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At least 559 records · Page 31
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Metabolic engineering of Caldicellulosiruptor bescii for 2,3-butanediol production from unpretreated lignocellulosic biomass and metabolic strategies for improving yields and titers

ABSTRACT The platform chemical 2,3-butanediol (2,3-BDO) is used to derive products, such as 1,3-butadiene and methyl ethyl ketone, for the chemical and fuel production industries. Efficient microbial 2,3-BDO production at industrial scales has not been achieved yet for various reasons, including product inhibition to host organisms, mixed stereospecificity in product formation, and dependence on expensive substrates (i.e., glucose). In this study, we explore engineering of a 2,3-BDO pathway inCaldicellulosiruptor bescii, an extremely thermophilic (optimal growth temperature = 78°C) and anaerobic bacterium that can break down crystalline cellulose and hemicellulose into fermentable C 5 and C 6 sugars. In addition, C. besciigrows on unpretreated plant biomass, such as switchgrass. Biosynthesis of 2,3-BDO involves three steps: two molecules of pyruvate are condensed into acetolactate; acetolactate is decarboxylated to acetoin, and finally, acetoin is reduced to 2,3-BDO.C. besciinatively produces acetoin; therefore, in order to complete the 2,3-BDO biosynthetic pathway,C. besciiwas engineered to produce a secondary alcohol dehydrogenase (sADH) to catalyze the final step. Two previously characterized, thermostable sADH enzymes with high affinity for acetoin, one from a bacterium and one from an archaeon, were tested independently. When either sADH was present inC. bescii,the recombinant strains were able to produce up to 2.5-mM 2,3-BDO from crystalline cellulose and xylan and 0.2-mM 2,3-BDO directly from unpretreated switchgrass. This serves as the basis for higher yields and productivities, and to this end, limiting factors and potential genetic targets for further optimization were assessed using the genome-scale metabolic model ofC. bescii. IMPORTANCE Lignocellulosic plant biomass as the substrate for microbial synthesis of 2,3-butanediol is one of the major keys toward cost-effective bio-based production of this chemical at an industrial scale. However, deconstruction of biomass to release the sugars for microbial growth currently requires expensive thermochemical and enzymatic pretreatments. In this study, the thermo-cellulolytic bacteriumCaldicellulosiruptor besciiwas successfully engineered to produce 2,3-butanediol from cellulose, xylan, and directly from unpretreated switchgrass. Genome-scale metabolic modeling ofC. besciiwas applied to adjust carbon and redox fluxes to maximize productivity of 2,3-butanediol, thereby revealing bottlenecks that require genetic modifications.

Biotechnology & Applied Microbiology↗
DOE OSTI2026

Accelerating Traction Motor Optimization Design with AI Surrogate Models

The advancement of artificial intelligence systems enables the use of data-driven physics-based surrogate models to explore design spaces rapidly and deeply for engineering projects. This work presents a surrogate model workflow that accelerates electric traction motor design optimization by replacing finite element analysis (FEA) with an artificial neural network (ANN) and using this model in a genetic algorithm for design optimization. A baseline interior permanent-magnet motor is parameterized and sampled to generate FEA-labeled training data, after which a feed-forward ANN predicts key outputs (e.g., loss components and weight). The validated surrogate enables genetic-algorithm optimization and deep search over the design space without new FEA runs, producing Pareto-optimal trade-offs between weight and losses and set of optimized designs for rapid downselection of manufacturable motor designs.

Ribeiro, Pedro [ORNL] (ORCID:0009000921026641)↗
DOE OSTI2025

Data for "Evaluating the industrial potential of emerging biomass pretreatment technologies in bioethanol production and lipid recovery from transgenic sugarcane"

The selection of pretreatment methods is critical to achieving high product yields during bioconversion of lignocellulosic biomass. Hydrothermal, soaking-in-aqueous ammonia, and ionic liquid pretreatment methods are viable candidates for minimizing sugar decomposition, permitting the effective hydrolysis of structural carbohydrates, and producing a fermentable substrate suitable for achieving industrial ethanol titers and yields. In this study, the effect of these three pretreatment methods on non-modified sugarcane cultivar CP88-1762 and two transgenic lipid-accumulating sugarcane lines, oilcane 1565 and oilcane 1566, were investigated and compared in terms of lipid recovery, sugar yield, and ethanol yields within the lignocellulosic biomass conversion pipeline. Fed-batch enzymatic hydrolysis at high solid loading yielded hydrolysates capable of supporting industrial bioethanol titers across all conditions. The highest sugar yields were obtained on ammonia-pretreated biomass hydrolysate (253.73 g L−1), followed by hydrothermally pretreated hydrolysate (213.10 g L−1) and ionic liquid-pretreated hydrolysate (154.20 g L−1). Commercially viable ethanol titers of 100.62 g L−1, 64.47 g L−1, and 52.95 g L−1 were achieved from ammonia, hydrothermal, and ionic liquid pretreated hydrolysate with the corresponding ethanol productivities of 2.08 g L−1 h−1, 0.53 g L−1 h−1, and 0.36 g L−1 h−1. The lower acetic acid concentration in ammonia-pretreated hydrolysate may have enhanced its fermentability relative to the hydrothermal pretreatment condition, as indicated by the differences in ethanol titer and productivity. Lower sugar yields and ethanol productivities under the ionic liquid conditions likely resulted from the inhibitory effect of cholinium lysinate. Oilcane 1565 and oilcane 1566 bagasse accumulated over 16- and 3 times higher lipids than the non-modified sugarcane CP88-1762. The total fatty acid content in the oilcane samples was reduced in ammonia and ionic liquid-pretreated bagasse relative to the hydrothermal pretreatment condition. While all pretreatment techniques tested are industrially viable, the observed differences in titer, productivity, and lipid content indicate that careful selection and validation of upstream processing methods can contribute to improved economic and environmental outcomes.

biomass analytics↗
DOE OSTI2025

Nickase fidelity drives EvolvR-mediated diversification in mammalian cells

Abstract In vivo genetic diversifiers have previously enabled efficient searches of genetic variant fitness landscapes for continuous directed evolution. However, existing genomic diversification modalities for mammalian genomic loci exclusively rely on deaminases to generate transition mutations within target loci, forfeiting access to most missense mutations. Here, we engineer CRISPR-guided error-prone DNA polymerases (EvolvR) to diversify all four nucleotides within genomic loci in mammalian cells. We demonstrate that EvolvR generates both transition and transversion mutations throughout a mutation window of at least 40 bp and implement EvolvR to evolve previously unreported drug-resistantMAP2K1variants via substitutions not achievable with deaminases. Moreover, we discover that the nickase’s mismatch tolerance limits EvolvR’s mutation window and substitution biases in a gRNA-specific fashion. To compensate for gRNA-to-gRNA variability in mutagenesis, we maximize the number of gRNA target sequences by incorporating a PAM-flexible nickase into EvolvR. Finally, we find a strong correlation between predicted free energy changes underlying R-loop formation and EvolvR’s performance using a given gRNA. The EvolvR system diversifies all four nucleotides to enable the evolution of mammalian cells, while nuclease and gRNA-specific properties underlying nickase fidelity can be engineered to further enhance EvolvR’s mutation rates.

Science & Technology - Other Topics↗
DOE OSTI2023

Heterologous expression of formate dehydrogenase enables photoformatotrophy in the emerging model microalga, Picochlorum renovo

Rising global greenhouse gas emissions and the impacts of resultant climate change necessitate development and deployment of carbon capture and conversion technologies. Amongst the myriad of bio-based conversion approaches under evaluation, a formate bio-economy has recently been proposed, wherein CO 2 -derived formate serves as a substrate for concurrent carbon and energy delivery to microbial systems. To date, this approach has been explored in chemolithotrophic and heterotrophic organisms via native or engineered formatotrophy. However, utilization of this concept in phototrophic organisms has yet to be reported. Herein, we have taken the first steps to establish formate utilization in Picochlorum renovo, a recently characterized eukaryotic microalga with facile genetic tools and promising applied biotechnology traits. Plastidial heterologous expression of a formate dehydrogenase (FDH) enabled P. renovo growth on formate as a carbon and energy source. Further, FDH expression enhanced cultivation capacity on ambient CO 2 , underscoring the potential for bypass of conventional CO 2 capture and concentration limitations. This work establishes a photoformatotrophic cultivation regime that leverages light energy-driven formate utilization. The resultant photosynthetic formate platform has widespread implications for applied phototrophic cultivation systems and the bio-economy at large.

09 BIOMASS FUELS↗
DOE OSTI2022

Engineering of holocellulase in biomass-degrading fungi for sustainable biofuel production

Biofuels, such as bioethanol, are a clean and sustainable form of energy and have emerged as a viable alternative to fossil fuels. Plant biomass is an important raw material for the production of clean and renewable energy. The holocellulose contained in the composition of plants may be broken down into simple sugars, such as glucose, which are fermented by yeast to produce bioethanol. The conversion of glucose polymers into fermentable sugars is accomplished by enzymes known as holocellulases, which are produced by lignocellulolytic fungi. These enzymes act synergistically for the efficient degradation of cellulose polymers, and the fine and coordinated regulation of this process is performed by transcription factors (TFs). TFs are regulatory proteins that bind to the promoter region of their target genes (CAZymes, sugar transporters, signaling proteins, other TFs, etc.) to induce or repress their transcription. This review aims to understand the main regulatory mechanisms involved in plant biomass degradation by the most studied lignocellulolytic fungi Trichoderma sp., Aspergillus sp., Penicillium sp., and Neurospora crassa. In this context, the most studied TFs related to holocellulose degradation and genetic modification of TFs or promoters as a valuable tool to improve enzyme production for biotechnological purposes have been discussed. Furthermore, this review enables the expansion of knowledge on the regulation of the cellulolytic system of filamentous fungi and the application of this knowledge to the improvement of numerous bioproducts. Engineering TFs and promoters may yield more efficient strains that may be active in plant biomass hydrolysis. In this way, the technological processes for obtaining ethanol from lignocellulose may become more commercially viable.

09 BIOMASS FUELS↗
DOE OSTI2023

CRISPR-COPIES: Web Tool

CRISPR/Cas system has emerged as a powerful genome-editing tool for metabolic engineering and human gene therapy. However, the conundrum of where to integrate heterologous genes on the chromosome using the CRISPR/Cas system remains an open question. Selecting a site for gene integration requires incorporation of complex criteria such as factors involved in CRISPR/Cas-mediated integration, genetic stability, and gene expression and therefore, usually requires strenuous characterization of sites on particular or different chromosomal locations. To address these issues, we developed CRISPR-COPIES, a COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites. The tool applies ScaNN, a state-of-the-art model on the embedding-based nearest neighbor search for fast and accurate off-target search and can identify genome-wide intergenic sites for most bacterial and fungal genomes within minutes. This submission contains the code we developed to create a user-friendly web interface for CRISPR-COPIES (https://biofoundry.web.illinois.edu/copies/). We anticipate CRISPR-COPIES will serve as a useful tool for targeted DNA integration and aid in the characterization of synthetic biology toolkits, rapid strain construction to produce valuable biochemicals, and human gene and cell therapy.

Bioinformatics↗
DOE OSTI2021

Kinetic proofreading of lipochitooligosaccharides determines signal activation of symbiotic plant receptors

Plant cell surface receptors perceive carbohydrate signaling molecules and hereby establish communication with surrounding microbes. Genetic studies have identified two different classes of lysin motif receptor kinases as gatekeepers that together trigger the symbiotic pathway in plants; however, no structural or functional data of the perception mechanisms switching these receptors from resting state into activation is known. In this study, we use structural biology, biochemical, and genetic approaches to demonstrate how the NFP/NFR5 class of lipochitooligosaccharide (LCO) receptors discriminate bacterial symbionts based on a kinetic proofreading mechanism that controls receptor activation and signaling specificity. We show that the LCO binding site can be engineered to support symbiotic functions, which greatly advance future opportunities for receptor engineering in legumes and nonlegumes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Plant-Enhanced Degradation Of Munitions by Engineered TERrestrial microbes (PEDOMETER) (Final Report)

LLNL led two major Technical Areas (TAs) within the PEDOMETER program: TA3 focused on biocontainment and TA4 focused on developing electrochemical TNT degradation sensors and testbeds. A key takeaway from our work is the importance of chassis host strain choice for kill switch design and actuator choice. Genetic instability of the kill switch circuit is a major barrier toward establishing a kill switch, which is host dependent. Addition of a host down-selection step to regulator and actuator screening stages would be beneficial to hasten kill switch development.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Investigation of the Unusual Ability of the [FeFe] Hydrogenase from Clostridium beijerinckii to Access an O 2 -Protected State

[FeFe] hydrogenases are enzymes capable of producing and oxidizing H 2 at staggering submillisecond time scales. A major limitation in applying these enzymes for industrial hydrogen production is their irreversible inactivation by oxygen. Recently, an [FeFe] hydrogenase from Clostridium beijerinckii (CbHydA1) was reported to regain its catalytic activity after exposure to oxygen. In this report, we have determined that artificially matured CbHydA1 is indeed oxygen tolerant in the absence of reducing agents and sulfides by means of reaching an O 2 -protected state (Hinact). We were also able to generate the H inact state anaerobically via both chemical and electrochemical oxidation. We use a combination of spectroscopy, electrochemistry, and density functional theory (DFT) to uncover intrinsic properties of the active center of CbHydA1, leading to its unprecedented oxygen tolerance. We have observed that reversible, low-potential oxidation of the active center leads to the protection against O 2 -induced degradation. The transition between the active oxidized state (H ox ) and the H inact state appears to proceed without any detectable intermediates. We found that the Hinact state is stable for more than 40 h in air, highlighting the remarkable resilience of CbHydA1 to oxygen. Using a combination of DFT and FTIR, we also provide a hypothesis for the chemical identity of the H inact state. These results demonstrate that CbHydA1 has remarkable stability in the presence of oxygen, which will drive future efforts to engineer more robust catalysts for biofuel production.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Mild hybridisation of turboprop engine with high-power-density integrated electric drives

Here this paper shares with the aerospace community a case study of turboprop mild hybridisation using a recently developed integrated drive system in the University of Nottingham, UK, within the ACHIEVE project under EU H2020 CleanSky 2 program (project No. 737814). The developed drive system enables green taxiing of a turboprop aircraft while on the ground with its engine off, and as an electrical generator when the turboprop is in the air. The entire system is designed to be able to integrate within the power auxiliary gear box (PAGB) of a turboprop aircraft. Some of the key features of the developed system include a high-speed permanent magnet machine (up to 14,200rpm) with dual three-phase design, SiC-based high power density (11.8kW/L for the power converter, 35.3kW/L and 7.2kW/kg for the machine active parts), integrated cooling design for high-temperature operation (>130°C ambient temperature), fault tolerance consideration with dual channel operation capabilities and sensorless control for entire operational conditions. This paper is giving an overview of the design process of the electrical machine, power converters, and its cooling of the entire drive. Numerical analysis (FEM and CFD) and some experimental results are presented to demonstrate the effectiveness and the desired performance of the developed integrated drive system.

42 ENGINEERING↗
DOE OSTI2025

Structural analysis of the NifL-NifA complex reveals the molecular basis of anti-activation of nitrogen fixation gene expression in Azotobacter vinelandii

Understanding the molecular basis of regulated nitrogen (N 2 ) fixation is essential for engineering N 2 -fixing bacteria that fulfill the demand of crop plants for fixed nitrogen, reducing our reliance on synthetic nitrogen fertilizers. In Azotobacter vinelandii and many other members of Proteobacteria, the two-component system comprising the anti-activator protein (NifL) and the Nif-specific transcriptional activator (NifA)controls the expression of nif genes, encoding the nitrogen fixation machinery. The NifL-NifA system evolved the ability to integrate several environmental cues, such as oxygen, nitrogen, and carbon availability. The nitrogen fixation machinery is thereby only activated under strictly favorable conditions, enabling diazotrophs to thrive in competitive environments. While genetic and biochemical studies have enlightened our understanding of how NifL represses NifA, the molecular basis of NifA sequestration by NifL depends on structural information on their interaction. Here, we present mechanistic insights into how nitrogen fixation is regulated by combining biochemical and genetic approaches with a low-resolution cryo-electron microscopy (cryo-EM) map of the oxidized NifL-NifA complex. Our findings define the interaction surface between NifL and NifA and reveal how this interaction can be manipulated to generate bacterial strains with increased nitrogen fixation rates able to secrete surplus nitrogen outside the cell, a crucial step in engineering improved nitrogen delivery to crop plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

CRISPR-prime editing, a versatile genetic tool to create specific mutations with a single nucleotide resolution in Leptospira

ABSTRACT Leptospirosis, caused by pathogenic bacteria from the genusLeptospira, is a global zoonosis responsible for more than one million human cases and 60,000 deaths annually. The disease also affects many domestic animal species. Historically, genetic manipulation ofLeptospirahas been difficult to perform, resulting in limited knowledge on pathogenic mechanisms of disease and the identification of virulence factors. The application of CRISPR/Cas9 and its variations have helped fill these gaps but the generation of knockout mutants remains challenging because double-strand breaks (DSBs) inflicted by Cas9 nuclease are lethal toLeptospiracells. The novel CRISPR prime editing (PE) strategy is the first precise genome-editing technology that allows deletions, insertions, and base substitutions without introducing DSBs. This revolutionary technique utilizes a nickase Cas9 that cleaves a single strand of DNA, coupled with an engineered reverse transcriptase and a modified single-guide RNA (termed prime editing guide RNA) containing an extended 3′ end with the desired edits. We demonstrate the application of CRISPR-PE in both saprophytic and pathogenicLeptospirafrom multiple species and serovars by introducing deletions or insertions into target DNA with a remarkable precision of just one nucleotide. Additionally, we demonstrate the ability to genetically manipulateLeptospira borgpetersenii, a prevalent pathogenic species of humans, domestic cattle, and wildlife animals. Rapid plasmid loss by mutated strains in liquid culture allows for the generation of knockout strains without selective markers, which can be readily used to elucidate virulence factors and develop optimized bacterin and/or live vaccines against leptospirosis. IMPORTANCE Leptospirosis is a geographically widespread bacterial zoonosis. Genetic manipulation of pathogenicLeptospiraspp. has been laborious and difficult to perform, limiting our ability to understand how leptospires cause disease. The application of the CRISPR/Cas9 system toLeptospiraenhanced our ability to generate knockdown and knockout mutants; however, the latter remains challenging. Here, we demonstrate the application of the CRISPR prime editing technique inLeptospira, allowing the generation of knockout mutants in several pathogenic species, with mutations comprising just a single nucleotide resolution. Notably, we generated a mutant in theLeptospira borgpeterseniibackground, a prevalent pathogenic species of humans and cattle. Our application of this method opens new avenues for studying pathogenic mechanisms ofLeptospiraand the identification of virulence factors across multiple species. These methods can also be used to facilitate the generation of marker-less knockout strains for updated and improved bacterin and/or live vaccines.

Microbiology↗
DOE OSTI2023

Systems Biology-Based Optimization of Extremely Thermophilic Lignocellulose Conversion to Bioproducts

This was a collaborative project involving researchers at the University of Georgia, North Carolina State University, Sanford‐Burnham‐Prebys Med. Discovery Institute and the University of Rhode Island. The over-arching goal was to demonstrate that non-model microorganisms, specifically extreme thermophiles, can be a strategic metabolic engineering platform for industrial biotechnology. We engineered the most thermophilic lignocellulose-degrading organism known, Caldicellulosiruptor bescii (Cbes) , which grows optimally near 80°C, and the most thermophilic fermentative organism known, Pyrococcus furiosus (Pfu) , which grows optimally at 100°C, to produce several key industrial chemicals. This work leveraged recent breakthrough advances in the development of molecular genetic tools for these organisms, complemented by a deep understanding of its metabolism and physiology gained over the past decade of study in the PIs’ laboratories. We applied the latest metabolic reconstruction and modeling approaches to optimize biomass to product conversion. Bio-processing above 70°C can have important advantages over near-ambient operations. Highly genetically-modified microorganisms usually have a fitness disadvantage and can be easily overtaken in culture when contaminating microbes are present. The high growth temperature of extreme thermophiles precludes growth or survival of virtually any contaminating organism or phage. This reduces operating costs associated with reactor sterilization and maintaining a sterile facility. In addition, at industrial scales, heat production from microbial metabolic activity vastly outweighs heat loss through bioreactor walls such that cooling is required. Extreme thermophiles have the advantage that non-refrigerated cooling water can be used if needed, and heating requirements can be met with low-grade steam typically in excess capacity on plant sites. We assembled a highly interdisciplinary team that brought together all of the expertise for the project to have successful outcomes. This project also built upon and utilized extensive information already available in the PIs’ labs for both Cbes and Pfu to develop models that provide a comprehensive description of these organisms’ physiology and metabolism that were utilized to inform metabolic engineering strategies. The models were validated with experimental data and the results demonstrated that unpretreated lignocellulose has the potential to be converted into value-added industrial chemicals at high loading at bioreactor scale. The data generated from this research were published in twenty-one peer-reviewed papers in international journals with online access.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Membrane potential sensing: Material design and method development for single particle optical electrophysiology

We review the development of “single” nanoparticle-based inorganic and organic voltage sensors, which can eventually become a viable tool for “non-genetic optogenetics.” The voltage sensing is accomplished with optical imaging at the fast temporal response and high spatial resolutions in a large field of view. Inorganic voltage nanosensors utilize the Quantum Confined Stark Effect (QCSE) to sense local electric fields. Engineered nanoparticles achieve substantial single-particle voltage sensitivity (~2% Δλ spectral Stark shift up to ~30% ΔF/F per 160 mV) at room temperature due to enhanced charge separation. A dedicated home-built fluorescence microscope records spectrally resolved images to measure the QCSE induced spectral shift at the single-particle level. Biomaterial based surface ligands are designed and developed based on theoretical simulations. The hybrid nanobiomaterials satisfy anisotropic facet-selective coating, enabling effective compartmentalization beyond non-specific staining. Self-spiking- and patched-HEK293 cells and cortical neurons, when stained with hybrid nanobiomaterials, show clear photoluminescence intensity changes in response to membrane potential (MP) changes. Organic voltage nanosensors based on polystyrene beads and nanodisk technology utilize Fluorescence (Förster) Resonance Energy Transfer (FRET) to sense local electric fields. Voltage sensing FRET pairs achieve voltage sensitivity up to ~35% ΔF/F per 120 mV in cultures. Non-invasive MP recording from individual targeted sites (synapses and spines) with nanodisks has been realized. However, both of these QCSE- and FRET-based voltage nanosensors yet need to reach the milestone of recording individual action potentials from individual targeted sites.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

TCF High Efficiency Anaerobic Electroporation (CRADA Final Report)

The Joint BioEnergy Institute (JBEI) researchers were co-inventors of the technology that will be used on this project and have developed a more current version of the chip and controller. JBEI will also assist with the design of the pathways and implementation of pathways on the chip. LanzaTech has developed novel gas fermentation technology that captures and utilizes greenhouse gases for production of fuels and chemicals. In contrast to traditional fermentation that uses sugars as substrate (and releases CO2 as a byproduct), gas fermentation utilizes C1 substrates carbon monoxide (CO) or CO2. This enables a diverse range of feedstock options including waste gases from industrial sources (e.g., steel mills and processing plants) or syngas generated from any biomass resource (e.g., agricultural waste, municipal solid waste, or organic industrial waste). Biomass is then gasified, allowing for maximum yields and complete carbon utilization including the recalcitrant lignocellulosic fraction that cannot be utilized in traditional sugar fermentation. To maximize the value that can be added to the array of gas resources that the LanzaTech process can use as an input, LanzaTech has pioneered genetic modification of acetogens and developed a comprehensive set of genetic tools to perform routine strain modification, including genome editing tools as CRISPR/Cas9 and libraries of validated genetic parts as promoters and terminators. Using this platform, production of over 50 new molecules have been demonstrated directly from gas. For a few selected molecules production rates and yields have been optimized and surpass production of native producers and engineered E. coli or yeast strains, but a higher throughput approach for combinatorial optimization of pathways is required to further advance synthesis of additional products in parallel.

09 BIOMASS FUELS↗