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Quantitative analysis of complex proteins is a challenging task in modern bioanalytical chemistry. Commonly available isotope labels are still suffering from limitations and drawbacks, whereas new metal labels open numerous possibilities in mass spectrometric analyses. In this work, we have developed a newmetal labeling strategy to tag glycan structures of proteins, more particularly antibodies. The oligosaccharide glycans were selectively trimmed to the last N-acetylglucosamine to which an artificial azide containing galactose residue was bound. This azide can be used for subsequent cycloaddition of an alkyne. Therefore, we developed a lanthanide-containing macrocyclic reagent to selectively connect to this azido galactose. In summary, the glycan structures of an antibody can be labeled with a metal functionality using this approach. Furthermore, the functionality of the antibodies can be fully maintained by labeling the Fc glycans instead of using labeling reagents that target amino or thiol groups. This approach enables the possibility of using elemental, besides molecular mass spectrometry, for quantitative analyses or imaging experiments of antibodies in complex biological samples.
Protein adsorption at the air–water interface is a serious problem in cryogenic electron microscopy (cryoEM) as it restricts particle orientations in the vitrified ice-film and promotes protein denaturation. To address this issue, the preparation of a graphene-based modified support film for coverage of conventional holey carbon transmission electron microscopy (TEM) grids is presented. The chemical modification of graphene sheets enables the universal covalent anchoring of unmodified proteins via inherent surface-exposed lysine or cysteine residues in a one-step reaction. Langmuir–Blodgett (LB) trough approach is applied for deposition of functionalized graphene sheets onto commercially available holey carbon TEM grids. The application of the modified TEM grids in single particle analysis (SPA) shows high protein binding to the surface of the graphene-based support film. Suitability for high resolution structure determination is confirmed by SPA of apoferritin. Prevention of protein denaturation at the air–water interface and improvement of particle orientations is shown using human 20S proteasome, demonstrating the potential of the support film for structural biology.
Small-area/spot photoelectron spectroscopy (SAXPS) is a powerful tool for the investigation of small surface features like microstructures of electronic devices, sensors or other functional surfaces, and so forth. For evaluating the quality of such microstructures, it is often crucial to know whether a small signal in a spectrum is an unwanted contamination of the field of view (FoV), defined by the instrument settings, or it originated from outside. To address this issue, the d80/20 parameter of a line scan across a chemical edge is often used. However, the typical d80/20 parameter does not give information on contributions from the long tails of the X-ray beam intensity distribution or the electron-optical system as defined by apertures. In the VAMAS TWA2 A22 project “Applying planar, patterned, multi-metallic samples to assess the impact of analysis area in surface-chemical analysis,” new test specimen was developed and tested. The here presented testing material consists of a silicon wafer substrate with an Au-film and embedded Cr circular and square spots with decreasing dimensions from 200 μm down to 5 μm. The spot sizes are traceable to the length unit due to size measurements with a metrological SEM. For the evaluation of the FoV, we determined the Au4f intensities measured with the center of the FoV aligned with the center of the spot and normalized to the Au4f intensity determined on the Au-film. With this test specimen, it was possible to characterize, as an example, the FoV of a Kratos AXIS Ultra DLD XPS instrument.
We demonstrate the use of a 3D printed radial collimator in X-ray powder diffraction and surface sensitive grazing incidence X-ray diffraction. We find a significant improvement in the overall Signal to background ratio of up to 100 and a suppression of more than a factor 3⋅10⁵ for undesirable Bragg reflections generated by the X-ray “transparent” windows of the sample environment.
The background reduction and the removal of the high intensity signals from the windows, which limit the detector’s dynamic range, enable significantly higher sensitivity in experiments within sample environments such as vacuum chambers and gas- or liquid-cells. Details of the additively manufactured steel collimator geometry, alignment strategies using X-ray fluorescence, and data analysis are also briefly discussed. The flexibility and affordability of 3D prints enable designs optimized for specific detectors and sample environments, without compromising the degrees of freedom of the diffractometer.
A novel approach for rating fatigue-initiating inclusions in highly demanding steel (INCAFAT)
(2018)
INCAFAT project aimed to improve existing fatigue damage models by establishing the most suitable combination of measurement techniques to characterise harmful inclusion populations in highly demanding steels. The different inclusion assessments carried out confirm that, chemical composition, secondary metallurgy and manufacturing route affect content, nature, size and shape of inclusions. According to the FEM model, inclusions produce an alteration of the stress field in their surrounding region, which can promote a fatigue failure. Experimental work on fatigue testing has demonstrated that depending on the stressed direction fatigue failures in highly demanding steels could be produced by different types of inclusions. Fractography analyses confirmed that meso-inclusions harmful in fatigue cannot be rated by standard methods, nor 10 MHz ultrasonic testing (macro) or micro-cleanness assessments. The necessity of rating these meso-inclusions has led to critical evaluation of Extreme Value Analysis according to ASTM E2283-08 and the development of high frequency immersion ultrasonic testing. EVA methodology based on inclusion width can be applied reliably when principal stress is parallel to the rolling direction. On the contrary, if inclusions are testing in the elongated directions its fails. On the other hand, the guidelines and recommendations for high frequency ultrasonic testing have been compiled in a new European standard draft. This method based on focal beam probes and high-resolution devices is able to provide information on meso-inclusion distribution.
We propose a novel iterative segmentation algorithm (i.S.Sy.Da.T.A: Iterative Segmentation Synthetic Data Training Algorithm) employing Deep Convolutional Neural Networks and synthetic training data for X-ray tomographic reconstructions of complex microstructures. In our method, we reinforce the synthetic training data with experimental XCT datasets that were automatically segmented in the previous iteration. This strategy produces better segmentations in successive iterations. We test our algorithm with experimental XCT re constructions of a 6-phase Al-Si Matrix Composite reinforced with ceramic fibers and particles. We perform the analysis in 3D with a special network architecture that demonstrates good generalization with synthetic training data. We show that our iterative algorithm returns better segmentations compared to the standard single training approach. More specifically, phases possessing similar attenuation coefficients can be better segmented: for Al2O3 fibers, SiC particles, and Intermetallics, we see an increase of the Dice score with respect to the classic approach: from 0.49 to 0.54, from 0.66 to 0.72, and from 0.55 to 0.66 respectively. Furthermore, the overall Dice score increases from 0.77 to 0.79. The methods presented in this work are also applicable to other materials and imaging techniques.
The amount of data generated worldwide is constantly increasing. These data come from a wide variety of sources and systems, are processed differently, have a multitude of formats, and are stored in an untraceable and unstructured manner, predominantly in natural language in data silos. This problem can be equally applied to the heterogeneous research data from materials science and engineering. In this domain, ways and solutions are increasingly being generated to smartly link material data together with their contextual information in a uniform and well-structured manner on platforms, thus making them discoverable, retrievable, and reusable for research and industry. Ontologies play a key role in this context. They enable the sustainable representation of expert knowledge and the semantically structured filling of databases with computer-processable data triples.
In this perspective article, we present the project initiative Materials-open-Laboratory (Mat-o-Lab) that aims to provide a collaborative environment for domain experts to digitize their research results and processes and make them fit for data-driven materials research and development. The overarching challenge is to generate connection points to further link data from other domains to harness the promised potential of big materials data and harvest new knowledge.
The fundamental properties of a polymeric material are ultimately governed by its structure, which mainly relies on monomercomposition and connection, topology, chain length, and polydispersity. Thus far, these structural characteristics are typicallyset ex situ by the specific polymerization procedure, eventually limiting the future design space for the creation of moresophisticated polymers. Herein, we report on a single photoswitchable catalyst system, which enables in situ remote controlover the ring-opening polymerization of l-lactide and further allows regulation of the incorporation of trimethylene carbonateand δ -valerolactone monomers in copolymerizations. By implementing a phenol moiety into a diarylethene-type structure,we exploit light-induced keto–enol tautomerism to switch the hydrogen-bonding-mediated monomer activation reversiblyON and OFF. This general and versatile principle allows for exquisite external modulation of ground-state catalysis of a livingpolymerization process in a closed system by ultraviolet and visible light and should thereby facilitate the generation of newpolymer structures.
This paper describes a new ultrasonic measuring device called “W-Box”. It was developed based on the requirements of the DFG Forschergruppe (research unit) CoDA for a portable device for monitoring of concrete specimens, models and actual structures using embedded ultrasonic transducers as well as temperature and humidity sensors. The W-Box can send ultrasonic pulses with a variable frequency of 50–100 kHz to one selectable transducer and records signals from up to 75 multiplexed channels with a sample rate of 1 MHz and a resolution of 14 bits. In addition, it measures temperature and humidity with high accuracy, adjustable amplification, restarts automatically after a power failure and can be fully controlled remotely. The measured data are automatically stored locally on-site data quality checks and transferred to remote servers. The comparison of the W-Box with a laboratory setup using commercial devices proves that it is equally reliable and precise, at much lower cost. The W-Box also shows that their measurement capacities, with the used embedded ultrasonic transducers, can reach above 6 m in concrete.
Monitoring programs should generate high-quality data on the concentrations of substances and other pollutants in the aquatic environment to enable reliable risk assessment. Furthermore, the need for comparability over space and time is critical for analysis of trends and evaluation of restoration of natural environment. Additionally, research work and exercises at the European level have highlighted that reliable measurements of estrogenic substances at the PNEC level are still challenging to achieve. The project EDC-WFD “Metrology for monitoring endocrine disrupting compounds under the EU Water Framework Directive” aims to develop traceable analytical methods for determining endocrine disrupting compounds and their effects, with a specific focus on three estrogens of the first watch list (17-beta-estradiol (17βE2), 17-alpha-ethinylestradiol (EE2), and estrone (E1)). Estrogens 17-alpha-estradiol (17aE2) and estriol (E3) will be included to demonstrate the reliability of the developed methods - Mass Spectrometry based method and effect-based methods (EBM) - and to support the requirements of Directive 2013/39/EC, Directive 2009/90/EC and Commission Implementation Decision (EU) 2018/840, hence improving the comparability and compatibility of measurement results within Europe. During the EDC-WFD project four EBM will be deeply investigated in order to improve their rationale use and their support in water quality assessment.
Monitoring programs should generate high-quality data on the concentrations of substances and other pollutants in the aquatic environment to enable reliable risk assessment. Furthermore, the need for comparability over space and time is critical for analysis of trends and evaluation of restoration of natural environment. Additionally, research work and exercises at the European level have highlighted that reliable measurements of estrogenic substances at the PNEC level are still challenging to achieve. The project EDC-WFD “Metrology for monitoring endocrine disrupting compounds under the EU Water Framework Directive” aims to develop traceable analytical methods for determining endocrine disrupting compounds and their effects, with a specific focus on three estrogens of the first watch list (17-beta-estradiol (17βE2), 17-alpha-ethinylestradiol (EE2), and estrone (E1)). Estrogens 17-alpha-estradiol (17aE2) and estriol (E3) will be included to demonstrate the reliability of the developed methods - Mass Spectrometry based method and effect-based methods (EBM) - and to support the requirements of Directive 2013/39/EC, Directive 2009/90/EC and Commission Implementation Decision (EU) 2018/840, hence improving the comparability and compatibility of measurement results within Europe. During the EDC-WFD project four EBM will be deeply investigated in order to improve their rationale use and their support in water quality assessment.
Inputs of plastic impurities into the environment via the application of fertilizers are regulated in Germany and the EU by means of ordinances. Robust and fast analytical methods are the basis of legal regulations. Currently, only macro- and large microplastic contents (>1 mm) are measured. Microplastics (1–1,000 µm), are not yet monitored. Thermal analytical methods are suitable for this purpose, which can determine the mass content and can also be operated fully automatically in routine mode. Thermal extraction desorption-gas chromatography/mass spectrometry (TED-GC/MS) allows the identification of polymers and the determination of mass contents in solid samples from natural environments. In accordance with the German or European Commission (EC) Fertiliser Ordinance, composting plants should be monitored for microplastic particles with this method in the future. In this context a compost plant was sampled. At the end of the rotting process, the compost was sieved and separated in a coarse (>1 mm) and a fine fraction (<1 mm). The fine fraction was processed using density separation comparing NaCl and NaI as possible salt alternative and screened for microplastic masses by TED-GC/MS with additional validation and quality assurance experiments. With TED-GC/MS total microplastics mass contents of 1.1–3.0 μg/mg in finished compost could be detected with polyethylene mainly. What differs much to the total mass of plastics in the coarse fraction with up to 60 μg/mg, which were visually searched, identified via ATR-FTIR and gravimetrically weighted.
A brief introduction is given into our data collection and organization procedure, and why we have settled on the HDF5-based NeXus format for describing experimental data.
The links between NeXus and the SciCat data catalog is also provided, showing how the NeXus metadata is automatically added as searchable metadata in the catalog.
Increasing contamination of environmental waters with pharmaceuticals represents an emerging threat for the drinking water quality and safety. In this regard, fast and reliable analytical methods are required to allow quick countermeasures in case of contamination. Here, we report the development of a magnetic bead-based immunoassay (MBBA) for the fast and cost-effective determination of the analgesic diclofenac (DCF) in water samples, based on diclofenac-coupled magnetic beads and a robust monoclonal anti-DCF antibody. A novel synthetic strategy for preparation of the beads resulted in an assay that enabled for the determination of diclofenac with a significantly lower limit of detection (400 ng/L) than the respective enzyme-linked immunosorbent assay (ELISA). With shorter incubation times and only one manual washing step required, the assay demands for remarkably shorter time to result (< 45 min) and less equipment than ELISA. Evaluation of assay precision and accuracy with a series of spiked water samples yielded results with low to moderate intra- and inter-assay variations and in good agreement with LC–MS/MS reference analysis. The assay principle can be transferred to other, e.g., microfluidic, formats, as well as applied to other analytes and may replace ELISA as the standard immunochemical method.
Regardless of its ban in agricultural use, the triazine derivative terbutryn is still used as a biocide against biofouling in building materials, such as façade colors and roof tiles. From there, it is washed off and may contaminate soil and surface waters, where it shows ecotoxicological behavior. For understanding of these leaching processes, analytical methods that can detect terbutryn in traces are necessary. In contrast to separation methods (Gas (GC) or liquid chromatography (LC)) coupled to mass spectrometry (MS), enzyme immunoassays (EIAs) have proven to be adequate tools for environmental monitoring. Compared to GC-or LC-MS, they are cheap, require only limited time and experimental expertise and enable high throughput. For quantification of terbutryn, EIAs have been established, with a limit of detection (LOD) of 50 ng L-1. For leaching experiments however, a lower LOD would be advantageous.
For detection of terbutryn we developed a direct competitive ELISA based on a monoclonal antibody: Terbutryn and an enzyme-terbutryn conjugate (“tracer”) compete for the binding sites of the immobilized antibody. The bound tracer converts a colourless substrate into a blue-coloured product, which can be detected via spectrophotometry. For quantification of terbutryn, a sigmoidal calibration curve is used. For establishing of the EIA, a new tracer based on a terbutryn surrogate (“hapten”) was synthesized. After optimization of the experimental conditions, the immunoassay exhibited a more than ten-fold increased sensitivity (LOD: 3 ng L-1), high stability against sample compounds (Ca2+, NaCl) and lower cross-reactivities against structurally related compounds, than reported before. Analysis of spiked samples was possible with high precision (inter-assay CV: < 10 %) and accuracy (recoveries from spiked samples: 89 % ± 10%). We therefore propose it as quick and reliable method for leaching studies of terbutryn out of building materials.
The hard X-ray beamline BAMline at BESSY II (Berlin, Germany) has now been in service for 20 years. Several improvements have been implemented in this time, and this review provides an overview of the imaging methods available at the BAMline. Besides classic full-field synchrotron X-ray computed tomography (SXCT), also absorption edge CT, synchrotron X-ray refraction radiography (SXRR), and synchrotron X-ray refraction tomography (SXRCT) are used for imaging. Moreover, virtually any of those techniques are currently coupled in situ or operando with ancillary equipment such as load rigs, furnaces, or potentiostats. Each of the available techniques is explained and both the current and the potential usage are described with corresponding examples. The potential use is manifold, the examples cover organic materials, composite materials, energy-related materials, biological samples, and materials related to additive manufacturing. The article includes published examples as well as some unpublished applications.
The propagation of ultrasonic waves in concrete is affected by its micro- and macro-structure, geometry and properties as well as external influences as stress, temperature or moisture. In addition, age and degradation have a strong influence. Therefore, Ultrasound has been used to monitor concrete samples and structures since decades. However, early applications using conventional techniques as time-of flight or changes in amplitudes have been limited to detect changes in a late stage close to serviceability or ultimate load states.
Around 2000, several new, more sensitive techniques adopted from geophysics or other field of material sciences have been introduced to research in ultrasonic monitoring of concrete. The most discussed methodologies are coda wave interferometry, a technique which allows to detect very subtle changes from repeated ultrasonic measurements. Nonlinear acoustic techniques help to identify e. g. cracks even in an inhomogeneous background. Both techniques can be combined.
This paper reviews methods and results achieved so far on the laboratory scale and with full scale models the directions for future research and application is given as well.
The propagation of ultrasonic waves in concrete is affected by its micro- and macro-structure, geometry and properties as well as external influences as stress, temperature or moisture. In addition, age and degradation have a strong influence. Therefore, Ultrasound has been used to monitor concrete samples and structures since decades. However, early applications using conventional techniques as time-of flight or changes in amplitudes have been limited to detect changes in a late stage close to serviceability or ultimate load states.
Around 2000, several new, more sensitive techniques adopted from geophysics or other field of material sciences have been introduced to research in ultrasonic monitoring of concrete. The most discussed methodologies are coda wave interferometry, a technique which allows to detect very subtle changes from repeated ultrasonic measurements. Nonlinear acoustic techniques help to identify e. g. cracks even in an inhomogeneous background. Both techniques can be combined.
This paper reviews methods and results achieved so far on the laboratory scale and with full scale models the directions for future research and application is given as well.
Iron isotopes are used in a variety of fields from e.g., geologic question to medical applications. Measurements of iron isotopes are usually performed as delta measurements to an artificial based delta zero standard. In the case of Fe isotopes is that delta zero standard IRMM-014, a pure Fe metal. Unfortunately, that conventional delta zero reference material defining the 56/54Fe scale is out of stock and therefore unavailable. To overcome that situation and fulfill the need for laboratories that measure Fe isotope on a regular basis we will provide a set of solutions with IRMM-014 and a second anchor point for Fe isotope ratio measurements that is based on a pure Fe metal. This new second anchor point, a high purity Fe from BAM, will be calibrated against IRMM-014 and can be used as bracketing standard or as reference value for stable Fe isotope measurements.
We are in the good situation that BAM ordered a large stock of IRMM-014 several years ago. That stock of IRMM-014 Fe cubes and IRMM-014 Fe wires will be dissolved in 6M HCl in a large quantity. The new anchor point, the high purity Fe metal, that is commercially available at BAM, is a pure Fe metal with only trace amounts of impurities. The high purity BAM material will also be dissolved in 6M HCl in large quantity. Several aliquots of both solutions will be measured on the Neptune Plus MC-ICP-MS to define this second anchor point with a low uncertainty. Further will we send several aliquots of both solutions to different laboratories to also measure this second anchor point of high purity Fe on the 56/54Fe scale.
We will report the values of that study on BAM high purity Fe and will provide a guide for scale conversion to the IRMM-014 scale and for uncertainty calculation to use that new anchor point instead of the exhausted IRMM-014.
The damage caused by ionizing radiation to DNA and proteins is the reason to treat cancer by radiation therapy. A better understanding of the molecular processes and quantification of the different damaging mechanisms is the prerequisite to develop more efficient therapies. Hereby the understanding of the processes involved in the damage to DNA are of key interest due to its central role in reproduction and mutation.
For radiation with low linear energy transfer (LET), most of the damage is caused by the secondary particles produced by scattering of the ionizing radiation with water. Thereby a multitude of species are produced, whereby especially kinetic low energy electrons, prehydrated electrons, OH-radicals and ions are of importance. With higher LET the relative amount of the direct damaging effects increases. This is especially important considering the increased usage of high LET nucleons in radiation therapy. Therefore, the quantification of the contribution to DNA damage of direct and indirect effects and the different secondary species is of high interest due to the increase of radio biological efficiency when applying high LET radiation.
Here we present an approach to investigate the relative contributions to DNA strand break yield for radiation of different LET within a single electron microscope in combination with electron scattering simulations.