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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Optical and electronic functionality arising from controlled defect formation in nanoscale complex oxide lateral epitaxy

Epitaxial crystallization of complex oxides provides the means to create materials with precisely selected composition, strain, and orientation, thereby controlling their functionalities. Extending this control to nanoscale three-dimensional geometries can be accomplished via a three-dimensional analog of oxide solid-phase epitaxy, lateral epitaxial crystallization. The orientation of crystals within laterally crystallized SrTiO 3 systematically changes from the orientation of the SrTiO 3 substrate. This evolution occurs as a function of lateral crystallization distance, with a rate of approximately 50° μm -1 . The mechanism of the rotation is consistent with a steady-state stress of tens of megapascal over a 100–nanometer scale region near the moving amorphous/crystalline interface arising from the amorphous-crystalline density difference. Second harmonic generation and piezoelectric force microscopy reveal that the laterally crystallized SrTiO 3 is noncentrosymmetric and develops a switchable piezoelectric response at room temperature, illustrating the potential to use lateral crystallization to control the functionality of complex oxides.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis

We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named "pre-op" isolates) and then 6 days later from the anastomotic site (herein named "post-op" isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Monitoring the impact of confinement on hyphal penetration and fungal behavior

Through their expansive mycelium network, soil fungi alter the physical arrangement and chemical composition of their local environment. This can significantly impact bacterial distribution and nutrient transport and can play a dramatic role in shaping the rhizosphere around a developing plant. However, direct observation and quantitation of such behaviors is extremely difficult due to the opacity and complex porosity of the soil microenvironment. In this study, we demonstrate the development and use of an engineered microhabitat to visualize fungal growth in response to varied levels of confinement. Microfluidics were fabricated using photolithography and conventional soft lithography, assembled onto glass slides, and prepared to accommodate fungal cultures. Selected fungal strains across three phyla (Ascomycota: Morchella sextalata , Fusarium falciforme ; Mucoromycota: Linnemannia elongata , Podila minutissima , Benniella ; Basidiomycota: Laccaria bicolor , and Serendipita sp.) were cultured within microhabitats and imaged using time-lapse microscopy to visualize development at the mycelial level. Fungal hyphae of each strain were imaged as they penetrated through microchannels with well-defined pore dimensions. The hyphal penetration rates through the microchannels were quantified via image analysis. Other behaviors, including differences in the degree of branching, peer movement, and tip strength were also recorded for each strain. Our results provide a repeatable and easy-to-use approach for culturing fungi within a microfluidics platform and for visualizing the impact of confinement on hyphal growth and other fungal behaviors pertinent to their remodeling of the underground environment.

Guo, Yi-Syuan (ORCID:0000000340142225)↗
DOE OSTI2026

Gaseous Hydrogen Embrittlement of L-PBF Ni-Based Superalloys for Service in Natural Gas Turbines

Efforts to improve efficiency of industrial gas turbine engines have focused on increasing operating temperatures by use of fuel-flexible gas blends. Ni-based superalloys are susceptible to hydrogen embrittlement (HE), leading to potential risk of premature component failure. Certain turbine components exposed to hydrogen-rich environments are manufactured from additive processes like laser powder bed fusion (L-PBF). The HE susceptibility was evaluated for three Ni-based superalloys: solid solution strengthened Alloy 625, γ’/γ’’-precipitation strengthened Alloy 718, and γ’-precipitation strengthened Haynes® 282®. L-PBF samples were pre-charged under medium and high pressure gaseous hydrogen before tensile testing at temperatures up to 260 °C using a fast strain rate. Selected samples were subjected to a service conditioning heat treatment prior to hydrogen charging to evaluate the change in susceptibility after prolonged service. The susceptibility to HE and HE mechanisms of these three alloys is compared.

additive manufacturing↗
DOE OSTI2022

Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria

Abstract Carbon-negative synthesis of biochemical products has the potential to mitigate global CO 2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimize and implement r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screen 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generates designer strains for the selective production of butanoic acid (4.9 ± 0.1 gL −1 ), as well as hexanoic acid (3.06 ± 0.03 gL −1 ) and 1-hexanol (1.0 ± 0.1 gL −1 ) at the best performance reported to date in this bacterium. We also generate Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL −1 in a 1.5 L continuous fermentation. Our strategy enables optimization of r-BOX derived products for biomanufacturing and industrial biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Combining Random Mutagenesis and Metabolic Engineering for Enhanced Tryptophan Production in Synechocystis sp. Strain PCC 6803

Tryptophan (Trp) is an essential aromatic amino acid that has value as an animal feed supplement, as the amount found in plant-based sources is insufficient. An alternative to production by engineered microbial fermentation is to have tryptophan biosynthesized by a photosynthetic microorganism that could replace or supplement both the plant and industrially used microbes. We selected Synechocystis sp. strain PCC 6803, a model cyanobacterium, as the host and studied metabolic engineering and random mutagenesis approaches. Previous work on engineering heterotrophic microbes for improved Trp titers has targeted allosteric feedback regulation in enzymes 3-deoxy-d-arabinoheptulosonate 7-phosphate synthase (DAHPS) and anthranilate synthase (AS) as major bottlenecks in the shikimate pathway. In this work, the genes encoding feedback-resistant enzymes from Escherichia coli, aroG fbr and trpE fbr , were overexpressed in the host wild-type (WT) strain. Separately, the WT strain was subjected to random mutagenesis and selection using an amino acid analog to isolate tryptophan-overproducing strains. The randomly mutagenized strains were sequenced in order to identify the mutations that resulted in the desirable phenotypes. Interestingly, the tryptophan overproducers had mutations in the gene encoding chorismate mutase (CM), which catalyzes the conversion of chorismate to prephenate. The best tryptophan overproducer from random mutagenesis was selected as a host for metabolic engineering where aroG fbr and trpE fbr were overexpressed. The best strain developed produced 212 ± 23 mg/liter of tryptophan after 10 days of photoautotrophic growth under 3% (vol/vol) CO2. We demonstrated that a combination of random mutagenesis and metabolic engineering was superior to either individual approach.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Phosphoribosylpyrophosphate synthetase as a metabolic valve advances Methylobacterium/Methylorubrum phyllosphere colonization and plant growth

The proficiency of phyllosphere microbiomes in efficiently utilizing plant-provided nutrients is pivotal for their successful colonization of plants. The methylotrophic capabilities of Methylobacterium/Methylorubrum play a crucial role in this process. However, the precise mechanisms facilitating efficient colonization remain elusive. In the present study, we investigate the significance of methanol assimilation in shaping the success of mutualistic relationships between methylotrophs and plants. A set of strains originating from Methylorubrum extorquens AM1 are subjected to evolutionary pressures to thrive under low methanol conditions. A mutation in the phosphoribosylpyrophosphate synthetase gene is identified, which converts it into a metabolic valve. This valve redirects limited C1-carbon resources towards the synthesis of biomass by up-regulating a non-essential phosphoketolase pathway. These newly acquired bacterial traits demonstrate superior colonization capabilities, even at low abundance, leading to increased growth of inoculated plants. This function is prevalent in Methylobacterium/Methylorubrum strains. In summary, our findings offer insights that could guide the selection of Methylobacterium/Methylorubrum strains for advantageous agricultural applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Polarization rotation in a ferroelectric BaTiO 3 film through low-energy He-implantation

Domain engineering in ferroelectric thin films is crucial for next-generation microelectronic and photonic technologies. Here, a method is demonstrated to precisely control domain configurations in BaTiO 3 thin films through low-energy He ion implantation. The approach transforms a mixed ferroelectric domain state with significant in-plane polarization into a uniform out-of-plane tetragonal phase by selectively modifying the strain state in the film’s top region. This structural transition significantly improves domain homogeneity and reduces polarization imprint, leading to symmetric ferroelectric switching characteristics. The demonstrated ability to manipulate ferroelectric domains post-growth enables tailored functional properties without compromising the coherently strained bottom interface. The method’s compatibility with semiconductor processing and ability to selectively modify specific regions make it particularly promising for practical implementation in integrated devices. This work establishes a versatile approach for strain-mediated domain engineering that could be extended to a wide range of ferroelectric systems, providing new opportunities for memory, sensing, and photonic applications where precise control of polarization states is essential.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Polarization rotation in a ferroelectric BaTiO$_3$ film through low-energy He-implantation

Domain engineering in ferroelectric thin films is crucial for next-generation microelectronic and photonic technologies. Here, a method is demonstrated to precisely control domain configurations in BaTiO$_3$ thin films through low-energy He ion implantation. The approach transforms a mixed ferroelectric domain state with significant in-plane polarization into a uniform out-of-plane tetragonal phase by selectively modifying the strain state in the film's top region. This structural transition significantly improves domain homogeneity and reduces polarization imprint, leading to symmetric ferroelectric switching characteristics. The demonstrated ability to manipulate ferroelectric domains post-growth enables tailored functional properties without compromising the coherently strained bottom interface. The method's compatibility with semiconductor processing and ability to selectively modify specific regions make it particularly promising for practical implementation in integrated devices. This work establishes a versatile approach for strain-mediated domain engineering that could be extended to a wide range of ferroelectric systems, providing new opportunities for memory, sensing, and photonic applications where precise control of polarization states is essential.

Luo, Liang [Ames Laboratory (AMES), Ames, IA (Unit↗
DOE OSTI2022

Selection-enriched genomic loci (SEGL) reveals genetic loci for environmental adaptation and photosynthetic productivity in Chlamydomonas reinhardtii

This work demonstrates an approach to produce and select hybrid algal strains exhibiting increased photosynthetic productivity under multiple environmental conditions. This simultaneously addresses two major impediments to improving algal bioenergy production: 1) generating new genetic variants with improved performance; and 2) disentangling complex interactions between genetic and physiological factors contributing to these improvements. We pooled progeny generated from mating two environmental isolates of the green alga Chlamydomonas reinhardtii and cultured the pools under multiple environmental conditions. Strains from the outcompeting populations showed substantial (in some cases over 3 fold) increases in productivity over the parental lines under certain environments related to biomass production, including laboratory conditions as well as hyperoxia, fluctuating light, high salinity and high temperature. The results indicate that C. reinhardtii has remarkable, untapped, directed evolution capacity that may be harnessed using breeding and competition approaches. The populations were deep sequenced at multiple time points to identify “Selection-Enriched Genomic Loci” (SEGL) that accumulated in the populations, and thus likely confer increased fitness under the respective environmental conditions. With improved resolution, SEGL mapping can identify allelic combinations used for targeted breeding approaches, generating elite algal lines with multiple desirable traits, as well as to further understand the genetic and mechanistic bases of photosynthetic productivity. Increasing the photosynthetic efficiency of algae during biomass production is perhaps the most critical hurdle for economically sustainable algal based biofuels. This presents unique challenges because modifications designed to increase photosynthesis often result in decreased fitness, due to production of toxic reactive oxygen species when photosynthesis is not adequately regulated. These problems are exacerbated under natural and outdoor production environments because of the complex nature of photosynthesis and the multifaceted interactions between genetic, environmental and physiological factors. Here, we demonstrate a high throughput biotechnological screening approach that simultaneously produces algal strains with highly increased autotrophic productivity and identifies genomic loci contributing to these improvements. Our results demonstrate that Chlamydomonas reinhardtii exhibits high directed evolutionary capacity readily accessed through breeding and selection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Antibacterial and antioxidant activities of Streptomyces sp. strain FR7 isolated from forest soil

Abstract Actinomycetes produce secondary metabolites with many bioactivities such as antimicrobial, which can be useful as alternatives against resistant bacterial strains. Therefore, the screening of new habitats is likely to provide new strains with high potential. In this work, the antimicrobial capacity was used to select Streptomyces sp. strains isolated from Raf Raf forest (Tunisia). From the strain displaying higher activity, FR7, an ethyl acetate extract was prepared under optimized culturing conditions (10 days at 30°C in ISP2 medium with initial pH 8), showing significant antimicrobial activity against Micrococcus luteus and Staphylococcus aureus (MIC = 5 μg ml−1), and Listeria monocytogenes and Pseudomonas aeruginosa (MIC = 20 μg ml−1). The extract displayed strong DPPH radical scavenging activity (IC50 = 1.3 μg ml−1) and protection of yeast cells from H2O2-induced oxidative stress determined by flow cytometry with dichlorofluorescein diacetate. The crude extract showed the presence of polyketides, with methylsalicylic acid as moiety, a large and diverse group of secondary metabolites with a wide range of bioactivities, including antioxidant and antibacterial. Based on 16S RNA gene sequences, strain FR7 was identified as belonging to genus Streptomyces with high resemblance to S. iakyrus. Streptomyces sp. FR7 has great potential as a source of antibacterial and antioxidant metabolites.

Weslati, Imen↗
DOE OSTI2022

Direct Air Capture of CO 2 and Delivery to Photobioreactors for Algal Biofuel Production (Final Report)

A mobile DAC system was designed and constructed to pair with photobioreactors growing algae for biofuel production. The DAC system was designed as a versatile research system, rather than a compact production unit. The system was constructed and mounted on a mobile skid to facilitate transportation to the algae production site. Within the DAC system, CO 2 was captured using amine-loaded monoliths that allow for high CO 2 uptake with low pressure drop. The CO 2 is collected using a Global Thermostat patented temperature/vacuum swing adsorption (TVSA) process. Amine sorbents and process conditions were optimized to produce 10 to >20 g CO 2 .h-1. The stability of the amine sorbents was also studied, with sorbent modifications made to improve stability to degradation by oxidation. An Algenol-developed Spirulina strain (Arthrospira platensis AB2293) was selected as the production cyanobacterial strain. AB2293 cultured was inoculum for outdoor production following PBR installation by Algenol. The PBR system was composed of three independent PBRs, with each PBR composed of four hanging bags internally recirculated by a liquid turnover pump. The PBRs were operated outdoors in Atlanta, GA, and integrated with the DAC system. Algae were grown with similar productivity using DAC-CO 2 as algae grown using pure CO 2 obtained commercially (Airgas). Throughout the experimental duration, no discoloration was observed, and cellular morphology was consistent between the two experimental treatments. An LCA including lifecycle greenhouse gas emissions, full life cycle inventory of the Algenol system and the DAC system and integrated DAC+PBR system was developed. Lifecycle greenhouse gas emissions were calculated for capture of carbon dioxide using input from Global Thermostat and the National Renewable Energy Laboratory. Three scenarios for energy provision were evaluated: a natural gas combined heat and power system sized to meet the electricity requirement, a natural gas combined heat and power system sized to meet the process heat requirements, and a system without on-site power that procures the electricity from the grid. In all three cases, as expected, the major contributor to the emissions is the energy consumption associated with the desorption step of the DAC process. The LCA quantified the reduced potential energy and greenhouse gas emissions of heat and mass integration of DAC and Algenol compared to unintegrated DAC and Algenol systems. A life cycle assessment of the role of sorbent productivity and lifetime was also developed. The development of more robust, oxidation resistant DAC sorbents may enable small reductions in energy requirements and in lifecycle greenhouse gas emissions and other environmental impacts. NREL performed techno-economic analysis (TEA) to identify the integration scenario most likely to achieve a 15% cost reduction target versus the baseline. Heat and mass integration of DAC and the PBR is critical to minimizing the MFSP. The baseline case utilizes no heat and mass integration, and the DAC system provides 100% of the CO 2 required by the photobioreactors (20 tonnes/hr), operating for 12 hours/day capturing 40 tonnes CO 2 /operating hour. The minimum fuel selling price (MFSP) of ethanol calculated from the baseline case was $10.68/gal ethanol. This corresponds with a targeted MFSP of $9.07/gal ethanol (or 15% reduction). This target was achieved by integration Option 2a with the greatest cost reduction of 17.8% (or $8.78/gal) and integration Option 2b with a cost reduction of 16.4% (or $8.93/gal). Reductions in MFSP are attributed to two primary process considerations: (a) CO 2 storage at night reduces the capital expenses associated with DAC (i.e., increasing on-stream time); and (b) distributed DAC scenarios (DAC-PBR integration Options 2a and 2b) make use of boiler and DAC CHP flue gas CO 2 (free). Direct air capture on-stream time was one of the largest contributors to MFSP reduction.

09 BIOMASS FUELS↗
DOE OSTI2024

Genome-resolved analysis of Serratia marcescens strain SMTT infers niche specialization as a hydrocarbon-degrader

Abstract Bacteria that are chronically exposed to high levels of pollutants demonstrate genomic and corresponding metabolic diversity that complement their strategies for adaptation to hydrocarbon-rich environments. Whole genome sequencing was carried out to infer functional traits of Serratia marcescens strain SMTT recovered from soil contaminated with crude oil. The genome size (Mb) was 5,013,981 with a total gene count of 4,842. Comparative analyses with carefully selected S. marcescens strains, 2 of which are associated with contaminated soil, show conservation of central metabolic pathways in addition to intra-specific genetic diversity and metabolic flexibility. Genome comparisons also indicated an enrichment of genes associated with multidrug resistance and efflux pumps for SMTT. The SMTT genome contained genes that enable the catabolism of aromatic compounds via the protocatechuate para-degradation pathway, in addition to meta-cleavage of catechol (meta-cleavage pathway II); gene enrichment for aromatic compound degradation was markedly higher for SMTT compared to the other S. marcescens strains analysed. Our data presents a valuable genetic inventory for future studies on strains of S. marcescens and provides insights into those genomic features of SMTT with industrial potential.

Genetics & Heredity↗
DOE OSTI2022

Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications

A variety of yeast species have been considered ideal hosts for metabolic engineering to produce value-added chemicals, including the model organism Saccharomyces cerevisiae, as well as non-conventional yeasts including Yarrowia lipolytica, Kluyveromyces marxianus, and Pichia pastoris. However, the metabolic capacity of these microbes is not simply dictated or implied by genus or species alone. Within the same species, yeast strains can display distinct variations in their phenotypes and metabolism, which affect the performance of introduced pathways and the production of interesting compounds. Moreover, it is unclear how this metabolic potential corresponds to function upon rewiring these organisms. These reports thus point out a new consideration for successful metabolic engineering, specifically: what are the best strains to utilize and how does one achieve effective metabolic engineering? Understanding such questions will accelerate the host selection and optimization process for generating yeast cell factories. In this review, we survey recent advances in studying yeast strain variations and utilizing non-type strains in pathway production and metabolic engineering applications. Additionally, we highlight the importance of employing portable methods for metabolic rewiring to best access this metabolic diversity. Finally, we conclude by highlighting the importance of considering strain diversity in metabolic engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multi-strain analysis of Pseudomonas putida reveals the metabolic and genetic diversity of the species

Pseudomonas putida is a gram-negative bacterial species increasingly utilized in biotechnology due to its robust growth, ability to degrade aromatic compounds, solvent tolerance, and genetic tractability. In this study, we report a comprehensive multi-strain analysis of 164 P. putida strains based on the reconstruction of a pan-putida metabolic network and the formulation of strain-specific genome-scale metabolic models (GEMs). We performed whole-genome sequencing and hybrid assembly for 40 strains, contributing a ~8% increase to the available genomic data for P. putida . Furthermore, high-throughput phenotypic profiling using the Biolog phenotype microarray system for 24 strains on 190 unique carbon sources, along with 15 aromatic compounds not present on Biolog plates, yielded 4,920 unique strain-phenotype measurements. These data were leveraged to curate GEMs for 24 representative strains, including a refined model for strain KT2440, which comprised 1,480 genes and 2,191 metabolites, achieving a prediction accuracy of 91.2% in carbon utilization. Systematic comparison of genomes and GEMs revealed both conserved core pathways and significant allelic and functional divergence across strains, highlighting strain-specific variation in aromatic degradation. While pathways for protocatechuate and phenylacetate degradation were widely conserved, metabolic capabilities for compounds such as ferulate, phenol, and cresols varied markedly, suggesting adaptation to distinct ecological niches. Alleleome analysis of enzymes, such as PcaI and PcaJ, revealed distinct, functionally similar clades, indicating possible convergent evolution or horizontal gene transfer. These results provide computable resources and informative models for selecting P. putida strains with desired traits for biomanufacturing and bioremediation and offer insights into the evolution and phylogeny of the P. putida species.

aromatics utilization↗
DOE OSTI2023

Disease phenotype of classical sheep scrapie is changed upon experimental passage through white-tailed deer

Prion agents occur in strains that are encoded by the structure of the misfolded prion protein (PrP Sc ). Prion strains can influence disease phenotype and the potential for interspecies transmission. Little is known about the potential transmission of prions between sheep and deer. Previously, the classical US scrapie isolate (No.13-7) had a 100% attack rate in white-tailed deer after oronasal challenge. The purpose of this study was to test the susceptibility of sheep to challenge with the scrapie agent after passage through white-tailed deer (WTD scrapie). Lambs of various prion protein genotypes were oronasally challenged with WTD scrapie. Sheep were euthanized and necropsied upon development of clinical signs or at the end of the experiment (72 months post-inoculation). Enzyme immunoassay, western blot, and immunohistochemistry demonstrated PrP Sc in 4 of 10 sheep with the fastest incubation occurring in VRQ/VRQ sheep, which contrasts the original No.13-7 inoculum with a faster incubation in ARQ/ARQ sheep. Shorter incubation periods in VRQ/VRQ sheep than ARQ/ARQ sheep after passage through deer was suggestive of a phenotype change, so comparisons were made in ovinized mice and with sheep with known strains of classical sheep scrapie: No. 13–7 and x-124 (that has a more rapid incubation in VRQ/VRQ sheep). After mouse bioassay, the WTD scrapie and x-124 isolates have similar incubation periods and PrP Sc conformational stability that are markedly different than the original No. 13–7 inoculum. Furthermore, brain tissues of sheep with WTD scrapie and x-124 scrapie have similar patterns of immunoreactivity that are distinct from sheep with No. 13–7 scrapie. Multiple lines of evidence suggest a phenotype switch when No. 13–7 scrapie prions are passaged through deer. This represents one example of interspecies transmission of prions resulting in the emergence or selection of new strain properties that could confound disease eradication and control efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Natural transformation as a tool in Acinetobacter baylyi : Evolution by amplification of gene copy number

For many years, the natural competency of Acinetobacter baylyi ADP1 facilitated studies of bacterial metabolism, biochemistry, and physiology. With the advent of synthetic biology, new opportunities arise to exploit the remarkable transformability and chromosomal plasticity of this model organism. In this chapter, we describe a recently developed method, “Evolution by Amplification and Synthetic Biology” (EASy). EASy allows the targeted amplification of chromosomal segments that give rise to new phenotypes. Increased gene dosage regulates protein expression in a rudimentary fashion by establishing a chromosomal array in which copy number adjusts via recombination between repeated DNA sequences. Selective conditions enrich for cells within the population that confer a growth advantage. Under continuous selective pressure, beneficial mutations may accumulate in any genomic region. Such mutations favor decreases in the average copy number of the target region. Thus, the genetic flexibility afforded by transient copy number variation helps accelerate the selection of engineered strains with desired traits during laboratory evolution. As a result, thanks to the extremely simple genetic manipulation of Acinetobacter baylyi ADP1, the EASy method can be readily implemented by researchers without the need for advanced instrumentation or complex cloning techniques.

59 BASIC BIOLOGICAL SCIENCES↗