130 research outputs found

    Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications

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    <p>Abstract</p> <p>Background</p> <p>A large portion of tissues stored worldwide for diagnostic purposes is formalin-fixed and paraffin-embedded (FFPE). These FFPE-archived tissues are an extremely valuable source for retrospective (genetic) studies. These include mutation screening in cancer-critical genes as well as pathogen detection. In this study we evaluated the impact of several widely used DNA extraction methods on the quality of molecular diagnostics on FFPE tissues.</p> <p>Findings</p> <p>We compared 4 DNA extraction methods from 4 identically processed FFPE mammary-, prostate-, colon- and lung tissues with regard to PCR inhibition, real time SNP detection and amplifiable fragment size. The extraction methods, with and without proteinase K pre-treatment, tested were: 1) heat-treatment, 2) QIAamp DNA-blood-mini-kit, 3) EasyMAG NucliSens and 4) Gentra Capture-Column-kit.</p> <p>Amplifiable DNA fragment size was assessed by multiplexed 200-400-600 bp PCR and appeared highly influenced by the extraction method used. Proteinase K pre-treatment was a prerequisite for proper purification of DNA from FFPE. Extractions with QIAamp, EasyMAG and heat-treatment were found suitable for amplification of fragments up to 400 bp from all tissues, 600 bp amplification was marginally successful (best was QIAamp). QIAamp and EasyMAG extracts were found suitable for downstream real time SNP detection. Gentra extraction was unsuitable. Hands-on time was lowest for heat-treatment, followed by EasyMAG.</p> <p>Conclusions</p> <p>We conclude that the extraction method plays an important role with regard to performance in downstream molecular applications.</p

    OPTICAL ABSORPTION OF Co2+ IN ZnO

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    On prĂ©sente des spectres d'absorption polarisĂ©s de l'ion CO2+ dans ZnO. Les transitions de l'Ă©tat fondamental 2A2 aux multiplets, 4T2(F), et 4T1(F) et 2E(G) sont analysĂ©es en dĂ©tail. Ces bandes sont composĂ©es de lignes aiguĂ«s de zĂ©ro phonon et leurs bandes vibratoires latĂ©rales. On a trouvĂ© que le couplage vibratoire est dominant avec des phonons optiques d'une Ă©nergie de 528 cm-1 et avec les phonons acoustiques du point M de la zone de Brillouin ayant une Ă©nergie de 100 cm-1. Pour expliquer les niveaux Ă©lectroniques dĂ©duits des spectres on a diagonalisĂ© l'opĂ©rateur hamiltonien reprĂ©sentant les champs cristallins cubique et trigonal, l'interaction coulombienne et le couplage spin-orbite regardant tous les niveaux de la configuration d7. Avec les paramĂštres Dq = 400, Îœ = 120, Îœ' = 320, B = 760, C = 3 500 et ζ = 430 cm-1 la thĂ©orie explique bien les centres des bandes d'absorption ainsi que leur structure fine. En plus les facteurs g|| et g⊄, de l'Ă©tat fondamental du Co2+ sont calculĂ©s correctement.Polarized optical absorption spectra of Co2+ in ZnO are reported. The crystal field transitions from the 4A2 ground state to the 4T2(F), 4T1(F) and 2E(G) multiplets are analyzed in detail. These bands consist of sharp zero phonon lines and their vibronic sidebands, where coupling to 528 cm-1 optical phonons and 100 cm-1 acoustical phonons from the M point of the ZnO Brillouin zone is shown to be dominant. In order to explain the level scheme derived from the spectra the Hamiltonian describing cubic and trigonal crystal field, Coulomb and spin-orbit interaction has been diagonalized within the full d7 configuration. With Dq = 400, Îœ = 120, Îœ' = 320, F = 760, C = 3 500 and ζ = 430 cm-1 both the band positions and the electronic fine structure splittings are satisfactorily accounted for. In addition the g-factors of the Co2+ ground state, g|| and g⊄, are correctly predicted

    Thermal gas effusion from hydrogenated amorphous carbon films

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    Hydrogenated amorphous carbon (a-C:H) films, deposited onto negatively biased substrates in a 13.56-MHz hydrocarbon glow discharge system, have been investigated by mass spectroscopic thermal effusion measurements. Depending on the bias voltage U sub B as the most important deposition parameter, hydrocarbons and/or H2 molecules are desorbed at threshold temperatures between 300 and 600 degrees C. The threshold temperature increases with increasing bias voltage while the mass of the desorbed molecules decreases. a-C:H films deposited at low bias release H2, CH4, and higher hydrocarbons whereas from hard a-C:H films deposited at U sub B above 500 V, only H2, is released. Using double-layer a-C:H/a-C:D films, it is shown that H2 and CH4 molecules are formed in the volume of the film followed by molecular diffusion through the a-C:H network. For high-bias voltages (U sub B above 500 V), the reduced pore size of the strongly crosslinked a-C:H network is shown to prevent diffusion of hydroca rbon molecules, while the films are still permeable for hydrogen. (IAF
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