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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 also reviews select issues Congress might consider should it legislate or conduct oversight in this area.
Date: January 9, 2014
Creator: James, Nathan
Partner: UNT Libraries Government Documents Department

Characterization of a Human 28S Ribosomal RNA Retropseudogene and Other Repetitive DNA Sequence Elements Isolated from a Human X Chromosome-Specific Library

Description: Three genomic clones encompassing human DNA segments (designated LhX-3, LhX-4, and LhX5) were isolated from an X chromosome-specific library and subjected to analysis by physical mapping and DNA sequencing. It was found that these three clones are very rich in repetitive DNA sequence elements and retropseudogenes.
Date: May 1994
Creator: Wang, Suyue
Partner: UNT Libraries

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.
Date: December 6, 2012
Creator: James, Nathan
Partner: UNT Libraries Government Documents Department

The effect of solvent dynamics on the low frequency collectivemotions of DNA in solution and unoriented films

Description: Infrared spectroscopy is used to probe the dynamics of invitro samples of DNA prepared as solutions and as solid unoriented films.The lowest frequency DNA mode identified in the far-infrared spectra ofthe DNA samples is found to shift in frequency when the solvent influencein the hydration shell is altered. The lowest frequency mode also hascharacteristics that are similar to beta - relaxations identified inother glass forming polymers.
Date: April 20, 2006
Creator: Woods, K.N.; Lee, S.A.; Holman, H.-Y.N. & Wiedemann, H.
Partner: UNT Libraries Government Documents Department

Quantum-Confined CdS Nanoparticles on DNA Templates

Description: As electronic devices became smaller, interest in quantum-confined semiconductor nanostructures increased. Self-assembled mesoscale semiconductor structures of II-VI nanocrystals are an especially exciting subject because of their controllable band gap and unique photophysical properties. Several preparative methods to synthesize and control the sizes of the individual nanocrystallites and the electronic and optical properties have been intensively studied. Fabrication of patterned nanostructures composed of quantum-confined nanoparticles is the next step toward practical applications. We have developed an innovative method to fabricate diverse nanostructures which relies on the size and a shape of a chosen deoxyribonucleic acid (DNA) template.
Date: May 1998
Creator: Rho, Young Gyu
Partner: UNT Libraries

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 also reviews select issues Congress might consider should it legislate or conduct oversight in this area.
Date: May 2, 2011
Creator: James, Nathan
Partner: UNT Libraries Government Documents Department

Genomic Sequencing of Single Microbial Cells from Environmental Samples

Description: Recently developed techniques allow genomic DNA sequencing from single microbial cells [Lasken RS: Single-cell genomic sequencing using multiple displacement amplification, Curr Opin Microbiol 2007, 10:510-516]. Here, we focus on research strategies for putting these methods into practice in the laboratory setting. An immediate consequence of single-cell sequencing is that it provides an alternative to culturing organisms as a prerequisite for genomic sequencing. The microgram amounts of DNA required as template are amplified from a single bacterium by a method called multiple displacement amplification (MDA) avoiding the need to grow cells. The ability to sequence DNA from individual cells will likely have an immense impact on microbiology considering the vast numbers of novel organisms, which have been inaccessible unless culture-independent methods could be used. However, special approaches have been necessary to work with amplified DNA. MDA may not recover the entire genome from the single copy present in most bacteria. Also, some sequence rearrangements can occur during the DNA amplification reaction. Over the past two years many research groups have begun to use MDA, and some practical approaches to single-cell sequencing have been developed. We review the consensus that is emerging on optimum methods, reliability of amplified template, and the proper interpretation of 'composite' genomes which result from the necessity of combining data from several single-cell MDA reactions in order to complete the assembly. Preferred laboratory methods are considered on the basis of experience at several large sequencing centers where >70% of genomes are now often recovered from single cells. Methods are reviewed for preparation of bacterial fractions from environmental samples, single-cell isolation, DNA amplification by MDA, and DNA sequencing.
Date: February 1, 2008
Creator: Ishoey, Thomas; Woyke, Tanja; Stepanauskas, Ramunas; Novotny, Mark & Lasken, Roger S.
Partner: UNT Libraries Government Documents Department

Purification and Analysis of Mycobacteriophage Alice

Description: This paper discusses research on the purification and analysis of mycobacteriophage Alice. The purpose of this research is to expand the knowledge of mycobacteriophage and analyze a single mycobacteriophage genome to be archived for future use.
Date: April 15, 2010
Creator: Manley, Coreen M.; Simon, Stephanie E.; Benjamin, Robert C. & Hughes, Lee E.
Partner: UNT Honors College

Characterization of the specificity of DNA uptake and transformation by naturally competent Acinetobacter calcoaceticus

Description: Although cultures of A. calcoaceticus BD413 are naturally competent at all growth phases, genetic markers can only be successfully transformed by DNA from the genus Acinetobacter. Transformation frequencies of nearly 1.2% were obtained with pcaA mutants were incubated in liquid culture with wild-type DNA.
Date: August 1990
Creator: Ahmadian-Tehrani, Mohsen
Partner: UNT Libraries

Contribution to Sequencing of the Deinococcus radiodurans Genome

Description: The stated goal of this project was to supply The Institute for Genomic Research (TIGR) with pure DNA from the bacterium Deinocmus radiodurans RI for purposes of complete genomic sequencing by TIGR. We subsequently decided to expand this project to include a second goal; this second goal was the development of a NotI chromosomal map of D. radiodurans R1 using Pulsed Field Gel Electrophoresis (PFGE).
Date: March 11, 1999
Creator: Minton, K.W.
Partner: UNT Libraries Government Documents Department

Overexpressed of RAD51 suppresses recombination defects: a possible mechanism to reverse genomic instability

Description: RAD51, a key protein in the homologous recombinational DNA repair (HRR) pathway, is the major strand-transferase required for mitotic recombination. An important early step in HRR is the formation of single-stranded DNA (ss-DNA) coated by RPA (a ss-DNA binding protein). Displacement of RPA by RAD51 is highly regulated and facilitated by a number of different proteins known as the 'recombination mediators'. To assist these recombination mediators, a second group of proteins also is required and we are defining these proteins here as 'recombination co-mediators'. Defects in either recombination mediators or comediators, including BRCA1 and BRCA2, lead to impaired HRR that can genetically be complemented for (i.e. suppressed) by overexpression of RAD51. Defects in HRR have long been known to contribute to genomic instability leading to tumor development. Since genomic instability also slows cell growth, precancerous cells presumably require genomic restabilization to gain a growth advantage. RAD51 is overexpressed in many tumors, and therefore, we hypothesize that the complementing ability of elevated levels of RAD51 in tumors with initial HRR defects limits genomic instability during carcinogenic progression. Of particular interest, this model may also help explain the high frequency of TP53 mutations in human cancers, since wild-type p53 represses RAD51.
Date: October 15, 2009
Creator: Schild, David & Wiese, Claudia
Partner: UNT Libraries Government Documents Department

Development of High Throughput Process for Constructing 454 Titanium and Illumina Libraries

Description: We have developed two processes with the Biomek FX robot to construct 454 titanium and Illumina libraries in order to meet the increasing library demands. All modifications in the library construction steps were made to enable the adaptation of the entire processes to work with the 96-well plate format. The key modifications include the shearing of DNA with Covaris E210 and the enzymatic reaction cleaning and fragment size selection with SPRI beads and magnetic plate holders. The construction of 96 Titanium libraries takes about 8 hours from sheared DNA to ssDNA recovery. The processing of 96 Illumina libraries takes less time than that of the Titanium library process. Although both processes still require manual transfer of plates from robot to other work stations such as thermocyclers, these robotic processes represent about 12- to 24-folds increase of library capacity comparing to the manual processes. To enable the sequencing of many libraries in parallel, we have also developed sets of molecular barcodes for both library types. The requirements for the 454 library barcodes include 10 bases, 40-60percent GC, no consecutive same base, and no less than 3 bases difference between barcodes. We have used 96 of the resulted 270 barcodes to construct libraries and pool to test the ability of accurately assigning reads to the right samples. When allowing 1 base error occurred in the 10 base barcodes, we could assign 99.6percent of the total reads and 100percent of them were uniquely assigned. As for the Illumina barcodes, the requirements include 4 bases, balanced GC, and at least 2 bases difference between barcodes. We have begun to assess the ability to assign reads after pooling different number of libraries. We will discuss the progress and the challenges of these scale-up processes.
Date: May 28, 2010
Creator: Deshpande, Shweta; Hack, Christopher; Tang, Eric; Malfatti, Stephanie; Ewing, Aren; Lucas, Susan et al.
Partner: UNT Libraries Government Documents Department

Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

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 DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation& Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.
Date: June 18, 2010
Creator: Tarver, Angela; Fern, Alison; Diego, Matthew San; Kennedy, Megan; Zane, Matthew; Daum, Christopher et al.
Partner: UNT Libraries Government Documents Department

Large Gap Size Paired-end Library Construction for Second Generation Sequencing

Description: Fosmid or BAC end sequencing plays an important role in de novo assembly of large genomes like fungi and plants. However construction and Sanger sequencing of fosmid or BAC libraries are laborious and costly. The current 454 Paired-End (PE) Library and Illumina Jumping Library construction protocols are limited with the gap sizes of approximately 20 kb and 8 kb, respectively. In the attempt to understand the limitations of constructing PE libraries with greater than 30Kb gaps, we have purified 18, 28, 45, and 65Kb sheared DNA fragments from yeast and circularized the ends using the Cre-loxP approach described in the 454 PE Library protocol. With the increasing fragment sizes, we found a general trend of decreasing library quality in several areas. First, redundant reads and reads containing multiple loxP linkers increase when the average fragment size increases. Second, the contamination of short distance pairs (<10Kb) increases as the fragment size increases. Third, chimeric rate increases with the increasing fragment sizes. We have modified several steps to improve the quality of the long span PE libraries. The modification includes (1) the use of special PFGE program to reduce small fragment contamination; (2) the increase of DNA samples in the circularization step and prior to the PCR to reduce redundant reads; and (3) the decrease of fragment size in the double SPRI size selection to get a higher frequency of LoxP linker containing reads. With these modifications we have generated large gap size PE libraries with a much better quality.
Date: May 28, 2010
Creator: Peng, Ze; Hamilton, Matthew; Froula, Jeff; Ewing, Aren; Foster, Brian & Cheng, Jan-Fang
Partner: UNT Libraries Government Documents Department