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DOE OSTI2024

Advanced Flexible Transformers

Advanced grid solutions are comprised of advanced transmission technologies and grid enhancing technologies. In this webinar, experts will provide participants with insights into eight advanced grid solutions. The advanced transmission technologies that will be discussed include point-to-point high voltage direct current and advanced conductoring and the grid enhancing technologies that experts will explore include topology optimization, advanced power flow control, dynamic line rating, energy storage, virtual power plants, and advanced flexible transformers

flexible power transformer, power flow controller,↗
DOE OSTI2021

The nth-plant scenario for blended feedstock conversion and preprocessing nationwide: biorefineries and depots

The sustainability of the biofuel industry depends on the development of a mature conversion technology on a national level that can take advantage of the economies of scale: the nth-plant. Defining the future location and supply logistics of conversion plants is imperative to ultimately transform the nation’s renewable biomass resources into cost-competitive, high-performance feedstock for production of biofuels and bioproducts. Since the US has put restrictions on production levels of conventional biofuels from edible resources, the nation needs to plan for the widespread accessibility and development of the cellulosic biofuel scenario. Conventional feedstock supply systems will be unable to handle cellulosic biomass nationwide, making it essential to expand the industry with an advanced feedstock supply system incorporating a distributed network of preprocessing depots and conversion plants, or biorefineries. Current studies are mostly limited to designing supply systems for specific regions of the country. We developed a national database with potential locations for depots and biorefineries to meet the nation’s target demand of cellulosic biofuel. Blended feedstock with switchgrass and corn stover (harvested by either a two- or three-pass method) are considered in a Mixed Integer Linear Programming model to deliver on-spec biomass that considers both, a desired quantity and quality at the biorefinery. A total delivered feedstock cost that is less than $79.07/dt (2016$) is evaluated for years 2022, 2030, and 2040. In 2022, 124 depots and 59 biorefineries could be supplied with 42.8 million dt of corn stover and switchgrass. In 2030 and 2040, the total accessible biomass could increase to 215% and 393% respectively when compared to 2022. However, an $8/dry tons reduction in targeted delivery cost could reduce total accessible biomass by 67%. Kansas, Nebraska, South Dakota and Texas were identified as potential states with a strong biofuel economy given that they had six or more biorefineries located in all scenarios. In some scenarios, Colorado, Alabama, Georgia, Minnesota, Mississippi and South Carolina would greatly benefit from a depot network as these could only deliver to a biorefinery in a nearby state. To elaborate the impact of a nationwide consideration, the findings were compared with existing literature for different US regions. We also present results for biorefinery capacities that are double, triple, and quadruple in size.

09 BIOMASS FUELS↗
DOE OSTI2020

Imaging of multiple fluorescent proteins in canopies enables synthetic biology in plants

Reverse genetics approaches have revolutionized plant biology and agriculture. Phenomics has the prospect of bridging plant phenotypes with genes, including transgenes, to transform agricultural fields. Genetically encoded fluorescent proteins (FPs) have revolutionized plant biology paradigms in gene expression, protein trafficking and plant physiology. While the first instance of plant canopy imaging of green fluorescent protein (GFP) was performed over 25 years ago, modern phenomics has largely ignored fluorescence as a transgene expression device despite the burgeoning FP colour palette available to plant biologists. Here, we show a new platform for stand-off imaging of plant canopies expressing a wide variety of FP genes. The platform-the fluorescence-inducing laser projector (FILP)-uses an ultra-low-noise camera to image a scene illuminated by compact diode lasers of various colours, coupled with emission filters to resolve individual FPs, to phenotype transgenic plants expressing FP genes. Each of the 20 FPs screened in plants were imaged at >3 m using FILP in a laboratory-based laser range. We also show that pairs of co-expressed fluorescence proteins can be imaged in canopies. The FILP system enabled a rapid synthetic promoter screen: starting from 2000 synthetic promoters transfected into protoplasts to FILP-imaged agroinfiltrated Nicotiana benthamiana plants in a matter of weeks, which was useful to characterize a water stress-inducible synthetic promoter. FILP canopy imaging was also accomplished for stably transformed GFP potato and in a split-GFP assay, which illustrates the flexibility of the instrument for analysing fluorescence signals in plant canopies.

abiotic stress↗
DOE OSTI2022

Rays for Roots - Integrating Backscatter X-Ray Phenotyping, Modeling and Genetics to Increase Carbon Sequestration and Switchgrass Resource Use (Final Report)

To increase carbon (C) deposition in the soil and enhance crop resource use efficiency, characterizing root form and function is essential. Several root and soil traits have been linked to increased root-to-soil C transfer. Technology that could provide high-resolution characterization of many of these traits in field conditions would revolutionize our ability to study and understand how to increase C sequestration. In this effort, we developed an initial early prototype backscatter X-ray system for non-destructive imaging of root traits. We collected initial backscatter X-ray data in field and lab settings and carried out early analysis of these data. Along with this prototype, we also developed a suite of root phenotyping approaches including advanced minirhizotron image analysis, soil core imaging, and mesocosm imaging. Minirhizotron (MR) tubes are clear tubes inserted into the soil in the field and used to image roots and the surrounding soil. Our team has developed deep learning-based methods that can segment roots from soil that can learn from imprecise image-level labels. The ability to learn or fine-tune our deep learning algorithms from image-level labels allows easier and faster application of these approaches to new locations and new plant species. We have successfully implemented and applied our MR analysis approaches to thousands of switchgrass MR images collected across geographical regions. An advantage of MR imaging is the ability to collect root and soil images over time. Our soil core analysis included collecting hundreds of soil core samples from harvested switchgrass fields and imaging these cores with both X-ray CT and backscatter X-ray imaging. Initial segmentation approaches for the X-ray CT images of these cores have been developed and applied. An advantage of soil core analysis is that it preserves the three-dimensional structures of the roots and soil in the core collected. Our group also developed photogrammetry-based mesocosm root imaging and phenotyping approaches. In this approach, a plant was grown in a large mesocosm with a three-dimensional grid of thin supporting lines inserted throughout the mesocosm. After the plant (and, correspondingly, the root architecture is grown and established) the soil media was removed and the supporting lines approximately preserved the three-dimensional root architecture. Then, we applied photogrammetry techniques to create a three-dimensional digital representation of the root architecture for which we developed analysis algorithms including skeletonization. We carried out our phenotyping development with powerful switchgrass resources and physiological and agroecosystem modeling to deliver novel technology. This project contributes to multiple ARPA-E missions including reduction of foreign imports of energy, reduction of energy-related emissions including greenhouse gases, and ensuring that the United States maintains a technological lead in developing and deploying advanced energy technology. Furthermore, the developed tools could transform public and private plant breeding and could be broadly applicable to other crops and, potentially, other application areas. Our team of engineers, plant and soil scientists, and modelers i) developed an early prototype backscatter X-ray platform that can operate in field conditions; ii) developed a suite of root phenotyping and characterization approaches as described above; iii) developed and carried out plant biology and physiology roots studies and; iv) developed and implemented mechanistic physiological modeling.

42 ENGINEERING↗
DOE OSTI2020

Safety-Related Instrumentation & Control Pilot Upgrade Initiation Phase Implementation Report

This research report (1) describes the process followed and products developed during the SR I&C Pilot Project Initial Scoping Phase, and (2) captures lessons learned. Exelon Generation and LWRS collaborated to develop a Digital Transformation Strategy as part of a larger Advanced Concept of Operations. The proposed SR I&C Pilot Upgrade provides a foundation stone for this Digital Transformation that will improve plant safety, reliability, and operational performance while lowering plant Total Cost of Ownership (TCO). Initial Scoping Phase activities for this Pilot Project have been performed in accordance with industry processes that have been adapted to better support digital upgrades. These processes include IP-ENG-001, Standard Design Process (SDP) [Reference 2], NISP-EN-04, Standard Digital Engineering Process (SDEP) [Reference 3], and Electric Power Research Institute (EPRI) Report 3002011816, Digital Engineering Guide (DEG). Completing Initial Scoping Phase Engineering and Operations, Licensing, and Project Management Activities was necessary to sufficiently bound the scope, schedule, and estimated cost of the Project to enable utility management to authorize moving into the Conceptual Design Phase. A significant finding of the Business Case Analysis (BCA) methodology developed and applied as part of this effort was that the growth rate of material costs for sustaining the operation of obsolete SR I&C equipment is accelerating. This directly contributed to the Project Economic Analysis created to justify continuing the Project. Project Initial Scoping Phase lessons learned have also been captured to assist the larger industry in understanding the Digital Transformation Strategy and SR I&C Pilot Project Initial Scoping Phase efforts. This is in keeping with the public/private partnership that has been established between the Department of Energy (DOE) and Exelon for this effort with engagement from the NRC. By addressing first-of-a-kind (FOAK) risks and capturing lessons learned, the SR I&C Pilot Upgrade Project addresses technical, regulatory, and business risks to enable subsequent implementers of similar upgrades.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2020

Safety-Related Instrumentation and Control Pilot Upgrade (Initial Scoping Phase Implementation Report)

This research report (1) describes the process followed and products developed during the SR I&C Pilot Project Initial Scoping Phase, and (2) captures lessons learned. Exelon Generation and LWRS collaborated to develop a Digital Transformation Strategy as part of a larger Advanced Concept of Operations. The proposed SR I&C Pilot Upgrade provides a foundation stone for this Digital Transformation that will improve plant safety, reliability, and operational performance while lowering plant Total Cost of Ownership (TCO). Initial Scoping Phase activities for this Pilot Project have been performed in accordance with industry processes that have been adapted to better support digital upgrades. These processes include IP-ENG-001, Standard Design Process (SDP), NISP-EN-04, Standard Digital Engineering Process (SDEP), and Electric Power Research Institute (EPRI) Report 3002011816, Digital Engineering Guide (DEG). Completing Initial Scoping Phase Engineering and Operations, Licensing, and Project Management Activities was necessary to sufficiently bound the scope, schedule, and estimated cost of the Project to enable utility management to authorize moving into the Conceptual Design Phase. A significant finding of the Business Case Analysis (BCA) methodology developed and applied as part of this effort was that the growth rate of material costs for sustaining the operation of obsolete SR I&C equipment is accelerating. This directly contributed to the Project Economic Analysis created to justify continuing the Project. Project Initial Scoping Phase lessons learned have also been captured to assist the larger industry in understanding the Digital Transformation Strategy and SR I&C Pilot Project Initial Scoping Phase efforts. This is in keeping with the public/private partnership that has been established between the Department of Energy (DOE) and Exelon for this effort with engagement from the NRC. By addressing first-of-a-kind (FOAK) risks and capturing lessons learned, the SR I&C Pilot Upgrade Project addresses technical, regulatory, and business risks to enable subsequent implementers of similar upgrade.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Diverse organic carbon dynamics captured by radiocarbon analysis of distinct compound classes in a grassland soil

Soil organic carbon (SOC) is a large, dynamic reservoir composed of a complex mixture of plant- and microbe-derived compounds with a wide distribution of cycling timescales and mechanisms. The distinct residence times of individual carbon components within this reservoir depend on a combination of factors, including compound reactivity, mineral association, and climate conditions. To better constrain SOC dynamics, bulk radiocarbon measurements are commonly used to trace biosphere inputs into soils and to estimate timescales of SOC cycling. However, understanding the mechanisms driving the persistence of organic compounds in bulk soil requires analyses of SOC pools that can be linked to plant sources and microbial transformation processes. Here, we adapt approaches, previously developed for marine sediments, to isolate organic compound classes from soils for radiocarbon ( 14 C) analysis. We apply these methods to a soil profile from an annual grassland in Hopland, California (USA), to assess changes in SOC persistence with depth (down to 1 m). We measured the radiocarbon values of water-extractable organic carbon (WEOC), total lipid extracts (TLEs), total hydrolyzable amino acids (AAs), and an acid-insoluble (AI) fraction from bulk and physically separated size fractions (< 2 mm, 2 mm–63 µm, and < 63 µm). Our results show that Δ 14 C values of bulk soil, size fractions, and extracted compound classes became more depleted with depth, and individual SOC components have distinct age–depth distributions that suggest distinguishable cycling rates. We found that AAs and TLEs cycle faster than the bulk soils and the AI fraction. The AI was the most 14 C-depleted fraction, indicating that it is the most chemically inert in this soil. Our approach enables the isolation and measurement of SOC fractions that separate functionally distinct SOC pools that can cycle relatively quickly (e.g., plant and microbial residues) from more passive or inert SOC pools (associated with minerals or petrogenic) from bulk soils and soil physical fractions. With the effort to move beyond SOC bulk analysis, we find that compound class 14 C analysis can improve our understanding of SOC cycling and disentangle the physical and chemical factors driving OC cycling rates and persistence.

58 GEOSCIENCES↗
DOE OSTI2022

Safety-Related Instrumentation and Control Pilot Upgrade: Initial Scoping Phase Implementation and Lessons Learned

In May 2016, the U.S. Nuclear Regulatory Commission (NRC) staff provided a digital instrumentation and control (I&C) regulatory infrastructure integrated action plan to the NRC for approval. One of the objectives of that plan was to establish a clear regulatory structure with reduced regulatory uncertainty to enable the expanded safe use of digital I&C in commercial nuclear reactors while continuing to ensure safety and security. To achieve this end, the NRC, with collaboration from industry, developed a streamlined License Amendment Request Alternate Review (AR) process for safety-related (SR) digital I&C upgrades. In spite of this effort, the industry has remained reluctant to perform such I&C upgrades because of perceived regulatory and financial risks associated with being the first or an early adopter of the AR process for SR I&C upgrades. The U.S. Department of Energy Light Water Reactor Sustainability Program at the Idaho National Laboratory performed Initial Scoping Phase research to help break this impasse by supporting a SR I&C Pilot Upgrade, working with MPR Associates, ScottMadden Inc., and Exelon Generation. Exelon’s Limerick Generating Station (LGS) was selected as the target for this research. This paper summarizes the Initial Scoping Phase engineering and operations, licensing, and project management activities necessary to bound the scope, schedule, and estimated cost of the project sufficiently to enable utility management authorization of Conceptual Design Phase activities. These efforts and associated products are intended to provide a template to support larger industry efforts to perform similar upgrades as a foundation stone for a digital transformation that will improve plant safety, reliability, and operational performance while lowering plant total cost of ownership. As a result of the combined effort of Exelon Generation and research participants, Conceptual Design Phase activities for the subject upgrade at LGS were approved by Exelon. Further, the U.S. Department of Energy also awarded a $50 million cost share award to Exelon in order to pave the way for SR I&C modernization and associated control room upgrades across the U.S. nuclear fleet. Additional research reports are planned for the Conceptual Design Phase, Detailed Design Phase, and the Implementation Phase of the LGS project to document the process followed and promulgate lessons learned to industry.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2026

Rewinding evolution in planta: A Rubisco-null platform validates high-performance ancestral enzymes

Improving the photosynthetic enzyme Rubisco is a key target for enhancing C3 crop productivity, but progress has been hampered by the difficulty of evaluating engineered variants in planta without interference from the native enzyme. Here, we report the creation of a Rubisco-null Nicotiana tabacum platform by using CRISPR-Cas9 to knock out all 11 nuclear-encoded small subunit (rbcS) genes. Knockout was achieved in a line expressing cyanobacterial Rubisco from the plastid genome, allowing the recovery of viable plants. We then developed a chloroplast expression system for coexpressing both large and small subunits from the plastid genome. We expressed two resurrected ancestral Rubiscos from the Solanaceae family. The resulting transgenic plants were phenotypically normal and accumulated Rubisco to wild-type levels. Importantly, kinetic analyses of the purified ancestral enzymes revealed they possessed a 16 to 20% higher catalytic efficiency (k cat,air /K c,air ) under ambient conditions, driven by a significantly faster turnover rate (k cat,air ). We have demonstrated that our system allows robust in vivo assessment of novel Rubiscos and that ancestral reconstruction is a powerful strategy for identifying superior enzymes to improve photosynthesis in C3 crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Safety-Related Instrumentation and Control Pilot Upgrade: Conceptual - Detailed Design Phase Report and Lessons Learned

Historically, regulatory barriers have precluded nuclear plant safety-related (SR) Instrumentation and Control (I&C) system modernizations. These barriers have been largely addressed by industry and United States Nuclear Regulatory Commission (NRC) efforts, including development of the License Amendment Request (LAR) Alternate Review (AR) process for digital I&C upgrades. The U.S. Department of Energy (DOE) and the Idaho National Laboratory (INL) are supporting a SR I&C pilot upgrade at the Limerick Generating Station (LGS) to demonstrate this process and capturing associated lessons learned for the benefit of industry. In 2021, a paper summarizing lessons learned as captured in INL/EXT-20-59809, Safety Related Instrumentation & Control Pilot Upgrade Initial Scoping Phase Implementation Report and Lessons Learned was presented at the 12th NPIC & HMIT conference. It is recommended that readers of this paper review reference 1 or the associated Nuclear Journal paper for context. This paper summarizes activities performed and lessons learned for the conceptual design phase and portions of the detailed design phase as captured in INL/RPT-23-XXXX, “Safety-Related Instrumentation and Control Pilot Upgrade: Conceptual - Detailed Design Phase Report and Lessons Learned.” The portions of the effort covered by reference 2 include conceptual design phase activities from December 2020, through completion in November 2021, and detailed design activities through September 2022. These efforts and associated detailed documentation in reference 3 are intended to support similar industry upgrades as a foundation stone for a Digital Transformation that will improve plant safety, reliability, and operational performance while lowering plant total cost of ownership.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Complete Evaluation of ION Cost Reduction Opportunities for LWRS Pathways

The Light Water Reactor Sustainability (LWRS) Program, sponsored by the U.S. Department of Energy (DOE), plays a pivotal role in enhancing the sustainability, safety, and economic viability of the nation's fleet of nuclear power plants. This program collaborates extensively with industry, vendors, suppliers, regulatory agencies, and research and development organizations within the nuclear energy sector. The overarching goals of the LWRS program are twofold: to provide innovative science and technology-based solutions to the nuclear industry, surpassing current performance models, and to manage the aging of systems, structures, and components (SSCs) to extend the operational lifetimes of nuclear power plants safely, efficiently, and economically. The program focuses on five research and development pathways: Plant Modernization: This pathway seeks to enhance the economic viability of nuclear power plants in evolving energy markets through innovation, efficiency improvements, and digital transformation. The integration of digital technologies into plant operations is a central theme, aiming to create a seamless digital environment that improves plant economics and safety. Flexible Plant Operation and Generation: Research efforts in this pathway explore opportunities for light-water reactors (LWRs) to directly supply energy to industrial processes, diversifying revenue generation approaches and improving economic sustainability.

42 ENGINEERING↗
DOE OSTI2026

Linking Plant and Microbial Traits to Soil Carbon for Reliable and Resilient Bioenergy Systems

Bioenergy systems in the United States offer a dual opportunity to supply renewable feedstocks while enhancing ecosystem services such as hydrologic regulation, erosion control, and soil carbon (C) storage. National assessments highlight the potential to grow perennial energy crops to improve soil function and ecosystem resilience. Realizing this potential requires understanding the ecological mechanisms that govern how C is added, transformed, and stabilized in soils. Plant traits determine the quantity, depth, and chemistry of organic inputs, while microbial processes—including carbon use efficiency, necromass formation, and trophic interactions—mediate their transformation and partitioning among soil carbon pools. These biological pathways are shaped by soil physical and chemical properties, including aggregation, texture, and mineralogy, and by environmental drivers such as temperature, moisture, and disturbance, leading to context-dependent outcomes across landscapes. Management practices that diversify feedstocks, minimize disturbance, and maintain soil cover can promote both biomass production and C retention, while microbial amendments and rhizosphere engineering offer emerging, but often context-dependent, tools to optimize plant–microbe interactions. Trade-offs between biomass yield and soil carbon storage may arise when systems favor rapid aboveground productivity at the expense of belowground inputs and microbial processing, underscoring the importance of trait combinations that support both functions. Advances in monitoring, reporting, and verification—spanning precision agriculture, remote sensing, and biosensing—are improving predictive capacity through microbial-explicit process models and model–experiment (ModEx) frameworks. By connecting soil, plant, and microbial processes with advances in modeling and biosensing, this review outlines research priorities focused on trait-based parameterization and ModEx integration. These priorities will support the design of bioenergy systems that are both reliable and resilient, enhancing renewable energy production and ecosystem sustainability.

bioenergy systems↗
DOE OSTI2025

Biotransformation of Pesticides across Biological Systems: Molecular Mechanisms, Omics Insights, and Biotechnological Advances for Environmental Sustainability

The widespread application of pesticides such as organophosphates, organochlorides, and triazines in modern agriculture has led to their notable presence in soils, water bodies, and food chains, raising concerns about persistence, bioaccumulation, and adverse effects on nontarget organisms. Biotransformation, the enzymatic transformation of xenobiotic compounds by microorganisms, plants, and animals, plays a pivotal role in the degradation and detoxification of these chemicals. This review provides a comprehensive examination of the mechanisms, key enzyme classes (e.g., hydrolases, oxidoreductases, transferases), and environmental factors influencing pesticide biotransformation across different biological systems. Recent advances in omics technologies have revolutionized the understanding of microbial and plant metabolism, while synthetic biology offers opportunities for engineering enhanced degradation capabilities. The environmental fate of transformation products is also discussed, together with a critical analysis of challenges, unresolved questions, and future research directions, offering a holistic perspective on pesticide biotransformation as a key process for mitigating chemical pollution.

Biotransformation↗
DOE OSTI2026

Effect of glutathione-coated Mn-doped ZnS quantum dots on nutrient delivery in basil ( Ocimum basilicum ) plants

Ensuring efficient nutrient delivery while minimizing environmental impacts remains a significant challenge for modern agriculture. Nanotechnology-based fertilizers offer promising strategies to improve nutrient uptake and bioavailability in plants. This research aims to evaluate the use of Glutathione-coated Manganese-doped Zinc Sulfide quantum dots (GSH-ZnS-Mn QDs) as a potential nano fertilizer for basil (Ocimum basilicum). QDs' physicochemical properties were characterized using UV–Vis spectroscopy, photoluminescence, FTIR, and energy-dispersive X-ray spectroscopy, confirming successful Mn doping and glutathione surface functionalization. Basil plants were exposed to different concentrations of GSH-ZnS-Mn QDs under soil and hydroponic conditions. Plant growth parameters, oxidative stress responses, photosynthetic pigments, and macro- and micronutrient uptake were assessed using biochemical assays and inductively coupled plasma optical emission spectrometry (ICP-OES). Elemental uptake, spatial distribution, and zinc speciation were further investigated using synchrotron-based micro-X-ray fluorescence (μ-XRF) imaging and X-ray absorption near-edge structure (XANES) spectroscopy. Results show that exposure to GSH-ZnS-Mn QDs resulted in a concentration-dependent increase in leaf and stem biomass, accompanied by enhanced Zn accumulation in plant tissues. Catalase activity decreased across all tested concentrations, suggesting a shift toward glutathione-dependent antioxidant pathways rather than oxidative damage. Chlorophyll levels exhibited moderate reductions at higher concentrations. The higher increase in macronutrient (K, Ca, and Mg) uptake was reported in plants exposed to 200 ppm of QDs. μ-XRF imaging indicated a selective accumulation of Zn in roots and stems, with partial translocation to leaves. XANES analyses revealed that Zn from QDs was mainly converted into organic Zn species, such as Zn-phytate, Zn-acetate, and Zn-cysteine, indicating transformation and complexation within the plant. The findings demonstrate that a glutathione coating on GSH-ZnS-Mn QDs improves biocompatibility and nutrient delivery efficiency. These results highlight the relevance of surface functionalization in regulating nanoparticle fate, transformation, and nutrient bioavailability, supporting the potential application of GSH–ZnS–Mn QDs as modern nano fertilizers.

Basil↗
DOE OSTI2023

An extensible vector toolkit and parts library for advanced engineering of plant genomes

Abstract Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T‐DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site‐specific recombinases. Finally, we use a series of dual‐luciferase assays to measure contributions to expression from promoters, terminators, and from cross‐cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.

42 ENGINEERING↗
DOE OSTI2024

X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction

Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. Here, to better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ~13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe–Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO 3 ) and K-citrate [K 3 (C 6 H 5 O 7 )·H 2 O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO 3 has both the lowest and highest lying energy features, and K 3 (C 6 H 5 O 7 )·H 2 O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Epigenetic Footprints of CRISPR/Cas9-Mediated Genome Editing in Plants

CRISPR/Cas9 has been widely applied to various plant species accelerating the pace of plant genome editing and precision breeding in crops. Unintended effects beyond off-target nucleotide mutations are still somewhat unexplored. We investigated the degree and patterns of epigenetic changes after gene editing. We examined changes in DNA methylation in genome-edited promoters of naturally hypermethylated genes (AT1G72350 and AT1G09970) and hypomethylated genes (AT3G17320 and AT5G28770) from Arabidopsis. Transgenic plants were developed via Agrobacterium-mediated floral dip transformation. Homozygous edited lines were selected from segregated T2 plants by an in vitro digestion assay using ribonucleoprotein complex. Bisulfite sequencing comparisons were made between paired groups of edited and non-edited plants to identify changes in DNA methylation of the targeted loci. We found that directed mutagenesis via CRISPR/Cas9 resulted in no unintended morphological or epigenetic alterations. Phenotypes of wild-type, transgenic empty vector, and transgenic edited plants were similar. Epigenetic profiles revealed that methylation patterns of promoter regions flanking target sequences were identical among wild-type, transgenic empty vector, and transgenic edited plants. There was no effect of mutation type on epigenetic status. We also evaluated off-target mutagenesis effects in the edited plants. Potential off-target sites containing up to 4-bp mismatch of each target were sequenced. No off-target mutations were detected in candidate sites. Our results showed that CRISPR/Cas9 did not leave an epigenetic footprint on either the immediate gene-edited DNA and flanking DNA or introduce off-target mutations.

59 BASIC BIOLOGICAL SCIENCES↗