Antonio H. H., author; Cole, Stewart T., author; Avanzi, Charlotte, author; Busso, Philippe, author; Frade, Marco A. C., author; Geluk, Annemieke, author; Salgado, Claudio G., author; Spencer, John S., author; Public Library of Science, publisher
Mycobacterium leprae (M. leprae) is a human pathogen and the causative agent for leprosy, a chronic disease characterized by lesions of the skin and peripheral nerve damage. Zoonotic transmission of M. leprae to humans by nine-banded armadillos (Dasypus novemcinctus) has been shown to occur in the southern United States, mainly in Texas, Louisiana, and Florida. Nine-banded armadillos are also common in South America, and residents living in some areas in Brazil hunt and kill armadillos as a dietary source of protein. This study examines the extent of M. leprae infection in wild armadillos and whether these New World mammals may be a natural reservoir for leprosy transmission in Brazil, similar to the situation in the southern states of the U.S. The presence of the M. leprae-specific repetitive sequence RLEP was detected by PCR amplification in purified DNA extracted from armadillo spleen and liver tissue samples. A positive RLEP signal was confirmed in 62% of the armadillos (10/16), indicating high rates of infection with M. leprae. Immunohistochemistry of sections of infected armadillo spleens revealed mycobacterial DNA and cell wall constituents in situ detected by SYBR Gold and auramine/rhodamine staining techniques, respectively. The M. leprae-specific antigen, phenolic glycolipid I (PGL-I) was detected in spleen sections using a rabbit polyclonal antibody specific for PGL-I. Anti-PGL-I titers were assessed by ELISA in sera from 146 inhabitants of Belterra, a hyperendemic city located in western Pará state in Brazil. A positive anti-PGL-I titer is a known biomarker for M. leprae infection in both humans and armadillos. Individuals who consumed armadillo meat most frequently (more than once per month) showed a significantly higher anti-PGL-I titer than those who did not eat or ate less frequently than once per month. Armadillos infected with M. leprae represent a potential environmental reservoir. Consequently, people who hunt, kill, or process or eat armadillo meat are at a higher risk for infection with M. leprae from these animals.
Open Access
A road damage and life-cycle greenhouse gas comparison of trucking and pipeline water delivery systems for hydraulically fractured oil and gas field development in Colorado
(Colorado State University. Libraries, 2017) Duthu, Ray C., author; Bradley, Thomas H., author; PLOS ONE, publisher
The process of hydraulic fracturing for recovery of oil and natural gas uses large amounts of fresh water and produces a comparable amount of wastewater, much of which is typically transported by truck. Truck transport of water is an expensive and energy-intensive process with significant external costs including roads damages, and pollution. The integrated development plan (IDP) is the industry nomenclature for an integrated oil and gas infrastructure system incorporating pipeline-based transport of water and wastewater, centralized water treatment, and high rates of wastewater recycling. These IDP have been proposed as an alternative to truck transport systems so as to mitigate many of the economic and environmental problems associated with natural gas production, but the economic and environmental performance of these systems have not been analyzed to date. This study presents a quantification of lifecycle greenhouse gas (GHG) emissions and road damages of a generic oil and gas field, and of an oil and gas development sited in the Denver-Julesburg basin in the northern Colorado region of the US. Results demonstrate that a reduction in economic and environmental externalities can be derived from the development of these IDP-based pipeline water transportation systems. IDPs have marginal utility in reducing GHG emissions and road damage when they are used to replace in-field water transport, but can reduce GHG emissions and road damage by factors of as much as 6 and 7 respectively, when used to replace fresh water transport and waste-disposal routes for exemplar Northern Colorado oil and gas fields.
Open Access
Effects of recreation on animals revealed as widespread through a global systematic review
(Colorado State University. Libraries, 2016-12-08) Larson, Courtney L., author; Reed, Sarah E., author; Merenlender, Adina M., author; Crooks, Kevin R., author; PLOS ONE, publisher
Outdoor recreation is typically assumed to be compatible with biodiversity conservation and is permitted in most protected areas worldwide. However, increasing numbers of studies are discovering negative effects of recreation on animals. We conducted a systematic review of the scientific literature and analyzed 274 articles on the effects of non-consumptive recreation on animals, across all geographic areas, taxonomic groups, and recreation activities. We quantified trends in publication rates and outlets, identified knowledge gaps, and assessed evidence for effects of recreation. Although publication rates are low and knowledge gaps remain, the evidence was clear with over 93% of reviewed articles documenting at least one effect of recreation on animals, the majority of which (59%) were classified as negative effects. Most articles focused on mammals (42% of articles) or birds (37%), locations in North America (37.7%) or Europe (26.6%), and individual-level responses (49%). Meanwhile, studies of amphibians, reptiles, and fish, locations in South America, Asia, and Africa, and responses at the population and community levels are lacking. Although responses are likely to be species-specific in many cases, some taxonomic groups (e.g., raptors, shorebirds, ungulates, and corals) had greater evidence for an effect of recreation. Counter to public perception, non-motorized activities had more evidence for a negative effect of recreation than motorized activities, with effects observed 1.2 times more frequently. Snow-based activities had more evidence for an effect than other types of recreation, with effects observed 1.3 times more frequently. Protecting biodiversity from potentially harmful effects of recreation is a primary concern for conservation planners and land managers who face increases in park visitation rates; accordingly, there is demand for sciencebased information to help solve these dilemmas.
Open Access
The method of attachment influences accelerometer-based activity data in dogs
(Colorado State University. Libraries, 2017-02-10) Martin, Kyle W., author; Olsen, Anastasia M., author; Duncan, Colleen G., author; Duerr, Felix M., author; BioMed Central, publisher
Background: Accelerometer-based activity monitoring is a promising new tool in veterinary medicine used to objectively assess activity levels in dogs. To date, it is unknown how device orientation, attachment method, and attachment of a leash to the collar holding an accelerometer affect canine activity data. It was our goal to evaluate whether attachment methods of accelerometers affect activity counts. Eight healthy, client-owned dogs were fitted with two identical neck collars to which two identical activity monitors were attached using six different methods of attachment. These methods of attachment evaluated the use of a protective case, positioning of the activity monitor and the tightness of attachment of the accelerometer. Lastly, the effect of leash attachment to the collar was evaluated. For trials where the effect of leash attachment to the collar was not being studied, the leash was attached to a harness. Activity data obtained from separate monitors within a given experiment were compared using Pearson correlation coefficients and across all experiments using the Kruskal-Wallis Test. Results: There was excellent correlation and low variability between activity monitors on separate collars when the leash was attached to a harness, regardless of their relative positions. There was good correlation when activity monitors were placed on the same collar regardless of orientation. There were poor correlations between activity monitors in three experiments: when the leash was fastened to the collar that held an activity monitor, when one activity monitor was housed in the protective casing, and when one activity monitor was loosely zip-tied to the collar rather than threaded on using the provided metal loop. Follow-up, pair-wise comparisons identified the correlation associated with these three methods of attachment to be statistically different from the level of correlation when monitors were placed on separate collars. Conclusions: While accelerometer-based activity monitors are useful tools to objectively assess physical activity in dogs, care must be taken when choosing a method to attach the device. The attachment of the activity monitor to the collar should utilize a second, dedicated collar that is not used for leash attachment and the attachment method should remain consistent throughout a study period.
Open Access
Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment
(Colorado State University. Libraries, 2016-10-23) Biddle, Wil, author; Schmitt, Margaret A., author; Fisk, John D., author; Oxford University Press, publisher
Breaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNAOpt. We suspected a modification of the tRNAOptAUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNAOptAUG is converted to inosine. We identified tRNAOptAUG anticodon loop variants that increase reassignment of the histidine CAU codon, decrease incorporation in response to the histidine CAC codon, and improve cell health and growth profiles. Recognizing tRNA modification as both a potential pitfall and avenue of directed alteration will be important as the field of genetic code engineering continues to infiltrate the genetic codes of diverse organisms.
Open Access
Accurate characterization of winter precipitation using multi-angle snowflake camera, visual hull, advanced scattering methods and polarimetric radar
(Colorado State University. Libraries, 2016-06-11) Notaroš, Branislav M., author; Bringi, Viswanathan N., author; Kleinkort, Cameron, author; Kennedy, Patrick, author; Huang, Gwo-Jong, author; Thurai, Merhala, author; Newman, Andrew J., author; Bang, Wonbae, author; Lee, GyuWon, author; MDPI, publisher
This article proposes and presents a novel approach to the characterization of winter precipitation and modeling of radar observables through a synergistic use of advanced optical disdrometers for microphysical and geometrical measurements of ice and snow particles (in particular, a multi-angle snowflake camera-MASC), image processing methodology, advanced method-of-moments scattering computations, and state-of-the-art polarimetric radars. The article also describes the newly built and established MASCRAD (MASC + Radar) in-situ measurement site, under the umbrella of CSU-CHILL Radar, as well as the MASCRAD project and 2014/2015 winter campaign. We apply a visual hull method to reconstruct 3D shapes of ice particles based on high-resolution MASC images, and perform "particle-by-particle" scattering computations to obtain polarimetric radar observables. The article also presents and discusses selected illustrative observation data, results, and analyses for three cases with widely-differing meteorological settings that involve contrasting hydrometeor forms. Illustrative results of scattering calculations based on MASC images captured during these events, in comparison with radar data, as well as selected comparative studies of snow habits from MASC, 2D video-disdrometer, and CHILL radar data, are presented, along with the analysis of microphysical characteristics of particles. In the longer term, this work has potential to significantly improve the radar-based quantitative winter-precipitation estimation.
Open Access
Linear plasmids and the rate of sequence evolution in plant mitochondrial genomes
(Colorado State University. Libraries, 2016) Warren, Jessica M., author; Simmons, Mark P., author; Wu, Zhiqiang, author; Sloan, Daniel B., author; Oxford University Press, publisher
The mitochondrial genomes of flowering plants experience frequent insertions of foreign sequences, including linear plasmids that also exist in standalone forms within mitochondria, but the history and phylogenetic distribution of plasmid insertions is not well known. Taking advantage of the increased availability of plant mitochondrial genome sequences, we performed phylogenetic analyses to reconstruct the evolutionary history of these plasmids and plasmid-derived insertions. Mitochondrial genomes from multiple land plant lineages (including liverworts, lycophytes, ferns, and gymnosperms) include fragmented remnants from ancient plasmid insertions. Such insertions are much more recent and widespread in angiosperms, in which approximately 75% of sequenced mitochondrial genomes contain identifiable plasmid insertions. Although conflicts between plasmid and angiosperm phylogenies provide clear evidence of repeated horizontal transfers, we were still able to detect significant phylogenetic concordance, indicating that mitochondrial plasmids have also experienced sustained periods of (effectively) vertical transmission in angiosperms. The observed levels of sequence divergence in plasmid-derived genes suggest that nucleotide substitution rates in these plasmids, which often encode their own viral-like DNA polymerases, are orders of magnitude higher than in mitochondrial chromosomes. Based on these results, we hypothesize that the periodic incorporation of mitochondrial genes into plasmids contributes to the remarkable heterogeneity in substitution rates among genes that has recently been discovered in some angiosperm mitochondrial genomes. In support of this hypothesis, we show that the recently acquired ψtrnP-trnW gene region in a maize linear plasmid is evolving significantly faster than homologous sequences that have been retained in the mitochondrial chromosome in closely related grasses.
Open Access
Local knowledge production, transmission, and the importance of village leaders in a network of Tibetan pastoralists coping with environmental change
(Colorado State University. Libraries, 2016) Hopping, Kelly A., author; Yangzong, Ciren, author; Klein, Julia A., author; Resilience Alliance, publisher
Changing climate, social institutions, and natural resource management policies are reshaping the dynamics of social-ecological systems globally, with subsistence-based communities likely to be among the most vulnerable to the impacts of global change. These communities’ local ecological knowledge is increasingly recognized as a source of adaptive capacity for them as well as a crucial source of information to be incorporated into scientific understanding and policy making. We interviewed Tibetan pastoralists about their observations of environmental changes, their interpretations of the causes of these changes, and the ways in which they acquire and transmit this knowledge. We found that community members tended to agree that changing climate is driving undesirable trends in grassland and livestock health, and some also viewed changing management practices as compounding the impacts of climate change. However, those nominated by their peers as experts on traditional, pastoral knowledge observed fewer changes than did a more heterogeneous group of people who reported more ways in which the environment is changing. Herders mostly discussed these changes among themselves and particularly with village leaders, yet people who discussed environmental changes together did not necessarily hold the same knowledge of them. These results indicate that members of the community are transferring knowledge of environmental change primarily as a means for seeking adaptive solutions to it, rather than for learning from others, and that local leaders can serve as critical brokers of knowledge transfer within and beyond their communities. This highlights not only the interconnectedness of knowledge, practice, and power, but also points toward the important role that local governance can have in helping communities cope with the impacts of global change.
Open Access
High transcript abundance, RNA editing, and small RNAs in intergenic regions within the massive mitochondrial genome of the angiosperm Silene noctiflora
(Colorado State University. Libraries, 2015) Wu, Zhiqiang, author; Stone, James D., author; Štorchovaá, Helena, author; Sloan, Daniel B., author; BMC Genomics, publisher
Background: Species within the angiosperm genus Silene contain the largest mitochondrial genomes ever identified. The enormity of these genomes (up to 11 Mb in size) appears to be the result of increased non-coding DNA, which represents >99 % of the genome content. These genomes are also fragmented into dozens of circular-mapping chromosomes, some of which contain no identifiable genes, raising questions about if and how these "empty" chromosomes are maintained by selection. To assess the possibility that they contain novel and unannotated functional elements, we have performed RNA-seq to analyze the mitochondrial transcriptome of Silene noctiflora. Results: We identified regions of high transcript abundance in almost every chromosome in the mitochondrial genome including those that lack any annotated genes. In some cases, these transcribed regions exhibited higher expression levels than some core mitochondrial protein-coding genes. We also identified RNA editing sites throughout the genome, including 97 sites that were outside of protein-coding gene sequences and found in pseudogenes, introns, UTRs, and transcribed intergenic regions. Unlike in protein-coding sequences, however, most of these RNA editing sites were only edited at intermediate frequencies. Finally, analysis of mitochondrial small RNAs indicated that most were likely degradation products from longer transcripts, but we did identify candidates for functional small RNAs that mapped to intergenic regions and were not associated with longer RNA transcripts. Conclusions: Our findings demonstrate transcriptional activity in many localized regions within the extensive intergenic sequence content in the S. noctiflora mitochondrial genome, supporting the possibility that the genome contains previously unidentified functional elements. However, transcription by itself is not proof of functional importance, and we discuss evidence that some of the observed transcription and post-transcriptional modifications are non-adaptive. Therefore, further investigations are required to determine whether any of the identified transcribed regions have played a functional role in the proliferation and maintenance of the enormous non-coding regions in Silene mitochondrial genomes.
Open Access
Foraging ecology of black bears in urban environments: guidance for human-bear conflict mitigation
(Colorado State University. Libraries, 2015-08) Lewis, D. L., author; Baruch-Mordo, S., author; Wilson, K. R., author; Breck, S. W., author; Mao, J. S., author; Broderick, J., author; Ecological Society of America, publisher
Urban environments offer wildlife novel anthropogenic resources that vary spatiotemporally at fine scales. Property damage, economic losses, human injury, or other human-wildlife conflicts can occur when wildlife use these resources; however, few studies have examined urban wildlife resource selection at fine scales to guide conflict mitigation. We studied black bears (Ursus americanus) in the urban area of Aspen, Colorado, USA from 2007 to 2010 to quantify bear foraging on natural and anthropogenic resources and to model factors associated with anthropogenic feeding events. We collected fine-scale spatiotemporal data by tracking GPS-collared bears at 30-min intervals and backtracked to bear locations within 24 hours of use. We used discrete choice models to assess bears' resource selection, modeling anthropogenic feeding (use) and five associated random (availability) locations as a function of attributes related to temporally changing natural (e.g., ripe mast) and human (e.g., garbage) food resources, urban characteristics (e.g., housing density), and land cover characteristics (e.g., distance to riparian area). We backtracked to 2,675 locations used by 24 bears and classified 20% as foraging locations. We found that bears foraged on both natural and anthropogenic food sources in the urban environment, with 77% of feeding events being anthropogenic. We documented inter- and intra-annual foraging patterns in which bears foraged extensively in urban areas when natural food production was poor, then switched to natural food sources when available. These patterns suggest that bears balance energy budgets and individual safety when making foraging decisions. Overwhelmingly, garbage was the main anthropogenic food source that bears used. Selection of foraging sites was not only influenced by presence of garbage but also by proximity to riparian habitat and presence of ripe anthropogenic fruit trees. We found that while 76% of the garbage containers at random locations were bear-resistant, 57% of these bear-resistant containers were not properly secured. We recommend conflict mitigation focus on reducing available garbage and anthropogenic fruit trees, particularly near riparian areas, to make urban environments less energetically beneficial for foraging. Additionally, deploying bear-resistant containers is inadequate without education and proactive enforcement to change human behavior to properly secure garbage and ultimately reduce human-bear conflict.
Open Access
Snow and albedo climate change impacts across the United States Northern Great Plains
(Colorado State University. Libraries, 2015) Fassnacht, S. R., author; Cherry, M. L., author; Venable, N. B. H., author; Copernicus, publisher
In areas with a seasonal snowpack, a warmer climate would cause less snowfall, a shallower snowpack and a change in the timing of snowmelt. Trends in temperature, precipitation (total and as snow), days with precipitation and snow, and winter albedo were investigated over the 60 year period from 1951 to 2010 for 20 meteorological stations across the Northern Great Plains. This is an area where snow accumulation is shallow but persistent for most of the winter (November through March). The most consistent trends were minimum temperature and days with precipitation, which both increased at a majority of the stations. The modeled winter albedo decreased at more stations than where it increased. There were substantial spatial variability in the climate trends. For most variables, the period of record used influenced the magnitude and sign of the significant trends.