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At least 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Feedstock Variability: Differences Among Biomass Anatomical Fractions and Tissues

Corn stover is a versatile feedstock for producing biofuels and other sustainable products. However, its diverse chemical and physical attributes can hinder the processes that convert it into these compounds. The composition of corn stover varies according to factors including corn plant variety, cultivation conditions and maturity at harvest. In essence, corn stover consists of the polymers cellulose, hemicellulose and lignin. The structural core of plant cell walls consists of elongated chains of glucose molecules arranged in bundles of cellulose. Additionally, lower concentrations of hemicellulose, a complex carbohydrate composed of various sugars, form part of the matrix surrounding cellulose bundles. Lignin is a complex aromatic polymer that reinforces plant cell walls. Corn stover generally comprises 40%-50% cellulose, 20%-30% hemicellulose, and 20%-30% lignin. The ratios of these components vary based on the specific type of corn plant and the growth conditions. For example, corn plants cultivated in drought conditions exhibit higher lignin levels than those grown under optimal conditions. The compositional diversity resulting from growth conditions is most pronounced among the different anatomical fractions of the corn plant. Understanding and accommodating the variation among the anatomical fractions of corn stover can enhance the effective utilization of this resource.

09 BIOMASS FUELS↗
DOE OSTI2021

Direct determination of cellulosic glucan content in starch-containing samples

A simple and highly selective analytical procedure is presented for the determination of cellulosic glucan content in samples that contain both cellulose and starch. This method eliminates the unacceptably large compounding errors of current two-measurement methods. If both starch and cellulose are present before analytical hydrolysis, both will be hydrolyzed to glucose causing bias and inaccuracy in the method. To prevent this interference, the removal of starch prior to cellulosic quantification is crucial. The method presented here is a concise in-series procedure with minimal measurements, eliminating large compounding errors. Sample preparation consists of a starch extraction employing enzymatic hydrolysis followed by a simple filtration and wash. The samples are then subjected to a two-stage acid hydrolysis. The concentration of glucose is determined by ion exchange high-performance liquid chromatography with a Pb 2+ column and a refractive index detector. The cellulosic glucan content is calculated based on the initial dry weight of the starting material. Data for the native biomass materials studied show excellent reproducibility, with coefficients of variance of 3.0% or less associated with the method. This selectivity for cellulosic glucan by the procedure was validated with several analytical techniques such as liquid chromatography coupled with mass spectrometry (LC–MS), Raman spectroscopy, and nuclear magnetic resonance.

09 BIOMASS FUELS↗
DOE OSTI2021

Renewable Polyurethanes from Sustainable Biological Precursors

Due to the depletion of fossil fuels, higher oil prices, and greenhouse gas emissions, the scientific community has been conducting an ongoing search for viable renewable alternatives to petroleum-based products, with the anticipation of increased adaptation in the coming years. New academic and industrial developments have encouraged the utilization of renewable resources for the development of ecofriendly and sustainable materials, and here, we focus on those advances that impact polyurethane (PU) materials. Vegetable oils, algae oils, and polysaccharides are included among the major renewable resources that have supported the development of sustainable PU precursors to date. Renewable feedstocks such as algae have the benefit of requiring only sunshine, carbon dioxide, and trace minerals to generate a sustainable biomass source, offering an improved carbon footprint to lessen environmental impacts. Incorporation of renewable content into commercially viable polymer materials, particularly PUs, has increasing and realistic potential. Biobased polyols can currently be purchased, and the potential to expand into new monomers offers exciting possibilities for new product development. This Review highlights the latest developments in PU chemistry from renewable raw materials, as well as the various biological precursors being employed in the synthesis of thermoset and thermoplastic PUs. We also provide an overview of literature reports that focus on biobased polyols and isocyanates, the two major precursors to PUs.

09 BIOMASS FUELS↗
DOE OSTI2020

An atypical lipoteichoic acid from Clostridium perfringens elicits a broadly cross-reactive and protective immune response

Clostridium perfringens is a leading cause of food-poisoning and causes avian necrotic enteritis, posing a significant problem to both the poultry industry and human health. No effective vaccine against C. perfringens is currently available. Using an antiserum screen of mutants generated from a C. perfringens transposon-mutant library, here we identified an immunoreactive antigen that was lost in a putative glycosyltransferase mutant, suggesting that this antigen is likely a glycoconjugate. Following injection of formalin-fixed whole cells of C. perfringens HN13 (a laboratory strain) and JGS4143 (chicken isolate) intramuscularly into chickens, the HN13-derived antiserum was cross-reactive in immunoblots with all tested 32 field isolates, whereas only 5 of 32 isolates were recognized by JGS4143-derived antiserum. The immunoreactive antigens from both HN13 and JGS4143 were isolated, and structural analysis by MALDI-TOF-MS, GC-MS, and 2D NMR revealed that both were atypical lipoteichoic acids (LTAs) with poly-(β1→4)-ManNAc backbones substituted with phosphoethanolamine. However, although the ManNAc residues in JGS4143 LTA were phosphoethanolamine-modified, a few of these residues were instead modified with phosphoglycerol in the HN13 LTA. The JGS4143 LTA also had a terminal ribose and ManNAc instead of ManN in the core region, suggesting that these differences may contribute to the broadly cross-reactive response elicited by HN13. In a passive-protection chicken experiment, oral challenge with C. perfringens JGS4143 lead to 22% survival, whereas co-gavage with JGS4143 and α-HN13 antiserum resulted in 89% survival. This serum also induced bacterial killing in opsonophagocytosis assays, suggesting that HN13 LTA is an attractive target for future vaccine-development studies.

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

Warming and elevated CO 2 alter tamarack C fluxes, growth and mortality: evidence for heat stress-related C starvation in the absence of water stress

Climate warming is increasing the frequency of climate-induced tree mortality events. While drought combined with heat is considered the primary cause of this mortality, little is known about whether moderately high temperatures alone can induce mortality, or whether rising CO 2 would prevent mortality at high growth temperatures. In this study, we grew tamarack ( Larix laricina ) under ambient (400 p.p.m.) and elevated (750 p.p.m.) CO 2 concentrations combined with ambient, ambient +4 °C and ambient +8 °C growth temperatures to investigate whether high growth temperatures lead to carbon (C) limitations and mortality. Growth at +8 °C led to 40% mortality in the ambient CO 2 (8TAC) treatment, but no mortality in the elevated CO 2 treatment. Thermal acclimation of respiration led to similar leaf C balances across the warming treatments, despite a lack of photosynthetic acclimation. Photosynthesis was stimulated under elevated CO 2 , increasing seedling growth, but not leaf C concentrations. However, growth and foliar C concentrations were lowest in the +8 °C treatments, even with elevated CO 2 . Dying 8TAC seedlings had lower needle C concentrations and lower ratios of photosynthesis to respiration than healthy 8TAC seedlings, indicating that C limitations were likely the cause of seedling mortality under high growth temperatures.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2000

Sugars as the optimal biosynthetic carbon substrate of aqueous life throughout the universe

Our previous analysis of the energetics of metabolism showed that both the biosynthesis of amino acids and lipids from sugars, and the fermentation of organic substrates, were energetically driven by electron transfer reactions resulting in carbon redox disproportionation (Weber, 1997). Redox disproportionation--the spontaneous (energetically favorable) direction of carbon group transformation in biosynthesis--is brought about and driven by the energetically downhill transfer of electron pairs from more oxidized carbon groups (with lower half-cell reduction potentials) to more reduced carbon groups (with higher half-cell reduction potentials). In this report, we compare the redox and kinetic properties of carbon groups in order to evaluate the relative biosynthetic capability of organic substrates, and to identify the optimal biosubstrate. This analysis revealed that sugars (monocarbonyl alditols) are the optimal biosynthetic substrate because they contain the maximum number of biosynthetically useful high energy electrons/carbon atom while still containing a single carbonyl group needed to kinetically facilitate their conversion to useful biosynthetic intermediates. This conclusion applies to aqueous life throughout the Universe because it is based on invariant aqueous carbon chemistry--primarily, the universal reduction potentials of carbon groups.

NASA Center ARC↗
DOE OSTI2020

A Glycan Array-Based Assay for the Identification and Characterization of Plant Glycosyltransferases

Growing plants with modified cell wall compositions is a promising strategy to improve resistance to pathogens, increase biomass digestibility, and tune other important properties. In order to alter biomass architecture, a detailed knowledge of cell wall structure and biosynthesis is a prerequisite. We report here a glycan array-based assay for the high-throughput identification and characterization of plant cell wall biosynthetic glycosyltransferases (GTs). We demonstrate that different heterologously expressed galactosyl-, fucosyl-, and xylosyltransferases can transfer azido-functionalized sugar nucleotide donors to selected synthetic plant cell wall oligosaccharides on the array and that the transferred monosaccharides can be visualized “on chip” by a 1,3-dipolar cycloaddition reaction with an alkynyl-modified dye. The opportunity to simultaneously screen thousands of combinations of putative GTs, nucleotide sugar donors, and oligosaccharide acceptors will dramatically accelerate plant cell wall biosynthesis research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Chemo-Enzymatic Synthesis of Long-Chain Oligosaccharides for Studying Xylan-Modifying Enzymes

Plant research is hampered in several aspects by a lack of pure oligosaccharide samples that closely represent structural features of cell wall glycans. An alternative to purely chemical synthesis to access these oligosaccharides is chemo-enzymatic synthesis using glycosynthases. These enzymes enable the ligation of oligosaccharide donors, when activated for example as α-glycosyl fluorides, with suitable acceptor oligosaccharides. Herein, the synthesis of xylan oligosaccharides up to dodecasaccharides is reported, with glycosynthase-mediated coupling reactions as key steps. The xylo-oligosaccharide donors were protected at the non-reducing end with a 4-O-tetrahydropyranyl (THP) group to prevent polymerization. Installation of an unnatural 3-O-methylether substituent at the reducing end xylose of the oligosaccharides ensured good water solubility. Biochemical assays demonstrated enzymatic activity for the xylan acetyltransferase XOAT1 from Arabidopsis thaliana, xylan arabinofuranosyl-transferase XAT3 enzymes from rice and switchgrass, and the xylan glucuronosyltransferase GUX3 from Arabidopsis thaliana. In case of the glucuronosyltransferase GUX3, MALDI-MS/MS analysis of the reaction product suggested that a single glucuronosyl substituent was installed primarily at the central xylose residues of the dodecasaccharide acceptor, demonstrating the value of long-chain acceptors for assaying biosynthetic glycosyltransferases.

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

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Explicit treatment of electronic polarizability in empirical force fields (FFs) represents an extension over a traditional additive or pairwise FF and provides a more realistic model of the variations in electronic structure in condensed phase, macromolecular simulations. To facilitate utilization of the polarizable FF based on the classical Drude oscillator model, Drude Prepper has been developed in CHARMM-GUI. Drude Prepper ingests additive CHARMM protein structures file (PSF) and pre-equilibrated coordinates in CHARMM, PDB, or NAMD format, from which the molecular components of the system are identified. These include all residues and patches connecting those residues along with water, ions, and other solute molecules. This information is then used to construct the Drude FF-based PSF using molecular generation capabilities in CHARMM, followed by minimization and equilibration. In addition, inputs are generated for molecular dynamics (MD) simulations using CHARMM, GROMACS, NAMD, and OpenMM. Validation of the Drude Prepper protocol and inputs is performed through conversion and MD simulations of various heterogeneous systems that include proteins, nucleic acids, lipids, polysaccharides, and atomic ions using the aforementioned simulation packages. Stable simulations are obtained in all studied systems, including 5 μs simulation of ubiquitin, verifying the integrity of the generated Drude PSFs. Additionally, the ability of the Drude FF to model variations in electronic structure is shown through dipole moment analysis in selected systems. Finally, the capabilities and availability of Drude Prepper in CHARMM-GUI is anticipated to greatly facilitate the application of the Drude FF to a range of condensed phase, macromolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

BdGT43B2 functions in xylan biosynthesis and is essential for seedling survival in Brachypodium distachyon

Abstract Xylan is the predominant hemicellulose in the primary cell walls of grasses, but its synthesis and interactions with other wall polysaccharides are complex and incompletely understood. To probe xylan biosynthesis, we generated CRISPR/Cas9 knockout and amiRNA knockdown lines of BdGT43B2 , an ortholog of the wheat TaGT43‐4 xylan synthase scaffolding protein in the IRX14 clade, in Brachypodium distachyon . Knockout of BdGT43B2 caused stunting and premature death in Brachypodium seedlings. Immunofluorescence labeling of xylans was greatly reduced in homozygous knockout BdGT43B2 mutants, whereas cellulose labeling was unchanged or slightly increased. Biochemical analysis showed reductions in digestible xylan in knockout mutant walls, and cell size was smaller in knockout leaves. BdGT43B2 knockdown plants appeared morphologically normal as adults, but showed slight reductions in seedling growth and small decreases in xylose content in isolated cell walls. Immunofluorescence labeling of xylan and cellulose staining was both reduced in BdGT43B2 knockdown plants. Together, these data indicate that BdGT43B2 functions in the synthesis of a form of xylan that is required for seedling growth and survival in Brachypodium distachyon .

36 MATERIALS SCIENCE↗
DOE OSTI2025

Empirical evidence that glucan-interacting amino acid side chains within the transmembrane channel collectively facilitate cellulose synthase function

The fundamental mechanism of cellulose synthesis is widely conserved across Kingdoms and depends on cellulose synthases, which are processive, dual-function, family 2 glycosyltransferases (GT-2). These enzymes polymerize glucose on the cytoplasmic side of the plasma membrane and export the glucan chain to the cell surface through an integral transmembrane (TM) channel. Structural studies of active plant cellulose synthases (CESAs) have revealed interactions between the nascent glucan chain and the side chains of polar, charged, and aromatic amino acid residues that line the TM channel. However, the functional consequences of modifying these side chains have not been tested in vivo in CESAs or other processive GT-2s. To test this, we used an established in vivo assay based on genetic complementation of CESA5 in the moss, Physcomitrium patens. For accurate prediction of glucan-interacting amino acid residues, we generated a complete homotrimeric molecular model of PpCESA5 using a combination of homology and de novo modeling. All-atom molecular dynamics-based analyses of contact metrics and interaction energy identified 23 amino acid residues with high propensity to interact with the nascent glucan chain within the TM channel or on the apoplastic surface of PpCESA5. Mutating any one of 18 of these amino acid residues to alanine, thereby removing their side chains, abolished or impaired CESA function, with the strongest effects observed upon the loss of charged amino acid side chains. This provides direct evidence to support the hypothesis that multiple amino acid residues collectively maintain a smooth energy landscape within the TM channel to facilitate glucan translocation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Carbon source-induced changes in the transcriptional landscape of Novacetimonas hansenii

Novacetimonas hansenii is a model organism for bacterial cellulose (BC) production, a biopolymer with broad industrial applications. To better understand its carbon source-dependent metabolism, we conducted the first time-resolved transcriptomic analysis of N. hansenii ATCC 23769 grown on five carbon sources (glucose, fructose, mannitol, galactose, and sucrose) across five time points (24–120h). Glucose, fructose, and mannitol supported growth and efficient BC production, whereas galactose and sucrose resulted in poor yields, likely due to limited transport and enzymatic capacity. Solid-state NMR revealed that cellulose crystallinity and polymorphism were carbon source-dependent, with reduced bcsD expression correlating with lower crystallinity. Transcriptomic profiling showed distinct metabolic responses. Cultures containing glucose and mannitol activated core metabolic pathways, fructose induced a delayed adaptive shift, and galactose and sucrose triggered stress-related gene expression. These results highlight the metabolic plasticity of N. hansenii and offer insights for enhancing BC production through carbon source optomization.

Bacterial cellulose↗
DOE OSTI2022

Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome

Ruminococcus bromii is a keystone species in the human gut that has the rare ability to degrade dietary resistant starch (RS). This bacterium secretes a suite of starch-active proteins that work together within larger complexes called amylosomes that allow R. bromii to bind and degrade RS. Starch adherence system protein 20 (Sas20) is one of the more abundant proteins assembled within amylosomes, but little could be predicted about its molecular features based on amino acid sequence. Here, we performed a structure–function analysis of Sas20 and determined that it features two discrete starch-binding domains separated by a flexible linker. We show that Sas20 domain 1 contains an N-terminal β-sandwich followed by a cluster of α-helices, and the nonreducing end of maltooligosaccharides can be captured between these structural features. Furthermore, the crystal structure of a close homolog of Sas20 domain 2 revealed a unique bilobed starch-binding groove that targets the helical α1,4-linked glycan chains found in amorphous regions of amylopectin and crystalline regions of amylose. Affinity PAGE and isothermal titration calorimetry demonstrated that both domains bind maltoheptaose and soluble starch with relatively high affinity (K d ≤ 20 μM) but exhibit limited or no binding to cyclodextrins. Finally, small-angle X-ray scattering analysis of the individual and combined domains support that these structures are highly flexible, which may allow the protein to adopt conformations that enhance its starch-targeting efficiency. Taken together, we conclude that Sas20 binds distinct features within the starch granule, facilitating the ability of R. bromii to hydrolyze dietary RS.

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

Development and evaluation of an agar capture system (ACS) for high-throughput screening of insoluble particulate substrates with bacterial growth and enzyme activity assays

In this work, we describe a method for containing insoluble particulates for use as substrates in either bacterial growth or enzyme assays. This method was designed for high-throughput screening of environmental or engineered bacteria. Benchmarking this method with several model bacteria uncovered phenotypes not observable with the particulate substrates alone.

59 BASIC BIOLOGICAL SCIENCES↗