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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

Characterisation of FUT4 and FUT6 α-(1→2)-Fucosyltransferases Reveals that Absence of Root Arabinogalactan Fucosylation Increases Arabidopsis Root Growth Salt Sensitivity

Plant type II arabinogalactan (AG) polysaccharides are attached to arabinogalactan proteins (AGPs) at hydroxyproline residues, and they are very diverse and heterogeneous structures. The AG consists of a β-(1→3)-linked galactan backbone with β-(1→6)-galactan side chains that are modified mainly with arabinose, but they may also contain glucuronic acid, rhamnose or other sugars. Here, we studied the positions of fucose substitutions in AGPs, and we investigated the functions of this fucosylation. Monosaccharide analysis of Arabidopsis leaf AGP extracts revealed a significant reduction in L-Fucose content in the fut4 mutant, but not in the fut6 mutant. In addition, Fucose was reduced in the fut4 mutant in root AGP extracts and was absent in the fut4/fut6 mutant. Curiously, in all cases reduction of fucose was accompanied with a reduction in xylose levels. The fucosylated AGP structures in leaves and roots in wild type and fut mutant plants were characterised by sequential digestion with AG specific enzymes, analysis by Polysaccharide Analysis using Carbohydrate gel Electrophoresis, and Matrix Assisted Laser Desorption/Ionisation (MALDI)-Time of Flight Mass spectrometry (MS). We found that FUT4 is solely responsible for the fucosylation of AGPs in leaves. The Arabidopsis thaliana FUT4 and FUT6 genes have been previously proposed to be non-redundant AG-specific fucosyltransferases. Unexpectedly, FUT4 and FUT6 enzymes both fucosylate the same AGP structures in roots, suggesting partial redundancy to each other. Detailed structural characterisation of root AGPs with high energy MALDI-Collision Induced Dissociation MS and NMR revealed an abundant unique AG oligosaccharide structure consisting of terminal xylose attached to fucose. The loss of this structure in fut4/fut6 mutants explains the reduction of both fucose and xylose in AGP extracts. Under salt-stress growth conditions the fut4/fut6 mutant lacking AGP fucosylation exhibited a shorter root phenotype than wild type plants, implicating fucosylation of AGPs in maintaining proper cell expansion under these conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Final Report for Award DE-FG02-09ER64721

The original goal of this award was to develop a proteoglycan “chip” containing suitable oligosaccharides that could be used as substrates for glycosyltransferases involved in synthesis or proteoglycans in higher plant cell walls. We had previously developed a suite of cloned enzymes that could be used to cleave most of the relevant glycosidic linkages in plant cell walls. The next step, supported by the previous award and this award, was to produce a series of transgenic plants in which synthetic proteins were introduced that contained each of the known sequence motifs that induce prolyl hydroxylation, and subsequent glycosylation. This work was completed and published in Estevez et al (2006). We then engaged on a series of experiments to define the properties of the prolyl hydroxylases that convert certain prolyl resides to hydroxyproline for subsequent glycosylation. This proved to be a challenging goal that required recruitment of an international team of complementary skills and several additional years or research. However, the effort was successful and has been published in Science recenty (Velasquez et al., 2011). In the course of this project, the postdoc supported by the award (Jose Estevez) was asked to provide technical assistance to a colleague at Stanford because of his expertise in marine polysaccharides. This led to the important discovery that marine algae have compounds that could be classified as lignin (Martone et al., 2009). Publications supported by the award Estévez, J.M., Kieliszewski, M.J., Khitrov, N., Somerville, C. (2006) Characterization of synthetic hydroxyproline-rich proteoglycans with AGP- and extensin-motifs in Arabidopsis. Plant Physiol., 142,458-470 Martone, P.T., Estevez, J.M., Lu, F., Ruel, K., Ralph, J., Denny, M.W., Somerville, C.R. (2009) Discovery of lignin in seaweed reveals convergent evolution of cell-wall architecture. Curr. Biol., 19, 169-175 Velasquez, S.M., M. Ricardi, M.M., Dorosz, J.G., Fernandez, P.V., Nadra, A.D., Pol-Fachin, L., Egelund, J., Gille, S., Harholt, J., Ciancia, M., Verli, H., Pauly, M., Bacic, A., Olsen, C.E., r Ulvskov, P., Petersen, B.L., Somerville, C., Iusem, N.D. & Estevez, J.M. (2011) O-glycosylated cell wall proteins are essential in root hair growth. Science 332,1401-1403

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deciphering exopolysaccharide functional specificity via visualization of chemical motifs that mediate microbial-microenvironment interactions in soil micromodels

Exopolysaccharides (EPS) are carbohydrate-based matrices of microbial biofilms that microbes use to adapt to their surroundings. Microbial EPS also promotes soil aggregate stability and contributes toward soil health by reducing erosion caused by continued land use. The chemical structure of EPS, even within single species biofilms, can vary greatly: from repeating units and branching patterns to the non-carbohydrate decorations. Despite the wealth of knowledge on EPS chemistry, many unresolved questions regarding the biological implications of EPS chemical variations remain. Here, we develop a mass spectrometry imaging toolbox that reveal how EPS chemistry enables microbial adaptation to different microenvironments such as specific moisture, soil-biofilm interfaces, and food source proximity. First, we developed emulated soil micromodels (ESMs), microfluidic channels that simulate the physical properties of soil, for biofilm formation in different microenvironments. Then, in order to map chemical features of EPS in these micromodels, we develop strategies for in-situ releasing of oligosaccharides using specific enzymes. Lastly, we optimized matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) to spatially analyze the released compounds in ESMs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Structural analysis and functional evaluation of the disordered ß–hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis

Hamamotoa (Sporobolomyces) singularis codes for an industrially important membrane bound ß-hexosyltransferase (BHT), (BglA, UniprotKB: Q564N5) that has applications in the production of natural fibers such as galacto-oligosaccharides (GOS) and natural sugars found in human milk. When heterologously expressed by Komagataella phaffii GS115, BHT is found both membrane bound and soluble secreted into the culture medium. In silico structural predictions and crystal structures support a glycosylated homodimeric enzyme and the presence of an intrinsically disordered region (IDR) with membrane binding potential within its novel N-terminal region (1–110 amino acids). Additional in silico analysis showed that the IDR may not be essential for stable homodimerization. Thus, we performed progressive deletion analyses targeting segments within the suspected disordered region, to determine the N-terminal disorder region’s impact on the ratio of membrane-bound to secreted soluble enzyme and its contribution to enzyme activity. The ratio of the soluble secreted to membrane-bound enzyme shifted from 40% to 53% after the disordered N-terminal region was completely removed, while the specific activity was unaffected. Furthermore, functional analysis of each glycosylation site found within the C-terminal domain revealed reduced total secreted protein activity by 58%–97% in both the presence and absence of the IDR, indicating that glycosylation at all four locations is required by the host for the secretion of active enzyme and independent of the removed disordered N-terminal region. Overall, the data provides evidence that the disordered region only partially influences the secretion and membrane localization of BHT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Leveraging microfluidic dielectrophoresis to distinguish compositional variations of lipopolysaccharide in E. coli

Lipopolysaccharide (LPS) is the unique feature that composes the outer leaflet of the Gram-negative bacterial cell envelope. Variations in LPS structures affect a number of physiological processes, including outer membrane permeability, antimicrobial resistance, recognition by the host immune system, biofilm formation, and interbacterial competition. Rapid characterization of LPS properties is crucial for studying the relationship between these LPS structural changes and bacterial physiology. However, current assessments of LPS structures require LPS extraction and purification followed by cumbersome proteomic analysis. This paper demonstrates one of the first high-throughput and non-invasive strategies to directly distinguish Escherichia coli with different LPS structures. Using a combination of three-dimensional insulator-based dielectrophoresis (3DiDEP) and cell tracking in a linear electrokinetics assay, we elucidate the effect of structural changes in E. coli LPS oligosaccharides on electrokinetic mobility and polarizability. We show that our platform is sufficiently sensitive to detect LPS structural variations at the molecular level. To correlate electrokinetic properties of LPS with the outer membrane permeability, we further examined effects of LPS structural variations on bacterial susceptibility to colistin, an antibiotic known to disrupt the outer membrane by targeting LPS. Our results suggest that microfluidic electrokinetic platforms employing 3DiDEP can be a useful tool for isolating and selecting bacteria based on their LPS glycoforms. Future iterations of these platforms could be leveraged for rapid profiling of pathogens based on their surface LPS structural identity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The regulation of the cell wall by glycosylphosphatidylinositol-anchored proteins in Arabidopsis

A polysaccharides-based cell wall covers the plant cell, shaping it and protecting it from the harsh environment. Cellulose microfibrils constitute the cell wall backbone and are embedded in a matrix of pectic and hemicellulosic polysaccharides and glycoproteins. Various environmental and developmental cues can regulate the plant cell wall, and diverse glycosylphosphatidylinositol (GPI)-anchored proteins participate in these regulations. GPI is a common lipid modification on eukaryotic proteins, which covalently tethers the proteins to the membrane lipid bilayer. Catalyzed by a series of enzymic complexes, protein precursors are post-translationally modified at their hydrophobic carboxyl-terminus in the endomembrane system and anchored to the lipid bilayer through an oligosaccharidic GPI modification. Ultimately, mature proteins reach the plasma membrane via the secretory pathway facing toward the apoplast and cell wall in plants. In Arabidopsis, more than three hundred GPI-anchored proteins (GPI-APs) have been predicted, and many are reported to be involved in diverse regulations of the cell wall. In this review, we summarize GPI-APs involved in cell wall regulation. GPI-APs are proposed to act as structural components of the cell wall, organize cellulose microfibrils at the cell surface, and during cell wall integrity signaling transduction. Besides regulating protein trafficking, the GPI modification is potentially governed by a GPI shedding system that cleaves and releases the GPI-anchored proteins from the plasma membrane into the cell wall.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Microbial Community Structure and Functional Potential Along a Hypersaline Gradient

© 2018 Kimbrel, Ballor, Wu, David, Hazen, Simmons, Singer and Jansson. Salinity is one of the strongest environmental drivers of microbial evolution and community composition. Here we aimed to determine the impact of salt concentrations (2.5, 7.5, and 33.2%) on the microbial community structure of reclaimed saltern ponds near San Francisco, California, and to discover prospective enzymes with potential biotechnological applications. Community compositions were determined by 16S rRNA amplicon sequencing revealing both higher richness and evenness in the pond sediments compared to the water columns. Co-occurrence network analysis additionally uncovered the presence of microbial seed bank communities, potentially primed to respond to rapid changes in salinity. In addition, functional annotation of shotgun metagenomic DNA showed different capabilities if the microbial communities at different salinities for methanogenesis, amino acid metabolism, and carbohydrate-active enzymes. There was an overall shift with increasing salinity in the functional potential for starch degradation, and a decrease in degradation of cellulose and other oligosaccharides. Further, many carbohydrate-active enzymes identified have acidic isoelectric points that have potential biotechnological applications, including deconstruction of biofuel feedstocks under high ionic conditions. Metagenome-assembled genomes (MAGs) of individual halotolerant and halophilic microbes were binned revealing a variety of carbohydrate-degrading potential of individual pond inhabitants.

Kimbrel, Jeffrey A.↗
DOE OSTI2021

A t FUT4 and A t FUT6 Are Arabinofuranose-Specific Fucosyltransferases

The bulk of plant biomass is comprised of plant cell walls, which are complex polymeric networks, composed of diverse polysaccharides, proteins, polyphenolics, and hydroxyproline-rich glycoproteins (HRGPs). Glycosyltransferases (GTs) work together to synthesize the saccharide components of the plant cell wall. The Arabidopsis thaliana fucosyltransferases (FUTs), At FUT4, and At FUT6, are members of the plant-specific GT family 37 (GT37). At FUT4 and At FUT6 transfer fucose (Fuc) onto arabinose (Ara) residues of arabinogalactan (AG) proteins (AGPs) and have been postulated to be non-redundant AGP-specific FUTs. At FUT4 and At FUT6 were recombinantly expressed in mammalian HEK293 cells and purified for biochemical analysis. We report an updated understanding on the specificities of At FUT4 and At FUT6 that are involved in the synthesis of wall localized AGPs. Our findings suggest that they are selective enzymes that can utilize various arabinogalactan (AG)-like and non-AG-like oligosaccharide acceptors, and only require a free, terminal arabinofuranose. We also report with GUS promoter-reporter gene studies that AtFUT4 and AtFUT6 gene expression is sub-localized in different parts of developing A. thaliana roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exogenous Enzymes Influenced Eimeria-Induced Changes in Cecal Fermentation Profile and Gene Expression of Nutrient Transporters in Broiler Chickens

Two 21-day experiments were conducted to investigate the effects of exogenous enzymes on growth performance, tight junctions, and nutrient transporters, jejunal oligosaccharides and cecal short-chain fatty acids (SCFA) of broiler chickens challenged with mixed Eimeria. Two different basal diets: high fiber-adequate protein (HFAP; Expt. 1) or low fiber-low protein (LFLP; Expt. 2) were used in the two experiments. In each experiment, birds were allocated to four treatments in a 2 × 2 factorial arrangement (with or without protease and xylanase combination; with or without Eimeria challenge). In Expt. 1, with HFAP diets, Eimeria upregulated (p < 0.05) the expression of claudin-1, but downregulated (p < 0.05) glucose transporters GLUT2/GLUT5. On the contrary, enzymes downregulated (p < 0.05) claudin-1 and alleviated the Eimeria-depressed GLUT2/GLUT5 expression. In both experiments, Eimeria decreased (p < 0.05) cecal saccharolytic SCFA and increased (p < 0.05) cecal branched-chain fatty acids. The challenge × enzyme interaction (p < 0.05) showed that enzymes reversed the Eimeria effects on fermentation pattern shift. In conclusion, Eimeria altered tight junctions and nutrient transporters expression promoted cecal proteolytic fermentation and inhibited saccharolytic fermentation. Exogenous enzymes showed the potential of alleviating the Eimeria-induced intestinal gene expression changes and reversing the unfavorable cecal fermentation pattern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Role of LysM receptors in chitin-triggered plant innate immunity

Recent research findings clearly indicate that lysin motif (LysM)-containing cell surface receptors are involved in the recognition of specific oligosaccharide elicitors (chitin and peptidoglycan), which trigger an innate immunity response in plants. These receptors are either LysM-containing receptor-like kinases (LYKs) or LysM-containing receptor proteins (LYPs). In Arabidopsis, five LYKs (AtCERK1/AtLYK1 and AtLYK2–5) and three LYPs (AtLYP1–3) are likely expressed on the plasma membrane. In this review, we summarize recent research results on the role of these receptors in plant innate immunity, including the recent structural characterization of AtCERK1 and composition of the various receptor complexes in Arabidopsis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Rapid Characterization Tools for Process Optimization: Cooperative Research and Development (Final Report)

In this project Prenexus Health, Inc. (Prenexus) and NLR will develop rapid characterization tools to improve the Prenexus production process. First, we will develop a tool to predict the overall performance of the Prenexus manufacturing process converting high-fiber sugarcane to xylo-oligosaccharides (XOS) (both the overall process yield and the composition of the XOS product) using rapid characterization of the incoming feedstock and knowledge of key process parameters. This tool will dramatically increase Prenexus’ understanding of the overall process. Second, we will develop a tool to predict the concentration of soluble oligomeric and monomeric xylose and organic acids in multiple process streams at-line in the Prenexus process, enabling real-time process control of the conversion process.

09 BIOMASS FUELS↗
DOE OSTI2018

Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer and a glycosylated HIV-1 gp120 core

VRC01 broadly neutralizing antibodies (bnAbs) target the CD4-binding site (CD4BS) of the human immunodeficiency virus-1 (HIV-1) envelope glycoprotein (Env). Unlike mature antibodies, corresponding VRC01 germline precursors poorly bind to Env. Immunogen design has mostly relied on glycan removal from trimeric Env constructs and has had limited success in eliciting mature VRC01 bnAbs. To better understand elicitation of such bnAbs, we characterized the inferred germline precursor of VRC01 in complex with a modified trimeric 426c Env by cryo-electron microscopy and a 426c gp120 core by X-ray crystallography, biolayer interferometry, immunoprecipitation, and glycoproteomics. Our results show VRC01 germline antibodies interacted with a wild-type 426c core lacking variable loops 1–3 in the presence and absence of a glycan at position Asn276, with the latter form binding with higher affinity than the former. Interactions in the presence of an Asn276 oligosaccharide could be enhanced upon carbohydrate shortening, which should be considered for immunogen design.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2013

Anthrax carbohydrates, synthesis and uses thereof

The present invention presents the isolation, characterization and synthesis of oligosaccharides of Bacillus anthracis. Also presented are antibodies that bind to such saccharide moieties and various methods of use for such saccharide moieties and antibodies.

Carlson, Russell W.↗
DOE OSTI2013

Anthrax carbohydrates, synthesis and uses thereof

The present invention presents the isolation, characterization and synthesis of oligosaccharides of Bacillus anthracis. Also presented are antibodies that bind to such saccharide moieties and various methods of use for such saccharide moieties and antibodies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Conversion of oligomeric starch, cellulose, hydrolysates or sugars to hydrocarbons

Embodiments of the present invention are directed to the conversion of a source material (e.g., a depolymerized oligosaccharide mixture, a monomeric sugar, a hydrolysate, or a mixture of monomeric sugars) to intermediate molecules containing 7 to 26 contiguous carbon atoms. These intermediates may also be converted to saturated hydrocarbons. Such saturated hydrocarbons are useful as, for example, fuels.

09 BIOMASS FUELS↗
DOE OSTI2021

Conversion of sugars to ionic liquids

Disclosed herein are methods for preparing sugar compositions. The methods include: i) forming a mixture including polysaccharide biomass and an ionic liquid solution, wherein the ionic liquid solution contains water and an ionic liquid, and the ionic liquid contains a) a cation and b) a sugar acid anion or a ketoacid anion; ii) maintaining the mixture under conditions sufficient to dissolve at least a portion of the polysaccharide present in the polysaccharide biomass; iii) adding at least one glycoside hydrolase to the mixture; and iv) maintaining the mixture containing the glycoside hydrolase under conditions sufficient to hydrolyze at least a portion of the dissolved polysaccharide, thereby forming the sugar compositions. The sugar compositions contain at least one monosaccharide or oligosaccharide. New sugar-based ionic liquids are also described.

Gladden, John M.↗
DOE OSTI2017

Chitosan–Sodium Tetradecyl Sulfate Hydrogel: Characterization and Preclinical Evaluation of a Novel Sclerosing Embolizing Agent for the Treatment of Endoleaks

PurposeTo compare the efficacy of an embolization agent with sclerosing properties (made of chitosan and sodium tetradecyl sulfate, CH–STS) with a similar embolization agent but without sclerosing properties (made of chitosan, CH) in treating endoleaks in a canine endovascular aneurysm repair model.MethodsTwo chitosan-based radiopaque hydrogels were prepared, one with STS and one without STS. Their rheological, injectability, and embolizing properties were assessed in vitro; afterwards, their efficacy in occluding endoleaks was compared in a canine bilateral aneurysm model reproducing type I endoleaks (n = 9 each). The primary endpoint was endoleak persistence at 3 or 6 months, assessed on a CT scan and macroscopic examination. Secondary endpoints were the occurrence of stent-graft (SG) thrombosis, the evolution of the aneurysm mean diameter, as well as aneurysm healing and inflammation scores in pathology examinations.ResultsIn vitro experiments showed that both products gelled rapidly and presented initial storage moduli greater than 800 Pa, which increased with time. Both gels were compatible with microcatheter injection and occlude flow up to physiological pressure in vitro. In a type I endoleak model, the injection of CH–STS sclerosing gel tended to reduce the risk of occurrence of endoleaks, compared to CH non-sclerosing agent (2/9 vs. 6/9, p = 0.069). No case of SG thrombosis was observed. Moderate inflammation was found around both gels, with a comparable intensity score in both CH and CH–STS groups (2.6 ± 0.9 and 2.7 ± 0.9, respectively; p = 0.789).ConclusionsFlow occlusion combined with chemical endothelial denudation appears promising for the treatment of endoleaks.Level of EvidenceN/A.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Optical Methods for the Analysis of the Temoprofin Photosensitizer Distribution Between Serum Proteins and Methyl-β-Cyclodextrin Nanocarriers in Blood Serum

Various optical methods for the analysis of the processes leading to temoporfin photosensitizer distribution between supramolecular nanosized inclusion complexes derived from β−cyclodextrins and blood serum proteins were examined. Methods involving induced circular dichroism, fluorescence anisotropy, and the variability of the shape of the photosensitizer fluorescence excitation spectra were compared with traditional methods such as gel chromatography and ultracentrifugation. The feasibility of using the photosensitizer optical characteristics for analyzing both equilibrium and kinetic processes of photosensitizer distribution in blood was demonstrated. The main advantages and limitations of these approaches in in vitro experiments were described.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗