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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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At least 631 records · Page 35
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DOE OSTI2014

The environmental impacts on the star formation main sequence: An Hα study of the newly discovered rich cluster at z = 1.52

We report the discovery of a strong over-density of galaxies in the field of a radio galaxy at z = 1.52 (4C 65.22) based on our broadband and narrow-band (Hα) photometry with the Subaru Telescope. We find that Hα emitters are located in the outskirts of the density peak (cluster core) dominated by passive red-sequence galaxies. This resembles the situation in lower-redshift clusters, suggesting that the newly discovered structure is a well-evolved rich galaxy cluster at z = 1.5. Our data suggest that the color-density and stellar mass-density relations are already in place at z ∼ 1.5, mostly driven by the passive red massive galaxies residing within r{sub c} ≲ 200 kpc from the cluster core. These environmental trends almost disappear when we consider only star-forming (SF) galaxies. We do not find SFR-density or SSFR-density relations amongst SF galaxies, and the location of the SF main sequence does not significantly change with environment. Nevertheless, we find a tentative hint that star-bursting galaxies (up-scattered objects from the main sequence) are preferentially located in a small group at ∼1 Mpc away from the main body of the cluster. We also argue that the scatter of the SF main sequence could be dependent on the distance to the nearest neighboring galaxy.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

POST-MERGER SIGNATURES OF RED-SEQUENCE GALAXIES IN RICH ABELL CLUSTERS AT z {approx}< 0.1

We have investigated the post-merger signatures of red-sequence galaxies in rich Abell clusters at z {approx}< 0.1: A119, A2670, A3330, and A389. Deep images in u', g', r', and medium-resolution galaxy spectra were taken using MOSAIC II CCD and Hydra MOS mounted on a Blanco 4 m telescope at Cerro Tololo Inter-American Observatory. Post-merger features are identified by visual inspection based on asymmetric disturbed features, faint structures, discontinuous halo structures, rings, and dust lanes. We found that {approx}25% of bright (M{sub r} < -20) cluster red-sequence galaxies show post-merger signatures in four clusters consistently. Most ({approx}71%) of the featured galaxies were found to be bulge dominated, and for the subsample of bulge-dominated red-sequence galaxies, the post-merger fraction rises to {approx}38%. We also found that roughly 4% of bulge-dominated red-sequence galaxies interact (ongoing merger). A total of 42% (38% post-merger, 4% ongoing merger) of galaxies show merger-related features. Compared to a field galaxy study with a similar limiting magnitude by van Dokkum in 2005, our cluster study presents a similar post-merger fraction but a markedly lower ongoing merger fraction. The merger fraction derived is surprisingly high for the high density of our clusters, where the fast internal motions of galaxies are thought to play a negative role in galaxy mergers. The fraction of post-merger and ongoing merger galaxies can be explained as follows. Most of the post-merger galaxies may have carried over their merger features from their previous halo environment, whereas interacting galaxies interact in the current cluster in situ. According to our semi-analytic calculation, massive cluster halos may very well have experienced tens of halo mergers over the last 4-5 Gyr; post-merger features last that long, allowing these features to be detected in our clusters today. The apparent lack of dependence of the merger fraction on the clustocentric distance is naturally explained this way. In this scenario, the galaxy morphology and properties can be properly interpreted only when the halo evolution characteristics are understood first.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

A DOUBLE WHITE-DWARF COOLING SEQUENCE IN {omega} CENTAURI

We have applied our empirical-point-spread-function-based photometric techniques on a large number of calibration-related WFC3/UVIS UV-B exposures of the core of {omega} Cen, and found a well-defined split in the bright part of the white-dwarf cooling sequence (WDCS). The redder sequence is more populated by a factor of {approx}2. We can explain the separation of the two sequences and their number ratio in terms of the He-normal and He-rich subpopulations that had been previously identified along the cluster main sequence. The blue WDCS is populated by the evolved stars of the He-normal component ({approx}0.55 M{sub Sun} CO-core DA objects), while the red WDCS hosts the end products of the He-rich population ({approx}0.46 M{sub Sun} objects, and {approx}10% CO-core and {approx}90% He-core WDs). The He-core WDs correspond to He-rich stars that missed the central He ignition, and we estimate their fraction by analyzing the population ratios along the cluster horizontal branch.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Broom: application for non-redundant storage of high throughput sequencing data

Abstract Motivation The data generation capabilities of high throughput sequencing (HTS) instruments have exponentially increased over the last few years, while the cost of sequencing has dramatically decreased allowing this technology to become widely used in biomedical studies. For small labs and individual researchers, however, storage and transfer of large amounts of HTS data present a significant challenge. The recent trends in increased sequencing quality and genome coverage can be used to reconsider HTS data storage strategies. Results We present Broom, a stand-alone application designed to select and store only high-quality sequencing reads at extremely high compression rates. Written in C++, the application accepts single and paired-end reads in FASTQ and FASTA formats and decompresses data in FASTA format. Availability and implementation C++ code available at https://scsb.utmb.edu/labgroups/fofanov/broom.asp. Supplementary information Supplementary data are available at Bioinformatics online.

Albayrak, Levent↗
DOE OSTI2022

The dark side of galaxy stellar populations – II. The dependence of star-formation histories on halo mass and on the scatter of the main sequence

Nearby galaxies are the end result of their cosmological evolution, which is predicted to be influenced by the growth of their host dark matter haloes. This co-evolution potentially leaves signatures in present-day observed galaxy properties, which might be essential to further understand how the growth and properties of galaxies are connected to those of their host haloes. In this work, we study the evolutionary histories of nearby galaxies both in terms of their host haloes and the scatter of the star-forming main sequence by investigating their time-resolved stellar populations using absorption optical spectra drawn from the Sloan Digital Sky Survey. We find that galaxy star-formation histories depend on the masses of their host haloes, and hence they shape the evolution of the star-forming main sequence over cosmic time. Additionally, we also find that the scatter around the z = 0 star-forming main sequence is not (entirely) stochastic, as galaxies with currently different star-formation rates have experienced, on average, different star-formation histories. Furthermore, our findings suggest that dark matter haloes might play a key role in modulating the evolution of star formation in galaxies, and thus of the main sequence, and further demonstrate that galaxies at different evolutionary stages contribute to the observed scatter of this relation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Effects of stratification on overshooting and waves atop the convective core of M ⊙ main-sequence stars

As a massive star evolves along the main sequence, its core contracts, leaving behind a stable stratification in helium. We simulate two-dimensional convection in the core at three different stages of evolution of a $5\,\mathrm{ M}_{\odot }$ star, with three different stratifications in helium atop the core. We study the propagation of internal gravity waves in the stably stratified envelope, along with the overshooting length of convective plumes above the convective boundary. We find that the stratification in helium in evolved stars hinders radial motions and effectively shields the radiative envelope against plume penetration. This prevents convective overshooting from being an efficient mixing process in the radiative envelope. In addition, internal gravity waves are less excited in evolved models compared to the zero-age-main-sequence model, and are also more damped in the stratified region above the core. As a result, the wave power is several orders of magnitude lower in mid- and terminal-main-sequence models compared to zero-age-main-sequence stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Atmospheric parameters and chemical abundances within 100 pc: a sample of G, K, and M main-sequence stars

ABSTRACT To date, we have access to enormous inventories of stellar spectra that allow the extraction of atmospheric parameters and chemical abundances essential in stellar studies. However, characterizing such a large amount of data is complex and requires a good understanding of the studied object to ensure reliable and homogeneous results. In this study, we present a methodology to measure homogenously the basic atmospheric parameters and detailed chemical abundances of over 1600 thin disc main-sequence stars in the 100 pc solar neighbourhood, using APOGEE-2 infrared spectra. We employed the code tonalli to determine the atmospheric parameters using a prior on $\log {g}$. The $\log {g}$ prior in tonalli implies an understanding of the treated population and helps to find physically coherent answers. Our atmospheric parameters agree within the typical uncertainties (100 K in $\mathrm{T_{eff}}$, 0.15 dex in $\log {g}$ and [M/H]) with previous estimations of ASPCAP and Gaia DR3. We use our temperatures to determine a new infrared colour–temperature sequence, in good agreement with previous works, that can be used for any main-sequence star. Additionally, we used the bacchus code to determine the abundances of Mg, Al, Si, Ca, and Fe in our sample. The five elements (Mg, Al, Si, Ca, Fe) studied have an abundance distribution centred around slightly subsolar values in agreement with previous results for the solar neighbourhood. The over 1600 main-sequence stars’ atmospheric parameters and chemical abundances presented here are useful in follow-up studies of the solar neighbourhood or as a training set for data-driven methods.

López-Valdivia, Ricardo (ORCID:0000000277950018)↗
DOE OSTI2024

The atomic gas sequence and mass–metallicity relation from dwarfs to massive galaxies

Galaxy scaling relations provide insights into the processes that drive galaxy evolution. The extension of these scaling relations into the dwarf galaxy regime is of particular interest. This is because dwarf galaxies represent a crucial stage in galaxy evolution, and understanding them could also shed light on their role in reionizing the early Universe. There is currently no consensus on the processes that dominate the evolution of dwarfs. In this work, we constrain the atomic gas sequence (stellar mass versus atomic gas fraction) and mass–metallicity relation (stellar mass versus gas-phase metallicity) from dwarf (⁠10 6.5 M ⊙ ⁠) to massive (⁠10 11.5 M ⊙ ) galaxies in the local Universe. The combined optical and 21-cm spectroscopic observations of the Dark Energy Spectroscopic Instrument and Arecibo Legacy Fast ALFA surveys allow us to constrain both scaling relations simultaneously. We find a slope change of the atomic gas sequence at a stellar mass of ~10 9 M ⊙ ⁠. We also find that the shape and scatter of the atomic gas sequence and mass–metallicity relation are strongly linked for both dwarfs and more massive galaxies. Consequently, the low-mass slope change of the atomic gas sequence is imprinted onto the mass–metallicity relation of dwarf galaxies. The mass scale of the measured slope change is consistent with a predicted escape velocity threshold below which low-mass galaxies experience significant supernova-driven gas loss, as well as with a reduction in cold gas accretion onto more massive galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2013

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.

Torella, JP↗
DOE OSTI2015

Base-resolution detection of N 4 -methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite-sequencing

Restriction-modification (R-M) systems pose a major barrier to DNA transformation and genetic engineering of bacterial species. Systematic identification of DNA methylation in R-M systems, including N 6 -methyladenine (6mA), 5-methylcytosine (5mC) and N 4 -methylcytosine (4mC), will enable strategies to make these species genetically tractable. Although single-molecule, real time (SMRT) sequencing technology is capable of detecting 4mC directly for any bacterial species regardless of whether an assembled genome exists or not, it is not as scalable to profiling hundreds to thousands of samples compared with the commonly used next-generation sequencing technologies. Here, we present 4mC-Tet-assisted bisulfite-sequencing (4mC-TAB-seq), a next-generation sequencing method that rapidly and cost efficiently reveals the genome-wide locations of 4mC for bacterial species with an available assembled reference genome. In 4mC-TAB-seq, both cytosines and 5mCs are read out as thymines, whereas only 4mCs are read out as cytosines, revealing their specific positions throughout the genome. We applied 4mC-TAB-seq to study the methylation of a member of the hyperthermophilc genus, Caldicellulosiruptor , in which 4mC-related restriction is a major barrier to DNA transformation from other species. Lastly, in combination with MethylC-seq, both 4mC- and 5mC-containing motifs are identified which can assist in rapid and efficient genetic engineering of these bacteria in the future.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence

La-related protein 1 (LARP1) regulates the stability of many mRNAs. These include 5'TOPs, mTOR-kinase responsive mRNAs with pyrimidine-rich 5' UTRs, which encode ribosomal proteins and translation factors. We determined that the highly conserved LARP1-specific C-terminal DM15 region of human LARP1 directly binds a 5'TOP sequence. The crystal structure of this DM15 region refined to 1.86 Å resolution has three structurally related and evolutionarily conserved helix-turn-helix modules within each monomer. These motifs resemble HEAT repeats, ubiquitous helical protein-binding structures, but their sequences are inconsistent with consensus sequences of known HEAT modules, suggesting this structure has been repurposed for RNA interactions. A putative mTORC1-recognition sequence sits within a flexible loop C-terminal to these repeats. We also present modelling of pyrimidine-rich single-stranded RNA onto the highly conserved surface of the DM15 region. Ultimately, these studies lay the foundation necessary for proceeding toward a structural mechanism by which LARP1 links mTOR signalling to ribosome biogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

RNAcentral: A comprehensive database of non-coding RNA sequences

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. Furthermore, the website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences

Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5'-AAAGTTT-3'. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications

Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping phenotypes are associated with WT1 mutations, including Wilms tumors, Denys-Drash syndrome (DDS), Frasier syndrome (FS) and WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). These conditions vary in severity from individual to individual; they can be fatal in early childhood, or relatively benign into adulthood. DDS mutations cluster predominantly in zinc fingers (ZF) 2 and 3 at the C-terminus of WT1, which together with ZF4 determine the sequence-specificity of DNA binding. We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we speculate, might derive from the ability of the mutant proteins to sequester WT1 into unproductive oligomers, or to erroneously bind to variant target sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Role for first zinc finger of WT1 in DNA sequence specificity: Denys–Drash syndrome-associated WT1 mutant in ZF1 enhances affinity for a subset of WT1 binding sites

Wilms tumor protein (WT1) is a Cys2-His2 zinc-finger transcription factor vital for embryonic development of the genitourinary system. The protein contains a C-terminal DNA binding domain with four tandem zinc-fingers (ZF1–4). An alternative splicing of Wt1 can add three additional amino acids—lysine (K), threonine (T) and serine (S)—between ZF3 and ZF4. In the –KTS isoform, ZF2–4 determine the sequence-specificity of DNA binding, whereas the function of ZF1 remains elusive. Three X-ray structures are described here for wild-type –KTS isoform ZF1–4 in complex with its cognate DNA sequence. We observed four unique ZF1 conformations. First, like ZF2–4, ZF1 can be positioned continuously in the DNA major groove forming a ‘near-cognate’ complex. Second, while ZF2–4 make base-specific interactions with one DNA molecule, ZF1 can interact with a second DNA molecule (or, presumably, two regions of the same DNA molecule). Third, ZF1 can intercalate at the joint of two tail-to-head DNA molecules. If such intercalation occurs on a continuous DNA molecule, it would kink the DNA at the ZF1 binding site. Fourth, two ZF1 units can dimerize. Furthermore, we examined a Denys–Drash syndrome-associated ZF1 mutation (methionine at position 342 is replaced by arginine). This mutation enhances WT1 affinity for a guanine base. X-ray crystallography of the mutant in complex with its preferred sequence revealed the interactions responsible for this affinity change. These results provide insight into the mechanisms of action of WT1, and clarify the fact that ZF1 plays a role in determining sequence specificity of this critical transcription factor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗
DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Reducing sequencing complexity in dynamical quantum error suppression by Walsh modulation

We study dynamical error suppression from the perspective of reducing sequencing complexity, with an eye toward facilitating the development of efficient semiautonomous quantum-coherent systems. To this end, we focus on digital sequences where all interpulse time periods are integer multiples of a minimum clock period and compatibility with digital classical control circuitry is intrinsic. We use so-called Walsh functions as a unifying mathematical framework; the Walsh functions are an orthonormal set of basis functions which may be associated directly with the control propagator for a digital modulation scheme. Using this insight, we characterize the suite of resulting Walsh dynamical decoupling sequences--including both familiar and novel control sequences--and identify the number of periodic square-wave (Rademacher) functions required to generate the associated Walsh function as the key determinant of the error-suppressing features. We also show how Walsh modulation may be employed for the protection of certain nontrivial logic gates. Based on these insights, we identify Walsh modulation as a digital-efficient approach for physical-layer error suppression.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗