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Improved Wood Properties Through Genetic Manipulation: Engineering of Syringyl Lignin in Softwood Species Through Xylem-Specific Expression of Hardwood Syringyl Monolignol Pathway Genes

Description: Project Objective: Our long-term goal is to genetically engineer higher value raw materials with desirable wood properties to promote energy efficiency, international competitiveness, and environmental responsiveness of the U.S. forest products industry. The immediate goal of this project was to produce the first higher value softwood raw materials engineered with a wide range of syringyl lignin quantities. Summary: The most important wood property affecting directly the levels of energy, chemi… more
Date: January 29, 2009
Creator: Joshi, Chandrashekhar P. & Chiang, Vincent L.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation

Description: “Molecular dissection of the roles of the SOD genes in mammalian response to low dose irradiation " was started on 09/01/03 and ended on 08/31/07. The primary objective of the project was to carry out mechanistic studies of the roles of the anti-oxidant SOD genes in mammalian cellular response to low dose ionizing radiation.
Date: January 27, 2009
Creator: Li, Dr. Chuan-Yaun
Item Type: Refine your search to only Text
Partner: UNT Libraries Government Documents Department
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Final Technical Report

Description: Bioremediation of radionuclides and metals in the subsurface necessitate an understanding of the metabolic capacities and interactions of the anaerobic microorganisms that are found there, including members of the sulfate-reducing bacteria (SRB). Genetic investigation into the pathway of reductant flow to U(VI) in the SRB belonging to the genus Desulfovibrio has been the focus of this project. In Dv. desulfuricans strain G20, we confirmed the importance of the tetraheme cytochrome c3 by disrupt… more
Date: February 27, 2009
Creator: Wall, Judy D.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

An Integrated Functional Genomics Consortium to Increase Carbon Sequestration in Poplars: Optimizing Aboveground Carbon Gain

Description: This project used gene expression patterns from two forest Free-Air CO2 Enrichment (FACE) experiments (Aspen FACE in northern Wisconsin and POPFACE in Italy) to examine ways to increase the aboveground carbon sequestration potential of poplars (Populus). The aim was to use patterns of global gene expression to identify candidate genes for increased carbon sequestration. Gene expression studies were linked to physiological measurements in order to elucidate bottlenecks in carbon acquisition in t… more
Date: February 17, 2009
Creator: Karnosky, David F (deceased); Podila, G Krishna & Burton, Andrew J (for DF Karnosky)
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

The Shewanella Federation: Functional Genomic Investigations of Dissimilatory Metal-Reducing Shewanella

Description: Generation and validation of a Shewanella oneidensis MR-1 clone set for protein expression and phage display. An ORF clone set for S. oneidensis was created using the lambda recombinase system. ORFs within entry vectors in this system can be readily transferred into multiple destination vectors, making the clone set a useful resource for research groups studying this microorganism. To establish that the S. oneidensis clone set could be used for protein expression and functional studies, three s… more
Date: January 30, 2009
Creator: Zhou, Jizhong & He, Zhili
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
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Implementation Plans for a Systems Microbiology and Extremophile Research Facility

Description: Introduction Biological organisms long ago solved many problems for which scientists and engineers seek solutions. Microbes in particular offer an astonishingly diverse set of capabilities that can help revolutionize our approach to solving many important DOE problems. For example, photosynthetic organisms can generate hydrogen from light while simultaneously sequestering carbon. Others can produce enzymes that break down cellulose and other biomass to produce liquid fuels. Microbes in water an… more
Date: April 20, 2009
Creator: Wiley, H. S.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Gene Expression in the Third Dimension: The ECM-nucleus Connection

Description: Decades ago, we and others proposed that the dynamic interplay between a cell and its surrounding environment dictates cell phenotype and tissue structure. Whereas much has been discovered about the effects of extracellular matrix molecules on cell growth and tissue specific gene expression, the nuclear mechanisms through which these molecules promote these physiological events remain unknown. Using mammary epithelial cells as a model, the purpose of this review is to discuss how the extracellu… more
Date: October 1, 2009
Creator: Spencer, Virginia A; Xu, Ren & Bissell, Mina
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Radiosensitivity profiles from a panel of ovarian cancer cell lines exhibiting genetic alterations in p53 and disparate DNA-dependent protein kinase activities

Description: The variability of radiation responses in ovarian tumors and tumor-derived cell lines is poorly understood. Since both DNA repair capacity and p53 status can significantly alter radiation sensitivity, we evaluated these factors along with radiation sensitivity in a panel of sporadic human ovarian carcinoma cell lines. We observed a gradation of radiation sensitivity among these sixteen lines, with a five-fold difference in the LD50 between the most radiosensitive and the most radioresistant cel… more
Date: September 7, 2009
Creator: Langland, Gregory T.; Yannone, Steven M.; Langland, Rachel A.; Nakao, Aki; Guan, Yinghui; Long, Sydney B.T. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Description: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor inte… more
Date: July 31, 2009
Creator: N. Price, Morgan; S. Dehal, Paramvir & P. Arkin, Adam
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Listening to the noise: random fluctuations reveal gene network parameters

Description: The cellular environment is abuzz with noise. The origin of this noise is attributed to the inherent random motion of reacting molecules that take part in gene expression and post expression interactions. In this noisy environment, clonal populations of cells exhibit cell-to-cell variability that frequently manifests as significant phenotypic differences within the cellular population. The stochastic fluctuations in cellular constituents induced by noise can be measured and their statistics qua… more
Date: January 1, 2009
Creator: Munsky, Brian & Khammash, Mustafa
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis

Description: Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high-resolution microarrays t… more
Date: February 3, 2009
Creator: Yamamoto, Miki L.; Clark, Tyson A.; Gee, Sherry L.; Kang, Jeong-Ah; Schweitzer, Anthony C.; Wickrema, Amittha et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair

Description: The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable… more
Date: May 11, 2009
Creator: Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

IMG ER: A System for Microbial Genome Annotation Expert Review and Curation

Description: A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and eff… more
Date: May 25, 2009
Creator: Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.; Chu, Ken & Kyrpides, Nikos C.
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Versatile P(acman) BAC Libraries for Transgenesis Studies in Drosophila melanogaster

Description: We constructed Drosophila melanogaster BAC libraries with 21-kb and 83-kb inserts in the P(acman) system. Clones representing 12-fold coverage and encompassing more than 95percent of annotated genes were mapped onto the reference genome. These clones can be integrated into predetermined attP sites in the genome using Phi C31 integrase to rescue mutations. They can be modified through recombineering, for example to incorporate protein tags and assess expression patterns.
Date: April 21, 2009
Creator: Venken, Koen J.T.; Carlson, Joseph W.; Schulze, Karen L.; Pan, Hongling; He, Yuchun; Spokony, Rebecca et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

AmiGO: online access to ontology and annotation data

Description: AmiGO is a web application that allows users to query, browse, and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium; it can also be downloaded and installed to browse local ontologies and annotations. AmiGO is free open source software developed and maintained by the GO Consortium.
Date: January 15, 2009
Creator: Carbon, Seth; Ireland, Amelia; Mungall, Christopher J.; Shu, ShengQiang; Marshall, Brad & Lewis, Suzanna
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Functional autonomy of distant-acting human enhancers

Description: Many human genes are associated with dispersed arrays of transcriptional enhancers that regulate their expression in time and space. Studies in invertebrate model systems have suggested that these elements function as discrete and independent regulatory units, but the in vivo combinatorial properties of vertebrate enhancers remain poorly understood. To explore the modularity and regulatory autonomy of human developmental enhancers, we experimentally concatenated up to four enhancers from differ… more
Date: February 19, 2009
Creator: Visel, Axel; Akiyama, Jennifer A.; Shoukry, Malak; Afzal, Veena; Rubin, Edward M. & Pennacchio, Len A.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Genome analysis of Elusimicrobium minutum, the first cultivated representative of the Elusimicrobia phylum (formerly Termite Group 1)

Description: The candidate phylum Termite group 1 (TG1), is regularly 1 encountered in termite hindguts but is present also in many other habitats. Here we report the complete genome sequence (1.64 Mbp) of Elusimicrobium minutum strain Pei191{sup T}, the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut and discuss the findings in light of physiological data. E. minutum has all genes required for uptake and … more
Date: February 1, 2009
Creator: Herlemann, D. P. R.; Geissinger, O.; Ikeda-Ohtsubo, W.; Kunin, V.; Sun, H.; Lapidus, A. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Cellulose Synthesizing Complexes in Vascular Plants and Procaryotes

Description: Continuing the work initiated under DE-FG03-94ER20145, the following major accomplishments were achieved under DE-FG02-03ER15396 from 2003-2007: (a) we purified the acsD gene product of the Acetobacter cellulose synthase operon as well as transferred the CesA cellulose gene from Gossypium into E. coli in an attempt to crystallize this protein for x-ray diffraction structural analysis; however, crystallization attempts proved unsuccessful; (b) the Acetobacter cellulose synthase operon was succes… more
Date: July 7, 2009
Creator: Brown, Richard M., Jr. & Saxena, Inder Mohan
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Homology with vesicle fusion mediator syntaxin-1a predicts determinants ofepimorphin/syntaxin-2 function in mammary epithelial morphogenesis

Description: We have shown that branching morphogenesis of mammary ductal structures requires the action of the morphogen epimorphin/syntaxin-2. Epimorphin, originally identified as an extracellular molecule, is identical to syntaxin-2, an intracellular molecule that is a member of the extensively investigated syntaxin family of proteins that mediate vesicle trafficking. We show here that although epimorphin/syntaxin-2 is highly homologous to syntaxin-1a, only epimorphin/syntaxin-2 can stimulate mammary bra… more
Date: June 3, 2009
Creator: Chen, Connie S.; Nelson, Celeste M.; Khauv, Davitte; Bennett, Simone; Radisky, Evette S.; Hirai, Yohei et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Bacterial Community Succession During in situ Uranium Bioremediation: Spatial Similarities Along Controlled Flow Paths

Description: Bacterial community succession was investigated in a field-scale subsurface reactor formed by a series of wells that received weekly ethanol additions to re-circulating groundwater. Ethanol additions stimulated denitrification, metal reduction, sulfate reduction, and U(VI) reduction to sparingly soluble U(IV). Clone libraries of SSU rRNA gene sequences from groundwater samples enabled tracking of spatial and temporal changes over a 1.5 y period. Analyses showed that the communities changed in a… more
Date: May 22, 2009
Creator: Hwang, Chiachi; Wu, Weimin; Gentry, Terry J.; Carley, Jack; Corbin, Gail A.; Carroll, Sue L. et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Transgenic Mouse Model of Chronic Beryllium Disease

Description: Animal models provide powerful tools for dissecting dose-response relationships and pathogenic mechanisms and for testing new treatment paradigms. Mechanistic research on beryllium exposure-disease relationships is severely limited by a general inability to develop a sufficient chronic beryllium disease animal model. Discovery of the Human Leukocyte Antigen (HLA) - DPB1Glu69 genetic susceptibility component of chronic beryllium disease permitted the addition of this human beryllium antigen pres… more
Date: May 26, 2009
Creator: Gordon, Terry
Item Type: Refine your search to only Report
Partner: UNT Libraries Government Documents Department
open access

Geochip: A high throughput genomic tool for linking community structure to functions

Description: GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of … more
Date: January 30, 2009
Creator: Van Nostrand, Joy D.; Liang, Yuting; He, Zhili; Li, Guanghe & Zhou, Jizhong
Item Type: Refine your search to only Book
Partner: UNT Libraries Government Documents Department
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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

Description: BACKGROUND: We previously established that six sequence-specific transcription factors that initiate anterior/posterior patterning in Drosophila bind to overlapping sets of thousands of genomic regions in blastoderm embryos. While regions bound at high levels include known and probable functional targets, more poorly bound regions are preferentially associated with housekeeping genes and/or genes not transcribed in the blastoderm, and are frequently found in protein coding sequences or in less … more
Date: May 15, 2009
Creator: MacArthur, Stewart; Li, Xiao-Yong; Li, Jingyi; Brown, James B.; Chu, Hou Cheng; Zeng, Lucy et al.
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
open access

Expanded breadth of the T-cell response to mosaic HIV-1 envelope DNA vaccination

Description: An effective AIDS vaccine must control highly diverse circulating strains of HIV-1. Among HIV -I gene products, the envelope (Env) protein contains variable as well as conserved regions. In this report, an informatic approach to the design of T-cell vaccines directed to HIV -I Env M group global sequences was tested. Synthetic Env antigens were designed to express mosaics that maximize the inclusion of common potential Tcell epitope (PTE) 9-mers and minimize the inclusion of rare epitopes likel… more
Date: January 1, 2009
Creator: Korber, Bette; Fischer, William & Wallstrom, Timothy
Item Type: Refine your search to only Article
Partner: UNT Libraries Government Documents Department
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