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At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018

Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod / nif / noeM gene clusters from C. taiwanensis LMG19424 T and “ Cupriavidus neocalidonicus” STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomic surveillance indicates clonal replacement of hypervirulent Klebsiella pneumoniae ST881 and ST29 lineage strains in vivo

The emergence of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant public health threat, particularly regarding its carriage in the healthy population. However, the genomic epidemiological characteristics and population dynamics of hvKp within a single patient across distinct infection episodes remain largely unknown. This study aimed to investigate the clonal replacement of hvKp K2-ST881 and K54-ST29 lineage strains in a single patient experiencing multiple-site infections during two independent episodes. Two strains, designated EDhvKp-1 and EDhvKp-2, were obtained from blood and cerebrospinal fluid during the first admission, and the strain isolated from blood on the second admission was named EDhvKp-3. Whole-genome sequencing, utilizing both short-read Illumina and long-read Oxford Nanopore platforms, was conducted. In silico multilocus sequence typing (MLST), identification of antimicrobial resistance and virulence genes, and the phylogenetic relationship between our strains and other K. pneumoniae ST881 and ST29 genomes retrieved from the public database were performed. Virulence potentials were assessed through a mouse lethality assay. Our study indicated that the strains were highly susceptible to multiple antimicrobial agents. Plasmid sequence analysis confirmed that both virulence plasmids, pEDhvKp-1 (166,008 bp) and pEDhvKp-3 (210,948 bp), belonged to IncFIB type. Multiple virulence genes, including rmpA , rmpA2 , rmpC , rmpD , iroBCDN , iucABCD , and iutA , were identified. EDhvKp-1 and EDhvKp-2 showed the closest relationship to strain 502 (differing by 51 SNPs), while EDhvKp-3 exhibited 69 SNPs differences compared to strain TAKPN-1, which all recovered from Chinese patients in 2020. In the mouse infection experiment, both ST881 EDhvKp-1 and ST29 EDhvKp-3 displayed similar virulence traits, causing 90 and 100% of the mice to die within 72 h after intraperitoneal infection, respectively. Our study expands the spectrum of hvKp lineages and highlights genomic alterations associated with clonal switching between two distinct lineages of hvKP that successively replaced each other in vivo . The development of novel strategies for the surveillance, diagnosis, and treatment of high-risk hvKp is urgently needed.

Liu, Ning↗
DOE OSTI2022

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

Genomic DNA from each sample was prepared using the Wizard Genomic DNA Purification Kit (Promega) and after, DNA was quantified using the QuantiFluor ONE dsDNA System (Promega). Genomic DNA underwent shearing to ~200 bp fragments via sonication and the gDNA fragments were prepared for sequencing using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). Bead-based size selection was used to select ~200 bp fragments and the fragments then underwent a splinkerette PCR using a Tn5-enriching forward primer and custom reverse primers for multiplexing. A final bead-based size selection was used to select for the correct length DNA. DNA was sequenced at the University of Michigan Advanced Genomics Core using Illumina sequencing with a custom read primer reading the last 10 nt of the transposon. PhiX174 DNA spike was added to the run to ensure sufficient sequence diversity on the flow cell. Then, a custom index read primer and standard Illumina primer were used to sequence the index reads and PhiX174, respectively.

Keck, James L.↗
NASA NTRS1974

The relation of variations in total magnetic field at high latitude with the parameters of the interplanetary magnetic field and with DP2 fluctuations

The maximum disturbances from the positive and negative regions of delta B (Bp and Bn, respectively) are investigated with respect to their correlation with (1) the average N-S component, Bz, (2) the average angle with respect to the solar magnetospheric equatorial plane, theta (3) the variance, sigma sub i, and (4) the magnitude, Bi, of the interplanetary magnetic field. These quantities were averaged over a period, T, ranging from 20 min. to 8 hours prior to the measurement of Bp or Bn. Variations (i.e., disturbances) in total magnetic field magnitude were studied utilizing data from the Polar Orbiting Geophysical Observatory satellites (OGO 2, 4, and 6), unofficially referred to as POGO.

Langel, R. A.↗
NASA NTRS1974

Evolution of the Moon's orbit and the origin of life

Indications about the past history of the lunar orbit that are yielded by palaeontological data derived from periodicities in fossil corals are shown to suggest that the moon approached the earth 2,850 plus or minus 250 Myr BP. Convergent evidence in the geological record indicates that a pulse of high temperature volcanism occurred about 2800 Myr BP. The implied catastrophe roughly coincides with the first records of life. It seems within the realm of possibility that a global thermal event might have been involved in the origin of life.

Turcotte, D. L.↗
NASA NTRS1983

Negatively supercoiled simian virus 40 DNA contains Z-DNA segments within transcriptional enhancer sequences

Three 8-base pair (bp) segments of alternating purine-pyrimidine from the simian virus 40 enhancer region form Z-DNA on negative supercoiling; minichromosome DNase I-hypersensitive sites determined by others bracket these three segments. A survey of transcriptional enhancer sequences reveals a pattern of potential Z-DNA-forming regions which occur in pairs 50-80 bp apart. This may influence local chromatin structure and may be related to transcriptional activation.

Nordheim, A.↗
NASA NTRS1984

Electrical characteristics of amorphous molybdenum-nickel contacts to silicon

The electrical characteristics of sputtered, amorphous Mo-Ni contacts have been measured on both p- and n-type Si, as functions of composition (30, 54, and 58 at. percent Mo). The contact resistivity on both p(+) and n(+) Si is in the 0.00000 ohm sq cm range. The barrier height for as-deposited samples varies between phi-bp = 0.47-0.42 V on p-type Si and between phi-bn = 0.63-0.68 V on n-type Si, as the composition of the amorphous layer goes from Ni-rich to Mo-rich. The sum phi-bp + phi-bn always equals 1.12 V, within experimental error. After thermal treatment at 500 C for 1/2 h, the contact resistivity changes by a factor of two or less, while the barrier height changes by at most approximately 0.05 V. In light of these results, the amorphous Mo-Ni film makes good ohmic contacts to silicon.

Kung, K. T.-Y.↗
NASA NTRS1985

Futher identifications of hydrogen in Grw +708247

Numerous spectra of the magnetic white dwarf Grw +70 8247 were obtained with the double CCD spectrograph at Palomar with signal-to-noise ratio above 100. Five weak absorptions in the blue and four in the red are produced by hydrogen in a strong magnetic field. New, precise, multiparameter, variational energy levels yielding intensity and wavelength, from 100 to 600 MG are presented. A search for those Zeeman components with wavelengths nearly constant with field is carried out. Two such Zeeman components which are relatively sharp and strong Pi transitions, explain the Minkowski band, 4137 A (known since 1938), as the 2s0-4f0 and the 5855 A band as the 2s0-3p0. Both have minimum wavelengths at B of about 300 MG. Their absorptions resemble band heads degraded to the red, as observed. The mixed nature of the 4f0 level results in an intensity ratio (2s0-4f0)/(2s0-3p0) = 0.58 at 280 MG, high for a line forbidden at zero field. Profiles computed for a pole-on dipole, near log Bp = 8.5, fit the two observed lines. Other hydrogen transitions (including the core of Ly-alpha) are consistent with the field strength. Six models with a variety of Bp and inclination are illustrated to show the quality of fit to the observations.

Greenstein, J. L.↗
NASA NTRS1986

Lunar nodal tide and distance to the moon during the Precambrian

The first direct determination of the lunar distance in the Precambrian is presented. A 23.3 + or - 0.3 yr periodicity preserved in 2500 Myr BP Australian banded iron formation is interpreted as reflecting the climatic influence of the lunar nodal tide, which has been detected with its modern 18.6-yr periodicity in some modern climate records. The lunar distance at 2500 Myr BP would then have been about 52 earth radii. The implied history of precambrian tidal friction is in accord with both the more recent paleontological evidence and the long-term stability of the lunar orbit. The length of the Milankovitch cycles that modulate the ice ages today also evolve with the earth-moon system. Their detection in the Precambrian sedimentary record would then permit an independent determination of the lunar distance.

Walker, J. C. G.↗
NASA NTRS1988

New evidence from the South China Sea for an abrupt termination of the last glacial period

Results demonstrating an abrupt change in the rate and character of sedimentation in the South China Sea at the close of the last glacial period are presented. Radiocarbon dating and its position in the oxygen isotope shift suggest that this change may be coincident with the abrupt change in climatic conditions seen at high latitudes in the North Atlantic and the Antarctic at 13 kyr BP. These results support the contention that a major global climatic change occurred between 14 and 13 kyr BP.

Broecker, W. S.↗
NASA NTRS1988

Compact non-thermal radio emission from B-peculiar stars

Some stars hotter than 10,000 K show propensity for unusual surface abundances and excessive magnetic fields. These peculiar stars, Ap and Bp in the spectral nomenclature, show unusually prominent absorption lines of heavier elements. Rapid rotation and strong magnetic fields are revealed by line shapes and Zeeman splitting. VLBI is here used to directly probe the source size and brightness temperature of weak radio emission recently discovered from two isolated Bp stars, sigma Orionis E and HD37017. The emitting zone for each star is no more than 6 stellar diameters in extent, reflecting brightness temperatures of more than one billion K. Such high surface brightness resembles gyrosynchrotron radiation from mildly relativistic electrons trapped in the strong magnetic fields surrounding these stars. Compact radio radiation from these two stars presents new opportunities for probing the physical environments of early-type stars and for precise radio astrometry.

Phillips, R. B.↗
NASA NTRS1988

A study of coronal bright points at 20 cm wavelength

The paper presents the results of a study of coronal bright points observed at 20 cm with the VLA on a day when the sun was exceptionally quiet. Microwave maps of bright points were obtained using data for the entire observing period of 5 hours, as well as for shorter periods of a few minutes. Most bright points, especially those appearing in the full-period maps, appear to be associated with small bipolar structures on the photospheric magnetogram. Overlays of bright point (BP) maps on the Ca(+) K picture, show that the brightest part of BP tends to lie on the boundary of a supergranulation network.

Nitta, N.↗
NASA NTRS1989

How to unveil a T Tauri star

A method for separating the 'veiling' continuum often present in T Tauri stars from the underlying photospheric spectrum is described. Echelle observations from 5100 to 6800 A of the partially veiled T Tauri star BP Tau were analyzed to determine the shape of the veiling spectrum. The residuals of the fit indicate the deviation of the veiling spectrum from a simple continuum and identify the location and strength of any emission-line components. It is shown, by means of goodness-of-fit tests, that the spectrum of BP Tau can be decomposed into a normal stellar spectrum plus a smooth veiling continuum with only a few emission lines superposed. The continuum dominates the veiling spectrum in this spectral region; the veiling does not arise from numerous deep photospheric absorption lines that are filled in by weak emission.

Hartigan, Patrick↗
NASA NTRS1990

The physiological cost of wearing the propellant handler's ensemble at the Kennedy Space Center

The potential for exposure to toxins used in the propulsion systems of spacecraft dictates the use of a whole body protective suit, the Propellant Handler's Ensemble (PHE) during preflight preparation and launching. The weight, structure, and operating parameters of the PHE may be expected to have a significant impact upon the metabolic, cardiovascular, and thermal responses of the user, especially during ambient temperature extremes and high workload situations. Four male subjects participated in tests in -7, 23, and 43 C (20, 74, and 110 F) environments in two versions of the PHE, the autonomous backpack (BP) and the hoseline (HL) supplied configuration. Measurements included heart rate (HR) rectal temperature, four skin temperatures, oxygen (O2), and carbon dioxide (CO2) in the helmet area, interior suit temperature, and suit pressure. Exercise metabolism was estimated from HR, PHE weight, and treadmill speed and grade. The HR responses between each PHE configuration were not statistically different. As a percentage of HR maximum, the mean values were 79 percent (COLD), 84 percent (LAB), and 90 percent (HOT). Helmet O2 and CO2 levels were correlated with percent HR max (P less than 0.001). Rectal temperatures were similar for each PHE configuration, except in the HOT exposure where the BP version exceeded the HL configuration (P less than 0.05). In nearly every instance the HR was driven to moderately high levels, the supplied respiratory gases were not optimum, and thermal adversity was a primary stressor. Our findings suggest that medical and physical fitness standards, along with operational restrictions, should be imposed upon PHE users to avoid situations that could adversely affect the worker.

Schonfeld, Brian R.↗
NASA NTRS1990

Calibration of the C-14 timescale over the past 30,000 years using mass spectrometric U-Th ages from Barbados corals

Uranium-thorium ages obtained by mass spectrometry from corals raised off the island of Barbados confirm the high precision of this technique over at least the past 30,000 years. Comparison of the U-Th ages with C-14 ages obtained on the Holocene samples shows that the U-Th ages are accurate, because they accord with the dendrochronological calibration. Before 9,000 yr BP, the C-14 ages are systematically younger than the U-Th ages, with a maximum difference of about 3500 yr at about 20,000 yr BP. The U-Th technique thus provides a way of calibrating the radiocarbon timescale beyond the range of dendrochronological calibration.

Bard, Edouard↗
NASA NTRS1992

Saline ingestion during lower body negative pressure as an end-of-mission countermeasure to post-space flight orthostatic intolerance

Lower body negative pressure (LBNP) in conjunction with saline ingestion can protect astronauts against post-space flight orthostatic intolerance. LBNP was used for both treatment and testing. The treatment was 4 hours of lower body decompression at 30 mm Hg below ambient pressure. One liter of water and 8 g of salt were ingested during the first hour. The treatment was evaluated by comparing heart rate (HR) and blood pressure (BP) responses to test decompressions on the days before and after treatment. It is concluded that cardiovascular responses to step-wise decompression duplicated Skylab findings. BP was maintained, but HR responses to each step were progressively greater in-flight than preflight. After the 4-hour treatment HR responses were closer to preflight values.

Charles, John B.↗
NASA NTRS1992

Annual, orbital, and enigmatic variations in tropical oceanography recorded by the Equatorial Atlantic amplifier

Equatorial Atlantic surface waters respond directly to changes in zonal and meridional lower tropospheric winds forced by annual insolation. This mechanism has its maximum effect along the equatorial wave guide centered on 10 deg W. The result is to amplify even subtle tropical climate changes such that they are recorded by marked amplitude changes in the proxy signals. Model realizations, NCAR AGCM and OGCM for 0 Ka and 126 Ka (January and July), and paleoceanographic proxy data show that these winds are also forced by insolation changes at the orbital periods of precession and obliquity. Perhelion in boreal summer produces a strengthened monsoon, e.g., increase meridional and decrease zonal wind stress. This reduces oceanic Ekman divergence and thermocline/nutricline shallowing. The result, in the equatorial Atlantic, is reduced primary productivity and higher euphotic zone temperatures; vice versa for perihelion in boreal winter. Perihelion is controlled by precession. Thus, the dominant period in spectra from a stacked SST record (0-252 Ka BP) at the site of the equatorial Atlantic amplifier is 23 Ky (53 percent of the total variance). This precessional period is coherent (k = 0.920) and in phase with boreal summer insolation. Oscillations of shorter period are present in records from cores sited beneath the amplifier region. These occur between 12.5 and 74.5 Ka BP, when eccentricity modulation of precession is at a minimum. Within this time interval there are 21 cycles with mean periods of 3.0 plus or minus 0.5 Ky. Similar periods have been documented from high latitude regions, e.g., Greenland ice cores from Camp Century. The Camp Century signal in this same time interval contains 21 cycles. A subjective correlation was made between the Camp Century and the equatorial records; the signals were statistically similar, r = 0.722 and k = 0.960.

Mcintyre, Andrew↗