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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

KBase Narrative - Draft Genome of Roseomonas Strain GC11

This narrative was used for the draft genome of a Roseomonas species Strain GC11. This genus includes 6 known species. The specimen was collected using a water grab method in Conservancy Park, a freshwater site in Belleview, KY. This species is often identified in aquatic environments and is a known pathogen to humans1. It has been reported in healthcare settings from bacteremia in the blood and has also been reported to be found in human catheters. Due to the the prevelance as a human pathogen and lack of isolation in a non-human environment this strain was of particular interest.

Cooper, Joshua [Northern Kentucky University, Depa↗
DOE OSTI2023

Five draft genome assemblies from Bacillaceae isolated from a degraded wetland environment

Abstract We isolated 5 Bacillaceae from a degraded wetland environment and sequenced their genomes using Illumina NextSeq. Here, we report draft genome sequences of Bacillus velezensus-SC119, Priestia megaterium-SC120, Bacillus zhangzhouensis-SC123, Bacillus pumilis-SC124, and Bacillus idriensis-SC127. The genomes range between 3,657,353 and 5,772,725 base pairs with %GC between 37.62% and 46.38%. Introduction Wetland environments play critical roles in the terrestrial carbon and water cycles and microbial communities are key players in healthy ecosystem function. Endospore forming bacteria in the Bacillaceae family are metabolically and genomically diverse soil heterotrophs that influence plant health, carbon and nitrogen cycling, and often produce diverse natural products that influence other bacterial and non-bacterial species in their environment (1). We collected two soil samples on January 19, 2023 from 42°43'12.7"N 73°45'01.4"W. One was highly hydrated and within a patch of invasive common reeds (Phragmites sp.) and the other was near the base of an Eastern cottonwood tree (Populus deltoides). Bacillus pumilis strain SC124 was isolated from the soil from near the cottonwood tree, while Bacillus velezensis strain SC119, Priestia megaterium strain SC120, Bacillus zhangzhouensis strain SC123, Bacillus idriensis strain SC127 and were isolated from the marshy soil.

isolate, wetlands, genome announcement↗
DOE OSTI2014

High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway

Olivivacter sitiensis Ntougias et al. 2007 is a member of the family Sphingobacteriaceae, phylum Bacteroidetes. Members of the genus Olivibacter are phylogenetically diverse and of significant interest. They occur in diverse habitats, such as rhizosphere and contaminated soils, viscous wastes, composts, biofilter clean-up facilities on contaminated sites and cave environments, and they are involved in the degradation of complex and toxic compounds. Here we describe the features of O. sitiensis AW-6T , together with the permanent-draft genome sequence and annotation. The organism was sequenced under the Genomic Encyclopedia for Bacteria and Archaea (GEBA) project at the DOE Joint Genome Institute and it is the first genome sequence of a species within the genus Olivibacter. The genome is 5,053,571 bp long and is comprised of 110 scaffolds with an average GC content of 44.61%. Of the 4,565 genes predicted, 4,501 were protein-coding genes and 64 were RNA genes. Most protein-coding genes (68.52%) were assigned to a putative function. The identification of 2-keto-4- pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase-coding genes indicates involvement of this organism in the catechol catabolic pathway. In addition, genes encoding for β-1,4-xylanases and β-1,4-xylosidases reveal the xylanolytic action of O. sitiensis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

High quality draft genome sequence of the slightly halophilic bacterium Halomonas zhanjiangensis type strain JSM 078169T (DSM 21076T) from a sea urchin in southern China

Halomonas zhanjiangensis Chen et al. 2009 is a member of the genus Halomonas, family Halomonadaceae, class Gammaproteobacteria. Representatives of the genus Halomonas are a group of halophilic bacteria often isolated from salty environments. The type strain H. zhanjiangensis JSM 078169T was isolated from a sea urchin (Hemicentrotus pulcherrimus) collected from the South China Sea. The genome of strain JSM 078169T is the fourteenth sequenced genome in the genus Halomonas and the fifteenth in the family Halomonadaceae. The other thirteen genomes from the genus Halomonas are H. halocynthiae, H. venusta, H. alkaliphila, H. lutea, H. anticariensis, H. jeotgali, H. titanicae, H. desiderata, H. smyrnensis, H. salifodinae, H. boliviensis, H. elongata and H stevensii. Here, we describe the features of strain JSM 078169T , together with the complete genome sequence and annotation from a culture of DSM 21076T . The 4,060,520 bp long draft genome consists of 17 scaffolds with the 3,659 protein-coding and 80 RNA genes and is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

Halomonadaceae↗
DOE OSTI2017

Data from: Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Intense artificial selection over the last 100 years has produced elite maize (Zea mays) inbred lines that combine to produce high-yielding hybrids. To further our understanding of how genome and transcriptome variation contribute to the production of high-yielding hybrids, we generated a draft genome assembly of the inbred line PH207 to complement and compare with the existing B73 reference sequence. B73 is a founder of the Stiff Stalk germplasm pool, while PH207 is a founder of Iodent germplasm, both of which have contributed substantially to the production of temperate commercial maize and are combined to make heterotic hybrids. Comparison of these two assemblies revealed over 2,500 genes present in only one of the two genotypes and 136 gene families that have undergone extensive expansion or contraction. Transcriptome profiling revealed extensive expression variation, with as many as 10,564 differentially expressed transcripts and 7,128 transcripts expressed in only one of the two genotypes in a single tissue. Genotype-specific genes were more likely to have tissue/condition-specific expression and lower transcript abundance. The availability of a high-quality genome assembly for the elite maize inbred PH207 expands our knowledge of the breadth of natural genome and transcriptome variation in elite maize inbred lines across heterotic pools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Seasonal controls on isolated convective storm drafts, precipitation intensity, and life cycle as observed during GoAmazon2014/5

Abstract. Isolated deep convective cloud life cycle and seasonal changes in storm properties are observed for daytime events during the US Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Green Ocean Amazon Experiment (GoAmazon2014/5) campaign to understand controls on storm behavior. Storm life cycles are documented using surveillance radar from initiation through maturity and dissipation. Vertical air velocity estimates are obtained from radar wind profiler overpasses, with the storm environment informed by radiosondes. Dry-season storm conditions favored reduced morning shallow cloud coverage and larger low-level convective available potential energy (CAPE) than wet-season counterparts. The typical dry-season storm reached its peak intensity and size earlier in its life cycle compared with wet-season cells. These cells exhibited updrafts in core precipitation regions (Z>35 dBZ) to above the melting level as well as persistent downdrafts aloft within precipitation adjacent to their cores. Moreover, dry-season cells recorded more intense updrafts to earlier life cycle stages as well as a higher incidence of strong updrafts (i.e., >5 m s−1) at low levels. In contrast, wet-season storms were longer-lived and featured a higher incidence of moderate (i.e., 2–5 m s−1) updrafts aloft. These storms also favored a shift in their most intense properties to later life cycle stages. Strong downdrafts were less frequent within wet-season cells aloft, indicating a potential systematic difference in draft behaviors, as linked to graupel loading and other factors between the seasons. Results from a stochastic parcel model suggest that dry-season cells may expect stronger updrafts at low levels because of larger low-level CAPE in the dry season. Wet-season cells anticipate strong updrafts aloft because of larger free-tropospheric relative humidity and reduced entrainment-driven dilution. Enhanced dry-season downdrafts are partially attributed to increased evaporation, dry-air entrainment mixing, and negative buoyancy in regions adjacent to sampled dry-season cores.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

INL Contributions to Draft HTTF Benchmark Specifications

The High-Temperature Test Facility (HTTF) is an integral effects thermal hydraulics test facility at Oregon State University designed as a 1/4 length scale model of the Modular High-Temperature Gas-Cooled Reactor 350 MW core (mHTGR-350). In the spring and summer of 2019, several experiments were conducted at HTTF providing a valuable source of gas-cooled reactor thermal hydraulics data. Idaho National Laboratory (INL), Oregon State University, Argonne National Laboratory, and Canadian Nuclear Laboratories have partnered to use this experimental data to develop a gas-cooled reactor thermal hydraulics benchmark led by INL under the auspices of the Advanced Reactor Technologies (ART) program. This report provides some context on the benchmark, HTTF, and previous Reactor Excursions and Leak Analysis Program (RELAP)5-3D modeling of HTTF. It also provides a draft of the benchmark specifications for the Depressurized Conduction Cooldown problem, which is the INL-led benchmark problem.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2022

ARC-100 Conceptual Design Phase Level 1 PSA Early Draft

This report represents the initial structure and content created for the ARC-100 nuclear reactor initial conceptual design Probabilistic Safety Assessment. The objective of the study is to assess the safety of the ARC-100 nuclear reactor conceptual design using a risk-informed approach. This early draft report is the first transmittal of the Probabilistic Safety Assessment approach and will be expanded over the remainder of the projects.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Comment Response for the Draft Combined TREAT-LOC & SATS Integral LOCA Experiment Plan

This document provides a detailed description of comments and responses, to the Advanced Fuel Campaign (AFC) loss-of-coolant accident (LOCA) experiment plan draft document shared in April 2022. Comments were provided from reviewers from U.S. nuclear fuel vendors, the Electric Power Research Institute (EPRI), the U.S. Nuclear Regulatory Commission (NRC), and the U.S. Department of Energy (DOE) all provided comments after solicitation. All comments have been carefully considered and responded to accordingly. Editorial and clarification comments are excluded from this writeup, but all have been addressed directly in the text of the revised plan document.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗