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At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microfluidic platform for multiplexed detection in single cells and methods thereof

The present invention relates to a microfluidic device and platform configured to conduct multiplexed analysis within the device. In particular, the device allows multiple targets to be detected on a single-cell level. Also provided are methods of performing multiplexed analyses to detect one or more target nucleic acids, proteins, and post-translational modifications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multiplex RNA-guided genome engineering

Methods of multiplex genome engineering in cells using Cas9 is provided which includes a cycle of steps of introducing into the cell a first foreign nucleic acid encoding one or more RNAs complementary to the target DNA and which guide the enzyme to the target DNA, wherein the one or more RNAs and the enzyme are members of a co-localization complex for the target DNA, and introducing into the cell a second foreign nucleic acid encoding one or more donor nucleic acid sequences, and wherein the cycle is repeated a desired number of times to multiplex DNA engineering in cells.

Church, George M.↗
DOE OSTI2022

An antibody-free platform for multiplexed, sensitive quantification of protein biomarkers in complex biomatrices

Sensitive, multiplexed protein quantification remains challenging despite recent advancements in LC-MS assays for targeted protein biomarker quantification. High-sensitivity protein biomarker measurements usually require immuno-affinity enrichment of target protein; a process which is highly dependent on capture reagent and limited in capability to measure multiple analytes. Herein, we report a novel antibody-free platform, which measures multiple biomarkers from complex matrices employing a strategically optimized solid-phase extraction cleanup and orthogonal multidimensional LC-MS. Eight human protein biomarkers with different specifications were spiked into canine plasma as a model investigation system. The developed strategy achieved the desired sensitivity, robustness, and throughput via the following steps: (1) post digestion mixed-mode cation exchange-reverse phase SPE enrichment cleaned up the sample initially; (2) rapid, high-pH peptide fractionation further eliminated background components efficiently while selectively enriched signature peptides (SP) to provide sufficient sensitivity for multiple targets; and (3) trapping-micro-LC-MS analysis delivered high sensitivity comparable to a nano-LC-MS method but with much better robustness and throughput for the final analysis. Compared with a conventional LC-MS assay with direct protein digestion and limited clean-up, analysis with this antibody-free platform improved the LLOQ by 1–2 orders of magnitude for the eight protein biomarkers, reaching as low as 5 ng/mL in plasma, with feasible robustness and throughput. In conclusion, this platform was applied for the quantification of biomarkers of respiratory conditions in patients with various lung diseases, demonstrating real-world applicability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates

Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, here we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Multiplexing and Demultiplexing Signals for Radiography Application Using the Discrete Fourier Transform

Our goal is to develop an X-ray phase-contrast imaging system that can provide excellent soft tissue contrast of phase, attenuation, and small-angle scatter. We propose to replace the common system of G0, G1, and G2 gradings with a biprism array to replace the G1 grading and introduce a novel X-ray tube designed to replace the motion of the phase stepping grading G2. The proposed X-ray tube uses temporal multiplexing to provide simultaneous virtual “electronic phase stepping.” In this work the discrete Fourier transform is used to separate from the composite measurement individual X-ray phase contrast measurements sampled at different frequencies. The method performs a discrete Fourier transform of a composite refence sequence to obtain using the frequency amplitudes calibration factors needed to extract the X-ray phase contrast measurement amplitudes from the composite image. The composite reference sequence is the sum of the individual sequences, at different frequencies, with amplitudes of one. The method takes the discrete Fourier transform of this composite reference sequence; whereby, the amplitude of each frequency component is compared with the total sum of its stand-alone sequence amplitude. A calibration factor is determined so that the amplitude of this composite reference frequency times the calibration factor must equal the total sum of the sequence amplitude—the zero-frequency amplitude of the discrete Fourier transform of its stand-alone sequence. To demultiplex the composite measured signal these calibration factors are multiplied by the amplitudes of the frequency components of the discrete Fourier transform of the composite X-phase-contrast measurement to obtain the amplitude of each frequency encoded measurement. Using these calibration factors, we demonstrate with the discrete Fourier transform in Mathematica the extraction of individual images from a composite image that one would expect obtaining from our proposed new X-ray phase contrast imaging system. We then demonstrate as an example how using images from X-ray phase contrast data one can calculate phase, attenuation and the dark field images using grading phase step data supplied to use from Microworks, GmbH in Karlsruhe, Germany.

42 ENGINEERING↗
DOE OSTI2022

PARA: A New Platform for the Rapid Assembly of gRNA Arrays for Multiplexed CRISPR Technologies

Multiplexed CRISPR technologies have great potential for pathway engineering and genome editing. However, their applications are constrained by complex, laborious and time-consuming cloning steps. In this research, we developed a novel method, PARA, which allows for the one-step assembly of multiple guide RNAs (gRNAs) into a CRISPR vector with up to 18 gRNAs. Here, we demonstrate that PARA is capable of the efficient assembly of transfer RNA/Csy4/ribozyme-based gRNA arrays. To aid in this process and to streamline vector construction, we developed a user-friendly PARAweb tool for designing PCR primers and component DNA parts and simulating assembled gRNA arrays and vector sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Wireless Frequency‐Multiplexed Acoustic Array‐Based Acoustofluidics

Abstract Acoustofluidics has shown great potential in enabling on‐chip technologies for driving liquid flows and manipulating particles and cells for engineering, chemical, and biomedical applications. To introduce on‐demand liquid sample processing and micro/nano‐object manipulation functions to wearable and embeddable electronics, wireless acoustofluidic chips are highly desired. This paper presents wireless acoustofluidic chips to generate acoustic waves carrying sufficient energy and achieve key acoustofluidic functions, including arranging particles and cells, generating fluid streaming, and enriching in‐droplet particles. To enable these functions, the wireless acoustofluidic chips leverage mechanisms, including inductive coupling‐based wireless power transfer (WPT), frequency multiplexing‐based control of multiple acoustic waves, and the resultant acoustic radiation and drag forces. For validation, the wirelessly generated acoustic waves are measured using laser vibrometry when different materials (e.g., bone, tissue, and hand) are inserted between the WPT transmitter and receiver. Moreover, the wireless acoustofluidic chips successfully arrange nanoparticles into different patterns, align cells into parallel pearl chains, generate streaming, and enrich in‐droplet microparticles. This research is anticipated to facilitate the development of embeddable wireless on‐chip flow generators, wearable sensors with liquid sample processing functions, and implantable devices with flow generation and acoustic stimulation abilities for engineering, veterinary, and biomedical applications.

Li, Jiali↗
DOE OSTI2024

Signatures of Thermal and Electrical Crosstalk in a Microwave Multiplexed Hard X-ray Transition Edge Sensor Array

We investigate the crosstalk between Transition-Edge Sensor (TES) pixels in a 24-pixel hard X-ray spectrometer array fabricated at the Advanced Photon Source, Argonne National Laboratory. Analysis shows thermal cross talk, possibly associated with insufficient thermalization, and rare but larger in magnitude electrical crosstalk between specific perpetrator-victim pixel combinations, potentially due to defects in the bias wiring or microwave multiplexing circuit. We use a method based on group-triggering and averaging to isolate the crosstalk response despite only having access to X-ray photon illumination uniform across the entire array. This allows us to identify thermal and electrical crosstalk between pixel pairs in repeated measurements to the level of 1 part in 1000 or better. In the array under study, the magnitude of observed crosstalk is small but comparable to the resolving power of this pixel design (E/Delta E similar to\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$E/\Delta {}E \sim$$\end{document} 1000 at 20 keV) and so potentially responsible for a degradation in energy resolution of the array at high incident photon rates. Having proven the methods to identify and quantify crosstalk in our setup, we can now consider mitigations.

Triamkitsawat, Panthita↗
DOE OSTI2024

Monte–Carlo ray-tracing studies of multiplexed prismatic graphite analyzers for the cold-neutron triple-axis spectrometer at the High Flux Isotope Reactor

A modern cold triple-axis spectrometer to study quantum condensed matter systems is planned for the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. Here, we describe the conceptual principles and design of a secondary spectrometer using a multiplexed, prismatic analyzer system relying on graphite crystals and inspired by the successful implementation of the Continuous Angle Multiple Energy Analysis (CAMEA) spectrometers at the Paul Scherrer Institute. This project is currently known as MANTA for Multi-Analyzer Neutron Triple-Axis. Here, we report Monte-Carlo ray-tracing simulations on a simple but realistic sample scattering kernel to further illustrate the prismatic analyzer concept’s workings, calibration, and performance. Then, we introduce a new statistical analysis approach based on the prismatic analyzer concept to improve the number of final energies measured on the spectrometer. We also study possible evolutions in the CAMEA design relevant for MANTA.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2022

Internal Standard Triggered-Parallel Reaction Monitoring Mass Spectrometry Enables Multiplexed Quantification of Candidate Biomarkers in Plasma

Despite advances in proteomic technologies, clinical translation of plasma biomarkers remains low, partly due to a major bottleneck between the discovery of candidate biomarkers and costly clinical validation studies. Due to a dearth of multiplexable assays, generally only a few candidate biomarkers are tested, and the validation success rate is accordingly low. Previously, mass spectrometry-based approaches have been used to fill this gap but feature poor quantitative performance and were generally limited to hundreds of proteins. Here, we demonstrate the capability of an internal standard triggered-parallel reaction monitoring (IS-PRM) assay to greatly expand the numbers of candidates that can be tested with improved quantitative performance. The assay couples immunodepletion and fractionation with IS-PRM and was developed and implemented in human plasma to quantify 5176 peptides representing 1314 breast cancer biomarker candidates. Characterization of the IS-PRM assay demonstrated the precision (median % CV of 7.7%), linearity (median R 2 > 0.999 over 4 orders of magnitude), and sensitivity (median LLOQ < 1 fmol, approximately) to enable rank-ordering of candidate biomarkers for validation studies. Using three plasma pools from breast cancer patients and three control pools, 893 proteins were quantified, of which 162 candidate biomarkers were verified in at least one of the cancer pools and 22 were verified in all three cancer pools. The assay greatly expands capabilities for quantification of large numbers of proteins and is well suited for prioritization of viable candidate biomarkers.

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

Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment

There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity in a cell-type-specific manner to better understand and predict the function of complex biological systems such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (microdroplet processing in one pot for trace samples), multiplexed isobaric labeling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram levels of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 μm2) and differentiate unique protein abundance patterns in pancreas. Furthermore, the use of the microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Multiplexed Quantitative Analysis of Germline Single Amino Acid Variants by Targeted Proteomics in Nondepleted Human Plasma

Single amino acid variants (SAAVs) in protein sequences are often a direct result of single-nucleotide polymorphisms (SNPs). Certain germline SAAVs have shown biological relevance in different disease conditions but lack precise quantification in circulation, which could hinder functional investigations and progress in biomarker development. Here, we have developed a multiplexed liquid chromatography-selected reaction monitoring (LC-SRM) assay that monitors 5 wild-type and variant peptide pairs (Complement Factor B: CFB-R32Q/R32W, Clusterin: CLU-N317H, Fetuin B: FETUB-K360R, and Kininogen: KNG1-L212P) in nondepleted human plasma. The assay was optimized for imprecision, linearity, stability, and calibration assessments with CVs of under 20%. The wild-type and variant peptide pairs were characterized in a set of healthy individual plasma samples. These target identifications were also validated by SNP genotyping with more than 99% accuracy. For all protein targets, we observed significantly lower concentrations of WT species in the presence variant peptides. In CFB, the concentration of R32Q was significantly lower than its counterpart R32W variant and WT species. Furthermore, our results distinguished phenotypes of homozygosity and heterozygosity of the SAAV presence through direct concentration level characterization. These findings provide some insights into how SAAVs affect quantitative assessments of target peptides. The assay demonstrates a platform for proteogenomic analyses with potential applications in both research and clinical settings.

genetics↗
DOE OSTI2020

Multiplex Evolution of Antibody Fragments Utilizing a Yeast Surface Display Platform

Advances in high-throughput synthetic biology technologies based on the CRISPR/Cas9 system have enabled a comprehensive assessment of mutations conferring desired phenotypes, as well as a better understanding of genotype-phenotype correlations in protein engineering. Engineering antibodies to enhance properties such as binding affinity and stability plays an essential role in therapeutic applications. Here we report a method, multiplex navigation of antibody structure (MINAS), that combines a CRISPR/Cas9-based trackable editing method and fluorescent-activated cell sorting (FACS) of yeast-displayed libraries. We designed mutations in all of the complementarity-determining and framework regions of a well-characterized scFv antibody and mapped the contribution of these regions to enhanced properties. We identified specific mutants that showed higher binding affinities up to 100-fold compared to the wild-type. This study expands the applicability of CRISPR/Cas9-based trackable protein engineering by combining it with a surface display platform.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multiplex base editing to convert $\mathrm{TAG}$ into $\mathrm{TAA}$ codons in the human genome

Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and highly multiplex editing in mammalian cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis

Enzymes with high activity are readily produced through protein engineering, but intentionally and efficiently engineering enzymes for an expanded substrate scope is a contemporary challenge. One approach to address this challenge is Substrate Multiplexed Screening (SUMS), where enzyme activity is measured on competing substrates. SUMS has long been used to rigorously quantitate native enzyme specificity, primarily for in vivo settings. SUMS has more recently found sporadic use as a protein engineering approach but has not been widely adopted by the field, despite its potential utility. Here, we develop principles of how to design and interpret SUMS assays to guide protein engineering. This rich information enables improving activity with multiple substrates simultaneously, identifies enzyme variants with altered scope, and indicates potential mutational hot-spots as sites for further engineering. These advances leverage common laboratory equipment and represent a highly accessible and customizable method for enzyme engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A substrate-multiplexed platform for profiling enzymatic potential of plant family 1 glycosyltransferases

Plants have expanded various biosynthetic enzyme families to produce a wide diversity of natural products; however, most enzymes encoded in plant genomes remain uncharacterized, highlighting the need for new functional genomic approaches. Here, we report a platform enabling the rapid functional characterization of plant family 1 glycosyltransferases, which serve important roles in plant development, defense, and communication. Using substrate-multiplexed reactions, mass spectrometry, and automated analysis, we screen 85 enzymes against a diverse library of 453 natural products, for a total of nearly 40,000 possible reactions. The resulting dataset reveals a widespread promiscuity and a strong preference for planar, hydroxylated aromatic substrates among family 1 glycosyltransferases. We also characterize glycosyltransferases with an unusually wide substrate scope and with a non-canonical Cys-Asp catalytic dyad. This work establishes a widely-applicable enzymatic screening pipeline, reflects the immense glycosylation capability of plants, and has implications in biocatalysis, metabolic engineering, and gene discovery.

Sirirungruang, Sasilada↗
DOE OSTI2021

Simulations of wavelength-multiplexed holography for single-shot spatiotemporal characterization of NIF’s advanced radiographic capability (ARC) laser

We simulate the use of a newly developed single-shot wavelength-multiplexed holography-based diagnostic, STRIPED FISH, to fully characterize the as-delivered laser pulses of the National Ignition Facility’s Advanced Radiographic Capability (NIF-ARC) laser. To that end, we have performed simulations of the NIF-ARC pulse incorporating (a) a time-integrated spatial-profile measurement and a complete temporal-intensity-and-phase measurement using a frequency resolved optical gating, but without any spatiotemporal pulse characterizations, and (b) simulated first-order spatiotemporal distortions, which could be measured on a single shot if a STRIPED FISH device were deployed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

First results from a multiplexed and massive instrument with sub-electron noise Skipper-CCDs

Here, we present a new instrument composed of a large number of sub-electron noise Skipper-CCDs operated with a two stage analog multiplexed readout scheme suitable for scaling to thousands of channels. New, thick, 1.35 Mpix sensors, from a new foundry, are glued into a Multi-Chip Module (MCM) printed circuit board on a ceramic substrate which has 16 sensors each. The instrument, that can hold up-to 16 MCMs, a total of 256 Skipper-CCD sensors (called a Super-Module with ≈ 130 grams of active mass and 346 Mpix), is part of the R&D effort of the OSCURA experiment which will have ≈ 94 super-modules. Experimental results with 10 MCMs and 160 Skipper-CCDs sensors are presented in this paper. This is already the largest ever built instrument with single electron sensitivity CCDs using nondestructive readout, both, in terms of active mass and number of channels.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗