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- Fluorescence (3)
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Organisationseinheit der BAM
Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability.
Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.
The calibration of fluorescence signals in assays as well as in biological systems is a key requirement. Especially for quantitative studies of living cells, e.g. expression of biomolecules the generation of concentration-proportional analytical statements obtained by the fluorescence intensity plays a significant role. This also applies for cell assays like immunofluorescence assays. Also, the determination of local concentrations of target proteins within cells or within their environment is a major challenge in modern biology.
Proper calibration of the fluorescence imaging systems is the prerequisite to ensure that test results from different instruments and different test environments are comparable. The existing calibration solutions for fluorescence imaging systems, however, mostly depend on simple instrument calibration without reference to absolute physical standards or with insufficient stability for multiple measurements. In order to obtain the necessary quantitative information, it is required to calibrate both instruments and the corresponding assays, ideally with one calibrating system.
We present several new calibration tools for the most commonly used platforms for cytometry, i.e. fluorescence microscope based systems and flow cytometry based systems. They are comprised of ultra-stable fluorophores that are encapsulated in bio- and cell-compatible polymer matrices. Each tool is tailored to the specific requirements of the different read-out platforms. Both re-usable single-color calibration slides for fluorescence microscopes as well as new multi-color calibration beads are presented.
The traceability of the calibration tools to international standards and the wide calibration range of the fluorescence intensity are illustrated. They are thus suitable for calibration of the signal over concentration and quantum yield to that of the targets.
Evaluation of an interlaboratory comparison of the chemical assay of U, Th oxide coated particles
(1981)
The Thorium High Temperature Prototype Reactor (THTR) at Schmehausen (Fed. Rep. Germany) burns a (Th, U)O2 nuclear fuel using 93% enriched uranium. This material is particularly safeguards sensitive. An interlaboratory test has been completed on the heavy metal determination in BISO type (Th, U)O2 particles. The laboratories involved were BAM, KFA, KfK, NUKEM and SAL (IAEA). The modified Davies and Gray titration was applied for uranium, oxalate precipitation followed by ignition to ThO2 and gravimetry for thorium.
The exercise allowed an estimate to be made of the various error components: the results indicate that the sampling techniques applied in this experiment ensure a representativity of the sample of 0.05% or better. The precision of the measurements (1σ) is better than or equal to 0.15%. Assuming the overall means are the true values, the accuracy of the methods is better than or equal to 0.1%. This fulfills safeguards requirements.
We present a novel, simple, and fast colorimetric method to quantify the total number of carboxy groups on polymer microparticle and nanoparticle surfaces. This method exploits that small divalent transition metal cations (M2+ = Ni2+, Co2+, Cd2+) are efficiently bound to these surface functional groups, which allows their extraction by a single centrifugation step. Remaining M2+ in the supernatant is subsequently quantified spectrophotometrically after addition of the metal ion indicator pyrocatechol violet, for which Ni2+ was identified to be the most suitable transition metal cation. We demonstrate that the difference between added and detected M2+ is nicely correlated to the number of surface carboxy groups as determined by conductometry, thereby affording a validated measure for the trueness of this procedure. The variation coefficient of ~5% found in reproducibility studies underlines the potential of this novel method that can find conceivable applications for the characterization of different types of poly(carboxylic acid)-functionalized materials, e.g., for quality control by manufacturers of such materials.
The fluorine content of polymer particles labelled with 2,2,2-trifluoroethylamine was reliably quantified with overlapping sensitivity ranges by XPS and solid-state NMR. This provides a first step towards reference materials for the metrological traceability of surface group quantifications. The extension of this concept to fluorescence spectroscopy is illustrated.
We introduce a method to determine the number of accessible functional groups on a polymer microsphere surface based on the interaction between the macrocyclic host cucurbit[7]uril (CB7) and a guest reacted to the microsphere surface. After centrifugation, CB7 in the supernatant is quantified by addition of a fluorescent dye. The difference between added and detected CB7 affords the number of accessible surface functional groups.
Dye-stained micrometer-sized polymer beads are important tools in the life sciences with applications in biomedical, biochemical, and clinical research. Here, bead-based assays are increasingly used, for example, in DNA sequencing and the detection of autoimmune diseases or pathogenic microorganisms. Moreover, stained beads are employed as calibration tools for fluorescence microscopy and flow cytometry methods with increasing complexity. To address the requirements concerning the relevant fluorescence features, the spectroscopic properties of representative polymer beads with diameters ranging from about 1 to 10 μm stained with varying concentrations of rhodamine 6G were systematically assessed. The observed dependence of the spectral properties, fluorescence decay kinetics, and fluorescence quantum yields on bead size and dye loading concentration is attributed to different fluorescence characteristics of fluorophores located in the particle core and near-surface dye molecules. Supported by the fluorescence anisotropy measurements, the origin of the observed alteration of fluorescence features is ascribed to a combination of excitation energy transfer and polarity-related effects that are especially pronounced at the interface of the bead and the surrounding medium. The results of our studies underline the need to carefully control and optimize all Parameters that can affect the fluorescence properties of the dye-stained beads.
We report a surface analytical study of poly(methyl methacrylate) (PMMA) microparticles (beads) with a grafted shell of poly(acrylic acid) (PAA) with thicknesses up to 4 nm using scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (ToF-SIMS), and near-edge X-ray adsorption fine structure (NEXAFS) spectroscopy. These polymer microparticles were analyzed before and after reaction of the surface carboxyl (CO2H) groups with 2,2,2-trifluoroethylamine (TFEA) to gain a better understanding of methods with use of covalently bound probe molecules for surface group analysis. The results obtained with chemical derivatization XPS using TFEA are discussed in terms of surface quantification of reactive CO2H groups on these PAA-coated microparticles. A labeling yield of about 50% was found for TFEA-derivatized particles with amounts of surface-grafted CO2H groups of 99 µmol/g or more, which is consistent with predicted reaction yields for homogeneously dispersed PAA hydrogels.
Commercial platforms consisting of ready-to-use microarrays printed with target-specific DNA probes, a microarray scanner, and software for data analysis are available for different applications in medical diagnostics and food analysis, detecting, e.g., viral and bacteriological DNA sequences. The transfer of these tools from basic research to routine analysis, their broad acceptance in regulated areas, and their use in medical practice requires suitable calibration tools for regular control of instrument performance in addition to internal assay controls. Here, we present the development of a novel assay-adapted calibration slide for a commercialized DNA-based assay platform, consisting of precisely arranged fluorescent areas of various intensities obtained by incorporating different concentrations of a 'green' dye and a 'red' dye in a polymer matrix. These dyes present 'Cy3' and 'Cy5' analogues with improved photostability, chosen based upon their spectroscopic properties closely matching those of common labels for the green and red channel of microarray scanners. This simple tool allows to efficiently and regularly assess and control the performance of the microarray scanner provided with the biochip platform and to compare different scanners. It will be eventually used as fluorescence intensity scale for referencing of assays results and to enhance the overall comparability of diagnostic tests.