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At least 181 records · Page 10

The CopA2-Type P 1B -Type ATPase CcoI Serves as Central Hub for cbb 3 -Type Cytochrome Oxidase Biogenesis

Copper (Cu)-transporting P 1B -type ATPases are ubiquitous metal transporters and crucial for maintaining Cu homeostasis in all domains of life. In bacteria, the P 1B -type ATPase CopA is required for Cu-detoxification and exports excess Cu(I) in an ATP-dependent reaction from the cytosol into the periplasm. CopA is a member of the CopA1-type ATPase family and has been biochemically and structurally characterized in detail. In contrast, less is known about members of the CopA2-type ATPase family, which are predicted to transport Cu(I) into the periplasm for cuproprotein maturation. One example is CcoI, which is required for the maturation of cbb 3 -type cytochrome oxidase (cbb 3 -Cox) in different species. Here, we reconstituted purified CcoI of Rhodobacter capsulatus into liposomes and determined Cu transport using solid-supported membrane electrophysiology. The data demonstrate ATP-dependent Cu(I) translocation by CcoI, while no transport is observed in the presence of a non-hydrolysable ATP analog. CcoI contains two cytosolically exposed N-terminal metal binding sites (N-MBSs), which are both important, but not essential for Cu delivery to cbb 3 -Cox. CcoI and cbb 3 -Cox activity assays in the presence of different Cu concentrations suggest that the glutaredoxin-like N-MBS1 is primarily involved in regulating the ATPase activity of CcoI, while the CopZ-like N-MBS2 is involved in Cu(I) acquisition. The interaction of CcoI with periplasmic Cu chaperones was analyzed by genetically fusing CcoI to the chaperone SenC. The CcoI-SenC fusion protein was fully functional in vivo and sufficient to provide Cu for cbb 3 -Cox maturation. In summary, our data demonstrate that CcoI provides the link between the cytosolic and periplasmic Cu chaperone networks during cbb 3 -Cox assembly.

59 BASIC BIOLOGICAL SCIENCES↗

Plant functional types broadly describe water use strategies in the Caatinga, a seasonally dry tropical forest in northeast Brazil

In seasonally dry tropical forests, plant functional type can be classified as deciduous low wood density, deciduous high wood density, or evergreen high wood density species. While deciduousness is often associated with drought-avoidance and low wood density is often associated with tissue water storage, the degree to which these functional types may correspond to diverging and unique water use strategies has not been extensively tested. We examined (a) tolerance to water stress, measured by predawn and mid-day leaf water potential; (b) water use efficiency, measured via foliar δ 13 C; and (c) access to soil water, measured via stem water δ 18 O. We found that deciduous low wood density species maintain high leaf water potential and low water use efficiency. Deciduous high wood density species have lower leaf water potential and variable water use efficiency. Both groups rely on shallow soil water. Evergreen high wood density species have low leaf water potential, higher water use efficiency, and access alternative water sources. These findings indicate that deciduous low wood density species are drought avoiders, with a specialized strategy for storing root and stem water. Deciduous high wood density species are moderately drought tolerant, and evergreen high wood density species are the most drought tolerant group. Our results broadly support the plant functional type framework as a way to understand water use strategies, but also highlight species-level differences.

54 ENVIRONMENTAL SCIENCES↗

Cyanobacteria from marine oxygen-deficient zones encode both form I and form II Rubiscos

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon into biomass. To date, all studied cyanobacterial lineages encode carbon fixation machinery relying upon form I Rubiscos within a CO 2 -concentrating carboxysome. Here, we report that the uncultivated anoxic marine zone (AMZ) IB lineage ofProchlorococcusfrom pelagic oxygen-deficient zones (ODZs) harbors both form I and form II Rubiscos, the latter of which are typically noncarboxysomal and possess biochemical properties tuned toward low-oxygen environments. We demonstrate that these cyanobacterial form II enzymes are functional in vitro and were likely acquired from proteobacteria. Metagenomic analysis reveals that AMZ IB are essentially restricted to ODZs in the Eastern Pacific, suggesting that form II acquisition may confer an advantage under low-O 2 conditions. AMZ IB populations express both forms of Rubisco in situ, with the highest form II expression at depths where oxygen and light are low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for carbon sequestration in natural and engineered systems.

Science & Technology - Other Topics↗

Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits

Abstract Climate warming is expected to stimulate plant growth in high‐elevation and high‐latitude ecosystems, significantly increasing aboveground net primary production (ANPP). However, the effects of simultaneous changes in temperature, snowmelt timing, and summer water availability on total net primary production (NPP)—and elucidation of both above‐ and belowground responses—remain an important area in need of further study. In particular, measures of belowground net primary productivity (BNPP) are required to understand whether ANPP changes reflect changes in allocation or are indicative of a whole plant NPP response. Further, plant functional traits provide a key way to scale from the individual plant to the community level and provide insight into drivers of NPP responses to environmental change. We used infrared heaters to warm an alpine plant community at Niwot Ridge, Colorado, and applied supplemental water to compensate for soil water loss induced by warming. We measured ANPP, BNPP, and leaf and root functional traits across treatments after 5 yr of continuous warming. Community‐level ANPP and total NPP (ANPP + BNPP) did not respond to heating or watering, but BNPP increased in response to heating. Heating decreased community‐level leaf dry matter content and increased total root length, indicating a shift in strategy from resource conservation to acquisition in response to warming. Water use efficiency (WUE) decreased with heating, suggesting alleviation of moisture constraints that may have enabled the plant community to increase productivity. Heating may have decreased WUE by melting snow earlier and creating more days early in the growing season with adequate soil moisture, but stimulated dry mass investment in roots as soils dried down later in the growing season. Overall, this study highlights how ANPP and BNPP responses to climate change can diverge, and encourages a closer examination of belowground processes, especially in alpine systems, where the majority of NPP occurs belowground.

54 ENVIRONMENTAL SCIENCES↗

Molar Absorptivities of U(VI), U(IV), and Pu(III) in Nitric Acid Solutions of Various Concentrations Relevant to Developing Nuclear Fuel Recycling Flowsheets

Testing of a co-decontamination (CoDCon) tributyl phosphate (TBP) based solvent extraction flowsheet is being performed to optimize conditions for achieving a target U/Pu ratio in the Pu-containing product. The flowsheet is designed to directly produce a mixture of U and Pu with a U/Pu mass ratio of 7/3. The system is monitored in real time using optical spectroscopy, which allows for control of the U/Pu ratio in the aqueous U/Pu nitrate product. On-line spectrophotometric monitoring of the aqueous stream at the reductive stripping step involves determination of U(VI), U(IV) and Pu(III) concentrations and relies on molar absorptivities of these species in nitric acid at a number of wavelengths corresponding to their peaks’ maxima. The magnitudes of these molar absorptivities are a sensitive function of nitric acid concentration and have to be determined as precisely as possible using an off-line spectrophotometry under well controlled conditions. This step (called training set acquisition) is typically performed not in a high contamination area of radiological glovebox where flow-through cells and other on-line equipment are installed but in a less aggressive environment of a radiological fume hood with much better control of stock solutions quality, dilution factors, optical absorbance scale calibration, etc. This is followed by the calibration transfer between the off-line instrument and the instrument deployed during extraction and stripping runs. This paper reports values of molar absorptivities of U(VI), U(IV), and Pu(III) in nitric acid solution of 0.5 M to 4 M concentration and compares them with available technical literature data. Results of off-line spectrophotometric analysis of selected aqueous grab samples from one of CoDCon runs show satisfactory agreement with total uranium and plutonium concentrations determined in the same samples by ICP-MS.

Sinkov, Sergey I.↗

Structural Studies of Alloyed and Nanoparticle Transition Metal Dichalcogenides by Selenium-77 Solid-State Nuclear Magnetic Resonance Spectroscopy

Layered transition metal dichalcogenides (TMDCs) such as MoS 2 , MoSe 2 , and WSe 2 are under intense investigation because they are atomically thin semiconductors with photophysical properties that can be tuned by changing their composition or morphology. Mechanochemical processing has been proposed as a method to obtain alloyed TMDCs in the series Mo 1–x W x S y Se 2–y (x = 0–1; y = 0–2). However, elucidating the chemical transformations occurring at the atomic scale following mechanochemical processing can be challenging because the products are often amorphous or microcrystalline. To address this challenge, we probe TMDC mixing and alloying by using a combination of powder X-ray diffraction, Raman spectroscopy, diffuse reflectance spectroscopy, 77 Se solid-state nuclear magnetic resonance (SSNMR) spectroscopy, and planewave density functional theory (DFT) calculations. The nature of the milling material and reaction atmosphere are shown to be essential factors in limiting the formation of undesired oxide byproducts. We demonstrate acquisition of 77 Se SSNMR spectra using different combinations of Carr-Purcell Meiboom-Gill acquisition (CPMG) pulse sequences, magic angle spinning (MAS), and MAS dynamic nuclear polarization. Further, the combination of SSNMR with the other characterization methods clearly demonstrates that high energy impact ball milling induces molecular level alloying of Mo, W and chalcogen atoms in the family Mo 1–x W x S y Se 2–y . Gauge including projector augmented wave DFT calculations yield accurate 77 Se chemical shift (CS) tensor components. 77 Se SSNMR spectroscopy was also applied to study the structure of WSe 2 nanocrystals intercalated with ethylenediamine. The intercalated WSe 2 nanocrystals exhibit a more positive isotropic 77 Se CS as compared to bulk WSe 2 , however, the 77 Se CS anisotropy is the same, confirming the WSe 2 layers have a similar structure as in their bulk counterparts.

36 MATERIALS SCIENCE↗

Illuminating gut microbiome signaling pathways that regulate host circadian rhythms

The gut microbiome affects host physiology by modulating nutrient acquisition and creating chemical signals that are received by host receptors. The molecular details of the orchestration of these microbial signaling processes remain largely unclear. We used a function-centric approach to interrogate the mechanistic links between gut microbiome metabolism and host circadian rhythms. We used rodent models, including germ-free mice, to determine how the gut microbiome influences host chronobiology by assaying metabolites in the gut and in circulation, and we used activity-based protein profiling to provide direct functional links to individual taxa. We specifically investigated how externally imposed behavioral schedules, such as feeding schedules, can desynchronize biological rhythms in metabolic organs (e.g., the gut, pancreas, and liver) from the central circadian rhythms regulated by the brain. We hypothesize that the gut microbiome creates chemical signals that can be entrained by feeding/fasting schedule to induce internal metabolic misalignment. Elaborating on the findings of this project will elucidate the chemical signals from the microbiome that modulate biological rhythms in the host’s metabolic organs.

59 BASIC BIOLOGICAL SCIENCES↗

Nutrient Dynamics in a Coupled Terrestrial Biosphere and Land Model (ELM-FATES-CNP)

We present a representation of nitrogen and phosphorus cycling in the Functionally Assembled Terrestrial Ecosystem Simulator, a demographic vegetation model within the Energy Exascale Earth System land model. This representation is modular, and designed to allow testing of multiple hypothetical approaches for carbon-nutrient coupling in plants. Novel model hypotheses introduced in this work include, (a) the controls on plant acquisition of aqueous mineralized nutrients in the soil and (b) fairly straight forward methods of allocating nutrients to specific plant organs and their losses through live plant turnover as well as litter fluxes generated through plant mortality. This combines the new with pre-existing hypotheses (such as nitrogen fixation and soil decomposition) into a system that can accommodate plant-soil dynamics for a large number of size- and functional-type-resolved plant cohorts within a time-since-disturbance-resolved ecosystem. Root uptake of nutrients is governed by fine root biomass, and plants vary in their fine root biomass allocation in order to balance carbon and nutrient limitations to growth. We test the sensitivity of the model to a wide range of parameter variations and structural representations, and in the context of observations at Barro Colorado Island, Panama. A key model prediction is that plants in the high-light-availability canopy positions allocate more carbon to fine roots than plants in low-light understory environments, given the widely different carbon versus nutrient constraints of these two niches within a given ecosystem. This model provides a basis for exploring carbon-nutrient coupling with vegetation demography within Earth system models.

54 ENVIRONMENTAL SCIENCES↗

Automated 3D cytoplasm segmentation in soft X-ray tomography

Cells’ structure is key to understanding cellular function, diagnostics, and therapy development. Soft X-ray tomography (SXT) is a unique tool to image cellular structure without fixation or labeling at high spatial resolution and throughput. Fast acquisition times increase demand for accelerated image analysis, like segmentation. Currently, segmenting cellular structures is done manually and is a major bottleneck in the SXT data analysis. This paper introduces ACSeg, an automated 3D cytoplasm segmentation model. ACSeg is generated using semi-automated labels and 3D U-Net and is trained on 43 SXT tomograms of immune T cells, rapidly converging to high-accuracy segmentation, therefore reducing time and labor. Furthermore, adding only 6 SXT tomograms of other cell types diversifies the model, showing potential for optimal experimental design. ACSeg successfully segmented unseen tomograms and is published on Biomedisa, enabling high-throughput analysis of cell volume and structure of cytoplasm in diverse cell types.

59 BASIC BIOLOGICAL SCIENCES↗

Optical and Plasmonic Properties of High-Electron-Density Epitaxial and Oxidative Controlled Titanium Nitride Thin Films

The present paper reports on the fabrication, detailed structural characterizations, and theoretical modeling of titanium nitride (TiN) and its isostructural oxide derivative, titanium oxynitride (TiNO) thin films that have excellent plasmonic properties and that also have the potential to overcome the limitation of noble metal and refractory metals. The TiNO films deposited at 700 °C in high vacuum conditions have the highest reflectance (R = ~ 95%), largest negative dielectric constant (ε 1 = –161), and maximal plasmonic figure of merit (FoM = –ε 1 /ε 2 ) of 1.2, followed by the 600 °C samples deposited in a vacuum (R = ~ 85%, ε 1 = –145, FoM = 0.8) and 700 °C–5 mTorr sample (R = ~ 82%, ε 1 = –8, FoM = 0.3). To corroborate our experimental observations, we calculated the phonon dispersions and Raman active modes of TiNO by using the virtual crystal approximation. From the experimental and theoretical studies, a multilayer optical model has been proposed for the TiN/TiNO epitaxial thin films for obtaining individual complex dielectric functions from which many other optical parameters can be calculated. The advantages of oxide derivatives of TiN are the continuation of similar free electron density as in TiN and the acquisition of additional features such as oxygen-dependent semiconductivity with a tunable bandgap.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Exoproteome and Surfaceome of Toxigenic Corynebacterium diphtheriae 1737 and Its Response to Iron Restriction and Growth on Human Hemoglobin

Toxin-producing Corynebacterium diphtheriae strains are the etiological agents of the severe upper respiratory disease, diphtheria. A global phylogenetic analysis revealed that biotype gravis is particularly lethal as it produces diphtheria toxin and a range of other virulence factors, particularly when it encounters low levels of iron at sites of infection. Here, to gain insight into how it colonizes its host, we have identified iron-dependent changes in the exoproteome and surfaceome of C. diphtheriae strain 1737 using a combination of whole-cell fractionation, intact cell surface proteolysis, and quantitative proteomics. In total, we identified 1414 of the predicted 2265 proteins (62%) encoded by its reference genome. For each protein, we quantified its degree of secretion and surface exposure, revealing that exoproteases and hydrolases predominate in the exoproteome, while the surfaceome is enriched with adhesins, particularly DIP2093. Our analysis provides insight into how components in the heme-acquisition system are positioned, showing pronounced surface exposure of the strain-specific ChtA/ChtC paralogues and high secretion of the species-conserved heme-binding HtaA protein, suggesting it functions as a hemophore. Profiling the response of the exoproteome and surfaceome after microbial exposure to human hemoglobin and iron limitation reveals potential virulence factors that may be expressed at sites of infection. Data are available via ProteomeXchange with identifier PXD051674.

cell envelope↗

Decadal changes in fire frequencies shift tree communities and functional traits

Global change has resulted in chronic shifts in fire regimes. Variability in the sensitivity of tree communities to multi-decadal changes in fire regimes is critical to anticipating shifts in ecosystem structure and function, yet remains poorly understood. Here, we address the overall effects of fire on tree communities and the factors controlling their sensitivity in 29 sites that experienced multi-decadal alterations in fire frequencies in savanna and forest ecosystems across tropical and temperate regions. Fire had a strong overall effect on tree communities, with an average fire frequency (one fire every three years) reducing stem density by 48% and basal area by 53% after 50 years, relative to unburned plots. Here, the largest changes occurred in savanna ecosystems and in sites with strong wet seasons or strong dry seasons, pointing to fire characteristics and species composition as important. Analyses of functional traits highlighted the impact of fire-driven changes in soil nutrients because frequent burning favoured trees with low biomass nitrogen and phosphorus content, and with more efficient nitrogen acquisition through ectomycorrhizal symbioses. Taken together, the response of trees to altered fire frequencies depends both on climatic and vegetation determinants of fire behaviour and tree growth, and the coupling between fire-driven nutrient losses and plant traits.

54 ENVIRONMENTAL SCIENCES↗

Towards functionalized lignin and its derivatives for high-value material applications

In pursuit of low-carbon development, the production of diverse functional materials from renewable resources, especially lignocellulosic biomass, is of vital importance. Lignin is a major component of lignocellulose, and it is nature's only true high-volume aromatic polymer, which has the advantages of biodegradability, biocompatibility, and low acquisition cost. After modification by a variety of physicochemical strategies, it can be applied as an alternative to basic industrial materials, including polyurethanes, phenolic, and epoxy resins, which stands comparably to conventional synthetic polymers in terms of both performance and reduced cost. To further unlock the potential of lignin, an alluring opportunity is the exploitation of lignin for high-value materials, especially nanomaterials, that find extensive applications in energy and environment areas. This review provides a systematic summary and perspective of research that has been devoted to lignin transformation to high-value materials, ranging from industrially well-established engineering materials to the recently emerged nanomaterials that were used for energy and environment applications. Latest cutting-edge innovations on lignin modification, controlled depolymerization, and assembly during the last five years are summarized. Structure-function relationships of lignin materials in terms of their specific applications are analyzed. Furthermore, challenges and future opportunities for lignin conversion to high-value materials are also provided. We wish this review will stimulate further advances in lignin based high-value materials, and promote “waste” into “wealth”.

36 MATERIALS SCIENCE↗

DAQExpert the service to increase CMS data-taking efficiency

The Data Acquisition (DAQ) system of the Compact Muon Solenoid (CMS) experiment at the LHC is a complex system responsible for the data readout, event building and recording of accepted events. Its proper functioning plays a critical role in the data-taking efficiency of the CMS experiment. In order to ensure high availability and recover promptly in the event of hardware or software failure of the subsystems, an expert system, the DAQ Expert, has been developed. It aims at improving the data taking efficiency, reducing the human error in the operations and minimising the on-call expert demand. Introduced in the beginning of 2017, it assists the shift crew and the system experts in recovering from operational faults, streamlining the post mortem analysis and, at the end of Run 2, triggering fully automatic recovery without human intervention. DAQ Expert analyses the real-time monitoring data originating from the DAQ components and the high-level trigger updated every few seconds. It pinpoints data flow problems, and recovers them automatically or after given operator approval. We analyse the CMS downtime in the 2018 run focusing on what was improved with the introduction of automated recovery; present challenges and design of encoding the expert knowledge into automated recovery jobs. Furthermore, we demonstrate the web-based, ReactJS interfaces that ensure an effective cooperation between the human operators in the control room and the automated recovery system. We report on the operational experience with automated recovery.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Design and commissioning of resistive foil bolometer diagnostics on the ST40 tokamak

Following successful campaigns on the compact high field spherical tokamak ST40, resistive gold foil bolometers have now been installed to measure the radiated power profile. Positioned on the midplane, two bolometer cameras offer perspectives of the horizontal and vertical planes, while the third camera, situated above the midplane, provides a vertical view of the top divertor plates, including the X-point and the strike points. Further, these cameras use a commercial off-the-shelf data acquisition platform with modules specifically designed for bolometers in a Wheatstone bridge configuration, providing both phase sensitive detection and in situ calibration. This paper presents an overview of the design and functionality of all three cameras and the commissioning of the horizontal plane camera. The commissioning of the horizontal camera shows data from a range of plasma pulses, presenting a positive correlation between the relative profiles measured from the bolometer camera and an absolute extreme ultraviolet diode camera viewing along similar lines of sight.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Regolith, rock and fluid distributions at the Upper Colorado River Basin via a multicomponent seismic imaging approach

In October 2018, we conducted an exploratory seismic survey of the East River Watershed Function Science Focus Area, near Crested Butte, CO. Our survey goals were to map seismic bedrock, regolith and sediment properties and relate them to geomorphic and hydrologic processes. We acquired ~12 km of seismic data along roads with a 72-channel, 1.25m spaced streamer, an average shot spacing of 2.5m and an average acquisition rate of 3 km/day. We also obtained ~3km of planted geophone data with geophone and shot spacing between 2.5 and 5 meters and an acquisition rate of 0.5 km/day. Vp results show a sharp transition between regolith and bedrock along hillslopes suggesting a similarly abrupt change in porosity. Vp anisotropy in the Mancos Shale is observable in the lower reaches of the watershed, but is absent in regions near crystalline intrusions where contact metamorphism has likely modified pore structure within the shale. Alluvium thickness varies along the river axis from 0 to > 20 meters reflecting variations in depositional processes as function of stream gradient. We show that when strong discontinuities at the regolith base are present, inhomogeneous waves that travel along subsurface interfaces are generated and can be measured on vertical component geophones. We present a summary manuscript in the report appendix.

58 GEOSCIENCES↗

Phase-weighted slant stacking for surface wave dispersion measurement

SUMMARY Surface wave retrieval from ambient noise records using seismic interferometry techniques has been widely used for multiscale shear wave velocity (Vs) imaging. One key step during Vs imaging is the generation of dispersion spectra and the extraction of a reliable dispersion curve from the retrieved surface waves. However, the sparse array geometry usually affects the ability for high-frequency (>1 Hz) seismic signals’ acquisition. Dispersion measurements are degraded by array response due to sparse sampling and often present smeared dispersion spectra with sidelobe artefacts. Previous studies usually focus on interferograms’ domain (e.g. cross-correlation function) and attempt to enhance coherent signals before dispersion measurement. We propose an alternative technique to explicitly deblur dispersion spectra through use of a phase-weighted slant-stacking algorithm. Numerical examples demonstrate the strength of the proposed technique to attenuate array responses as well as incoherent noise. Three different field examples prove the flexibility and superiority of the proposed technique: the first data set consists of ambient noise records acquired using a nodal seismometer array; the second data set utilizes distributed acoustic sensing (DAS) and a marine fibre-optic cable to acquire a similar ambient noise data set; the last data set is a vibrator-based active-source surface wave data. The enhanced dispersion measurements provide cleaner and higher-resolution spectra without distortions which will assist both human interpreters as well as ML algorithms in efficiently picking curves for subsequent Vs inversion.

58 GEOSCIENCES↗

CRADA Final Report: Open Microgrid Platform

Current microgrid control technology is mostly proprietary, expensive, and inflexible. An open-source, vendor-neutral, publish-subscribe controller will significantly lower the barrier to entry for new technologies and market entrants: inverter, battery, and load control manufacturers; cloud and services providers; and energy aggregators. An OpenFMB controller can significantly reduce the acquisition, integration, and ongoing operating and maintenance costs and increase revenue opportunities for energy producers and consumers. It allows distributed energy resource (DER) owners to replace individual DER components as richer-function, lower-cost devices become available or to incorporate new forecast and optimization algorithms as they are developed. A standard, secure, full-function DER field controller will also provide a low-cost means for grid operators to effectively manage the variability and uncertainty of solar photovoltaics (PV). Under the terms of this CRADA, ORNL has worked with Open Energy Solutions (OES) to advance the transition of ORNL’s existing open-source microgrid controller into a platform geared toward mainstream implementation. Using a more prevalent and memory-safe programming language, Rust, OES has converted ORNL’s current generation on-grid optimization into an application more suitable for industry use. The results of the ported optimization were analyzed by inputting the same arguments in both the current-generation and next-generation optimizers and verifying that the results were equivalent.

24 POWER TRANSMISSION AND DISTRIBUTION↗