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At least 181 records · Page 10
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Insights into controlling bacterial cellulose nanofiber film properties through balancing thermodynamic interactions and colloidal dynamics

In recent years, nanocellulose has emerged as a sustainable and environmentally friendly alternative to traditional petroleum-derived structural polymers. Sourced either from plants, algae, or bacteria, nanocellulose can be processed into colloid, gel, film and fiber forms. However, the required fundamental understanding of process parameters that govern the morphology and structure–property relationships of nanocellulose systems, from colloidal suspensions to bulk materials, has not been developed and generalized for all forms of cellulose. This further hinders the more widespread adoption of this biopolymer in applications. Our study investigates the dispersion of cellulose nanofibers (CNFs) produced by a bacterial–yeast co-culture, in solvents, highlighting the role of thermodynamic interactions in influencing their colloidal behavior. By adjusting Hansen solubility parameters, we controlled the thermodynamic relationship between CNFs and solvents across various concentrations, studying the dilute to semi-dilute regimes. Rheological measurements revealed that the threshold at which a concentration-based regime transition occurs is distinctly solvent-dependent. Complementing rheological analysis with small angle X-ray scattering and zeta potential measurements, our findings reveal that enhancing CNF–solvent interactions increases excluded volume in the dilute regime, emphasizing the importance of the balance between fiber–fiber and fiber–solvent interactions. Moreover, we investigated the transition from colloidal to solid state by creating films from dispersions with varying interaction parameters in semi-dilute regimes. Through mechanical testing and scanning electron microscopy imaging of the fracture surfaces, we highlight the significance of electrokinetic effects in such transitions, as dispersions with higher electrokinetic stabilization gave rise to stronger and tougher films despite having less favorable thermodynamic interaction parameters. Finally, our work provides insights into the thermodynamic and electrokinetic interplay that governs bacterial CNF dispersion, offering a foundation for future application and a deeper understanding of nanocellulose's colloidal and structure-property relationships.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Molecular insights into the in situ early-stage assembly of metal–organic frameworks on cellulose nanofibrils

The integration of metal–organic frameworks (MOFs) into renewable matrices, including those derived from cellulose, to create cellulose/MOF hybrids has attracted significant interest due to the synergistic combination of cellulosic biopolymer properties and MOFs' multifunctional features. The interfacial interactions between cellulose and MOF not only ensure stable bonding, but ultimately also determine the bulk physical properties of the macroscopic composites. However, the mechanistic understanding of the in situ assembly between the two materials remains unclear. In this study, we employ a combination study of synthesis, experimental characterization, and molecular dynamics simulations to explore the early-stage assembly of a cellulose/MOF hybrid. Our results revealed that the growth of MOF clusters on the 2,2,6,6-tetramethyl-1-piperidinyloxy oxidized cellulose nanofibrils (TOCNF) follows an inhomogeneous sequential transformation pathway. The carboxylates of TOCNF form coordination-like bonds with the metal ions, while the hydroxyl groups of TOCNF form hydrogen bonds with MOF ligands. These interactions provide the initial nucleation sites that mediate the growth of MOF clusters and also guide the assembly of larger MOF clusters onto the TOCNF substrate. In conclusion, the fundamental insights into the in situ assembly of MOF nanoparticles on cellulosic substrates are essential for the rational design of high-performance materials with tailored morphology and optimized properties.

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

The importance of ester cleavage in the butylamine pretreatment of hybrid poplar

Butylamine is an effective in-and-out pretreatment solvent for hybrid poplar. It penetrates the cell walls and breaks ester cross-linkages, facilitating lignin release and improving enzymatic digestion. This work explores the “in-and-out” pretreatment of hybrid poplar with butylamine as a distillable protic solvent and reagent. The butylamine solvent can be removed by vacuum distillation with >95% solvent removal in all cases, providing a valuable scheme for efficient solvent recovery and recycling. Running the reaction with neat butylamine at 140 °C for 3 hours results in high yields of monosaccharides (90% glucose and 71% xylose) after enzymatic digestion, and a good tolerance to water content with no significant reduction in glucose yield up to an 8 : 1 water : butylamine ratio. We investigate the mechanisms of this pretreatment using powder X-ray diffraction, thermogravimetric analysis, fluorescence microscopy, elemental analysis, solid state and solution state nuclear magnetic spectroscopy to observe chemical and material markers of the pretreatment chemistry. The results suggest that the butylamine leaves the macro and microstructural properties of the lignocellulose relatively unaltered, but conducts targeted ester cleavage chemistry to remove cross-links between the various biopolymers and partially solubilize the lignin component of the biomass. These findings should act to guide future development of pretreatment chemistry for the development of biorefinery processes, and assist in the utilization of biomass as a starting point for chemical syntheses.

Palasz, Joseph M↗
DOE OSTI2025

Integration of Metabolic and Bioprocess Engineering for the Production of B-Ketoadipic Acid from Glucose and Xylose by Pseudomonas Putida

..beta..-Ketoadipic acid is a common intermediate in aerobic microbial aromatic catabolism that can be used as a monomer in performance-advantaged biopolymers. Here, we engineered Pseudomonas putida KT2440 to produce ..beta..-ketoadipate from glucose and xylose, the most prevalent carbohydrates derived from lignocellulosic polysaccharides. With the top-performing strain, P. putida GR038, we conducted bioprocess development using glucose and xylose as substrates in a 2 : 1 molar ratio to mimic lignocellulosic hydrolysate. Fed-batch cultivations achieved a titer of 65.8 g L-1 and a rate of 0.69 g L-1 h-1, with a C-mol yield of 0.52. Application of adsorptive in situ product recovery further improved the effective titer to 92.0 g L-1 and the rate to 0.83 g L-1 h-1, while also improving the downstream purity of ..beta..-ketoadipate from 88.3 wt% to 99.0 wt%. These results show promise towards industrial production of ..beta..-ketoadipate from lignocellulosic sugars.

09 BIOMASS FUELS↗
DOE OSTI2026

Cooperative effect of local active stresses on the macroscopic contractility of elastic fiber networks

The collective action of actively contractile units embedded in elastic biopolymer networks plays a crucial role in regulating the network's macroscopic mechanical response. Here, in this study, we investigate how the macroscopic boundary stress in model elastic fiber networks depends on the number and nature of embedded contractile units, each exerting an isotropic force dipole, as well as on the bending stiffness of fibers. We find that the macroscopic stress increases nonlinearly with the number of dipoles due to mutual stiffening of initially soft, bending-dominated networks. Using effective medium theory, we relate this enhanced contractility to an increase in the effective average network coordination number due to constraints imposed by the force dipoles. By comparing three distinct force dipole models that differ in their local structures, we demonstrate that the specific manner in which an active unit constrains the network strongly influences the onset and nature of the stiffening transition. Our results highlight that not only the quantity but also the local geometry of force-generating units critically determines the macroscopic mechanical behavior. This framework provides a physical basis for understanding how biological systems—such as molecular motors in the cytoskeleton, or adherent cells in the extracellular matrix—can modulate network-scale nonlinear elastic properties through local tuning of active force-generating units.

Biological and medical sciences↗
DOE OSTI2021

A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1

Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. In this work, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major β-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

36 MATERIALS SCIENCE↗
DOE OSTI2021

RNA nanotechnology to build a dodecahedral genome of single-stranded RNA virus

The quest for artificial RNA viral complexes with authentic structure while being non-replicative is on its way for the development of viral vaccines. RNA viruses contain capsid proteins that interact with the genome during morphogenesis. The sequence and properties of the protein and genome determine the structure of the virus. For example, the Pariacoto virus ssRNA genome assembles into a dodecahedron. Virus-inspired nanotechnology has progressed remarkably due to the unique structural and functional properties of viruses, which can inspire the design of novel nanomaterials. RNA is a programmable biopolymer able to self-assemble sophisticated 3D structures with rich functionalities. RNA dodecahedrons mimicking the Pariacoto virus quasi-icosahedral genome structures were constructed from both native and 2'-F modified RNA oligos. The RNA dodecahedron easily self-assembled using the stable pRNA three-way junction of bacteriophage phi29 as building blocks. The RNA dodecahedron cage was further characterized by cryo-electron microscopy and atomic force microscopy, confirming the spontaneous and homogenous formation of the RNA cage. The reported RNA dodecahedron cage will likely provide further studies on the mechanisms of interaction of the capsid protein with the viral genome while providing a template for further construction of the viral RNA scaffold to add capsid proteins for the assembly of the viral nucleocapsid as a model. Understanding the self-assembly and RNA folding of this RNA cage may offer new insights into the 3D organization of viral RNA genomes. Finally, the reported RNA cage also has the potential to be explored as a novel virus-inspired nanocarrier.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Cuticle development and the underlying transcriptome–metabolome associations during early seedling establishment

Abstract The plant cuticle is a complex extracellular lipid barrier that has multiple protective functions. This study investigated cuticle deposition by integrating metabolomics and transcriptomics data gathered from six different maize seedling organs of four genotypes, the inbred lines B73 and Mo17, and their reciprocal hybrids. These datasets captured the developmental transition of the seedling from heterotrophic skotomorphogenic growth to autotrophic photomorphogenic growth, a transition that is highly vulnerable to environmental stresses. Statistical interrogation of these data revealed that the predominant determinant of cuticle composition is seedling organ type, whereas the seedling genotype has a smaller effect on this phenotype. Gene-to-metabolite associations assessed by integrated statistical analyses identified three gene networks associated with the deposition of different elements of the cuticle: cuticular waxes; monomers of lipidized cell wall biopolymers, including cutin and suberin; and both of these elements. These gene networks reveal three metabolic programs that appear to support cuticle deposition, including processes of chloroplast biogenesis, lipid metabolism, and molecular regulation (e.g. transcription factors, post-translational regulators, and phytohormones). This study demonstrates the wider physiological metabolic context that can determine cuticle deposition and lays the groundwork for new targets for modulating the properties of this protective barrier.

Plant Sciences↗
DOE OSTI2025

Exact statistics of helical wormlike chains with twist-bend coupling

Here, we present a solution for the Green's function for the general case of a helical wormlike chain with twist-bend coupling and demonstrate the applicability of our solution for evaluating general structural and mechanical chain properties. We find that twist-bend coupling renormalizes the persistence length and the force-extension curves relative to wormlike chains. Analysis of intrinsically twisted polymers shows that incorporation of twist-bend coupling results in the oscillatory behavior in principal tangent correlations that are observed in some studies of synthetic polymers. The exact nature of our solution provides a framework to evaluate the role of twist-bend coupling on polymer properties, such as DNA bound to histones and motivates the reinterpretation of existing biopolymer experimental data.

Ghosh, Ashesh [University of California, Berkeley,↗
DOE OSTI2021

Low friction bio-inspired polydopamine/polytetrafluoroethylene coating performance in hydrodynamic bearings

Purpose Low friction polymer coatings able to withstand high loadings and many years of continuous operation are difficult to formulate at low cost, but could find many applications in industry. This study aims to analyze and compare friction and wear performance of novel polydopamine/polytetrafluoroethylene (PDA/PTFE) and traditional tin Babbitt coatings applied to an industrial journal bearing. Design/methodology/approach This paper tested PTFE based coating, co-deposited with PDA, a biopolymer allowing sea mussels to adhere to ocean rocks. This coating was deposited on flat steel substrates and on a curved cast iron hydrodynamic journal bearing surface. The flat substrates were analyzed with a tribometer and an optical microscope, while the coated bearing liners were tested in an industrial laboratory setting at different speeds and different radial loads. Findings PDA/PTFE coating showed 2-3 times lower friction compared to traditional tin Babbitt for flat substrates, but higher friction in the bearing liners. PDA/PTFE also showed considerable wear through coating delamination and abrasion in the bearing liners. Research limitations/implications Five future modifications to mitigate coating flaws are provided, which include modifications to coating thickness and its surface finish. Originality/value While the novel coating showed excellent results on flat substrates, coating performance in a large scale bearing was found to be poor. This study shows that coating preparation needs to be improved to avoid frictional losses and unwanted damage to bearings. We provide several routes that could improve coating performance in industrial applications.

Engineering↗
DOE OSTI2025

Evolutionary and functional relationships between plant and microbial C 1 metabolism in terrestrial ecosystems

One-carbon (C 1 ) metabolism, centered on the universal methyl donor S-adenosyl methionine (SAM), plays critical roles in biosynthesis, redox regulation, and stress responses across plants and microbes. A recently proposed photosynthetic C 1 pathway links SAM methyl groups directly to RuBisCO-mediated CO 2 assimilation and integrates with nitrogen and sulfur metabolism. Light-dependent SAM synthesis may regulate the methylation of biopolymers and specialized metabolites and help mitigate photorespiratory stress under elevated temperature and drought. Phylogenetic analysis of two core enzymes suggests evolutionary continuity from methylotrophic microbes to land plants, supporting microbial origins via endosymbiotic gene transfer. Beyond intracellular roles, C 1 metabolism drives biosphere–atmosphere exchange via gases such as methane, methanol, formic acid, and formaldehyde, and numerous specialized volatiles synthesized through SAM methylation. S-methylmethionine, a mobile C 1 metabolite, may mediate phloem transport of reduced sulfur, nitrogen, and methyl groups, linking above- and belowground C 1 cycling in plants. Advances in real-time gas sensing now allow the high-frequency quantification of C 1 fluxes from leaves, stems, and soils, highlighting C 1 metabolism as a critical and underrecognized component of terrestrial carbon and nutrient cycling. Given its microbial ancestry and the production of diverse volatile biosignatures, C 1 metabolism may also offer unique insights into life's origins and biosignature detection on exoplanets.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Cell‐type‐specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems

SUMMARY Bioenergy sorghum is a low‐input, drought‐resilient, deep‐rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4–5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell‐type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell‐type‐specific and cell‐preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell‐type‐specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell‐specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data ( https://mc‐lab.shinyapps.io/lcm‐dataset/ ).

09 BIOMASS FUELS↗
DOE OSTI2020

Three-dimensional super line-localization in low signal-to-noise microscope images via prior-apprised unsupervised learning (PAUL)

Biological processes such as processive enzyme turnover and intracellular cargo tracking involve the dynamic motion of a small "article" along a curvilinear biopolymer track. To understand these processes that occur across multiple length and time scales, one must acquire both the trajectory of the particle and the position of the track along which it moves, possibly by combining high-resolution single-particle tracking with conventional microscopy. Yet, usually there is a significant resolution mismatch between these modalities: while the tracked particle is localized with a precision of 10 nm, the image of the surroundings is limited by optical difraction, with 200 nm lateral and 500 nm axial resolutions. Compared to the particle's trajectory, the surrounding curvilinear structure appears as a blurred and noisy image. This disparity in the spatial resolutions of the particle trajectory and the surrounding curvilinear structure image makes data reconstruction, as well as interpretation, particularly challenging. Analysis is further complicated when the curvilinear structures are oriented arbitrarily in 3D space. Here, we present a prior-apprised unsupervised learning (PAUL) approach to extract information from 3D images where the underlying features resemble a curved line such as a filament or microtubule. This three-stage framework starts with a Hessian-based feature enhancement, which is followed by feature registration, where local line segments are detected on repetitively sampled subimage tiles. In the final stage, statistical learning, segments are clustered based on their geometric relationships. Principal curves are then approximated from each segment group via statistical tools including principal component analysis, bootstrap and kernel transformation. This procedure is characterized on simulated images, where sub-voxel medium deviations from true curves have been achieved. The 3D PAUL approach has also been implemented for successful line localization in experimental 3D images of gold nanowires obtained using a multifocal microscope. Lastly, this work not only bridges the resolution gap between two microscopy modalities, but also allows us to conduct 3D super line-localization imaging experiments, without using super-resolution techniques.

42 ENGINEERING↗
DOE OSTI2023

Molecular insights into the evolution of woody plant decay in the gut of termites

Plant cell walls represent the most abundant pool of organic carbon in terrestrial ecosystems but are highly recalcitrant to utilization by microbes and herbivores owing to the physical and chemical barrier provided by lignin biopolymers. Termites are a paradigmatic example of an organism’s having evolved the ability to substantially degrade lignified woody plants, yet atomic-scale characterization of lignin depolymerization by termites remains elusive. We report that the phylogenetically derived termite Nasutitermes sp. efficiently degrades lignin via substantial depletion of major interunit linkages and methoxyls by combining isotope-labeled feeding experiments and solution-state and solid-state nuclear magnetic resonance spectroscopy. Exploring the evolutionary origin of lignin depolymerization in termites, we reveal that the early-diverging woodroach Cryptocercus darwini has limited capability in degrading lignocellulose, leaving most polysaccharides intact. Conversely, the phylogenetically basal lineages of “lower” termites are able to disrupt the lignin-polysaccharide inter- and intramolecular bonding while leaving lignin largely intact. These findings advance knowledge on the elusive but efficient delignification in natural systems with implications for next-generation ligninolytic agents.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Biochemical parallels between catabolic pathways for lignin-associated aromatic dimers

Lignin is one of the most common biopolymers on Earth. In nature, lignin is primarily deconstructed by fungi into mixtures of aromatic compounds that are then assimilated by bacteria and fungi. Industrially, lignin is primarily generated as a byproduct of pulp and paper production and burned for process heat. However, if the appropriate assimilatory pathways were identified, deconstructed lignin could be funneled into value-added products using engineered bacteria. Foundational work has described pathways for assimilation of diverse monomeric aromatic compounds such as protocatechuate, ferulate, and syringate, as well as select dimers including those with β-O-4 and 5-5 interunit linkages. Recent advances have elucidated additional pathways for dimer assimilation, including pathways for new substrates as well as parallel pathways for previously characterized substrates. Comparing these dimer assimilation pathways can illuminate the underlying biochemical logic of assimilation for lignin-associated aromatic dimers and provide opportunities for metabolic engineering to enhance lignin valorization.

Sphingomonas↗
DOE OSTI2020

Genome-based analysis for the bioactive potential of Streptomyces yeochonensis CN732, an acidophilic filamentous soil actinobacterium

Background: Acidophilic members of the genus Streptomyces can be a good source for novel secondary metabolites and degradative enzymes of biopolymers. In this study, a genome-based approach on Streptomyces yeochonensis CN732, a representative neutrotolerant acidophilic streptomycete, was employed to examine the biosynthetic as well as enzymatic potential, and also presence of any genetic tools for adaptation in acidic environment. Results: A high quality draft genome (7.8Mb) of S. yeochonensis CN732 was obtained with a G+C content of 73.53% and 6549 protein coding genes. The in silico analysis predicted presence of multiple biosynthetic gene clusters (BGCs), which showed similarity with those for antimicrobial, anticancer or antiparasitic compounds. However, the low levels of similarity with known BGCs for most cases suggested novelty of the metabolites from those predicted gene clusters. The production of various novel metabolites was also confirmed from the combined high performance liquid chromatography-mass spectrometry analysis. Through comparative genome analysis with related Streptomyces species, genes specific to strain CN732 and also those specific to neutrotolerant acidophilic species could be identified, which showed that genes for metabolism in diverse environment were enriched among acidophilic species. In addition, the presence of strain specific genes for carbohydrate active enzymes (CAZyme) along with many other singletons indicated uniqueness of the genetic makeup of strain CN732. The presence of cysteine transpeptidases (sortases) among the BGCs was also observed from this study, which implies their putative roles in the biosynthesis of secondary metabolites. Conclusions: This study highlights the bioactive potential of strain CN732, an acidophilic streptomycete with regard to secondary metabolite production and biodegradation potential using genomics based approach. The comparative genome analysis revealed genes specific to CN732 and also those among acidophilic species, which could give some insights into the adaptation of microbial life in acidic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum

Sorghum bicolor is a deep-rooted, heat- and drought-tolerant crop that thrives on marginal lands and is increasingly valued for its applications in biofuel, bioenergy, and biopolymer production. The sorghum stem, which can reach 4–5 m in length, serves as the primary reservoir of both lignocellulosic biomass and soluble sugars, making it a promising bioenergy feedstock. Although recent advances in genetic, genomic, and transcriptomic resources have improved our understanding of sorghum biology, comprehensive genome-wide analyses of functional dynamics across diverse organ types and developmental stages remain limited. In particular, candidate genes with stem preferred expression pattern or their associated cis-regulatory elements, which may program key stem-related functions and enable organ- or tissue-specific engineering, have not yet been identified.

59 BASIC BIOLOGICAL SCIENCES↗