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At least 703 records · Page 39
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling

The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.

58 GEOSCIENCES↗
DOE OSTI2022

A toolkit for plant lipid engineering: surveying the efficacies of lipogenic factors for accumulating specialty lipids

Plants produce energy-dense lipids from carbohydrates using energy acquired via photosynthesis, making plant oils an economically and sustainably attractive feedstock for conversion to biofuels and value-added bioproducts. A growing number of strategies have been developed and optimized in model plants, oilseed crops and high-biomass crops to enhance the accumulation of storage lipids (mostly triacylglycerols, TAGs) for bioenergy applications and to produce specialty lipids with increased uses and value for chemical feedstock and nutritional applications. Most successful metabolic engineering strategies involve heterologous expression of lipogenic factors that outperform those from other sources or exhibit specialized functionality. In this review, we summarize recent progress in engineering the accumulation of triacylglycerols containing - specialized fatty acids in various plant species and tissues. We also provide an inventory of specific lipogenic factors derived from a wide variety of organisms, along with their reported efficacy in supporting the accumulation of desired lipids. A review of previously obtained results serves as a foundation to guide future efforts to optimize combinations of factors to achieve further enhancements to the production and accumulation of desired lipids in a variety of plant tissues and species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Field performance of switchgrass plants engineered for reduced recalcitrance

Switchgrass ( Panicum virgatum L.) is a promising perennial bioenergy crop that achieves high yields with relatively low nutrient and energy inputs. Modification of cell wall composition for reduced recalcitrance can lower the costs of deconstructing biomass to fermentable sugars and other intermediates. We have engineered overexpression of OsAT10 , encoding a rice BAHD acyltransferase and QsuB , encoding dehydroshikimate dehydratase from Corynebacterium glutamicum , to enhance saccharification efficiency in switchgrass. These engineering strategies demonstrated low lignin content, low ferulic acid esters, and increased saccharification yield during greenhouse studies in switchgrass and other plant species. In this work, transgenic switchgrass plants overexpressing either OsAT10 or QsuB were tested in the field in Davis, California, USA for three growing seasons. No significant differences in the content of lignin and cell wall-bound p -coumaric acid or ferulic acid were detected in transgenic OsAT10 lines compared with the untransformed Alamo control variety. However, the transgenic overexpressing QsuB lines had increased biomass yield and slightly increased biomass saccharification properties compared to the control plants. This work demonstrates good performance of engineered plants in the field, and also shows that the cell wall changes in the greenhouse were not replicated in the field, emphasizing the need to validate engineered plants under relevant field conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency

Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied. We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency. In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency. Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Editorial: Artificial Intelligence and Machine Learning Applications in Plant Genomics and Genetics

In plants, as in other species, genotypic variation in combination with environmental variation leads to differences in the biochemical makeup of cells, measurable as molecular phenotypes. These in turn influence physiological and developmental traits such as organ formation and plant growth, and eventually traits relevant in agriculture, such as yield and stress tolerance. Thus, relating genotypes to phenotypes yields fundamental insights into the regulation of important processes in plant development and physiology, but also provides the ability to predict yield and quality traits in specific environments, which is essential in basic plant science and molecular breeding of resilient plants in changing environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Harnessing Plant Sugar Metabolism for Glycoengineering

Plants possess an innate ability to generate vast amounts of sugar and produce a range of sugar-derived compounds that can be utilized for applications in industry, health, and agriculture. Nucleotide sugars lie at the unique intersection of primary and specialized metabolism, enabling the biosynthesis of numerous molecules ranging from small glycosides to complex polysaccharides. Plants are tolerant to perturbations to their balance of nucleotide sugars, allowing for the overproduction of endogenous nucleotide sugars to push flux towards a particular product without necessitating the re-engineering of upstream pathways. Pathways to produce even non-native nucleotide sugars may be introduced to synthesize entirely novel products. Heterologously expressed glycosyltransferases capable of unique sugar chemistries can further widen the synthetic repertoire of a plant, and transporters can increase the amount of nucleotide sugars available to glycosyltransferases. In this opinion piece, we examine recent successes and potential future uses of engineered nucleotide sugar biosynthetic, transport, and utilization pathways to improve the production of target compounds. Additionally, we highlight current efforts to engineer glycosyltransferases. Ultimately, the robust nature of plant sugar biochemistry renders plants a powerful chassis for the production of target glycoconjugates and glycans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii—A Blueprint for Nitrogen-Fixing Plants?

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Microbiology↗
DOE OSTI2021

Biogeochemical and plant trait mechanisms drive enhanced methane emissions in response to whole-ecosystem warming

Abstract. Climate warming perturbs ecosystem carbon (C) cycling, causing both positive and negative feedbacks on greenhouse gas emissions. In 2016, we began a tidal marsh field experiment in two vegetation communities to investigate the mechanisms by which whole-ecosystem warming alters C gain, via plant-driven sequestration in soils, and C loss, primarily via methane (CH4) emissions. Here, we report the results from the first 4 years. As expected, warming of 5.1 ∘C more than doubled CH4 emissions in both plant communities. We propose this was caused by a combination of four mechanisms: (i) a decrease in the proportion of CH4 consumed by CH4 oxidation, (ii) more C substrates available for methanogenesis, (iii) reduced competition between methanogens and sulfate-reducing bacteria, and (iv) indirect effects of plant traits. Plots dominated by Spartina patens consistently emitted more CH4 than plots dominated by Schoenoplectus americanus, indicating key differences in the roles these common wetland plants play in affecting anaerobic soil biogeochemistry and suggesting that plant composition can modulate coastal wetland responses to climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The curled wake model: a three-dimensional and extremely fast steady-state wake solver for wind plant flows

Abstract. Wind turbine wake models typically require approximations, such as wake superposition and deflection models, to accurately describe wake physics. However, capturing the phenomena of interest, such as the curled wake and interaction of multiple wakes, in wind power plant flows comes with an increased computational cost. To address this, we propose a new hybrid method that uses analytical solutions with an approximate form of the Reynolds-averaged Navier–Stokes equations to solve the time-averaged flow over a wind plant. We compare results from the solver to supervisory control and data acquisition data from the Lillgrund wind plant obtaining wake model predictions which are generally within 1 standard deviation of the mean power data. We perform simulations of flow over the Columbia River Gorge to demonstrate the capabilities of the model in complex terrain. We also apply the solver to a case with wake steering, which agreed well with large-eddy simulations. This new solver reduces the time – and therefore the related cost – it takes to simulate a steady-state wind plant flow (on the order of seconds using one core). Because the model is computationally efficient, it can also be used for different applications including wake steering for wind power plants and layout optimization.

17 WIND ENERGY↗
DOE OSTI2022

Fast yaw optimization for wind plant wake steering using Boolean yaw angles

Abstract. In wind plants, turbines can be yawed into the wind to steer their wakes away from downstream turbines and achieve an overall increase in plant power. Mathematical optimization is typically used to determine the best yaw angles at which to operate the turbines in a plant. In this paper, we present a new heuristic to rapidly determine the yaw angles in a wind plant. In this method, we define the turbine yaw angles as Boolean – either yawed at a predefined angle or nonyawed – as opposed to the typical methods of defining yaw angles as continuous or with fine discretizations. We then optimize which turbines should be yawed with an algorithm that sweeps through the turbines from the most upstream to the most downstream. We demonstrate that our new Boolean optimization method can find turbine yaw angles that perform well compared to a traditionally used gradient-based optimizer for which the yaw angles are defined as continuous. There is less than 0.6 % difference in the optimized power between the two optimization methods for randomly placed turbine layouts and less than a 0.6 % difference in the optimal annual energy production between the two optimization methods for a real wind farm. Additionally, we show that our new method is much more computationally efficient than the traditional method. For plants with nonzero optimal yaw angles, our new method is generally able to solve for the turbine yaw angles 50–150 times faster, and in some extreme cases up to 500 times faster, than the traditional method.

17 WIND ENERGY↗
DOE OSTI2021

Integrating New Arctic Plant Functional Types in a Land Surface Model Using Above- and Belowground Field Observations: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication "Integrating New Arctic Plant Functional Types in a Land Surface Model Using Above- and Belowground Field Observations". We used field observations of biomass and leaf traits (Salmon et al., 2019b) across a gradient of plant communities on the Seward Peninsula in northwest Alaska (Breen et al., 2020; Iversen et al., 2017) to replace the original ELM configuration with nine, arctic-specific PFTs. Original arctic PFTs in the model were (1) broadleaf deciduous boreal shrub and (2) C3 arctic grass. New PFTs were (1) lichen, (2) bryophyte, (3) evergreen dwarf shrub, (4) deciduous dwarf shrub, (5) deciduous low shrub, (6) deciduous low to tall shrub, (7) alder shrub, (8) forb, and (9) graminoid. New PFTs were parameterized and evaluated using site-level trait and biomass measurements (Salmon et al., 2019b), root C:N ratios and rooting depth patterns (Salmon et al., 2019c), and root biomass (Salmon et al., 2020). This archive contains forcing data and model output from ELM simulations conducted at the Kougarok Hillslope site (Kougarok Road Mile Marker 64). Simulations were conducted for the Kougarok Hillslope site using meteorological driving data from the Scenarios Network for Alaska and Arctic Planning (SNAP) downscaled climate projection dataset using NCAR-CCSM forcing (Bieniek et al., 2020 dataset; Walsh et al., 2018). The archive includes three versions of model simulations representing a progression from the original model configuration to an Arctic-specific configuration (see Output section below). Simulation 1 used grid cell data from a global E3SM configuration, including the fractional area of E3SM PFTs assigned to the grid cell containing the Kougarok Hillslope site in global simulations. This simulation did not distinguish between different plant communities on the Kougarok Hillslope, but instead used a single point simulation to represent the entire area. Simulation 2 used default E3SM PFT definitions combined with adjusted depth to bedrock for plant communities with shallow rocky layers to represent the role of abiotic soil factors in driving site differences (based on depth measurements of Iversen et al., 2019a), and adjusted the relative areas of the broadleaf deciduous boreal shrub and C3 arctic grass PFTs to reflect the observed spatial coverage of shrub and non-shrub PFTs across Kougarok Hillslope plant communities. Simulation 3 used the new arctic PFT definitions and parameterizations based on the vegetation types present at the site, along with the adjusted soil depths used in Simulation 2. Included are *.pdf, *.nc (NetCDF), *tar.gz, *.py, and *.bash files. We would like to thank Mary's Igloo Native Corporation for allowing us to perform this research on their land and giving us the opportunity to share this research with their community. Thanks to Shawn Serbin and Alistair Rogers for helpful discussions. Holly Vander Stel, Joanne Childs, and Stan Wullschleger helped with collection of field data. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Heat Pump Retrofits for Central Plant Hydronic Heating Systems: A Software Toolkit for Screening and Design

Retrofitting existing central plants with high-efficiency heat pump technologies can play a crucial role in achieving long-term planning goals. Modern heat pump technologies are able to use waste heat recovery to meet a building's heating demand, but there is a lack of accessible tools designed for non-HVAC experts, such as building owners, to quickly and easily conduct what-if analysis, e.g., estimating retrofit costs and payback period for their partial or full equipment replacement. This paper introduces an open-source software toolkit designed to facilitate the initial screening and decision-making of heat pump retrofits in existing central plants using a building's yearly load profile from metered or utility bill data. The toolkit evaluates the technical and economic viability of replacing traditional central plant equipment with various options including water-to-water or air-to-water heat pumps, which can provide efficient and lower-cost heating and cooling. It allows users to compare current central plant configurations with retrofit scenarios, assessing energy consumption, life-cycle costs, and environmental impact. The toolkit offers (1) a web-based tool designed for user-friendly access by a broad audience and (2) Python-based source code for researchers and engineers conducting parametric studies and design parameter optimization. The toolkit compares a typical central plant configuration to a configuration that uses a heat pump to supply hydronic heating and cooling. The output metrics include energy consumption and output of each equipment, life-cycle cost analyses and metrics, and environmental impact of the system.

Excell, L↗
DOE OSTI2020

Building customizable auto-luminescent luciferase-based reporters in plants

Bioluminescence is a powerful biological signal that scientists have repurposed as a reporter for gene expression in plants and animals. However, there are downsides associated with the need to provide a substrate to these reporters, including its high cost and non-uniform tissue penetration. In this work we reconstitute a fungal bioluminescence pathway (FBP) in planta using a composable toolbox of parts. We demonstrate that the FBP can create luminescence across various tissues in a broad range of plants without external substrate addition. We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes. A low-cost imaging platform for gene expression profiling is also described. These experiments lay the groundwork for future construction of programmable auto-luminescent plant traits, such as light driven plant-pollinator interactions or light emitting plant-based sensors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Carbon fixation systems in plants and algae

Provided are methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

NREL's Biochemical Conversion Pilot Plant Capabilities

NREL's biochemical conversion plant is a flexible pilot plant for testing a wide range of bio-based technologies for producing renewable fuels and byproducts. The biochemical conversion pilot plant is housed in the Integrated Biorefinery Research Facility located on the National Renewable Energy Laboratory's (NREL's) main campus. The facility provides industry partners the opportunity to test and develop their own biorefining technology using NREL equipment or rental equipment that can be brought into the plant. The pilot plant can process materials up to one dry ton per day in an integrated fashion using a variety of operating modes including batch, fed-batch, and continuous processing.

biochemical↗
DOE OSTI2021

Carbon fixation systems in plants and algae

Provided are heterologous nucleic acid constructs, vectors and methods for elevating cyclic electron transfer activity, improving carbon concentration, and enhancing carbon fixation in C3 and C4 plants, and algae, and producing biomass or other products from C3 or C4 plants, and algae, selected from among, for example, starches, oils, fatty acids, lipids, cellulose or other carbohydrates, alcohols, sugars, nutraceuticals, pharmaceuticals, fragrance and flavoring compounds, and organic acids, as well as transgenic plants produced thereby. These methods and transgenic plants and algae encompass the expression, or overexpression, of various combinations of genes that improve carbon concentrating systems in plants and algae, such as bicarbonate transport proteins, carbonic anhydrase, light driven proton pump, cyclic electron flow regulators, etc.

Sayre, Richard Thomas↗
DOE OSTI2021

Genes for enhancing drought and heat tolerance in plants and methods of use

The present disclosure provides methods for increasing drought resistance and heat resistance of a plant. The methods encompass expression of at least one heat shock protein (HSP) from the group consisting of HSP40, HSP60 or HSP70 together with a phosphoenolpyruvate carboxylase (PEPC) comprising an aspartic acid (D) at a position that corresponds to the position 509 of SEQ ID NO: 4, in the plant. In comparison to a plant not manipulated in this manner, the disclosed, genetically-modified, plants display improved drought resistance and heat resistance. Also provided are plants that can be obtained by the method according to the invention, and nucleic acid vectors to be used in the described methods.

Yang, Xiaohan↗
DOE OSTI2021

Microneedle-based electrical impedance sensor to monitor plant water status in real time

A sensor uses microneedle electrodes and multi-frequency electrical impedance spectroscopy to monitor plant water status in real time. The microneedle can be between 10 and 1000 microns in length, enabling precise placement in a variety of plant tissues. The impedance behavior can distinguish electrical properties and physiological functions of different plant tissue types. Therefore, impedance measurements can be used to monitor water stress to prevent irreversible damage to a plant and to enable improvement of plant biomass or fruit yield.

Hanson, David T.↗