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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Novel symmetry-preserving neural network model for phylogenetic inference

Abstract Motivation Scientists world-wide are putting together massive efforts to understand how the biodiversity that we see on Earth evolved from single-cell organisms at the origin of life and this diversification process is represented through the Tree of Life. Low sampling rates and high heterogeneity in the rate of evolution across sites and lineages produce a phenomenon denoted “long branch attraction” (LBA) in which long nonsister lineages are estimated to be sisters regardless of their true evolutionary relationship. LBA has been a pervasive problem in phylogenetic inference affecting different types of methodologies from distance-based to likelihood-based. Results Here, we present a novel neural network model that outperforms standard phylogenetic methods and other neural network implementations under LBA settings. Furthermore, unlike existing neural network models in phylogenetics, our model naturally accounts for the tree isomorphisms via permutation invariant functions which ultimately result in lower memory and allows the seamless extension to larger trees. Availability and implementation We implement our novel theory on an open-source publicly available GitHub repository: https://github.com/crsl4/nn-phylogenetics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A systems genetic analysis identifies putative mechanisms and candidate genes regulating vessel traits in poplar wood

Wood is the water conducting tissue of tree stems. Like most angiosperm trees, poplar wood contains water-conducting vessel elements whose functional properties affect water transport and growth rates, as well as susceptibility to embolism and hydraulic failure during water stress and drought. Here we used a unique hybrid poplar pedigree carrying genomically characterized chromosomal insertions and deletions to undertake a systems genomics analysis of vessel traits. We assayed gene expression in wood forming tissues from clonal replicates of genotypes covering dosage quantitative trait loci with insertions and deletions, genotypes with extreme vessel trait phenotypes, and control genotypes. A gene co-expression analysis was used to assign genes to modules, which were then used in integrative analyses to identify modules associated with traits, to identify putative molecular and cellular processes associated with each module, and finally to identify candidate genes using multiple criteria including dosage responsiveness. These analyses identified known processes associated with vessel traits including stress response, abscisic acid and cell wall biosynthesis, and in addition identified previously unexplored processes including cell cycle and protein ubiquitination. We discuss our findings relative to component processes contributing to vessel trait variation including signaling, cell cycle, cell expansion, and cell differentiation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Learning epistatic polygenic phenotypes with Boolean interactions

Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1 , a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Exploring the Structural, Biochemical, and Functional Diversity of Glycoside Hydrolase Family 12 from Penicillium subrubescens

Glycoside hydrolases (GHs) play an essential role in plant biomass degradation and modification for the sustainable production of biochemicals. The filamentous Ascomycete fungus Penicillium subrubescens contains a higher number of GH12 candidates compared to related species. Therefore, we aimed to compare P. subrubescens GH12s for their ability and substrate specificity for plant cell wall polysaccharide degradation and species’ potential as a source of novel enzymes for plant biomass valorization. Our re-evaluated phylogenetic analysis of fungal GH12 members showed that the P. subrubescens GH12s were located in different (new) clades. Biochemical characterization marked PsEglA as an endoglucanase and four other P. subrubescens GH12s (i.e., PsXegA–D) as xyloglucanases. Interestingly, structural features of PsXegD and PsXegE were more comparable to those of Basidiomycete GH12 xyloglucanases with a unique open substrate-binding cleft. PsUegA displayed dual xyloglucanase and endoglucanase activity and also showed distinct structural features. Comparative transcriptome analysis supported the functional diversity of P. subrubescens GH12s in plant biomass degradation. The gene encoding PsUegA was expressed under diverse conditions, suggesting a scouting role for this enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Responses of the Plant Cell Wall to Sub-Zero Temperatures: A Brief Update

Our general understanding of plant responses to sub-zero temperatures focuses on mechanisms that mitigate stress to the plasma membrane. The plant cell wall receives comparatively less attention, and questions surrounding its role in mitigating freezing injury remain unresolved. Despite recent molecular discoveries that provide insight into acclimation responses, the goal of reducing freezing injury in herbaceous and woody crops remains elusive. This is likely due to the complexity associated with adaptations to low temperatures. Understanding how leaf cell walls of herbaceous annuals promote tissue tolerance to ice does not necessarily lead to understanding how meristematic tissues are protected from freezing by tissue-level barriers formed by cell walls in overwintering tree buds. In this mini-review, we provide an overview of biological ice nucleation and explain how plants control the spatiotemporal location of ice formation. We discuss how sugars and pectin side chains alleviate adhesive injury that develops at sub-zero temperatures between the matrix polysaccharides and ice. The importance of site-specific cell-wall elasticity to promote tissue expansion for ice accommodation and control of porosity to impede ice growth and promote supercooling will be presented. How specific cold-induced proteins modify plant cell walls to mitigate freezing injury will also be discussed. The opinions presented in this report emphasize the importance of a plant’s developmental physiology when characterizing mechanisms of freezing survival.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Streamlining heterologous expression of top carbonic anhydrases in Escherichia coli : bioinformatic and experimental approaches

Carbonic anhydrase (CA) enzymes facilitate the reversible hydration of CO 2 to bicarbonate ions and protons. Identifying efficient and robust CAs and expressing them in model host cells, such as Escherichia coli, enables more efficient engineering of these enzymes for industrial CO 2 capture. However, expression of CAs in E. coli is challenging due to the possible formation of insoluble protein aggregates, or inclusion bodies. This makes the production of soluble and active CA protein a prerequisite for downstream applications. In this study, we streamlined the process of CA expression by selecting seven top CA candidates and used two bioinformatic tools to predict their solubility for expression in E. coli. The prediction results place these enzymes in two categories: low and high solubility. Our expression of high solubility score CAs (namely CA5-SspCA, CA6-SazCAtrunc, CA7-PabCA and CA8-PhoCA) led to significantly higher protein yields (5 to 75 mg purified protein per liter) in flask cultures, indicating a strong correlation between the solubility prediction score and protein expression yields. Furthermore, phylogenetic tree analysis demonstrated CA class-specific clustering patterns for protein solubility and production yields. Unexpectedly, we also found that the unique N-terminal, 11-amino acid segment found after the signal sequence (not present in its homologs), was essential for CA6-SazCA activity. Overall, this work demonstrated that protein solubility prediction, phylogenetic tree analysis, and experimental validation are potent tools for identifying top CA candidates and then producing soluble, active forms of these enzymes in E. coli. The comprehensive approaches we report here should be extendable to the expression of other heterogeneous proteins in E. coli.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Factors underlying a latitudinal gradient in the S/G lignin monomer ratio in natural poplar variants

The chemical composition of wood plays a pivotal role in the adaptability and structural integrity of trees. However, few studies have investigated the environmental factors that determine lignin composition and its biological significance in plants. Here, we examined the lignin syringyl-to-guaiacyl (S/G) ratio in members of a Populus trichocarpa population sourced from their native habitat and conducted a genome wide association study to identify genes linked to lignin formation. Our results revealed many significant associations, suggesting that lignin biosynthesis is a complex polygenic trait. Additionally, we found an increase in the S/G ratio from northern to southern geographic origin of the trees sampled, along with a corresponding metabolic and transcriptional reprogramming of xylem cell wall biosynthesis. Further molecular analysis identified a mutation in a cell wall laccase genetically associated with higher S/G ratios that predominate in trees from warmer lower latitudes. Collectively, our findings suggest that lignin heterogeneity arises from an evolutionary process enabling poplar adaptation to different climatic challenges.

adaptation↗
DOE OSTI2022

Heterogeneous isotope effects decouple conifer leaf and branch sugar δ 18 O and δ 13 C

Isotope ratios of tree-ring cellulose are a prominent tool to reconstruct paleoclimate and plant responses to environmental variation. Current models for cellulose isotope ratios assume a transfer of the environmental signals recorded in bulk leaf water to carbohydrates and ultimately into stem cellulose. However, the isotopic signal of carbohydrates exported from leaf to branch may deviate from mean leaf values if spatial heterogeneity in isotope ratios exists in the leaf. We tested whether the isotopic heterogeneity previously observed along the length of a ponderosa pine (Pinus ponderosa) leaf water was preserved in photosynthetic products. We observed an increase in both sugar and bulk tissue δ 18 O values along the needle, but the increase in carbohydrate δ 18 O values was dampened relative to the trend observed in leaf water. In contrast, δ 13 C values of both sugar and bulk organic matter were invariant along the needle. Additionally, phloem-exported sugar measured in the branch below the needles did not match whole-needle values of δ 18 O or δ 13 C. Instead, there was a near-constant offset observed between the branch and needle sugar δ 13 C values, while branch δ 18 O values were most similar to δ 18 O values observed for sugar at the base of the needle. The observed offset between the branch and needle sugar δ 18 O values likely arises from partial isotope oxygen exchange between sugars and water during phloem loading and transport. An improved understanding of the conditions producing differential δ 13 C and δ 18 O isotope effects between branch phloem and needle sugars could improve tree-ring-based climate reconstructions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Little vertical and circumferential variations in stem xylem water Δ 2 H and Δ 18 O in three tree species

Vertical and circumferential patterns of xylem water isotope signatures in large trees are rarely characterized but may influence interpretation of water source investigations and soil/xylem water isotope offsets. Furthermore, to examine vertical and circumferential variation in xylem water δ 2 H and δ 18 O, we collected xylem tissue at 5 heights (0, 1, 4, 7 and 10 m) from three replicate trees of three species with contrasting xylem anatomy, two angiosperms (Liquidambar styraciflua and Quercus nigra) and one gymnosperm (Pinus taeda). Concurrently, we also determined δ 2 H and δ 18 O of groundwater, soil water, and recent precipitation. On a different day, we collected circumferential samples at 1 m from the same trees to test for sectorality effects. Water from stem and soil samples were cryogenically extracted and analyzed for δ 2 H and δ 18 O. Mean xylem water δ 2 H and δ 18 O were significantly different between species, both vertically and circumferentially. We did not find significant (p = 0.05) systematic variation in δ 2 H or δ 18 O with height. We found no significant evidence for sectorality effects on δ 2 H, δ 18 O. Variances of vertical synoptic xylem water δ 2 H or δ 18 O were similar between species, 7.2–10.4‰ for δ 2 H and 0.58–0.81‰ for δ 18 O. Circumferential variances were also similar between species, 4.0–6.0 for δ 2 H and 0.37–0.44 for δ 18 O. A mixing model showed that sweetgum, water oak and loblolly pine, were drawing most of their water from deep soil from 45 to 190 cm (84.7, 68.4 and 53.2%, respectively) however, soil water-excess values indicate δ 2 H fractionation effects on these estimates. Dual isotope mixing model evaluation with single and multiple sample configurations showed that source water estimates were not affected by within tree variability of xylem water signatures. Xylem water δ 2 H and δ 18 O variability with height or circumference, was 3.2 and 2.7 times less than between tree variation because of transient temporal and spatial processes and is, therefore, not likely to affect interpretations of water sourcing in these three species.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1971

Evolution of proteins.

The amino acid sequences of proteins from living organisms are dealt with. The structure of proteins is first discussed; the variation in this structure from one biological group to another is illustrated by the first halves of the sequences of cytochrome c, and a phylogenetic tree is derived from the cytochrome c data. The relative geological times associated with the events of this tree are discussed. Errors which occur in the duplication of cells during the evolutionary process are examined. Particular attention is given to evolution of mutant proteins, globins, ferredoxin, and transfer ribonucleic acids (tRNA's). Finally, a general outline of biological evolution is presented.

Dayhoff, M. O.↗
NASA NTRS2020

Shedding Light on Microbial Dark Matter with A Universal Language of Life

The majority of microbial genomes have yet to be cultured, and most proteins predicted from microbial genomes or sequenced from the environment cannot be functionally annotated. As a result, current computational approaches to describe microbial systems rely on incomplete reference databases that cannot adequately capture the full functional diversity of the microbial tree of life, limiting our ability to model high-level features of biological sequences. The scientific community needs a means to capture the functionally and evolutionarily relevant features underlying biology, independent of our incomplete reference databases. Such a model can form the basis for transfer learning tasks, enabling downstream applications in environmental microbiology, medicine, and bioengineering. Here we present LookingGlass, a deep learning model capturing a “universal language of life”. LookingGlass encodes contextually-aware, functionally and evolutionarily relevant representations of short DNA reads, distinguishing reads of disparate function, homology, and environmental origin. We demonstrate the ability of LookingGlass to be fine-tuned to perform a range of diverse tasks: to identify novel oxidoreductases, to predict enzyme optimal temperature, and to recognize the reading frames of DNA sequence fragments. LookingGlass is the first contextually-aware, general purpose pre-trained “biological language” representation model for short-read DNA sequences. LookingGlass enables functionally relevant representations of otherwise unknown and unannotated sequences, shedding light on the microbial dark matter that dominates life on Earth.

A Hoarfrost↗
DOE OSTI2023

Phylogenomics and diversification of Sordariomycetes

The Sordariomycetes is a specious, morphologically diverse, and widely distributed class of the phylum Ascomycota that forms a well-supported clade diverged from Leotiomycetes. Aside from their ecological significance as plant and human pathogens, saprobes, endophytes, and fungicolous taxa, species of Sordariomycetes produces a wide range of chemically novel and diverse metabolites used in important fields. Recent phylogenetic analyses derived from a small number of genes have considerably increased our understanding of the family, order, and subclass relationships within Sordariomycetes, but several important groups have not been resolved well. In addition, there are various paraphyletic or polyphyletic groups. Moreover, the criteria used to establish higher ranks remain highly variable across different studies. Therefore, the taxonomy of Sordariomycetes is in constant flux, remains poorly understood, and is subject to much controversy. Here, for the first time, we have assembled a phylogenetic dataset containing 638 genomes representing the 156 genera, 50 families, and 17 orders and 5 subclasses of Sordariomycetes. This data set is based on 1124 genes and results in a well-resolved phylogenomic tree. We further constructed an evolutionary timeline of Sordariomycetes diversification based on the genomic data sets. Our divergence time estimate results are inconsistent with previous studies, suggesting estimates of node ages are less precise and varied. Based on these results, we discuss the higher ranks of Sordariomycetes and empirically propose an unprecedented taxonomic framework for the class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Tropical Cyclone Ecology: A Scale-Link Perspective

Tropical cyclones are increasing in intensity and size and, thus, are poised to increase in importance as disturbance agents. Our understanding of cyclone ecology is biased towards the North Atlantic Basin, because cyclone effects do differ across oceanic basins. Cyclones have both short and long-term effects across the levels of biological organization, but we lack a scale-perspective of cyclone ecology. Effects on individual trees, such as defoliation or branch stripping and uprooting, are mechanistically linked to effects at the community and ecosystem levels, including forest productivity and stand regeneration time. Forest dwarfing via the gradual removal of taller trees by cyclones over many generations illustrates that cyclones shape forest structure through the accumulation of short-term effects over longer timescales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Understanding the impacts of elevated CO2 and vapor pressure deficit on tree mortality - CRADA 599 (Abstract)

Many studies have examined the effects of rising CO2 on gas exchange and growth of plants. However, concurrent with the rise in CO2 has been the rise in temperature and associated drying of the atmosphere, or vapor pressure deficit (VPD), which increases tree mortality. Little attention has been given to the net outcome of these antagonistic drivers of plant performance. The net balance of rising CO2 and VPD upon plant and ecosystem function is possibly the largest uncertainty in model projections of the terrestrial carbon and water cycles. The purpose of this CRADA is to improve our predictive understanding of tree mortality under our changing environment. We will collaborate with WSU to provide a mechanistic understanding of the relative impacts of CO2 and VPD on tree mortality that scales across the globe. Ultimately, we will understand the potential impacts and mechanisms underlying CO2 and VPD responses and will enable improved prediction of future tree mortality.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Case Study: Can you find Delftia?

Delftia is a genus of bacteria with a bunch of cool features! The best studied species, Delftia acidovorans can produce gold nanoparticles from gold ions in solution. This bacteria has been found living in biofolms with Cupriavidis metallidurans on gold nuggets. It is also found in soil, in sinks and in rhizospheres of different plants where it promotes their growth. Delftia acidovorans forms gold nuggets by producing a short nonribosomal peptide called delftibactin. The 16 genes responsible for the production of delftibactin are called the del cluster (delA-delP). These genes were originally discovered in Delftia acidovorans SPH-1, but our research shows that the del cluster appears to be present across the genus. We'll start with a number of raw reads, clean them up and do a little taxonomy to figure out what we might be able to assemble. Next, we'll assemble the reads using 4 different methods and pick out the best assembly. Then we'll take those reads and sort them by genome and assess the quality of those genomes. We'll select the high quality genomes to annotate and insert into phylogenetic trees to find relatives.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1991

Software For Design Of Life-Support Systems

Design Assistant Workstation (DAWN) computer program is prototype of expert software system for analysis and design of regenerative, physical/chemical life-support systems that revitalize air, reclaim water, produce food, and treat waste. Incorporates both conventional software for quantitative mathematical modeling of physical, chemical, and biological processes and expert system offering user stored knowledge about materials and processes. Constructs task tree as it leads user through simulated process, offers alternatives, and indicates where alternative not feasible. Also enables user to jump from one design level to another.

Rudokas, Mary R.↗
NASA NTRS1997

Biosphere 2's Marsh Biome

The Marsh Biome, which was modeled after the mangroves and marshes of southwest Florida, has an area of 441.2 sq m separated into three hydrologically independent sections: the Freshwater, Oligohaline and Salt Marshes. The divisions are made based on their salinity (approximately 0, 4, and 34 ppt. respectively), but they also contain different biological communities. The Freshwater and Oligohaline Marshes are mostly filled with various grasses and several trees, while the Salt Marsh houses regions of red, black, and white mangroves (Rhizophora mangle, Avicennia germinans, and Languncularia racemosa respectively). Overall, there are an estimated 80 species of plants within the biome. Water in the Salt Marsh follows a meandering stream from the algal turf scrubbers (apparatuses that clean the water of its nutrients and heavy metals while increasing dissolved oxygen levels) which have an outlet in the Salt Marsh section near sites 4 and 5 to the Fringing Red Mangrove section. The sections of the Salt Marsh are separated by walls of concrete with openings to allow the stream to flow through. Throughout this study, conducted through the months of June and July, many conditions within the biome remained fairly constant. The temperature was within a degree or two of 25 C, mostly depending on whether the sample site was in direct sunlight or shaded. The pH throughout the Salt Marsh was 8.0 +/- 0.2, and the lower salinity waters only dropped below this soon after rains. The water rdepth and dissolved oxygen varied, however, between sites.

Molnar, Jennifer↗
DOE OSTI2022

Seasonal non-structural carbohydrate dynamics differ between twig bark and xylem tissues

Despite extensive research non-structural carbohydrate (NSC), the distribution of total NSC (TNC) and its primary components (sugar and starch) to the bark and xylem of twigs remains poorly understood. We determined seasonal NSC dynamics in twig bark and xylem in seven temperate tree species exhibiting different xylem anatomies and leaf habits. Seasonal trends in sugar were similar across species with concentrations peaking at least 15 days earlier in the spring for xylem than bark. Furthermore, evergreens exhibited maximum bark starch concentrations in early spring, followed by declines throughout the growing season, whereas deciduous species exhibited early spring declines in bark starch, followed by late growing season increases. Evergreens exhibited limited seasonal variation in xylem starch concentrations, whereas deciduous species exhibited variation in xylem starch concentrations that was similar to variation in bark starch. With a few exceptions, concentrations and seasonal amplitudes for sugar, starch, and TNC were generally higher in bark than xylem. Sugar concentrations were generally higher than starch, especially in the bark, which resulted in variability of TNC concentrations in bark or xylem. NSC concentrations varied significantly between xylem and the entire twig when bark was not explicitly considered. Averaged across species, sugar, starch, and TNC content in bark accounted for 66%, 54%, and 61% of total twig content, respectively, even though bark only accounted for 53% of the total twig mass. We recommend quantifying bark sugar and starch separately from xylem when determining twig NSC concentration and content.

59 BASIC BIOLOGICAL SCIENCES↗