Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “cell wall”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,315 records · Page 73
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H 2 and CO 2 compared to organotrophic growth with fructose

Clostridium ljungdahlii derives energy by lithotrophic and organotrophic acetogenesis. C. ljungdahlii was grown organotrophically with fructose and also lithotrophically, either with syngas - a gas mixture containing hydrogen (H 2 ), carbon dioxide (CO 2 ), and carbon monoxide (CO), or with H 2 and CO 2 . Gene expression was compared quantitatively by microarrays using RNA extracted from all three conditions. Gene expression with fructose and with H 2 /CO 2 was compared by RNA-Seq. Upregulated genes with both syngas and H 2 /CO 2 (compared to fructose) point to the urea cycle, uptake and degradation of peptides and amino acids, response to sulfur starvation, potentially NADPH-producing pathways involving (S)-malate and ornithine, quorum sensing, sporulation, and cell wall remodeling, suggesting a global and multicellular response to lithotrophic conditions. With syngas, the upregulated (R)-lactate dehydrogenase gene represents a route of electron transfer from ferredoxin to NAD. With H 2 /CO 2 , flavodoxin and histidine biosynthesis genes were upregulated. Downregulated genes corresponded to an intracytoplasmic microcompartment for disposal of methylglyoxal, a toxic byproduct of glycolysis, as 1-propanol. Several cytoplasmic and membrane-associated redox-active protein genes were differentially regulated. In conclusion, the transcriptomic profiles of C. ljungdahlii in lithotrophic and organotrophic growth modes indicate large-scale physiological and metabolic differences, observations that may guide biofuel and commodity chemical production with this species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

Dark septate endophytes (DSE) are a form-group of root endophytic fungi with elusive functions. Here, the genomes of two common DSE of semiarid areas, Cadophora sp. and Periconia macrospinosa were sequenced and analyzed with another 32 ascomycetes of different lifestyles. Cadophora sp. (Helotiales) and P. macrospinosa (Pleosporales) have genomes of 70.46 Mb and 54.99 Mb with 22,766 and 18,750 gene models, respectively. The majority of DSE-specific protein clusters lack functional annotation with no similarity to characterized proteins, implying that they have evolved unique genetic innovations. Both DSE possess an expanded number of carbohydrate active enzymes (CAZymes), including plant cell wall degrading enzymes (PCWDEs). Those were similar in three other DSE, and contributed a signal for the separation of root endophytes in principal component analyses of CAZymes, indicating shared genomic traits of DSE fungi. Number of secreted proteases and lipases, aquaporins, and genes linked to melanin synthesis were also relatively high in our fungi. In spite of certain similarities between our two DSE, we observed low levels of convergence in their gene family evolution. This suggests that, despite originating from the same habitat, these two fungi evolved along different evolutionary trajectories and display considerable functional differences within the endophytic lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Genome sequencing of Rigidoporus microporus provides insights on genes important for wood decay, latex tolerance and interspecific fungal interactions

Fungal plant pathogens remain a serious threat to the sustainable agriculture and forestry, despite the extensive efforts undertaken to control their spread. White root rot disease is threatening rubber tree (Hevea brasiliensis) plantations throughout South and Southeast Asia and Western Africa, causing tree mortality and severe yield losses. Here, we report the complete genome sequence of the basidiomycete fungus Rigidoporus microporus, a causative agent of the disease. Our phylogenetic analysis confirmed the position of R. microporus among the members of Hymenochaetales, an understudied group of basidiomycetes. Our analysis further identified pathogen's genes with a predicted role in the decay of plant cell wall polymers, in the utilization of latex components and in interspecific interactions between the pathogen and other fungi. We also detected putative horizontal gene transfer events in the genome of R. microporus. The reported first genome sequence of a tropical rubber tree pathogen R. microporus should contribute to the better understanding of how the fungus is able to facilitate wood decay and nutrient cycling as well as tolerate latex and utilize resinous extractives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy

Root biology is pivotal in addressing global challenges including sustainable agriculture and climate change. However, roots have been relatively understudied among plant organs, partly due to the difficulties in imaging root structures in their natural environment. Here we used microfabricated ecosystems (EcoFABs) to establish growing environments with optical access and employed nonlinear multimodal microscopy of third-harmonic generation (THG) and three-photon fluorescence (3PF) to achieve label-free, in situ imaging of live roots and microbes at high spatiotemporal resolution. THG enabled us to observe key plant root structures including the vasculature, Casparian strips, dividing meristematic cells, and root cap cells, as well as subcellular features including nuclear envelopes, nucleoli, starch granules, and putative stress granules. THG from the cell walls of bacteria and fungi also provides label-free contrast for visualizing these microbes in the root rhizosphere. With simultaneously recorded 3PF signal, we demonstrated our ability to investigate root-microbe interactions by achieving single-bacterium tracking and subcellular imaging of fungal spores and hyphae in the rhizosphere.

Pan, Daisong [University of California, Berkeley, ↗
DOE OSTI2019

Downregulation of pectin biosynthesis gene GAUT4 leads to reduced ferulate and lignin-carbohydrate cross-linking in switchgrass

Abstract Knockdown (KD) expression of GAlactUronosylTransferase 4 ( GAUT4 ) in switchgrass improves sugar yield and ethanol production from the biomass. The reduced recalcitrance of GAUT4 -KD transgenic biomass is associated with reduced cell wall pectic homogalacturonan and rhamnogalacturonan II content and cross-linking, and the associated increases in accessibility of cellulose to enzymatic deconstruction. To further probe the molecular basis for the reduced recalcitrance of GAUT4 -KD biomass, potential recalcitrance-related factors including the physicochemical properties of lignin and hemicellulose are investigated. We show that the transgenic switchgrass have a lower abundance of ferulate and lignin-carbohydrate complex cross-linkages, reduced amounts of residual arabinan and xylan in lignin-enriched fractions after enzymatic hydrolysis, and greater coalescence and migration of lignin after hydrothermal pretreatment in comparison to the wild-type switchgrass control. The results reveal the roles of both decreased lignin-polymer and pectin cross-links in the reduction of recalcitrance in PvGAUT4 -KD switchgrass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

In situ plant materials hyperspectral imaging by multimodal scattering near-field optical microscopy

Plant cells are elaborate three-dimensional polymer nano-constructs with complex chemistry. The bulk response of plants to light, in the far-field, is ultimately encoded by optical scattering from these nano-constructs. Their chemical and physical properties may be acquired through their interaction with a modulated nano-tip using scattering scanning near-field optical microscopy. Here, using this technique, we present 20 nm spatial resolution mechanical, spectral and optical mappings of plant cell walls. We first address the problem of plant polymers tracking through pretreatment and processing. Specifically, cellulose and lignin footprints are traced within a set of delignified specimen, establishing the factors hindering complete removal of lignin, an important industrial polymer. Furthermore, we determine the frequency dependent dielectric function ${\epsilon }(\omega)={(n+ik)}^{2}$ of plant material in the range 28 ≤ ω ≤ 58 THz, and show how the environmental chemical variation is imprinted in the nanoscale variability of n and k . This nanometrology is a promise for further progress in the development of plant-based (meta-)materials.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Electronically transparent graphene replicas of diatoms: a new technique for the investigation of frustule morphology

The morphogenesis of the silica cell walls (called frustules) of unicellular algae known as diatoms is one of the most intriguing mysteries of the diatoms. To study frustule morphogenesis, optical, electron and atomic force microscopy has been extensively used to reveal the frustule morphology. However, since silica frustules are opaque, past observations were limited to outer and fracture surfaces, restricting observations of interior structures. Here we show that opaque silica frustules can be converted into electronically transparent graphene replicas, fabricated using chemical vapor deposition of methane. Chemical vapor deposition creates a continuous graphene coating preserving the frustule’s shape and fine, complicated internal features. Subsequent dissolution of the silica with hydrofluoric acid yields a free-standing replica of the internal and external native frustule morphologies. Electron microscopy renders these graphene replicas highly transparent, revealing previously unobserved, complex, three-dimensional, interior frustule structures, which lend new insights into the investigation of frustule morphogenesis.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Synchrotron-based X-ray fluorescence microscopy enables multiscale spatial visualization of ions involved in fungal lignocellulose deconstruction

Ions play an important role in the growth and development of filamentous fungi, particularly in the fungal decay process of lignocellulose materials. The role of ions in wood degradation, and more broadly fungal metabolism, have implications for diverse research disciplines ranging from plant pathology and forest ecology, to wood protection. Despite the importance of ions in both enzymatic and non-enzymatic fungal decay mechanisms, the spatial distribution of ions in wood and fungal hyphae during decay is not known. Here we employ synchrotron based X-ray fluorescence microscopy (XFM) to map physiologically relevant ions, such as K, Ca, Mn, Fe, and Zn, in wood being decayed by the model brown rot fungus Serpula lacrymans . Two-dimensional XFM maps were obtained to study the ion spatial distributions from mm to submicron length scales in wood and hyphae. Three-dimensional ion volume reconstructions with submicron spatial resolution were also acquired of wood cell walls and fungal hyphae, and an estimation of oxalate concentration at the microscale was made. Results show that the fungus actively transports some ions, such as Fe, into the wood and controls the distribution of ions at both the bulk wood and cellular length scales. Within the fungal hyphae, ion volume reconstructions show inhomogeneous ion distributions at the micron length scale and this localization may be indicative of both physiological status and requirements or in some cases, potentially sites associated with the initiation of metal-catalyzed wood degradation. Finally, these measurements illustrate how synchrotron based XFM is uniquely qualified for probing the role of ions in the growth and metabolic processes of filamentous fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Lignin Valorization: Emerging Approaches

Lignin, an aromatic biopolymer found in plant cell walls, is a key component of lignocellulosic biomass and generally utilized for heat and power. However, lignin's chemical composition makes it an attractive source for biological and catalytic conversion to fuels and chemicals. Bringing together experts from biology, catalysis, engineering, analytical chemistry, and techno-economic/life-cycle analysis, Lignin Valorization presents a comprehensive, interdisciplinary picture of how lignocellulosic biorefineries could potentially employ lignin valorization technologies. Chapters will specifically focus on the production of fuels and chemicals from lignin and topics covered include (i) methods for isolating lignin in the context of the lignocellulosic biorefinery, (ii) thermal, chemo-catalytic, and biological methods for lignin depolymerization, (iii) chemo-catalytic and biological methods for upgrading lignin, (iv) characterization of lignin, and (v) techno-economic and life-cycle analysis of integrated processes to utilize lignin in an integrated biorefinery. The book provides the latest breakthroughs and challenges in upgrading lignin to fuels and chemicals for graduate students and researchers in academia, governmental laboratories, and industry interested in biomass conversion.

09 BIOMASS FUELS↗
DOE OSTI2018

Chapter 1: A Brief Introduction to Lignin Structure

Lignin is an alkyl-aromatic polymer found in the cell walls of terrestrial plants. Lignin provides structure and rigidity to plants, is a natural, highly effective barrier against microbial attack, and enables water and nutrient transport through plant tissues. Depending on the plant species, the constituents of lignin can vary considerably, leading to substantial diversity in lignin chemistry and structure. Despite nearly a century of research and development attempting to convert lignin into valuable products, lignin in most current and planned biorefinery contexts remains underutilized, most often being burned to generate heat and power. However, the drive towards effective lignin valorization processes has witnessed a significant resurgence in the past decade, catalyzed by advances in improved understanding of lignin chemistry, structure, and plasticity in parallel with new catalytic and biological approaches to valorize this important, prevalent biopolymer. As a preface to the subsequent chapters in this book, this chapter briefly highlights the known aspects of lignin structure.

09 BIOMASS FUELS↗
DOE OSTI2014

Why genetic modification of lignin leads to low-recalcitrance biomass

Genetic modification of plants via down-regulation of cinnamyl alcohol dehydrogenase leads to incorporation of aldehyde groups in the lignin polymer. Moreover, the resulting lignocellulosic biomass has increased bioethanol yield. However, a molecular-scale explanation of this finding is currently lacking. We perform molecular dynamics simulation of the copolymer with hemicellulose of wild type and the genetically modified lignin, in aqueous solution. We find that the non-covalent association with hemicellulose of lignin containing aldehyde groups is reduced compared to the wild-type. This phase separation may increase the cell wall porosity in the mutant plants, thus explaining their easier deconstruction to biofuels. The thermodynamic origin of the reduced lignin-hemicellulose association is found to be a more favorable self-interaction energy and less favorable interaction with hemicellulose for the mutant lignin. Furthermore, reduced hydration water density fluctuations are found for the mutant lignin, implying a more hydrophobic lignin surface. Our results provide a detailed description of how aldehyde incorporation makes lignin more hydrophobic and reduces its association with hemicellulose, thus suggesting that increased lignin hydrophobicity may be an optimal characteristic required for improved biofuel production.

09 BIOMASS FUELS↗
DOE OSTI2017

Lignocellulose fermentation and residual solids characterization for senescent switchgrass fermentation by Clostridium thermocellum in the presence and absence of continuous in situ ball-milling

Milling during lignocellulosic fermentation, henceforth referred to as cotreatment, is investigated as an alternative to thermochemical pretreatment as a means of enhancing biological solubilization of lignocellulose. We investigate the impact of milling on soluble substrate fermentation by Clostridium thermocellum with comparison to yeast, document solubilization for fermentation of senescent switchgrass with and without ball milling, and characterize residual solids. Soluble substrate fermentation by C. thermocellum proceeded readily in the presence of continuous ball milling but was completely arrested for yeast. Total fractional carbohydrate solubilization achieved after fermentation of senescent switchgrass by C. thermocellum for 5 days was 0.45 without cotreatment or pretreatment, 0.81 with hydrothermal pretreatment (200 degrees C, 15 minutes, severity 4.2), and 0.88 with cotreatment. Acetate and ethanol were the main fermentation products, and were produced at similar ratios with and without cotreatment. Analysis of solid residues was undertaken using molecular beam mass spectrometry (PyMBMS) and solid-state nuclear magnetic resonance spectroscopy (NMR) in order to provide insight into changes in plant cell walls during processing via various modes. The structure of lignin present in residual solids remaining after fermentation with cotreatment appeared to change little, with substantially greater changes observed for hydrothermal pretreatment - particularly with respect to formation of C-C bonds. The observation of high solubilization with little apparent modification of the residue is consistent with cotreatment enhancing solubilization primarily by increasing the access of saccharolytic enzymes to the feedstock, and C. thermocellum being able to attack all the major linkages in cellulosic biomass provided that these linkages are accessible.

09 BIOMASS FUELS↗
DOE OSTI2017

Effects of organosolv and ammonia pretreatments on lignin properties and its inhibition for enzymatic hydrolysis

Lignin offers structural support and protection for plant cell walls; but, it also contributes to biomass recalcitrance and the costs of biofuel production via the biological pathway. Organosolv and ammonia pretreatments have been developed to reduce biomass recalcitrance and improve sugar release performance during enzymatic hydrolysis. It is believed that lignin properties are related to its inhibition on enzymatic hydrolysis; therefore, understanding the characteristics of lignin is a key for effective biomass conversion to biofuels. In this study, an organosolv pretreatment using 60% ethanol with 1.25% H 2 SO 4 significantly deconstructed poplar lignin and reduced its molecular weights due to the cleavage of lignin inter-unit linkages. The organosolv pretreatment increased the contents of phenolic OH units and the lignin residue showed a high cellulase maximum adsorption capacity. Ammonia pretreatment with 5% ammonium hydroxide was not as effective as organosolv pretreatment on lignin deconstruction. Organosolv lignin residue had lower lignin S/G ratio than the untreated one. Furthermore, when compared to the organosolv lignin residue and untreated lignin, ammonia lignin residue had a higher cellulase adsorption affinity. In addition, the effects of lignin on cellulose hydrolysis was investigated and the results suggested that the presence of lignin with cellulose substrates reduced cellulose hydrolysis, and its inhibitory effect was primarily determined by the lignin properties after each pretreatment. The organosolv pretreatment resulted in a slightly lower cellulase binding strength (249.7 mL g -1 ) on poplar lignin than that on untreated samples (261.1 mL g -1 ), while ammonia lignin residue showed a higher cellulase binding strength (402.8 mL g -1 ) and had more significant inhibition effect on cellulose hydrolysis. Our results demonstrated that the binding strength significantly affected the lignin-derived inhibition on enzymatic hydrolysis of cellulose in the cellulose-lignin mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Temperature-dependent phase behaviour of tetrahydrofuran–water alters solubilization of xylan to improve co-production of furfurals from lignocellulosic biomass

Xylose, Xylan, Hemicellulose, CELF, THF, Co-solvent, Pretreatment, Biomass ABSTRACT: Xylan is an important polysaccharide found in the hemicellulose fraction of lignocellulosic biomass that can be hydrolysed to xylose and further dehydrated to the furfural, an important renewable platform fuel precursor. Here, pairing molecular simulation and experimental evidences, we reveal how the unique temperature-dependent phase behaviour of water-tetrahydrofuran (THF) co-solvent can delay xylan solubilization to synergistically improve catalytic co-processing of biomass to furfural and 5-HMF. Our results indicate, based on polymer correlations between polymer conformational behaviour and solvent quality, that both co-solvent and aqueous environments serve as ‘good’ solvents for xylan. Interestingly, the simulations also revealed that unlike other cell-wall components (i.e., lignin and cellulose), the make-up of the solvation shell of xylan in THF-water is dependent on the temperature-phase behaviour. At temperatures between 333K and 418K, THF and water become immiscible, and THF is evacuated from the solvation shell of xylan, while above and below this temperature range, THF and water are both present in the polysaccharide’s solvation shell. This suggested that the solubilization of xylan in THF-water may be similar to aqueous-only solutions at temperatures between 333K and 418K and different outside this range. Experimental reactions on beachwood xylan corroborate this hypothesis by demonstrating 2-fold reduction of xylan solubilization in THF-water within a miscible temperature regime (445K) and unchanged solubilization within an immiscible regime (400K). Translating this phase-dependent behaviour to processing of maple wood chips, we demonstrate how the weaker xylan solvation in THF-water under miscible conditions can delay furfural production from xylose, allowing 5-HMF production from cellulose to “catch-up” such that their high yield production from biomass can be synergized in a single pot reaction.

09 BIOMASS FUELS↗
DOE OSTI2018

Impact of hydration and temperature history on the structure and dynamics of lignin

The full utilization of plant biomass for the production of energy and novel materials often involves high temperature treatment. Examples include melt spinning of lignin for manufacturing low-cost carbon fiber and the relocalization of lignin to increase the accessibility of cellulose for production of biofuels. These temperature-induced effects arise from poorly understood changes in lignin flexibility. Here, we combine molecular dynamics simulations with neutron scattering and dielectric spectroscopy experiments to probe the dependence of lignin dynamics on hydration and thermal history. We find a dynamical and structural hysteresis: at a given temperature, the lignin molecules are more expanded and their dynamics faster when the lignin is cooled than when heated. The structural hysteresis is more pronounced for dry lignin. The difference in dynamics, however, follows a different trend, it is found to be more significant at high temperatures and high hydration levels. The simulations also reveal syringyl units to be more dynamic than guiacyl. The results provide an atomic-detailed description of lignin dynamics, important for understanding lignin role in plant cell wall mechanics and for rationally improving lignin processing. The lignin glass transition, at which the polymer softens, is lower when lignin is cooled than when heated, therefore extending the cooling phase of processing and shortening the heating phase may offer ways to lower processing costs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Dynamics of the lignin glass transition

The dynamics of lignin, a complex and heterogeneous major plant cell-wall macromolecule, is of both fundamental and practical importance. Lignin is typically heated to temperatures above its glass transition to facilitate its industrial processing. Here, we performed molecular dynamics simulations to investigate the segmental (α) relaxation of lignin, the dynamical process that gives rise to the glass transition. It is found that lignin dynamics involves mainly internal motions below T g , while segmental inter-molecular motions are activated above T g . The segments whose mobility is enhanced above T g consist of 3–5 lignin monomeric units. The temperature dependence of the lignin segmental relaxation time changes from Arrhenius below T g to Vogel–Fulcher–Tamman above T g . This change in temperature dependence is determined by the underlying energy landscape being restricted below T g but exhibiting multiple minima above T g . The Q-dependence of the relaxation time is found to obey a power-law up to Q max , indicative of sub-diffusive motion of lignin above T g . Temperature and hydration affect the segmental relaxation similarly. Increasing hydration or temperature leads to: (1) the α process starting earlier, i.e. the beta process becomes shortened, (2) Q max decreasing, i.e. the lengthscale above which subdiffusion is observed increases, and (3) the number of monomers constituting a segment increasing, i.e. the motions that lead to the glass transition become more collective. The above findings provide molecular-level understanding of the technologically important segmental motions of lignin and demonstrate that, despite the heterogeneous and complex structure of lignin, its segmental dynamics can be described by concepts developed for chemically homogeneous polymers.

09 BIOMASS FUELS↗
DOE OSTI2019

A critical review on the analysis of lignin carbohydrate bonds

Replacing fossil-based resources with renewable alternatives is generally acknowledged as a critical component to address several of today's environmental concerns. In this context, lignocellulosic biomass is an attractive, sustainable resource. Yet, the constitutional biopolymers of interest are locked in the structural complexity of the plant cell walls, which defines their properties and contributes to fractionation recalcitrance. One of the key elements restricting fractionation of the biopolymers in high yield is the presence of lignin–carbohydrate bonds forming a matrix referred to as lignin–carbohydrate complex (LCC). Nonetheless, covalent bonds between lignin and carbohydrates, remain one of the most controversial topics in lignocellulose chemistry. This challenge can be attributed to the slow progress made in their research, which also forms the basis for this review. Herein, we will critically discuss the literature with a particular focus on the latest characterization and analytical techniques. Discussions on existing techniques and, importantly the drawbacks with them should be compelling to researchers in the area, especially at this time when crucial issues surrounding the realization of biorefineries need to be addressed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗