Search NASA⌕ Search

SEARCH · Search NASA

Results for “Laboratory 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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

raogroupuiuc/yl_variantcalling

NGS analysis for mutation analysis in Yarrowia lipolytica evolved strains. Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Deewan, Anshu↗
DOE OSTI2016

Comprehensive molecular characterization of Methylobacterium extorquens AM1 adapted for 1-butanol tolerance

In this study, the toxicity of alcohols is one of the major roadblocks of biological fermentation for biofuels production. Methylobacterium extorquens AM1, a facultative methylotrophic α-proteobacterium, has been engineered to generate 1-butanol from cheap carbon feedstocks through a synthetic metabolic pathway. However, M. extorquens AM1 is vulnerable to solvent stress, which impedes further development for 1-butanol production. Only a few studies have reported the general stress response of M. extorquens AM1 to solvent stress. Therefore, it is highly desirable to obtain a strain with ameliorated 1-butanol tolerance and elucidate the molecular mechanism of 1-butnaol tolerance in M. extorquens AM1 for future strain improvement. In this work, adaptive laboratory evolution was used as a tool to isolate mutants with 1-butanol tolerance up to 0.5 %. The evolved strains, BHBT3 and BHBT5, demonstrated increased growth rates and higher survival rates with the existence of 1-butanol. Whole genome sequencing revealed a SNP mutation at kefB in BHBT5, which was confirmed to be responsible for increasing 1-butanol tolerance through an allelic exchange experiment. Global metabolomic analysis further discovered that the pools of multiple key metabolites, including fatty acids, amino acids, and disaccharides, were increased in BHBT5 in response to 1-butanol stress. Additionally, the carotenoid synthesis pathway was significantly down-regulated in BHBT5. In conclusion, we successfully screened mutants resistant to 1-butanol and provided insights into the molecular mechanism of 1-butanol tolerance in M. extorquens AM1. This research will be useful for uncovering the mechanism of cellular response of M. extorquens AM1 to solvent stress, and will provide the genetic blueprint for the rational design of a strain of M. extorquens AM1 with increased 1-butanol tolerance in the future.

global metabolome analysis↗
DOE OSTI2020

Metabolic and evolutionary responses of Clostridium thermocellum to genetic interventions aimed at improving ethanol production

Engineering efforts targeted at increasing ethanol by modifying the central fermentative metabolism of Clostridium thermocellum have been variably successful. Here, we aim to understand this variation by a multifaceted approach including genomic and transcriptomic analysis combined with chemostat cultivation and high solids cellulose fermentation. Three strain lineages comprising 16 strains total were examined. Two strain lineages in which genes involved in pathways leading to organic acids and/or sporulation had been knocked out resulted in four end-strains after adaptive laboratory evolution (ALE). A third strain lineage recapitulated mutations involving adhE that occurred spontaneously in some of the engineered strains.

Biotechnology & Applied Microbiology↗
DOE OSTI2019

Coupling S -adenosylmethionine–dependent methylation to growth: Design and uses

We present a selection design that couples S -adenosylmethionine-dependent methylation to growth. We demonstrate its use in improving the enzyme activities of not only N-type and O-type methyltransferases by 2-fold but also an acetyltransferase of another enzyme category when linked to a methylation pathway in Escherichia coli using adaptive laboratory evolution. We also demonstrate its application for drug discovery using a catechol O-methyltransferase and its inhibitors entacapone and tolcapone. Implementation of this design in Saccharomyces cerevisiae is also demonstrated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

PKA regulatory subunit Bcy1 couples growth, lipid metabolism, and fermentation during anaerobic xylose growth in Saccharomyces cerevisiae

Organisms have evolved elaborate physiological pathways that regulate growth, proliferation, metabolism, and stress response. These pathways must be properly coordinated to elicit the appropriate response to an ever-changing environment. While individual pathways have been well studied in a variety of model systems, there remains much to uncover about how pathways are integrated to produce systemic changes in a cell, especially in dynamic conditions. We previously showed that deletion of Protein Kinase A (PKA) regulatory subunit BCY1 can decouple growth and metabolism in Saccharomyces cerevisiae engineered for anaerobic xylose fermentation, allowing for robust fermentation in the absence of division. This provides an opportunity to understand how PKA signaling normally coordinates these processes. Here, we integrated transcriptomic, lipidomic, and phospho-proteomic responses upon a glucose to xylose shift across a series of strains with different genetic mutations promoting either coupled or decoupled xylose-dependent growth and metabolism. Together, results suggested that defects in lipid homeostasis limit growth in the bcy1Δ strain despite robust metabolism. To further understand this mechanism, we performed adaptive laboratory evolutions to re-evolve coupled growth and metabolism in the bcy1Δ parental strain. The evolved strain harbored mutations in PKA subunit TPK1 and lipid regulator OPI1 , among other genes, and evolved changes in lipid profiles and gene expression. Deletion of the evolved opi1 gene partially reverted the strain’s phenotype to the bcy1Δ parent, with reduced growth and robust xylose fermentation. We suggest several models for how cells coordinate growth, metabolism, and other responses in budding yeast and how restructuring these processes enables anaerobic xylose utilization.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community

The recalcitrance of complex organic polymers such as lignocellulose is one of the major obstacles to sustainable energy production from plant biomass, and the generation of toxic intermediates can negatively impact the efficiency of microbial lignocellulose degradation. Here, we describe the development of a model microbial consortium for studying lignocellulose degradation, with the specific goal of mitigating the production of the toxin formaldehyde during the breakdown of methoxylated aromatic compounds. Included are Pseudomonas putida, a lignin degrader; Cellulomonas fimi, a cellulose degrader; and sometimes Yarrowia lipolytica, an oleaginous yeast. Unique to our system is the inclusion of Methylorubrum extorquens, a methylotroph capable of using formaldehyde for growth. We developed a defined minimal “Model Lignocellulose” growth medium for reproducible coculture experiments. We demonstrated that the formaldehyde produced by P. putida growing on vanillic acid can exceed the minimum inhibitory concentration for C. fimi, and, furthermore, that the presence of M. extorquens lowers those concentrations. We also uncovered unexpected ecological dynamics, including resource competition, and interspecies differences in growth requirements and toxin sensitivities. Finally, we introduced the possibility for a mutualistic interaction between C. fimi and M. extorquens through metabolite exchange. This study lays the foundation to enable future work incorporating metabolomic analysis and modeling, genetic engineering, and laboratory evolution, on a model system that is appropriate both for fundamental eco-evolutionary studies and for the optimization of efficiency and yield in microbially-mediated biomass transformation.

Methylorubrum extorquens↗
DOE OSTI2021

BETO 2021 Peer Review - Improving Formate Upgrading by Cupriavidus Necator 2.3.2.111

Formate can be generated by electrocatalytic reduction of CO2 and has been proposed as a soluble intermediate for the storage of carbon and energy. Biological systems capable of assimilating formate could enable conversion of formate generated from low-cost renewable energy and waste CO2 to myriad fuels and chemicals. To that end, the goal of this project is to develop the natural formatotroph Cupriavidus necator as a robust microbial chassis for efficient conversion of formate to value-added products. Using a combination of laboratory evolution and rational engineering, we have identified mutations and genetic deletions that improve its growth rate and biomass yield on formate by 1.2X. Using RNA-seq transcriptomics, we are elucidating the mechanisms that underly these improvements and anticipate this will contribute to our understanding of formate conversion. We have also engineered C. necator to convert formate to the potential polymer precursor 2-hydroxymuconate semialdehyde (2HMS) by introducing an exogenous pathway and deleting competing pathways and demonstrated production and robust growth using a pH-stat bioreactor. Final techno-economic analysis and life-cycle assessment on biological production of 2HMS from formate will enable the DOE and other stake holders to evaluate the economic and environmental impact of this project and related technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2023

Laboratory Experiments Examining the Effect of Thermal and Mechanical Processes on Hydraulic Transmissivity Evolution

Using laboratory slide-hold-slide experiments, at temperatures from 22 to 200 degrees C, to examine effects of fracture reactivation and quasi-static loading on the evolution of fluid transport properties of simulated fractures in Westerly granite. At all temperatures, the in-plane hydraulic transmissivity consistently decays during hold periods resulting in an overall reduction in transmissivity. During the first three to fifteen hours of an experiment, transmissivity decreases rapidly due to the generation of wear products, development of a sliding surface, and compaction of the resulting gouge. Once the sliding surface has developed, the long-term transmissivity decay rate at 22 and 100 degrees C is significantly lower than the transmissivity decay rate during the initial 3-15 hours of the experiment. However, at 200 degrees C, the decay of hydraulic transmissivity remains high throughout the experiment. The long-term decay of hydraulic transmissivity can be fitted with a power law model with more rapid reduction of hydraulic transmissivity at higher temperature. Periods of sliding on the fracture surface result in transient increases in the transmissivity, due to shear dilation, as is expected for Coulomb materials. These transients are superimposed on the long-term decay. When sliding ceases and a new hold period commences, there is a rapid reduction in transmissivity and return to the long-term rate of transmissivity decay. The rate of decay of the transmissivity transients is inversely correlated with temperature, in contrast to the long-term decay and the expected behavior for processes like subcritical crack growth and indentation creep. The higher decay rates that are observed during the initial 3-15 hours of the tests and following sliding, are associated with times that the porosity of the gouge is expected to be high. The difference in decay rates suggests that when the gouge is driven far from equilibrium by active shearing, densification may be dominated by a different mechanism from long-term compaction.

15 GEOTHERMAL ENERGY↗
DOE OSTI2015

Disease Diagnostics Research at Los Alamos National Laboratory

Human evolution and persistent diseases have existed side-by-side. A recent concern is the re-emergence of tuberculosis, one of the oldest and most challenging diseases known to man. Effective diagnosis can save lives and prevent its spread. This talk will cover how our immune system discriminates between itself and foreign entities and how a new laboratory and nature inspired strategy can detect tuberculosis equally well in human and animal populations. The approach is being extended to other applications such as the identification of strep throat and respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evolution of an arched magnetized laboratory plasma in a sheared magnetic field

Arched magnetized structures are a common occurrence in space and laboratory plasmas. Results from a laboratory experiment on spatio-temporal evolution of an arched magnetized plasma ( $\beta \approx 10^{-3}$ , Lundquist number $\approx 10^{4}$ , plasma radius/ion gyroradius $\approx 20$ ) in a sheared magnetic configuration are presented. The experiment is designed to model conditions relevant to the formation and destabilization of similar structures in the solar atmosphere. The magnitude of a nearly horizontal overlying magnetic field was varied to study its effects on the writhe and twist of the arched plasma. In addition, the direction of the guiding magnetic field along the arch was varied to investigate its role in the formation of either forward- or reverse-S shaped plasma structures. The electrical current in the arched plasma was well below the current required to make it kink unstable. A significant increase in the writhe of the arched plasma was observed with larger magnitudes of overlying magnetic field. A forward-S shaped arched plasma was observed for a guiding magnetic field oriented nearly antiparallel to the initial arched plasma current, while the parallel orientation yielded the reverse-S shaped arched plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2019

Laboratory Foamed-Cement-Curing Evolution Using CT Scanning: Insights From Elevated-Pressure Generation

Computed-tomography (CT) scanning has become a mainstay among scientists (Wildenschild and Sheppard 2013) because it enables nondestructive observation of material processes and formation in real time. Foamed cement is a high-strength, low-density material containing nitrogen gas, and is used to stabilize wellbore casings both onshore and offshore. In-situ foamed cement is subject to pressure changes because the slurry is pumped downhole and cures at depth. To correlate the influence of pressure to the gas-void size and the curing evolution of a foamed cement, two laboratory foamed cements were generated and CT scanned as they cured. One cement was generated following the American Petroleum Institute (API) industry standard API RP 10B-4 (2015) at atmospheric conditions using a blender, and the other cement was created using a foamed-cement generator (FCG) (resembling that of de Rozières and Ferrière 1991) to produce a sample at an elevated pressure. FCG-generated cement qualities (in the range of 20, 25, 30, 35, and 40%) were scanned at their cured state for comparison. From the CT-image time series and the single FCG scans, the volumetric void properties were characterized and compared. The time-series blender voids were an order of magnitude larger than the FCG voids, and void growth was stagnant after a curing period of 100 minutes, whereas the FCG voids gradually increased in volume after 100 minutes. The Hsü-Nadai plots (Brandon 1995) reveal that the FCG and blender voids are weakly prolate, and all FCG voids, regardless of generation quality, relax to a greater final-magnitude strain than the blender voids. Furthermore, these findings confirm that both the void size and the curing process are influenced by the pressure at which a foamed cement is generated.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Pore habit of methane hydrate and its evolution in sediment matrix – Laboratory visualization with phase-contrast micro-CT

Describing the pore habit of methane hydrate in sediment matrices is essential for understanding natural distribution of methane hydrate, methane trace (transport and solidification) in the hydrate stability zone, physical properties of hydrate-bearing sediments, and the associated influence on potential gas production. Pore habit visualization in natural media at pore scale even with laboratory synthesized cores has been challenging due to the similar densities of methane hydrate from pore liquid. In this work, we used phase-contrast assisted micro-CT with potassium iodine-doped brine to visualize four phases: sand particles, pore fluid, methane hydrate and methane gas. This study visualizes the pore habit of methane hydrate at various stages including during hydrate formation in excess-gas systems, its evolution after brine injection to replace pore fluid, and hydrate formation in excess-water systems. Hydrate tends to adopt round and smooth surfaces when in contact with water while exhibits relatively angular interfaces when in contact with methane gas. Hydrate formation in excess-gas systems results in a partial cementing and partial mineral-coating pore habit, while hydrate in excess-water systems develops mainly as pore-filling, and locally cementing or mineral-coating where big gas pockets exist at the initial state. Pore liquid replacement from methane gas to brine triggers a shift of hydrate pore habit towards pore-filling. Methane hydrate evolution over time produces bigger hydrate particles but with less contact area with sand particles. The effects of hydrate pore habit become less important as hydrate particle size exceeds the pore size. Additionally, hydrate formation could trap residual methane gas and brine as inclusions.

58 GEOSCIENCES↗
DOE OSTI2016

On the evolution of elastic properties during laboratory stick‐slip experiments spanning the transition from slow slip to dynamic rupture

Abstract The physical mechanisms governing slow earthquakes remain unknown, as does the relationship between slow and regular earthquakes. To investigate the mechanism(s) of slow earthquakes and related quasi‐dynamic modes of fault slip we performed laboratory experiments on simulated fault gouge in the double direct shear configuration. We reproduced the full spectrum of slip behavior, from slow to fast stick slip, by altering the elastic stiffness of the loading apparatus ( k ) to match the critical rheologic stiffness of fault gouge ( k c ). Our experiments show an evolution from stable sliding, when k > k c , to quasi‐dynamic transients when k ~ k c , to dynamic instabilities when k < k c . To evaluate the microphysical processes of fault weakening we monitored variations of elastic properties. We find systematic changes in P wave velocity ( V p ) for laboratory seismic cycles. During the coseismic stress drop, seismic velocity drops abruptly, consistent with observations on natural faults. In the preparatory phase preceding failure, we find that accelerated fault creep causes a V p reduction for the complete spectrum of slip behaviors. Our results suggest that the mechanics of slow and fast ruptures share key features and that they can occur on same faults, depending on frictional properties. In agreement with seismic surveys on tectonic faults our data show that their state of stress can be monitored by V p changes during the seismic cycle. The observed reduction in V p during the earthquake preparatory phase suggests that if similar mechanisms are confirmed in nature high‐resolution monitoring of fault zone properties may be a promising avenue for reliable detection of earthquake precursors.

Tinti, E.↗
DOE OSTI2023

Foreshock properties illuminate nucleation processes of slow and fast laboratory earthquakes

Understanding the connection between seismic activity and the earthquake nucleation process is a fundamental goal in earthquake seismology with important implications for earthquake early warning systems and forecasting. We use high-resolution acoustic emission (AE) waveform measurements from laboratory stick-slip experiments that span a spectrum of slow to fast slip rates to probe spatiotemporal properties of laboratory foreshocks and nucleation processes. We measure waveform similarity and pairwise differential travel-times (DTT) between AEs throughout the seismic cycle. AEs broadcasted prior to slow labquakes have small DTT and high waveform similarity relative to fast labquakes. We show that during slow stick-slip, the fault never fully locks, and waveform similarity and pairwise differential travel times do not evolve throughout the seismic cycle. In contrast, fast laboratory earthquakes are preceded by a rapid increase in waveform similarity late in the seismic cycle and a reduction in differential travel times, indicating that AEs begin to coalesce as the fault slip velocity increases leading up to failure. These observations point to key differences in the nucleation process of slow and fast labquakes and suggest that the spatiotemporal evolution of laboratory foreshocks is linked to fault slip velocity.

58 GEOSCIENCES↗
DOE OSTI2026

RNAseq data for P. putida with vanillate

Illumina sequencing reads from RNA sequencing of vanillate-utilizing strains of Pseudomonas putida, described in Evolution and engineering of pathways for aromatic O-demethylation in Pseudomonas putida KT2440 by A. Bleem, et al. (2024)

Adaptive laboratory evolution↗