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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2025

Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Data for "Efficient Mutagenesis and Genotyping of Maize Inbreds Using Biolistics, Multiplex CRISPR/Cas9 Editing, and Indel-Selective PCR"

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

gene editing↗
DOE OSTI2025

Nanopore Activity Assays for Detection of Biomarker Protease Activity: Design and Testing of Substrates for Both Nanopore Sequencing and PCR-Based Detection Methods

The work performed in this project has demonstrated the ability to construct proteolytic enzyme substrates that are PCR and sequencing-readable reporter molecules. Specifically, the goal was to detect those reporter molecules via PCR and Oxford Nanopore Technologies MinION sequencing methods following exposure to the biomarker protease thrombin. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. The action of thrombin on the peptide portion of the molecule released the oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing. Additional steps to remove background release of reporter molecules during the assay was used to improve the difference in detected oligonucleotide reporter following protease activity. Additional steps in assay development will be to (1) test the assay in an appropriate matrix, (2) investigate detection using additional DNA sequencing platforms and (3) demonstrate multiplexed detection of multiple protease markers in a single reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Real-time PCR assays that detect genes for botulinum neurotoxin A–G subtypes

The role of Real-Time PCR assays for surveillance and rapid screening for pathogens is garnering more and more attention because of its versatility and ease of adoption. The goal of this study was to design, test, and evaluate Real-Time TaqMan PCR assays for the detection of botulinum neurotoxin (bont/A-G) genes from currently recognized BoNT subtypes. Assays were computationally designed and then laboratory tested for sensitivity and specificity using DNA preparations containing bont genes from 82 target toxin subtypes, including nine bivalent toxin types; 31 strains representing other clostridial species; and an extensive panel that consisted of DNA from a diverse set of prokaryotic (bacterial) and eukaryotic (fungal, protozoan, plant, and animal) species. In addition to laboratory testing, the assays were computationally evaluated using in silico analysis for their ability to detect bont gene sequences from recently identified toxin subtypes. Seventeen specific assays (two for each of the bont/C, bont/D, bont/E, and bont/G subtypes and three for each of the bont/A, bont/B, and bont/F subtypes) were designed and evaluated for their ability to detect bont genes encoding multiple subtypes from all seven serotypes. These assays could provide an additional tool for the detection of botulinum neurotoxins in clinical, environmental and food samples that can complement other existing methods used in clinical diagnostics, regulatory, public health, and research laboratories.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Extraction of Pure Plastic Resins From PCR Plastic Waste by Solvent-Targeted Recovery and Precipitation (STRAP)

For this work, we have been developing a solvent‐based plastic recycling technology called STRAP. The technology is based on dissolving a targeted plastic resin in a specific solvent that does not dissolve other resins. We have demonstrated STRAP in thousands of bench scale experiments for a large variety of wastes. Recently we have demonstrated the technology for PCR, using mixed plastic wastes (MPWs), from a wet Material Recovery Facility (MRF). The process includes (1) infrared (IR) characterization to determine the plastic composition for accurate selection of the solvent to be used for the extraction of the pure resins. (2) Shredding to the right size and aspect ratio required for flowable and fast dissolvable process. (3) Mixing the MPW in the first solvent to dissolve the first resin. (4) Filtration of the solution plastic blend, to separate the nondissolved plastic from the solution. (5) Further filtration of the solution to remove micron‐sized particle of pigments and fibers. (6) Cooling for precipitation. (7) Filtration of pure resins. (8) Drying of a pure resin. (9) Extrusion of the resin to pellets. (10) Generating films or other products from the pure resin. Steps 1–10 can be considered as one‐cycle that extracted the first resin. (11) A second resin can be extracted with a respective solvent from the plastic that did not dissolve in the first cycle and following steps 1–10 described above. The process also includes characterization of interim and final products. The effort includes building a pilot system at 25 kg/h throughput. We will present specific results for various PCR.

IR characterization↗
DOE OSTI2024

Assessment of Different Application Grades of Post-Consumer Recycled (PCR) Polyolefins from Material Recovery Facilities (MRFs) in the United States

The recycling of plastics has been gaining traction in the following years as many companies, organizations, and governments are pushing toward a more circular economy. However, plastic recycling rates are still small compared to those of plastic production, especially for polyolefins, such as high-density polyethylene (HDPE) and polypropylene (PP). With the goal of finding applications for recycled plastic resin, recyclers can face some challenges associated with the heterogeneity in the polymer properties of plastic waste streams, which could hinder the full potential of recycling due to the lack of a consistent feedstock. Here, this study assessed how an additional sorting step of recycled HDPE and PP streams, separating them into two categories based on the previous application, impacts the recycled polymer properties, such as physical, molecular, and thermal. It was demonstrated that manually separating HDPE articles previously processed by extrusion blow molding (EBM) or injection molding (IM) and PP articles by thermoforming (TF) or IM could yield recycled resins with more consistent properties, considering the significant differences between them. This highlights that an additional sorting step would allow recyclers to target more premium or currently unattainable plastic processing applications with postconsumer recycled (PCR) resins, which could significantly promote an increase in plastic recycling rates. Nevertheless, the development of new technologies is needed to automate this extra sorting step, as with the increase in scale manual sortation could not be feasible and cost-effective, reducing the attractiveness of using PCR resins in comparison to virgin ones.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Digital Droplet PCR and Mesocosm-Based Methods to Evaluate Biocontainment Strategies in a Native Soil Ecosystem

Genetically modified industrial production microbes and their associated bioproducts have emerged as an integral component of a sustainable bioeconomy. However, the rapid development of these innovative technologies raises biosecurity concerns, namely, the risk of environmental escape. Thus, the realization of a bioeconomy hinges not only on the development and deployment of microbial production hosts, but also on the development of secure biosystems and biocontainment designs. Current laboratory-based biocontainment testing systems do not accurately reflect the complexities found in natural environments, necessitating an environmentally relevant analysis pipeline that allows for the detection of rare escapees within a complex soil microbiome and differentiation between closely related strains. To this end, we have developed an approach that utilizes soil mesocosms and integrated digital droplet PCR (ddPCR) system to evaluate the efficacy of novel biocontainment strategies. We demonstrate the utility of this approach by modeling contamination with industrial microbial chasses versus their biocontained counterparts. Here we demonstrate the broad utility of this system by highlighting findings from strains of Saccharomyces cerevisiae that are contained with an inducible toxin anti-toxin system, strains of Synechocystis sp. PCC 6803 contained via gene knockout or toxin anti-toxin system, and strains of Escherichia coli that are contained via genomic recoding. We also show that ddPCR can be used to detect gene copies from E. coli equal to those counted by traditional spot plating assays. The resultant data demonstrates that this system has broad utility across diverse microbial chassis and biocontainment strategies and enables researchers to track the fate of our contaminating microbe with high sensitivity in the soil. The findings presented here support the use of this mesocosm-based approach to assess the environmental impact of industrial microbes and to validate biocontainment strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR)

An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 10 1 to 10 4 viruses per cell, and H1N1 ranging from 10 1 to 10 3 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

The Effects of Polyolefin Structure and Source on Pyrolysis-Derived Plastic Oil Composition

Seven types of plastics were pyrolyzed in a fluidized bed reactor: post-consumer recycled (PCR) high-density polyethylene (HDPE), PCR polypropylene (PP), virgin resins of varying molecular weights of HDPE, virgin resins of low-density polyethylene (LDPE), linear low-density polyethylene (LLDPE), and (PP). Pyrolysis produced non-condensable gases (C1-C3), liquid phase products (C4-C40), and solids (C40+ and chars), with alkane, alkene, alkadiene, aromatic, and multi-cycloaromatics as the predominant compounds. Polymer structure had the greatest impact on product distribution, with minimal influence from molecular weight. Branches in polyethylene (PE) acted as thermal defects initiating degradation. Higher branch density in PE led to increased concentrations of aromatics, branched alkanes, and internal alkenes. PP and PE exhibited distinct degradation mechanisms, with PP requiring less energy for decomposition and yielding more oil. Here, pyrolysis oil from PCR HDPE and PCR PP contained a higher proportion of branched compounds. Additives in PCR plastics may promote isomerization during pyrolysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

High Throughput Genome Releaser

In this study, we present the development of a High Throughput Genome Releaser, an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed for rapid, cost-effective, and efficient DNA extraction, optimized for subsequent PCR reactions. Our experimentation with various synthetic materials led us to select a particular type of plastic that mirrors the properties of glass cover slides, providing a smooth surface and effective compression capabilities. We engineered a 96-well device equipped with a 96-well plate and a top rod, operable both manually and automatically, which is compatible with widely used liquid-handling robot decks. This compatibility enhances ease of use in high-throughput PCR setups. Additionally, we developed software to support its automatic functions. The genome releaser facilitates the extraction of PCR-amplifiable genomic DNA from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells. This versatility could significantly advance biomanufacturing processes.

42 ENGINEERING↗
DOE OSTI2026

Upcycling plastic waste into polyhydroxyalkanoates with high carbon conversion via CO 2 plasma-enabled deconstruction

Plastic deconstruction into fermentable intermediates is a key step for microbial bio-upcycling into value-added products. In this study, CO 2 plasma deconstruction was used as an electrified route to convert polyethylene into oxygenated intermediates and liquid (OIL). The resulting OIL was rich in fatty acids, fatty alcohols, and hydrocarbons, making it a suitable feedstock for medium-chain-length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida NRRL B-14688 and Pseudomonas resinovorans NRRL B-2649. Compared with batch fermentation and monocultures, fed-batch co-cultivation markedly improved biomass formation and PHA accumulation, likely due to complementary substrate utilization, particularly hydrocarbon conversion by P. resinovorans. Using virgin polyethylene-derived OIL (Vir-OIL), the co-culture achieved 40.11% mcl-PHA content and about 18% PHA yield based on total OIL fed. More importantly, OIL produced from post-consumer single-use plastic films (PCR-OIL) was directly fermented and well supported the cell growth and PHA accumulation, achieving 38.11% PHA content and about 14.7% PHA yield. Based on emulsified OIL fractions, PHA yields for Vir-OIL and PCR-OIL were comparable (∼28%). PHA granules were extracted from PCR-OIL-grown cells with high recovery (88.25%) and purity (94.8%). Five monomers were identified in the polymer, including 3-hydroxyhexanoate (3HHx), 3-hydroxyoctanoate (3HO), 3-hydroxydecanoate (3HD), 3-hydroxydodecanoate (3HDD), and 3-hydroxytetradecanoate (3HTD), with 3HO (44.28%) and 3HD (40.60%) as the dominant units. The polymer exhibited moderate molecular weight and narrow dispersity (M n = 65.4 kDa, M w = 92.1 kDa, Đ = 1.40) and low crystallinity (T m ≈ 76.6 °C, X c ≈ 15.5%). These characteristics indicate elastomer-like behavior, making the material suitable for flexible applications such as films, coatings, adhesives, and blend modifiers. Overall, this study establishes a CO 2 plasma-assisted route for generating fermentable polyethylene-derived intermediates and demonstrates that fed-batch co-culture fermentation can effectively funnel plastic-derived carbon into mcl-PHA.

42 ENGINEERING↗
DOE OSTI2025

A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data

Wastewater testing can be used to monitor SARS-CoV-2 infections in communities. Data from PCR-based wastewater testing are usually available to public health authorities within 5–7 days after excreta and other body fluids enter the sewer. While PCR-based methods can accurately detect and quantify SARS-CoV-2, sequencing-based methods are usually required to distinguish between variants, delaying the results and adding cost to the process. We developed and assessed a novel, customizable digital PCR (dPCR)-based genotyping method for SARS-CoV-2 variant detection in wastewater, which is more cost-effective, faster, and more accessible than sequencing. This approach was applied to more than 1,400 wastewater samples

Wilton, Rose↗
DOE OSTI2024

A cell-based Papain-like Protease (PLpro) activity assay for rapid detection of active SARS-CoV-2 infections and antivirals

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants are a continuous threat to human life. An urgent need remains for simple and fast tests that reliably detect active infections with SARS-CoV-2 and its variants in the early stage of infection. Here we introduce a simple and rapid activity-based diagnostic (ABDx) test that identifies SARS-CoV-2 infections by measuring the activity of a viral enzyme, Papain-Like protease (PLpro). The test system consists of a peptide that fluoresces when cleaved by SARS PLpro that is active in crude, unprocessed lysates from human tongue scrapes and saliva. Test results are obtained in 30 minutes or less using widely available fluorescence plate readers, or a battery-operated portable instrument for on-site testing. Proof-of-concept was obtained in a study on clinical specimens collected from patients with COVID-19 like symptoms who tested positive (n = 10) or negative (n = 10) with LIAT RT-PCR using nasal mid turbinate swabs. When saliva from these patients was tested with in-house endpoint RT-PCR, 17 were positive and only 5 specimens were negative, of which 2 became positive when tested 5 days later. PLpro activity correlated in 17 of these cases (3 out of 3 negatives and 14 out of 16 positives, with one invalid specimen). Despite the small number of samples, the agreement was significant (p value = 0.01). Two false negatives were detected, one from a sample with a late Ct value of 35 in diagnostic RT-PCR, indicating that an active infection was no longer present. The PLpro assay is easily scalable and expected to detect all viable SARS-CoV-2 variants, making it attractive as a screening and surveillance tool. Additionally, we show feasibility of the platform as a new homogeneous phenotypic assay for rapid screening of SARS-CoV-2 antiviral drugs and neutralizing antibodies.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Surface Trap Dynamics and Gamma‐Ray Detection Enhancement in Passivated FAPbBr 3 Perovskite Crystals

Perovskite‐based direct radiation detectors offer a compelling platform for room‐temperature gamma spectroscopy due to their high sensitivity, tunable optoelectronic properties, and compatibility with solution processing. While prior studies on formamidinium lead tribromide (FAPbBr 3 ) have shown that surface passivation mitigates deep trap state impact on the charge collection efficiency (CCE), the influence of surface‐based shallow traps on time‐resolved detector response remains largely unexplored. In this article, a digital signal processing (DSP) method is applied to analyze waveform rising edge dynamics in FAPbBr 3 single‐crystal detectors, identifying prompt and delayed charge collection components. Using the second derivative of the collected charge signal, the onset of shallow trap reemission is isolated, occurring 1.1 µs after carrier generation. Surface passivation suppressed deep trap states, shifting carrier occupancy toward shallower traps and extending the temporal window of delayed charge collection. This delayed contribution correlates with measurable changes in the temporal and amplitude distributions of detector events. By leveraging time‐domain filtering informed by these dynamics, a selective enhancement in signal quality and gamma peak‐to‐Compton ratio (PCR) is achieved, while preserving over 90% of photoelectric events. An improvement in the PCR to 1.80, from the original 1.09, is enabled by focusing on high collection efficiency events corresponding to reemitted carriers in the 1.1 to 3 µs range after the generation event. These results demonstrate a pathway for leveraging shallow trap dynamics to enhance spectral fidelity in time‐resolved perovskite detectors.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Upcycling of Waste Plastics into Carboxylic Acids for Biodegradable Surfactants

This work outlines a process for producing high‐purity (>95%) carboxylate surfactants from post‐consumer recycled high‐density polyethylene (PCR‐HDPE). The approach involves the thermal depolymerization of PCR‐HDPE via pyrolysis, followed by fractional distillation to isolate C9–C14 olefins. These olefins undergo hydroformylation using cobalt carbonyl catalysts to generate aldehydes, which are subsequently oxidized to carboxylic acids using Pinnick oxidation under mild aqueous‐phase conditions. Neutralization of the resulting carboxylic acids with sodium hydroxide produces plastic‐derived carboxylate surfactants (PDCs) in the form of sodium carboxylates. Subsequent purification steps ensure surfactant‐grade purity and enable accurate assessment of physicochemical properties. The resulting PDCs are evaluated for critical micelle concentration (CMC), foamability, surface tension reduction, and calcium ion tolerance, demonstrating competitive behavior with conventional anionic carboxylate surfactants. This route provides a sustainable alternative for surfactant production, reducing reliance on fossil‐derived feedstocks and valorizing plastic waste streams through chemical upcycling.

Biodegradable surfactants↗
DOE OSTI2024

Robust surfactant-assisted one-pot sample preparation for label-free single-cell and nanoscale proteomics

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk cells. However, such bulk measurement obscures cell to cell heterogeneity, precluding proteome profiling of single cells and small numbers of cells of interest. To address this issue, in recent 5 years there are a surge of small sample preparation methods developed for robust effective collection and processing of single cells and small numbers of cells for in-depth MS-based proteome profiling. Based on their broad accessibility, they can be categorized into two types: specific device- and standard PCR tube- or multi-well plate-based methods. Herein we describe the detailed protocol of our recently developed, easily adoptable, Surfactant-assisted One-Pot (SOP) sample preparation coupled with MS method termed SOP-MS for label-free single-cell and nanoscale proteomics. SOP-MS capitalizes on the combination of a MS-compatible surfactant, DDM (n-Dodecyl-ß-D-maltoside), and standard low-bind PCR tube or multi-well plate for ‘all-in-one’ one-pot sample preparation without sample transfer. With its robust and convenient features, SOP-MS can be readily implemented in any MS laboratory for single-cell and nanoscale proteomics. With further improvements in MS detection sensitivity and sample throughput, we believe that SOP-MS could open an avenue for single-cell proteomics with broad applicability in the biological and biomedical research.

Single-cell proteomics, nanoscale proteomics, SOP-↗