Results for “Sample Collection” — Page 58

DOE OSTI2023

Saccharomycopsis sp. KB-2023a isolate UFMG-CM-Y6991, whole genome shotgun sequencing project

Three yeast isolates were obtained from soil and rotting wood samples collected in an Amazonian rainforest biome in Brazil. Comparison of the intergenic spacer 5.8S region and the D1/D2 domains of the large subunit rRNA gene showed that the isolates represent a novel species of the genus Saccharomycopsis. A tree inferred from the D1/D2 sequences placed the novel species near a subclade containing Saccharomycopsis lassenensis, Saccharomycopsis fermentans, Saccharomycopsis javanensis, Saccharomycopsis babjevae, Saccharomycopsis schoenii and Saccharomycopsis oosterbeekiorum, but with low bootstrap support. In terms of sequence divergence, the novel species had the highest identity in the D1/D2 domains with Saccharomycopsis capsularis, from which it differed by 36 substitutions. In contrast, a phylogenomic analysis based on 1061 single-copy orthologs for a smaller set of Saccharomycopsis species whose whole genome sequences are available indicated that the novel species represented by strain UFMG-CM-Y6991 is phylogenetically closer to Saccharomycopsis fodiens and Saccharomycopsis sp. TF2021a (=Saccharomycopsis phalluae). The novel yeast is homothallic and produces asci with one spheroidal ascospore with an equatorial or subequatorial ledge. The name Saccharomycopsis praedatoria sp. nov. is proposed to accommodate the novel species. The holotype of Saccharomycopsis praedatoria is CBS 16589(T). The MycoBank number is MB849369. S. praedatoria was able to kill cells of Saccharomyces cerevisiae by means of penetration with infection pegs, a trait common to most species of Saccharomycopsis.

Amazonian Forest↗

DOE OSTI2023

SRX13165144: yHMH446_Pichia_sp_nov_plate33_SPADES

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

genome sequence↗

DOE OSTI2022

Pichia sp. yHMH446, whole genome shotgun sequencing project

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

genome sequence↗

DOE OSTI2021

Pichia sp. strain yHMH446 internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

genome sequence↗

DOE OSTI2021

Pichia sp. strain yHMH446 internal transcribed spacer 2 and large subunit ribosomal RNA gene, partial sequence

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

genome sequence↗

DOE OSTI2022

Pichia sp. yHMH446 translation elongation factor 1-alpha gene, partial cds

A novel budding yeast species was isolated from a soil sample collected in the United States of America. Phylogenetic analyses of multiple loci and phylogenomic analyses conclusively placed the species within the genus Pichia. Strain yHMH446 falls within a clade that includes Pichia norvegensis, Pichia pseudocactophila, Candida inconspicua, and Pichia cactophila. Whole genome sequence data were analyzed for the presence of genes known to be important for carbon and nitrogen metabolism, and the phenotypic data from the novel species were compared to all Pichia species with publicly available genomes. Across the genus, including the novel species candidate, we found that the inability to use many carbon and nitrogen sources correlated with the absence of metabolic genes. Based on these results, Pichia galeolata sp. nov. is proposed to accommodate yHMH446(T) (=NRRL Y-64187 = CBS 16864). This study shows how integrated taxogenomic analysis can add mechanistic insight to species descriptions.

genome sequence↗

DOE OSTI2011

The Mars Hopper: a radioisotope powered, impulse driven, long-range, long-lived mobile platform for exploration of Mars

Planetary exploration mission requirements are becoming more demanding. Due to the increasing cost, the missions that provide mobile platforms that can acquire data at multiple locations are becoming more attractive. Wheeled vehicles such as the MER rovers have proven extremely capable but have very limited range and cannot traverse rugged terrain. Flying vehicles such as balloons and airplanes have been proposed but are problematic due to the very thin atmospheric pressure and the strong, dusty winds present on Mars. The Center for Space Nuclear Research has designed an instrumented platform that can acquire detailed data at hundreds of locations during its lifetime - a Mars Hopper. The Mars Hopper concept utilizes energy from radioisotopic decay in a manner different from any existing radioisotopic power sources—as a thermal capacitor. By accumulating the heat from radioisotopic decay for long periods, the power of the source can be dramatically increased for short periods. The platform will be able to "hop" from one location to the next every 5-7 days with a separation of 5-10 km per hop. Preliminary designs show a platform that weighs around 52 kgs unfueled which is the condition at deployment. Consequently, several platforms may be deployed on a single launch from Earth. With sufficient lifetime, the entire surface of Mars can be mapped in detail by a couple dozen platforms. In addition, Hoppers can collect samples from all over the planet, including gorges, mountains and crevasses, and deliver them to a central location for eventual pick-up by a Mars Sample Return mission. The status of the Mars Hopper development project at the CSNR is discussed.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2012

Cellulolytic Microorganisms from Thermal Environments

Thermal, anaerobic environments rich in decaying plant material are a potential source of novel cellulolytic bacteria. Samples collected from geothermal aquifers in the Yellowstone National Park (YNP) were used to select for cellulolytic thermophiles. Laboratory enrichments on dilute-acid pretreated plant biomass (switchgrass, Populus), and crystalline cellulose (Avicel) resulted in the isolation of 247 environmental clones. The majority of individual clones were affiliated with the cellulolytic bacteria of phylum Firmicutes, followed by xylanolytic and saccharolytic members of the phylum Dictyoglomi. Among the Firmicutes, the clones were affiliated with the genera Caldicellulosiruptor (54.4%), Caloramator (11.5%), Thermoanaerobacter (8.8%), Thermovenabulum (4.1%), and Clostridium (2.0%). From established anaerobic thermophilic enrichments a total of 81 single strains of the genera Caldicellulosiruptor (57%) and Thermoanaerobacter (43%) were isolated. With continuous flow enrichment on Avicel, increases in the relative abundance of Caloramator sp. was observed over clones detected from the Caldicellulosiruptor. Complex communities of interacting microorganisms bring about cellulose decomposition in nature, therefore using up-to-date approaches may yield novel cellulolytic microorganisms with high activity and a rapid rate of biomass conversion to biofuels.

09 BIOMASS FUELS↗

DOE OSTI2011

Searches for Fourth Generation Fermions

We present the results from searches for fourth generation fermions performed using data samples collected by the CDF II and D0 Detectors at the Fermilab Tevatron p{bar p} collider. Many of these results represent the most stringent 95% C. L. limits on masses of new fermions to-date. A fourth chiral generation of massive fermions with the same quantum numbers as the known fermions is one of the simplest extensions of the SM with three generations. The fourth generation is predicted in a number of theories, and although historically have been considered disfavored, stands in agreement with electroweak precision data. To avoid Z {yields} {nu}{bar {nu}} constraint from LEP I a fourth generation neutrino {nu}{sub 4} must be heavy: m({nu}{sub 4}) > m{sub Z}/2, where m{sub Z} is the mass of Z boson, and to avoid LEP II bounds a fourth generation charged lepton {ell}{sub 4} must have m({ell}{sub 4}) > 101 GeV/c{sup 2}. At the same time due to sizeable radiative corrections masses of fourth generation fermions cannot be much higher the current lower bounds and masses of new heavy quarks t' and b' should be in the range of a few hundred GeV/c{sup 2}. In the four-generation model the present bounds on the Higgs are relaxed: the Higgs mass could be as large as 1 TeV/c{sup 2}. Furthermore, the CP violation is significantly enhanced to the magnitude that might account for the baryon asymmetry in the Universe. Additional chiral fermion families can also be accommodated in supersymmetric two-Higgs-doublet extensions of the SM with equivalent effect on the precision fit to the Higgs mass. Another possibility is heavy exotic quarks with vector couplings to the W boson Contributions to radiative corrections from such quarks with mass M decouple as 1/M{sup 2} and easily evade all experimental constraints. At the Tevatron p{bar p} collider 4-th generation chiral or vector-like quarks can be either produced strongly in pairs or singly via electroweak production, where the latter can be enhanced for vector-like quarks. In the following we present searches for both pair and single production of heavy quarks performed by CDF and D0 Collaborations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2011

Search for Lepton Flavour Violating Decays Tau- to L- K0(S) and Tau- to L- (Rho0, K0, Anti-K0, Phi) at BaBar

We report on recent searches for lepton flavour violating decays of the {tau} lepton: {tau}{sup -} {yields} {ell}{sup -} K{sub S}{sup 0}, {tau}{sup -} {yields} {ell}{sup -}({rho}{sup 0}, K*{sup 0}, {bar K}*{sup 0}, {phi}). These preliminary results use data samples collected by the BaBar detector at the SLAC PEP-II B factory corresponding to integrated luminosities of 469 fb{sup -1} for the {tau}{sup -} {yields} {ell}{sup -}K{sub S}{sup 0} and 451 fb{sup -1} for the {tau}{sup -} {yields} {ell}{sup -}({rho}{sup 0}, K*{sup 0}, {bar K}*{sup 0}, {phi}) searches. No statistically significant signal has been observed in any of these channels and we set upper limits on their branching fractions between 0.8-18.2 x 10{sup -8} at 90% confidence level.

43 PARTICLE ACCELERATORS↗

DOE OSTI2011

Search for signatures of extra dimensions in the diphoton mass spectrum at the Large Hadron Collider

A search for signatures of extra dimensions in the diphoton invariant-mass spectrum has been performed with the CMS detector at the LHC. No excess of events above the standard model expectation is observed using a data sample collected in proton-proton collisions at {radical}s = 7 TeV corresponding to an integrated luminosity of 2.2 fb{sup -1}. In the context of the large-extra-dimensions model, lower limits are set on the effective Planck scale in the range of 2.3-3.8 TeV at the 95% confidence level. These limits are the most restrictive bounds on virtual-graviton exchange to date. The most restrictive lower limits to date are also set on the mass of the first graviton excitation in the Randall-Sundrum model in the range of 0.86-1.84 TeV, for values of the associated coupling parameter between 0.01 and 0.10.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2012

Search for Scalar Top Quark Production in $p\bar{p}$ Collisions at $\sqrt{s}=1.96$ TeV

We report on a search for the supersymmetric partner of the top quark (scalar top) decaying into a charm quark and a neutralino in p{bar p} collisions at {radical}s = 1.96 TeV. The data sample, collected by the CDF II detector at the Fermilab Tevatron, corresponds to an integrated luminosity of 2.6 fb{sup -1}. Candidate events are selected by requiring two or more jets and a large imbalance in the transverse momentum. To enhance the analysis sensitivity, at least one of the jets is required to be identified as originating from a charm quark using an algorithm specifically designed for this analysis. The selected events are in good agreement with standard model predictions. In the case of large mass splitting between the scalar top quark and the neutralino we exclude a scalar top quark mass below 180 GeV/c{sup 2} at 95% confidence level.

43 PARTICLE ACCELERATORS↗

DOE OSTI2010

Predicting reaerosolization

Outdoor studies of the environmental persistence of bacteria have led to many interesting results. It turns out that the initial deposition of bacteria is not the end of the story. We examined both the ongoing daily deposition and aerosolization of bacteria for two weeks following an initial deposition event. Differences between samples collected in a clearing and those collected beneath a forest canopy were also examined. There were two important results: first, bacteria were still moving about in significant quantities after two weeks, though the local environment where they were most prevalent appeared to shift over time; second, we were able to develop a simple mathematical model that could fairly accurately estimate the average daily airborne concentration of bacteria over the duration of the experiment using readily available environmental information. The implication is that deposition patterns are very likely to shift over an extended period of time following a release, possibly quite significantly, but there is hope that we may be able to estimate these changes fairly accurately.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2012

Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Search for contact interactions in dilepton events from pp collisions at root s=7 TeV with the ATLAS detector

This Letter presents a search for contact interactions in the dielectron and dimuon channels using data from proton-proton collisions produced by the LHC at {radical}s = 7 TeV and recorded by the ATLAS detector. The data sample, collected in 2011, corresponds to an integrated luminosity of 1.08 and 1.21 fb{sup -1} in the e{sup +}e{sup -} and {mu}{sup +}{mu}{sup -} channels, respectively. No significant deviations from the standard model are observed. Using a Bayesian approach with a prior flat in 1/{Lambda}{sup 2}, the following 95% CL lower limits are placed on the energy scale of {ell}{ell}qq contact interactions: {Lambda}{sup -} > 10.1 TeV ({Lambda}{sup +} > 9.4 TeV) in the electron channel and {Lambda}{sup -} > 8.0 TeV ({Lambda}{sup +} > 7.0 TeV) in the muon channel for constructive (destructive) interference in the left-left isoscalar contact interaction model. Limits are also provided for a prior flat in 1/{Lambda}{sup 4}.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2012

A Robust Infrastructure Design for Gas Centrifuge Enrichment Plant Unattended Online Enrichment Monitoring

An online enrichment monitor (OLEM) is being developed to continuously measure the relative isotopic composition of UF6 in the unit header pipes of a gas centrifuge enrichment plant (GCEP). From a safeguards perspective, OLEM will provide early detection of a facility being misused for production of highly enriched uranium. OLEM may also reduce the number of samples collected for destructive assay and if coupled with load cell monitoring can provide isotope mass balance verification. The OLEM design includes power and network connections for continuous monitoring of the UF6 enrichment and state of health of the instrument. Monitoring the enrichment on all header pipes at a typical GCEP could require OLEM detectors on each of the product, tails, and feed header pipes. If there are eight process units, up to 24 detectors may be required at a modern GCEP. Distant locations, harsh industrial environments, and safeguards continuity of knowledge requirements all place certain demands on the network robustness and power reliability. This paper describes the infrastructure and architecture of an OLEM system based on OLEM collection nodes on the unit header pipes and power and network support nodes for groupings of the collection nodes. A redundant, self-healing communications network, distributed backup power, and a secure communications methodology. Two candidate technologies being considered for secure communications are the Object Linking and Embedding for Process Control Unified Architecture cross-platform, service-oriented architecture model for process control communications and the emerging IAEA Real-time And INtegrated STream-Oriented Remote Monitoring (RAINSTORM) framework to provide the common secure communication infrastructure for remote, unattended monitoring systems. The proposed infrastructure design offers modular, commercial components, plug-and-play extensibility for GCEP deployments, and is intended to meet the guidelines and requirements for unattended and remotely monitored safeguards systems.

On Line Enrichment Monitor GCEP↗

DOE OSTI2013

Unlocking a Sea Ice Secret

Dr. Rachel Obbard and her research group from Dartmouth College traveled to the Antarctic to collect samples of sea ice. Next stop: the GeoSoilEnviroCARS x-ray beamline at the Advanced Photon Source at Argonne National Laboratory in Illinois. This U.S. Department of Energy Office of Science synchrotron x-ray research facility gave the Obbard team the frontier scientific tools they needed to study the path bromide takes as it travels from the ocean to the atmosphere.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2013

Apparatus and method for monitoring of gas having stable isotopes

Gas having stable isotopes is monitored continuously by using a system that sends a modulated laser beam to the gas and collects and transmits the light not absorbed by the gas to a detector. Gas from geological storage, or from the atmosphere can be monitored continuously without collecting samples and transporting them to a lab.

47 OTHER INSTRUMENTATION↗