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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2011

The Plant Cell Wall–Decomposing Machinery Underlies the Functional Diversity of Forest Fungi

Brown rot decay removes cellulose and hemicellulose from wood residual lignin contributing up to 30% of forest soil carbon and is derived from an ancestral white rot saprotrophy in which both lignin and cellulose are decomposed. Comparative and functional genomics of the dry rot fungus Serpula lacrymans, derived from forest ancestors, demonstrated that the evolution of both ectomycorrhizal biotrophy and brown rot saprotrophy were accompanied by reductions and losses in specific protein families, suggesting adaptation to an intercellular interaction with plant tissue. Transcriptome and proteome analysis also identified differences in wood decomposition in S. lacrymans relative to the brown rot Postia placenta. Furthermore, fungal nutritional mode diversification suggests that the boreal forest biome originated via genetic coevolution of above- and below-ground biota.

fungi, plant cell wall, brown rot, soil carbon, sa↗
DOE OSTI2013

A new structural framework for integrating replication protein A into DNA processing machinery

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Differential response of the photosynthetic machinery to dehydration in older and younger resurrection plants

Abstract A group of vascular plants called homoiochlorophyllous resurrection plants evolved unique capabilities to protect their photosynthetic machinery against desiccation-induced damage. This study examined whether the ontogenetic status of the resurrection plant Craterostigma pumilum has an impact on how the plant responds to dehydration at the thylakoid membrane level to prepare cells for the desiccated state. Thus, younger plants (<4 months) were compared with their older (>6 months) counterparts. Ultrastructural analysis provided evidence that younger plants suppressed senescence-like programs that are realized in older plants. During dehydration, older plants degrade specific subunits of the photosynthetic apparatus such as the D1 subunit of PSII and subunits of the cytochrome b6f complex. The latter leads to a controlled down-regulation of linear electron transport. In contrast, younger plants increased photoprotective high-energy quenching mechanisms and maintained a high capability to replace damaged D1 subunits. It follows that depending on the ontogenetic state, either more degradation-based or more photoprotective mechanisms are employed during dehydration of Craterostigma pumilum.

Plant Sciences↗
DOE OSTI2022

Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceutical compounds is a pathway to treating COVID-19. Conventional tools, e.g., cryo-electron microscopy and all-atom molecular dynamics (AAMD), do not provide sufficiently high resolution or timescale to capture important dynamics of this molecular machine. Consequently, we develop an innovative workflow that bridges the gap between these resolutions, using mesoscale fluctuating finite element analysis (FFEA) continuum simulations and a hierarchy of AI-methods that continually learn and infer features for maintaining consistency between AAMD and FFEA simulations. We leverage a multi-site distributed workflow manager to orchestrate AI, FFEA, and AAMD jobs, providing optimal resource utilization across HPC centers. Our study provides unprecedented access to study the SARS-CoV-2 RTC machinery, while providing general capability for AI-enabled multi-resolution simulations at scale.

Trifan, Anda↗
DOE OSTI2025

High-Temperature Active Magnetic Bearing Development for Supercritical CO 2 Machinery Applications

Hermetic machinery utilizing gas bearings for MW-scale supercritical CO 2 (sCO 2 ) machinery applications can have significantly lower power loss and enable improved cycle efficiency compared to conventional machinery with oil-lubricated bearings. Active magnetic bearings (AMBs) are another option anticipated to have similar power loss and load capacity to gas bearings as well as offering larger mechanical tolerances, the ability to tune properties, and high reliability due to lack of mechanical wear. AMBs also have proven commercial experience at MW-scale, though environments for high-temperature sCO 2 power cycle machinery conditions are novel. Besides the potential impact of AMBs for sCO 2 turbomachinery, the technology also offers promising benefits for steam and gas turbines for power generation, compressors and expanders for industrial heat and power, and in other oil and gas and space applications. The goals of this project were to conceptual design an AMB and perform material testing. Conceptual designs for radial and thrust AMBs were produced based on a hermetically-sealed sCO 2 machinery waste-heat recovery (WHR) application for sizing and loads, and choosing a target design temperature of 540°C useful for high-temperature sCO 2 turbines for concentrating solar power (CSP) applications. Conceptual designs were initially developed for multiple radial and thrust AMBs with spreadsheet-based calculations before selecting one of each to develop further using higher-fidelity design methods for magnetic and structural performance. It was found that the radial AMB at 540°C was feasible, but the thrust AMB needed to be limited to 315°C for high-speed operation. The decision for a reduced-temperature thrust AMB was the result of several significant conclusions: 1) Hiperco 50A, originally chosen for good magnetic performance at high temperature, had insufficient strength for high-speed operation, so it was replaced with 17-4 PH. 2) The reduced magnetic performance from 17-4 PH yielded a larger bearing size, reducing the strength margin. 3) This ultimately led to a creative design implementing a more-compact E-core topology, compared to the original (conventional) C-core, and an integral shaft-disk with Hirth joint connection. These conceptual designs are unique for the size and temperature in CO 2 , relevant for MW-scale CSP applications. Long term, high temperature test data was generated for several materials, filling a void in the current body of literature. Corrosion and magnetic performance measurements were produced for PM materials (Alnico 5-7C, Alnico 9C, and SmCo) with and without nickel-coating for environments of high-temperature CO 2 up to 550°C at atmospheric pressure and 450°C at 103 bar for up to 6,000 hours. Corrosion measurements were also produced for Hiperco 50, a SM material relevant for AMB laminations, with and without C5 coating. Comparisons were also made for 450°C and 550°C, atmospheric pressure air exposures up to 5,000 hours. Results generally show that coatings can be effective at improving oxidation resistance of the bare materials, and Alnicos generally outperformed SmCo after high-temperature exposure. In addition to technical feasibility demonstrated by the design, economic feasibility was demonstrated by updating the TEA from the reference machine, re-evaluating it with CAPEX and OPEX to reflect estimated changes from process-lubricated bearings to AMBs. AMBs were shown to be comparable in performance to process-lubricated bearings, still showing a notable improvement over conventional machinery architecture with oil-lubricated bearings.

42 ENGINEERING↗
DOE OSTI2021

The core autophagy machinery is not required for chloroplast singlet oxygen-mediated cell death in the Arabidopsis thaliana plastid ferrochelatase two mutant

Chloroplasts respond to stress and changes in the environment by producing reactive oxygen species (ROS) that have specific signaling abilities. The ROS singlet oxygen ( 1 O 2 ) is unique in that it can signal to initiate cellular degradation including the selective degradation of damaged chloroplasts. This chloroplast quality control pathway can be monitored in the Arabidopsis thaliana mutant plastid ferrochelatase two ( fc2 ) that conditionally accumulates chloroplast 1 O 2 under diurnal light cycling conditions leading to rapid chloroplast degradation and eventual cell death. The cellular machinery involved in such degradation, however, remains unknown. Recently, it was demonstrated that whole damaged chloroplasts can be transported to the central vacuole via a process requiring autophagosomes and core components of the autophagy machinery. The relationship between this process, referred to as chlorophagy, and the degradation of 1 O 2 -stressed chloroplasts and cells has remained unexplored. Results To further understand 1 O 2 -induced cellular degradation and determine what role autophagy may play, the expression of autophagy-related genes was monitored in 1 O 2 -stressed fc2 seedlings and found to be induced. Although autophagosomes were present in fc2 cells, they did not associate with chloroplasts during 1 O 2 stress. Mutations affecting the core autophagy machinery ( atg5 , atg7 , and atg10 ) were unable to suppress 1 O 2 -induced cell death or chloroplast protrusion into the central vacuole, suggesting autophagosome formation is dispensable for such 1 O 2 –mediated cellular degradation. However, both atg5 and atg7 led to specific defects in chloroplast ultrastructure and photosynthetic efficiencies, suggesting core autophagy machinery is involved in protecting chloroplasts from photo-oxidative damage. Finally, genes predicted to be involved in microautophagy were shown to be induced in stressed fc2 seedlings, indicating a possible role for an alternate form of autophagy in the dismantling of 1 O 2 -damaged chloroplasts. Conclusions Our results support the hypothesis that 1 O 2 -dependent cell death is independent from autophagosome formation, canonical autophagy, and chlorophagy. Furthermore, autophagosome-independent microautophagy may be involved in degrading 1 O 2 -damaged chloroplasts. At the same time, canonical autophagy may still play a role in protecting chloroplasts from 1 O 2 -induced photo-oxidative stress. Together, this suggests chloroplast function and degradation is a complex process utilizing multiple autophagy and degradation machineries, possibly depending on the type of stress or damage incurred.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Distinct amyloid precursor protein processing machineries of the olfactory system

Highlights: • Under healthy condition, active γ-secretase is highly expressed in the olfactory system. • During Alzheimer disease progression, the expressions of presenilin2(γ-secretases) are increased in the OE, not in the OB, in turn neurotoxic Aβ*56 is accumulated more quickly in the OE. • Distinct APP processing machineries in the OE can be a feasible biomarker for the early diagnosis of AD onset. Processing of amyloid precursor protein (APP) occurs through sequential cleavages first by β-secretase and then by the γ-secretase complex. However, abnormal processing of APP leads to excessive production of β-amyloid (Aβ) in the central nervous system (CNS), an event which is regarded as a primary cause of Alzheimer's disease (AD). In particular, gene mutations of the γ-secretase complex—which contains presenilin 1 or 2 as the catalytic core—could trigger marked Aβ accumulation. Olfactory dysfunction usually occurs before the onset of typical AD-related symptoms (eg, memory loss or muscle retardation), suggesting that the olfactory system may be one of the most vulnerable regions to AD. To date however, little is known about why the olfactory system is affected so early by AD prior to other regions. Thus, we examined the distribution of secretases and levels of APP processing in the olfactory system under either healthy or pathological conditions. Here, we show that the olfactory system has distinct APP processing machineries. In particular, we identified higher expressions levels and activity of γ-secretase in the olfactory epithelium (OE) than other regions of the brain. Moreover, APP c-terminal fragments (CTF) are markedly detected. During AD progression, we note increased expression of presenilin2 of γ-secretases in the OE, not in the OB, and show that neurotoxic Aβ*56 accumulates more quickly in the OE. Taken together, these results suggest that the olfactory system has distinct APP processing machineries under healthy and pathological conditions. This finding may provide a crucial understanding of the unique APP-processing mechanisms in the olfactory system, and further highlights the correlation between olfactory deficits and AD symptoms.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Edge-cloud computing performance benchmarking for IoT based machinery vibration monitoring

Advances in low cost and reliable sensing, connectivity (Internet of Things), computational power, and advanced analytics, are leading to a new wave of innovation in machinery status sensing and condition monitoring. Significant research efforts are directed towards cloud computing architectures. However, given the latency, bandwidth, cost, security, and privacy concerns, further supported by the ever-increasing capabilities of edge computing devices, there is a need to consider both edge and cloud computing together to make informed decisions based upon context and performance. In this work, we present an edge-cloud performance evaluation for IoT based machinery vibration monitoring, to foster deployment for the contexts considered.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors

Xyloglucans are highly substituted and recalcitrant polysaccharides found in the primary cell walls of vascular plants, acting as a barrier against pathogens. Here, we reveal that the diverse and economically relevant Xanthomonas bacteria are endowed with a xyloglucan depolymerization machinery that is linked to pathogenesis. Using the citrus canker pathogen as a model organism, we show that this system encompasses distinctive glycoside hydrolases, a modular xyloglucan acetylesterase and specific membrane transporters, demonstrating that plant-associated bacteria employ distinct molecular strategies from commensal gut bacteria to cope with xyloglucans. Notably, the sugars released by this system elicit the expression of several key virulence factors, including the type III secretion system, a membrane-embedded apparatus to deliver effector proteins into the host cells. Together, these findings shed light on the molecular mechanisms underpinning the intricate enzymatic machinery of Xanthomonas to depolymerize xyloglucans and uncover a role for this system in signaling pathways driving pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes dissociation of the S1 domains and exposure of the fusion machinery, although the molecular details of this process have yet to be observed. We report the development of bottom-up coarse-grained (CG) models consistent with cryo-electron tomography data, and the use of CG molecular dynamics simulations to investigate viral binding and S2 core exposure. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces in a manner distinct from binding between soluble proteins, which processively induces S1 dissociation. We also simulate possible variant behavior using perturbed CG models, and find that ACE2-induced S1 dissociation is primarily sensitive to conformational state populations and the extent of S1/S2 cleavage, rather than ACE2 binding affinity. These simulations reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides

Here, RNA interference (RNAi) is a conserved mechanism of genome defence that can also have a role in the regulation of endogenous functions through endogenous small RNAs (esRNAs). In fungi, knowledge of the functions regulated by esRNAs has been hampered by lack of clear phenotypes in most mutants affected in the RNAi machinery. Mutants of Mucor circinelloides affected in RNAi genes show defects in physiological and developmental processes, thus making Mucor an outstanding fungal model for studying endogenous functions regulated by RNAi. Some classes of Mucor esRNAs map to exons (ex-siRNAs) and regulate expression of the genes from which they derive. To have a broad picture of genes regulated by the silencing machinery during vegetative growth, we have sequenced and compared the mRNA profiles of mutants in the main RNAi genes by using RNA-seq. In addition, we have achieved a more complete phenotypic characterization of silencing mutants Deletion of any main RNAi gene provoked a deep impact in mRNA accumulation at exponential and stationary growth. Genes showing increased mRNA levels, as expected for direct ex-siRNAs targets, but also genes with decreased expression were detected, suggesting that, most probably, the initial ex-siRNA targets regulate the expression of other genes, which can be up- or down-regulated. Expression of 50% of the genes was dependent on more than one RNAi gene in agreement with the existence of several classes of ex-siRNAs produced by different combinations of RNAi proteins. These combinations of proteins have also been involved in the regulation of different cellular processes. Besides genes regulated by the canonical RNAi pathway, this analysis identified processes, such as growth at low pH and sexual interaction that are regulated by a dicer -independent non-canonical RNAi pathway. In conclusion, this work shows that the RNAi pathways play a relevant role in the regulation of a significant number of endogenous genes in M. circinelloides during exponential and stationary growth phases and opens up an important avenue for in-depth study of genes involved in the regulation of physiological and developmental processes in this fungal model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Recombineering machinery to increase homology directed genome editing in thermophilic microbes

A native Type I-B and heterologous Type II Clustered Regularly-Interspaced Short Palindromic Repeat/cas systems were developed and characterize to improve the ability to engineer C. thermocellum and other thermophilic microbes. The native Type I-B system was engineered for genome editing. For the Type I-B system, an engineered strain, termed LL1586, yielded 40% genome editing efficiency at the pyrF locus. When recombineering machinery was expressed the efficiency was increased to 71%. For the Type II GeoCas9 system, 12.5% genome editing efficiency was observed. When recombineering machinery was expressed, this increased to 94%. By combining the thermophilic CRISPR system (either Type I-B or Type II) with the recombinases, a new tool was developed that allows for efficient CRISPR editing. The tools provided herein enable CRISPR technologies to better engineer C. thermocellum, including engineering C. thermocellum for both increased lignocellulose degradation and biofuel production.

Eckert, Carrie↗
DOE OSTI2024

Non-Invasive Biophysical Techniques to Monitor the Structural Plasticity of the Photosynthetic Machinery of Live Diatom Cells

The photosynthetic performance of diatoms depends largely on the organization and structural flexibility of their thylakoid membranes, the densely packed, highly organized membrane vesicles in which light reactions of photosynthesis occur. Different regulatory mechanisms that fine tune the photosynthetic functions affect the organization of the photosynthetic machinery at different levels of structural complexity, from the level of individual protein complexes to the macroarray of membrane proteins and the remodeling of the entire thylakoid membrane system. To monitor these reorganizations, non-invasive techniques are of special value. In this chapter, we focus our attention on three of these techniques, which have been demonstrated to provide unique and useful information on the structure and structural and functional plasticity of live diatom cells: (i) circular dichroism (CD) spectroscopy, which has provided unique information on the chiral (macro-)organization of protein complexes and on their rapid, reversible reorganizations, fine-tuning the light-harvesting processes, as well as on variations in the short-range excitonic interactions in the antenna complexes; (ii) small-angle neutron scattering (SANS), which has been used to determine the periodic organization of the thylakoid membranes and to monitor reversible ultrastructural changes on the time-scale of minutes, induced by variations in the environmental conditions such as changes in temperature or light intensity; and (iii) electrochromic shift absorbance transients (ΔA ECS ), a spectroscopic tool which has been shown to be capable of identifying distinct functional groups of the light-harvesting carotenoid fucoxanthin in different diatoms and in cells exposed to different light intensities. Future use of these techniques will most certainly contribute to the deeper understanding of key regulatory mechanisms of photosynthesis in diatoms.

Szabo, Milan↗
DOE OSTI2015

Developmental exposure to 50 parts-per-billion arsenic influences histone modifications and associated epigenetic machinery in a region- and sex-specific manner in the adult mouse brain

Epidemiological studies report that arsenic exposure via drinking water adversely impacts cognitive development in children and, in adults, can lead to greater psychiatric disease susceptibility, among other conditions. While it is known that arsenic toxicity has a profound effect on the epigenetic landscape, very few studies have investigated its effects on chromatin architecture in the brain. We have previously demonstrated that exposure to a low level of arsenic (50 ppb) during all three trimesters of fetal/neonatal development induces deficits in adult hippocampal neurogenesis in the dentate gyrus (DG), depressive-like symptoms, and alterations in gene expression in the adult mouse brain. As epigenetic processes control these outcomes, here we assess the impact of our developmental arsenic exposure (DAE) paradigm on global histone posttranslational modifications and associated chromatin-modifying proteins in the dentate gyrus and frontal cortex (FC) of adult male and female mice. DAE influenced histone 3 K4 trimethylation with increased levels in the male DG and FC and decreased levels in the female DG (no change in female FC). The histone methyltransferase MLL exhibited a similar sex- and region-specific expression profile as H3K4me3 levels, while histone demethylase KDM5B expression trended in the opposite direction. DAE increased histone 3 K9 acetylation levels in the male DG along with histone acetyltransferase (HAT) expression of GCN5 and decreased H3K9ac levels in the male FC along with decreased HAT expression of GCN5 and PCAF. DAE decreased expression of histone deacetylase enzymes HDAC1 and HDAC2, which were concurrent with increased H3K9ac levels but only in the female DG. Levels of H3 and H3K9me3 were not influenced by DAE in either brain region of either sex. These findings suggest that exposure to a low, environmentally relevant level of arsenic during development leads to long-lasting changes in histone methylation and acetylation in the adult brain due to aberrant expression of epigenetic machinery based on region and sex. - Highlights: • Brain tissue from adult mice with developmental arsenic exposure (DAE) was used. • DAE impacted histone methylation and associated methyltransferases based on sex. • DAE differentially altered histone acetylation based on brain region. • DAE altered HATs in males and HDACs in females. • Epigenetic modifier expression correlated with the associated histone modification.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2010

Dynamin-like protein 1 at the Golgi complex: A novel component of the sorting/targeting machinery en route to the plasma membrane

The final step in the liberation of secretory vesicles from the trans-Golgi network (TGN) involves the mechanical action of the large GTPase dynamin as well as conserved dynamin-independent fission mechanisms, e.g. mediated by Brefeldin A-dependent ADP-ribosylated substrate (BARS). Another member of the dynamin family is the mammalian dynamin-like protein 1 (DLP1/Drp1) that is known to constrict and tubulate membranes, and to divide mitochondria and peroxisomes. Here, we examined a potential role for DLP1 at the Golgi complex. DLP1 localized to the Golgi complex in some but not all cell lines tested, thus explaining controversial reports on its cellular distribution. After silencing of DLP1, an accumulation of the apical reporter protein YFP-GL-GPI, but not the basolateral reporter VSVG-SP-GFP at the Golgi complex was observed. A reduction in the transport of YFP-GL-GPI to the plasma membrane was confirmed by surface immunoprecipitation and TGN-exit assays. In contrast, YFP-GL-GPI trafficking was not disturbed in cells silenced for BARS, which is involved in basolateral sorting and trafficking of VSVG-SP-GFP in COS-7 cells. Our data indicate a new role for DLP1 at the Golgi complex and thus a role for DLP1 as a novel component of the apical sorting machinery at the TGN is discussed.

60 APPLIED LIFE SCIENCES↗