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At least 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Comparative genomics of Mortierella elongata and its bacterial endosymbiont Mycoavidus cysteinexigens

Endosymbiosis of bacteria by eukaryotes is a defining feature of cellular evolution. In addition to well-known bacterial origins for mitochondria and chloroplasts, multiple origins of bacterial endosymbiosis are known within the cells of diverse animals, plants and fungi. Early-diverging lineages of terrestrial fungi harbor endosymbiotic bacteria belonging to the Burkholderiaceae. Furthermore, we sequenced the metagenome of the soil-inhabiting fungus Mortierella elongata and assembled the complete circular chromosome of its endosymbiont, Mycoavidus cysteinexigens, which we place within a lineage of endofungal symbionts that are sister clade to Burkholderia. The genome of M. elongata strain AG77 features a core set of primary metabolic pathways for degradation of simple carbohydrates and lipid biosynthesis, while the M. cysteinexigens (AG77) genome is reduced in size and function. Experiments using antibiotics to cure the endobacterium from the host demonstrate that the fungal host metabolism is highly modulated by presence/ absence of M. cysteinexigens. In independent comparative phylogenomic analyses of fungal and bacterial genomes we find that they are consistent with an ancient origin for M. elongata M. cysteinexigens symbiosis, most likely over 350 million years ago and concomitant with the terrestrialization of Earth and diversification of land fungi and plants.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics

Summary Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus ( Ca . N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca . Nitrosotalea strains, extracted an almost complete Ca . Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca . Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca . Nitrosotalea strains represent separate species within the genus. The four Ca . Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca . Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca . Nitrosotalea lineage in acidic environments.

Microbiology↗
DOE OSTI2024

Comparative proteomics of a versatile, marine, iron-oxidizing chemolithoautotroph

This study conducted a comparative proteomic analysis to identify potential genetic markers for the biological function of chemolithoautotrophic iron oxidation in the marine bacterium Ghiorsea bivora. To date, this is the only characterized species in the class Zetaproteobacteria that is not an obligate iron-oxidizer, providing a unique opportunity to investigate differential protein expression to identify key genes involved in iron-oxidation at circumneutral pH. Over 1000 proteins were identified under both iron- and hydrogen-oxidizing conditions, with differentially expressed proteins found in both treatments. Notably, a gene cluster upregulated during iron oxidation was identified. This cluster contains genes encoding for cytochromes that share sequence similarity with the known iron-oxidase, Cyc2. Interestingly, these cytochromes, conserved in both Bacteria and Archaea, do not exhibit the typical β-barrel structure of Cyc2. This cluster potentially encodes a biological nanowire-like transmembrane complex containing multiple redox proteins spanning the inner membrane, periplasm, outer membrane, and extracellular space. The upregulation of key genes associated with this complex during iron-oxidizing conditions was confirmed by quantitative reverse transcription-PCR. These findings were further supported by electromicrobiological methods, which demonstrated negative current production by G. bivora in a three-electrode system poised at a cathodic potential. This research provides significant insights into the biological function of chemolithoautotrophic iron oxidation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

In‐depth comparative analysis of Illumina ® MiSeq run metrics: Development of a wet‐lab quality assessment tool

Abstract Whole genome sequencing of bacterial isolates has become a daily task in many laboratories, generating incredible amounts of data. However, data acquisition is not an end in itself; the goal is to acquire high‐quality data useful for understanding genetic relationships. Having a method that could rapidly determine which of the many available run metrics are the most important indicators of overall run quality and having a way to monitor these during a given sequencing run would be extremely helpful to this effect. Therefore, we compared various run metrics across 486 MiSeq runs, from five different machines. By performing a statistical analysis using principal components analysis and a K ‐means clustering algorithm of the metrics, we were able to validate metric comparisons among instruments, allowing for the development of a predictive algorithm, which permits one to observe whether a given MiSeq run has performed adequately. This algorithm is available in an Excel spreadsheet: that is, MiSeq Instrument & Run (In‐Run) Forecast. Our tool can help verify that the quantity/quality of the generated sequencing data consistently meets or exceeds recommended manufacturer expectations. Patterns of deviation from those expectations can be used to assess potential run problems and plan preventative maintenance, which can save valuable time and funding resources.

Kastanis, George John↗
DOE OSTI2022

Clinical pharmacology information in regulatory submissions and labeling: A comparative analysis of orphan and non-orphan drugs approved by the FDA

Clinical pharmacology is an integral discipline supporting the development, regulatory evaluation, and clinical use of drugs for the treatment of both common and rare diseases. Here, we evaluated the recommendations and information available from select clinical pharmacology studies in the therapeutic product labeling of new molecular entities (NMEs) approved from 2017 to 2019 for both common and rare diseases. A total of 151 NMEs, including 72 orphan and 79 non-orphan drugs, were analyzed for recommendations and information available related to food–drug interaction, drug–drug interaction, renal impairment, hepatic impairment, QT assessment, and human radiolabeled mass balance studies using data collected from the original labeling and other regulatory documents. The analysis showed no statistically significant difference in the recommendations between orphan and non-orphan drugs except for renal impairment related recommendations in section 8 of the labeling. Although not significant, fewer hepatic impairment labeling recommendations were available for orphan drugs when compared with non-orphan drugs. At the time of initial approval, 79 postmarketing requirements (PMRs) and postmarketing commitments (PMCs) for 33 orphan drugs and 39 PMRs and PMCs for 19 non-orphan drugs were established; with most difference observed for drug–drug interaction, hepatic impairment, and QT assessment. Overall, although there was a trend for more labeling recommendations and fewer postmarketing studies and clinical trials for non-orphan drugs, there appeared to be no substantial differences in how these select clinical pharmacology studies are leveraged during the development and approval of orphan and non-orphan drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Microstructural origin of high‐strength Tyranno SA4 SiC fiber studied by comparative Raman spectroscopy #

Tyranno SA4 grade SiC fiber is an emerging continuous fiber with excellent mechanical properties. The origin of the fiber's high-performance was studied by comparative Raman spectroscopy of four different grades of SiC fibers and reference SiC monolith. Analysis of the Raman spectra of fiber cross-sections, surface and homogeneity, and fibers under stress, revealed how differences in microstructure, such as crystalline order, size, and the presence of critical flaws, dictate mechanical properties. In conclusion, this information can help optimize SiC fiber manufacturing.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Phenotypic and comparative genomic analysis of two Lactobacillus amylolyticus strains from naturally fermented tofu whey

Summary The differences in aspects of morphology, fermentation and probiotic characteristics between Lactobacillus amylolyticus L5 (Lam1.5) and L6 (Lam1.6) isolated from naturally fermented tofu whey were investigated by phenotypic and comparative genomic analysis. The results indicated that morphological difference between two strains may attribute to the mutation of ftsW and ftsK genes responsible for cell division. The optimum growth temperatures of Lam1.5 and Lam1.6 were different, and the acid‐producing ability of Lam1.6 was stronger than that of Lam1.5. And the growth rate of Lam1.6 exhibited better growth performance than that of Lam1.5 in MRS with initial pH 3.0–5.0. Besides, Lam1.5 was proved to be safe to be used in fermented food with safety evaluation. In respect of probiotic traits, Lam1.5 displayed the same performance in tolerance of intestinal juice, antimicrobial activity and adhesion properties as that of Lam1.6. However, Lam1.5 was more sensitive to simulated gastric juice than Lam1.6 at pH 2.5 and 3.0, which might be due to its long‐rod shape and lack of K+‐ATPase and Na+‐H+ antiporters. This study unveiled morphological and physiological differences between Lam1.5 and Lam1.6, raising the potential effect of ftsW and ftsK on the morphological development of lactobacilli that further affects their metabolic properties.

Fei, Yongtao↗
DOE OSTI2024

Comparative nutrient drawdown capacities of farmed kelps and implications of metabolic strategy and nutrient source

Abstract Seaweed aquaculture, particularly kelp farming, is a popular topic as a potential solution for mitigating anthropogenic pollutants and enhancing coastal drawdown of carbon and nitrogen. Using a common garden approach, this study evaluated nutrient drawdown capacities of Alaria marginata (ribbon kelp) and Saccharina latissima (sugar kelp) across four commercial kelp farms in Southeast and Southcentral Alaska. Our findings show that A. marginata exhibited ~30% more carbon and 21% more nitrogen content compared to S. latissima . These results demonstrate the potential for A. marginata to serve as a more efficient species for nutrient drawdown into farmed kelp tissues (per unit biomass) for consideration of potential mitigative actions. The efficacy of this drawdown is likely to be driven by the careful pairing of kelp species with farming environment. Temporally, there was a noted increase in carbon content and a decline in nitrogen content from March to May for both species, consistent with known seasonal nutrient dynamics in coastal waters. Notably, differences in the carbon stable isotope signatures (δ 13 C) between the kelps may hint at variations in metabolic pathways and nutrient sourcing, particularly concerning the preferential assimilation of CO 2 versus , and highlight the need for further work on this topic for applied macroalgal research.

Stephens, Tiffany↗
DOE OSTI2017

The bias of a two‐dimensional view: comparing two‐dimensional and three‐dimensional mesophyll surface area estimates using noninvasive imaging

Summary The mesophyll surface area exposed to intercellular air space per leaf area ( S m ) is closely associated with CO 2 diffusion and photosynthetic rates. S m is typically estimated from two‐dimensional (2D) leaf sections and corrected for the three‐dimensional (3D) geometry of mesophyll cells, leading to potential differences between the estimated and actual cell surface area. Here, we examined how 2D methods used for estimating S m compare with 3D values obtained from high‐resolution X‐ray microcomputed tomography (microCT) for 23 plant species, with broad phylogenetic and anatomical coverage. Relative to 3D, uncorrected 2D S m estimates were, on average, 15–30% lower. Two of the four 2D S m methods typically fell within 10% of 3D values. For most species, only a few 2D slices were needed to accurately estimate S m within 10% of the whole leaf sample median. However, leaves with reticulate vein networks required more sections because of a more heterogeneous vein coverage across slices. These results provide the first comparison of the accuracy of 2D methods in estimating the complex 3D geometry of internal leaf surfaces. Because microCT is not readily available, we provide guidance for using standard light microscopy techniques, as well as recommending standardization of reporting S m values.

Théroux‐Rancourt, Guillaume↗
DOE OSTI2017

Comparative plastome genomics and phylogenomics of Brachypodium : flowering time signatures, introgression and recombination in recently diverged ecotypes

Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B. distachyon, we detected two main lineages, a mostly Extremely Delayed Flowering (EDF+) clade and a mostly Spanish (S+) – Turkish (T+) clade, plus nine chloroplast capture and two plastid DNA (ptDNA) introgression and micro-recombination events. Early Oligocene (30.9 million yr ago (Ma)) and Late Miocene (10.1 Ma) divergence times were inferred for the respective stem and crown nodes of Brachypodium and a very recent Mid-Pleistocene(0.9 Ma) time for the B. distachyon split. Flowering time variation is a main factor driving rapid intraspecific divergence in B. distachyon, although it is counterbalanced by repeated introgression between previously isolated lineages. Swapping of plastomes between the three different genomic groups, EDF+,T+, S+, probably resulted from random backcrossing followed by stabilization through selection pressure.

Sancho, Rubén↗
DOE OSTI2019

Comparative genomics of Rhizophagus irregularis , R. cerebriforme , R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina

Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology. Here, we compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle. Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein-coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis-related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation. The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis-related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Comparative genomics reveals unique wood-decay strategies and fruiting body development in the Schizophyllaceae

Agaricomycetes are fruiting body-forming fungi that produce some of the most efficient enzyme systems to degrade wood. Despite decades-long interest in their biology, the evolution and functional diversity of both wood-decay and fruiting body formation are incompletely known. We performed comparative genomic and transcriptomic analyses of wood-decay and fruiting body development in Auriculariopsis ampla and Schizophyllum commune (Schizophyllaceae), species with secondarily simplified morphologies, an enigmatic wood-decay strategy and weak pathogenicity to woody plants. The plant cell wall-degrading enzyme repertoires of Schizophyllaceae are transitional between those of white rot species and less efficient wood-degraders such as brown rot or mycorrhizal fungi. Rich repertoires of suberinase and tannase genes were found in both species, with tannases restricted to Agaricomycetes that preferentially colonize bark-covered wood, suggesting potential complementation of their weaker wood-decaying abilities and adaptations to wood colonization through the bark. Fruiting body transcriptomes revealed a high rate of divergence in developmental gene expression, but also several genes with conserved expression patterns, including novel transcription factors and small-secreted proteins, some of the latter which might represent fruiting body effectors. Finally, taken together, our analyses highlighted novel aspects of wood-decay and fruiting body development in an important family of mushroom-forming fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Comparing Experimental Results for Large Particle Separation from Non-Newtonian Slurries Using Full and Tapered Bump Arrays

To separate particles from carrier fluids arrays of staggered posts inserted into the flow stream can be employed. The smaller particles follow the flow stream while the larger particles move laterally to one side. During flow, the concentration of particulate increases in one direction and decreases in the other crosswise direction. This technique separates the particles from the carrier fluid. Experiments using a slurry with non-Newtonian rheology were conducted to evaluate large particle separation from the non-Newtonian carrier fluid using bump arrays. The bentonite kaolin clay slurry with non-Newtonian rheology was spiked with large diameter inert glass particles. Experiments with flow through lateral displacement arrays evaluated the performance of particle separation using two array configurations: a full array with all posts and a tapered array with posts removed in a triangular portion of the array past the rows of anticipated particle of separation. The posts are staggered posts to promote particle segregation to one side of the flow channel. Using this type of array for removing particles from non-Newtonian yield stress slurries is novel and we present unique results. In this paper, the performance of full and tapered arrays are compared. These results have many industrial applications including removing particles from slurries of nuclear waste. Large particle removal is an important step in waste processing.

slurry, solids removal, deterministic lateral disp↗
DOE OSTI2023

Comparative Study on Deep Learning Methods for Defect Identification and Classification in Composite Aerostructure Material

Aircraft structures are required to have a high level of quality to satisfy their need for light weight, efficient flight, and withstanding high loads over their lifespan. These aerostructures are typically made from composite material due to their good tensile strength and resistance to compression. To ensure their structural integrity, the composite material requires inspection for common flaws such as porosity, delaminations, voids, foreign object debris, and other defects. Ultrasonic testing (UT) is a popular non-destructive inspection (NDI) technique used for effectively evaluating composite material. Current inspection methods rely heavily on human experience and are extremely time consuming. Therefore, there is a need for the development of techniques to reduce the manual inspection time. This work compares the performance of different deep learning-based methods in the identification and classification of defects. Deep learning has shown great promise in numerous fields, and we show its effectiveness in the evaluation of composite aerostructure material. Furthermore, the methods developed here are both highly reliable with a top recall value of 98.63% as well as extremely efficient requiring an average of 4 seconds during the inferencing stage to evaluate new composites.

composites↗
DOE OSTI2016

Comparative study of ITO and TiN fabricated by low-temperature RF biased sputtering

Radio frequency (RF) biasing induced by a second plasma source at the substrate is applied to low-temperature sputtering processes for indium tin oxide (ITO) and titanium nitride (TiN) thin films. Investigations on crystal structure and surface morphology show that RF-biased substrate plasma processes result in a changed growth regime with different grain sizes and orientations than those produced by processes without a substrate bias. The influence of the RF bias is shown comparatively for reactive RF-sputtered ITO and reactive direct-current-sputtered TiN. The ITO layers exhibit an improved electrical resistivity of 0.5 mΩ cm and an optical absorption coefficient of 0.5 × 10{sup 4 }cm{sup −1} without substrate heating. Room-temperature sputtered TiN layers are deposited that possess a resistivity (0.1 mΩ cm) of 3 orders of magnitude lower than, and a density (5.4 g/cm{sup 3}) up to 45% greater than, those obtained from layers grown using the standard process without a substrate plasma.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Study of shot noise in photoresists for extreme ultraviolet lithography through comparative analysis of line edge roughness in electron beam and extreme ultraviolet lithography

In this paper, the influence of the absorption shot noise on line edge roughness (LER) of photoresists for extreme ultraviolet (EUV) lithography is studied experimentally through the comparative analysis of LER obtained by EUV (92 eV photons) and 100 keV e-beam lithography. Techniques for performing EUV and e-beam lithography with a matched image log slope for a fair comparison of LER values are described. Measurements of absorption of 100 keV electrons estimated through a transmissive electron energy loss spectroscopy measurement with a 120 keV electron beam showed that despite having access to core levels in the material (e.g., 284 eV edge in carbon), these electrons mostly just excite the energy levels less than 100 eV in the resist, with a mean deposited energy of 35 eV. By combining the incident flux and the absorption probabilities, the absorbed quanta for patterning of 50 nm half-pitch line/space features was found to be similar between the two patterning technologies.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2013

Comparative dose evaluations between XVI and OBI cone beam CT systems using Gafchromic XRQA2 film and nanoDot optical stimulated luminescence dosimeters

Purpose: To investigate the effect of energy (kVp) and filters (no filter, half Bowtie, and full Bowtie) on the dose response curves of the Gafchromic XRQA2 film and nanoDot optical stimulated luminescence dosimeters (OSLDs) in CBCT dose fields. To measure surface and internal doses received during x-ray volume imager (XVI) (Version R4.5) and on board imager (OBI) (Version 1.5) CBCT imaging protocols using these two types of dosimeters. Methods: Gafchromic XRQA2 film and nanoDot OSLD dose response curves were generated at different kV imaging settings used by XVI (software version R4.5) and OBI (software version 1.5) CBCT systems. The settings for the XVI system were: 100 kVp/F0 (no filter), 120 kVp/F0, and 120 kVp/F1 (Bowtie filter), and for the OBI system were: 100 kVp/full fan, 125 kVp/full fan, and 125 kVp/half fan. XRQA2 film was calibrated in air to air kerma levels between 0 and 11 cGy and scanned using reflection scanning mode with the Epson Expression 10000 XL flat-bed document scanner. NanoDot OSLDs were calibrated on phantom to surface dose levels between 0 and 14 cGy and read using the inLight{sup TM} MicroStar reader. Both dosimeters were used to measure in field surface and internal doses in a male Alderson Rando Phantom. Results: Dose response curves of XRQA2 film and nanoDot OSLDs at different XVI and OBI CBCT settings were reported. For XVI system, the surface dose ranged between 0.02 cGy in head region during fast head and neck scan and 4.99 cGy in the chest region during symmetry scan. On the other hand, the internal dose ranged between 0.02 cGy in the head region during fast head and neck scan and 3.17 cGy in the chest region during chest M20 scan. The average (internal and external) dose ranged between 0.05 cGy in the head region during fast head and neck scan and 2.41 cGy in the chest region during chest M20 scan. For OBI system, the surface dose ranged between 0.19 cGy in head region during head scan and 4.55 cGy in the pelvis region during spot light scan. However, the internal dose ranged between 0.47 cGy in the head region during head scan and 5.55 cGy in the pelvis region during spot light scan. The average (internal and external) dose ranged between 0.45 cGy in the head region during head scan and 3.59 cGy in the pelvis region during spot light scan. Both Gafchromic XRQA2 film and nanoDot OSLDs gave close estimation of dose (within uncertainties) in many cases. Though, discrepancies of up to 20%-30% were observed in some cases. Conclusions: Dose response curves of Gafchromic XRQA2 film and nanoDot OSLDs indicated that the dose responses of these two dosimeters were different even at the same photon energy when different filters were used. Uncertainty levels of both dosimetry systems were below 6% at doses above 1 cGy. Both dosimetry systems gave almost similar estimation of doses (within uncertainties) in many cases, with exceptions of some cases when the discrepancy was around 20%-30%. New versions of the CBCT systems (investigated in this study) resulted in lower imaging doses compared with doses reported on earlier versions in previous studies.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2013

Comparative performance of modern digital mammography systems in a large breast screening program

Purpose: To compare physical measures pertaining to image quality among digital mammography systems utilized in a large breast screening program. To examine qualitatively differences in these measures and differences in clinical cancer detection rates between CR and DR among sites within that program. Methods: As part of the routine quality assurance program for screening, field measurements are made of several variables considered to correlate with the diagnostic quality of medical images including: modulation transfer function, noise equivalent quanta, d′ (an index of lesion detectability) and air kerma to allow estimation of mean glandular dose. In addition, images of the mammography accreditation phantom are evaluated. Results: It was found that overall there were marked differences between the performance measures of DR and CR mammography systems. In particular, the modulation transfer functions obtained with the DR systems were found to be higher, even for larger detector element sizes. Similarly, the noise equivalent quanta, d′, and the phantom scores were higher, while the failure rates associated with low signal-to-noise ratio and high dose were lower with DR. These results were consistent with previous findings in the authors’ program that the breast cancer detection rates at sites employing CR technology were, on average, 30.6% lower than those that used DR mammography. Conclusions: While the clinical study was not large enough to allow a statistically powered system-by-system assessment of cancer detection accuracy, the physical measures expressing spatial resolution, and signal-to-noise ratio are consistent with the published finding that sites employing CR systems had lower cancer detection rates than those using DR systems for screening mammography.

62 RADIOLOGY AND NUCLEAR MEDICINE↗