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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 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Middleware for a Heterogeneous CAV Fleet

This paper introduces CAN to ROS, a model-based code generation tool used in development, testing, and deployment of a heterogeneous fleet of vehicles with robotic sensing in ROS. Code generation supports two main features: (1) self-configuration for deployment in a heterogeneous vehicle fleet, and (2) quick iteration for testing and development of reading vehicle sensors and robotic control. This tool features the ability to detect the vehicle it is in and regenerate and rebuild itself at runtime to provide the proper two-way bridge between ROS and the sensed on-board vehicle sensor network. Code generation relies on a per-model defined JSON to map a CAN database (DBC) to the desired ROS topic names and message types. The live ROS publishing of CAN messages allows for instant feedback, and the code regeneration allows for adjustments in DBC or vehicle JSON to iteratively hone in on new vehicle signals. Generated ROS nodes are written in C++ for runtime use in lightweight embedded computers. This has been tested in vehicles from three different Original Equipment Manufacturers (OEMs), and can be extended to support a wide array of vehicles. By using a unifying ROS specification, a heterogeneous set of vehicles can be unified into a fleet with abstracted model-specific details; this opens the door for developing cross-model software applications for vehicle control, connected vehicle applications, or fleet monitoring systems.

42 ENGINEERING↗
DOE OSTI2021

High-Current Density Durability of Pt/C and PtCo/C Catalysts at Similar Particle Sizes in PEMFCs

The durability of carbon supported PtCo-alloy based nanoparticle catalysts play a key role in the longevity of proton-exchange membrane fuel cells (PEMFC) in electric vehicle applications. To improve its durability, it is important to understand and mitigate the various factors that cause PtCo-based cathode catalyst layers (CCL) to lose performance over time. These factors include i) electrochemical surface area (ECSA) loss, ii) specific activity loss, iii) H + /O 2 -transport changes and iv) Co 2+ contamination effects. We use a catalyst-specific accelerated stress test (AST) voltage cycling protocol to compare the durability of Pt and PtCo catalysts at similar average nanoparticle size and distribution. Our studies indicate that while Pt and PtCo nanoparticle catalysts suffer from similar magnitudes of electrochemical surface area (ECSA) losses, PtCo catalyst shows a significantly larger cell voltage loss at high current densities upon durability testing. The distinctive factor causing the large cell voltage loss of PtCo catalyst appears to be the secondary effects of the leached Co 2+ cations that contaminate the electrode ionomer. A 1D performance model has been used to quantify the cell voltage losses arising from various factors causing degradation of the membrane electrode assembly (MEA).

08 HYDROGEN↗
DOE OSTI2024

Electrolyte and Cutoff Potential Effects on Cycle Life of Li4Ti5O12/LiNi0.9Mn0.1O2 Batteries for Behind-the-Meter Storage Applications

Behind-the-Meter Storage (BTMS) is a stationary battery energy storage system that is connected to the electrical distribution system on the customer's side of the utility's service meter. BTMS systems are used to store electrical energy from the grid as well as inconstant, renewable energy, such as local solar and wind generation. A successful BTMS system will allow the customer to pair their energy generation and storage to optimize electrical consumption from the grid, improving reliability and minimizing cost. For BTMS applications, batteries must be designed and optimized with different set of criteria from other leading segments of the Li-ion battery market, like transportation, due the system being stationary and proximal to the residential or commercial building it's benefitting. BTMS applications prioritize safety, cost (low/no-critical materials), reliability (20-year calendar life), and durability (10,000 cycle life), while having the ability to (minimally) compromise energy density and rate capability. Lithium titanate (Li4Ti5O12-, LTO) is a promising anode candidate for BTMS applications due to its high safety and capacity retention, while maintaining a reasonable 160 mAhg-1 reversable capacity and composition of relatively abundant materials. (1) Specifically, LTO has a high working voltage which helps to prevent Li dendrite formation, improving safety. Furthermore, LTO also has negligible lithiation-based volume change, leading to less mechanical pulverization, or loss of active material, upon cycling. For the cathode, materials with little or no Co are of high interest due to the high cost and low abundance of Co. LiMn2O4 (LMO) has been paired with LTO for BTMS applications in the past due to its safety, low cost (abundancy), and reasonably high operating voltage. (2-4) However, the low capacity of LMO limits energy density and specific energy. While not the highest priority for BTMS applications, increasing energy density will enable deployment in space constrained BTMS applications and decrease total cost. LiNi0.9Mn0.1O2 (LN-MO) is a recently developed material with promise due to its high operating voltage and relatively low price. (5) However, Ni-rich layered oxides, including LNMO, tend to struggle with capacity retention during high-voltage cycling due to mechanical pulverization, irreversible phase transitions, and unstable solid-electrolyte interphase. The study presented here focuses on building an understanding of how electrolyte solvent and varied cutoff potentials will impact the cycle life of LTO/LN-MO cells. Specifically, a comparison is provided between ethylene carbonate (EC), ethyl methyl carbonate (EMC), fluoroethylene carbonate (FEC), and Gen2 electrolyte solvents with 1M Lithium hexafluorophosphate (LiPF6) salt, cycling to two upper termination potentials, 2.6V and 2.7V. Electrochemical testing and diagnostics (e.g., differential capacity analysis, area specific impedance, constant voltage hold, and rate capability) and post-mortem characterization will be used to understand the aging behavior and failure mechanisms of the 8 cell combinations (four electrolytes and two voltage cutoffs). Cells with FEC electrolyte showed a lower initial capacity compared to cells with Gen2, EMC, and EC cycling at both voltages; however, the cells with FEC showed consistent trends in capacity retention with 2.6V and 2.7V termination potentials, while the cells with the other electrolytes showed much higher rates of capacity loss when cycling to the higher voltage. These results indicate that FEC may play a role in improving durability of high-voltage, Ni-rich electrode systems for use in high-cycle applications, such as BTMS.

electrolyte↗
DOE OSTI2021

Quantile-Dependent Expressivity of Serum Uric Acid Concentrations

“Quantile-dependent expressivity” occurs when the effect size of a genetic variant depends upon whether the phenotype (e.g., serum uric acid) is high or low relative to its distribution. Analyses were performed to test whether serum uric acid heritability is quantile-specific and whether this could explain some reported gene-environment interactions. Methods. Serum uric acid concentrations were analyzed from 2151 sibships and 12,068 offspring-parent pairs from the Framingham Heart Study. Quantile-specific heritability from offspring-parent regression slopes (β OP , h 2 = 2β OP /(1 + r spouse )) and full-sib regression slopes (β FS ,h 2 = {(1 + 8r spouse β FS ) 0.5 - 1}/(2r spouse ) was robustly estimated by quantile regression with nonparametric significance assigned from 1000 bootstrap samples. Results. Quantile-specific h 2 (±SE) increased with increasing percentiles of the offspring’s sex- and age-adjusted uric acid distribution when estimated from β OP (P trend = 0.001): 0.34 ± 0.03 at the 10th, 0.36 ± 0.03 at the 25th, 0.41 ± 0.03 at the 50th, 0.46 ± 0.04 at the 75th, and 0.49 ± 0.05 at the 90th percentile and when estimated from β FS (P trend = 0.006). This is consistent with the larger genetic effect size of (1) the SLC2A9 rs11722228 polymorphism in gout patients vs. controls, (2) the ABCG2 rs2231142 polymorphism in men vs. women, (3) the SLC2A9 rs13113918 polymorphism in obese patients prior to bariatric surgery vs. two-year postsurgery following 29 kg weight loss, (4) the ABCG2 rs6855911 polymorphism in obese vs. nonobese women, and (5) the LRP2 rs2544390 polymorphism in heavier drinkers vs. abstainers. Quantile-dependent expressivity may also explain the larger genetic effect size of an SLC2A9/PKD2/ABCG2 haplotype for high vs. low intakes of alcohol, chicken, or processed meats. Conclusions. Heritability of serum uric acid concentrations is quantile-specific.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Polyglot Framework

Polyglot utilizes a combination of custom and open source tools and libraries to provide developers with a consistent environment for building tools, etc. for a wide variety of targets with minimal changes to the code being built. It supports a variety of architectures and operating systems/firmware in as target-agnostic way as possible. This allows for developers to minimize the amount of time/effort required to port tools—in particular, forensic tools—to a wide variety of targets. The project is comprised of two main components: a frontend toolchain that understands how to utilize other tools in order to build code for a specific target, and a minimalistic C library specific to Polyglot. These collectively provide the method to build code for a specific target, and the capability for code to interact with the underlying operating system when run on the target. Both components are written in a way to minimize the amount of target-specific knowledge required to both develop and utilize the project.

Huddleston, TimothyA.↗
DOE OSTI2024

Polyglot C Library

The C library component of Polyglot. Polyglot utilizes a combination of custom and open source tools and libraries to provide developers with a consistent environment for building tools, etc. for a wide variety of targets with minimal changes to the code being built. It supports a variety of architectures and operating systems/firmware in as target-agnostic way as possible. This allows for developers to minimize the amount of time/effort required to port tools-in particular, forensic tools-to a wide variety of targets. The project is comprised of two main components: a frontend toolchain that understands how to utilize other tools in order to build code for a specific target, and a minimalistic C library specific to Polyglot. These collectively provide the method to build code for a specific target, and the capability for code to interact with the underlying operating system when run on the target. Both components are written in a way to minimize the amount of target-specific knowledge required to both develop and utilize the project.

Huddleston, TimothyA.↗
DOE OSTI2026

Asi Nuclear Energy Sensors Data Portal Chatbot And Data Structuring Tool

The Idaho National Laboratory (INL) is advancing the development of an AI-powered chatbot and data structuring tool specifically designed to accelerate data mining processes for sensor-related information and seamlessly integrate the results into the ASI Sensors Data Portal (https://nes.energy.gov/). By doing so, the software aims to enhance the accessibility, usability, and organization of sensor data for nuclear energy applications. The software initial phase focuses on retrieving comprehensive datasets, prioritizing the past five years of publicly available information from the Office of Scientific and Technical Information (OSTI). These datasets will be meticulously processed to ensure compatibility, employing cleaning and preprocessing steps to eliminate irrelevant, incomplete, or corrupted information, thus establishing a robust foundation for subsequent AI use. The data will serve as the backbone for training an AI model and chatbot, which will act as an interactive tool enabling users to ask complex, context-specific questions and receive accurate, validated answers derived from constrained literature. In parallel, the project incorporates a data structuring process supported by AI to organize sensor information from multiple sources into a standardized format. This structured data will include detailed sensor specifications, such as measurement range, applications, accuracy, and operating conditions, generated and documented with AI. These specifications will be systematically integrated into the sensor portal. To maintain the highest levels of accuracy and relevance, all AI-generated outputs will be reviewed and validated by subject matter experts (SMEs), with additional fields or parameters added as needed. Future stages of the project aim to expand the dataset beyond OSTI to include other sources and potentially incorporate unclassified controlled information (UCI) with restricted access protocols to address security and confidentiality requirements.

Mapes, NormanJ. [Idaho National Laboratory (INL), ↗
DOE OSTI2023

Immunotherapy-induced neutralizing antibodies disrupt allergen binding and sustain allergen tolerance in peanut allergy

In IgE-mediated food allergies, exposure to the allergen activates systemic allergic responses. Oral immunotherapy (OIT) treats food allergies through incremental increases in oral allergen exposure. However, OIT only induces sustained clinical tolerance and decreased basophil sensitivity in a subset of individuals despite increases in circulating allergen-specific IgG in all treated individuals. Therefore, we examined the allergen-specific antibodies from 2 OIT cohorts of patients with sustained and transient responses. Here, we compared antibodies from individuals with sustained or transient responses and discovered specific tolerance-associated conformational epitopes of the immunodominant allergen Ara h 2 recognized by neutralizing antibodies. First, we identified what we believe to be previously unknown conformational, intrahelical epitopes using x-ray crystallography with recombinant antibodies. We then identified epitopes only recognized in sustained tolerance. Finally, antibodies recognizing tolerance-associated epitopes effectively neutralized allergen to suppress IgE-mediated effector cell activation. Our results demonstrate the molecular basis of antibody-mediated protection in IgE-mediated food allergy, by defining how these antibodies disrupt IgE-allergen interactions to prevent allergic reactions. Our approach to studying the structural and functional basis for neutralizing antibodies demonstrates the clinical relevance of specific antibody clones in antibody-mediated tolerance. We anticipate that our findings will form the foundation for treatments of peanut allergy using neutralizing antibodies and hypoallergens.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A novel post-processing method for progressive failure analysis of brittle composite compression

Finite element analysis of brittle materials in axial compression typically uses element deletion to allow continued global deformation post-element-failure. However, element deletion produces cyclic load-displacement curves that underestimate energy absorption and are not representative of a continuum system. Two key observations support the conclusion that results from an appropriately discretized model can be an adequate representation of a continuum system. Specifically, the frequency of the oscillations in the load-displacement curve is directly dependent upon element length in the loading direction, and the peak amplitudes of oscillations are mesh size independent. A method of post-processing the analysis results, by connecting the peak amplitudes of oscillations, is proposed and applied to a series of continuous carbon fiber composite crush tubes. The load-displacement curve, stable crushing load, and specific energy absorption of the post-processed results compare well to an experimental study of crush tubes with similar layups.

Materials Science↗
DOE OSTI2022

Experimental study of the impact of scavenging efficiency on diesel combustion in an opposed-piston two-stroke engine

The opposed-piston two-stroke (OP2S) engine is a promising alternative powertrain technology that can offer thermal and brake efficiency improvements over conventional four-stroke engines. In recent years, many of the technical barriers of the OP2S engine architecture have been overcome. However, there is still a need for fundamental studies to provide insight into the scavenging and combustion processes of the OP2S engine to help design and operate the most efficient combustion systems using this engine architecture. This work aims to provide such insights by analyzing experimental data collected on a 3-cylinder, 4.9 L OP2S engine. Specifically, a scavenging efficiency sweep, an engine speed sweep with a constant scavenging efficiency, and an engine speed with a constant pressure differential across the engine were studied in detail. It was found that in diesel combustion, as the scavenging efficiency decreased, the increase in temperature of the hot, internal residuals resulted in a significant increase in heat transfer. Despite lowering pumping losses, this resulted in an overall decrease in brake efficiency. When the bulk thermodynamic conditions of two different scavenging efficiency cases (67% and 72%) were matched at port closing, the lower scavenging efficiency case still displayed a 0.7 percentage point penalty in net thermal efficiency and an increase in engine-out indicated specific emissions of NOx of 18% due to residual stratification in the cylinder. The results presented in this work show that the optimal breathing strategy in diesel combustion on an OP2S engine architecture is one that results in a slightly under-scavenged environment at port closing. However, the results did show potential system-level efficiency benefits of decreasing scavenging efficiency, meaning that alternative fuels and combustion strategies without the constraints of diesel combustion could achieve system-level efficiency gains by running significantly under-scavenged.

Engineering↗
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 OSTI2024

Systemic immunological responses are dependent on sex and ovarian hormone presence following acute inhaled woodsmoke exposure

Background: Rural regions of the western United States have experienced a noticeable surge in both the frequency and severity of acute wildfire events, which brings significant challenges to both public safety and environmental conservation efforts, with impacts felt globally. Identifying factors contributing to immune dysfunction, including endocrinological phenotypes, is essential to understanding how hormones may influence toxicological susceptibility. Methods: This exploratory study utilized male and female C57BL/6 mice as in vivo models to investigate distinct responses to acute woodsmoke (WS) exposure with a focus on sex-based differences. In a second set of investigations, two groups were established within the female mouse cohort. In one group, mice experienced ovariectomy (OVX) to simulate an ovarian hormone-deficient state similar to surgical menopause, while the other group received Sham surgery as controls, to investigate the mechanistic role of ovarian hormone presence in driving immune dysregulation following acute WS exposure. Each experimental cohort followed a consecutive 2-day protocol with daily 4-h exposure intervals under two conditions: control HEPA-filtered air (FA) and acute WS to simulate an acute wildfire episode. Results: Metals analysis of WS particulate matter (PM) revealed significantly increased levels of 63 Cu, 182 W, 208 Pb, and 238 U, compared to filtered air (FA) controls, providing insights into the specific metal components most impacted by the changing dynamics of wildfire occurrences in the region. Male and female mice exhibited diverse patterns in lung mRNA cytokine expression following WS exposure, with males showing downregulation and females displaying upregulation, notably for IL-1β, TNF-α, CXCL-1, CCL-5, TGF-β, and IL-6. After acute WS exposure, there were notable differences in the responses of macrophages, neutrophils, and bronchoalveolar lavage (BAL) cytokines IL-10, IL-6, IL-1β, and TNF-α. Significant diverse alterations were observed in BAL cytokines, specifically IL-1β, IL-10, IL-6, and TNF-α, as well as in the populations of immune cells, such as macrophages and polymorphonuclear leukocytes, in both Sham and OVX mice, following acute WS exposure. These findings elucidated the profound influence of hormonal changes on inflammatory outcomes, delineating substantial sex-related differences in immune activation and revealing altered immune responses in OVX mice due to ovarian hormone deficiency. In addition, the flow cytometry analysis highlighted the complex interaction between OVX surgery, acute WS exposure, and their collective impact on immune cell populations within the hematopoietic bone marrow niche. Conclusions: In summary, both male and female mice, alongside females subjected to OVX and those who had sham surgery, exhibit significant variations in the expression of proinflammatory cytokines, chemokines, lung mRNA gene expression, and related functional networks linked to signaling pathways. These differences potentially act as mediators of sex-specific and hormonal influences in the systemic inflammatory response to acute WS exposure during a wildfire event. Understanding the regulatory roles of genes expressed differentially under environmental stressors holds considerable implications, aiding in identifying sex-specific therapeutic targets for addressing acute lung inflammation and injury.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

CHIQUITA1 maintains the temporal transition between proliferation and differentiation in Arabidopsis thaliana

ABSTRACT Body size varies widely among species, populations and individuals, depending on the environment. Transitioning between proliferation and differentiation is a crucial determinant of final organ size, but how the timing of this transition is established and maintained remains unknown. Using cell proliferation markers and genetic analysis, we show that CHIQUITA1 (CHIQ1) is required to maintain the timing of the transition from proliferation to differentiation in Arabidopsis thaliana. Combining kinematic and cell lineage-tracking studies, we found that the number of actively dividing cells in chiquita1-1 plants decreases prematurely compared with wild-type plants, suggesting CHIQ1 maintains the proliferative capacity in dividing cells and ensures that cells divide a specific number of times. CHIQ1 belongs to a plant-specific gene family of unknown molecular function and genetically interacts with three close members of its family to control the timing of proliferation exit. Our work reveals the interdependency between cellular and organ-level processes underlying final organ size determination.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Assessing United States County-Level Exposure for Research on Tropical Cyclones and Human Health

Tropical cyclone epidemiology can be advanced through exposure assessment methods that are comprehensive and consistent across space and time, as these facilitate multiyear, multistorm studies. Further, an understanding of patterns in and between exposure metrics that are based on specific hazards of the storm can help in designing tropical cyclone epidemiological research. a) Provide an open-source data set for tropical cyclone exposure assessment for epidemiological research; and b) investigate patterns and agreement between county-level assessments of tropical cyclone exposure based on different storm hazards. We created an open-source data set with data at the county level on exposure to four tropical cyclone hazards: peak sustained wind, rainfall, flooding, and tornadoes. The data cover all eastern U.S. counties for all land-falling or near-land Atlantic basin storms, covering 1996–2011 for all metrics and up to 1988–2018 for specific metrics. We validated measurements against other data sources and investigated patterns and agreement among binary exposure classifications based on these metrics, as well as compared them to use of distance from the storm’s track, which has been used as a proxy for exposure in some epidemiological studies. Our open-source data set was typically consistent with data from other sources, and we present and discuss areas of disagreement and other caveats. Over the study period and area, tropical cyclones typically brought different hazards to different counties. Therefore, when comparing exposure assessment between different hazard-specific metrics, agreement was usually low, as it also was when comparing exposure assessment based on a distance-based proxy measurement and any of the hazard-specific metrics. Our results provide a multihazard data set that can be leveraged for epidemiological research on tropical cyclones, as well as insights that can inform the design and analysis for tropical cyclone epidemiological research.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Data for A Transcriptomic Atlas of Acute Stress Response to Low pH in Multiple Issatchenkia orientalis Strains

Because of its natural stress tolerance to low pH, Issatchenkia orientalis (a.k.a. Pichia kudriavzevii ) is a promising non-model yeast for bio-based production of organic acids. Yet, this organism is relatively unstudied, and specific mechanisms of its tolerance to low pH are poorly understood, limiting commercial use. In this study, we selected 12 I. orientalis strains with varying acid stress tolerance (six tolerant and six susceptible) and profiled their transcriptomes in different pH conditions to study potential mechanisms of pH tolerance in this species. We identified hundreds of genes whose expression response is shared by tolerant strains but not by susceptible strains, or vice versa, as well as genes whose responses are reversed between tolerant and susceptible strains. We mapped regulatory mechanisms of transcriptomic responses via motif analysis as well as differential network reconstruction, identifying several transcription factors, including Stb5, Mac1, and Rtg1/Rtg3, some of which are known for their roles in acid response in Saccharomyces cerevisiae . Functional genomics analysis of short-listed genes and transcription factors suggested significant roles for energy metabolism and translation-related processes, as well as the cell wall integrity pathway and RTG-dependent retrograde signaling pathway. Finally, we conducted additional experiments for two organic acids, 3-hydroxypropionate and citramalate, to eliminate acid-specific effects and found potential roles for glycolysis and trehalose biosynthesis specifically for response to low pH. In summary, our approach of comparative transcriptomics and phenotypic contrasting, along with a multi-pronged bioinformatics analysis, suggests specific mechanisms of tolerance to low pH in I. orientalis that merit further validation through experimental perturbation and engineering.

Conversion↗
DOE OSTI2026

Data for Resourceful and Economical Designing of Fermentation Medium for Lab and Commercial Strains of Yeast from Alternative Feedstock: Transgenic Oilcane

Sugarcane plant engineered to accumulate lipids in its vegetative tissue is being developed as a new bioenergy crop. The new crop would be a source of juice, oil, and cellulosic sugars. However, limited tolerance of industrially recognized yeasts towards inhibitors generated during the processing of lignocellulosic biomass to produce fermentable sugars is a major challenge in developing scalable processes for second-generation drop-in fuel production. To this end, hydrolysates generated from engineered sugarcane—‘oilcane’ bagasse contain added phenolics and fatty acids that further restrict the growth of fermenting microorganisms and necessitate nutrient supplementation and/or detoxification of hydrolysate which makes the fermentation process expensive. Herein, we propose a resourceful and economical approach for growing lab and commercial strains of S. cerevisiae on unrefined cellulosic sugars aerobically and fermentatively. An equal ratio of hydrolysate and juice was found optimum for growth and fermentation by lab and commercial strains of Saccharomyces cerevisiae engineered for xylose fermentation. The industrial strain grew and fermented efficiently under low aeration conditions having an ethanol titer, yield, specific and volumetric productivities of 46.96 ± 0.19 g/l, 0.51 ± 0.00 g/g, 0.27 ± 0.02 g/g.h and 1.95 ± 0.01 g/l.h, respectively, while the lab strain grew better under higher aeration conditions having the ethanol titer, yield, specific and volumetric productivities of 24.93 ± 0.09, 0.27 ± 0.00 g/g, 0.17 ± 0.00 g/g.h and 1.04 ± 0.00 g/l.h, respectively. Acclimation of cultures in a blended medium significantly improved the performance of the yeast strains. The addition of transgenic oilcane juice, which is inedible and rich in amino acids, to the hydrolysate averted the need for expensive nutrient supplementation and detoxification steps of hydrolysate. The approach provides an economical solution to reduce the cost of fermentation at an industrial scale for second-generation drop-in fuel production.

Biomass Analytics↗
DOE OSTI2020

SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique

A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Characterizing inhibitors of human AP endonuclease 1

AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg 2+ -bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.

59 BASIC BIOLOGICAL SCIENCES↗