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We report the complete genome sequences of five Variovorax strains isolated from the roots of Populus species in greenhouse and field settings. Genome sizes range from 7.44 to 7.71 Mbp and encode 6,077–6,879 predicted protein-coding genes. These genome assemblies expand the known genomic catalog of Variovorax in plant-associated environments.
GATA factors are evolutionarily conserved transcription factors that are found in animals, fungi, and plants. Compared to that of animals, the size of the plant GATA family is increased. In angiosperms, four main GATA classes and seven structural subfamilies can be defined. In recent years, knowledge about the biological role and regulation of plant GATAs has substantially improved. Individual family members have been implicated in the regulation of photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, and stomata formation, as well as root, leaf, and flower development. In this review, we summarize the current knowledge of plant GATA factors. Using phylogenomic analysis, we trace the evolutionary origin of the GATA classes in the green lineage and examine their relationship to animal and fungal GATAs. Lastly, we speculate about a possible conservation of GATA-regulated functions across the animal, fungal, and plant kingdoms.
Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.
Integrated energy systems (IES) combine different energy technologies in synergistic ways to achieve a more secure and economical energy supply. The RAVEN-based HYBRID framework and the RAVEN plugin for grid and capacity optimization (HERON) are used to find the optimal installed capacity and the optimal economical dispatch of each component of the IES, by respecting the limits on the production variables and the corresponding rates of variation (explicit constraints). Besides, there are other process variables whose evolution needs to be bounded to avoid damaging the components (e.g., condensers, heat exchangers, steam generators, etc.) or degrading the process efficiency (e.g., electrolysis in the hydrogen production process). To avoid violating these latter limits (implicit constraints), a proof-of-concept HERON validator based on Feasible Actuator Range Modifier (FARM-Alpha) was developed by Argonne National Laboratory in January 2021. This FARM-Alpha validator calculates the evolution of process variables on whom the implicit constraints are placed, and then provides feedback to HERON dispatcher to adjust the power setpoints of three IES components, i.e., Balance of Plant, Secondary Energy Source, and Thermal Energy Storage, so as to meet both the explicit and implicit constraints. FARM-Alpha was designed to assess the performance of FARM as a HERON validator only, i.e., the list of components and implicit operational constraints were hard-coded within the source code. The lack of flexibility of the corresponding software structure does not allow the deployment in production environment. This report describes the development and the implementation of an enhanced version of the FARM-based validator (FARM-Beta), which ensures more flexibility for the end user in modeling multiple IES configurations and scenarios. Several test cases of the power dispatch problem were then selected to demonstrate the capabilities offered by FARM-beta. The test cases illustrate the efficiency of the closed-loop optimization scheme and the capability to calculate set-point trajectories satisfying both explicit and implicit constraints.
Sex chromosomes are expected to coevolve with their respective sex, potentially disfavoring their co-occurrence as cosexuality evolves. This effect is expected to be stronger where sex chromosomes are restricted to one sex, such as in plants expressing sex in their haploid stage. We assess this hypothesis in liverworts with U/V sex chromosomes, ancestral dioicy, and several independent transitions to monoicy (cosexuality). We report the chromosome-level genome assembly of Marchantia quadrata, which recently evolved monoicy, and perform comparative genomic analyses with its dioicous relative M. polymorpha. We find that monoicy evolved via retention of the V chromosome as a small ninth chromosome, complete loss of the U chromosome, and translocation of key U-linked genes to autosomes, among which the major sex-determining gene (Feminizer) acquired environmental/developmental regulation. Our findings parallel recent observations on Ricciocarpos natans, which evolved monoicy independently, suggesting genetic constraints that may make transitions to monoicy predictable in liverworts.
Plant cell walls are largely composed of polysaccharide polymers, including cellulose, hemicelluloses (xyloglucan, xylan, mannan, and mixed-linkage β-1,3/1,4-glucan), and pectins. Among these cell wall polysaccharides, xyloglucan, xylan, mannan, and pectins are often O-acetylated, and polysaccharide O-acetylation plays important roles in cell wall assembly and disease resistance. Genetic and biochemical analyses have implicated the involvement of three groups of proteins in plant cell wall polysaccharide O-acetylation: trichome birefringence-like (TBL)/domain of unknown function 231 (DUF231), reduced wall acetylation (RWA), and altered xyloglucan 9 (AXY9). Although the exact roles of RWAs and AXY9 are yet to be identified, members of the TBL/DUF231 family have been found to be O-acetyltransferases responsible for the O-acetylation of xyloglucan, xylan, mannan, and pectins. Here, we provide a comprehensive overview of the occurrence of O-acetylated cell wall polysaccharides, the biochemical properties, structural features, and evolution of cell wall polysaccharide O-acetyltransferases, and the potential biotechnological applications of manipulations of cell wall polysaccharide acetylation. Further in-depth studies of the biochemical mechanisms of cell wall polysaccharide O-acetylation will not only enrich our understanding of cell wall biology, but also have important implications in engineering plants with increased disease resistance and reduced recalcitrance for biofuel production.
A major challenge for sustainable food, fuel, and fiber production is simultaneous genetic improvement of yield, biomass quality, and resilience to episodic environmental stress and climate change. For Populus and other forest trees, quality traits involve alterations in the secondary cell wall (SCW) of wood for traditional uses, as well as for a growing diversity of biofuels and bioproducts. Alterations in wood properties that are desirable for specific end uses can have negative effects on growth and stress tolerance. Understanding of the diverse roles of SCW genes is necessary for the genetic improvement of fast-growing, short-rotation trees that face perennial challenges in their growth and development. Here, we review recent progress into the synergies and antagonisms of SCW development and abiotic stress responses, particularly, the roles of transcription factors, SCW biogenesis genes, and paralog evolution.
Mythology is replete with good and evil shapeshifters, who, by definition, display great adaptability and assume many different forms—with several even turning themselves into trees. Cell walls certainly fit this definition as they can undergo subtle or dramatic changes in structure, assume many shapes, and perform many functions. In this review, we cover the evolution of knowledge of the structures, biosynthesis, and functions of the 5 major cell wall polymer types that range from deceptively simple to fiendishly complex. Along the way, we recognize some of the colorful historical figures who shaped cell wall research over the past 100 years. The shapeshifter analogy emerges more clearly as we examine the evolving proposals for how cell walls are constructed to allow growth while remaining strong, the complex signaling involved in maintaining cell wall integrity and defense against disease, and the ways cell walls adapt as they progress from birth, through growth to maturation, and in the end, often function long after cell death. We predict the next century of progress will include deciphering cell type–specific wall polymers; regulation at all levels of polymer production, crosslinks, and architecture; and how walls respond to developmental and environmental signals to drive plant success in diverse environments.
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Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype‐resolved chromosome‐scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus , certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species – as are the chromosomal locations of R gene clusters – but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus . Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus .
Potassium ion (K + ) plays a critical role as an essential electrolyte in all biological systems. Genetically-encoded fluorescent K + biosensors are promising tools to further improve our understanding of K + -dependent processes under normal and pathological conditions. Here, we report the crystal structure of a previously reported genetically-encoded fluorescent K + biosensor, GINKO1, in the K + -bound state. Using structure-guided optimization and directed evolution, we have engineered an improved K + biosensor, designated GINKO2, with higher sensitivity and specificity. We have demonstrated the utility of GINKO2 for in vivo detection and imaging of K + dynamics in multiple model organisms, including bacteria, plants, and mice.
The main objectives of this project are to construct plant N flux maps (NFMs) from plant genomes and to determine functionality of AT enzymes and plant N metabolic network. To address this grand challenge, this project made use of rapidly growing numbers of plant genomes, high-throughput functional characterization platforms, and computational modeling to deduce both biochemical and systems level functionality of ATs and NFMs. The obtained NFMs will provide a novel framework to advance basic understanding of plant N metabolism and facilitate rational engineering of plants with high productivity even under limited N input.
Here, this study develops a thermal stress model of solid-oxide electrolysis cells (SOECs) including a model for creep strain and failure probability that is integrated with a dynamic plant-wide model of a hydrogen production process. Uncertainties in key material properties of the cell are quantified to assess their impact on stress profile variability. The oxygen electrode is found to have about 10 times higher failure probability compared to the fuel electrode. The study shows that if the stack operation is not optimized, cycling operation would lead to stress build-up eventually leading to catastrophic failure. A dynamic optimization problem is set up for obtaining the optimal operational profile considering a variable hydrogen production rate. Due to the tradeoff between the efficiency and stress build-up, the dynamic optimization problem is multi-objective. It is observed that the optimizer can considerably reduce the stress build-up (i.e., can increase the stack life) albeit at the cost of a lower efficiency thus exhibiting strong tradeoffs between capital and operating costs. For example, if the stack would be replaced in 0.5 yr, specific energy requirement would be 48.5 kWh/kg H 2 while for a stack replacement time of about 6 yr, the specific energy requirement rises by about 4.2 %.
Radiation of fuel rods with neutrons during a fission reaction in a nuclear reactor is known to affect the material microstructure of the fuel as a result of fission fragment damage, and lead to the formation of atomic-level defects such as voids, dislocation loops, and lattice swelling from fission-gas release. A consequence of the radiation-induced damage in nuclear fuels is the drastic alteration of material properties, in particular, the reduction of the thermal conductivity – a key parameter that governs the transport of thermal energy released from fissile fuel atoms to the surrounding coolant. Swelling can induce high stresses and ultimate failure of the cladding. A fundamental understanding of the role of radiation-induced damage on the thermal transport and mechanical properties of nuclear fuels is therefore critical for efficient, reliable and safe operation of a nuclear power plant. As opposed to conventional post-irradiation examination techniques that are often time-consuming and require significant sample preparation, laser-based characterization methods have emerged as promising non-contact, non-destructive tools to measure the evolution of microstructure-induced material property changes. Moreover, laser methods offer the promise of in-situ characterization while the material is being irradiated. This project aims to develop an improved understanding of the impact of radiation-induced changes to material microstructure on the thermal and elastic properties of nuclear materials. A laser ultrasonic technique, known as the transient grating (TG) spectroscopy method, is used to simultaneously measure thermal diffusivity and elastic properties in unirradiated and ion-irradiated oxide nuclear fuel samples. The results will complement on-going investigations on electron- and phonon-mediated thermal transport in nuclear materials and will provide foundational work for incorporating the influence of defects in fuel performance codes.
Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.
Concrete structures in nuclear installations are subject to time-dependent degradation mechanisms that can deteriorate their physical and mechanical properties, potentially exacerbating the risk of structural failure under external forces such as a seismic event. Previous research has extensively investigated the seismic response of nuclear concrete structures and the associated risk, as well as their effect on structural components safety margins. However, substantial work is still necessary to incorporate concrete aging effects into such evaluations. In fact, most models in the literature assume pristine concrete conditions and do not account for the impact of aging on the structural components’ fragility curves. This work identifies relevant time-dependent degradation mechanisms and provides simplified models to predict the the evolution of key material properties based on data from the literature. Namely, this work focuses on the aging effects of corrosion, alkali–silica reaction (ASR), and irradiation on reinforced concrete within US Department of Energy (DOE) nuclear facilities and nuclear power plants (NPP) structures. Furthermore, degradation models based on literature data are presented that define the relationship between probabilistic material properties and the concrete’s age. In this work, sampled material properties served as input for a simplified finite element model (FEM) of a critical nuclear structural system, with the output of the FEM being the seismic response for a given ground motion. The results of the FEM were then used within a probabilistic performance assessment with a statistically significant number of samples. The research presented herein addresses the detrimental effects of hazards caused by natural phenomena on deteriorated concrete elements of nuclear installations. This work directly benefits the safety analysis performed on US DOE/ National Nuclear Security Administration (NNSA) nuclear facilities located in areas prone to seismic activity. The results presented herein could aid in the improvement of DOE-STD-1020, the DOE Standard that addresses seismic risk analysis and capacity evaluation in DOE facilities. DOE-STD-1020 refers to the requirements in American Society of Civil Engineers (ASCE) 4-98, now superseded by ASCE 4-16, that shall be met in performing dynamic response analyses and generating in-structure response spectra, provided that such requirements are consistent with the requirements of ASCE/Structural Engineering Institute (SEI) 43-05. Moreover, the results presented herein could also aid in the updating of section C3.1.1. of ASCE 4-16 to account for the effects of aging on the stiffness of reinforced elements and American Concrete Institute (ACI) 349.3R-18, “Report on Evaluation and Repair of Existing Nuclear Safety-Related Concrete Structures.” Ultimately, this work can assist the risk assessment of potential lifetime extension of the existing US commercial nuclear fleet (light water reactors) and the safety analysis of the emerging advanced nuclear reactors. The proposed proof-of-concept methodology employs open-source DOE computational tools and is transferable to commercial software commonly used by engineering firms.
Sucrose is the current baseline additive at the Hanford Waste Treatment and Immobilization Plant in Washington, USA to control foaming during waste feed to glass transitions and the redox state of the glass melt. Alternative reductants are being investigated to alleviate strain on effluent treatment from toxic acetonitrile production from incomplete combustion of sucrose. This study evaluates ceramic additive options including B4C, B6Si, SiC and VB2 in simulated low-activity waste feed, as well as coke dust, probing the feed volume expansion during melting as well as the gas evolution. All alternative reductant options examined significantly reduced acetonitrile production, however there was variability in their effectiveness as foam-reducing agents. VB2 and coke at the appropriate ratios were similarly effective as sucrose in controlling both foam volume and glass redox state, but with considerably less acetonitrile production. B4C, B6Si and SiC showed more promising foam control and very little acetonitrile production, however all of the final glasses were over reduced, i.e., Fe2+/FeT = 0.5. These alternative reductant studies provide operational flexibility to the operation of the vitrification plant, as well as options for alternative raw materials in industrial glass melting.
The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.