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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 343 records · Page 19
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Multiplexed Knockouts in the Model Diatom Phaeodactylum by Episomal Delivery of a Selectable Cas9

Marine diatoms are eukaryotic microalgae that play significant ecological and biogeochemical roles in oceans. They also have significant potential as organismal platforms for exploitation to address biotechnological and industrial goals. In order to address both modes of research, sophisticated molecular and genetic tools are required. We presented here new and improved methodologies for introducing CRISPRCas9 to the model diatom Phaeodactylum tricornutum cells and a streamlined protocol for genotyping mutant cell lines with previously unknown phenotypes. First, bacterialconjugation was optimized for the delivery of Cas9 by transcriptionally fusing Cas9 to a selectable marker by the 2A peptide. An episome cloning strategy using both negative and positive selection was developed to streamline CRISPR-episome assembly. Next, cell line picking and genotyping strategies, that utilize manual sequencing curation, TIDE sequencing analysis, and a T7 endonuclease assay, were developed to shorten the time required to generate mutants. Following this new experimental pipeline, both singlegene and two-gene knockout cell lines were generated at mutagenesis efficiencies of 48% and 25%, respectively. Lastly, a protocol for precise gene insertions via CRISPRCas9 targeting was developed using particle-bombardment transformation methods. Overall, the novel Cas9 episome design and improved genotyping methods presented here allow for quick and easy genotyping and isolation of Phaeodactylum mutant cell lines (less than 3 weeks) without relying on a known phenotype to screen for mutants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Synergistic Integration of Chemo-Resistive and SERS Sensing for Label-Free Multiplex Gas Detection

Practical sensing applications such as real-time safety alerts and clinical diagnoses require sensor devices to differentiate between various target molecules with high sensitivity and selectivity, yet conventional devices such as oxide-based chemo-resistive sensors and metal-based surface-enhanced Raman spectroscopy (SERS) sensors usually do not satisfy such requirements. In this report a label-free, chemo-resistive/SERS multimodal sensor based on a systematically assembled 3D cross-point multifunctional nanoarchitecture (3D-CMA), which has unusually strong enhancements in both “chemo-resistive” and “SERS” sensing characteristics is introduced. 3D-CMA combines several sensing mechanisms and sensing elements via 3D integration of semiconducting SnO 2 nanowire frameworks and dual-functioning Au metallic nanoparticles. It is shown that the multimodal sensor can successfully estimate mixed-gas compositions selectively and quantitatively at the sub-100 ppm level, even for mixtures of gaseous aromatic compounds (nitrobenzene and toluene) with very similar molecular structures. This is enabled by combined chemo-resistive and SERS multimodal sensing providing complementary information.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Multiplexed Quantitative Proteomics in Prostate Cancer Biomarker Development

Prostate cancer (PCa) is the most common non-skin cancer among men in the United States. However, the widely used protein biomarker in PCa, prostate-specific antigen (PSA), while useful for initial detection, its use alone cannot detect aggressive PCa and can lead to overtreatment. This chapter provides an overview of PCa protein biomarker development. It reviews the state-of-the-art liquid chromatography-mass spectrometry-based proteomics technologies for PCa biomarker development, such as enhancing the detection sensitivity of low-abundance proteins through antibody-based or antibody-independent protein/peptide enrichment, enriching post-translational modifications such as glycosylation as well as information-rich extracellular vesicles, and increasing accuracy and throughput using advanced data acquisition methodologies. This chapter also summarizes recent PCa biomarker validation studies that applied those techniques in diverse specimen types, including cell lines, tissues, proximal fluids, urine, and blood, developing novel protein biomarkers for various clinical applications, including early detection and diagnosis, prognosis, and therapeutic intervention of PCa.

Prostate cancer, SRM, PRM, DIA, protein biomarker↗
DOE OSTI2023

Multiplexed fitness profiling by RB-TnSeq elucidates pathways for lignin-related aromatic catabolism in Sphingobium sp. SYK-6

Bioconversion of lignin-related aromatic compounds relies on robust catabolic pathways in microbes. Sphingobium sp. SYK-6 (SYK-6) is a well-characterized aromatic catabolic organism that has served as a model for microbial lignin conversion, and its utility as a biocatalyst could potentially be further improved by genome-wide metabolic analyses. To this end, we generate a randomly barcoded transposon insertion mutant (RB-TnSeq) library to study gene function in SYK-6. The library is enriched under dozens of enrichment conditions to quantify gene fitness. Several known aromatic catabolic pathways are confirmed, and RB-TnSeq affords additional detail on the genome-wide effects of each enrichment condition. Selected genes are further examined in SYK-6 or Pseudomonas putida KT2440, leading to the identification of new gene functions. The findings from this study further elucidate the metabolism of SYK-6, while also providing targets for future metabolic engineering in this organism or other hosts for the biological valorization of lignin.

09 BIOMASS FUELS↗
DOE OSTI2025

Quantitative multiplexed analysis of gene and protein expression patterns in Yarrowia lipolytica

In this report, we present coordinated observations of protein and mRNA transcript counts at the single-cell level in the oleaginous yeast model Yarrowia lipolytica. The transcription factor Xbp1p regulates entry into a quiescent state, representing a shift of resources to sequestration of nutrients rather than cell division. We observed the responses of wild-type and Δxbp1 cells to protein (by fluorescence) and transcript quantification and localization at both single-cell and population-averaged levels. Data were collected via single-molecule fluorescence in situ hybridization (smFISH) and qPCR under nitrogen depletion, a condition that drives lipid accumulation. These techniques reveal a complex and heterogeneous population of Xbp1p dynamics and downstream regulation. Our findings highlight the need for single-cell resolution analyses to describe cellular dynamics and regulatory processes.

Yarrowia lipolytica↗
DOE OSTI2023

Grafting-To and From for Multiplexed Chemical-Warfare-Agent Responsive Polymer Brushes

Surface-tethered polymers have important applications in functional polymer coatings, particularly for the development of chemically responsive surfaces. Here, we combined the traditional grafting-to and grafting-from methods to create a new surface grafting strategy, termed grafting-to and from, using surface-initiated ring-opening metathesis polymerization (SI-ROMP). In this method, poly(pentafluorophenyl methacrylate) is grafted to an amine terminated surface. Surplus reactive esters after reaction with surface amines render this polymer a connecting or tie layer that can be further reacted to provide dense ROMP initiation sites. This amplification of grafting sites results in thick and environmentally stable polymer brushes upon SI-ROMP. With the goal of developing polymer-grafted breathable membranes that autonomously react to multiple chemical warfare agents (CWAs), we demonstrate the benefit of this method by employing amine reactive monomers in the grafting-from step. This enables diverse postsynthetic functionalization for the facile screening of chemical motifs to enhance response capabilities to mustard blister agents. Surface-tethered triarylmethanol-containing polymers with four distinct functional groups are prepared and challenged with the vapor of 2-chloroethyl ethyl sulfide (CEES), a simulant of mustard agent, in humid air. Importantly, hydroxyl groups effectively improve CWA response and the resulting polymer brushes show chain collapse after both CEES and diethylchlorophosphate (DCP) treatment. Our results illustrate that the grafting-to and from method can be used to grow functional and robust polymer coatings for various applications.

36 MATERIALS SCIENCE↗