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Results for “multiple displacement amplification”

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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5 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing

Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

DNA viruses from different stages of a wastewater treatment plant in southwest Ohio

Wastewater treatment plants (WWTPs) house diverse populations of microbial communities that are dynamic across treatment stages. Although viruses, especially non-pathogenic ones are relatively less studied compared to their bacterial counterparts, they are equally important players in WWTP microbiomes. In this study, we sampled influent, activated sludge, and effluent stages of a WWTP in southwest Ohio to sequence their viral population using multiple displacement amplification (MDA) and metagenomic approaches. We recovered 1003 viral genomes, the majority of which were ssDNA (single-stranded DNA) viruses that formed distinct clusters representing novel species and phylogenetic groups not closely related to known human gut or terrestrial viruses. Additionally, tracking viruses across treatment stages showed several persisted across multiple treatment stages. These results suggest that further studies are needed to understand the persistence of viral populations, particularly non-pathogenic ones, across different stages of WWTPs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

scMicrobe PTA: near complete genomes from single bacterial cells

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1980

Strouhal number influence on flight effects on jet noise radiated from convecting quadrupoles

The paper reports a complementary extension of previous work to include the high-frequency features reflected in the discussion of the higher Strouhal number influence on flight effects. It is found that, in addition to the usual features of flight effects on noise from ordinary flows, the high Strouhal number flows exhibit some more interesting features which are uniquely characteristic to them. The additional features are as follows: (1) Flight effects are more favorable to hot jets than to cold jets; (2) the higher the Strouhal number of the jet flow, the lesser the forward arc amplification due to flight; (3) as the Strouhal number increases, the peak amplification angle in the forward quadrant and the peak suppression angle in the aft quadrant move toward 90 deg and get closer, thus reducing the amplification exposure to a constricted angular region; (4) the silence zone is disturbed and displaced from its normal position parallel to the jet flow to give rise to multiple crossings of flight curves with the static line; and (5) the occurrence of multiple crossings is a strange phenomenon solely characteristic of high Strouhal number with high subcritical jet flows in flight.

Dash, R.↗
DOE OSTI2025

Fundamental limits to the generation of highly displaced bright squeezed light using linear optics and parametric amplifiers

High-quality squeezed light is an important resource for a variety of applications. Multiple methods for generating squeezed light are known, having been demonstrated theoretically and experimentally. However, the effectiveness of these methods—in particular, the inherent limitations to the signals that can be produced—has received little consideration. Here we present a comparative theoretical analysis for generating a highly displaced squeezed light from a linear optical method—a beamsplitter mixing a squeezed vacuum and a strong coherent state—and well-studied parametric amplification methods including an optical parametric oscillator, an optical parametric amplifier, and a dissipative optomechanical squeezer seeded with coherent states. We show that the quality of highly displaced squeezed states that can be generated using these methods is limited on a fundamental level by the physical mechanism utilized; across all methods there are significant trade-offs between displacement, squeezing, and overall uncertainty. We explore the nature and extent of these trade-offs specific to each mechanism and identify the optimal operation modes for each. Finally, we identify the conditions for minimum-uncertainty squeezing in arbitrary parametric amplifying systems and show that displacing the output signal will in general violate these conditions, adding noise and degrading squeezing. Published by the American Physical Society 2025

Young, Steve M. (ORCID:0000000173839366)↗