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open access

DNA Degradation as an Indicator of Post-Mortem Interval

Description: The question of post-mortem interval (PMI) or time since death is often the most sought after piece of information associated with a medical death investigation. Based on the observation that DNA degradation disproportionately affects the analysis of larger genetic loci, it was proposed that DNA degradation, as a result of autolysis or putrefaction, could prove suitable as a potential rate-of-change indicator of PMI. Nine randomly amplified polymorphic DNA (RAPD) analysis primers and three se… more
Date: August 2010
Creator: Watson, William H.
Partner: UNT Libraries
open access

DNA Testing in Criminal Justice: Background, Current Law, Grants, and Issues

Description: This report provides an overview of how DNA is used to investigate crimes and help protect the innocent. It also reviews current statutory law on collecting DNA samples, sharing DNA profiles generated from those samples, and providing access to post-conviction DNA testing. The report also includes a summary of grant programs authorized by Congress to assist state and local governments with reducing DNA backlogs, provide post-conviction DNA testing, and promote new technology in the field. It al… more
Date: May 2, 2011
Creator: James, Nathan
Partner: UNT Libraries Government Documents Department
open access

DNA Databanking: Selected Fourth Amendment Issues and Analysis

Description: This report looks at how the practice of DNA database programs, which have been looked at favorably by Congress, are in possible violation of the Fourth Amendment's prohibition on unreasonable searches and seizures. It looks at how the databases' legality has currently been holding up in court, as well as how new advances and revelations in the science of forensic analysis and databanking may have potentially significant legal implications.
Date: June 6, 2011
Creator: Barbour, Emily C.
Partner: UNT Libraries Government Documents Department
open access

Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant

Description: This article reports on the dynamics of E coli DNA polymerase III proofreading in the presence of its processivity factor, the β₂-sliding clamp, at varying base pair termini using single-molecule FRET.
Date: September 3, 2018
Creator: Gahlon, Hailey L.; Walker, Alice R.; Cisneros, Gerardo Andrés; Lamers, Meindert H. & Rueda, David S.
Partner: UNT College of Science
open access

Influence of Translation Initiation on Organellar Protein Targeting in Arabidopsis

Description: A primary focus of the Mackenzie laboratory is the elucidation of processes and machinery for mitochondrial genome maintenance and transmission in higher plants. We have found that numerous organellar DNA maintenance components in plants appear to be dual targeted to mitochondria and plastids. Of particular interest was the observation that some twin (tandemly arrayed) dual targeting presequences appeared to utilize non-AUG alternative translation initiation, allowing for multiple translation s… more
Date: April 18, 2011
Creator: Mackenzie, Sally A.
Partner: UNT Libraries Government Documents Department
open access

Adult Human Pancreatic Islet Beta-Cells Display Limited Turnover and Long Lifespan as Determined by In-Vivo Thymidine Analog Incorporation and Radiocarbon Dating

Description: Diabetes mellitus results from an absolute or relative deficiency of insulin producing pancreatic beta-cells. The adult human beta-cell's turnover rate remains unknown. We employed novel techniques to examine adult human islet beta-cell turnover and longevity in vivo. Subjects enrolled in NIH clinical trials received thymidine analogues [iododeoxyuridine (IdU) or bromodeoxyuridine (BrdU)] 8-days to 4-years prior to death. Archival autopsy samples from ten patients (aged 17-74 years) were employ… more
Date: March 15, 2010
Creator: Perl, S.; Kushner, J. A.; Buchholz, B. A.; Meeker, A. K.; Stein, G. M.; Hsieh, M. et al.
Partner: UNT Libraries Government Documents Department
open access

Illumina Unamplified Indexed Library Construction: An Automated Approach

Description: Manual library construction is a limiting factor in Illumina sequencing. Constructing libraries by hand is costly, time-consuming, low-throughput, and ergonomically hazardous, and constructing multiple libraries introduces risk of library failure due to pipetting errors. The ability to construct multiple libraries simultaneously in automated fashion represents significant cost and time savings. Here we present a strategy to construct up to 96 unamplified indexed libraries using Illumina TruSeq … more
Date: March 21, 2011
Creator: Hack, Christopher A.; Sczyrba, Alexander & Cheng, Jan-Fang
Partner: UNT Libraries Government Documents Department
open access

Metabolic Design and Control for Production in Prokaryotes

Description: Prokaryotic life on earth is manifested by its diversity and omnipresence. These microbes serve as natural sources of a large variety of compounds with the potential to serve the ever growing, medicinal, chemical and transportation needs of the human population. However, commercially viable production of these compounds can be realized only through significant improvement of the native production capacity of natural isolates. The most favorable way to achieve this goal is through the genetic ma… more
Date: November 10, 2010
Creator: Chhabra, Swapnil R. & Keasling, J.D.
Partner: UNT Libraries Government Documents Department
open access

High Performance Computing Facility Operational Assessment, CY 2011 Oak Ridge Leadership Computing Facility

Description: Oak Ridge National Laboratory's Leadership Computing Facility (OLCF) continues to deliver the most powerful resources in the U.S. for open science. At 2.33 petaflops peak performance, the Cray XT Jaguar delivered more than 1.4 billion core hours in calendar year (CY) 2011 to researchers around the world for computational simulations relevant to national and energy security; advancing the frontiers of knowledge in physical sciences and areas of biological, medical, environmental, and computer sc… more
Date: February 1, 2012
Creator: Baker, Ann E; Barker, Ashley D; Bland, Arthur S Buddy; Boudwin, Kathlyn J.; Hack, James J; Kendall, Ricky A et al.
Partner: UNT Libraries Government Documents Department
open access

Engineering the Cyanobacterial Carbon Concentrating Mechanism for Enhanced CO2 Capture and Fixation

Description: In cyanobacteria CO2 fixation is localized in a special proteinaceous organelle, the carboxysome. The CO2 fixation enzymes are encapsulated by a selectively permeable protein shell. By structurally and functionally characterizing subunits of the carboxysome shell and the encapsulated proteins, we hope to understand what regulates the shape, assembly and permeability of the shell, as well as the targeting mechanism and organization of the encapsulated proteins. This knowledge will be used to enh… more
Date: June 2, 2011
Creator: Sandh, Gustaf; Cai, Fei; Shih, Patrick; Kinney, James; Axen, Seth; Salmeen, Annette et al.
Partner: UNT Libraries Government Documents Department
open access

Salt Dependence of the Radius of Gyration and Flexibility of Single-stranded DNA in Solution probed by Small-angle X-ray Scattering

Description: Short single-stranded nucleic acids are ubiquitous in biological processes and understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flex… more
Date: July 6, 2012
Creator: Sim, Adelene Y.L.; Lipfert, Jan; Herschlag, Daniel & Doniach, Sebastian
Partner: UNT Libraries Government Documents Department
open access

Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

Description: Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear t… more
Date: April 18, 2011
Creator: Goldfarb, K. C.; Karaoz, U.; Hanson, C. A.; Santee, C. A.; Bradford, M. A.; Treseder, K. K. et al.
Partner: UNT Libraries Government Documents Department
open access

The DNA repair endonuclease XPG interacts directly and functionally with the WRN helicase defective in Werner syndrome

Description: XPG is a structure-specific endonuclease required for nucleotide excision repair (NER). XPG incision defects result in the cancer-prone syndrome xeroderma pigmentosum, whereas truncating mutations of XPG cause the severe postnatal progeroid developmental disorder Cockayne syndrome. We show that XPG interacts directly with WRN protein, which is defective in the premature aging disorder Werner syndrome, and that the two proteins undergo similar sub-nuclear redistribution in S-phase and co-localiz… more
Date: April 20, 2011
Creator: Trego, Kelly S.; Chernikova, Sophia B.; Davalos, Albert R.; Perry, J. Jefferson P.; Finger, L. David; Ng, Cliff et al.
Partner: UNT Libraries Government Documents Department
open access

Reconstruction of a Bacterial Genome from DNA Cassettes

Description: This basic research program comprised two major areas: (1) acquisition and analysis of marine microbial metagenomic data and development of genomic analysis tools for broad, external community use; (2) development of a minimal bacterial genome. Our Marine Metagenomic Diversity effort generated and analyzed shotgun sequencing data from microbial communities sampled from over 250 sites around the world. About 40% of the 26 Gbp of sequence data has been made publicly available to date with a compl… more
Date: 2012~
Creator: Dupont, Christopher; Glass, John; Sheahan, Laura; Yooseph, Shibu; Allen, Lisa Zeigler; Thiagarajan, Mathangi et al.
Partner: UNT Libraries Government Documents Department
open access

Methods for Engineering Sulfate Reducing Bacteria of the Genus Desulfovibrio

Description: Sulfate reducing bacteria are physiologically important given their nearly ubiquitous presence and have important applications in the areas of bioremediation and bioenergy. This chapter provides details on the steps used for homologous-recombination mediated chromosomal manipulation of Desulfovibrio vulgaris Hildenborough, a well-studied sulfate reducer. More specifically, we focus on the implementation of a 'parts' based approach for suicide vector assembly, important aspects of anaerobic cult… more
Date: March 15, 2011
Creator: Chhabra, Swapnil R; Keller, Kimberly L. & Wall, Judy D.
Partner: UNT Libraries Government Documents Department
open access

Chromosomal Rainbows detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors

Description: Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumo… more
Date: August 19, 2010
Creator: O'Brien, Benjamin; Jossart, Gregg H.; Ito, Yuko; Greulich-Bode, Karin M.; Weier, Jingly F.; Munne, Santiago et al.
Partner: UNT Libraries Government Documents Department
open access

Somatic genomic variations in extra-embryonic tissues

Description: In the mature chorion, one of the membranes that exist during pregnancy between the developing fetus and mother, human placental cells form highly specialized tissues composed of mesenchyme and floating or anchoring villi. Using fluorescence in situ hybridization, we found that human invasive cytotrophoblasts isolated from anchoring villi or the uterine wall had gained individual chromosomes; however, chromosome losses were detected infrequently. With chromosomes gained in what appeared to be a… more
Date: May 21, 2010
Creator: Weier, Jingly F.; Ferlatte, Christy & Weier, Heinz-Ulli G.
Partner: UNT Libraries Government Documents Department
open access

Final Report on ``Theories of Strong Electron Correlations in Molecules and Solids’’ - DE-FG02-97ER45640

Description: The PI led theoretical studies of correlated hybridization in transition metal complexes, compounds, and molecules, and of electron transport in DNA associated with nanoelectronic conformations attached to gold electrodes and in the presence of DNA repair proteins.
Date: April 15, 2013
Creator: Cox, Daniel L.
Partner: UNT Libraries Government Documents Department
open access

Hybridization and Selective Release of DNA Microarrays

Description: DNA microarrays contain sequence specific probes arrayed in distinct spots numbering from 10,000 to over 1,000,000, depending on the platform. This tremendous degree of multiplexing gives microarrays great potential for environmental background sampling, broad-spectrum clinical monitoring, and continuous biological threat detection. In practice, their use in these applications is not common due to limited information content, long processing times, and high cost. The work focused on characteriz… more
Date: November 29, 2011
Creator: Beer, N R; Baker, B; Piggott, T; Maberry, S; Hara, C M; DeOtte, J et al.
Partner: UNT Libraries Government Documents Department
open access

Fleet DNA Project (Fact Sheet)

Description: The Fleet DNA Project - designed by the U.S. Department of Energy's National Renewable Energy Laboratory (NREL) in partnership with Oak Ridge National Laboratory - aims to accelerate the evolution of advanced vehicle development and support the strategic deployment of market-ready technologies that reduce costs, fuel consumption, and emissions. At the heart of the Fleet DNA Project is a clearinghouse of medium- and heavy-duty commercial fleet transportation data for optimizing the design of adv… more
Date: October 1, 2012
Partner: UNT Libraries Government Documents Department
open access

Regulation of Meiotic Recombination

Description: Meiotic recombination results in the heritable rearrangement of DNA, primarily through reciprocal exchange between homologous chromosome or gene conversion. In plants these events are critical for ensuring proper chromosome segregation, facilitating DNA repair and providing a basis for genetic diversity. Understanding this fundamental biological mechanism will directly facilitate trait mapping, conventional plant breeding, and development of genetic engineering techniques that will help support… more
Date: November 9, 2011
Creator: Copenhaver, Gregory P.
Partner: UNT Libraries Government Documents Department
open access

Mammalian Tissue Response to Low Dose Ionizing Radiation: The Role of Oxidative Metabolism and Intercellular Communication

Description: The objective of the project was to elucidate the mechanisms underlying the biological effects of low dose/low dose rate ionizing radiation in organs/tissues of irradiated mice that differ in their susceptibility to ionizing radiation, and in human cells grown under conditions that mimic the natural in vivo environment. The focus was on the effects of sparsely ionizing cesium-137 gamma rays and the role of oxidative metabolism and intercellular communication in these effects. Four Specific Aims… more
Date: January 16, 2013
Creator: Azzam, Edouard I.
Partner: UNT Libraries Government Documents Department
open access

Illumina GA IIx&HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute

Description: The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Illumina Genome Analyzer and HiSeq pipeline has been established. Optimization of the sesequencer pipelines has been ongoing with the aim of cont… more
Date: January 31, 2011
Creator: Daum, Christopher; Zane, Matthew; Han, James; Kennedy, Megan; San Diego, Matthew; Copeland, Alex et al.
Partner: UNT Libraries Government Documents Department
open access

2010 IRON-SULFUR ENZYMES GORDON RESEARCH CONFERENCE, JUNE 6-11, 2010

Description: Iron-sulfur (FeS) centers are essential for biology and inspirational in chemistry. These protein cofactors are broadly defined as active sites in which Fe is coordinated by S-donor ligands, often in combination with extra non-protein components, for example, additional metal atoms such as Mo and Ni, and soft ligands such as CN{sup -} and CO. Iron-sulfur centers are inherently air sensitive: they are found in essentially all organisms and it is possible that they were integral components of the… more
Date: June 11, 2010
Creator: Gray, Nancy Ryan
Partner: UNT Libraries Government Documents Department
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