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There are a large number of non-family (NF) genes that do not cluster into families with three or more members per genome. While gene families have been extensively studied, a systematic analysis of NF genes has not been reported. We performed comparative studies on NF genes in 14 plant species. Based on the clustering of protein sequences, we identified ~94,000 NF genes across these species that were divided into five evolutionary groups: Viridiplantae-wide, angiosperm-specific, monocot-specific, dicot-specific, and those that were species-specific. Our analysis revealed that the NF genes resulted largely from less frequent gene duplications and/or a higher rate of gene loss after segmental duplication relative to genes in both low-copy-number families (LF; 3 10 copies per genome) and high-copy-number families (HF; >10 copies). Furthermore, we identified functions enriched in the NF gene set as compared with the HF genes. We found that NF genes were involved in essential biological processes shared by all plant lineages (e.g., photosynthesis and translation), as well as gene regulation and stress responses associated with phylogenetic diversification. In particular, our analysis of an Arabidopsis protein-protein interaction network revealed that hub proteins with the top 10% most connections were over-represented in the NF set relative to the HF set. This research highlights the roles that NF genes may play in evolutionary and functional genomics research.
The genome sequence of Bacillus amyloliquefaciens strain Co1-6, a plant growth-promoting rhizobacterium (PGPR) with broad-spectrum antagonistic activities against plant pathogenic fungi, bacteria and nematodes, consists of a single 3.9 Mb circular chromosome. The genome reveals genes putatively responsible for its promising biocontrol and PGP properties.
Unlike most other fungi, molds of the genus Trichoderma (Hypocreales, Ascomycota) are aggressive parasites of other fungi and efficient decomposers of plant biomass. Although nutritional shifts are common among hypocrealean fungi, there are no examples of such broad substrate versatility as that observed in Trichoderma . A phylogenomic analysis of 23 hypocrealean fungi (including nine Trichoderma spp. and the related Escovopsis weberi) revealed that the genus Trichoderma has evolved from an ancestor with limited cellulolytic capability that fed on either fungi or arthropods. The evolutionary analysis of Trichoderma genes encoding plant cell wall-degrading carbohydrate-active enzymes and auxiliary proteins (pcwdCAZome, 122 gene families) based on a gene tree / species tree reconciliation demonstrated that the formation of the genus was accompanied by an unprecedented extent of lateral gene transfer (LGT). Nearly one-half of the genes in Trichoderma pcwdCAZome (41%) were obtained via LGT from plant-associated filamentous fungi belonging to different classes of Ascomycota, while no LGT was observed from other potential donors. In addition to the ability to feed on unrelated fungi (such as Basidiomycota), we also showed that Trichoderma is capable of endoparasitism on a broad range of Ascomycota, including extant LGT donors. This phenomenon was not observed in E. weberi and rarely in other mycoparasitic hypocrealean fungi. Thus, our study suggests that LGT is linked to the ability of Trichoderma to parasitize taxonomically related fungi (up to adelphoparasitism in strict sense). This may have allowed primarily mycotrophic Trichoderma fungi to evolve into decomposers of plant biomass.
Here, lignin plays important structural and functional roles in plants by forming a hydrophobic matrix in secondary cell walls that enhances mechanical strength and resists microbial decay. While the importance of the lignin matrix is well documented and the biosynthetic pathways for monolignols are known, the process by which lignin precursors or monolignols are transported and polymerized to form this matrix remains a subject of considerable debate. In this study, we have synthesized and tested an analog of coniferyl alcohol that has been modified to contain an ethynyl group at the C-3 position. This modification enables fluorescent tagging and imaging of this molecule after its incorporation into plant tissue by click chemistry-assisted covalent labeling with a fluorescent azide dye, and confers a distinct Raman signature that could be used for Raman imaging. We found that this monolignol analog is incorporated into in vitro -polymerized dehydrogenation polymer (DHP) lignin and into root epidermal cell walls of 4-day-old Arabidopsis seedlings. Incorporation of the analog in stem sections of 6-week-old Arabidopsis thaliana plants and labeling with an Alexa-594 azide dye revealed the precise locations of new lignin polymerization. Results from this study indicate that this molecule can provide high-resolution localization of lignification during plant cell wall maturation and lignin matrix assembly.
As the uncertainty of a sustained water supply, regulatory constraints, competition among end users, and public scrutiny increases, a growing number of manufacturing sectors are adapting to current and emerging water-related risks by optimizing productivity and reducing waste. As a step toward increasing water use efficiency and making informed business decisions, corporations must make an effort to understand and track their water demands, losses, and costs associated with each subsystem within their facilities. Manufacturers are often unaware of the “true cost of water” (i.e., the total costs associated with procurement, treatment, and consumption of water, and wastewater disposal), which reduces the visibility of the actual impact of water-saving measures. To help manufacturers account for water procurement and use in manufacturing operations, quantify the true cost of water, and identify potential areas for water and associated energy cost savings, an open access tool—Plant Water Profiler (PWP)—was developed. The tool is based on water mass balance analysis and has been adopted as the core analysis tool for plant water use assessments, Water In-Plant Training (Water INPLT), as part of the US Department of Energy’s Better Plants program. During three pilot INPLTs conducted in 2019 at three manufacturing facilities, the PWP tool allowed users to understand water flows within the facilities and provided additional capabilities to analyze their water use. This paper describes the methodology behind the PWP tool and its implementation through pilot Water INPLT trainings delivered in three manufacturing facilities in the United States. The three case studies demonstrate opportunities to improve water efficiency and reduce associated costs and the challenges encountered in three different manufacturing sectors.
Approximately two-thirds of U.S. energy consumption in the industrial and transportation sectors relies on fossil fuels. These sectors require high-quality heat, i.e., thermal energy at very high temperatures, for molecular transformation processes. The Integrated Energy Systems (IES) program aims to assess the economic potential of utilizing nuclear-grade heat from Advanced Reactors (ARs) to meet the high-quality heat demands. By having industrial processes (IPs) supplied with nuclear-generated heat, manufacturers could benefit from more stable and potentially lower energy costs, reducing reliance on volatile fossil fuel markets. The main outcome of the FY24 research was the thermodynamic assessment and gap analysis of steam generation for IP applications. The study completed in June 2024 demonstrated that the required steam temperatures could be achieved by integrating a heat pump into an AR power plant. After identifying the thermal demands of target IPs, multiple balance of plant configurations for the Xe-100 reactor by X-energy, incorporating a heat pump, were analyzed. Their technical feasibilities were assessed, including the design of suitable axial compressors for these applications. Comparative performance analysis showed that thermal efficiency alone is insufficient to evaluate system suitability. To address this, a new indicator (heat factor) was introduced in the report released in September 2024 to quantify the low-quality thermal power needed to produce one unit of high-quality heat for the IP. Results showed that integrating heat pumps into Rankine cycles enables higher steam temperatures, though at the expense of increased thermal energy input. This report builds upon and completes the foundational work previously undertaken. It focuses on the design of two Balance of Plant (BOP) configurations, both based on Rankine energy conversion cycles: “Case 1”, which involves electricity generation only, and “Case 2”, which combines electricity and high-temperature heat generation for industrial use. For each configuration, a comprehensive equipment list was developed, detailing all major components such as turbines, compressors, heat exchangers, pumps, and control systems. These lists will serve as the basis for future comparative cost analyses, with the goal of assessing the number and type of components required to integrate a heat pump into the Rankine cycle and to establish a heat transport system capable of delivering thermal energy from the nuclear plant to an industrial facility. Using the constitutive equations presented in the June 2024 milestone, the operating conditions of all BOP components for both “Case 1” and “Case 2” were evaluated. These parameters—such as temperature, pressure, mass flow rate, and steam quality—served as the basis for calculating the associated thermal and mechanical power flows. The net power required from the heat pump to raise the steam temperature to the target level was also determined. The thermodynamic performance of the configuration was then assessed using the heat factor metric. The key outcome of this analysis is a comparative table that presents the equipment that was used in the “Case 1” and “Case 2” configurations. This study offers a preliminary comparison of the two designs, providing insight into the impact of integrating a heat pump in terms of component requirements and thermal efficiency. This equipment list, together with the evaluated operating conditions, also serves as a foundation for the economic analyses scheduled for the current fiscal year.
Crassulacean acid metabolism (CAM) improves photosynthetic efficiency under limited water availability relative to C 3 photosynthesis. It is widely accepted that CAM plants have evolved from C 3 plants and it is hypothesized that CAM is under the control of the internal circadian clock. However, the role that the circadian clock plays in the evolution of CAM is not well understood. To identify the molecular basis of circadian control over CAM evolution, rhythmic gene sets were identified in a CAM model plant species ( Kalanchoë fedtschenkoi ) and a C 3 model plant species ( Arabidopsis thaliana ) through analysis of diel time-course gene expression data using multiple periodicity detection algorithms. Based on protein sequences, ortholog groups were constructed containing genes from each of these two species. The ortholog groups were categorized into five gene sets based on conservation and diversification of rhythmic gene expression. Interestingly, minimal functional overlap was observed when comparing the rhythmic gene sets of each species. Specifcally, metabolic processes were enriched in the gene set under circadian control in K. fedtschenkoi and numerous genes were found to have retained or gained rhythmic expression in K. fedtsechenkoi . Additonally, several rhythmic orthologs, including CAM-related orthologs, displayed phase shifts between species. Results of this analysis point to several mechanisms by which the circadian clock plays a role in the evolution of CAM. These genes provide a set of testable hypotheses for future experiments.
Standard descriptions for solar thermal power plants are established and uniform costing methodologies for nondevelopmental balance of plant (BOP) items are developed. The descriptions and methodologies developed are applicable to the major systems. These systems include the central receiver, parabolic dish, parabolic trough, hemispherical bowl, and solar pond. The standard plant is defined in terms of four categories comprising (1) solar energy collection, (2) power conversion, (3) energy storage, and (4) balance of plant. Each of these categories is described in terms of the type and function of components and/or subsystems within the category. A detailed description is given for the BOP category. BOP contains a number of nondevelopmental items that are common to all solar thermal systems. A standard methodology for determining the costs of these nondevelopmental BOP items is given. The methodology is presented in the form of cost equations involving cost factors such as unit costs. A set of baseline values for the normalized cost factors is also given.
The Biomass Production Chamber at John F. Kennedy Space Center is a closed plant growth chamber facility that can be used to monitor the level of biogenic emissions from large populations of plants throughout their entire growth cycle. The head space atmosphere of a 26-day-old lettuce (Lactuca sativa cv. Waldmann's Green) stand was repeatedly sampled and emissions identified and quantified using GC-mass spectrometry. Concentrations of dimethyl sulphide, carbon disulphide, alpha-pinene, furan and 2-methylfuran were not significantly different throughout the day; whereas, isoprene showed significant differences in concentration between samples collected in light and dark periods. Volatile organic compounds from the atmosphere of wheat (Triticum aestivum cv. Yecora Rojo) were analysed and quantified from planting to maturity. Volatile plant-derived compounds included 1-butanol, 2-ethyl-1-hexanol, nonanal, benzaldehyde, tetramethylurea, tetramethylthiourea, 2-methylfuran and 3-methylfuran. Concentrations of volatiles were determined during seedling establishment, vegetative growth, anthesis, grain fill and senescence and found to vary depending on the developmental stage. Atmospheric concentrations of benzaldehyde and nonanal were highest during anthesis, 2-methylfuran and 3-methylfuran concentrations were greatest during grain fill, and the concentration of the tetramethylurea peaked during senescence.
The Space Chile Grow a Pepper Plant Challenge (SCGAPPC) is a citizen outreach activity performed in conjunction with NASA technical demonstration, Plant Habitat (PH)-04 which grew a New Mexico chile pepper as the first fruit in the Advanced Plant Habitat (APH). Growing a related pepper variety from Chimayo, New Mexico, the activity tasked citizen “Space Farmers” to grow a pepper plant indoors, at home, or in controlled environments to document the details of growth, and search for solutions to growing consistently productive and flavorful peppers under these conditions. Launched in February of 2020, a scientist on the PH04 team shared an introduction on social media to provide information about the activity and instructions on how to participate. Each space farmer received an envelopecontaining seeds and a mission sticker. They conducted their own pepper growth trials to record environment and horticultural data and submit one pepper to the University of New Mexico for capsaicin analysis. This activity was available online at the onset of the COVID-19 shutdown. During 2020-2021, over 1,800 envelopes were mailed across the globe, tens of thousands of seed pouches were shared, the SCGAPPC was featured during a virtual Growing Beyond Earth Educator Workshop with the challenge of becoming a critical part of that program when students were working remotely. Citizen space farmers around the world contributed to space biology and crop production research while learning about CE agriculture. Members of the space biology community volunteered participation, skills, and interaction. An online community page provided a format for scientists, and the general publicto interact. A portion of data was documented in an online database. The primary outcome served to inform the publicabout NASA space crop production, while creating a channel to share experiences and compare results from a singlecrop growing under varying controlled environments.
The present disclosure is directed to methods of improving mycorrhization in a plant or plant cell. Another aspect of this disclosure is directed to a genetically modified plant or plant cell with improved mycorrhization.
The primary objective of this project is to characterize coal contaminants in coal-fired power plant wastewater as a function of coal type, unit configurations, and unit operation profile with uncertainty analysis. This project was in response to the U.S. Department of Energy (DOE) Solicitation DE-FOA-0001842. The project duration was between September 01, 2018, and December 31, 2021 (no-cost extension filed, due to the Covid-19 pandemic restrictions, and approved). Field and lab test program was conducted with the main goal to characterize coal contaminants in coal-fired power plant wastewater as a function of coal type, unit configurations, and unit operation profile with uncertainty analysis. In this project, the team of Lehigh University (prime recipient) and Western Kentucky University identified two suitable Thermoelectric Power Plants (TTPs) firing bituminous and sub-bituminous coals respectively, designed test plans, and performed sample collection. Sampling included coal from each TTPs power generation units, Wet Flue Gas Desulfurization (WFGD) slurry material and waste-water samples taken from the outlet of the water treatment tank prior to discharge and other pertinent locations. Coal samples are dried, crushed, and pulverized according to the American Society for Testing and Materials (ASTM) methods. The prepared coal samples are analyzed for normal proximate and ultimate analysis tests in addition to the toxic metals and anions according to ASTM methods. The FGD slurry materials are analyzed for toxic metals and anions according to Electric Power Research Institute (EPRI) or Environmental Protection Agency (EPA) methods, as appropriate. The wastewater samples from the water treatment tank outlet are analyzed for toxic metals and anions according to EPA methods. The effluent species analyzed include mercury, arsenic, selenium, nitrate/nitrite, bromide, and chlorine. This project provided results of effluent conditions as a function of coal type, unit configuration, and unit operation profile, and identified the levels of uncertainty in the effluent results.
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The objective of this paper is to present test cases for wind turbine generator and wind power plant models commonly used during commissioning of wind power plants to ensure grid integration compatibility. In this paper, different types of wind power plant models based on the Western Electricity Coordinating Council Wind Generator Modeling Group's standardization efforts are implemented on areal-time digital simulator, and different test cases are used to gauge their grid integration capability. The low-voltage ride through and reactive power support capability and limitations of wind turbine generators under different grid conditions are explored. Several types of transient events (e.g., symmetrical and unsymmetrical faults, frequency dips) are included in the test cases. Thedifferences in responses from different types of wind turbine are discussed in detail.
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Camelina sativa is a Brassicaceae oilseed species being explored as a biofuel and industrial oil crop. A growing number of studies have indicated that the turnover of phosphatidylcholine plays an important role in the synthesis and modification of triacylglycerols. This study manipulated the expression of a patatin-related phospholipase AIIIδ ( pPLAIIIδ ) in camelina to determine its effect on seed oil content and plant growth. Constitutive overexpression of pPLAIIIδ under the control of the constitutive cauliflower mosaic 35S promoter resulted in a significant increase in seed oil content and a decrease in cellulose content. In addition, the content of major membrane phospholipids, phosphatidylcholine and phosphatidylethanolamine, in 35S::pPLAIIIδ plants was increased. However, these changes in 35S::pPLAIIIδ camelina were associated with shorter cell length, leaves, stems, and seed pods and a decrease in overall seed production. When pPLAIIIδ was expressed under the control of the seed specific, β-conglycinin promoter, the seed oil content was increased without compromising plant growth. In conclusion, the results suggest that pPLAIIIδ alters the carbon partitioning by decreasing cellulose content and increasing oil content in camelina.