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At least 451 records · Page 25
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Selection-enriched genomic loci (SEGL) reveals genetic loci for environmental adaptation and photosynthetic productivity in Chlamydomonas reinhardtii

This work demonstrates an approach to produce and select hybrid algal strains exhibiting increased photosynthetic productivity under multiple environmental conditions. This simultaneously addresses two major impediments to improving algal bioenergy production: 1) generating new genetic variants with improved performance; and 2) disentangling complex interactions between genetic and physiological factors contributing to these improvements. We pooled progeny generated from mating two environmental isolates of the green alga Chlamydomonas reinhardtii and cultured the pools under multiple environmental conditions. Strains from the outcompeting populations showed substantial (in some cases over 3 fold) increases in productivity over the parental lines under certain environments related to biomass production, including laboratory conditions as well as hyperoxia, fluctuating light, high salinity and high temperature. The results indicate that C. reinhardtii has remarkable, untapped, directed evolution capacity that may be harnessed using breeding and competition approaches. The populations were deep sequenced at multiple time points to identify “Selection-Enriched Genomic Loci” (SEGL) that accumulated in the populations, and thus likely confer increased fitness under the respective environmental conditions. With improved resolution, SEGL mapping can identify allelic combinations used for targeted breeding approaches, generating elite algal lines with multiple desirable traits, as well as to further understand the genetic and mechanistic bases of photosynthetic productivity. Increasing the photosynthetic efficiency of algae during biomass production is perhaps the most critical hurdle for economically sustainable algal based biofuels. This presents unique challenges because modifications designed to increase photosynthesis often result in decreased fitness, due to production of toxic reactive oxygen species when photosynthesis is not adequately regulated. These problems are exacerbated under natural and outdoor production environments because of the complex nature of photosynthesis and the multifaceted interactions between genetic, environmental and physiological factors. Here, we demonstrate a high throughput biotechnological screening approach that simultaneously produces algal strains with highly increased autotrophic productivity and identifies genomic loci contributing to these improvements. Our results demonstrate that Chlamydomonas reinhardtii exhibits high directed evolutionary capacity readily accessed through breeding and selection.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2001

Nature of Fluctuations on Directional Discontinuities Inside a Solar Ejection: Wind and IMP 8 Observations

A solar ejection passed the Wind spacecraft between December 23 and 26, 1996. On closer examination, we find a sequence of ejecta material, as identified by abnormally low proton temperatures, separated by plasmas with typical solar wind temperatures at 1 AU. Large and abrupt changes in field and plasma properties occurred near the separation boundaries of these regions. At the one boundary we examine here, a series of directional discontinuities was observed. We argue that Alfvenic fluctuations in the immediate vicinity of these discontinuities distort minimum variance normals, introducing uncertainty into the identification of the discontinuities as either rotational or tangential. Carrying out a series of tests on plasma and field data including minimum variance, velocity and magnetic field correlations, and jump conditions, we conclude that the discontinuities are tangential. Furthermore, we find waves superposed on these tangential discontinuities (TDs). The presence of discontinuities allows the existence of both surface waves and ducted body waves. Both probably form in the solar atmosphere where many transverse nonuniformities exist and where theoretically they have been expected. We add to prior speculation that waves on discontinuities may in fact be a common occurrence. In the solar wind, these waves can attain large amplitudes and low frequencies. We argue that such waves can generate dynamical changes at TDs through advection or forced reconnection. The dynamics might so extensively alter the internal structure that the discontinuity would no longer be identified as tangential. Such processes could help explain why the occurrence frequency of TDs observed throughout the solar wind falls off with increasing heliocentric distance. The presence of waves may also alter the nature of the interactions of TDs with the Earth's bow shock in so-called hot flow anomalies.

Vasquez, Bernard J.↗
DOE OSTI2020

Fluorescent amplification for next generation sequencing (FA-NGS) library preparation

BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa

The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Period-activity relations in close binary systems

The question as to whether the amount of activity observed in stars with the same fundamental stellar parameters depends on rotational velocity is considered in view of close binary systems, making use of their orbital rather than their rotational period. It is noted that the main sequence G star binaries lie systematically lower than the K subgiants for the same rotational periods, so that relations including a variety of spectral classes cannot be used to directly deduce correlations between magnetic fields and activity without suitable correction. The behavior of the present sample suggests that activity increases with later spectral type and with evolution off the main sequence. The chromosphere shows a minor reaction to rotational velocity increase.

Basri, G.↗
NASA NTRSDate not supplied

Commanding Constellations (Pipeline Architecture)

Providing ground command software for constellations of spacecraft is a challenging problem. Reliable command delivery requires a feedback loop; for a constellation there will likely be an independent feedback loop for each constellation member. Each command must be sent via the proper Ground Station, which may change from one contact to the next (and may be different for different members). Dynamic configuration of the ground command software is usually required (e.g. directives to configure each member's feedback loop and assign the appropriate Ground Station). For testing purposes, there must be a way to insert command data at any level in the protocol stack. The Pipeline architecture described in this paper can support all these capabilities with a sequence of software modules (the pipeline), and a single self-identifying message format (for all types of command data and configuration directives). The Pipeline architecture is quite simple, yet it can solve some complex problems. The resulting solutions are conceptually simple, and therefore, reliable. They are also modular, and therefore, easy to distribute and extend. We first used the Pipeline architecture to design a CCSDS (Consultative Committee for Space Data Systems) Ground Telecommand system (to command one spacecraft at a time with a fixed Ground Station interface). This pipeline was later extended to include gateways to any of several Ground Stations. The resulting pipeline was then extended to handle a small constellation of spacecraft. The use of the Pipeline architecture allowed us to easily handle the increasing complexity. This paper will describe the Pipeline architecture, show how it was used to solve each of the above commanding situations, and how it can easily be extended to handle larger constellations.

Tim Ray↗
DOE OSTI2024

Structural and electronic characteristics of amorphous Ge 8 Sb 2 Te 11

GeTe-rich phase-change materials can be utilized in rewriteable optical memory due to the large contrast in reflectivity between amorphous and crystalline phases. Here we explored the structure and electronic properties of amorphous Ge 8 Sb 2 Te 11 using ab initio molecular dynamics simulations. The results indicate that amorphous Ge 8 Sb 2 Te 11 is dominantly composed of Ge-, Sb- and Te-centered octahedrons with distortions, while 30.4 % of Ge-centered clusters are in the form of tetrahedrons which are randomly distributed. The 5-fold rings possess a large proportion, and the Gesingle bondTe and Sbsingle bondTe bonds present larger formation energies than other bonds, leading to the ABAB bonding sequence (A: Ge and Sb, B: Te). The lone pair electrons locating at the opposite direction of bonds possess a large fraction of 14.8 %, which may enhance the distortions of local clusters. Importantly, these structural properties lead to the high stability of amorphous Ge 8 Sb 2 Te 11 and thus long data retention in the information storage.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Disruption of the endogenous indole glucosinolate pathway impacts the Arabidopsis thaliana root exudation profile and rhizobacterial community

Root exudates are composed of primary and secondary metabolites known to modulate the rhizosphere microbiota. Glucosinolates are defense compounds present in the Brassicaceae family capable of deterring pathogens, herbivores and biotic stressors in the phyllosphere. In addition, traces of glucosinolates and their hydrolyzed byproducts have been found in the soil, suggesting that these secondary metabolites could play a role in the modulation and establishment of the rhizosphere microbial community associated with this family. Here, we used Arabidopsis thaliana mutant lines, including the cyp79B2cyp79B3 double mutant line with a disruption in the indole glucosinolate pathway and atr1D, which overexpresses ATR1 and increases glucosinolate production. These lines were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing to evaluate how genetic modifications to the indole glucosinolate pathway affects the root exudate profile of Arabidopsis thaliana, and, in turn, impacts the rhizosphere microbial community. Metabolic analysis of root exudates from the wild-type Columbia (Col-0), along with the mutant lines, confirmed that alterations to the indole glucosinolate biosynthetic pathway result in shifts in the root exudate profile of the plant. We observed changes in the relative abundance of exuded metabolites. Moreover, 16S rRNA amplicon sequencing results provided evidence that the rhizobacterial communities associated with the plant lines used were directly impacted in diversity and community composition. Here, this work provides further information on the involvement of secondary metabolites and their role in modulating the rhizobacterial community. Root metabolites dictate the presence of different bacterial species, including plant growth-promoting rhizobacteria (PGPR). Our results suggest that genetic alterations in the indole glucosinolate pathway cause disruptions beyond the endogenous levels of the plant, significantly changing the abundance and presence of different metabolites in the root exudates of the plants as well as the microbial rhizosphere community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase

All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Observations of Disequilibrium CO Chemistry in the Coldest Brown Dwarfs

Cold brown dwarfs are excellent analogs of widely separated, gas giant exoplanets, and provide insight into the potential atmospheric chemistry and physics we may encounter in objects to be discovered by future direct imaging surveys. We present a low-resolution, R ∼ 300, M-band spectroscopic sequence of seven brown dwarfs with effective temperatures between 750 and 250 K along with Jupiter. These spectra reveal disequilibrium abundances of carbon monoxide (CO) produced by atmospheric quenching. We use the eddy diffusion coefficient (K {sub zz}) to estimate the strength of vertical mixing in each object. The K {sub zz} values of cooler gaseous objects are close to their theoretical maximum, and warmer objects show weaker mixing, likely due to less efficient convective mixing in primarily radiative layers. The CO-derived K {sub zz} values imply that disequilibrium phosphine (PH{sub 3}) should be easily observable in all of the brown dwarfs, but none as yet show any evidence for PH{sub 3} absorption. We find that ammonia is relatively insensitive to atmospheric quenching at these effective temperatures. We are able to improve the fit to WISE 0855's M-band spectrum by including both CO and water clouds in the atmospheric model.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1970

Analysis of a Decision-Directed Receiver with Unknown Priors

A decision-directed receiver (DDR) uses previous outputs (decisions) to estimate unknown parameters and, on the basis of these estimates, modifies the detector structure for subsequent decisions. Although the DDR is less complex to instrument than other adaptive schemes, inherent in the decision-directed approach is the possibility of a runaway. This occurs when the detector commits a sequence of decision errors resulting in a degradation of parameter estimates, which, in turn, results in a further deterioration of detector performance. Because of the dependencies introduced by the learning process, runaway is difficult to analyze. In this paper, a DDR with unknown a priori probabilities is considered. The priors are estimated by the relative frequency of decisions of that event. For binary detection, it is shown that there is a positive probability of a runaway (the estimates converge to 1 or 0), which equals 1 if the signal-to-noise ratio is below a critical value. A tight bound on the probability of a runaway is obtained by approximating the learning process by a random walk with independent increments. The analysis demonstrates that a runaway is quite improbable even for moderate signal-to-noise ratios. The analysis is extended to multiple signals and to the situation where the estimates of the priors are updated continuously through exponential weighting rather than allowed to converge.

Davisson, Lee D.↗
NASA NTRS1972

Metal-poor stars. IV - The evolution of red giants.

Detailed evolutionary calculations for six Population-II red giants are presented. The first five of these models are followed from the zero age main sequence to the onset of the helium flash. The sixth model allows the effect of direct electron-neutrino interactions to be estimated. The updated input physics and evolutionary code are described briefly. The results of the calculations are presented in a manner pertinent to later stages of evolutions and suitable for comparison with observations.

Rood, R. T.↗
NASA NTRS1980

Thermal deformations and stresses in composite materials

Residual stresses are induced during curing in angle-ply laminates as a result of anisotropic thermal deformations of the variously oriented plies. Residual strains are measured experimentally using embedded strain gage techniques, and residual stresses are computed using orthotropic stress-strain relations. The results show that, for graphite and Kevlar laminates, residual stresses at room temperature are high enough to cause damage in the plies in the transverse to the fiber direction. It is also shown that residual stresses do not relax appreciably. The ply stacking sequence is found to have no effect on the magnitude of average residual stresses. Residual stresses and susceptibility to cracking during curing depend to a marked extent on ply layup.

Daniel, I. M.↗
NASA NTRS1984

IUE observations of weak G-band stars

High- and low-resolution ultraviolet spectra of several weak G-band giants have been obtained with the IUE satellite, to derive Be abundances and to search for degenerate companions. The abundances of Be in these stars are about log epsilon (Be) approximately -0.5. These values are in good agreement with the Be abundances of Hyades giants, and are consistent with standard theories of post-main-sequence Be depletion in stars. However, the Be abundances do not fit with the large Li abundances in weak G-band stars. Post-main-sequence production of Li or element segregation in main-sequence stars may explain the high Li abundance in weak G-band stars. No direct evidence is seen for the presence of hot subluminous companions. The peculiar abundances in these stars probably are not due to binary mass transfer.

Parthasarathy, M.↗
NASA NTRS1988

A mechanism for strong shock electron heating in supernova remnants

It is shown that collisionless shock waves propagating away from a supernova may be directly responsible for the 10 keV X-ray emission seen in supernova remnants. A sequence of plasma instabilities (Buneman and ion acoustic) between the reflected and/or transmitted ions and the background electrons at the foot of the shock front can give rise to rapid anomalous heating of electrons. Hybrid simulations of a perpendicular collisionless shock are presented to demonstrate that this heating can arise within a self-consistently computed shock structure.

Cargill, P. J.↗
NASA NTRS1988

Evidence for and implications of an Early Archean terrestrial impact record

Early Archean, 3.5 to 3.2 Ga, greenstone sequences in South Africa and Western Australia contain a well-preserved record of early terrestrial meteorite impacts. The main impact-produced deposits are layers, 10 cm to over 1 m thick, composed largely of sand-sized spherules, 0.1 to 4 mm in diameter. The beds studied to date show an assemblage of features indicating formation by the fall of debris from impact-generated ejecta clouds. Some presented data effectively rule out normal magmatic or sedimentary processes in the origin of these units and provide substantial support for an origin by large impacts on the early earth. The presence of at least four, remarkably thick, nearly pure spherule layers suggests that smaller-scale impact deposits may be even more abundant in these sequences. The existence of a well-preserved Archean terrestrial impact record suggests that a direct source of evidence is available regarding a number of important aspects of early earth history.

Lowe, Donald R.↗
NASA NTRS1995

Direct binding of F actin to the cytoplasmic domain of the alpha 2 integrin chain in vitro

The transmembrane integrins have been shown to interact with the cytoskeleton via noncovalent binding between cytoplasmic domains (CDs) of integrin beta chains and various actin binding proteins within the focal adhesion complex. Direct or indirect integrin alpha chain CD binding to the actin cytoskeleton has not been reported. We show here that actin, as an abundant constituent of focal adhesion complex proteins isolated from fibroblasts, binds strongly and specifically to alpha 2 CD, but not to alpha 1 CD peptide. Similar specific binding to alpha 2 CD peptide was seen for highly purified F actin, free of putative actin-binding proteins. The bound complex of actin and peptide was visualized directly by coprecipitation, and actin binding was abrogated by removal of a five amino acid sequence from the alpha 2 CD peptide. Our findings may explain the earlier observation that, while integrins alpha 2 beta 1 and alpha 1 beta 1 both bind to collagen, only alpha 2 beta 1 can mediate contraction of extracellular collagen matrices.

Non-NASA Center↗
NASA NTRS2005

Isolation and Identification of Microorganisms in JSC Mars-1 Simulant Soil

Microorganisms were isolated and identified in samples of JSC Mars-1, a Mars simulant soil. JSC Mars-1 is an altered volcanic ash from a cinder cone south of Mauna Kea, Hawaii. This material was chosen because of its similarity to the Martian soil in physical and chemical composition. The soil was obtained by excavating 40 cm deep in a vegetated area to prevent contamination. In previous studies, bacteria from this soil has been isolated by culturing on different types of media, including minimal media, and using biochemical techniques for identification. Isolation by culturing is successful only for a small percentage of the population. As a result, molecular techniques are being employed to identify microorganisms directly from the soil without culturing. In this study, bacteria were identified by purifying and sequencing the DNA encoding the 16s ribosomal RNA (16s rDNA). This gene is well conserved in species and demonstrates species specificity. In addition, biofilm formation, an indicator of microbial life, was studied with this soil. Biofilms are microbial communities consisting of microbes and exopolysaccharides secreted by them. This is a protective way of life for the microbes as they are more resistant to environmental pressures.

Mendez, Claudia↗