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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 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment

Abstract Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae . The strain was isolated from surface sediment (0–1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase ( mttB ) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. Among the ability to convert other sulfur compounds it has the genetic capacity to produce climatically active dimethyl sulfide. Growth on glutamate as a sole carbon source results in formation of cell-connecting filaments, a putative phenotypic adaptation of the surface-associated strain to the environmental conditions at the seafloor. Genome analysis revealed the presence of a flagellum ( fla 1) and a type IV pilus biogenesis, which is speculated to be a prerequisite for biofilm formation. This is also related to genes responsible for signalling such as N-acyl homoserine lactones, as well as quip-genes responsible for quorum quenching and antibiotic biosynthesis. Pairwise similarities of 16S rRNA genes (98.56 % sequence similarity to the next relative S. haliotis ) and the in silico DNA-DNA hybridization (21.20 % sequence similarity to S. haliotis ) indicated Shimia str. SK013 to be considered as a new species. The genome analysis of Shimia str. SK013 offered first insights into specific physiological and phenotypic adaptation mechanisms of Roseobacter- affiliated bacteria to the benthic environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Complete genome of Erwinia spp. str . LJJL01 isolated from waste charcoal

We present the complete genome sequence of Erwinia spp. str. LJJL01, isolated from waste charcoal in Colorado, USA, using Oxford Nanopore sequencing. This sequence provides important insights into this bacterium’s metabolic and catabolic robustness to utilize sugars, acids, and aromatics, highlighting its potential as a bio-industrial strain for various feedstocks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

A selection approach using high‑oxygen and pond-mimicking culture conditions increases biomass productivity in the industrially relevant diatom Nitzschia inconspicua str. hildebrandi

To meet the energy and food challenges of the 21st century, renewable and sustainable sources of fuel and nutrients are required. Microalgae offer promise in meeting these challenges but must achieve higher rates of areal productivity to compete with fully scaled, existing industries. In this study, we used selective O 2 pressure to attain a ~90% increase in areal biomass productivity relative to the parental strain in the diatom Nitzschia inconspicua str. hildebrandi under pond-mimicking conditions with high O 2 stress. The resulting strain (GAI-337) was tested further for dilution time, culture density, CO 2 supplementation, pH, temperature, and dissolved O 2 concentration under outdoor pond-mimicking conditions to improve areal productivities. These experiments yielded an optimum harvest and dilution time just after sunset, ~0.45 g AFDW L -1 initial culture density for maximal productivities, no requirement for CO 2 gas supplementation or pH control, maximal performance under a diel temperature curve going from 24 °C at night to 36 °C during the day, and benefits from some O 2 removal from the culture by bubbling with air. Using pond-mimicking laboratory bioreactors, N. inconspicua GAI-337 achieved ~42 g AFDW m -2 d -1 , placing it among the most productive microalgal strains tested to date. Nutrient limitation experiments resulted in a biomass composition with 36% of AFDW comprised of lipids (measured as FAMEs) that equated to ~160 Gallons of Gasoline Equivalent energy per ton AFDW, highlighting the potential of GAI337 as a promising renewable fuel feedstock strain.

09 BIOMASS FUELS↗
DOE OSTI2015

High quality draft genome sequence of Meganema perideroedes str. Gr1 T and a proposal for its reclassification to the family Meganemaceae fam. nov.

Meganema perideroedes Gr1 T is a filamentous bacterium isolated from an activated sludge wastewater treatment plant where it is implicated in poor sludge settleability (bulking). M. perideroedes is the sole described species of the genus Meganema and of the proposed novel family “Meganemaceae” . Here we describe the features of the type strain Gr1 T along with its annotated genome sequence. The 3,409,949 bp long draft genome consists of 22 scaffolds with 3,033 protein-coding and 59 RNA genes and is a part of Genomic Encyclopedia of Type Strains , Phase I: the one thousand microbial genomes KMG project. Notably, genome annotation indicated the potential for facultative methylotrophy. However, the ability to utilize methanol as a carbon source could not be empirically demonstrated for the type strain or for in situ Meganema spp. strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Metallic artifact mitigation and organ-constrained tissue assignment for Monte Carlo calculations of permanent implant lung brachytherapy

Purpose: To investigate methods of generating accurate patient-specific computational phantoms for the Monte Carlo calculation of lung brachytherapy patient dose distributions. Methods: Four metallic artifact mitigation methods are applied to six lung brachytherapy patient computed tomography (CT) images: simple threshold replacement (STR) identifies high CT values in the vicinity of the seeds and replaces them with estimated true values; fan beam virtual sinogram replaces artifact-affected values in a virtual sinogram and performs a filtered back-projection to generate a corrected image; 3D median filter replaces voxel values that differ from the median value in a region of interest surrounding the voxel and then applies a second filter to reduce noise; and a combination of fan beam virtual sinogram and STR. Computational phantoms are generated from artifact-corrected and uncorrected images using several tissue assignment schemes: both lung-contour constrained and unconstrained global schemes are considered. Voxel mass densities are assigned based on voxel CT number or using the nominal tissue mass densities. Dose distributions are calculated using the EGSnrc user-code BrachyDose for{sup 125}I, {sup 103}Pd, and {sup 131}Cs seeds and are compared directly as well as through dose volume histograms and dose metrics for target volumes surrounding surgical sutures. Results: Metallic artifact mitigation techniques vary in ability to reduce artifacts while preserving tissue detail. Notably, images corrected with the fan beam virtual sinogram have reduced artifacts but residual artifacts near sources remain requiring additional use of STR; the 3D median filter removes artifacts but simultaneously removes detail in lung and bone. Doses vary considerably between computational phantoms with the largest differences arising from artifact-affected voxels assigned to bone in the vicinity of the seeds. Consequently, when metallic artifact reduction and constrained tissue assignment within lung contours are employed in generated phantoms, this erroneous assignment is reduced, generally resulting in higher doses. Lung-constrained tissue assignment also results in increased doses in regions of interest due to a reduction in the erroneous assignment of adipose to voxels within lung contours. Differences in dose metrics calculated for different computational phantoms are sensitive to radionuclide photon spectra with the largest differences for{sup 103}Pd seeds and smallest but still considerable differences for {sup 131}Cs seeds. Conclusions: Despite producing differences in CT images, dose metrics calculated using the STR, fan beam + STR, and 3D median filter techniques produce similar dose metrics. Results suggest that the accuracy of dose distributions for permanent implant lung brachytherapy is improved by applying lung-constrained tissue assignment schemes to metallic artifact corrected images.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2012

Microbial Iron Cycling in Acidic Geothermal Springs of Yellowstone National Park: Integrating Molecular Surveys, Geochemical Processes, and Isolation of Novel Fe-Active Microorganisms

Geochemical, molecular, and physiological analyses of microbial isolates were combined to study the geomicrobiology of acidic iron oxide mats inYellowstone National Park. Nineteen sampling locations from 11 geothermal springs were studied ranging in temperature from 53 to 88°C and pH 2.4 to 3.6. All iron oxide mats exhibited high diversity of crenarchaeal sequences from the Sulfolobales, Thermoproteales, and Desulfurococcales. The predominant Sulfolobales sequences were highly similar to Metallosphaera yellowstonensis str. MK1, previously isolated from one of these sites. Other groups of archaea were consistently associated with different types of iron oxide mats, including undescribed members of the phyla Thaumarchaeota and Euryarchaeota. Bacterial sequences were dominated by relatives of Hydrogenobaculum spp. above 65–70°C, but increased in diversity below 60°C. Cultivation of relevant iron-oxidizing and iron-reducing microbial isolates included Sulfolobus str. MK3, Sulfobacillus str. MK2, Acidicaldus str. MK6, and a new candidate genus in the Sulfolobales referred to as Sulfolobales str. MK5. Strains MK3 and MK5 are capable of oxidizing ferrous iron autotrophically, while strain MK2 oxidizes iron mixotrophically. Similar rates of iron oxidation were measured for M. yellowstonensis str. MK1 and Sulfolobales str. MK5. Biomineralized phases of ferric iron varied among cultures and field sites, and included ferric oxyhydroxides, K-jarosite, goethite, hematite, and scorodite depending on geochemical conditions. Strains MK5 and MK6 are capable of reducing ferric iron under anaerobic conditions with complex carbon sources. The combination of geochemical and molecular data as well as physiological observations of isolates suggests that the community structure of acidic Fe mats is linked with Fe cycling across temperatures ranging from 53 to 88°C.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Partitioning of Fe(II) in reduced nontronite (NAu-2) to reactive sites: Reactivity in terms of Tc(VII) reduction

Abstract Clay minerals impart important chemical properties to soils, in part, by virtue of changes in the redox state of Fe in their crystal structures. Therefore, measurement of Fe(III)/Fe(II) and partitioning of Fe(II) in different reactive sites in clay minerals (during biological and chemical Fe(III) reduction) is essential to understand their role and their relative reactivity in terms of reduction and immobilization of heavy metal contaminants such as technetium. This study had three objectives: (1) to understand the degree of dissolution of nontronite (Fe-rich smectite) as a result of chemical and biological reduction of Fe(III) in the structure; (2) to quantify partitioning of chemically and biologically produced Fe(II) into different reactive sites in reduced nontronite, including aqueous Fe 2+ , ammonium chloride-extractable Fe(II) (mainly from the ion-exchangeable sites, denoted as Fe ( II ) NH 4 Cl ${\rm{Fe}}{\left( {{\rm{II}}} \right)_{{\rm{N}}{{\rm{H}}_4}{\rm{Cl}}}}$ ), sodium acetate-extractable Fe(II) (mainly from the surface complexation sites, denoted as Fe(II) acetate ), and structural Fe(II) (denoted as Fe(II) str ); and (3) to evaluate the reactivity of these Fe(II) species in terms of Tc(VII) reduction. Chemical and biological reduction of Fe(III) in nontronite (NAu-2) was performed, and reduced nontronite samples with different extents of Fe(III) reduction (1.2–71%) were prepared. The extent of reductive dissolution was measured as a function of the extent of Fe(III) reduction. Our results demonstrated that chemically and biologically produced Fe(II) in NAu-2 may be accommodated in the NAu-2 structure if the extent of Fe(III) reduction is small (< ∼30%). When the extent of reduction was >∼30%, dissolution of nontronite occurred with a corresponding decrease in crystallinity of residual nontronite. The Fe(II) produced was available for partitioning into four species: Fe ( ab ) 2 + ${\rm{Fe}}_{\left( {{\rm{ab}}} \right)}^{2 + }$ , Fe(II) acetate , Fe ( II ) NH 4 Cl ${\rm{Fe}}{\left( {{\rm{II}}} \right)_{{\rm{N}}{{\rm{H}}_4}{\rm{Cl}}}}$ , and Fe(II) str . The increase in Fe(II) acetate during the early stages of Fe(III) reduction indicated that the Fe(II) released had the greatest affinity for the surface-complexation sites, but this site had a limited capacity (∼60 µmol of Fe(II)/g of NAu-2). The subsequent increase in Fe ( II ) NH 4 Cl ${\rm{Fe}}{\left( {{\rm{II}}} \right)_{{\rm{N}}{{\rm{H}}_4}{\rm{Cl}}}}$ indicated that the released Fe(II) partitioned into the exchangeable sites once the amount of Fe at the surface-complexation sites reached half of its maximum site capacity. The fraction of Fe(II) str decreased concomitantly, as a result of Fe(II) release from the NAu-2 structure, from 100% when the extent of Fe(III) reduction was <30% to nearly 65% when the extent of Fe(III) reduction reached 71%. The Fe(II) acetate and Fe(II) str exhibited greater reactivity in terms of Tc(VII) reduction than the Fe ( II ) NH 4 Cl ${\rm{Fe}}{\left( {{\rm{II}}} \right)_{{\rm{N}}{{\rm{H}}_4}{\rm{Cl}}}}$ . Clearly, the surface-complexed and structural Fe(II) are the desirable species when reduced clay minerals are used to reduce and immobilize soluble heavy metals in contaminated groundwater and soils. These results have important implications for understanding microbe—clay mineral interactions and heavy metal immobilization in clay-rich natural environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2013

The Role of Postoperative Radiation Therapy in the Treatment of Meningeal Hemangiopericytoma—Experience From the SEER Database

Purpose: The aim of this study was to examine the effect of postoperative radiation therapy (RT) on cause-specific survival in patients with meningeal hemangiopericytomas. Methods and Materials: The Surveillance, Epidemiology, and End Results database from 1990-2008 was queried for cases of surgically resected central nervous system hemangiopericytoma. Patient demographics, tumor location, and extent of resection were included in the analysis as covariates. The Kaplan-Meier product-limit method was used to analyze cause-specific survival. A Cox proportional hazards regression analysis was conducted to determine which factors were associated with cause-specific survival. Results: The mean follow-up time is 7.9 years (95 months). There were 76 patients included in the analysis, of these, 38 (50%) underwent gross total resection (GTR), whereas the other half underwent subtotal resection (STR). Postoperative RT was administered to 42% (16/38) of the patients in the GTR group and 50% (19/38) in the STR group. The 1-year, 10-year, and 20-year cause-specific survival rates were 99%, 75%, and 43%, respectively. On multivariate analysis, postoperative RT was associated with significantly better survival (HR = 0.269, 95% CI 0.084-0.862; P=.027), in particular for patients who underwent STR (HR = 0.088, 95% CI: 0.015-0.528; P<.008). Conclusions: In the absence of large prospective trials, the current clinical decision-making of hemangiopericytoma is mostly based on retrospective data. We recommend that postoperative RT be considered after subtotal resection for patients who could tolerate it. Based on the current literature, the practical approach is to deliver limited field RT to doses of 50-60 Gy while respecting the normal tissue tolerance. Further investigations are clearly needed to determine the optimal therapeutic strategy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2013

Increased Subventricular Zone Radiation Dose Correlates With Survival in Glioblastoma Patients After Gross Total Resection

Purpose: Neural progenitor cells in the subventricular zone (SVZ) have a controversial role in glioblastoma multiforme (GBM) as potential tumor-initiating cells. The purpose of this study was to examine the relationship between radiation dose to the SVZ and survival in GBM patients. Methods and Materials: The study included 116 patients with primary GBM treated at the Johns Hopkins Hospital between 2006 and 2009. All patients underwent surgical resection followed by adjuvant radiation therapy with intensity modulated radiation therapy (60 Gy/30 fractions) and concomitant temozolomide. Ipsilateral, contralateral, and bilateral SVZs were contoured on treatment plans by use of coregistered magnetic resonance imaging and computed tomography. Multivariate Cox regression was used to examine the relationship between mean SVZ dose and progression-free survival (PFS), as well as overall survival (OS). Age, Karnofsky Performance Status score, and extent of resection were used as covariates. The median age was 58 years (range, 29-80 years). Results: Of the patients, 12% underwent biopsy, 53% had subtotal resection (STR), and 35% had gross total resection (GTR). The Karnofsky Performance Status score was less than 90 in 54 patients and was 90 or greater in 62 patients. The median ipsilateral, contralateral, and bilateral mean SVZ doses were 48.7 Gy, 34.4 Gy, and 41.5 Gy, respectively. Among patients who underwent GTR, a mean ipsilateral SVZ dose of 40 Gy or greater was associated with a significantly improved PFS compared with patients who received less than 40 Gy (15.1 months vs 10.3 months; P=.028; hazard ratio, 0.385 [95% confidence interval, 0.165-0.901]) but not in patients undergoing STR or biopsy. The subgroup of GTR patients who received an ipsilateral dose of 40 Gy or greater also had a significantly improved OS (17.5 months vs 15.6 months; P=.027; hazard ratio, 0.385 [95% confidence interval, 0.165-0.895]). No association was found between SVZ radiation dose and PFS and OS among patients who underwent STR or biopsy. Conclusion: A mean radiation dose of 40 Gy or greater to the ipsilateral SVZ was associated with a significantly improved PFS and OS in patients with GBM after GTR.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2014

Long-Term Outcomes and Complications in Patients With Craniopharyngioma: The British Columbia Cancer Agency Experience

Purpose: We report long-term outcomes and complications of craniopharyngioma patients referred to our institution. Methods and Materials: Between 1971 and 2010, 123 consecutive patients received primary treatment for craniopharyngioma in British Columbia and were referred to our institution. The median age was 30 years (range, 2-80 years). Thirty-nine percent of patients were treated primarily with subtotal resection (STR) and radiation therapy (RT), 28% with STR alone, 15% with gross total resection, 11% with cyst drainage (CD) alone, 5% with CD+RT, and 2% with RT alone. Eight percent of patients received intracystic bleomycin (ICB) therapy. Results: Median follow-up was 8.9 years, and study endpoints were reported at 10 years. Ten-year Kaplan-Meier progression-free survival (PFS) was 46%. Patients treated with STR+RT or CD+RT had the highest PFS (82% and 83%, respectively). There were no significant differences between PFS after adjuvant versus salvage RT (84% vs 74%, respectively; P=.6). Disease-specific survival (DSS) was 88%, and overall survival (OS) was 80%. Primary treatment modality did not affect DSS or OS, while older age was a negative prognostic factor for OS but not DSS. Kaplan-Meier rates for visual deterioration, anterior pituitary hormone deficiency, diabetes insipidus, seizure disorder, and cerebrovascular events (CVE) due to treatment, not tumor progression, were 27%, 76%, 45%, 16%, and 11%, respectively. The CVE rate was 29% in patients who received ICB compared to 10% in those who did not (P=.07). Conclusions: We report favorable PFS in patients with craniopharyngioma, especially in those who received RT after surgery. DSS and OS rates were excellent regardless of primary treatment modality. We observed a high incidence of hypopituitarism, visual deterioration, and seizure disorder. Eleven percent of patients experienced CVEs after treatment. There was a suggestion of increased CVE risk in patients treated with ICB.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Candidatus Mycoplasma girerdii replicates, diversifies, and co-occurs with Trichomonas vaginalis in the oral cavity of a premature infant

Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis). The completed 629,409-bp 'Mnola' genome (Candidatus Mycoplasma girerdii str. UC-B3) was distinct at the strain level from its closest relative, vaginally-derived Ca. M. girerdii str. VCU-M1, which is also associated with T. vaginalis. Replication rate measurements indicated growth of str. UC-B3 within the infant. Genes encoding surface-associated proteins and restriction-modification systems were especially diverse within and between strains. In UC-B3, the population genetic underpinnings of phase variable expression were evident in vivo. Unique among mycoplasmas, Ca. M. girerdii encodes pyruvate-ferredoxin oxidoreductase and may be sensitive to metronidazole. This study reveals a metabolically unique mycoplasma colonizing a premature neonate, and establishes the value of genome-resolved metagenomics in tracking phase variation.

60 APPLIED LIFE SCIENCES↗