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At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

A native IgE in complex with profilin provides insights into allergen recognition and cross-reactivity

Allergies have become a rising health problem, where plentiful substances can trigger IgE-mediated allergies in humans. While profilins are considered minor allergens, these ubiquitous proteins are primary molecules involved in cross-reactivity and pollen-food allergy syndrome. Here we report the first crystal structures of murine Fab/IgE, with its chains naturally paired, in complex with the allergen profilin from Hevea brasiliensis (Hev b 8). The crystallographic models revealed that the IgE’s six complementarity-determining regions (CDRs) interact with the allergen, comprising a rigid paratope-epitope surface of 926 Å 2 , which includes an extensive network of interactions. Interestingly, we also observed previously unreported flexibility at Fab/IgE’s elbow angle, which did not influence the shape of the paratope. The Fab/IgE exhibits a high affinity for Hev b 8, even when using 1 M NaCl in BLI experiments. Finally, based on the encouraging cross-reactivity assays using two mutants of the maize profilin (Zea m 12), this antibody could be a promising tool in IgE engineering for diagnosis and research applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Elevated CO 2 shifts the functional structure and metabolic potentials of soil microbial communities in a C 4 agroecosystem

Atmospheric CO 2 concentration is continuously increasing, and previous studies have shown that elevated CO 2 (eCO 2 ) significantly impacts C 3 plants and their soil microbial communities. However, little is known about effects of eCO 2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C 4 plants. Here we showed that a C 4 maize agroecosystem exposed to eCO 2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0–5 cm and 5–15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO 2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO 2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO 2 explained 5.2% and 3.8%, respectively. This study implies that eCO 2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C 4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C 4 agroecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Agriculture intensifies soil moisture decline in Northern China

Northern China is one of the most densely populated regions in the world. Agricultural activities have intensified since the 1980s to provide food security to the country. However, this intensification has likely contributed to an increasing scarcity in water resources, which may in turn be endangering food security. Based on in-situ measurements of soil moisture collected in agricultural plots during 1983–2012, we find that topsoil (0–50 cm) volumetric water content during the growing season has declined significantly (p<0.01), with a trend of -0.011 to -0.015 m3 m-3 per decade. Observed discharge declines for the three large river basins are consistent with the effects of agricultural intensification, although other factors (e.g. dam constructions) likely have contributed to these trends. Practices like fertilizer application have favoured biomass growth and increased transpiration rates, thus reducing available soil water. In addition, the rapid proliferation of water-expensive crops (e.g., maize) and the expansion of the area dedicated to food production have also contributed to soil drying. Adoption of alternative agricultural practices that can meet the immediate food demand without compromising future water resources seem critical for the sustainability of the food production system.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Quadrupolar density structures in driven magnetic reconnection experiments with a guide field

Magnetic reconnection is a ubiquitous process in plasma physics, driving rapid and energetic events such as coronal mass ejections. Reconnection between magnetic fields with arbitrary shear can be decomposed into an anti-parallel reconnecting component and a non-reconnecting guide-field component, which is parallel to the reconnecting electric field. This guide field modifies the structure of the reconnection layer and the reconnection rate. We present results from experiments on the MAIZE pulsed-power generator (500 kA peak current, 200 ns rise time), which use two exploding wire arrays, tilted in opposite directions, to embed a guide field in the plasma flows with a relative strength b≡B g /B rec =0, 0.4, or 1. The reconnection layers in these experiments have widths that are less than the ion skin depth, d i =c/ω pi , indicating the importance of the Hall term, which generates a distinctive quadrupolar magnetic field structure along the separatrices of the reconnection layer. Using laser imaging interferometry, we observe quadrupolar structures in the line-integrated electron density, consistent with the interaction of the embedded guide field with the quadrupolar Hall field. Our measurements extend over much larger length scales (40d i ) at higher β (∼1) than previous experiments, providing an insight into the global structure of the reconnection layer.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Impact of nano iron and manganese metal-oxides on contaminant interaction and micronutrient uptake in agricultural systems – a review

Rising population growth and increase global food demand has made meeting the demands of food production and security a major challenge world-wide. Nanotechnology has become a remediation strategy of interest as a sustainable tool in agricultural systems, where it aims to increase efficiency in techniques such as food monitoring, pathogen control, water treatment, and targeted delivery of agrochemicals. In addition to these platforms, nanoparticles, such as nano metal-oxides, have been engineered to act as contaminant scavengers and could be applied to wide range of systems. Numerous studies have looked at scavenging ability of nano metal-oxides (NMOs) but few have looked at them in agricultural and food systems. In this review, we specifically address previous research that has used nano Fe and Mn oxides in agricultural systems, particularly world-wide crop production of four major staple foods – rice, wheat, maize, and soybean. Nano Fe and Mn oxides are strong candidates for immobilization of agricultural contaminants in soils and, because they are naturally ubiquitous, have the potential to be a cost-effective and sustainable technology compared to other remediation strategies.

Gillispie, Elizabeth C.↗
DOE OSTI2016

Grasses suppress shoot-borne roots to conserve water during drought

Significance Grasses, whose members constitute key food and bioenergy crops worldwide, use unique developmental programs to establish the root system from the shoot. Shoot-borne crown roots originate near the soil surface and provide the main conduits through which the plant takes up water and nutrients. We show that crown root development is the major target of drought stress signaling. Water deficit-triggered crown root arrest provides an important mechanism to conserve water under drought, and this response is widely conserved across grass species. Substantial phenotypic variation exists in maize for this trait, which may be a useful target in breeding efforts to improve drought tolerance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Simulated vs. empirical weather responsiveness of crop yields: US evidence and implications for the agricultural impacts of climate change

Global gridded crop models (GGCMs) are the workhorse of assessments of the agricultural impacts of climate change. Yet the changes in crop yields projected by different models in response to the same meteorological forcing can differ substantially. Through an inter-method comparison, we provide a first glimpse into the origins and implications of this divergence—both among GGCMs and between GGCMs and historical observations. We examine yields of rainfed maize, wheat, and soybeans simulated by six GGCMs as part of the Inter-Sectoral Impact Model Intercomparison Project-Fast Track (ISIMIP-FT) exercise, comparing 1981–2004 hindcast yields over the coterminous United States (US) against US Department of Agriculture (USDA) time series for about 1000 counties. Leveraging the empirical climate change impacts literature, we estimate reduced-form econometric models of crop yield responses to temperature and precipitation exposures for both GGCMs and observations. We find that up to 60% of the variance in both simulated and observed yields is attributable to weather variation. A majority of the GGCMs have difficulty reproducing the observed distribution of percentage yield anomalies, and exhibit aggregate responses that show yields to be more weather-sensitive than in the observational record over the predominant range of temperature and precipitation conditions. In conclusion, this disparity is largely attributable to heterogeneity in GGCMs' responses, as opposed to uncertainty in historical weather forcings, and is responsible for widely divergent impacts of climate on future crop yields.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

CO 2 fertilization of crops offsets yield losses due to future surface ozone damage and climate change

Tropospheric ozone (O 3 ) is harmful to plant productivity and negatively impacts crop yields. O3 concentrations are projected to decrease globally in the optimistic Representative Concentration Pathway of 2.6 W m –2 (RCP2.6) but increase globally following the high-emission scenario under the RCP8.5, with substantial implications for global food security. The damaging effect of O 3 on future crop yield is affected by CO 2 fertilization and climate change, and their interactions for RCP scenarios have yet to be quantified. In this study, we used the Joint UK Land Environment Simulator modified to include crops (JULES-crop) to quantify the impacts, and relative importance of present-day and future O3, CO 2 concentration and meteorology on crop production at the regional scale until 2100 following RCP2.6 and RCP8.5 scenarios. We focus on eight major crop-producing regions that cover the production of wheat, soybean, maize, and rice. Our results show that CO 2 alone has the largest effect on regional yields, followed by climate and O 3 . However, the CO 2 fertilization effect is offset by the negative impact of tropospheric O 3 in regions with high O 3 concentrations, such as South Asia and China. Simulated crop yields in 2050 were compared with Food and Agriculture Organisation (FAO) statistics to investigate the differences between a socioeconomic and a biophysical process-based approach. Results showed that FAO estimates are closer to our JULES-crop RCP8.5 scenario. This study demonstrates that air pollution could be the biggest threat to future food production and highlights an urgent policy need to mitigate the threat of climate change and O 3 pollution on food security.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Theoretical evidence that root penetration ability interacts with soil compaction regimes to affect nitrate capture

Abstract Background and Aims Although root penetration of strong soils has been intensively studied at the scale of individual root axes, interactions between soil physical properties and soil foraging by whole plants are less clear. Here we investigate how variation in the penetration ability of distinct root classes and bulk density profiles common to real-world soils interact to affect soil foraging strategies. Methods We utilize the functional–structural plant model ‘OpenSimRoot’ to simulate the growth of maize (Zea mays) root systems with variable penetration ability of axial and lateral roots in soils with (1) uniform bulk density, (2) plow pans and (3) increasing bulk density with depth. We also modify the availability and leaching of nitrate to uncover reciprocal interactions between these factors and the capture of mobile resources. Key Results Soils with plow pans and bulk density gradients affected overall size, distribution and carbon costs of the root system. Soils with high bulk density at depth impeded rooting depth and reduced leaching of nitrate, thereby improving the coincidence of nitrogen and root length. While increasing penetration ability of either axial or lateral root classes produced root systems of comparable net length, improved penetration of axial roots increased allocation of root length in deeper soil, thereby amplifying N acquisition and shoot biomass. Although enhanced penetration ability of both root classes was associated with greater root system carbon costs, the benefit to plant fitness from improved soil exploration and resource capture offset these. Conclusions While lateral roots comprise the bulk of root length, axial roots function as a scaffold determining the distribution of these laterals. In soils with high soil strength and leaching, root systems with enhanced penetration ability of axial roots have greater distribution of root length at depth, thereby improving capture of mobile resources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species

Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Chromosome assembled and annotated genome sequence of Aspergillus flavus NRRL 3357

Abstract Aspergillus flavus is an opportunistic pathogen of crops, including peanuts and maize, and is the second leading cause of aspergillosis in immunocompromised patients. A. flavus is also a major producer of the mycotoxin, aflatoxin, a potent carcinogen, which results in significant crop losses annually. The A. flavus isolate NRRL 3357 was originally isolated from peanut and has been used as a model organism for understanding the regulation and production of secondary metabolites, such as aflatoxin. A draft genome of NRRL 3357 was previously constructed, enabling the development of molecular tools and for understanding population biology of this particular species. Here, we describe an updated, near complete, telomere-to-telomere assembly and re-annotation of the eight chromosomes of A. flavus NRRL 3357 genome, accomplished via long-read PacBio and Oxford Nanopore technologies combined with Illumina short-read sequencing. A total of 13,715 protein-coding genes were predicted. Using RNA-seq data, a significant improvement was achieved in predicted 5’ and 3’ untranslated regions, which were incorporated into the new gene models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High-resolution mapping reveals hotspots and sex-biased recombination in Populus trichocarpa

Abstract Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DCT4 —A New Member of the Dicarboxylate Transporter Family in C 4 Grasses

Malate transport shuttles atmospheric carbon into the Calvin–Benson cycle during NADP-ME C 4 photosynthesis. Previous characterizations of several plant dicarboxylate transporters (DCT) showed that they efficiently exchange malate across membranes. Here, we identify and characterize a previously unknown member of the DCT family, DCT4, in Sorghum bicolor. We show that SbDCT4 exchanges malate across membranes and its expression pattern is consistent with a role in malate transport during C 4 photosynthesis. SbDCT4 is not syntenic to the characterized photosynthetic gene ZmDCT2, and an ortholog is not detectable in the maize reference genome. We found that the expression patterns of DCT family genes in the leaves of Zea mays, and S. bicolor varied by cell type. Our results suggest that subfunctionalization, of members of the DCT family, for the transport of malate into the bundle sheath plastids, occurred during the process of independent recurrent evolution of C 4 photosynthesis in grasses of the PACMAD clade. We also show that this subfunctionalization is lineage independent. Our results challenge the dogma that key C 4 genes must be orthologues of one another among C 4 species, and shed new light on the evolution of C 4 photosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Evolution of Centromeric Retrotransposons in Grasses

Centromeric retrotransposons (CRs) constitute a family of plant retroelements, some of which have the ability to target their insertion almost exclusively to the functional centromeres. Our exhaustive analysis of CR family members in four grass genomes revealed not only horizontal transfer (HT) of CR elements between the oryzoid and panicoid grass lineages but also their subsequent recombination with endogenous elements that in some cases created prolific recombinants in foxtail millet and sorghum. HT events are easily identifiable only in cases where host genome divergence significantly predates HT, thus documented HT events likely represent only a fraction of the total. If the more difficult to detect ancient HT events occurred at frequencies similar to those observable in present day grasses, the extant long terminal repeat retrotransposons represent the mosaic products of HT and recombination that are optimized for retrotransposition in their host genomes. This complicates not only phylogenetic analysis but also the establishment of a meaningful retrotransposon nomenclature, which we have nevertheless attempted to implement here. In contrast to the plant-centric naming convention used currently for CR elements, we classify elements primarily based on their phylogenetic relationships regardless of host plant, using the exhaustively studied maize elements assigned to six different subfamilies as a standard. The CR2 subfamily is the most widely distributed of the six CR subfamilies discovered in grass genomes to date and thus the most likely to play a functional role at grass centromeres.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Predicted range expansion of Prostephanus truncatus (Coleoptera: Bostrichidae) under projected climate change scenarios

Abstract The larger grain borer (Prostephanus truncatus [Horn] [Coleoptera: Bostrichidae]) is a wood-boring insect native to Central America and adapted to stored maize and cassava. It was accidentally introduced to Tanzania and became a pest across central Africa. Unlike many grain pests, P. truncatus populations can establish and move within forests. Consequently, novel infestations can occur without human influence. The objectives of our study were to (i) develop an updated current suitability projection for P. truncatus, (ii) assess its potential future distribution under different climate change scenarios, and (iii) identify climate variables that best inform the model. We used WALLACE and MaxEnt to predict potential global distribution by incorporating bioclimatic variables and occurrence records. Future models were projected for 2050 and 2070 with Representative Concentration Pathways (RCPs) 2.6 (low change) and 8.5 (high change). Distribution was most limited by high precipitation and cold temperatures. Globally, highly suitable areas (> 75%) primarily occurred along coastal and equatorial regions with novel areas in northern South America, India, southeastern Asia, Indonesia, and the Philippines, totaling 7% under current conditions. Highly suitable areas at RCPs 2.6 and 8.5 are estimated to increase to 12% and 15%, respectively, by 2050 and increase to 19% in 2070 under RCP 8.5. Centroids of highly suitable areas show distribution centers moving more inshore and away from the equator. Notably, the result is a range expansion, not a shift. Results can be used to decrease biosecurity risks through more spatially explicit and timely surveillance programs for targeting the exclusion of this pest.

Entomology↗
DOE OSTI2021

Can improved canopy light transmission ameliorate loss of photosynthetic efficiency in the shade? An investigation of natural variation in Sorghum bicolor

Abstract Previous studies have found that maximum quantum yield of CO2 assimilation (Φ CO2,max,app) declines in lower canopies of maize and miscanthus, a maladaptive response to self-shading. These observations were limited to single genotypes, leaving it unclear whether the maladaptive shade response is a general property of this C4 grass tribe, the Andropogoneae. We explored the generality of this maladaptation by testing the hypothesis that erect leaf forms (erectophiles), which allow more light into the lower canopy, suffer less of a decline in photosynthetic efficiency than drooping leaf (planophile) forms. On average, Φ CO2,max,app declined 27% in lower canopy leaves across 35 accessions, but the decline was over twice as great in planophiles than in erectophiles. The loss of photosynthetic efficiency involved a decoupling between electron transport and assimilation. This was not associated with increased bundle sheath leakage, based on 13C measurements. In both planophiles and erectophiles, shaded leaves had greater leaf absorptivity and lower activities of key C4 enzymes than sun leaves. The erectophile form is considered more productive because it allows a more effective distribution of light through the canopy to support photosynthesis. We show that in sorghum, it provides a second benefit, maintenance of higher Φ CO2,max,app to support efficient use of that light resource.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy

Abstract Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.

59 BASIC BIOLOGICAL SCIENCES↗