Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Directed evolution”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Unlocking nature’s biosynthetic potential by directed genome evolution

Microorganisms have been increasingly explored as microbial cell factories for production of fuels, chemicals, drugs, and materials. Among the various metabolic engineering strategies, directed genome evolution has emerged as one of the most powerful tools to unlock the full biosynthetic potential of microorganisms. Furthermore we summarize the directed genome evolution strategies that have been developed in recent years, including adaptive laboratory evolution and various targeted genome-scale engineering strategies, and discuss their applications in basic and applied biological research.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1986

Isotopic constraints on planetary evolution

Direct observations are considered that have been made on terrestrial and lunar materials in the search for answers to questions such as: when did the major structural elements (core, mantle, and crust) come into being and evolved. Measurements of isotope ratios of Pb, Sr, Nd, Hf, Ar, and other elements provide information about the internal evolution of the earth and moon since their formation 4.5 Gyr ago. The existing evidence indicates the core formed more than 4.4 Gyr ago, possibly while the earth was still accreting. Though the moon crust is similarly very old, the moon ceased to differentiate after about 1 Gyr whereas earth differentiation has continued to the present. Cataclysmic episodes have occurred, the largest 2.8 Gyr ago, when about half of the present continental mass formed.

Depaolo, D. J.↗
NASA NTRS1988

Outgassing asymmetry of periodic Comet Encke. II - Apparitions 1868-1918 and a study of the nucleus evolution

Directed outgassing from isolated sources on P/Encke's rotating nucleus is investigated based on observations made between 1868 and 1918. A model of a collimated particle flow which identifies a sunward fan-like coma with the emission cone described by the ejecta from a discrete active region is shown to account for physical observations of the comet's perihelion. The results support nucleus precession, with a time-variable rate averaging about 1 degree per revolution. It is suggested that wall collapse and other processes limit the lifespans of individual vents to only a few hundred years or so. Differences between new and old vents are considered.

Sekanina, Z.↗
DOE OSTI2025

A Route to Design Novel Functional Peptides by Applying a Denoising Diffusional Model to mRNA Display Libraries

In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B‐cell lymphoma extra‐large (Bcl‐x L ), a key cancer target. Starting with high‐throughput sequencing data from previous selections, a DDIM is trained to produce novel sequences with high affinity binding. Experimental validation confirms that most generated sequences are functionally equivalent to the original library members for Bcl‐x L binding and demonstrated comparable binding kinetics and affinity relative to the wildtype and nearest original neighbors. Importantly, this approach generated rare sequences not easily accessible via mutation and directed evolution. These results indicate that DDIMs can complement and expand directed evolution data, efficiently exploring underrepresented regions of sequence space. This approach provides a broadly applicable framework for accelerating ligand discovery and optimizing molecular properties across diverse targets.

Qi, Pearl [Mork Family Department of Chemical Engi↗
DOE OSTI2022

“Multiagent” Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations

Enzyme evolution has enabled numerous advances in biotechnology and synthetic biology, yet still requires many iterative rounds of screening to identify optimal mutant sequences. This is due to the sparsity of the fitness landscape, which is caused by epistatic mutations that only offer improvements when combined with other mutations. We report an approach that incorporates diverse substrate analogues in the screening process, where multiple substrates act like multiple agents navigating the fitness landscape, identifying epistatic mutant residues without a need for testing the entire combinatorial search space. We initially validate this approach by engineering a malonyl-CoA synthetase and identify numerous epistatic mutations improving activity for several diverse substrates. The majority of these mutations would have been missed upon screening for a single substrate alone. We expect that this approach can accelerate a wide array of enzyme engineering programs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Integrating continuous hypermutation with high–throughput screening for optimization of cis,cis –muconic acid production in yeast

Directed evolution is a powerful method to optimize proteins and metabolic reactions towards user-defined goals. It usually involves subjecting genes or pathways to iterative rounds of mutagenesis, selection and amplification. While powerful, systematic searches through large sequence-spaces is a labour-intensive task, and can be further limited by a priori knowledge about the optimal initial search space, and/or limits in terms of screening throughput. Here, we demonstrate an integrated directed evolution workflow for metabolic pathway enzymes that continuously generate enzyme variants using the recently developed orthogonal replication system, OrthoRep and screens for optimal performance in high-throughput using a transcription factor-based biosensor. We demonstrate the strengths of this workflow by evolving a rate-limiting enzymatic reaction of the biosynthetic pathway for cis,cis-muconic acid (CCM), a precursor used for bioplastic and coatings, in Saccharomyces cerevisiae. After two weeks of simply iterating between passaging of cells to generate variant enzymes via OrthoRep and high-throughput sorting of best-performing variants using a transcription factor-based biosensor for CCM, we ultimately identified variant enzymes improving CCM titers > 13-fold compared with reference enzymes. Taken together, the combination of synthetic biology tools as adopted in this study is an efficient approach to debottleneck repetitive workflows associated with directed evolution of metabolic enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A combinatorially complete epistatic fitness landscape in an enzyme active site

Protein engineering often targets binding pockets or active sites which are enriched in epistasis—nonadditive interactions between amino acid substitutions—and where the combined effects of multiple single substitutions are difficult to predict. Few existing sequence-fitness datasets capture epistasis at large scale, especially for enzyme catalysis, limiting the development and assessment of model-guided enzyme engineering approaches. We present here a combinatorially complete, 160,000-variant fitness landscape across four residues in the active site of an enzyme. Assaying the native reaction of a thermostable β-subunit of tryptophan synthase (TrpB) in a nonnative environment yielded a landscape characterized by significant epistasis and many local optima. These effects prevent simulated directed evolution approaches from efficiently reaching the global optimum. There is nonetheless wide variability in the effectiveness of different directed evolution approaches, which together provide experimental benchmarks for computational and machine learning workflows. The most-fit TrpB variants contain a substitution that is nearly absent in natural TrpB sequences—a result that conservation-based predictions would not capture. Thus, although fitness prediction using evolutionary data can enrich in more-active variants, these approaches struggle to identify and differentiate among the most-active variants, even for this near-native function. Overall, this work presents a large-scale testing ground for model-guided enzyme engineering and suggests that efficient navigation of epistatic fitness landscapes can be improved by advances in both machine learning and physical modeling.

biocatalysis↗
DOE OSTI2022

Ephemeral antibubbles: Spatiotemporal evolution from direct numerical simulations

Antibubbles, which consist of a shell of a low-density fluid inside a high-density fluid, have several promising applications. We show, via extensive direct numerical simulations (DNSs), in both two and three dimensions, that the spatiotemporal evolution of antibubbles can be described naturally by the coupled Cahn-Hilliard-Navier-Stokes (CHNS) equations for a binary fluid. Our DNSs capture elegantly the gravity-induced thinning and breakup of an antibubble via the time evolution of the Cahn-Hilliard scalar-order-parameter field $\phi$, which varies continuously across interfaces, so we do not have to enforce complicated boundary conditions at the moving antibubble interfaces. To ensure that our results are robust, we supplement our CHNS simulations with sharp-interface volume-of-fluid DNSs. We track the thickness of the antibubble and calculate the dependence of the lifetime of an antibubble on several parameters; we show that our DNS results agree with various experimental results; in particular, the velocity with which the arms of the antibubble retract after breakup scales as σ 1/2 , where σ is the surface tension.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

A Chemoselective and Stereodivergent Platform of Heme‐Nitrene Transferases to Access Chiral Aryl‐β‐Amino Esters and An Investigation of the Sequence‐Activity Landscape

Engineered biocatalysts can utilize nitrene precursors to access enantioenriched amination products, yet they have not been applied to produce valuable, enantiomerically enriched noncanonical β-amino esters. Current approaches to synthesizing β-amino acids rely on pre-oxidized precursors and multistep synthetic approaches involving various protecting groups. We engineered a platform of heme enzymes for stereoselective C–H bond amination of readily available carboxylic ester derivatives to install primary amines. A directed evolution campaign coupled with sequencing of over 1000 variants enabled us to develop engineered variants that use either O-pivaloylhydroxylamine triflic acid (PONT) or hydroxylamine hydrochloride (H 2 NOH∙HCl) as aminating reagents. An analysis of the resulting sequence–activity dataset revealed additional improvements that could be made to the final variant, highlighting the utility of sequencing data to guide future steps in directed evolution campaigns. Furthermore, the evolved nitrene transferases expand the scope of accessible chiral β-amino acid building blocks for peptidomimetic applications and provide new starting points for the design and synthesis of enantioenriched β-amino acid motifs.

amino ester building blocks↗
DOE OSTI2023

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries.

Choe, Kisurb↗
DOE OSTI2020

Tracking atomic structure evolution during directed electron beam induced Si-atom motion in graphene via deep machine learning

Using electron beam manipulation, we enable deterministic motion of individual Si atoms in graphene along predefined trajectories. Structural evolution during the dopant motion was explored, providing information on changes of the Si atom neighborhood during atomic motion and providing statistical information of possible defect configurations. The combination of a Gaussian mixture model and principal component analysis applied to the deep learning-processed experimental data allowed disentangling of the atomic distortions for two different graphene sublattices. This approach demonstrates the potential of e-beam manipulation to create defect libraries of multiple realizations of the same defect and explore the potential of symmetry breaking physics. The rapid image analytics enabled via a deep learning network further empowers instrumentation for e-beam controlled atom-by-atom fabrication. Here, the analysis described in the paper can be reproduced via an interactive Jupyter notebook at https://git.io/JJ3Bx.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
NASA NTRSDate not supplied

Three-dimensional in Situ Observations of Polycrystalline Microstructure Evolution During Directional Solidification of Transparent Alloys Aboard the ISS and Quantitative Comparison with Numerical Modeling

Cellular/dendritic microstructures formed during solidification have a crucial influence on the mechanical properties of a wide range of structural alloys. By minimizing the amount of gravity-induced convection in the liquid, directional solidification experiments using transparent organic alloys conducted in the DECLIC-DSI onboard the International Space Station have provided unique 3D in situ observations of the spatiotemporal evolution of the solid-liquid interface during the formation of cellular and dendritic microstructures under purely diffusive growth conditions in polycrystalline samples containing several grains with a small misorientation with respect to the temperature gradient. Those observations have made it possible to perform benchmark quantitative comparisons with the predictions of state-of-the-art phase-field simulations of microstructure formation in 3D on experimentally relevant length and time scales. This talk will report quantitative comparisons between microgravity experiments and phase-field simulations in succinonitrile-camphor alloys of two different compositions that shed new light on the role of subgrain boundaries in the spatiotemporal evolution of the primary cellular spacing and the selection of dendritic array structures.

Kaihua Ji↗
NASA NTRSDate not supplied

Three-Dimensional In Situ Observations of Polycrystalline Microstructure Evolution During Directional Solidification of Transparent Alloys Aboard the ISS and Quantitative Comparison with Numerical Modeling

Cellular/dendritic microstructures formed during solidification have a crucial influence on the mechanical properties of a wide range of structural alloys. By minimizing the amount of gravity-induced convection in the liquid, directional solidification experiments using transparent organic alloys conducted in the DECLIC-DSI onboard the International Space Station have provided unique 3D in situ observations of the spatiotemporal evolution of the solid-liquid interface during the formation of cellular and dendritic microstructures under purely diffusive growth conditions. Those observations have made it possible to perform benchmark quantitative comparisons with the predictions of state-of-the-art phase-field simulations of microstructure formation in 3D on experimentally relevant length and time scales. This talk will report quantitative comparisons between microgravity experiments and phase-field simulations in succinonitrile-camphor alloys of two different compositions, which shed new light on the selection of dendritic array structures, and on roles of macroscopic curvatures and subgrain boundaries between grains with a small misorientation with respect to the temperature gradient in the spatiotemporal evolution of the primary cellular spacing.

Kaihua Ji↗
NASA NTRS2008

Effect of Stepwise Pressure Change on Porosity Evolution during Directional Solidification in Small Cylindrical Channels

Controlled directional solidification experiments were performed in capillary channels, using nitrogen-saturated succinonitrile, to examine the effect of an in-situ stepwise processing pressure increase on an isolated pore evolution. Two experiments were performed using different processing pressure input profiles. The results indicate that a processing pressure increase has a transient effect on pore growth geometry characterized by an initial phase of decreasing pore diameter, followed by a recovery phase of increasing pore diameter. The experimental results also show that processing pressure can be used as a control parameter to either increase or terminate porosity formation. A theoretical model is introduced which indicates that the pore formation process is limited by the diffusion of solute-gas through the melt, and that the observed response toa pressure increase is attributed to the re-equilibration of solute concentration in the melt associated with the increased melt pressure.

Grugel, R.N.↗
NASA NTRS2005

Morphological Evolution of Directional Solidification Interfaces in Microgravity: An Analysis of Model Experiments Performed on the International Space Station

A series of experiments performed using the Pore Formation and Mobility Investigation (PFMI) apparatus within the glovebox facility (GBX) on board the International Space Station (ISS) has provided video images of the morphological evolution of a three-dimensional interface in a diffusion controlled regime. The experimental samples were prepared on ground by filling glass tubes, 1 cm ID and approximately 30 cm in length, with "alloys" of succinonitrile (SCN) and water in an atmosphere of nitrogen at 450 millibar pressure. The compositions of the samples processed and analyzed are 0.25,0.5 and 1.0 wt% water. Experimental processing parameters of temperature gradient and translation speed, as well as camera settings, were remotely monitored and manipulated from the ground Telescience Center (TSC) at the Marshall !3pace Flight Center. During the experiments, the sample was first subjected to a unidirectional melt back, generally at 10 microns per second, with a constant temperature gradient ahead of the melting interface. Following the melt back, the interface was allowed to stabilize before translation is initiated. The temperatures in the sample were monitored by six in situ thermocouples and the position is monitored by an optical linear encoder. For the experiments performed and analyzed, the gradients ranged from 2.5 - 3.3 K/mm and the initial pulling velocities ranged from 0.7 micron per second to 1 micron per second with subsequent transition velocities of up to 100 microns per second. The data provided by the PFMI for analysis includes near-real-time (NRT) video captured on the ground during the experiment runs, ISS Video Tape Recorder (VTR) data dumped from the VTR at the end of the experiment run and recorded on the ground, telemetry data including temperature and position measurements, and limited flight HI-8 tapes in 2 camera views of experiment runs for which tapes have been returned to the investigators from ISS. Because of limited down mass from the ISS, the majority of the initial analysis has been performed using the NRT and VTR video data but will be supplemented with the HI-8 video as it becomes available. hardware and procedures required to prepare samples for correlation to flight samples is described. Using this ground-based system, a series of experiments have been performed for direct comparison with the flight data. The results of these comparisons as well as implications to future microgravity experiments are presented and discussed. A ground-based thin-sample directional solidification system as well as all associated

Strutzenberg, Louise L.↗
DOE OSTI2023

Adapting enzymes to improve their functionality in plants: why and how

Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context (‘plantized’) even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can — or cannot — be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.

Biochemistry & Molecular Biology↗