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At least 235 records · Page 13

Modifying a covarying protein–DNA interaction changes substrate preference of a site-specific endonuclease

Abstract Identifying and validating intermolecular covariation between proteins and their DNA-binding sites can provide insights into mechanisms that regulate selectivity and starting points for engineering new specificity. LAGLIDADG homing endonucleases (meganucleases) can be engineered to bind non-native target sites for gene-editing applications, but not all redesigns successfully reprogram specificity. To gain a global overview of residues that influence meganuclease specificity, we used information theory to identify protein–DNA covariation. Directed evolution experiments of one predicted pair, 227/+3, revealed variants with surprising shifts in I-OnuI substrate preference at the central 4 bases where cleavage occurs. Structural studies showed significant remodeling distant from the covarying position, including restructuring of an inter-hairpin loop, DNA distortions near the scissile phosphates, and new base-specific contacts. Our findings are consistent with a model whereby the functional impacts of covariation can be indirectly propagated to neighboring residues outside of direct contact range, allowing meganucleases to adapt to target site variation and indirectly expand the sequence space accessible for cleavage. We suggest that some engineered meganucleases may have unexpected cleavage profiles that were not rationally incorporated during the design process.

59 BASIC BIOLOGICAL SCIENCES↗

Understanding variation in salamander ionomes: A nutrient balance approach

1. Ecological stoichiometry uses information on a few key biological elements (C, N and P) to explain complex ecological patterns. Although factors driving variation in these elements are well established, expanding stoichiometric principles to explore dynamics of the many other essential elements comprising biological tissues (i.e. the ionome) is needed to determine their metabolic relationships and better understand biological control of elemental flows through ecosystems. 2. Here in this paper, we report observations of ionomic variation in two species of salamander (Ambystoma opacum and A. talpoideum) across ontogenic stages using specimens from biological collections of two wetlands sampled over a 30-year period. This unique data set allowed us to explore the extent of ionomic variation between species, among ontogenic stages, between sites and through time. 3. We found species- and, to a lesser extent, site-specific differences in C, N and P along with 13 other elements forming salamander ionomes but saw no evidence of temporal changes. Salamander ionomic composition was most strongly related to ontogeny with relatively higher concentrations of many elements in adult males (i.e. Ca, P, S, Mg, Zn and Cu) compared to metamorphic juveniles, which had greater amounts of C, Fe and Mn. 4. In addition to patterns of individual elements, covariance among elements was used to construct multi-elemental nutrient balances, which revealed differences in salamander elemental composition between species and sites and changes in elemental proportions across ontogenic development. These multi-elemental balances distinguished among species-site-ontogenic stage groups better than using only C, N and P. 5. Overall, this study highlights the responsiveness of consumer ionomes to life-history and environmental variation while reflecting underlying relationships among elements tied to biological function. As such, ionomic studies can provide important insights into factors shaping consumer elemental composition and for predicting how these changes might affect higher-order ecological processes.

59 BASIC BIOLOGICAL SCIENCES↗

Beyond leaf habit: generalities in plant function across 97 tropical dry forest tree species

Leaf habit has been hypothesized to define a linkage between the slow-fast plant economic spectrum and the drought resistance-avoidance trade-off in tropical forests (‘slow-safe vs fast-risky’). However, variation in hydraulic traits as a function of leaf habit has rarely been explored for a large number of species. We sampled leaf and branch functional traits of 97 tropical dry forest tree species from four sites to investigate whether patterns of trait variation varied consistently in relation to leaf habit along the ‘slow-safe vs fast-risky’ trade-off. Leaf habit explained from 0% to 43.69% of individual trait variation. We found that evergreen and semi-deciduous species differed in their location along the multivariate trait ordination when compared to deciduous species. While deciduous species showed consistent trait values, evergreen species trait values varied as a function of the site. Last, trait values varied in relation to the proportion of deciduous species in the plant community. Here We found that leaf habit describes the strategies that define drought avoidance and plant economics in tropical trees. However, leaf habit alone does not explain patterns of trait variation, which suggests quantifying site-specific or species-specific uncertainty in trait variation as the way forward.

59 BASIC BIOLOGICAL SCIENCES↗

SU-E-T-760: Tolerance Design for Site-Specific Range in Proton Patient QA Process Using the Six Sigma Model

Purpose: To show how tolerance design and tolerancing approaches can be used to predict and improve the site-specific range in patient QA process in implementing the Six Sigma. Methods: In this study, patient QA plans were selected according to 6 site-treatment groups: head &neck (94 cases), spine (76 cases), lung (89 cases), liver (53 cases), pancreas (55 cases), and prostate (121 cases), treated between 2007 and 2013. We evaluated a model of the Six Sigma that determines allowable deviations in design parameters and process variables in patient-specific QA, where possible, tolerance may be loosened, then customized if it necessary to meet the functional requirements. A Six Sigma problem-solving methodology is known as DMAIC phases, which are used stand for: Define a problem or improvement opportunity, Measure process performance, Analyze the process to determine the root causes of poor performance, Improve the process by fixing root causes, Control the improved process to hold the gains. Results: The process capability for patient-specific range QA is 0.65 with only ±1 mm of tolerance criteria. Our results suggested the tolerance level of ±2–3 mm for prostate and liver cases and ±5 mm for lung cases. We found that customized tolerance between calculated and measured range reduce that patient QA plan failure and almost all sites had failure rates less than 1%. The average QA time also improved from 2 hr to less than 1 hr for all including planning and converting process, depth-dose measurement and evaluation. Conclusion: The objective of tolerance design is to achieve optimization beyond that obtained through QA process improvement and statistical analysis function detailing to implement a Six Sigma capable design.

60 APPLIED LIFE SCIENCES↗

Identification of Novel Protein Lysine Acetyltransferases in Escherichia coli

ABSTRACT Posttranslational modifications, such as N ε-lysine acetylation, regulate protein function. N ε-lysine acetylation can occur either nonenzymatically or enzymatically. The nonenzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donor to modify an N ε-lysine residue of a protein. The enzymatic mechanism uses N ε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to N ε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified in Escherichia coli . Here, we demonstrate the existence of 4 additional E. coli KATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap among KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the posttranslational modification of bacterial proteins. We alos showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Lastly, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific nonenzymatic and enzymatic protein acetylation mechanisms present in bacteria. IMPORTANCE N ε-Lysine acetylation is one of the most abundant and important posttranslational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, N ε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed an E. coli strain that lacked both known acetylation mechanisms to identify four new N ε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate nonenzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellum-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial posttranslational modification.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of substrate specificity in bacterial AA10 lytic polysaccharide monooxygenases

Background: Understanding the diversity of lignocellulose-degrading enzymes in nature will provide insights for the improvement of cellulolytic enzyme cocktails used in the biofuels industry. Two families of enzymes, fungal AA9 and bacterial AA10, have recently been characterized as crystalline cellulose or chitin-cleaving lytic polysaccharide monooxygenases (LPMOs). Here we analyze the sequences, structures, and evolution of LPMOs to understand the factors that may influence substrate specificity both within and between these enzyme families. Results: Comparative analysis of sequences, solved structures, and homology models from AA9 and AA10 LPMO families demonstrated that, although these two LPMO families are highly conserved, structurally they have minimal sequence similarity outside the active site residues. Phylogenetic analysis of the AA10 family identified clades with putative chitinolytic and cellulolytic activities. Estimation of the rate of synonymous versus non-synonymous substitutions (dN/dS) within two major AA10 subclades showed distinct selective pressures between putative cellulolytic genes (subclade A) and CBP21-like chitinolytic genes (subclade D). Estimation of site-specific selection demonstrated that changes in the active sites were strongly negatively selected in all subclades. Furthermore, all codons in the subclade D had dN/dS values of less than 0.7, whereas codons in the cellulolytic subclade had dN/dS values of greater than 1.5. Positively selected codons were enriched at sites localized on the surface of the protein adjacent to the active site. Conclusions: The structural similarity but absence of significant sequence similarity between AA9 and AA10 families suggests that these enzyme families share an ancient ancestral protein. Combined analysis of amino acid sites under Darwinian selection and structural homology modeling identified a subclade of AA10 with diversifying selection at different surfaces, potentially used for cellulose-binding and protein-protein interactions. Together, these data indicate that AA10 LPMOs are under selection to change their function, which may optimize cellulolytic activity. This work provides a phylogenetic basis for identifying and classifying additional cellulolytic or chitinolytic LPMOs.

09 BIOMASS FUELS↗

Site-specific programming of the host epithelial transcriptome by the gut microbiota

The intestinal epithelium separates us from the microbiota but also interacts with it and thus affects host immune status and physiology. Previous studies investigated microbiota-induced responses in the gut using intact tissues or unfractionated epithelial cells, thereby limiting conclusions about regional differences in the epithelium. Here, we sought to investigate microbiota-induced transcriptional responses in specific fractions of intestinal epithelial cells. To this end, we used microarray analysis of laser capture microdissection (LCM)-harvested ileal and colonic tip and crypt epithelial fractions from germ-free and conventionally raised mice and from mice during the time course of colonization. We found that about 10% of the host’s transcriptome was microbially regulated, mainly including genes annotated with functions in immunity, cell proliferation, and metabolism. The microbial impact on host gene expression was highly site specific, as epithelial responses to the microbiota differed between cell fractions. Specific transcriptional regulators were enriched in each fraction. In general, the gut microbiota induced a more rapid response in the colon than in the ileum. Our study indicates that the microbiota engage different regulatory networks to alter host gene expression in a particular niche. Understanding host-microbiota interactions on a cellular level may facilitate signaling pathways that contribute to health and disease and thus provide new therapeutic strategies.

59 BASIC BIOLOGICAL SCIENCES↗

A divalent cation-dependent variant of the glmS ribozyme with stringent Ca 2+ selectivity co-opts a preexisting nonspecific metal ion-binding site

Ribozymes use divalent cations for structural stabilization, as catalytic cofactors, or both. Because of the prominent role of Ca 2+ in intracellular signaling, engineered ribozymes with stringent Ca 2+ selectivity would be important in biotechnology. The wild-type glmS ribozyme (glmSWT) requires glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. Previously, a glmS ribozyme variant with three adenosine mutations (glm SAAA ) was identified, which dispenses with GlcN6P and instead uses, with little selectivity, divalent cations as cofactors for site-specific RNA cleavage. We now report a Ca 2+ -specific ribozyme (glmSCa) evolved from glm SAAA that is >10,000 times more active in Ca 2+ than Mg 2+ , is inactive in even 100 mM Mg2+, and is not responsive to GlcN6P. This stringent selectivity, reminiscent of the protein nuclease from Staphylococcus, allows rapid and selective ribozyme inactivation using a Ca 2+ chelator such as EGTA. Because glmSCa functions in physiologically relevant Ca 2+ concentrations, it can form the basis for intracellular sensors that couple Ca 2+ levels to RNA cleavage. Biochemical analysis of glmSCa reveals that it has co-opted for selective Ca 2+ binding a nonspecific cation-binding site responsible for structural stabilization in glmSWT and glmSAAA. Fine-tuning of the selectivity of the cation site allows repurposing of this preexisting molecular feature.

59 BASIC BIOLOGICAL SCIENCES↗

2013 Annual Site Inspection and Monitoring Report for Uranium Mill Tailings Radiation Control Act Title I Disposal Sites

This report, in fulfillment of a license requirement, presents the results of long-term surveillance and maintenance activities conducted by the U.S. Department of Energy (DOE) Office of Legacy Management (LM) in 2013 at 19 uranium mill tailings disposal sites established under Title I of the Uranium Mill Tailings Radiation Control Act (UMTRCA) of 1978.1 These activities verified that the UMTRCA Title I disposal sites remain in compliance with license requirements. DOE operates 18 UMTRCA Title I sites under a general license granted by the U.S. Nuclear Regulatory Commission (NRC) in accordance with Title 10 Code of Federal Regulations Part 40.27 (10 CFR 40.27). As required under the general license, a long-term surveillance plan (LTSP) for each site was prepared by DOE and accepted by NRC. The Grand Junction, Colorado, Disposal Site, one of the 19 Title I sites, will not be included under the general license until the open, operating portion of the cell is closed. The open portion will be closed either when it is filled or in 2023. This site is inspected in accordance with an interim LTSP. Long-term surveillance and maintenance services for these disposal sites include inspecting and maintaining the sites; monitoring environmental media and institutional controls; conducting any necessary corrective actions; and performing administrative, records, stakeholder relations, and other regulatory stewardship functions. Annual site inspections and monitoring are conducted in accordance with site-specific LTSPs and procedures established by DOE to comply with license requirements. Each site inspection is performed to verify the integrity of visible features at the site; to identify changes or new conditions that may affect the long-term performance of the site; and to determine the need, if any, for maintenance, follow-up or contingency inspections, or corrective action in accordance with the LTSP. LTSPs and site compliance reports are available on the Internet at http://www.lm.doe.gov/.

2013↗

Solar Photovoltaics Resilient Fasteners Levelized Cost of Energy (LCOE) Tool

Solar photovoltaics (PV) module fasteners are one of the most common structural failure points on PV systems, particularly in high winds and coastal areas with ocean spray. Some fastener types have been shown to survive these conditions at higher rates than others. The fastener type, material, quantity, and placement all impact performance. Fasteners that fail less often typically have a higher upfront cost, but this investment can pay off in savings from less frequent torque audits (which reduces O&M costs), reduced system damage, and decreased system downtime. We developed an Excel-based tool to evaluate different module fasteners for a PV system - either a new or retrofit project - and compare differences in upfront and outyear costs to determine the expected life cycle costs and simple payback periods of different fastener options. The tool is site-specific, with inputs including system attributes (such as system size, location, price of power) and fastener attributes (such as design, washer type, nut type, use of locking hardware, materials, installation time, and torque audit requirements). A baseline fastener scenario can be compared to up to four proposed fastener scenarios. In addition to presenting expected life cycle cost implications of the different fastener options, the tool produces results showing the reductions in outyear costs needed to offset any initial cost premiums for more reliable fasteners across four categories: preventative O&M, avoided damage, reduced downtime, and reduced insurance premiums. These numbers can serve as decision aids for users when considering fastener options on new or existing projects. This poster will present the tool, methodology, and scenarios using example sites to highlight the tool capabilities and how it can inform different fastener decisions on different projects. Future work includes incorporating lifetime expected damage costs by embedding damage function curves that the authors are developing from field data.

14 SOLAR ENERGY↗

Different methods of estimating riverbed sediment grain size diverge at the basin scale

Introduction: The distribution of sediment grain size in streams and rivers is often quantified by the median grain size (D50), a key metric for understanding and predicting hydrologic and biogeochemical function of streams and rivers. Manual D50 measurements are time-consuming and ignore larger grains, while approaches to model D50 based on catchment characteristics may over-generalize and miss site-scale heterogeneity. Machine learning-enabled object detection methods like You Only Look Once (YOLO) provides an alternative that enables estimation of D50 that is faster than manual measurements and more site-specific than predictions based on catchment characteristics. Methods: To understand the potential role of object detection methods for improving understanding of D50, we compared D50 estimates made manually, predicted from catchment characteristics, and using a YOLO-enabled approach across the Yakima River Basin. Results: We found distinct differences between methods for D50 averages and variability, and relationships between D50 estimates and basin characteristics. Discussion: We discuss the advantages and limitations of object detection methods versus current methods, and explore potential future directions to combine D50 methods to better estimate spatiotemporal variation of D50, and improve incorporation into basin-scale models.

grain size distribution↗

Enhanced Production of Bioethanol by Fermentation of Autohydrolyzed and C4mimOAc-Treated Sugarcane Bagasse Employing Various Yeast Strains

Natural dissolved organic matter (DOM) affects mercury (Hg) redox reactions and anaerobic microbial Hg methylation in the environment. Several studies have shown that DOM can enhance Hg methylation, especially under sulfidic conditions, whereas others show that DOM inhibits Hg methylation due to strong Hg-DOM complexation. Here, we investigated and compared the effects of DOM on Hg methylation by an iron-reducing bacterium Geobacter sulfurreducens PCA and a sulfate-reducing bacterium Desulfovibrio desulfuricans ND132 under non-sulfidic conditions. The methylation experiment was performed with washed cells either in the absence or presence of DOM or glutathione, both of which form strong complexes with Hg via thiol-functional groups. DOM was found to greatly inhibit Hg methylation by G. Sulfurreducens PCA but enhance Hg methylation by D. desulfuricans ND132 cells with increasing DOM concentration. These strain-dependent opposing effects of DOM were also observed with glutathione, suggesting that thiols in DOM likely played an essential role in affecting cell Hg uptake and methylation. Additionally, DOM and glutathione decreased Hg sorption by G. sulfurreducens PCA, but not by D. desulfuricans ND132 cells, demonstrating that ND132 has a higher affinity to sorb or take up Hg than the PCA strain. Our observations indicate that DOM effects on Hg methylation are bacterial strain specific, depend on the DOM:Hg ratio or site-specific conditions, and may thus offer new insights into the role of DOM in methylmercury production in the environment.

54 ENVIRONMENTAL SCIENCES↗

Long-Range Allosteric Communication Modulated by Active Site Mn(II) Coordination Drives Catalysis in Xanthobacter autotrophicus Acetone Carboxylase

Acetone carboxylase (AC) from Xanthobacter autotrophicus is a 360 KDa α2β2γ2 heterohexamer that catalyzes the ATP-dependent formation of phosphorylated acetone and bicarbonate intermediates that react at Mn(II) metal active sites to form acetoacetate. Structural models of X. autotrophicus AC (XaAC) with and without nucleotides reveal that the binding and phosphorylation of the two substrates occurs ~40 Å from the Mn(II) active sites where acetoacetate is formed. Based on the crystal structures, a significant conformational change was proposed to open and close a tunnel that facilitates the passage of reaction intermediates between the sites for nucleotide binding and phosphorylation of substrates and Mn(II) sites of acetoacetate formation. We have employed electron paramagnetic resonance (EPR), kinetic assays, and hydrogen/deuterium exchange mass spectrometry (HDX-MS) of poised ligand-bound states and site-specific amino acid variants to complete an in-depth analysis of Mn(II) coordination and allosteric communication throughout the catalytic cycle. In contrast with the established paradigms for carboxylation, our analyses of XaAC suggested a carboxylate shift that couples both local and long-range structural transitions. Shifts in the coordination mode of a single carboxylic acid residue (αE89) mediate both catalysis proximal to a Mn(II) center and communication with an ATP active site in a separate subunit of a 180 kDa α2β2γ2 complex at a distance of 40 Å. This work demonstrates the power of combining structural models from X-ray crystallography with solution-phase spectroscopy and biophysical techniques to elucidate functional aspects of a multi-subunit enzyme.

Biochemistry & Molecular Biology↗

Photovoltaic System Health-State Architecture for Data-Driven Failure Detection

The timely detection of photovoltaic (PV) system failures is important for maintaining optimal performance and lifetime reliability. A main challenge remains the lack of a unified health-state architecture for the uninterrupted monitoring and predictive performance of PV systems. To this end, existing failure detection models are strongly dependent on the availability and quality of site-specific historic data. The scope of this work is to address these fundamental challenges by presenting a health-state architecture for advanced PV system monitoring. The proposed architecture comprises of a machine learning model for PV performance modeling and accurate failure diagnosis. The predictive model is optimally trained on low amounts of on-site data using minimal features and coupled to functional routines for data quality verification, whereas the classifier is trained under an enhanced supervised learning regime. The results demonstrated high accuracies for the implemented predictive model, exhibiting normalized root mean square errors lower than 3.40% even when trained with low data shares. The classification results provided evidence that fault conditions can be detected with a sensitivity of 83.91% for synthetic power-loss events (power reduction of 5%) and of 97.99% for field-emulated failures in the test-bench PV system. Finally, this work provides insights on how to construct an accurate PV system with predictive and classification models for the timely detection of faults and uninterrupted monitoring of PV systems, regardless of historic data availability and quality. Such guidelines and insights on the development of accurate health-state architectures for PV plants can have positive implications in operation and maintenance and monitoring strategies, thus improving the system’s performance.

photovoltaics↗

Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator

MarR (multiple antibiotic resistance repressor) family proteins are bacterial repressors that regulate transcription in response to a wide range of chemical signals. Although specific features of MarR family function have been described, the role of atomic motions in MarRs remains unexplored thus limiting insights into the evolution of allostery in this ubiquitous family of repressors. Here, we provide the first experimental evidence that internal dynamics play a crucial functional role in MarR proteins. Streptococcus pneumoniae AdcR (adhesin-competence repressor) regulates ZnII homeostasis and ZnII functions as an allosteric activator of DNA binding. ZnII coordination triggers a transition from somewhat independent domains to a more compact structure. We identify residues that impact allosteric activation on the basis of ZnII-induced perturbations of atomic motions over a wide range of timescales. These findings appear to reconcile the distinct allosteric mechanisms proposed for other MarRs and highlight the importance of conformational dynamics in biological regulation.

Capdevila, Daiana A.↗

An Ecosystem Simulation Model for Methane Production and Emission from Wetlands

Previous experimental studies suggest that methane emission from wetland is influenced by multiple interactive pathways of gas production and transport through soil and sediment layers to the atmosphere. The objective of this study is to evaluate a new simulation model of methane production and emission in wetland soils that was developed initially to help identify key processes that regulate methanogenesis and net flux of CH4 to the air, but which is designed ultimately for regional simulation using remotely sensed inputs for land cover characteristics. The foundation for these computer simulations is based on a well-documented model (CASA) of ecosystem production and carbon cycling in the terrestrial blaspheme. Modifications to represent flooded wetland soils and anaerobic decomposition include three new sub-models for: (1) layered soil temperature and water table depth (WTD) as a function of daily climate drivers, (2) CH4 production within the anoxic soil layer as a function of WTD and CO2 production under poorly drained conditions, and (3) CH4 gaseous transport pathways (molecular diffusion, ebullition, and plant vascular transport) as a function of WTD and ecosystem type. The model was applied and tested using climate and ecological data to characterize tundra wetland sites near Fairbanks, Alaska studied previously by Whalen and Reeburgh. Comparison of model predictions to measurements of soil temperature and thaw depth, water-table depth, and CH4 emissions over a two year period suggest that inter-site differences in soil physical conditions and methane fluxes could be reproduced accurately for selected periods. Day-to-day comparison of predicted emissions to measured CH4 flux rates reveals good agreement during the early part of the thaw season, but the model tends to underestimate production of CH4 during the months of July and August in both test years. Important seasonal effects, including that of falling WTD during these periods, are apparently overlooked in the model formulation. Nevertheless, reasonably close agreement was achieved between the model's mean daily and seasonal estimates of CH4 flux and observed emission rates for northern wetland ecosystems. Several features of the model are identified as crucial to more accurate prediction of wetland methane emission, including the capacity to incorporate influences of localized topographic and hydrologic features on site-specific soil temperature and WTD dynamics, and mechanistic simulation of methane emission transport pathways from within the soil profile.

Potter, C. S.↗

Using airborne and DESIS imaging spectroscopy to map plant diversity across the largest contiguous tract of tallgrass prairie on earth

Grassland ecosystems are under threat globally, primarily due to land-use and land-cover changes that have adversely affected their biodiversity. Given the negative ecological impacts of biodiversity loss in grasslands, there is an urgent need for developing an operational biodiversity monitoring system that functions in these ecosystems. In this paper, we assessed the capability of airborne and spaceborne imaging spectroscopy (also known as hyperspectral imaging) to capture plant α-diversity in a large naturally-assembled grassland while considering the impact of common management practices, specifically prescribed fire. We collected a robust in-situ plant diversity data set, including species composition and percent cover from 2500 sampling points with different burn ages, from recently-burned to transitional and pre-prescribed fire at the Joseph H. Williams Tallgrass Prairie Preserve in Oklahoma, USA. We expressed in-situ plant α-diversity using the first three Hill numbers, including species richness (number of observed species in a plant community), exponential Shannon entropy index (hereafter Shannon diversity; effective number of common species, where species are weighed proportional to their percent cover), and inverse Simpson concentration index (hereafter Simpson diversity; effective number of dominant species, where more weight is given to dominant species) at four different plot sizes, including 60 m × 60 m, 120 m × 120 m, 180 m × 180 m, and 240 m × 240 m. We collected full-range airborne hyperspectral data with fine spatial resolution (1 m) and visible and near-infrared spaceborne hyperspectral data from DESIS sensor with coarse spatial resolution (30 m), and used the spectral diversity hypothesis—i.e., that the variability in spectral data is largely driven by plant diversity—to estimate α-diversity remotely. In recently-burned plots and those at the transitional stage, both airborne and spaceborne data were capable of capturing Simpson diversity—a metric that calculates the effective number of dominant species by emphasizing abundant species and discounting rare species—but not species richness or Shannon diversity. Further, neither airborne nor spaceborne hyperspectral data sets were capable of capturing plant α-diversity of 60 m × 60 m or 120 m × 120 m plots. Based on these results, three main findings emerged: (1) management practices influence grassland biodiversity patterns that can be remotely detected, (2) both fine- and coarse-resolution remotely-sensed data can detect the effective number of dominant species (e.g., Simpson diversity), and (3) attention should be given to site-specific plant diversity field data collection to appropriately interpret remote sensing results. Findings of this study indicate the feasibility of estimating Simpson diversity in naturally-assembled grasslands using forthcoming spaceborne imagers such as National Aeronautics and Space Administration's Surface Biology and Geology mission.

Hamed Gholizadeh↗

XRootD Third Party Copy for the WLCG and HL- LHC

A Third Party Copy (TPC) mechanism has existed in the pure XRootD storage environment for many years. However, using the XRootD TPC in the WLCG environment presents additional challenges due to the diversity of the storage systems involved such as EOS, dCache, DPM and ECHO, requiring that we carefully navigate the unique constraints imposed by these storage systems and their site-specific environments through customized configuration and software development. To support multitenant setups seen at many WLCG sites, X509 based authentication and authorization in XRootD was significantly improved to meet both security and functionality requirements. This paper presents architecture of the pull based TPC with optional X509 credential delegation, and how it is implemented in native XRootD and dCache. The paper discusses technical requirements, challenges, design choices and implementation details in the WLCG storage systems, as well as in FTS/gfal2. It also outlines XRootD's plan to support newer TPC and security models such as token based authorization. 1

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗