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DNA Mixtures (dna + mixture)
Selected AbstractsEvaluation of DNA Mixtures from Database SearchBIOMETRICS, Issue 1 2010Yuk-Ka Chung Summary With the aim of bridging the gap between DNA mixture analysis and DNA database search, a novel approach is proposed to evaluate the forensic evidence of DNA mixtures when the suspect is identified by the search of a database of DNA profiles. General formulae are developed for the calculation of the likelihood ratio for a two-person mixture under general situations including multiple matches and imperfect evidence. The influence of the prior probabilities on the weight of evidence under the scenario of multiple matches is demonstrated by a numerical example based on Hong Kong data. Our approach is shown to be capable of presenting the forensic evidence of DNA mixtures in a comprehensive way when the suspect is identified through database search. [source] Hybridization of short complementary PNAs to G-quadruplex forming oligonucleotides: An electrospray mass spectrometry studyBIOPOLYMERS, Issue 4 2009Jussara Amato Abstract We investigated the interaction of the short peptide nucleic acid (PNA) strand [acccca]-PNA with oligodeoxynucleotides containing one, two, or four tracts of TGGGGT units. Electrospray ionization mass spectrometry allowed exploring the wide variety of complex stoichiometries that were found to coexist in solution. In water, the PNA strand forms short heteroduplexes with the complementary DNA sequences, but higher-order structures are also found, with PNA2n·DNAn triplex units, culminating in precipitation at very low ionic strength. In the presence of ammonium acetate, there is a competition between PNA·DNA heteroduplex formation and DNA G-quadruplex formation. Heteroduplex formation is favored when the PNA + DNA mixture in ammonium acetate is heated and cooled at room temperature, but not if the PNA is added at room temperature to the preformed G-quadruplex. We also found that the short [acccca]-PNA strand binds to G-quadruplexes. © 2008 Wiley Periodicals, Inc. Biopolymers 91: 244,255, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Design and testing of ,genome-proxy' microarrays to profile marine microbial communitiesENVIRONMENTAL MICROBIOLOGY, Issue 2 2008Virginia I. Rich Summary Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a ,genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to 13 of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual open reading frame, and distributed along each ,40,160 kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having , ,75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of ,0.1% of the community, corresponding to ,103 cells ml,1 in these samples. Signal correlated to cell concentration with an R2 of 1.0 across six orders of magnitude. In addition, the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R2 = 0.9999 and a limit of detection of ,1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array's multiple-probe, ,genome-proxy' approach and consequent ability to track both target genotypes and their close relatives is important for the array's environmental application given the recent discoveries of considerable intrapopulation diversity within marine microbial communities. [source] Interpreting DNA Evidence: A ReviewINTERNATIONAL STATISTICAL REVIEW, Issue 3 2003L.A. Foreman Summary The paper provides a review of current issues relating to the use of DNA profiling in forensic science. A short historical section gives the main statistical milestones that occurred during a rapid development of DNA technology and operational uses. Greater detail is then provided for interpretation issues involving STR DNA profiles, including: , methods that take account of population substructure in DNA calculations; , parallel work carried out by the US National Research Council; , the move away from multiple independence testing in favour of experiments that demonstrate the robustness of casework procedures; , the questionable practice of source attribution ,with reasonable scientific certainty'; , the effect on the interpretation of profiles obtained under increasingly sensitive techniques, the LCN technique in particular; , the use of DNA profiles as an intelligence tool; , the interpretation of DNA mixtures. Experience of presenting DNA evidence within UK courts is also discussed. The paper then summarises a generic interpretation framework based on the concept of likelihood ratio within a hierarchy of propositions. Finally the use of Bayesian networks to interpret DNA evidence is reviewed. Résumé Cet article présente un inventaire des questions relativesá l'utilisation du profilage ADN dans la science légale. Une courte section historique décrit les principales étapes statistiques qui ont eu lieu pendant le rapide développement de la technologie ADN et ses utilisations opérationnelles. De plus grands détails sont ensuite donnés pour l'interprétation de questions sur les profils AND STR, ce qui inclut: ,les méthodes qui tiennent compte des sous-structures de population dans les calculs ADN; ,le travail conduit en paralléle par le Conseil de Recherche Nationale des Etats-Unis (NRC); ,l'évolution depuis les tests d'indépendance multiple vers des expériences qui démontrent la robustesse des procédures; ,la pratique contestable de l'attribution de source avec "certitude scientifique raisonnable"; ,l'effet de l'interprétation des profils obtenus sous techniques de plus en plus sensibles, la technique LCN en particulier ,l'utilisation de profils ADN comme outil d'intelligence; ,l'interprétation de mélanges ADN. L'expérience de ce type de preuve dans les tribunaux britanniques sera également présentée et commentée. L'article présentera un cavenas d'interprétation centré sur le concept de rapport de vraisemblance, inscrit dans une hérarchie de propositions. Finalement, l'utilisation de réseaux Bayesien pour interpréter la preuve par ADN sera abordée. [source] Evaluation of DNA Mixtures from Database SearchBIOMETRICS, Issue 1 2010Yuk-Ka Chung Summary With the aim of bridging the gap between DNA mixture analysis and DNA database search, a novel approach is proposed to evaluate the forensic evidence of DNA mixtures when the suspect is identified by the search of a database of DNA profiles. General formulae are developed for the calculation of the likelihood ratio for a two-person mixture under general situations including multiple matches and imperfect evidence. The influence of the prior probabilities on the weight of evidence under the scenario of multiple matches is demonstrated by a numerical example based on Hong Kong data. Our approach is shown to be capable of presenting the forensic evidence of DNA mixtures in a comprehensive way when the suspect is identified through database search. [source] Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2007Suncerae I. Smith Abstract Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding. Copyright © 2007 John Wiley & Sons, Ltd. [source] | |||||||||||||