Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “pathway analysis”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Targeted inhibition of MASTL kinase activity induces apoptosis in breast cancer

Microtubule-associated serine/threonine kinase-like (MASTL) (or Greatwall kinase (GWL)) is an important cell cycle regulating kinase that regulates the G2-M transition. Uncontrolled MASTL activity is implicated in breast cancer progression. To date, very few inhibitors have been reported against this protein. Here, structure-based computational modeling indicates that the natural product flavopiridol (FLV) binds strongly to MASTL and these results are validated using molecular dynamics simulation studies. Further, an in vitro kinase assay reveals an EC 50 (effective concentration) value of FLV to be 82.1 nM and a better IC 50 compared to the positive reference compound, staurosporine. FLV is found to inhibit MASTL kinase activity, arresting the cell growth in the G1 phase and inducing apoptosis in breast cancer cells. Consistent with these results differential gene expression obtained using RNA sequencing studies, and validated by RT PCR and immunoblot analysis, indicate that MASTL inhibition induces cell cycle arrest and apoptotic-related genes. Furthermore, metastasis- and inflammation- related genes are downregulated. Thus, the deregulation of MASTL signaling pathways on targeted inhibition of its kinase activity is revealed. This study lays a strong foundation for investigating FLV as a lead compound in breast cancer therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale

Many industrial chemicals that are produced from fossil resources could be manufactured more sustainably through fermentation. In this work, we describe the development of a carbon-negative fermentation route to producing the industrially important chemicals acetone and isopropanol from abundant, low-cost waste gas feedstocks, such as industrial emissions and syngas. Using a combinatorial pathway library approach, we first mined a historical industrial strain collection for superior enzymes that we used to engineer the autotrophic acetogen Clostridium autoethanogenum. Next, we used omics analysis, kinetic modeling and cell-free prototyping to optimize flux. Finally, we scaled-up our optimized strains for continuous production at rates of up to ~3 g/L/h and ~90% selectivity. Life cycle analysis confirmed a negative carbon footprint for the products. Unlike traditional production processes, which result in release of greenhouse gases, our process fixes carbon. These results show that engineered acetogens enable sustainable, high-efficiency, high-selectivity chemicals production. We expect that our approach can be readily adapted to a wide range of commodity chemicals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Field-driven ion pairing dynamics in concentrated electrolytes

Here, we investigate ion pairing dynamics in electrolytes driven far from equilibrium using molecular simulations and nonequilibrium rate theory. Focusing on 0.5M LiPF 6 in water and acetonitrile under uniform electric fields, we compute transition path theory observables, including reactive fluxes and mean first-passage times of ion pairing. Moreover, we introduce a dynamical proxy of free-ion population, where its field-induced change is strongly correlated with the nonlinear enhancement of conductivity, yielding an increase of 40% at 50 mV/Å in acetonitrile, compared to that of less than 10% in aqueous electrolytes. Further kinetic analysis elucidates that Onsager’s classical theory substantially overestimates field-induced enhancement of ion pair dissociation in molecular electrolytes. This discrepancy arises from solvent-mediated dynamical pathways and field-induced dielectric decrement that suppress ion pair dissociation within explicit solvents, highlighting that a faithful description of molecular details is essential. Our results provide a molecular interpretation of nonlinear electrolyte transport beyond continuum theories and establish a general framework for quantifying nonequilibrium reaction kinetics in condensed phase systems.

Moon, Seokjin [University of California, Berkeley,↗
DOE OSTI2024

The impact of regional resources and technology availability on carbon dioxide removal potential in the United States

To achieve net zero carbon emissions by mid-century, the United States may need to rely on carbon dioxide removal (CDR) to offset emissions from difficult-to-decarbonize sectors and/or shortfalls in near-term mitigation efforts. CDR can be delivered using many approaches with different requirements for land, water, geologic carbon storage capacity, energy, and other resources. The availability of these resources varies by region in the U.S. suggesting that CDR deployment will be uneven across the country. Using the global change analysis model for the United States (GCAM-USA), we modeled six classes of CDR and explored their potential using four scenarios: a scenario where all the CDR pathways are available (Full Portfolio), a scenario with restricted carbon capture and storage (Low CCS), a scenario where the availability of bio-based CDR options is limited (Low Bio), and a scenario with constraints on enhanced rock weathering (ERW) capabilities (Low ERW). We find that by employing a diverse set of CDR approaches, the U.S. could remove between 1 and 1.9 GtCO 2 /yr by midcentury. In the Full Portfolio scenario, direct air carbon capture and storage (DACCS) predominates, delivering approximately 50% of CO 2 removal, with bioenergy with carbon capture and storage contributing 25%, and ERW delivering 11.5%. Texas and the agricultural Midwest lead in CDR deployment due to their abundant agricultural land and geological storage availability. In the Low CCS scenario, reliance on DACCS decreases, easing pressure on energy systems but increasing pressure on the land. In all cases CDR deployment was found to drive important impacts on energy, land, or materials supply chains (to supply ERW, for example) and these effects were generally more pronounced when fewer CDR technologies were available.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗
DOE OSTI2026

Multi‐season analysis reveals hundreds of drought‐responsive genes in sorghum

Persistent drought affects global crop production and is becoming more severe in many parts of the world in recent decades. Deciphering how plants respond to drought will facilitate the development of flexible mitigation strategies. Sorghum bicolor L. Moench (sorghum), a major cereal crop and an emerging bioenergy crop, exhibits remarkable resilience to drought. To better understand the molecular traits that underlie sorghum's remarkable drought tolerance, we undertook a large-scale sorghum gene expression profiling effort, totaling nearly 1500 transcriptome profiles, across a 3-year field study with replicated plots in California's Central Valley. This study included time-resolved gene expression data from roots and leaves of two sorghum genotypes, BTx642 and RTx430, with different pre-flowering and post-flowering drought-tolerance adaptations under control and drought conditions. Quantification of genotype-specific drought tolerance effects was enabled by de novo sequencing, assembly, and annotation of both BTx642 and RTx430 genomes. These reference-quality genomes were used to construct a pangene set for characterizing conserved and genotype-specific expression. By integrating time-resolved transcriptomic responses to drought in the field across three consecutive years, we identified a set of 726 drought-responsive genes that responded similarly in all 3 years of our field study. Functional enrichment analysis identified abiotic stress, secondary cell wall-related processes and metabolism as particularly affected under both types of drought stress. We also found that some glyoxylate cycle pathway genes, including malate synthase and isocitrate lyase, are differentially regulated particularly during post-flowering drought stress, implicating this pathway as potentially important for drought responsiveness. This expansive dataset represents a unique resource for sorghum and drought research communities and provides a methodological framework for the integration of multi-faceted time-resolved transcriptomic datasets.

Cole, Benjamin [USDOE Joint Genome Institute (JGI)↗
DOE OSTI2022

Opportunities for Recovering Resources from Municipal Wastewater

Municipal wastewater contains valuable resources including water, energy, and nutrients that often enter and leave wastewater treatment plants (WWTPs) without being captured. Currently, plants are increasingly seeking to recover resources and reuse them in a sustainable way. Therefore, the purpose of this project was to assess the potential for recovery and reuse of water and products from municipal wastewater treatment plants across the United States and to examine how this potential varies by region. To accomplish this, three main tasks were set: first, to characterize wastewater treatment plants; second, to characterize technologies and pathways used to recover energy, nutrients, and water from treatment plants; third, to assess the demand for reclaimed resources and products at a regional level by performing spatial analysis. These three tasks were then synthesized to present key findings in this report and a geospatial dataset with the hope of guiding the increased use of resource recovery technologies in the U.S.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Rapid AI-based Dissection of Ashes using Raman and XRF Spectroscopy (RADAR-X)

Waste-to-energy (WTE) facilities incinerate ~35 million tons of municipal solid waste annually in the United States. The incineration process reduces the mass and the volume of the waste fraction by over 75 and 95%, respectively. The fraction left after incineration remains as ash residues and is referred to as WTE ash, compromising of bottom and fly ash. In the United States, ~10 million tons of WTE ashes are generated annually and predominantly landfilled because of the lack of secondary end-use pathways. This incurs a significant financial burden (landfilling costs) on U.S. WTE facilities and also results in the loss of materials to the landfill. The primary objective of this research is to understand better the elemental and mineralogical composition of WTE ashes from diverse origins and find composition dependent upcycling pathways for diverting these ashes from landfills. This primary objective was addressed through three research tasks –(Task I) An AI-led Multi-Modal Approach for Compositional Analysis, (Task II) Developing a Dissolution-Based Test for Real Time Analysis, and (Task III) Establishing composition-dependent end uses. The chemical composition of WTE ash is dependent on two factors, i.e., the input waste composition and the operational parameters of a WTE facility (combustion conditions). Amongst these two factors, the input waste composition will likely show spatial and temporal variation. As a result, the chemical composition of WTE ash will also fluctuate. To understand the spatial and temporal variation in WTE ash composition, in Task I, we collected 128 ash samples (62 bottom ash and 66 fly ash samples) from 11 WTE facilities located in 11 U.S. states and characterized them via X-ray Fluorescence, powder X-ray Diffraction, and Raman Spectroscopy. The findings from this extensive characterization work indicated that the key elements in WTE fly ashes are Ca, Cl (greater than 10 wt. %), Si, S, K, Zn ( between 1 and 10 wt. %), Mg, Al, P, Ti, Fe, Cu, Br, and Pb (between 0.1 and 1 wt. %). Similarly, the key elements in WTE bottom ash fraction finer than 45μm are Ca (greater than 10 wt. %), Mg, Al, Si, S, Cl, K, Ti, Fe, Zn (between 1 and 10 wt. %), P, V, Cr, Mn, Cu, Br, and Pb (between 0.1 and 1 wt. %). Here, we note that the dominant fraction of WTE bottom ash is the coarse fraction. The coarse WTE bottom ash fraction (rich in silicon) was not characterized in this study because of excessive grinding requirements and their unsuitability as a supplementary cementitious material due to their coarse nature. The elements in WTE bottom ashes are present as calcite, anhydrite, vaterite, hydroxyapatite, quartz, bassanite, gehlenite, akermanite, hydrocalumite, and portlandite. Similarly, the mineralogical species present in WTE fly ashes are calcium chloride hydroxide, halite, calcite, anhydrite, sylvite, hydrocalumite, vaterite, hannebachite, quartz, and bassanite. Temporal variation in ash composition may also result in significant fluctuations in chemical compositions. Therefore, a WTE facility may need to monitor the ash composition (elemental and mineralogical composition) in real time. In Task I, we evaluated the possibility of using a portable X-ray fluorescence (XRF) spectrometer to monitor the elemental composition in real-time. Specifically, we collected XRF data on identical specimens via a portable XRF spectrometer (low-end) and a lab-based benchtop XRF spectrometer (high-end). The collected data was used to train an A.I. algorithm (portable XRF data as an input and benchtop XRF data as an output) to predict accurate elemental composition using portable XRF data. Finally, we developed a 2-minute photobleaching protocol to monitor the mineralogical characteristics of WTE ashes via Raman spectroscopy. Overall, the activities in Task I improved our understanding of ash composition and developed techniques to monitor elemental and mineralogical composition in near real-time. Based on the findings of Task I, we find that WTE ashes exhibit wide variability in mineralogy. For ICP-based elemental analysis, all the mineralogical species in WTE ashes must be brought into solution. This is traditionally accomplished with acid digestion using a combination of multiple acids. However, acid digestion with multiple acids is time-consuming and often fails to ensure complete digestion of the ash matrix. To address this limitation, in Task II, we developed an alkali-fusion-based digestion protocol using a combination of lithium tetraborate, lithium metaborate, and their combinations as possible alkali fluxes for digesting WTE ashes entirely and rapidly. The validity of the developed method was evaluated on two standard ash specimens, i.e., SRM 1633c coal fly ash and BCR-176R incineration fly ash specimen. The findings suggest that the developed protocol can ensure complete digestion of elements such as Al, Ba, Ca, Cr, Cu, Mg, Mn, P, Sr, V, Zn, Be, K, and rare earth elements. The recent changes in the energy market towards renewables and increased metal recycling have resulted in reduced supplies of supplementary cementitious materials (coal fly ash and slag). Therefore, in Task III, we evaluated the possibility of employing WTE ashes as SCMs. As the chemical composition of WTE ashes varies temporally (on an hourly basis), there was also a need to develop tests that can evaluate the suitability of material to act as supplementary cementitious material rapidly, i.e., in a few minutes. Therefore, in Task II, we also developed a rapid test to assess the suitability of a material to act as an SCM in 5 minutes. This represents a significant advance over the state-of-the-art R 3 test, which takes ~144 hours. This test was initially validated on amorphous aluminosilicates, such as calcined clays, and could be extended to evaluate other industrial by-products, such as WTE ashes. In Task III, we evaluated the possibility of employing WTE ashes for two applications, i.e., as an SCM and a lime substitute for clay stabilization. The findings from Task I indicated that WTE ashes are enriched in chlorine and, therefore, cannot be used directly as an SCM due to corrosion-related risks and altered hydration kinetics. Accordingly, we developed an ash treatment protocol to reduce the solubility of chlorine-containing species in WTE ashes. The developed treatment protocol also immobilized lead in certain mineral forms. As a result of the treatment, WTE ashes can be used as SCMs without any corrosion or heavy metal leaching concerns. The second application examined in this study was clay stabilization. WTE ashes are calcium-rich and can be an adequate lime replacement for clay stabilization. Our findings reveal that the sum of the concentrations of Ca(OH) 2 and CaClOH controls the clay stabilization capability of WTE ashes. In summary, in this work, we evaluated the elemental and mineralogical characteristics of U.S. WTE ashes from diverse origins and developed tests to evaluate the chemical characteristics of these ashes in real time through a portable XRF and a benchtop Raman spectrometer. Based on the chemical characteristics of these ashes, we developed an ash treatment process to enable the use of WTE ashes as an SCM and also evaluated the possibility of employing these ashes for clay stabilization. Overall, the findings from this work enables the diversion of WTE ashes from landfills for multiple end-uses, i.e., as an SCM or a lime substitute for clay stabilization.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Unraveling the Threads of Environmental Justice in Critical Mineral Extraction: A Framework for Regionalized Life Cycle Data

As we transition to a more sustainable energy system, the extraction and processing of critical minerals becomes increasingly important. However, these industries often raise concerns about environmental and social impacts, particularly in disadvantaged communities. To address these concerns, our research focuses on regionalizing environmental life cycle data to connect it with communities affected by mineral extraction. A framework was developed for collecting life cycle background data that supports the Justice40 Toolset, a market-based approach to evaluating net benefits and costs of critical mineral material recovery pathways. A goal was to alleviate public skepticism around mineral extraction processes, including secondary and unconventional feedstocks, by highlighting both environmental and social impacts. To achieve this, computational analysis and geospatial data science techniques were employed, such as within-scale and across-scale methods and proxy dataset usage. By doing so, we were able to develop a framework for identifying and disaggregating data down to regions small enough to support Justice40 goals. Our approach not only provides valuable tools fo insight into the environmental implications of mineral extraction but also helps policymakers evaluate the social impacts on local communities. This research contributes to a more just and equitable transition to a sustainable energy system, ensuring that marginalized voices are heard in decision-making process.

Davis, Tyler [NETL Site Support Contractor, Nation↗
DOE OSTI2026

Boride-based Ceramic Super-high Temperature Thermocouples in Harsh Environments (Final Scientific/Technical Report)

An electromotive force (emf) can be generated along a temperature gradient between the cold end and hot end of a thermoelectric material, termed the Seebeck effect. Based on the Seebeck effect, metallic alloys have been extensively employed to detect temperatures for centuries, named thermocouples. However, commercially available thermocouple alloys suffer from limitations, such as oxidation, chemical degradation, and poor long-term stability under high-temperature harsh environments. This DOE-funded project aimed to develop high-temperature, chemically tolerant thermocouples suitable for operation in extreme environments relevant to semiconducting thermoelectric materials. The research focused on boride-based semiconducting thermoelectric compounds as candidates for next-generation thermocouples with enhanced oxidation resistance, chemical stability, and thermal robustness under conditions representative of charcoal-fired electricity facilities. During the funded years, boride materials were synthesized using an arc-plasma technique under ambient air and argon atmospheres, enabling scalable and cost-effective production compared with conventional boride fabrication methods. The synthesized borides were processed into nanostructured powders, followed by consolidation into dense bulk materials using a spark plasma sintering (SPS) bottom-up approach. Comprehensive characterization was performed, including microstructural analysis, electrical transport measurements, and optical and thermal property evaluation. Both p-type and n-type boride electric legs were fabricated and integrated into boride-based thermocouples. The thermal and irradiation stabilities of the boride nanomaterials and bulk thermoelectric materials were systematically evaluated to assess suitability for long-term operation in harsh environments. Additionally, 12 students were broadly hands-on trained spanning the full research workflow, including word processing and technical editing (e.g., LATEX for manuscript and poster preparation), data collection and analysis (using Python and related libraries and hardware interfaces), sample preparation (including arc-plasma synthesis and spark plasma sintering), and advanced characterization techniques (such as X-ray diffraction, UV–vis spectroscopy, electron microscopy, differential thermal analysis (DTA), and Seebeck coefficient measurements, etc). Overall, this project demonstrated the feasibility of boride-based thermoelectric materials as durable high-temperature thermocouples, providing a promising pathway toward robust temperature sensing technologies aligned with DOE energy infrastructure and extreme-environment monitoring needs.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2020

Silencing Folylpolyglutamate Synthetase1 (FPGS1) in Switchgrass (Panicum virgatum L.) Improves Lignocellulosic Biofuel Production

Switchgrass (Panicum virgatum L.) is a lignocellulosic perennial grass with great potential in bioenergy field. Lignocellulosic bioenergy crops are mostly resistant to cell wall deconstruction, and therefore yield suboptimal levels of biofuel. The one-carbon pathway (also known as C1 metabolism) is critical for polymer methylation, including that of lignin and hemicelluloses in cell walls. Folylpolyglutamate synthetase (FPGS) catalyzes a biochemical reaction that leads to the formation of folylpolyglutamate, an important cofactor for many enzymes in the C1 pathway. In this study, the putatively novel switchgrass PvFPGS1 gene was identified and its functional role in cell wall composition and biofuel production was examined by RNAi knockdown analysis. The PvFPGS1-downregulated plants were analyzed in the field over three growing seasons. Transgenic plants with the highest reduction in PvFPGS1 expression grew slower and produced lower end-of-season biomass. Transgenic plants with low-to-moderate reduction in PvFPGS1 transcript levels produced equivalent biomass as controls. There were no significant differences observed for lignin content and syringyl/guaiacyl lignin monomer ratio in the low-to-moderately reduced PvFPGS1 transgenic lines compared with the controls. Similarly, sugar release efficiency was also not significantly different in these transgenic lines compared with the control lines. However, transgenic plants produced up to 18% more ethanol while maintaining congruent growth and biomass as non-transgenic controls. Severity of rust disease among transgenic and control lines were not different during the time course of the field experiments. Altogether, the unchanged lignin content and composition in the low-to-moderate PvFPGS1-downregulated lines may suggest that partial downregulation of PvFPGS1 expression did not impact lignin biosynthesis in switchgrass. In conclusion, the manipulation of PvFPGS1 expression in bioenergy crops may be useful to increase biofuel potential with no growth penalty or increased susceptibility to rust in feedstock.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Two Alternative Splicing Variants of AtERF73/HRE1, HRE1α and HRE1β, Have Differential Transactivation Activities in Arabidopsis

AtERF73/HRE1 is an AP2/ERF transcription factor in Arabidopsis and has two distinct alternative splicing variants, HRE1α and HRE1β. In this study, we examined the differences between the molecular functions of HRE1α and HRE1β. We found that HRE1α and HRE1β are both involved in hypoxia response and root development and have transactivation activity. Two conserved motifs in the C-terminal region of HRE1α and HRE1β, EELL and LWSY-like, contributed to their transactivation activity, specifically the four E residues in the EELL motif and the MGLWS amino acid sequence at the end of the LWSY-like motif. The N-terminal region of HRE1β also showed transactivation activity, mediated by the VDDG motif, whereas that of HRE1α did not. The transactivation activity of HRE1β was stronger than that of HRE1α in Arabidopsis protoplasts. Both transcription factors transactivated downstream genes via the GCC box. RNA-sequencing analysis further supported that both HRE1α and HRE1β might regulate gene expression associated with the hypoxia stress response, although they may transactivate different subsets of genes in downstream pathways. Our results, together with previous studies, suggested that HRE1α and HRE1β differentially transactivate downstream genes in hypoxia response and root development in Arabidopsis.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Investigating the impact of donor atoms of single-source precursors on f-element nanomaterial formation and mechanisms of initial bond cleavage

Nanotechnology is advancing exponentially, with novel discoveries and applications emerging every day across various fields, including environmental remediation, biomedicine, electronics, and textiles. Nanoparticles (NPs) are defined as particles with sizes ranging from 1 to 100 nm, and their properties are influenced by factors such as composition, phase, size, and shape. Single-source precursors (SSPs) offer a promising method for controlling the synthesis of phase-pure nanoparticles with the desired stoichiometry and have been successfully applied to prepare transition metal and lanthanide NPs. SSPs are molecular compounds that contain all the necessary components to form the final nanomaterial and decompose under mild conditions, such as heating, to create the solid-state product. The objective of this work was to garner a mechanistic understanding of cerium oxide NP formation from cerium SSPs. To achieve these goals, first, ligands with oxygen and sulfur donor atoms were synthesized; among the array of ligands synthesized, some were novel. These ligands were then chelated to cerium ions to synthesize cerium precursors. Initially, known cerium alkoxide precursors were synthesized. Subsequently, these basic cerium complexes were further manipulated through acid-base protonolysis reactions to install a diverse set of ligands. Within this body of work, 10 novel cerium precursors were successfully synthesized. The ligands and the SSPs were analyzed using nuclear magnetic resonance (NMR) and thermogravimetric analysis coupled with differential scanning calorimetry (TGA-DSC). These SSPs were then introduced to a collision-induced dissociation mass spectrometer (CID-MS), and their dissociation pathways were studied.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
DOE OSTI2021

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, a-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.

Arabidopsis, arogenate dehydratases, lignin, multi↗
DOE OSTI2022

The contribution of bioenergy to the decarbonization of transport: a multi-model assessment

The expected growth in the demand for passenger and freight services exacerbates the challenges of reducing transport GHG emissions, especially as commercial low-carbon alternatives to petroleum fuels are limited for shipping, air and long-distance road travel. Biofuels can offer a pathway to significantly reduce emissions from these sectors, as they can easily substitute for conventional liquid fuels in internal combustion engines. In this paper, we assess the potential of bioenergy to reduce transport GHG emissions through an analysis leveraging various integrated assessment models and scenarios, as part of the 33rd Energy Modeling Forum study (EMF-33). Furthermore, we find that bioenergy can contribute a significant, albeit not dominant, proportion of energy supply to the future transport sector: in scenarios aiming to keep the temperature increase below 2 °C by the end of the twenty-first century, models project that in 2100 bioenergy can provide on average 42 EJ/yr (ranging from 5 to 85 EJ/yr) for transport (compared to 3.7 EJ in 2018), mainly through lignocellulosic fuels. This makes up 9–62% of final transport energy use. Only a small amount of bioenergy is projected to be used in transport through electricity and hydrogen pathways, with a larger role for biofuels in road passenger transport than in freight. The association of carbon capture and storage (CCS) with bioenergy technologies (BECCS) is a key determinant in the role of biofuels in transport, because of the competition for biomass feedstock to provide other final energy carriers along with carbon removal. Among models that consider CCS in the biofuel conversion process the average market share of biofuels is 21% in 2100 (ranging from 2 to 44%), compared to 10% (0–30%) for models that do not. Cumulative direct emissions from the transport sector account for half of the emission budget (from 306 to 776 out of 1,000 GtCO 2 ). However, the carbon intensity of transport decreases as much as other energy sectors in 2100 when accounting for process emissions, including carbon removal from BECCS. Lignocellulosic fuels become more attractive for transport decarbonization if BECCS is not feasible for any energy sectors. Since global transport service demand increases and biomass supply is limited, its allocation to and within the transport sector is uncertain and sensitive to assumptions about political as well as technological and socioeconomic factors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

An Analysis Framework for Distribution Network DER Integration Analysis in India: Distributed Solar in Tamil Nadu

This report is part of a two-part series that represents a year-long collaboration with the Tamil Nadu Generation and Distribution Corporation Limited (TANGEDCO) on power sector planning. The first report in this series, the Pathways for Tamil Nadu’s Electric Power Sector 2017-2030 report outlines NREL’s work with TANGEDCO's electricity sector planning department to develop a model of the State’s power system and evaluate multiple scenarios of system growth given resource constraints, costs of technologies, and power sector policies. This second report in this series focuses on the rapidly transforming distribution network in the State. The report outlines a framework developed by NREL with TANGEDCO's distribution utility to quickly and accurately analyze the impacts of integrating renewable energy, specifically rooftop solar PV onto Tamil Nadu's distribution system. Together these studies help to prepare Tamil Nadu for a rapidly transforming power system.

14 SOLAR ENERGY↗
DOE OSTI2023

Functional analysis of a conserved site mutation in the DNA end processing enzyme PNKP leading to ataxia with oculomotor apraxia type 4 in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved glutamine (Gln) in PNKP leads to late-onset ataxia with oculomotor apraxia type 4 (AOA4) in humans and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant versus WT PNKP are comparable; however, cells expressing mutant PNKP and peripheral blood mononuclear cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break accumulation and consequent activation of the DNA damage response. Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DNA damage response due to persistent accumulation of double-strand breaks in the mutant cells, triggering death of vulnerable brain cells—a potential cause of neurodegeneration in AOA4 patients.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Stochastic simulations of temporally and spatially variable Fe cycling within a floodplain aquifer

This data package contains model input and output files for local and global sensitivity analysis (SA) of a reactive transport model simulating redox cycling within a floodplain aquifer. The reaction network is implemented in CrunchFlow and focuses on spatially and temporally heterogeneous Fe cycling, though it contains several other species and redox pathways (37 aqueous species and 7 minerals in total). The package contains data from 600 Monte Carlo simulations (for global SA) and 104 one-at-a-time simulations (for local SA). It includes all input files required to run the CrunchFlow model, as well as limited model output – .csv files containing time series of primary species concentrations at 21 grid cells within the domain. These time series files contain the following species: H+, CO32-, SO42-, Cl-, Ca2+, Mg2+, Na+, K+, Fe(II), Fe(III), HS-, CH3COO-, O2(aq), S(aq), and Br-.These data were used to demonstrate the application of a novel form of global SA, distance-based generalized sensitivity analysis (DGSA) to a reactive transport model. The 2D model simulates the export of reduced species from pockets of fine-grained, organic-rich sediments embedded in a coarse sand aquifer. Stochastic simulations jointly varied 17 key model input parameters across several orders of magnitude, including the spatial variability of each parameter. DGSA on the model results reveal that the amplitude and variability of exported Fe(II) are most sensitive to the interaction between sand permeability and individual reaction rates. By contrast, the propagation of reducing conditions downgradient from the fine-grained lenses depends most heavily on the rate of dissolved organic carbon and sulfate release from the fines.

54 ENVIRONMENTAL SCIENCES↗