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At least 73 records · Page 4
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 OSTI2024

SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network

ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

Microbiology↗
DOE OSTI2024

raogroupuiuc/yl_variantcalling

NGS analysis for mutation analysis in Yarrowia lipolytica evolved strains. Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.

Deewan, Anshu↗
DOE OSTI2024

HWO Pupil Chopping Wavefront Sensing and Control FY24 Mini-Project Writeup

This document is a summary of work completed in June through July 2024 to assess the feasibility of implementing non-coronagraphic pupil chopping (PC) for Habitable Worlds Observatory (HWO) primary mirror segment stabilization with an on- and/or off-axis Natural Guide Star (NGS) or Laser Guide Star (LGS). This work considers three different PC configurations: (1) a non-common path (NCP) continuous low-order Deformable Mirror (DM), (2) using the telescope’s primary mirror (M1) segment(s), and (3) using a NCP low-order segmented DM. We show that option 2 likely needs a LGS for guiding, while options 1 and 3 may be able to guide on NGSs. We also separately evaluate spectral bandwidth limitations in the absence of photon noise, showing that the technique is limited to Δλ/λ ≲ 25% in a standard imaging configuration but Δλ/λ ≲ 150% when using a NCP Wynne corrector.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Diversity of Sordariales Fungi: Identification of Seven New Species of Naviculisporaceae Through Morphological Analyses and Genome Sequencing

Thanks to next-generation sequencing (NGS) technologies, the diversity of fungi can now be investigated through the analysis of their genome sequences. Naviculisporaceae is a family within the Sordariales, whose diversity is not well-known, with only one genome sequence published for this family. Here, we report on the isolation and cultivation of 20 new strains of Naviculisporaceae. Their genome sequences, as well as those of the five commercially available strains, were determined, thus providing complete genome sequences for 25 new Naviculisporaceae strains. Species delimitation was conducted using a combination of (1) ITS + LSU phylogenetic analysis of the new isolates along with other known species of the family, (2) comparisons between DNA barcode sequences of the new strains with those of the known species, and (3) average genome-wide nucleotide identity calculation. We built a phylogenomic tree and studied the organization of the mating-type locus. In vitro fruiting was obtained for 16 strains, enabling the definition of seven new species, namely Pseudorhypophila gallica, Pseudorhypophila guyanensis Rhypophila alpibus, Rhypophila brasiliensis, Rhypophila camarguensis, Rhypophila reunionensis and Rhypophila thailandica, as well as two new combinations, namely Pseudorhypophila latipes and Pseudorhypophila oryzae. Eight strains for which in vitro fruiting was not obtained may belong to additional new species. These results expand the known diversity of the Naviculisporaceae and greatly enlarge the genomic data available for the family.

Naviculisporaceae↗
NASA NTRS1979

Observations of far-infrared fine structure lines: o III88.35 micrometer and oI 63.2 micrometer

Observations of the O III 88.35 micrometer line and the O I63.2 micrometer were made with a far infrared spectrometer. The sources M17, NGC 7538, and W51 were mapped in the O III line with 1 arc minute resolution and the emission is found to be quite widespread. In all cases the peak of the emission coincides with the maximum radio continuum. The far infrared continuum was mapped simultaneously and in M17, NGC 7538, and W51 the continuum peak is found to be distinct from the center of ionization. The O III line was also detected in W3, W49, and in a number of positions in the Orion nebula. Upper limits were obtained on NGS 7027, NGC 6572, DR21, G29.9-0.0 and M82. The 63.2 micrometer O I line was detected in M17, M42, and marginally in DR21. A partial map of M42 in this line shows that most of the emission observed arises from the Trapezium and from the bright optical bar to the southeast.

Storey, J. W. V.↗
NASA NTRS1980

Red and nebulous objects in dark clouds - A survey

A search on the NGS-PO Sky Survey photographs has revealed 150 interesting nebulous and/or red objects, mostly lying in dark clouds and not previously catalogued. Spectral classifications are presented for 55 objects. These indicate a small number of new members of the class of Herbig-Haro objects, a significant number of new T Tauri stars, and a few emission-line hot stars. It is argued that hot, high-mass stars form preferentially in the dense cores of dark clouds. The possible symbiosis of high and low mass stars is considered. A new morphology class is defined for cometary nebulae, in which a star lies on the periphery of a nebulous ring.

Cohen, M.↗
NASA NTRS1983

Crustal dynamics project session 4 validation and intercomparison experiments 1979-1980 report

As part of the Crustal Dynamics Project, an experiment was performed to verify the ability of Satellite Laser Ranging (SLR), Very Long Baseline interferometry (VLBI) and Doppler Satellite Positioning System (Doppler) techniques to estimate the baseline distances between several locations. The Goddard Space Flight Center (GSFC) lasers were in operation at all five sites available to them. The ten baselines involved were analyzed using monthly orbits and various methods of selecting data. The standard deviation of the monthly SLR baseline lengths was at the 7 cm level. The GSFC VLBI (Mark III) data was obtained during three separate experiments. November 1979 at Haystack and Owens Valley, and April and July 1980 at Haystack, Owens Valley, and Fort Davis. Repeatability of the VLBI in determining baseline lengths was calculated to be at the 2 cm level. Jet Propulsion Laboratory (JPL) VLBI (Mark II) data was acquired on the Owens Valley to Goldstone baseline on ten occasions between August 1979 and November 1980. The repeatability of these baseline length determinations was calculated to be at the 5 cm level. National Geodetic Survey (NGS) Doppler data was acquired at all five sites in January 1980. Repeatability of the Doppler determined baseline lengths results were calculated at approximately 30 cm. An intercomparison between baseline distances and associated parameters was made utilizing SLR, VLBI, and Doppler results on all available baselines. The VLBI and SLR length determinations were compared on four baselines with a resultant mean difference of -1 cm and a maximum difference of 12 cm. The SLR and Doppler length determinations were compared on ten baselines with a resultant mean difference of about 30 cm and a maximum difference of about 60 cm. The VLBI and Doppler lengths from seven baselines showed a resultant mean difference of about 30 cm and maximum difference of about 1 meter. The intercomparison of baseline orientation parameters were consistent with past analysis.

Liebrecht, P.↗
NASA NTRS1988

The celestial reference frame defined by VLBI

VLBI currently produces the most accurate positions of celestial objects. From 1979 to 1987, 114 extragalactic radio sources have been observed with dual-frequency Mark III VLBI as part of the NASA Crustal Dynamics Project and the NGS POLARIS/IRIS program. The formal statistical errors of conventional celestial coordinates are as small as 0.3 milliarcseconds. The fundamental quantity measured by VLBI is the arc length between radio sources. Thus, it is suggested that VLBI be used to establish a coordinate reference frame based solely on radio positions, and that this system not necessarily be coupled to right ascension and declination.

Ma, C.↗
NASA NTRS1990

GPS-based orbit determination and point positioning under selective availability

Selective availability (SA) degrades the positioning accuracy for nondifferential users of the GPS Standard Positioning Service (SPS). The often quoted SPS accuracy available under normal conditions is 100 m 2DRMS. In the absence of more specific information, many prospective SPS users adopt the 100 m value in their planning, which exaggerates the error in many cases. SA error is examined for point positioning and dynamic orbit determination for an orbiting user. To minimize SA error, nondifferential users have several options: expand their field of view; observe as many GPS satellites as possible; smooth the error over time; and employ precise GPS ephemerides computed independently, as by NASA and the NGS, rather than the broadcast ephemeris. Simulations show that 3D point position error can be kept to 30 m, and this can be smoothed to 3 m in a few hours.

Bar-Sever, Yoaz E.↗
NASA NTRS1992

Advanced Communications Technology Satellite (ACTS)

An overview of the NASA ACTS program is presented. The key technologies of ACTS include spot beams, on-board baseband processing and routing, wide bandwidth (900 MHz), and Ka-band transponders. The discussion covers system description, current status of the spacecraft development, ACTS earth stations, NGS traffic terminal, USAT, land and aeronautical mobiles, high data rate and propagation receive only terminals, and ACTS experiments program.

Schertler, Ronald J.↗
NASA NTRS1996

Design and Development of a Baseband Processor for the Advanced Communications Technology Satellite

This paper describes the implementation of the operational baseband processor (BBP) subsystem on board the NASA Advanced Communications Technology Satellite (ACTS). The BBP supports the network consisting of the NASA ground station (NGS) low burst rate (LBR) terminals, and the T1 very small aperture terminals (VSAT's), to provide flexible, demand assigned satellite switched (SS), baseband processed frequency division modulated (FDM)/time division multiple access (TDMA) operations. This paper presents an overview of the baseband processor and includes a description of the data flow, functional block diagrams, and a discussion of the implementation of BBP. A discussion of the supporting technologies for the BBP is presented. A brief summary of BBP-level performance testing is also presented. Finally, a discussion of the implications of current technology on the BBP design, if it were to be developed today, is presented.

Lee, Kerry D.↗
NASA NTRS2000

WFPC2 Stellar Photometry with HSTphot

HSTphot, a photometry package designed to handle the undersampled PSFs found in WFPC2 images, is introduced and described, as well as some of the considerations that have to be made in order to obtain accurate PSF-fitting stellar photometry with WFPC2 data. Tests of HSTphot's internal reliability are made using multiple observations of the same field, and tests of external reliability are made by comparing with DoPHOT reductions of the same data. Subject headz'ngs: techniques: photometric

Dolphin, Andrew E.↗
NASA NTRS2000

ACTS Ka-Band Earth Stations: Technology, Performance, and Lessons Learned

The Advanced Communications Technology Satellite (ACTS) Project invested heavily in prototype Ka-band satellite ground terminals to conduct an experiments program with ACTS. The ACTS experiments program proposed to validate Ka-band satellite and ground-station technology, demonstrate future telecommunication services, demonstrate commercial viability and market acceptability of these new services, evaluate system networking and processing technology, and characterize Ka-band propagation effects, including development of techniques to mitigate signal fading. This paper will present a summary of the fixed ground terminals developed by the NASA Glenn Research Center and its industry partners, emphasizing the technology and performance of the terminals and the lessons learned throughout their 6-year operation, including the inclined orbit phase-of-operations. The fixed ground stations used for experiments by government, academic, and commercial entities used reflector-based offset-fed antenna systems with antennas ranging in size from 0.35 to 3.4 in. in diameter. Gateway earth stations included two systems referred to as the NASA Ground Station (NGS) and the Link Evaluation Terminal (LET).

Reinhart, Richard C.↗
NASA NTRS2001

The Secret Lives of Galaxies

The ground-based image in visible light locates the hub imaged with the Hubble Space Telescope. This barred galaxy feeds material into its hub, igniting star birth. The Hubble NICMOS instrument penetrates beneath the dust to reveal clusters of young stars. Footage shows ground-based, WFPC2, and NICMOS images of NGS 1365. An animation of a large spiral galaxy zooms from the edge to the galactic bulge.

Source record↗
NASA NTRS1961

A Theoretical Investigation of Vortex-Sheet Deformation Behind a Highly Loaded Wing and Its Effect on Lift

The induced drag polar is developed for wt-ngs capable of attaining extremely high loadings while possessing an elliptical distribution of circulation. This development is accomplished through a theoretical investigation of the vortex-wake deformation process and the deduction of the airfoil forces from the impulse and kinetic energy contents of the ultimate wake form. The investigation shows that the induced velocities of the wake limit the maximum lift coefficient to a value of 1.94 times the wing aspect ratio, for aspect ratios equal to or less than 6.5, and that the section properties of the airfoil limit the lift coefficient to 12.6 for aspect ratios greater than 6.5. Relations are developed for the rate of deformation of the vortex wake. It is also shown that linear wing theory is app1icable up to lift coefficients equal to 1.1 times the aspect ratio.

Cone, Clarence D., Jr.↗
NASA NTRS2004

Comparative NIR Detector Characterization for NGST

List of publications for final perfomance report are: Detectors for the JWST Near-Infrared Spectrometer Rauscher, B.J., Strada, P., Regan, M.W., Figer, D.F., Jakobsen, P., Moseley, H.S., & Boeker, T. 2004, SPIE Detectors for the JWST Near-Infrared Spectrometer Rauscher, B.J., Strada, P., Regan, M.W., Figer, D.F., Jakobsen, P., Moseley, H.S., & Boeker, T. 2004, AAS, 203, 124.07 Independent Testing of JWST Detector Prototypes Figer, D.F., Rauscher, B. J., Regan, M. W., Morse, E., Balleza, J., Bergeron, L., & Stockman, H. S. 2003 , SPIE, 5 167 The Independent Detector Testing Laboratory and the NGST Detector Program Figer, D.F., Agronin, M., Balleza, J., Barkhouser, R., Bergeron, L., Greene, G. R., McCandliss, S. R., Rauscher, B. J., Reeves, T., Regan, M. W., Sharma, U., Stockman, H. S. 2003, SPIE, 4850,981 Intra-Pixel Sensitivity in NIR Detectors for NGST Sharma, U., Figer, D.F., Sivaramakrishnan, A., Agronin, M., Balleza, J., Barkhouser, R., Bergeron, L., Greene, G. R., McCandliss, S. R., Rauscher, B. J., Reeves, T., Regan, M. W., Stockman, H. S. 2003, SPIE, 4850,1001 NIRCAM Image Simulations for NGST Wavefiont SensinglPS A. Sivaramakrishnan, D. Figer, H. Bushouse, H. S. Stockman (STScI),C. Ohara , D. Redding (JPL), M. Im (IPAC), & J. Offenberg (Raytheon) 2003, SPIE, 4850,388 Ultra-Low Background Operation of Near-Infrared Detectors for NGS Rauscher, B. J., Figer, D. F., Agronin, M., Balleza, J., Barkhouser, R., Bergeron, L., Greene, G. R., McCandliss, S. R., Reeves, T., Regan, M. W., Sharma, U., Stockman, H. S. 2003, SPIE, 4850,962 The Independent Detector Testing Laboratory and the JWST Detector Program Figer, D.F. et a1.2003, AAS201, #131.05

Greenhouse, Matthew↗
NASA NTRS2004

An Evaluation of Quantitative Methods of Determining the Degree of Melting Experienced by a Chondrule

Many workers have considered the degree to which partial melting occurred in chondrules they have studied, and this has led to attempts to find reliable methods of determining the degree of melting. At least two quantitative methods have been used in the literature: a convolution index (CVI), which is a ratio of the perimeter of the chondrule as seen in thin section divided by the perimeter of a circle with the same area as the chondrule, and nominal grain size (NGS), which is the inverse square root of the number density of olivines and pyroxenes in a chondrule (again, as seen in thin section). We have evaluated both nominal grain size and convolution index as melting indicators. Nominal grain size was measured on the results of a set of dynamic crystallization experiments previously described, where aliquots of LEW97008(L3.4) were heated to peak temperatures of 1250, 1350, 1370, and 1450 C, representing varying degrees of partial melting of the starting material. Nominal grain size numbers should correlate with peak temperature (and therefore degree of partial melting) if it is a good melting indicator. The convolution index is not directly testable with these experiments because the experiments do not actually create chondrules (and therefore they have no outline on which to measure a CVI). Thus we had no means to directly test how well the CVI predicted different degrees of melting. Therefore, we discuss the use of the CVI measurement and support the discussion with X-ray Computed Tomography (CT) data.

Nettles, J. W.↗