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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 1,441 records · Page 80
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Comparative genomics reveals phylogenetic distribution patterns of secondary metabolites in Amycolatopsis species

Background: Genome mining tools have enabled us to predict biosynthetic gene clusters that might encode compounds with valuable functions for industrial and medical applications. With the continuously increasing number of genomes sequenced, we are confronted with an overwhelming number of predicted clusters. In order to guide the effective prioritization of biosynthetic gene clusters towards finding the most promising compounds, knowledge about diversity, phylogenetic relationships and distribution patterns of biosynthetic gene clusters is necessary. Results: Here, we provide a comprehensive analysis of the model actinobacterial genus Amycolatopsis and its potential for the production of secondary metabolites. A phylogenetic characterization, together with a pan-genome analysis showed that within this highly diverse genus, four major lineages could be distinguished which differed in their potential to produce secondary metabolites. Furthermore, we were able to distinguish gene cluster families whose distribution correlated with phylogeny, indicating that vertical gene transfer plays a major role in the evolution of secondary metabolite gene clusters. Still, the vast majority of the diverse biosynthetic gene clusters were derived from clusters unique to the genus, and also unique in comparison to a database of known compounds. Our study on the locations of biosynthetic gene clusters in the genomes of Amycolatopsis’ strains showed that clusters acquired by horizontal gene transfer tend to be incorporated into non-conserved regions of the genome thereby allowing us to distinguish core and hypervariable regions in Amycolatopsis genomes. Conclusions: Using a comparative genomics approach, it was possible to determine the potential of the genus Amycolatopsis to produce a huge diversity of secondary metabolites. Furthermore, the analysis demonstrates that horizontal and vertical gene transfer play an important role in the acquisition and maintenance of valuable secondary metabolites. Our results cast light on the interconnections between secondary metabolite gene clusters and provide a way to prioritize biosynthetic pathways in the search and discovery of novel compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

Background: Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny. Results: Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered. Conclusions: The divergence time of subgenus Vetrix and Salix was about 17.6–16.0 Mya during the period of Middle Miocene Climate Transition (21–14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Identifying spatiotemporal patterns in opioid vulnerability: investigating the links between disability, prescription opioids and opioid-related mortality

Background: The opioid crisis remains one of the most daunting and complex public health problems in the United States. This study investigates the national epidemic by analyzing vulnerability profiles of three key factors: opioid-related mortality rates, opioid prescription dispensing rates, and disability rank ordered rates. Methods: This study utilizes county level data, spanning the years 2014 through 2020, on the rates of opioid-related mortality, opioid prescription dispensing, and disability. To successfully estimate and predict trends in these opioid-related factors, we augment the Kalman Filter with a novel spatial component. To define opioid vulnerability profiles, we create heat maps of our filter’s predicted rates across the nation’s counties and identify the hotspots. In this context, hotspots are defined on a year-by-year basis as counties with rates in the top 5% nationally. Results: Our spatial Kalman filter demonstrates strong predictive performance. From 2014 to 2018, these predictions highlight consistent spatiotemporal patterns across all three factors, with Appalachia distinguished as the nation’s most vulnerable region. Starting in 2019 however, the dispensing rate profiles undergo a dramatic and chaotic shift. Conclusions: The initial primary drivers of opioid abuse in the Appalachian region were likely prescription opioids; however, it now appears that abuse is sustained by illegal drugs. Additionally, we find that the disabled subpopulation may be more at risk of opioid-related mortality than the general population. Public health initiatives must extend beyond controlling prescription practices to address the transition to and impact of illicit drug use.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Differential patterns of reproductive and lifestyle risk factors for breast cancer according to birth cohorts among women in China, Japan and Korea

Background: The birth cohort effect has been suggested to influence the rate of breast cancer incidence and the trends of associated reproductive and lifestyle factors. We conducted a cohort study to determine whether a differential pattern of associations exists between certain factors and breast cancer risk based on birth cohorts. Methods: This was a cohort study using pooled data from 12 cohort studies. We analysed associations between reproductive (menarche age, menopause age, parity and age at first delivery) and lifestyle (smoking and alcohol consumption) factors and breast cancer risk. We obtained hazard ratios (HRs) with 95% confidence intervals (CIs) using the Cox proportional hazard regression analysis on the 1920s, 1930s, 1940s and 1950s birth cohorts. Results: Parity was found to lower the risk of breast cancer in the older but not in the younger birth cohort, whereas lifestyle factors showed associations with breast cancer risk only among the participants born in the 1950s. In the younger birth cohort group, the effect size was lower for parous women compared to the other cohort groups (HR [95% CI] 0.86 [0.66–1.13] compared to 0.60 [0.49–0.73], 0.46 [0.38–0.56] and 0.62 [0.51–0.77]). Meanwhile, a higher effect size was found for smoking (1.45 [1.14–1.84] compared to 1.25 [0.99–1.58], 1.06 [0.85–1.32] and 0.86 [0.69–1.08]) and alcohol consumption (1.22 [1.01–1.48] compared to 1.10 [0.90–1.33], 1.15 [0.96–1.38], and 1.07 [0.91–1.26]). Conclusion: We observed different associations of parity, smoking and alcohol consumption with breast cancer risk across various birth cohorts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Phase patterning of metallic glasses through superfast quenching of ion irradiation-induced thermal spikes

Amorphous metallic glasses (MGs) convert to crystalline solids upon annealing at a high temperature. Such a phase change, however, does not occur with the local melting caused by damage cascades introduced by ion irradiation, although the resulting thermal spikes can reach temperatures > 1000 K. This is because the quenching rate of the local melting zone is several orders of magnitude higher than the critical cooling rate for MG formation. Thus the amorphous structure is sustained. This mechanism increases the highest temperature at which irradiated MG sustains amorphous phase. More interestingly, if an irradiated MG is pre-annealed to form a polycrystalline structure, ion irradiation can locally convert this crystalline phase to an amorphous phase if the grains are nanometers in size and comparable to the damage cascade volume size. Combining pre-annealing and site selective ion irradiation, patterned crystalline-amorphous heterogeneous structures have been fabricated. This finding opens new doors for various applications.

36 MATERIALS SCIENCE↗
DOE OSTI2021

SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning

SMAD4 regulates gene expression in response to BMP and TGFβ signal transduction, and is required for diverse morphogenetic processes, but its target genes have remained largely elusive. Here, we identify the SMAD4 target genes in mouse limb buds using an epitope-tagged Smad4 allele for ChIP-seq analysis in combination with transcription profiling. This analysis shows that SMAD4 predominantly mediates BMP signal transduction during early limb bud development. Unexpectedly, the expression of cholesterol biosynthesis enzymes is precociously downregulated and intracellular cholesterol levels are reduced in Smad4-deficient limb bud mesenchymal progenitors. Most importantly, our analysis reveals a predominant function of SMAD4 in upregulating target genes in the anterior limb bud mesenchyme. Analysis of differentially expressed genes shared between Smad4- and Shh-deficient limb buds corroborates this function of SMAD4 and also reveals the repressive effect of SMAD4 on posterior genes that are upregulated in response to SHH signaling. This analysis uncovers opposing trans-regulatory inputs from SHH- and SMAD4-mediated BMP signal transduction on anterior and posterior gene expression during the digit patterning and outgrowth in early limb buds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Power distribution estimation method for SMR using ex-core detectors: experimental demonstration by plural control rod patterns at KUCA

The power distribution estimation method based on the ex-core detectors, or PHOEBE, was demonstrated at Kyoto University Critical Assembly, KUCA. Generally, core monitoring systems use in-core neutron detectors. Since inside the core is a harsh environment, the maintainability and reliability of the detectors are deteriorated. On the other hand, the environment outside the core is milder: core monitoring by the ex-core detectors improves the maintainability and reliability especially for small modular reactors and micro-reactors. However, neutron information from the inner region of the core is lost at the ex-core detectors. To recover the information, the authors proposed to utilize the power correlation between the fuel regions. PHOEBE concept was demonstrated at KUCA with distorted power distributions simulated by control rod patterns. The relative power distribution estimated by PHOEBE agreed with that calculated by Monte Carlo simulation code MVP. PHOEBE approximately reproduced the trend of the distorted power distributions calculated by MVP code. By contrast, the case of without power correlation between fuel regions produced significant different power distributions. Therefore, the advantage of considering the power correlation between fuel regions was also demonstrated. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2015

Ppb-level formaldehyde detection using a CW room-temperature interband cascade laser and a miniature dense pattern multipass gas cell

A ppb-level formaldehyde (H 2 CO) sensor was developed using a thermoelectrically cooled (TEC), continuous-wave (CW) room temperature interband cascade laser (ICL) emitting at 3.59 μm and a miniature dense pattern multipass gas cell with >50 m optical path length. Performance of the sensor was investigated with two measurement schemes: direct absorption (DAS) and wavelength modulation spectroscopy (WMS). With an integration time of less than 1.5 second, a detection limit of ~3 ppbv for H 2 CO measurement with precision of 1.25 ppbv for DAS and 0.58 ppbv for WMS, respectively, was achieved without zero air based background subtraction. An Allan-Werle variance analysis indicated that the precisions can be further improved to 0.26 ppbv @ 300s for DAS and 69 pptv @ 90 s for WMS, respectively. Finally, a side-by-side comparison between two measurement schemes is also discussed in detail.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Polarization mode control of long-wavelength VCSELs by intracavity patterning

Polarization mode control is enhanced in wafer-fused vertical-cavity surface-emitting lasers emitting at 1310 nm wavelength by etching two symmetrically arranged arcs above the gain structure within the laser cavity. The intracavity patterning introduces birefringence and dichroism, which discriminates between the two polarization states of the fundamental transverse modes. We find that the cavity modifications define the polarization angle at threshold with respect to the crystal axes, and increase the gain anisotropy and birefringence on average, leading to an increase in the polarization switching current. As a result, experimental measurements are explained using the spin-flip model of VCSEL polarization dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Electrically pumped continuous wave quantum dot lasers epitaxially grown on patterned, on-axis (001) Si

High performance III-V lasers at datacom and telecom wavelengths on on-axis (001) Si are needed for scalable datacenter interconnect technologies. We demonstrate electrically injected quantum dot lasers grown on on-axis (001) Si patterned with {111} v-grooves lying in the [110] direction. No additional Ge buffers or substrate miscut was used. The active region consists of five InAs/InGaAs dot-in-a-well layers. Here, we achieve continuous wave lasing with thresholds as low as 36 mA and operation up to 80°C.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2023

High external quantum efficiency (6.5%) InGaN V-defect LEDs at 600 nm on patterned sapphire substrates

Highly efficient long-wavelength InGaN LEDs have been a research focus in nitride LEDs for their potential applications in displays and solid-state lighting. A key breakthrough has been the use of laterally injected quantum wells via naturally occurring V-defects which promote hole injection through semipolar sidewalls and help to overcome the barriers to carrier injection that plague long wavelength nitride LEDs. In this article, we study V-defect engineered LEDs on (0001) patterned sapphire substrates (PSS) and GaN on (111) Si. V-defects were formed using a 40-period InGaN/GaN superlattice and we report a packaged external quantum efficiency (EQE) of 6.5% for standard 0.1 mm 2 . LEDs on PSS at 600 nm. We attribute the high EQE in these LEDs to lateral injection via V-defects.

Ewing, Jacob J.↗
DOE OSTI2019

Deterministic stabilization of eight-way 2D diffractive beam combining using pattern recognition

We demonstrate a new method for controlling diffractive, high-power beam combination, sensing phase errors by analyzing the intensity pattern of uncombined side beams at the output. A square array of eight beams is combined with <0.3% stability and 84.6% efficiency. As the channel count is increased, so does the usable information, enabling scaling to large channel counts without significant slowing of control loop response time, an advantage over single-input algorithms.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Enhancement of second-order optical nonlinearities and nanoscale periodic domain patterning in ferroelectric boron-substituted aluminum nitride thin films

The discovery and development of CMOS-compatible, nonlinear optical materials is essential to produce integrated photonic devices with advanced functionalities. AlN is a strong candidate for on-chip device demonstration due to its intrinsic second-order optical nonlinearities, large bandgap, and well-established fabrication techniques. However, AlN is not easily phase matched for the largest coefficient d 33 ; the coefficients that could potentially be dispersion phase-matched, d 31 and d 15 , have weak nonlinearities. This work investigates ferroelectric Al 1-x B x N (x = 0 to 0.11) for viability as a large bandgap nonlinear optical material with unique suitability towards ultraviolet light generation using second harmonic generation. The linear and nonlinear optical properties are characterized accounting for material anisotropy. With increasing B concentration, a large enhancement from near negligible values to d 31 = 0.9 ± 0.1 pm/V and d 15 = 1.2 ± 0.1 pm/V is observed. This compares favorably to other large bandgap materials like β-Ba(BO 2 ) 2 , where the largest nonlinear coefficient is d 22 ~ 2.3 pm/V at 800 nm. This is accompanied by a change in the bandgap from 6.1 eV to 5.8 eV as B substitution goes from 0 to 11%. A periodically poled, quasi-phase-matched ferroelectric domain pattern with 400 nm domain size and a wall roughness of <16 nm is demonstrated.

36 MATERIALS SCIENCE↗
DOE OSTI2013

A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis

Dark-grown seedlings exhibit skotomorphogenic development. Genetic and molecular evidence indicates that a quartet of Arabidopsis Phytochrome (phy)-Interacting bHLH Factors (PIF1, 3, 4, and 5) are critically necessary to maintaining this developmental state and that light activation of phy induces a switch to photomorphogenic development by inducing rapid degradation of the PIFs. Here, using integrated ChIP–seq and RNA–seq analyses, we have identified genes that are direct targets of PIF3 transcriptional regulation, exerted by sequence-specific binding to G-box (CACGTG) or PBE-box (CACATG) motifs in the target promoters genome-wide. In addition, expression analysis of selected genes in this set, in all triple pif-mutant combinations, provides evidence that the PIF quartet members collaborate to generate an expression pattern that is the product of a mosaic of differential transcriptional responsiveness of individual genes to the different PIFs and of differential regulatory activity of individual PIFs toward the different genes. Together with prior evidence that all four PIFs can bind to G-boxes, the data suggest that this collective activity may be exerted via shared occupancy of binding sites in target promoters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016–2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Stone, Nathan E.↗
DOE OSTI2014

Comparative Analyses of Three Chlorella Species in Response to Light and Sugar Reveal Distinctive Lipid Accumulation Patterns in the Microalga C. sorokiniana

While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG) lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold's basal medium (BBM) and heterotrophy in BBM supplemented with glucose (10 g L –1 ). Heterotrophic growth rates of UTEX 411, 265, and 1230 were found to be 1.5-, 3.7-, and 5-fold higher than their respective autotrophic rates. With a rapid nine-hour heterotrophic doubling time, Chlorella sorokiniana UTEX 1230 maximally accumulated 39% total lipids by dry weight during heterotrophy compared to 18% autotrophically. Furthermore, the discrete fatty acid composition of each strain was examined in order to elucidate lipid accumulation patterns under the two trophic conditions. In both modes of growth, UTEX 411 and 265 produced 18:1 as the principal fatty acid while UTEX 1230 exhibited a 2.5-fold enrichment in 18:2 relative to 18:1. Although the total lipid content was highest in UTEX 411 during heterotrophy, UTEX 1230 demonstrated a two-fold increase in its heterotrophic TAG fraction at a rate of 28.9 mg L –1 d –1 to reach 22% of the biomass, corresponding to as much as 90% of its total lipids. Interestingly, UTEX 1230 growth was restricted during mixotrophy and its TAG production rate was suppressed to 18.2 mg L –1 d –1 . This constraint on carbon flow raises intriguing questions about the impact of sugar and light on the metabolic regulation of microalgal lipid biosynthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Cell Context Dependent p53 Genome-Wide Binding Patterns and Enrichment at Repeats

The p53 ability to elicit stress specific and cell type specific responses is well recognized, but how that specificity is established remains to be defined. Whether upon activation p53 binds to its genomic targets in a cell type and stress type dependent manner is still an open question. Here we show that the p53 binding to the human genome is selective and cell context-dependent. We mapped the genomic binding sites for the endogenous wild type p53 protein in the human cancer cell line HCT116 and compared them to those we previously determined in the normal cell line IMR90. We report distinct p53 genome-wide binding landscapes in two different cell lines, analyzed under the same treatment and experimental conditions, using the same ChIP-seq approach. This is evidence for cell context dependent p53 genomic binding. The observed differences affect the p53 binding sites distribution with respect to major genomic and epigenomic elements (promoter regions, CpG islands and repeats). We correlated the high-confidence p53 ChIP-seq peaks positions with the annotated human repeats (UCSC Human Genome Browser) and observed both common and cell line specific trends. In HCT116, the p53 binding was specifically enriched at LINE repeats, compared to IMR90 cells. The p53 genome-wide binding patterns in HCT116 and IMR90 likely reflect the different epigenetic landscapes in these two cell lines, resulting from cancer-associated changes (accumulated in HCT116) superimposed on tissue specific differences (HCT116 has epithelial, while IMR90 has mesenchymal origin). In conclusion, our data support the model for p53 binding to the human genome in a highly selective manner, mobilizing distinct sets of genes, contributing to distinct pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Multi-scale temporal patterns in fish presence in a high-velocity tidal channel

The natural variation of fish presence in high-velocity tidal channels is not well understood. A better understanding of fish use of these areas would aid in predicting fish interactions with marine hydrokinetic (MHK) devices, the effects of which are uncertain but of high concern. To characterize the patterns in fish presence at a tidal energy site in Cobscook Bay, Maine, we examined two years of hydroacoustic data continuously collected at the proposed depth of an MHK turbine with a bottom-mounted, side-looking echosounder. The maximum number of fish counted per hour ranged from hundreds in the early spring to over 1,000 in the fall. Counts varied greatly with tidal and diel cycles in a seasonally changing relationship, likely linked to the seasonally changing fish community of the bay. In the winter and spring, higher hourly counts were generally confined to ebb tides and low slack tides near sunrise and sunset. In summer and fall of each year, the highest fish counts shifted to night and occurred during ebb, low slack, and flood tides. Fish counts were not linked to current speed, and did not decrease as current speed increased, contrary to observations at other tidal power sites. As fish counts may be proportional to the encounter rate of fish with an MHK turbine at the same depth, highly variable counts indicate that the risk to fish is similarly variable. The links between fish presence and environmental cycles at this site will likely be present at other locations with similar environmental forcing, making these observations useful in predicting potential fish interactions at tidal energy sites worldwide.

54 ENVIRONMENTAL SCIENCES↗