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At least 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

UrbanPop: A spatial microsimulation framework for exploring demographic influences on human dynamics

Ensuring the social equity of planning measures in social systems requires an understanding of human dynamics, particularly how individual relationships, activities, and interactions intersect with individual needs. Spatial microsimulation models (SMSMs) support planning for human security goals by representing human dynamics through realistic, georeferenced synthetic populations, that a) provide a complete representation of social systems while b) also protecting individual privacy. In this paper, we present UrbanPop, an open and reproducible SMSM framework for analysis of human dynamics with high spatial, temporal, and demographic resolution. UrbanPop creates synthetic populations of demographically detailed worker and student agents, positioning them first at probable nighttime locations (home), then moving them to probable daytime locations (work/school). Summary aggregations of these populations match the granular detail available at the census block group level in the American Community Survey Summary File (SF), providing realistic approximations of the actual population. UrbanPop users can select particular demographic traits important in their application, resulting in a highly tailored agent population. We first lay out UrbanPop's baseline methodology, including population synthesis, activity modeling, and diagnostics, then demonstrate these capabilities by developing case studies of shifting population distributions and high-risk populations in Knox County, TN during the global COVID-19 pandemic.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Improving biomass and lipid yields of Desmodesmus armatus and Chlorella vulgaris through mutagenesis and high-throughput screening

Advancement of microalgae for use as biofuel feedstock depends on bioprospecting novel strains and then applying classical strain improvement techniques to enhance desirable traits. Here we successfully demonstrate this approach using two novel strains of green algae, identified as Desmodesmus armatus and Chlorella vulgaris, to improve biomass and lipid yields. UV irradiation was utilized to generate random mutations and the resulting populations were analyzed via flow cytometry to quantify lipid fluorescence while enriching for high lipid variants using fluorescence activated cell sorting. Secondary screening was performed via in situ fluorescence staining to identify the single highest lipid producing mutants from each strain. This approach produced a Desmodesmus armatus mutant that exhibited both increased biomass productivity and higher lipid content, which doubled lipid yield from the culture. The resulting Chlorella vulgaris mutant exhibited an increase in growth only, resulting in a 33% increase in lipid yield.

09 BIOMASS FUELS↗
DOE OSTI2020

Effect of digestate and digestate supplemented with biochar on switchgrass growth and chemical composition

Digestate, a by-product of anaerobic digestion, can be an excellent source of nutrients for bioenergy crop production, while biochar, resulting from pyrolyzing biomass, can valorize the nutrients of digestate. The objective of this study was to evaluate the nutritional value of digestate and digestate + biochar for switchgrass production. The greenhouse experiment was conducted to determine the effects of a nitrogen (N) source including 0 N (control), urea (nutrient control), sewage sludge digestate, and sewage sludge digestate + corn stover biochar on switchgrass growth and feedstock composition. Nitrogen sources were observed to significantly increase plant weight at the 32-week harvest, with weight ranging from 94.2 to 125.2 g plant -1 , depending on the N source, compared to 70.7 g plant -1 from the negative control. Moreover, switchgrass treated with digestate + biochar showed higher plant weight than samples treated only with digestate. Nitrogen application of urea, digestate, and digestate + biochar had positive effects on plant height and total leaf area in the 32-week harvests and chlorophyll content in the 8-week harvests. Feedstock quality traits including hemicellulose, cellulose, and lignin content were not affected by N sources in either the 8 or 32-week harvests with the exception of ash concentration in the 32-week harvests. Our results indicate that digestate and digestate + biochar can be a potential substitute for chemical fertilizer, resulting in increased biomass yield.

09 BIOMASS FUELS↗
DOE OSTI2020

Microalgae as a future food source

One of the key challenges that we face in the 21st century is the need to feed an ever-increasing human population with increasingly limited natural resources. Even today it is estimated that roughly 1 out of 9 people in the world are undernourished, of which the most important factor is protein-energy malnutrition. By establishing microalgae as a new food and feed platform, we have the opportunity to increase the supply of these essential products to address global demands in a more efficient and environmentally sustainable way. Many types of algae are nutritionally complete foods, their yields outperform most plant crops, and there is a growing set of tools to develop improved strains of algae. Similar improvements were achieved in traditional crops through thousands of years of breeding and strain selection, whereas with the newest genetic engineering tools and advanced strain selection techniques, similar changes can be implemented in microalgae in just a few years. Here we describe different strategies that could be used to enhance the nutritional content, productivity, and organoleptic traits of algae to help drive development of this new crop. Clearly developing more efficient, sustainable, and nutritious foods and feed would be an enormous benefit for the planet, and algae represents an opportunity to develop a new crop that would complement traditional agriculture, and one that could potential result in a more efficient means to meet the world's food and feed supply.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Building an expanded bio-based economy through synthetic biology

The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.

09 BIOMASS FUELS↗
DOE OSTI2026

A novel xylosylated fucoglucuronan in Penium reveals structural parallels to rhamnogalacturonan-I and its broad evolutionary footprint in lower plants

Green algae inhabit aquatic environments across the planet and play a crucial role in sustaining the global ecosystem. Ancestors of some Charophytes adapted to terrestrial conditions and eventually evolved into land plants. Extant green algae have inherited traits from their ancestors and evolved into their current morphological and chemical forms, as reflected by their cell walls with distinct shapes and compositions. To illuminate the evolution of plant cell walls and bridge the gap between green algae and land plants, we investigated the charophyte Penium margaritaceum, a close relative of terrestrial plants. We discovered a previously unknown polysaccharide in both its culture medium and cell wall. This polysaccharide, termed xylosylated fucoglucuronan (XFG), possesses a rhamnogalacturonan-I (RG-I)-like backbone composed of repeating [-3-α-Fucp-(1,4)-α-GlcpA-] disaccharides that are extensively xylosylated and acetylated. Surveying approximately 20 non-vascular plants revealed that XFG and RG-I (or related structures) first emerge in certain Chlorophyceae and subsequently co-occur throughout lineages along the evolutionary trajectory to bryophytes, thereby bridging aquatic green algae to early land plants. The striking structural parallels between XFG, RG-I, and ulvan suggest a shared evolutionary origin, offering new insight into how plant cell walls adapted during the transition from marine to freshwater environments and ultimately to land.

Algae↗
DOE OSTI2020

Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types

Characterizing the tissue-specific binding sites of transcription factors (TFs) is essential to reconstruct gene regulatory networks and predict functions for non-coding genetic variation. DNase-seq footprinting enables the prediction of genome-wide binding sites for hundreds of TFs simultaneously. Despite the public availability of high-quality DNase-seq data from hundreds of samples, a comprehensive, up-to-date resource for the locations of genomic footprints is lacking. Here, we develop a scalable footprinting workflow using two state-of-the-art algorithms: Wellington and HINT. We apply our workflow to detect footprints in 192 ENCODE DNase-seq experiments and predict the genomic occupancy of 1,515 human TFs in 27 human tissues. We validate that these footprints overlap true-positive TF binding sites from ChIP-seq. We demonstrate that the locations, depth, and tissue specificity of footprints predict effects of genetic variants on gene expression and capture a substantial proportion of genetic risk for complex traits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience

Roots remain understudied as the site of complex and important biological interactions mediating plant productivity. In grain and bioenergy crops, grass root specialized metabolites (GRSM) are central to key interactions, yet our basic knowledge of the chemical language remains fragmentary. Continued improvements in plant genome assembly and metabolomics are enabling large-scale advances in the discovery of specialized metabolic pathways as a means of regulating root-biotic interactions. Metabolomics, transcript coexpression analyses, forward genetic studies, gene synthesis and heterologous expression assays drive efficient pathway discoveries. Functional genetic variants identified through genome wide analyses, targeted CRISPR/Cas9 approaches, and both native and non-native overexpression studies critically inform novel strategies for bioengineering metabolic pathways to improve plant traits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Advances in engineering algae for biofuel production

While algae demonstrate potential as a sustainable fuel source, low productivities limit the economic realization of algal biofuels. High-throughput strain engineering, omics-informed genome-scale modeling, and microbiome engineering are key technologies for enabling algal biofuels. High-throughput strain engineering efforts generate improved traits, including high biomass productivity and lipid content, in diverse algal species. Genome-scale models, constructed with the aid of omics data, provide insight into metabolic limitations and guide rational algal strain engineering efforts. As outdoor cultivation systems introduce exogenous organisms, microbiome engineering seeks to eliminate harmful organisms and introduce beneficial species. In conclusion, optimizing algal biomass production and lipid content using these technologies may overcome the productivity barrier for the commercialization of algal biofuels.

09 BIOMASS FUELS↗
DOE OSTI2021

The deep-DRT: A deep neural network approach to deconvolve the distribution of relaxation times from multidimensional electrochemical impedance spectroscopy data

Electrochemical impedance spectroscopy (EIS) is an experimental technique ubiquitously used to study electrochemical systems. However, conventional EIS data interpretation through physical and equivalent circuit models is challenging because physical models are problem-specific, and equivalent circuits are often just lumped-element analogs lacking physical meaning. The distribution of relaxation times (DRT) has emerged as a complementary approach to resolve these issues. One drawback of conventional DRT deconvolution is that the EIS data is understood to be (only) a function of frequency (i.e. 1D data) and deconvolved accordingly. This work proposes a novel deconvolution method based on deep neural networks (DNNs), allowing the analysis of multidimensional EIS spectra to bridge data dependency on both frequencies and experimental conditions. Two particularly appealing traits of the deep-DRT method developed in this article are that neither regularization nor specific spacing on the state variables defining the experiment are required. Finally, leveraging DNN to examine complex EIS spectra and their dependence on experimental conditions, this work opens a new research direction in the area of EIS analysis and DRT deconvolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

How will United States commercial building energy use be impacted by IPCC climate scenarios?

Climate change and anthropogenically-forced shift of weather in the future will impact energy use and resilience of both the built environment and the electric grid. The aim of this analysis is to understand how future climate scenarios will impact electricity and natural gas use of commercial buildings in the United States. Here, this study analyzes this impact for 2030, 2045, and 2100 using Representative Concentration Pathways (RCP) scenarios defined in Intergovernmental Panel on Climate Change (IPCC) Assessment Report 5. The large, gridded simulation of meteorological variables for RCPs 2.6, 4.5, 6.0, and 8.5 are selected and downscaled to make available hourly Future Meteorological Year (FMY) weather files for use and improvement in subsequent studies. High performance computing resources use these FMYs to simulate commercial prototype buildings in every American Society of Heating, Refrigeration, and Air Conditioning Engineers (ASHRAE) climate zone of the United States (US), and results are scaled to nation-wide energy use using conditioned floor area multipliers. The analysis is conducted without speculating the physical and performance traits of future buildings or the grid characteristics. This analysis quantifies the impact of climate change on source electrical and natural gas usage for commercial buildings in the United States over the next 80 years. If US commercial floorspace remained constant, total energy use by 2100 is predicted between an 1.75% decrease under the greatest emission scenario (8.5) and a 1.76% increase under the lowest emission scenario (2.6). When adjusted for anticipated urban growth by 2100, the predicted range is 65% increase (8.5) and 71% increase (2.6). Under a global temperature rise climate scenario, the warmest US climate zones will see a large increases in electricity use derived from space cooling while the coldest US climate zones will see significant decreases in natural gas use caused by the decrease in heating necessary. While climate change may ultimately require adaptations of the built environment to withstand its effects and because the United States is a country that requires more heating than cooling, from a building energy perspective, climate change (average temperature rise) is a net energy saver for the United States.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Migrating Populus with climate change: Phenology, coppice management, cold spell susceptibility, leaf dynamics, and biomass production

Understanding the phenology and productivity of Populus species is crucial for effective management and conservation strategies amid climate change. We investigated leaf budbreak timing, susceptibility to cold damage, leaf dynamics, and biomass production of 168 Populus genotypes with diverse provenances in the southeastern United States. Our study revealed significant variation in budbreak timing across different taxa and years, with genotypes inheriting traits adapted to their parents’ local climates. Temperature emerged as a key factor triggering budbreak, while leaf development depended on other environmental cues such as photoperiod. Notably, budbreak occurred approximately 20 days earlier in 2023 compared to 2022 due to higher accumulated degree days (ADDs). Short-rotation-coppice (SRC) management delayed budbreak by five to ten days. Cold damage was significant in 2023, particularly for genotypes from northern provenances and those with P. maximowiczii parentage. Severe damage was also observed in eastern cottonwood ( Populus deltoides ​× ​ Populus deltoides (D ​× ​D)) genotypes, despite most having southeastern US parentages. Leaf dynamics, including leaf duration and leaf area index (LAI), varied across taxa and sites, with earlier budbreak correlating with extended growing seasons and increased LAI. Biomass production was intricately linked to phenological events, with earlier budbreak leading to increased biomass production and greater susceptibility to cold damage. Our findings highlight the importance of genetics, environment, and coppicing management in understanding and managing Populus phenology and biomass production. These insights provide valuable guidance for developing effective breeding, conservation, and management strategies for Populus species in the context of climate change.

Accumulated degree days (ADDs)↗
DOE OSTI2023

Hydraulic safety and growth rather than climate of origin influence survival in desert shrubs and trees

The species-poor woodlands and forests in arid regions are particularly vulnerable to climate change induced plant die-off. Searching for species suitable to replant in these areas is an effective way to prevent further expansion of land desertification. Good knowledge of drought resistance of species is critical for current replanting efforts, however, the related plant survival mechanisms in the process of restoration remain limited. Here, we tested the dominant drivers of plant survival in relation to climate factors, growth characteristics and functional traits including hydraulics and gas exchange across 35 multiple shrub and tree woody species in a common garden at the Tengger Desert, northwest China. We found the desert plants had a wide range of hydraulic thresholds among these desert species, with relative high hydraulic safety, and low xylem hydraulic conductivity. Pant survival was largely determined by hydraulic safety and growth status, but was not affected by the climate of the species’ site of origin. Shrubs and trees diverged in hydraulic and growth characteristics, while there was no difference between native and introduced species. In this study, our results highlight the critical roles of hydraulic safety and growth on determining the survival and drought adaptation during desert vegetation development, which provide a new insight into ecological restoration in arid regions under changing climate conditions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Salinity exposure affects lower-canopy specific leaf area of upland trees in a coastal deciduous forest

Sea level rise and increasing storm surges are likely to affect the canopy physiology, ecology, and structure of coastal forests, even well in advance of tree mortality. Laboratory and greenhouse studies have documented that saltwater exposure can trigger changes in leaf-level physiology and morphology, but few in situ studies have examined how tree-specific leaf area (SLA), the ratio of leaf area to mass and a crucial trait and model parameter, is affected by saline soils. We conducted an observational study of SLA in a mid-Atlantic (USA) coastal deciduous forest, taking advantage of a natural gradient in salinity along a tidal creek. Measured SLA of the 239 trees and seven species sampled ranged from Carya glabra (N = 6 trees, mean SLA = 277.9±36.3cm 2 /g) to Fagus grandifolia (N=60, 321.9±62.9cm 2 g); as expected, trees species and canopy position (sun versus shade) significantly affected SLA. For trees (N=100) directly exposed to the tidal creek, salinity was highly significant after accounting for species (P<0.001), with trees in the lower reaches of the creek having lower SLA. Leaf area index (LAI), computed from SLA and litter traps, ranged from 4.8 to 15.8 and was inversely related to salinity exposure; the spatial variability in leaf litter production contributed much more to LAI uncertainty than did SLA variability. These in situ results are correlative but consistent with the hypothesis, based on previous greenhouse studies, that the stress of chronic salinity exposure changes species’ leaf morphology. Our findings are useful for understanding the growing effects of saltwater intrusion into upland forests, as well as parameterizing and testing ecosystem-scale models simulating forest stressors and disturbances at the terrestrial-aquatic interface.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Recent advances in biological activities of lignin and emerging biomedical applications: A short review

As an abundant biopolymer, lignin gains interest owing to its renewable nature and polyphenolic structure. It possesses many biological activities such as antioxidant activity, antimicrobial activity, and biocompatibility. Studies are being carried out to relate the biological activities to the polyphenolic structures. These traits present lignin as a natural compound being used in biomedical field. Lignin nanoparticles (LNPs) are being investigated for safe use in drug and gene delivery, and lignin-based hydrogels are being explored as wound dressing materials, in tissue engineering and 3D printing. In addition, lignin and its derivatives have shown the potential to treat diabetic disease. This review summarizes latest research results on the biological activities of lignin and highlights potential applications exampled by selective studies. It helps to transform lignin from a waste material into valuable materials and products.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Introduction: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic trait that can cause hemolytic anemia. To date, over 150 nonsynonymous mutations have been identified in G6PD, with pathogenic mutations clustering near the dimer and/or tetramer interface and the allosteric NADP + -binding site. Recently, our lab identified a small molecule that activates G6PD variants by stabilizing the allosteric NADP + and dimer complex, suggesting therapeutics that target these regions may improve structural defects. Here, we elucidated the connection between allosteric NADP + binding, oligomerization, and pathogenicity to determine whether oligomer stabilization can be used as a therapeutic strategy for G6PD deficiency (G6PD def ). We first solved the crystal structure for G6PD K403Q , a mutant that mimics the physiological acetylation of wild-type G6PD in erythrocytes and demonstrated that loss of allosteric NADP + binding induces conformational changes in the dimer. These structural changes prevent tetramerization, are unique to Class I variants (the most severe form of G6PD def ), and cause the deactivation and destabilization of G6PD. We also introduced nonnative cysteines at the oligomer interfaces and found that the tetramer complex is more catalytically active and stable than the dimer. Furthermore, stabilizing the dimer and tetramer improved protein stability in clinical variants, regardless of clinical classification, with tetramerization also improving the activity of G6PD K403Q and Class I variants. These findings were validated using enzyme activity and thermostability assays, analytical size-exclusion chromatography (SEC), and SEC coupled with small-angle X-ray scattering (SEC-SAXS). Taken together, our findings suggest a potential therapeutic strategy for G6PD def and provide a foundation for future drug discovery efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Ancestral archaea expanded the genetic code with pyrrolysine

The pyrrolysyl-tRNA synthetase (PylRS) facilitates the cotranslational installation of the 22nd amino acid pyrrolysine. Owing to its tolerance for diverse amino acid substrates, and its orthogonality in multiple organisms, PylRS has emerged as a major route to install noncanonical amino acids into proteins in living cells. Recently, a novel class of PylRS enzymes was identified in a subset of methanogenic archaea. Enzymes within this class (ΔPylSn) lack the N-terminal tRNA-binding domain that is widely conserved amongst PylRS enzymes, yet remain active and orthogonal in bacteria and eukaryotes. In this study, we use biochemical and in vivo UAG-readthrough assays to characterize the aminoacylation efficiency and substrate spectrum of a ΔPylSn class PylRS from the archaeon Candidatus Methanomethylophilus alvus. We show that, compared with the full-length enzyme from Methanosarcina mazei, the Ca. M. alvus PylRS displays reduced aminoacylation efficiency but an expanded amino acid substrate spectrum. To gain insight into the evolution of ΔPylSn enzymes, we performed molecular phylogeny using 156 PylRS and 105 pyrrolysine tRNA (tRNA Pyl ) sequences from diverse archaea and bacteria. This analysis suggests that the PylRS•tRNA Pyl pair diverged before the evolution of the three domains of life, placing an early limit on the evolution of the Pyl-decoding trait. Furthermore, our results document the coevolutionary history of PylRS and tRNA Pyl and reveal the emergence of tRNA Pyl sequences with unique A73 and U73 discriminator bases. The orthogonality of these tRNA Pyl species with the more common G73-containing tRNA Pyl will enable future efforts to engineer PylRS systems for further genetic code expansion.

59 BASIC BIOLOGICAL SCIENCES↗