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Best Experimental Conditions (best + experimental_condition)
Selected AbstractsTesting and improving experimental parameters for the use of low molecular weight targets in array-CGH experiments,HUMAN MUTATION, Issue 11 2006Marianne Stef Abstract Array,comparative genomic hybridization (CGH) has evolved as a useful technique for the detection and characterization of deletions, and, to a lesser extent, of duplications. The resolution of the technique is dictated by the genomic distance between targets spotted on the microarray, and by the targets' sizes. The use of region-specific, high-resolution microarrays is a specific goal when studying regions that are prone to rearrangements, such as those involved in deletion syndromes. The aim of the present study was to evaluate the best experimental conditions to be used for array-CGH analysis using low molecular weight (LMW) targets. The parameters tested were: the target concentration, the way LMW targets are prepared (either as linearized plasmids or as purified PCR products), and the way the targets are attached to the array-CGH slide (in a random fashion on amino-silane coated slides, or by one amino-modified end on epoxysilane-coated slides). As a test case, we constructed a microarray harboring LMW targets located in the CREBBP gene, mutations of which cause the Rubinstein-Taybi syndrome (RTS). From 10 to 15% of RTS patients have a CREBBP deletion. We showed that aminosilane- and epoxysilane-coated slides were equally efficient with targets above 1,000,bp in size. On the other hand, with the smallest targets, especially those below 500,bp, epoxysilane-coated slides were superior to aminosilane-coated slides, which did not allow deletion detection. Use of the high resolution array allowed us to map intragenic breakpoints with precision and to identify a very small deletion and a duplication that were not detected by the currently available techniques for finding CREBBP deletions. Hum Mutat 27(11), 1143,1150, 2006. © 2006 Wiley-Liss, Inc. [source] Surface-enhanced Raman scattering study of the red dye laccaic acidJOURNAL OF RAMAN SPECTROSCOPY, Issue 10 2007M. V. Cañamares Abstract FT-Raman and surface-enhanced Raman scattering (SERS) spectroscopy were applied to the study of lac dye, a highly fluorescent anthraquinone red dye. The SERS spectra were obtained at different pH values, on Ag nanoparticles prepared by chemical reduction with citrate and hydroxylamine, and at several excitation wavelengths, in order to find the best experimental conditions for the detection of the lac dye. The lower detection limit was achieved using nanoparticles prepared by reduction with hydroxylamine, excitation at 514.5 nm, and slightly acidic pH conditions, thus exploiting a combination of factors including lower electrostatic repulsion between dye and nanoparticles and resonance Raman enhancement. A comparison between the adsorption of laccaic acid (LA) and carminic acid (CA), another anthraquinone red dye, was also done, based on the SERS spectra of both dyes. Copyright © 2007 John Wiley & Sons, Ltd. [source] SAXSANA: an interactive program for the analysis and monitoring of static and time-resolved small-angle X-ray solution scattering measurementsJOURNAL OF SYNCHROTRON RADIATION, Issue 2 2003Yuzuru Hiragi An interactive analytical program, SAXSANA, for small-angle X-ray scattering measurements of solutions is described. The program processes scattered data without disciplined knowledge of small-angle scattering. SAXSANA also assists in finding the best experimental conditions, thus avoiding blind runs of experiments. SAXSANA consists of the following procedures: (i) determination of the centre of scattered X-rays and moment transfer Q (Q,=,4,sin,/,, where 2, is the scattering angle and , is the wavelength) for each measured channel; (ii) conversion of the data format to the format of Q versus scattered intensities J(Q); (iii) truncation of unnecessary data and smoothing of scattering curves by cubic-spline function; (iv) correction of the absorption effect and subtraction of the scattered intensity of the buffer (solvent) solution from that of the sample solution; (v) creation of a data file for a three-dimensional representation of time-resolved scattering curves; (vi) determination of radii of gyration by Guinier plots; (vii) determination of persistent lengths by Kratky plots; (viii) extrapolation of the small-angle part by Guinier plots; (ix) extrapolation of the wide-angle part by Porod's & Luzzati's laws for the Hankel transformation in order to obtain the distance distribution function p(r); (x) calculation of p(r) and computation of the invariant, the chord length, the volume, the spherical radius, the maximum dimension Dmax and the radius of gyration (Rg). SAXSANA also serves as an on-site monitor for the validity of an experimental result during the measurements. [source] Use of flow injection atmospheric pressure photoionization quadrupole time-of-flight mass spectrometry for fast olive oil fingerprintingRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 8 2006J. L. Gómez-Ariza The recently introduced technique of an atmospheric pressure photoionization (APPI) source coupled to quadrupole time-of-flight mass spectrometry (QqTOFMS) has been applied to fast olive oil fingerprinting on the basis of the accurate mass measurements obtained with this instrumentation. The key compounds can be characterized as [M+H]+ (produced by proton transfer) or as [M]+. (by charge transfer) ions in the mass spectra. [M+H]+ ions, however, show higher abundance, especially for triacylglycerols. Other ions present in APPI-MS are the acylium ion [RiCO]+ and [RiCOH2O]+. This latter ion is absent in the electrospray ionization (ESI)-MS spectra, and this represents valuable complementary information. Several critical parameters in the APPI source were optimized such as LC eluent composition, ion spray voltage and, especially, declustering potential. APPI-QqTOFMS allows easy discrimination among different edible oils: olive, extra virgin olive, olive-pomace, hazelnut, sunflower, corn and several mixed oils, with high throughput (approximately 1,min per sample). Cluster analysis was applied to obtain the best experimental conditions for oil discrimination on the basis of declustering potential. Principal components analyses of these APPI-MS spectra show that the approach can be used for studies of olive oil adulteration with other oils, even in the case of hazelnut oil that exhibits a high chemical similarity with olive oil. Copyright © 2006 John Wiley & Sons, Ltd. [source] Theory of pH-stat titrationBIOTECHNOLOGY & BIOENGINEERING, Issue 1 2003Elena Ficara Abstract Innovative techniques are being studied to assess the activity of bioreactors and to improve the performance and operational stability of biological processes. Among these techniques, the pH-stat titration is applicable to any bioreaction involving pH variations. Up to now, the main application of the pH-stat titration has been for nitrification monitoring. In this article, we present a theoretical model of pH-stat titration, which predicts the response to any reaction involving the production or consumption of protons, hydroxyl ions, or inorganic carbon chemical species (CO2, HCO3,, CO3=). This model is a useful tool to understand pH-stat titrations, to define their applicability and limits, and to select the best experimental conditions for specific applications. Tests have been performed to compare experimental pH-stat titration rates in the presence of carbon dioxide and HCO3, producing reactions to the values predicted by the model and a very satisfying correspondence was found. © 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 82: 28,37, 2003. [source] | |||||||||||||