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At least 1,333 records · Page 74

Links between autophagy and lipid droplet dynamics

Abstract Autophagy is a catabolic process in which cytoplasmic components are delivered to vacuoles or lysosomes for degradation and nutrient recycling. Autophagy-mediated degradation of membrane lipids provides a source of fatty acids for the synthesis of energy-rich, storage lipid esters such as triacylglycerol (TAG). In eukaryotes, storage lipids are packaged into dynamic subcellular organelles, lipid droplets. In times of energy scarcity, lipid droplets can be degraded via autophagy in a process termed lipophagy to release fatty acids for energy production via fatty acid β-oxidation. On the other hand, emerging evidence suggests that lipid droplets are required for the efficient execution of autophagic processes. Here, we review recent advances in our understanding of metabolic interactions between autophagy and TAG storage, and discuss mechanisms of lipophagy. Free fatty acids are cytotoxic due to their detergent-like properties and their incorporation into lipid intermediates that are toxic at high levels. Thus, we also discuss how cells manage lipotoxic stresses during autophagy-mediated mobilization of fatty acids from lipid droplets and organellar membranes for energy generation.

59 BASIC BIOLOGICAL SCIENCES↗

Knocksideways in plants: an inducible system for in planta visualization of protein interactions

Understanding protein-protein interactions (PPIs) is key to unlocking the secrets of various cellular processes. While many tools have been developed to detect PPIs, such as the yeast two-hybrid assay, bimolecular fluorescence complementation, and affinity purification, there is great demand for additional methods to complement existing ones. As all approaches have limitations, evidence from at least two independent assays is required to validate PPIs. In a Breakthrough Report, Joanna Winkler and colleagues present here a promising method, named “knocksideways in plants” (KSP), for inducible visualization of PPIs in planta.

59 BASIC BIOLOGICAL SCIENCES↗

Inducing thermodynamically blocked atomic ordering via strongly driven nonequilibrium kinetics

Ultrafast light-matter interactions enable inducing exotic material phases by promoting access to kinetic processes blocked in equilibrium. Despite potential opportunities, actively using nonequilibrium kinetics for material discovery is limited by the poor understanding on intermediate states of driven systems. Here, using single-pulse time-resolved imaging with x-ray free-electron lasers, we found intermediate states of photoexcited bismuth nanoparticles that showed kinetically reversed surface ordering during ultrafast melting. This entropy-lowering reaction was further investigated by molecular dynamics simulations to reveal that observed kinetics were thermodynamically buried in equilibrium, which emphasized the critical role of electron-mediated ultrafast free-energy modification in inducing exotic material phases. This study demonstrated that ultrafast photoexcitations of electrons provide an efficient strategy to induce hidden material phases by overcoming thermodynamic barriers via nonequilibrium reaction pathways.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass, Avena fatua. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of Thaumarch aeota and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). In conclusion, our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats.

54 ENVIRONMENTAL SCIENCES↗

Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme Thermophile Caldicellulosiruptor bescii

To develop functional metabolic engineering platforms for nonmodel microorganisms, a comprehensive understanding of the physiological and metabolic characteristics is critical. Caldicellulosiruptor bescii and other species in this genus have untapped potential for conversion of unpretreated plant biomass into industrial fuels and chemicals. The highly interactive and complex machinery used by C. bescii to acquire and process complex carbohydrates contained in lignocellulose was elucidated here to complement related efforts to develop a metabolic engineering platform with this bacterium.

comparative genomics↗

Social Evolution and Cheating in Plant Pathogens

Plant pathogens are a critical component of the microbiome that exist as populations undergoing ecological and evolutionary processes within their host. Many aspects of virulence rely on social interactions mediated through multiple forms of public goods, including quorum-sensing signals, exoenzymes, and effectors. Virulence and disease progression involve life-history decisions that have social implications with large effects on both host and microbe fitness, such as the timing of key transitions. Considering the molecular basis of sequential stages of plant–pathogen interactions highlights many opportunities for pathogens to cheat, and there is evidence for ample variation in virulence. Case studies reveal systems where cheating has been demonstrated and others where it is likely occurring. Harnessing the social interactions of pathogens, along with leveraging novel sensing and -omics technologies to understand microbial fitness in the field, will enable us to better manage plant microbiomes in the interest of plant health.

Plant Sciences↗

rmon (Resource monitor) [SWR-24-128]

The resource monitor application provides monitoring, collection, and visualization of resource utilization in compute nodes. This package contains utilities to monitor system resource utilization (CPU, memory, disk, network). Here are the ways you can use it: -Monitor resource utilization for a compute node for a given set of resource types and process IDs. -Start a process and monitor its resource utilization. -Monitor resource utilization for a compute node asynchronously with the ability to dynamically change the resource types and process IDs being monitored. -Produce JSON reports of aggregated metrics. -Produce interactive HTML plots of the statistics.

Thom, Daniel [National Renewable Energy Laboratory↗

Self-assembly for electronics

Self-assembly, a process in which molecules, polymers, and particles are driven by local interactions to organize into patterns and functional structures, is being exploited in advancing silicon electronics and in emerging, unconventional electronics. Additionally, silicon electronics has relied on lithographic patterning of polymer resists at progressively smaller lengths to scale down device dimensions. Yet, this has become increasingly difficult and costly. Assembly of block copolymers and colloidal nanoparticles allows resolution enhancement and the definition of essential shapes to pattern circuits and memory devices. As we look to a future in which electronics are integrated at large numbers and in new forms for the Internet of Things and wearable and implantable technologies, we also explore a broader material set. Semiconductor nanoparticles and biomolecules are prized for their size-, shape-, and composition-dependent properties and for their solution-based assembly and integration into devices that are enabling unconventional manufacturing and new device functions.

36 MATERIALS SCIENCE↗

The mechanical response of micron-sized molecular crystals

Abstract Microstructures and corresponding properties of compacted powders ultimately depend on the mechanical response of individual particles. In principle, computational simulations can predict the results of powder compaction processes, but the selection of appropriate models for both particle–particle interactions and particle deformations across all relevant length scales remain nontrivial tasks, especially in material systems lacking detailed mechanical property information. The work presented here addresses these issues by conducting uniaxial compressions in situ inside of a scanning electron microscope to characterize the mechanical response of individual micron-sized particles of a molecular crystal, hexanitrohexaazaisowurtzitane (CL-20). This experimental approach enabled the collection of quantitative force and displacement data alongside simultaneous imaging to capture morphology changes. The results reveal information about elastic deformation, yield, plastic deformation, creep, and fracture phenomena. Accordingly, this work demonstrates a generalizable approach for assessing the mechanical response of individual micron-sized molecular crystal particles and utilizing those responses in particle-level models. Graphic abstract

36 MATERIALS SCIENCE↗

Chemical Recommender System: Replacement Suggestions for Small Molecules

The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.

Nair, Parthiv Anand [Sandia National Laboratories ↗

Hybrid Ceramic-CMC Vane with EBC for Future Coal Derived Syngas Fired 65% Efficient Turbine Combined Cycle

The efficiency of both simple cycle and combined cycle power generation systems scale with the peak temperature at which the gas exits the combustor to drive the turbine. In conventional systems, a substantial fraction of the total turbine core flow exiting the compressor is diverted downstream to cool metallic turbine hardware rather than power the turbine, much of which is used to cool the first-stage turbine vane. The use of coal derived syngas fuels provides an additional challenge to the lifetime of materials utilized in the turbine, as particulate byproducts created in the coal gasification process melt in the combustion gas, and can subsequently deposit and interact with the turbine hardware. The development of durable hot-section materials capable of operating at temperature well above that of single crystal superalloy airfoil/zirconia based thermal barrier coatings is critical to realizing 65% efficient coal derived syngas fired gas turbine based power systems. To enable higher turbine inlet temperatures while lowering cooling air requirements, United Technologies Research Center (UTRC), the central R&D laboratory supporting UT Pratt & Whitney, led the conceptual design of a new type of ceramic composite turbine hot section materials system. The design focused on a novel hybrid monolithic ceramic-fiber reinforced ceramic matrix composite (CMC) first stage turbine vane having an environmental barrier coating. By utilizing ceramic construction in the turbine hot-section, the core flow normally used to cool metallic components will be substantially reduced, increasing efficiency and reducing emissions. To provide the framework for future demonstration testing, UTRC partnered with University of North Dakota Energy and Environmental Research Center (UNDEERC) to provide a conceptual design for a gasified coal fed high-pressure turbine combustor system designed to mimic the conditions expected in a future 65% fuel to busbar efficient syngas fueled gas turbine based combined cycle. The UNDEERC and UTRC collaborated on characterizing dusts from coal gasifier filtration systems.

10 SYNTHETIC FUELS↗

Subcomponent Validation of Composite Joints for the Marine Energy Advanced Materials Project

The Marine Energy Advanced Materials project is an ongoing multi-year, multi-lab project with the main goals of addressing barriers and uncertainties facing marine energy developers in adopting advanced materials for structural applications. NREL's goals of the project were to address subcomponents testing needs for marine energy materials, to improve understanding of design allowables at the full-scale and provide near net-scale static and fatigue data of composite subcomponents using materials applicable to the marine energy industry. In the long term, the test method development and data generated would be used to inform standards development. This report outlines perhaps one of the largest-scale studies conducted with regards to saltwater conditioning of various composite material subcomponents and their subsequent structural validation, specifically directed at the marine renewable energy industry. A variety of fiberglass composite panels with epoxy and vinyl ester epoxy resin systems were manufactured at Montana State University, which were then used to manufacture an array of different types of subcomponent test specimens at the National Renewable Energy Laboratory's Flatirons Campus. These subcomponents were in the form of T-bolt and double-ended-insert specimens, which were intended to represent bonded and mechanical bolted connections for thick composite laminates, metal-metal and composite lap shear specimens to evaluate adhesion of constituent materials, and adhesive beam-shear specimens as part of an effort to better evaluate the characteristics of thick adhesive bondlines. Overall, the materials used were fiberglass reinforced epoxy and vinyl ester matrix composites, epoxy and methacrylate adhesives, and 316 and 2507 stainless steels. Specimens were then conditioned in salt water at various temperatures and for various periods of time at Florida Atlantic University and Pacific Northwest National Laboratory. All specimens were then mechanically characterized and validated using various test methods under static and fatigue loading conditions at NREL's Structural Technology Laboratory. Throughout the conditioning and mechanical validation process, valuable experience was gained, which will help guide future test method development for marine energy materials. In many instances, the results indicated similar observations as to what had been observed during previous coupon scale characterization efforts that provided a vital understanding of the scale up process. However in some instances, unexpected phenomena were observed, such as interactions between the adhesives and 316 steel. Furthermore, some materials exhibited significant degradation due to the saltwater conditioning. Ultimately, this report provides a detailed summary of the specimens that were designed, the subcomponent test methods that were developed, and the results that were generated, which will serve as important guidance for marine renewable energy developers and researchers for future structural designs and validation.

16 TIDAL AND WAVE POWER↗

Large-Volume Stimulation of Rock for Greatly Enhanced Fluids Recovery using Targeted Seismic-Assisted Hydraulic Fracturing (Final Technical Report)

This project has developed and demonstrated a new technology for large-volume and targeted comminution of rock in low permeability formations to enhance recovery from unconventional oil and gas (UOG) resources. The technology is based on a strategically designed interaction of multiple induced seismic pulses that assist the hydraulic fracturing process to enhance shear and multi-planar crack formation. This greatly increased rock stimulation, through bulk comminution, is expected to cause significant increase in permeability leading to enhancement of recovery factors for sub- surface fluids. The proposed technology is especially applicable for enhanced recovery in emerging UOG plays, such as ductile shales that are resistant to opening-mode fracturing by conventional hydraulic fracturing processes. The project combines an integrated experimental and computation approach to develop and demonstrate a modular technology that can be easily implement in the field to augment current practices. The effort integrates a fundamental scientific understanding of dynamic material response under constraint and damage-induced permeability and porosity enhancements at multiple length scales, along with models of comminution due to the local release of kinetic energy associated with high shear strain rate of dynamic deformation. The results will be validated through small-scale experiments and then implemented in a lab-scale field test to demonstrate the developed technology. The project involves collaboration between a solid mechanician, a materials scientist, and a petroleum engineering geo-mechanician. It builds on a successful history of success and collaboration that includes both fundamental scientific exploration and technology development.

04 OIL SHALES AND TAR SANDS↗

Beyond Price-Taker: Multiscale Optimization of a Wind-Battery Integrated Energy System within the Wholesale Electricity Market

This work presents the optimization of a wind-battery IES using the multiscale optimization framework proposed in our previous work to quantify errors from the price-taker assumption. The framework, built over Prescient (an open-source package for solving production cost models), is applied to the RTS-GMLC dataset, an open-source dataset that is representative of the southwest U.S. wholesale electricity market. The framework provides detailed bidding, market clearing, and control processes of an IES, and it can quantify how the IES interacts with the market. In this work, we use the retrofit of a wind farm with a battery storage system as an example to show the difference in the market outcomes and revenues obtained from both price-taker and multiscale optimization approaches. Our work goes beyond price-taker and deep dives into quantifying IES-market interaction in optimizing IES. This framework enables users to explore how different design and operation decisions of energy systems interact with the market and provides a more accurate evaluation than the price-taker assumption.

Chen, Xinhe↗

Next-Generation Parametrically Induced QUantum Engineering (PIQUE 2.0) (Final Technical Report)

This final technical report summarizes the key accomplishments on the project Next-Generation Parametrically-Induced QUantum Engineering (PIQUE) , a BES-funded award received by PI Archana Kamal at University of Massachusetts Lowell. The focus of this award was to enable new quantum information processing functionalities for multi-qubit entanglement and control, using parametric interactions in superconducting quantum circuits.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Beyond the Standard Model physics prospects at the Deep Underground Neutrino Experiment

The Deep Underground Neutrino Experiment (DUNE) is an international project for neutrino physics and proton-decay searches, currently in the design and planning stages. Once built, DUNE will consist of two detectors exposed to the world's most intense neutrino beam. The near detector at Fermilab will record neutrino interactions near the beginning of the beam line. The other, much larger, detector, comprising four 10-kton liquid argon time projection chambers (LArTPCs), will be installed at a depth of 1.5 km at the Sanford Underground Research Facility in South Dakota, about 1,300 km away from the neutrino source. The unique combination of the high-intensity neutrino beam, DUNE's high-resolution near detector system, and massive LArTPC far detector enables a variety of probes of Beyond-the-Standard-Model (BSM) physics, from the discovery of new particles (sterile neutrinos or dark matter), to precision tests of beyond the three-flavor mixing paradigm, non-standard neutrino interactions (NSIs), heavy neutral leptons, and the detailed study of rare processes (e.g., neutrino trident production). This article reviews these physics topics and discusses the prospects for their discovery at the DUNE experiment.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Summary Data for paper titled: Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

59 BASIC BIOLOGICAL SCIENCES↗

Data for Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry: Summary Data

Climate change is causing an increase in drought in many soil ecosystems and a loss of soil organic carbon. Calcareous soils may partially mitigate these losses via carbon capture and storage. Here, we aimed to determine how irrigation-supplied soil moisture and perennial plants impact biotic and abiotic soil properties that underpin deep soil carbon chemistry in an unfertilized calcareous soil. Soil was sampled up to one meter in depth from irrigated and planted field treatments and analyzed using a suite of omics and chemical analyses. Carbon cycling processes in the surface soil were dominated by plant-microbe interactions that drive organic carbon cycling, whereas inorganic carbon chemistry dominated in deeper soil layers. Both irrigation and plant cover impacted organic and inorganic carbon pools in the soil profiles. This study reveals the complex interactions between water, plants, minerals, and microorganisms that govern organic and inorganic pools of soil carbon at different depths.

Naasko, Katherine I↗