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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS1971

Mechanisms and kinetics of cellulose fermentation for protein production

The development of a process (and ancillary processing and analytical techniques) to produce bacterial single-cell protein of good nutritional quality from waste cellulose is discussed. A fermentation pilot plant and laboratory were developed and have been in operation for about two years. Single-cell protein (SCP) can be produced from sugarcane bagasse--a typical agricultural cellulosic waste. The optimization and understanding of this process and its controlling variables are examined. Both batch and continuous fermentation runs have been made under controlled conditions in the 535 liter pilot plant vessel and in the laboratory 14-liter fermenters.

Dunlap, C. A.↗
DOE OSTI2021

Towards an Understanding of Oxidative Damage in an a-L-Arabinofuranosidase of Trichoderma reesei : a Molecular Dynamics Approach

Trichoderma reesei is a ‘workhorse’ fungus that produces glycosyl hydrolases (e.g., cellulases) at high titers for use in industrial bioprocessing. In this study, we focused on two side-chain hemicellulases, a-L-arabinofuranosidases and a-D-galactosidases, which are important for the treatment of lignocellulosic biomass, but susceptible to oxidative damage that can occur during industrial processing. The molecular details that render these enzymes inactive have not yet been identified. To approach this issue, we used proteomics to identify amino acid residues that were oxidized after a relevant oxidative treatment (Fenton reaction). These oxidative modifications were included in the 3D-protein structures, and using molecular dynamics simulations, we then studied the behaviors of non-modified and oxidized enzymes. These simulations showed significant alterations of the conformational stability of proteins when oxidized, as evidenced by changes in root mean square deviation (RMSD) and principal component analyses (PCA) trajectories. Likewise, enzyme-ligand interactions such as hydrogen bonds were greatly reduced in quantity and quality in the oxidized proteins. Finally, free energy landscape plots showed that there was a more rugged energy surface in the oxidized proteins, implying a less favorable reaction pathway. These results reveal the basis for loss of function in these carbohydrate active enzymes (CAZYs) in T. reesei.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Automated instant labeling chemistry workflow for real-time monitoring of monoclonal antibody N -glycosylation

With the transition toward continuous bioprocessing, process analytical technology (PAT) is becoming necessary for rapid and reliable in-process monitoring during biotherapeutics manufacturing. Bioprocess 4.0 is looking to build end-to-end bioprocesses that include PAT-enabled real-time process control. This is especially important for drug product quality attributes that can change during bioprocessing, such as protein N-glycosylation, a critical quality attribute for most monoclonal antibody (mAb) therapeutics. Glycosylation of mAbs is known to influence their efficacy as therapeutics and is regulated for a majority of mAb products on the market today. Currently, there is no method to truly measure N-glycosylation using on-line PAT, hence making it impractical to design upstream process control strategies. We recently described the N-GLYcanyzer workflow: an integrated PAT unit that measures mAb N-glycosylation within 3 hours of automated sampling from a bioreactor. Here, we integrated Agilent's Instant Procainamide (InstantPC) based chemistry workflow into the N-GLYcanyzer PAT unit to allow for nearly 10× faster near real-time analysis of mAb glycoforms. Furthermore, our methodology is explained in detail to allow for replication of the PAT workflow as well as present a case study demonstrating the use of this PAT to autonomously monitor a mammalian cell perfusion process at the bench scale to gain increased knowledge of mAb glycosylation dynamics during continuous biologics manufacturing using Chinese hamster ovary (CHO) cells.

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

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting

Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledge or artificial intelligence driven, and physics-guided computational methods to build, fit, and refine molecular structures. Going beyond a single stationary- structure determination scheme, it is becoming more common to interpret the experimental data with an ensemble of models, which contributes to an average observation. Hence, there is a need to decide on the quality of an ensemble of protein structures on-the-fly, while refining them against the density maps. Here, we introduce such an adaptive decision making scheme during the molecular dynamics flexible fitting (MDFF) of biomolecules. Using RADICAL-Cybertools, and the new RADICAL augmented MDFF implementation (R-MDFF) is examined in high-performance computing environments for refinement of two protein systems, Adenylate Kinase and Carbon Monoxide Dehydrogenase. For the test cases, use of multiple replicas in flexible fitting with adaptive decision making in R-MDFF improves the overall correlation to the density by 40% relative to the refinements of the brute-force MDFF. The improvements are particularly significant at high, 2 - 3 Å, map resolutions. More importantly, the ensemble model captures key features of biologically relevant molecular dynamics that is inaccessible to a single-model interpretation. Finally, the pipeline is applicable to systems of growing sizes, which is demonstrated using ensemble refinement of capsid proteins from Chimpanzee adenovirus. The overhead for decision making remaining low and robust to computing environments. The software is publicly available on GitHub and includes a short user guide to install the R-MDFF on different computing environments, from local Linux based workstations to High Performance Computing (HPC) environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1987

Non-conventional approaches to food processing in CELSS. I - Algal proteins: Characterization and process optimization

Protein isolate obtained from green algae (Scenedesmus obliquus) cultivated under controlled conditions was characterized. Molecular weight determination of fractionated algal proteins using SDS-polyacrylamide gel electrophoresis revealed a wide spectrum of molecular weights ranging from 15,000 to 220,000. Isoelectric points of dissociated proteins were in the range of 3.95 to 6.20. Amino acid composition of protein isolate compared favorably with FAO standards. High content of essential amino acids leucine, valine, phenylalanine and lysine makes algal protein isolate a high quality component of CELSS diets. To optimize the removal of algal lipids and pigments supercritical carbon dioxide extraction (with and without ethanol as a co-solvent) was used. Addition of ethanol to supercritical CO2 resulted in more efficient removal of algal lipids and produced protein isolate with a good yield and protein recovery. The protein isolate extracted by the above mixture had an improved water solubility.

Nakhost, Z.↗
DOE OSTI2024

Self-healing macromolecular crystal materials

Hybrid materials are disclosed including molecular/protein crystals integrated with synthetic polymers. The disclosed materials combine the structural order and periodicity of crystals, the adaptiveness and tunable mechanical properties of polymeric networks, and the chemical versatility of protein building blocks. Some of the properties of the disclosed materials include the following: 1) allows crystals—which are typically rigid and brittle—to expand and contract reversibly; 2) incorporates polymers to increase the mechanical toughness of the crystals and allow self-healing; 3) reversibly expand/contract crystal lattices and mobilize the protein components therein may provide a new means to improve X-ray diffraction quality and explore otherwise inaccessible protein structural states using 3D protein crystallography; 4) creation of chemically and mechanically differentiated domains within single crystals. Some example embodiments combine the properties of hydrogels (flexibility, adaptability, elasticity, self-healing), crystals (structural order) and proteins (chemical and genetic tailorability).

Tezcan, Faik↗
DOE OSTI2024

Modeling Radiation-Induced Epithelial Cell Injury in Murine Three-Dimensional Esophageal Organoids

Esophageal squamous cell carcinoma (ESCC) is a deadly consequence of radiation exposure to the esophagus. ESCC arises from esophageal epithelial cells that undergo malignant transformation and features a perturbed squamous cell differentiation program. Understanding the dose- and radiation quality-dependence of the esophageal epithelium response to radiation may provide insights into the ability of radiation to promote ESCC. We have explored factors that may play a role in esophageal epithelial radiosensitivity and their potential relationship to ESCC risk. We have utilized a murine three-dimensional (3D) organoid model that recapitulates the morphology and functions of the stratified squamous epithelium of the esophagus to study persistent dose- and radiation quality-dependent changes. Interestingly, although high-linear energy transfer (LET) Fe ion exposure induced a more intense and persistent alteration of squamous differentiation and 53BP1 DNA damage foci levels as compared to Cs, the MAPK/SAPK stress pathway signaling showed similar altered levels for most phospho-proteins with both radiation qualities. In addition, the lower dose of high-LET exposure also revealed nearly the same degree of morphological changes, even though only ~36% of the cells were predicted to be hit at the lower 0.1 Gy dose, suggesting that a bystander effect may be induced. Although p38 and ERK/MAPK revealed the highest levels following high-LET exposure, the findings reveal that even a low dose (0.1 Gy) of both radiation qualities can elicit a persistent stress signaling response that may critically impact the differentiation gradient of the esophageal epithelium, providing novel insights into the pathogenesis of radiation-induced esophageal injury and early stage esophageal carcinogenesis.

3D organoid culture↗
NASA NTRS1986

Utilization of non-conventional systems for conversion of biomass to food components: Recovery optimization and characterizations of algal proteins and lipids

Protein isolate obtained from green algae (Scenedesmus obliquus) cultivated under controlled conditions was characterized. Molecular weight determination of fractionated algal proteins using SDS-polyacrylamide gel electrophoresis revealed a wide spectrum of molecular weights ranging from 15,000 to 220,000. Isoelectric points of dissociated proteins were in the range of 3.95 to 6.20. Amino acid composition of protein isolate compared favorably with FAO standards. High content of essential amino acids leucine, valine, phenylalanine and lysine makes algal protein isolate a high quality component of closed environment life support system (CELSS) diets. To optimize the removal of algal lipids and pigments supercritical carbon dioxide extraction (with and without ethanol as a co-solvent) was used. Addition of ethanol to supercritical CO2 resulted in more efficient removal of algal lipids and produced protein isolate with a good yield and protein recovery. The protein isolate extracted by the above mixture had an improved water solubility.

Karel, M.↗
NASA NTRS1987

Non-conventional approaches to food processing in CELSS, 1. Algal proteins: Characterization and process optimization

Protein isolate obtained from green algae cultivated under controlled conditions was characterized. Molecular weight determination of fractionated algal proteins using SDS-polyacrylamide gel electrophoresis revealed a wide spectrum of molecular weights ranging from 15,000 to 220,000. Isoelectric points of dissociated proteins were in the range of 3.95 to 6.20. Amino acid composition of protein isolate compared favorably with FAO standards. High content of essential amino acids leucine, valine, phenylalanine and lysine make algal protein isolate a high quality component of closed ecological life support system diets. To optimize the removal of algal lipids and pigments supercritical carbon dioxide extraction (with and without ethanol as a co-solvent) was used. Addition of ethanol to supercritical carbon dioxide resulted in more efficient removal of algal lipids and produced protein isolate with a good yield and protein recovery. The protein isolate extracted by the above mixture had an improved water solubility.

Nakhost, Z.↗
NASA NTRS1983

Rain-induced spring wheat harvest losses

When rain or a combination of rain and high humidity delay wheat harvest, losses can occur in grain yield and/or grain quality. Yield losses can result from shattering, from reduction in test weight, and in the case of windrowed grain, from rooting of sprouting grain at the soil: windrow contact. Losses in grain quality can result from reduction in test weight and from sprouting. Sprouting causes a degradation of grain proteins and starches, hence flour quality is reduced, and the grain price deteriorates to the value of feed grain. Although losses in grain yield and quality are rain-induced, these losses do not necessarily occur because a standing or windrowed crop is wetted by rain. Spike water concentration in hard red spring wheat must be increased to about 45-49% before sprouting is initiated in grain that has overcome dormancy. The time required to overcome this dormancy after the cultivar has dried to 12 to 14% water concentration differs with hard red spring cultivars. The effect of rain on threshing-ready standing and windrowed hard red spring wheat grain yeild and quality was evaluated. A goal was to develop the capability to forecast the extent of expected loss of grain yield and quality from specific climatic events that delay threshing.

Bauer, A.↗
DOE OSTI2023

Trends in Light and Temperature Sensitivity Recommendations among Licensed Biotechnology Drug Products

Inherent structural and functional properties of biotechnology-derived therapeutic biologics make them susceptible to light- and temperature-induced degradation and consequently can influence their quality. Photosensitivity of therapeutic proteins continues to be examined, but the commonalities and trends of storage conditions and information about light and temperature sensitivity among currently licensed therapeutic proteins has not been previously surveyed. Using a comprehensive and relational database approach, we conducted a scientific survey of all licensed biotechnology-derived drug products with the goal of providing evidence-based information about recommended storage conditions of formulations sorted by light- and temperature-related attributes as described for each product at licensure. We report the prevalence of indications for light and temperature sensitivity in formulations categorized by their presentation type, number of doses, container type, dosage form and active molecule type. We also report the storage temperature range across formulations and diluents for reconstitution and dilution. Formulations with excipients that potentially facilitate light-induced and thermal degradation were also noted. The result of our analysis indicates that light and temperature sensitivity are prevalent across therapeutic protein formulations. However, when a formulation is reconstituted or diluted, both light and temperature sensitivity are less clear. In addition, light and temperature sensitivity are more well defined in liquid formulations than lyophilized powder formulations, and more well defined in products manufactured in autoinjectors, prefilled-syringes, and pens than products in vials. Overall, our report provides a data-driven summary of storage conditions among therapeutic protein formulations to support the development of future biologic drug products.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Technology Case Study: Techno-Economic and Life Cycle Analysis for Microalgae Conversion Pathways to Fuels and Products

This technology case study report details the cost and sustainability prospects for an emerging feedstock - microalgae - converted to fuels and products via a fractionation and upgrading approach termed combined algae processing (CAP). Detailed techno-economic analysis (TEA) and life cycle analysis (LCA) are conducted for the conversion of farmed algae biomass, with two primary scenarios considering the conversion of either high-compositional-quality biomass enriched in lipids (high-lipid [HL]) or lower-quality biomass enriched in protein (high-protein [HP]). Each scenario employs a different biorefinery configuration tailored towards extracting the maximum value from the given biomass composition. The HL scenario produces fuels and non-isocyanate polyurethane (NIPU) as the primary products, while the HP scenario products fuels and a residual solid coproduct which can be used as a co-feed for producing thermoplastics. The results for the HL scenario were particularly promising, with a minimum fuel selling price (MFSP) of $\$$3.68 per gasoline gallon equivalent (GGE) and fuel GHG emissions translating to 54%-76% reduction compared to petroleum fuels depending on the coproduct handling method used. In contrast, the HP scenario faced more challenges in producing biofuels economically, projecting an MFSP of $\$$7.92/GGE despite significant revenues from the residual algae solids. LCA results for the HP case reflected a 24% reduction potential in biorefinery-level GHG emissions. However, these GHG reductions were primarily associated with the thermoplastic coproduct, which accounted for 93% of all biorefinery outputs by mass. Using a process-level allocation method, carbon intensity results were less promising, indicating a net increase in fuel GHG emissions versus petroleum fuels and highlighting the reliance of this scenario on the thermoplastic coproduct.

09 BIOMASS FUELS↗
NASA NTRS1991

The effect of microgravity on protein crystal growth

Based on the results of microgravity crystallization experiments using the protein canavalin aboard four separate U.S. Space Shuttle missions, visual observations and diffraction data are presented that support the contention that protein crystals of improved quality can be obtained in a microgravity environment. With canavalin, no significant increase in resolution was noted, but an overall improvement in diffraction quality, as judged by statistical analyses of the data, was clear. This improvement in quality may be due primarily to the elimination of defects and dislocations rather than an overall enhancement of order. The mechanism for this improvement may be microgravity-stabilized depletion zones that develop around growing crystals that establish and maintain optimal growth conditions more rapidly following nucleation. Such zones would be destroyed by convective flow effects in earth's gravity.

Mcpherson, Alexander↗
NASA NTRS2003

Structural Biology of Proteins of the Multi-enzyme Assembly Human Pyruvate Dehydrogenase Complex

Objectives and research challenges of this effort include: 1. Need to establish Human Pyruvate Dehydrogenase Complex protein crystals; 2. Need to test value of microgravity for improving crystal quality of Human Pyruvate Dehydrogenase Complex protein crystals; 3. Need to improve flight hardware in order to control and understand the effects of microgravity on crystallization of Human Pyruvate Dehydrogenase Complex proteins; 4. Need to integrate sets of national collaborations with the restricted and specific requirements of flight experiments; 5. Need to establish a highly controlled experiment in microgravity with a rigor not yet obtained; 6. Need to communicate both the rigor of microgravity experiments and the scientific value of results obtained from microgravity experiments to the national community; and 7. Need to advance the understanding of Human Pyruvate Dehydrogenase Complex structures so that scientific and commercial advance is identified for these proteins.

Source record↗
NASA NTRS2003

New Programs Utilizing Light Scattering and Flow Imaging Techniques for Macromolecular Crystal Growth and Fluid Dynamics Studies

Dr. Phil Segre, a physicist by training, is a recent addition to the Biotech group, SD46, having joined NASA in August of 2000. Over the past two years he has been developing a laboratory for the study of macromolecular and protein crystal growth. The main apparatus for this work is a Dynamic Light Scattering apparatus, DLS, which is capable of making highly precise measurements of size distributions of both protein solutions and protein crystals. With Drs. Chernov and Thomas (USRA), he has begun a collaboration studying the affects of protein impurities on protein crystal growth and subsequent crystal quality. One of the hypotheses behind the differences between Earth and space grown protein crystals is that the absorption of harmful impurities is reduced in space due to the absence of convective flows. Using DLS measurements we are examining crystal growth with varying amounts of impurities and testing whether there is a strong physical basis behind this hypothesis. With Dr. Joe Ng of UAH he has been collaborating on a project to examine the folding/unfolding dynamics of large RNA complexes. A detailed understanding of this process is necessary for the handling of RNA in biotech applications, and the DLS instrument gives details and results beyond that of other instruments. With Prof. Jim McClymer of the University of Maine (summer faculty visitor to NASA in 2001, 2002), we have been studying the crystallization process in model colloidal suspensions whose behavior in some cases can mimic that of much smaller protein solutions. An understanding of the self-assembly of colloids is the first step in the process of engineering novel materials for photonic and light switching applications. Finally, he has begun an investigation into the physics of particle sedimentation. In addition to the DLS instrument he also has an instrument (called PIV) that can measure flow fields of fluids. The applications are to the dynamics of protein crystal motions both on earth and in low-gravity.

Source record↗
DOE OSTI2021

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Rye as an Energy Cover Crop: Management, Forage Quality, and Revenue Opportunities for Feed and Bioenergy

Harvesting a winter rye energy cover crop (Secale cereale L.) could help sustain growing food and energy demand, provide new revenue streams, and enhance ecosystem services without inducing land-use change. A two-year field experiment with three planting methods and three N fertilization rates (0, 60, and 120 kg N ha -1 ) that produced >5.0 Mg ha -1 yr -1 of biomass was evaluated for (1) fresh and anaerobically digested rye forage quality; (2) revenue potential from renewable bioenergy, carbon markets, and digestate feed protein; and (3) potential greenhouse gas (GHG) offsets. We showed that rye can be harvested as forage for animals or anaerobically digested to produce renewable natural gas (RNG), with the residue after digestion (digestate) still available as a feed protein concentrate. Anaerobically digesting rye improved forage quality indicators. Digestion significantly decreased acid- and neutral-detergent fiber (ADF and NDF) by 5.2% and 17.8%, respectively, while significantly increasing crude protein (CP) (33.6%), total digestible nutrients (TDN) (2.0%), relative feed value (RFV) (23.6%), net energy for lactation (8.3%), maintenance (7.5%), and gain (20.0%). Using market prices for RNG, high protein feed, and GHG mitigation, potential on-farm revenue ranged from USD 307 Mg -1 and USD 502 Mg -1 dry matter with an average of USD 402 Mg -1 . However, there are substantial costs associated with RNG and the revenue potential does not represent the profitability of this system. Evaluation of the integrated system showed GHG emissions associated with rye fertilization were more than offset by the benefits of increasing yield in the 60 kg N ha -1 treatment. The overall carbon footprint of the integrated system was strongly carbon negative, confirming the potential of this strategy to sustainably intensify land use in the Midwestern United States.

09 BIOMASS FUELS↗