Digital Commons Network^™

Science Fiction And Shed Dna, D. H. Kaye

NULR Online

No abstract provided.

Searching For A Needle In A Haystack: The Constitutionality Of Police Dna Dragnets, Sepideh Esmaili

Chicago-Kent Law Review

DNA dragnets—the mass warrantless DNA testing of individuals whom authorities have neither probable cause nor reasonable suspicion to believe perpetrated a crime, but who merely live or work near a crime scene—have increasingly been used by police departments in a desperate attempt to solve puzzling crimes. The lack of success and the Fourth Amendment constitutional concerns raised by DNA dragnets, however, lead this practice to be suspect. Under the Fourth Amendment, all searches of an individual must be reasonable. The reasonableness of any search typically depends on the government obtaining a warrant prior to the search. While there are well-established …

Rapid Isolation Of Dna From The Mucus Of Asian Arowana (Scleropages Formosus, Osteoglossidae), Nantarika Chansue

The Thai Journal of Veterinary Medicine

Owing to arowana being listed in CITES, DNA diagnostics should not rely on conventional methods of obtaining tissue samples. A non-invasive method of obtaining material containing DNA has been developed. Mucus samples for DNA isolation can be obtained by cotton swabbing the arowana body surface with subsequent purification of DNA fragments by using phenol/chloroform. DNA sample quality is assessed by UV absorbancy at wave lengths of 260 nm and 280 nm, as well as by calculating the absorbancy ratio involving 260 nm/280 nm results in order to determine DNA sample quality and quantity. Electrophoresis is employed to assess DNA quantity …

A Comparison Of The Amely Gene Sequence In Argali (Ovis Ammon) And Domestic (Ovis Aries) Sheep, Kimberly Elwood

Undergraduate Honors Capstone Projects

Amelogenin (AMEL) is a gene responsible for tooth bud development. It is located on the X-chromosome, thus called AMELX, in mammals. AMEL has been shown to be present in fish, amphibians, and reptiles, though the exact location on the chromosome has not been determined. Amelogenin-like gene (AMELY), an AMEL homolog encoded on the Y-chromosome in some mammals, including sheep, cattle, deer, bears, humans, and some primates, is shorter than the sequence on the X-chromosome. It is unknown whether AMELY is transcriptionally active, but it has been found to be useful for human sexing purposes in forensics, archaeology and prenatal diagnosis, …

Regulation Of A Dna-Compacting Plastid Nucleoid Protein, Steven William Adamson

Dissertations

DCP68, a DNA-compacting nucleoid protein, was further characterized in order to understand how plastid nucleoid proteins affect the structure and function of chloroplast DNA. Previously, DCP68 was identified as ferredoxin: sulfite reductase, an enzyme that participates in reductive sulfur assimilation and inhibits chloroplast DNA replication and transcription in vitro [1, 2]. In this study, the portion of SiR that was found to be present in soluble and plastid nucleoid-enriched fractions indicated that most SiR was stromal in Arabidopsis and soybean plants. Although SiR was detected in Arabidopsis chloroplast nucleoid-enriched fractions, the study of nucleoid dynamics proved to be difficult due …

Insights Into Transcription Enhancer Factor 1 (Tef-1) Activity From The Solution Structure Of The Tea Domain, Asokan Anbanandam, Diana C Albarado, Catherine T Nguyen, Georg Halder, Xiaolian Gao, Sudha Veeraraghavan

Journal Articles

Transcription enhancer factor 1 is essential for cardiac, skeletal, and smooth muscle development and uses its N-terminal TEA domain (TEAD) to bind M-CAT elements. Here, we present the first structure of TEAD and show that it is a three-helix bundle with a homeodomain fold. Structural data reveal how TEAD binds DNA. Using structure-function correlations, we find that the L1 loop is essential for cooperative loading of TEAD molecules on to tandemly duplicated M-CAT sites. Furthermore, using a microarray chip-based assay, we establish that known binding sites of the full-length protein are only a subset of DNA elements recognized by TEAD. …

The Daily Gamecock, Tuesday, October 17, 2006, University Of South Carolina, Office Of Student Media

October

No abstract provided.

Bayesian Hidden Markov Modeling Of Array Cgh Data, Subharup Guha, Yi Li, Donna Neuberg

Harvard University Biostatistics Working Paper Series

Genomic alterations have been linked to the development and progression of cancer. The technique of Comparative Genomic Hybridization (CGH) yields data consisting of fluorescence intensity ratios of test and reference DNA samples. The intensity ratios provide information about the number of copies in DNA. Practical issues such as the contamination of tumor cells in tissue specimens and normalization errors necessitate the use of statistics for learning about the genomic alterations from array-CGH data. As increasing amounts of array CGH data become available, there is a growing need for automated algorithms for characterizing genomic profiles. Specifically, there is a need for …

A Missense Mutation In Pmel17 Is Associated With The Silver Coat Color In The Horse, Emma Brunberg, Leif Andersson, Gus Cothran, Kaj Sandberg, Sofia Mikko, Gabriella Lindgren

Veterinary Science Faculty Publications

BACKGROUND: The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype.

RESULTS: Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34 …

Turning A Blind Eye To Misleading Scientific Testimony: Failure Of Procedural Safeguards In A Capital Case, William C. Thompson

ExpressO

In September 1999, Robin Lovitt was convicted and sentenced to death for the murder of a pool hall manager in Arlington, Virginia. The DNA evidence that was a key part of the government’s case was presented in a misleading and unfair manner. In this case study, we first examine the way in which DNA evidence was misused. We then discuss the failure of the legal system at all levels to recognize and remedy this problem. Our goal is to explain how a system that supposedly leaves no stone unturned in capital trials managed to miss or ignore a crucial problem …

Cyclin D1 Repression Of Nuclear Respiratory Factor 1 Integrates Nuclear Dna Synthesis And Mitochondrial Function., Chenguang Wang, Zhiping Li, Yinan Lu, Runlei Du, Sanjay Katiyar, Jianguo Yang, Maofu Fu, Jennifer E Leader, Andrew Quong, Phyllis M Novikoff, Richard Pestell

Department of Cancer Biology Faculty Papers

Cyclin D1 promotes nuclear DNA synthesis through phosphorylation and inactivation of the pRb tumor suppressor. Herein, cyclin D1 deficiency increased mitochondrial size and activity that was rescued by cyclin D1 in a Cdk-dependent manner. Nuclear respiratory factor 1 (NRF-1), which induces nuclear-encoded mitochondrial genes, was repressed in expression and activity by cyclin D1. Cyclin D1-dependent kinase phosphorylates NRF-1 at S47. Cyclin D1 abundance thus coordinates nuclear DNA synthesis and mitochondrial function.

Saccharomyces Cerevisiae-Based Molecular Tool Kit For Manipulation Of Genes From Gram-Negative Bacteria, Robert M. Q. Shanks, Nicky C. Caiazza, Shannon M. Hinsa, Christine M. Toutain, George A. O'Toole

Dartmouth Scholarship

A tool kit of vectors was designed to manipulate and express genes from a wide range of gram-negative species by using in vivo recombination. Saccharomyces cerevisiae can use its native recombination proteins to combine several amplicons in a single transformation step with high efficiency. We show that this technology is particularly useful for vector design. Shuttle, suicide, and expression vectors useful in a diverse group of bacteria are described and utilized. This report describes the use of these vectors to mutate clpX and clpP of the opportunistic pathogen Pseudomonas aeruginosa and to explore their roles in biofilm formation and surface …

Bacillus Anthracis Virulent Plasmid Px02 Genes Found In Large Plasmids Of Two Other Bacillus Species, Vicki A. Luna, Debra S. King, K. Kealy Peak, Frank Reeves, Lea Heberlein-Larson, William Veguilla, L. Heller, Kathleen E. Duncan, Andrew C. Cannons, Philip Amuso, Jacqueline Cattani

Bioelectrics Publications

In order to cause the disease anthrax, Bacillus anthracis requires two plasmids, pX01 and pX02, which carry toxin and capsule genes, respectively, that are used as genetic targets in the laboratory detection of the bacterium. Clinical, forensic, and environmental samples that test positive by PCR protocols established by the Centers for Disease Control and Prevention for B. anthracis are considered to be potentially B. anthracis until confirmed by culture and a secondary battery of tests. We report the presence of 10 genes (acpA, capA, capB, capC, capR, capD, IS1627, ORF 48, ORF 61, and repA) and the sequence for the …

The “Csi Effect”: Better Jurors Through Television And Science?, Michael D. Mann

ExpressO

This Comment discusses how television shows such as CSI and Law & Order create heightened juror expectations. This will be published in the Buffalo Public Interest Law Journal's 2005-2006 issue.

Biomolecular Study Of The Correlation Between Papillomatosis Of The Vulvar Vestibule In Adolescents And Human Papillomavirus, Geni Beznos, Verônica Coates, Jose Focchi, Hatim A. Omar

Pediatrics Faculty Publications

The main goal of this study was to investigate, through a biomolecular study, the correlation between papillomatosis of the vulvar vestibule and human papillomavirus (HPV) infection, as well as to establish the necessity of treatment. A total of 44 female adolescents between 12 and 18 years of age were selected through a prospective study with a confirmed diagnosis of papillomatosis of the vulvar vestibule. Vulvar biopsies were obtained for the histological and biomolecular detection of HPV DNA through polymerase chain reaction (PCR). Twenty (45%) adolescents were virgins (group A), the other 24 (55%) were sexually active. The virgin adolescents (group …

The “Csi Effect”: Better Jurors Through Television And Science?, Michael Mann

Michael D. Mann

This Comment explores how television shows such as CSI and Law & Order have created heightened juror expectations in courtrooms across America. Surprise acquitals often have prosectors scratching their heads as jurors hold them to this new "Hollywood" standard. The Comment also analyzes the CSI phenomena by reflecting on past legal television shows that have influenced the public's perception of the legal profession and how the "CSI effect" has placed an even greater burden on parties to proffer some kind of forensic evidence at trial.

The Comment was published in volume 24 of the Buffalo Public Interest Law Journal (2006).

Electrochemical Impedance Spectrum Of Ferrocene At A Rotating Disk Glassy Carbon Electrode And Its Interaction With Dna, Can-Hui Chen

Journal of Electrochemistry

The electrochemical impedance spectrum(EIS) of ferrocene(Fc) at a rotating glassy carbon(GC) electrode and its interaction with calf thymus DNA in Tris-NaCl buffer solution(pH=7.2) have been investigated by using electrochemical techniques such as rotating disk electrode(RDE),EIS and its data fitting.A plateau of the limiting current for the voltammetric curve and two capacitance arches obtained at the rotating GC electrode are exhibited.The interaction of Fc with DNA is represented by the decrease of limiting diffusion current and the increase of electrochemical reaction resistances with the increase of DNA concentration,respectively.On the other hand,based on the theoretical analysis and data fitting of RDE and …

X-Irradiation Of Dna Components In The Solid State: Experimental And Computational Studies Of Stabilized Radicals In Guanine Derivatives, Nayana Kumudini Jayatilaka

Physics and Astronomy Dissertations

Single crystals of sodium salt of guanosine dihydrate and 9 Ethyl Guanine were X-irradiated with the objective of identifying the radical products. Study with K-band EPR, ENDOR, and ENDOR-Induced EPR techniques indicated at least four radical species to appear in both crystals in the temperature range of 6K to room temperature. Three of these radicals (Radicals R1, R2, and R3) were present immediately after irradiation at 6K. Computational chemistry and EPR spectrum simulation methods were also used to assist in radical identifications. Radical R1, the product of net hydrogen addition to N7, and Radical R2, the product of electron loss …

A Determination Of Phylogeny And Hybridization History Within Clematis L. (Ranunculaceae) Using Actin And Nitrate Reductase Intron Sequences, Kimberly Fearn Do

USF Tampa Graduate Theses and Dissertations

The phylogeny of Clematis, section Viorna, was characterized in this study using molecular data. Two nuclear introns were sequenced for a variety of taxa: actin and nitrate reductase. Actin intron sequence data yielded very little phylogenetic information. Some basal clades were resolved, but there were very few well supported relationships between species of the Viorna section in both the neighbor joining and maximum parsimony analyses. Nitrate reductase intron sequence data was slightly more variable. The number of well supported relationships in both the neighbor joining and maximum parsimony analyses for nitrate reductase was greater, but still not sufficient …

Plasmid Probes For Screening Specific Genes In Large Fragment Dna Libraries, Leah Ferguson

Senior Honors Projects

Heliothis virescens, a member of the lepidopteran family, is of great importance to many people who rely on agriculture as a source of income because it is a pest of many important crops. Because H. virescens feeds on a broad array of hosts including cotton, tobacco, tomato, and soybean it has earned its place as a major nuisance in the United States. Heliothis subflexa is a close taxonomic relative of H. virescens, but the two species differ in that H. subflexa is a specialized herbivore that only feeds on plants in the genus Physalis. Studies have been performed to determine …

Measuring Inter-Dna Potentials In Solution, Xiangyun Qiu, Lisa W. Kwok, Hye Yoon Park, Jessica S. Lamb, Kurt Andresen, Lois Pollack

Physics and Astronomy Faculty Publications

Interactions between short strands of DNA can be tuned from repulsive to attractive by varying solution conditions and have been quantified using small angle x-ray scattering techniques. The effective DNA interaction charge was extracted by fitting the scattering profiles with the generalized one-component method and inter-DNA Yukawa pair potentials. A significant charge is measured at low to moderate monovalent counterion concentrations, resulting in strong inter-DNA repulsion. The charge and repulsion diminish rapidly upon the addition of divalent counterions. An intriguing short range attraction is observed at surprisingly low divalent cation concentrations, ~16 mM Mg2+. Quantitative measurements of inter- DNA potentials …

Length-Dependent Degradation Of Single-Stranded 3' Ends By The Werner Syndrome Protein (Wrn): Implications For Spatial Orientation And Coordinated 3' To 5' Movement Of Its Atpase/Helicase And Exonuclease Domains, Amrita Machwe, Liren Xiao, David K. Orren

Toxicology and Cancer Biology Faculty Publications

BACKGROUND: The cancer-prone and accelerated aging disease Werner syndrome is caused by loss of function of the WRN gene product that possesses ATPase, 3' to 5' helicase and 3' to 5' exonuclease activities. Although WRN has been most prominently suggested to function in telomere maintenance, resolution of replication blockage and/or recombinational repair, its exact role in DNA metabolism remains unclear. WRN is the only human RecQ family member to possess both helicase and exonuclease activity, but the mechanistic relationship between these activities is unknown. In this study, model single-stranded and 3' overhang DNA substrates of varying length and structure were …

Demarcation Of Coding And Non-Coding Regions Of Dna Using Linear Transforms, Krithika Venkat

Theses

Deoxyribonucleic Acid (DNA) strand carries genetic information in the cell. A strand of DNA consists of nitrogenous molecules called nucleotides. Nucleotides triplets, or the codons, code for amino acids. There are two distinct regions in DNA, the gene and the intergenic DNA, or the junk DNA. Two regions can be distinguished in the gene- the exons, or the regions that code for amino acid, and the introns, or the regions that do not code for amino acid. The main aim of the thesis is to study signal processing techniques that help distinguish between the regions of the exons and the …

Competition Between The Dna Unwinding And Strand Pairing Activities Of The Werner And Bloom Syndrome Proteins, Amrita Machwe, Enerlyn M. Lozada, Liren Xiao, David K. Orren

Toxicology and Cancer Biology Faculty Publications

BACKGROUND: The premature aging and cancer-prone Werner and Bloom syndromes are caused by defects in the RecQ helicase enzymes WRN and BLM, respectively. Recently, both WRN and BLM (as well as several other RecQ members) have been shown to possess a strand annealing activity in addition to the requisite DNA unwinding activity. Since an annealing function would appear to directly oppose the action of a helicase, we have examined in this study the dynamic equilibrium between unwinding and annealing mediated by either WRN or BLM.

RESULTS: Our investigation into the competition between annealing and unwinding demonstrates that, under standard reaction …

The Development Of An All-Dna-Based Electro-Optic Waveguide Modulator, Emily Marie Heckman

Graduate Theses and Dissertations

No abstract provided.

A Comparison And Combination Of Plastid Atpb And Rbcl Gene Sequences For Inferring Phylogenetic Relationships Within Orchidaceae, Kenneth M. Cameron

Aliso: A Journal of Systematic and Floristic Botany

Parsimony analyses of DNA sequences from the plastid genes atpB and rbcL were completed for 173 species of Orchidaceae (representing 150 different genera) and nine genera from outgroup families in Asparagales. The atpB tree topology is similar to the rbcL tree, although the atpB data contain less homoplasy and provide greater jackknife support than rbcL alone. In combination, the two-gene tree recovers five monophyletic clades corresponding to subfamilies within Orchidaceae, and fully resolves them with moderate to high jackknife support as follows: Epidendroideae are sister to Orchidoideae, followed by Cypripedioideae, then Vanilloideae, and with …

A Nuclear Rdna Phylogeny Of Smilax (Smilacaceae), Kenneth M. Cameron, Chengxin Fu

Aliso: A Journal of Systematic and Floristic Botany

Smilacaceae are a taxonomically confused, cosmopolitan family of Liliales characterized by climbing habit, reticulate leaf venation, paired petiolar tendrils, unisexual flowers, and superior ovaries. Deviations from this generalized morphology have led to the division of Smilacaceae into at least seven different genera and five sections within the large genus Smilax. In particular, taxa with connate tepals (Heterosmilax), more than six stamens (Pleiosmilax, Oligosmilax), or herbaceous habit (Hemexia) have been variously classified. Using DNA sequences of 96 taxa from the nuclear rDNA ITS gene region, parsimony analyses provide moderate resolution, but generally poor bootstrap support …

The Never-Ending Story: Multigene Approaches To The Phylogeny Of Amaryllidaceae, Alan W. Meerow, Deirdre A. Snuman

Aliso: A Journal of Systematic and Floristic Botany

a whole, strongly supported the mostly African tribe Amaryllideae as sister to the rest of the family, and resolved geographically-based monophyletic groups, but failed to resolve the relationships among several basal lineages in the family (the African Haemantheae and Cyrtantheae, the Australasian Calostemmateae, and the American and Eurasian sister clades). We present analysis of plastid ndhF sequences that fully resolved the major clades of the family. The baccate-fruited Haemantheae and Calostemmateae are sister tribes, and the African endemic Cyrtantheae is sister to them both. This clade is sister to an American/Eurasian clade. We also present preliminary nuclear ribosomal ITS …

Hiv Dna And Dementia In Treatment-Naive Hiv-1-Infected Individuals In Bangkok, Thailand, Robert H. Paul, Bruce Shiramizu, Silvia Ratto-Kim, Pasiri Sithinamsuwan

Psychology Faculty Works

High HIV-1 DNA (HIV DNA) levels in peripheral blood mononuclear cells (PBMC) correlate with HIV-1-associated dementia (HAD) in patients on highly active antiretroviral therapy (HAART). If this relationship also exists among HAART-naïve patients, then HIV DNA may be implicated in the pathogenesis of HAD. In this study, we evaluated the relationship between HIV DNA and cognition in subjects naïve to HAART in a neuro AIDS cohort in Bangkok, Thailand. Subjects with and without HAD were recruited and matched for age, gender, education, and CD4 cell count. PBMC and cellular subsets were analyzed for HIV DNA using real-time PCR. The median …

Site-Specific Labeling Of Supercoiled Dna., Alexander Y. Lushnikov, Vladimir N. Potaman, Yuri L. Lyubchenko

Journal Articles: Pharmaceutical Sciences

Visualization of site-specific labels in long linear or circular DNA allows unambiguous identification of various local DNA structures. Here we describe a novel and efficient approach to site-specific DNA labeling. The restriction enzyme SfiI binds to DNA but leaves it intact in the presence of calcium and therefore may serve as a protein label of 13 bp recognition sites. Since SfiI requires simultaneous interaction with two DNA recognition sites for stable binding, this requirement is satisfied by providing an isolated recognition site in the DNA target and an additional short DNA duplex also containing the recognition site. The SfiI/DNA complexes …