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in creator/contributor: "United States. Department of Energy. Office of Biological and Environmental Research."

open access

Horizontal gene transfer and the evolution of transcriptionalregulation in Escherichia coli

Background: Most bacterial genes were acquired by horizontalgene transfer from other bacteria instead of being inherited bycontinuous vertical descent from an ancient ancestor}. To understand howthe regulation of these {acquired} genes evolved, we examined theevolutionary histories of transcription factors and of regulatoryinteractions from the model bacterium Escherichia coli K12. Results:Although most transcription factors have paralogs, these usually arose byhorizontal gene transfer rather t… more

Date: December 20, 2007

Creator: Price, Morgan N.; Dehal, Paramvir S. & Arkin, Adam P.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Extending the cereus group genomics to putative food-borne pathogens of different toxicity

The cereus group represents sporulating soil bacteriacontaining pathogenic strains which may cause diarrheic or emetic foodpoisoning outbreaks. Multiple locus sequence typing revealed a presencein natural samples of these bacteria of about thirty clonal complexes.Application of genomic methods to this group was however biased due tothe major interest for representatives closely related to B. anthracis.Albeit the most important food-borne pathogens were not yet defined,existing dataindicate that… more

Date: August 24, 2006

Creator: Lapidus, Alla; Goltsman, Eugene; Auger, Sandrine; Galleron, Nathalie; Segurens, Beatrice; Dossat, Carole et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Pathway confirmation and flux analysis of central metabolicpathways in Desulfovibrio vulgaris Hildenborough using gaschromatography-mass spectrometry and fourier transform-ion cyclotronresonance mass spectrometry

It has been proposed that during growth under anaerobic oroxygen-limited conditions Shewanella oneidensis MR-1 uses theserine-isocitrate lyase pathway common to many methylotrophic anaerobes,in which formaldehyde produced from pyruvate is condensed with glycine toform serine. The serine is then transformed through hydroxypyruvate andglycerate to enter central metabolism at phosphoglycerate. To examine itsuse of the serine-isocitrate lyase pathway under anaerobic conditions, wegrew S. oneidensis… more

Date: July 11, 2006

Creator: Tang, Yinjie; Pingitore, Francesco; Mukhopadhyay, Aindrila; Phan,Richard; Hazen, Terry C. & Keasling, Jay D.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Evaluation of production samples of the scintillators LaBr3:Ce and LaCl3:Ce

We report on the evaluation of the performance of two recently developed scintillator materials, LaCl{sub 3}:Ce and LaBr{sub 3}:Ce, at the task of gamma ray spectroscopy. Their performance is compared to a standard scintillator used for gamma ray spectroscopy--a 25 mm diameter 25 mm tall cylinder of NaI:Tl. We measure the pulse height, energy resolution, and full-energy efficiency of production LaBr{sub 3}:Ce and LaCl{sub 3}:Ce scintillation crystals of different sizes and geometries for a vari… more

Date: September 15, 2005

Creator: Choong, Woon-Seng; Derenzo, Stephen E. & Moses, William W.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

IMG/M: A data management and analysis system for metagenomes

IMG/M is a data management and analysis system for microbial community genomes (metagenomes) hosted at the Joint Genome Institute (JGI). IMG/M consists of metagenome data integrated with isolate microbial genomes from the Integrated Microbial Genomes (IMG) system. IMG/M provides IMG's comparative data analysis tools extended to handle metagenome data, together with metagenome-specific analysis tools. IMG/M is available at http://img.jgi.doe.gov/m. Studies of the collective genomes (also known a… more

Date: August 1, 2007

Creator: Markowitz, Victor M.; Ivanova, Natalia N.; Szeto, Ernest; Palaniappan, Krishna; Chu, Ken; Dalevi, Daniel et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Targeting the tumor microenvironment

Despite some notable successes cancer remains, for the most part, a seemingly intractable problem. There is, however, a growing appreciation that targeting the tumor epithelium in isolation is not sufficient as there is an intricate mutually sustaining synergy between the tumor epithelial cells and their surrounding stroma. As the details of this dialogue emerge, new therapeutic targets have been proposed. The FDA has already approved drugs targeting microenvironmental components such as VEGF a… more

Date: November 7, 2006

Creator: Kenny, P. A.; Lee, G. Y. & Bissell, M. J.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Comparative Genome Analysis in the Integrated Microbial Genomes (IMG) System

Comparative genome analysis is critical for the effectiveexploration of a rapidly growing number of complete and draft sequencesfor microbial genomes. The Integrated Microbial Genomes (IMG) system(img.jgi.doe.gov) has been developed as a community resource thatprovides support for comparative analysis of microbial genomes in anintegrated context. IMG allows users to navigate the multidimensionalmicrobial genome data space and focus their analysis on a subset ofgenes, genomes, and functions of i… more

Date: March 1, 2006

Creator: Kyrpides, Nikos C. & Markowitz, Victor M.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Spatiotemporal variations in growing season exchanges of CO2, H2O,and sensible heat in agricultural fields of the Southern GreatPlains

Climate, vegetation cover, and management create fine-scaleheterogeneity in unirrigated agricultural regions, with important but notwell-quantified consequences for spatial and temporal variations insurface CO2, water, and heat fluxes. We measured eddy covariance fluxesin seven agricultural fields--comprising winter wheat, pasture, andsorghum--in the U.S. Southern Great Plains (SGP) during the 2001-2003growing seasons. Land-cover was the dominant source of variation insurface fluxes, with 50-10… more

Date: June 13, 2007

Creator: Fischer, Marc L.; Billesbach, David P.; Berry, Joseph A.; Riley,William J. & Torn, Margaret S.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Using IMG: Comparative Analysis with the Integrated Microbial Genomes System

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Date: December 3, 2007

Creator: Markowitz, Victor M.; Ivanova, Natalia; Anderson, Iain; Lykidis,Athanasios; Mavromatis, Konstantinos; Szeto, Ernest et al.

Item Type: Report

Partner: UNT Libraries Government Documents Department

open access

Process Control Minitoring by Stress Response

Environmental contamination with a variety of pollutants hasprompted the development of effective bioremediation strategies. But howcan these processes be best monitored and controlled? One avenue underinvestigation is the development of stress response systems as tools foreffective and general process control. Although the microbial stressresponse has been the subject of intensive laboratory investigation, theenvironmental reflection of the laboratory response to specific stresseshas been litt… more

Date: April 17, 2006

Creator: Hazen, Terry C. & Stahl, David A.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

The Life-cycle of Operons

Operons are a major feature of all prokaryotic genomes, buthow and why operon structures vary is not well understood. To elucidatethe life-cycle of operons, we compared gene order between Escherichiacoli K12 and its relatives and identified the recently formed anddestroyed operons in E. coli. This allowed us to determine how operonsform, how they become closely spaced, and how they die. Our findingssuggest that operon evolution may be driven by selection on geneexpression patterns. First, both … more

Date: March 15, 2007

Creator: Price, Morgan N.; Arkin, Adam P. & Alm, Eric J.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Galvanic interpretation of self-potential signals associated withmicrobial sulfate-reduction

We have evaluated the usefulness of the self-potential (SP)geophysical method to track the onset and location of microbialsulfate-reduction in saturated sediments during organic carbon amendment.Following stimulation of sulfate-reducing bacteria (SRB) by addition oflactate, anomalous voltages exceeding 600 mV correlated in space and timewith the accumulation of dissolved sulfide. Abiotic experiments in whichthe sulfide concentration at the measurement electrode was systematicallyvaried showed a… more

Date: May 2, 2007

Creator: Williams, Kenneth H.; Hubbard, Susan S. & Banfield, Jillian F.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

The morphologies of breast cancer cell lines in three-dimensionalassays correlate with their profiles of gene expression

3D cell cultures are rapidly becoming the method of choice for the physiologically relevant modeling of many aspects of non-malignant and malignant cell behavior ex vivo. Nevertheless, only a limited number of distinct cell types have been evaluated in this assay to date. Here we report the first large scale comparison of the transcriptional profiles and 3D cell culture phenotypes of a substantial panel of human breast cancer cell lines. Each cell line adopts a colony morphology of one of four … more

Date: January 31, 2007

Creator: Kenny, Paraic A.; Lee, Genee Y.; Myers, Connie A.; Neve, RichardM.; Semeiks, Jeremy R.; Spellman, Paul T. et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

FINAL REPORT: A Study of the Abundance and 13C/12C Ratio of Atmospheric Carbon Dioxide to Advance the Scientific Understanding of Terrestrial Processes Regulating the GCC

The main objective of this project was to continue research to develop carbon cycle relationships related to the land biosphere based on remote measurements of atmospheric CO2 concentration and its isotopic composition. The project continued time-series observations of atmospheric carbon dioxide and isotopic composition begun by Charles D. Keeling at remote sites, including Mauna Loa, the South Pole, and eight other sites. The program also included the development of methods for measuring radio… more

Date: December 23, 2008

Creator: Keeling, R. F. & Piper, S. C.

Item Type: Report

Partner: UNT Libraries Government Documents Department

open access

Use of simulated data sets to evaluate the fidelity of Metagenomic processing methods

Metagenomics is a rapidly emerging field of research for studying microbial communities. To evaluate methods presently used to process metagenomic sequences, we constructed three simulated data sets of varying complexity by combining sequencing reads randomly selected from 113 isolate genomes. These data sets were designed to model real metagenomes in terms of complexity and phylogenetic composition. We assembled sampled reads using three commonly used genome assemblers (Phrap, Arachne and JAZZ… more

Date: December 1, 2006

Creator: Mavromatis, Konstantinos; Ivanova, Natalia; Barry, Kerri; Shapiro, Harris; Goltsman, Eugene; McHardy, Alice C. et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

The integrated microbial genomes (IMG) system in 2007: datacontent and analysis tool extensions

The Integrated Microbial Genomes (IMG) system is a data management, analysis and annotation platform for all publicly available genomes. IMG contains both draft and complete JGI microbial genomes integrated with all other publicly available genomes from all three domains of life, together with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and annotating genomes, genes and functions, individually or in a comparative context. Since its first release in 2005,… more

Date: August 1, 2007

Creator: Markowitz, Victor M.; Szeto, Ernest; Palaniappan, Krishna; Grechkin, Yuri; Chu, Ken; Chen, I-Min A. et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

A comparison of DNA damage probes in two HMEC lines with X-irradiation

In this study, we investigated {gamma}H2AX{sup ser139} and 53BP1{sup ser25}, DNA damage pathway markers, to observe responses to radiation insult. Two Human Mammary Epithelial Cell (HMEC) lines were utilized to research the role of immortalization in DNA damage marker expression, HMEC HMT-3522 (S1) with an infinite lifespan, and a subtype of HMEC 184 (184V) with a finite lifespan. Cells were irradiated with 50 cGy X-rays, fixed with 4% paraformaldehyde after 1 hour repair at 37 C, and processed… more

Date: January 19, 2007

Creator: Wisnewski, Christy L.; Bjornstad, Kathleen A.; Rosen, ChristoperJ.; Chang, Polly Y. & Blakely, Eleanor A.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Effect of Saline Waste Solution Infiltration Rates on Uranium Retention and Spatial Distribution in Hanford Sediments

The accidental overfilling of waste liquid from tank BX-102 at the Hanford Site in 1951 put about 10 metric tons of U(VI) into the vadose zone. In order to understand the dominant geochemical reactions and transport processes occurred during the initial infiltration and help understand current spatial distribution, we simulated the waste liquid spilling event in laboratory sediment columns using synthesized metal waste solution. We found that, as the plume propagating through sediments, pH decr… more

Date: March 15, 2007

Creator: Wan, Jiamin; Tokunaga, Tetsu K.; Kim, Yongman; Wang, Zheming; Lanzirotti, Antonio; Saiz, Eduardo et al.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Epigenetic reversion of breast carcinoma phenotype is accompanied by DNA sequestration

The importance of microenvironment and context in regulation of tissue-specific genes is finally well established. DNA exposure to, or sequestration from, nucleases can be used to detect differences in higher order chromatin structure in intact cells without disturbing cellular or tissue architecture. To investigate the relationship between chromatin organization and tumor phenotype, we utilized an established 3-D assay where normal and malignant human breast cells can be easily distinguished b… more

Date: July 19, 2006

Creator: Sandal, Tone; Valyi-Nagy, Klara; Spencer, Virginia A.; Folberg,Robert; Bissell, Mina J. & Maniotis, Andrew J.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Proteomic Analysis of Calcium- and Phosphorylation-dependentCalmodulin Complexes in Mammalian Cells

Protein conformational changes due to cofactor binding (e.g. metal ions, heme) and/or posttranslational modifications (e.g. phosphorylation) modulate dynamic protein complexes. Calmodulin (CaM) plays an essential role in regulating calcium (Ca{sup 2+}) signaling and homeostasis. No systematic approach on the identification of phosphorylation-dependent Ca{sup 2+}/CaM binding proteins has been published. Herein, we report a proteome-wide study of phosphorylation-dependent CaM binding proteins fro… more

Date: May 26, 2006

Creator: Jang, Deok-Jin & Wang, Daojing

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Complete chloroplast genome of Trachelium caeruleum: extensiverearrangements are associated with repeats and tRNAs

Chloroplast genome structure, gene order and content arehighly conserved in land plants. We sequenced the complete chloroplastgenome sequence of Trachelium caeruleum (Campanulaceae) a member of anangiosperm family known for highly rearranged chloroplast genomes. Thetotal genome size is 162,321 bp with an IR of 27,273 bp, LSC of 100,113bp and SSC of 7,661 bp. The genome encodes 115 unique genes, with 19duplicated in the IR, a tRNA (trnI-CAU) duplicated once in the LSC and aprotein coding gene (p… more

Date: January 9, 2006

Creator: Haberle, Rosemarie C.; Fourcade, Matthew L.; Boore, Jeffrey L. & Jansen, Robert K.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

Field evidence for strong chemical separation of contaminants in the Hanford Vadose Zone

Water and chemical transport from a point source withinvadose zone sediments at Hanford were examined with a leak testconsisting of five 3800-liter aliquots of water released at 4.5 m depthevery week over a 4-week period. The third aliquot contained bromide, D2Oand 87Sr. Movement of the tracers was monitored for 9 months by measuringpore water compositions of samples from boreholes drilled 2-8 m from theinjection point. Graded sedimentary layers acting as natural capillarybarriers caused signif… more

Date: April 10, 2007

Creator: Conrad, Mark E.; DePaolo, Donald J.; Maher, Katharine; Gee,Glendon W. & Ward, Anderson L.

Item Type: Article

Partner: UNT Libraries Government Documents Department

open access

An Integrated Assessment of Geochemical and Community Structure Determinants of Metal Reduction Rates in Subsurface Sediments

This project represented a joint effort between Oak Ridge National Laboratory (ORNL), the University of Tennessee (UT), and Florida State University (FSU). ORNL served as the lead in-stitution with Dr. A.V. Palumbo responsible for project coordination, integration, and deliver-ables. In situ uranium bioremediation is focused on biostimulating indigenous microorganisms through a combination of pH neutralization and the addition of large amounts of electron donor. Successful biostimulation of U(V… more

Date: March 24, 2008

Creator: Kostka, Joel E.

Item Type: Report

Partner: UNT Libraries Government Documents Department

open access

The Shewanella oneidensis MR-1 Fluxome under Various OxygenConditions

The central metabolic fluxes of Shewanella oneidensis MR-1were examined under carbon-limited (aerobic) and oxygen-limited(micro-aerobic) chemostat conditions using 13C labeled lactate as thesole carbon source. The carbon labeling patterns of key amino acids inbiomass were probed using both GC-MS and 13C-NMR. Based on the genomeannotation, a metabolic pathway model was constructed to quantify thecentral metabolic flux distributions. The model showed that thetricarboxylic acid (TCA) cycle is the … more

Date: March 17, 2006

Creator: Tang, Yinjie J.; Hwang, Judy S.; Wemmer, David E. & Keasling, Jay D.

Item Type: Article

Partner: UNT Libraries Government Documents Department