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Paper des Monats
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Gene-V protein (G5P/GVP) is a single-stranded (ss)DNA-binding protein (SBP) of bacteriophage f1 that is required for DNA synthesis and repair. In solution, it exists as a dimer that binds two antiparallel ssDNA strands with high affinity in a cooperative manner, forming a left-handed helical protein–DNA filament. Here, we report on fluorescence studies of the interaction of G5P with different DNA oligonucleotides having a hairpin structure (molecular beacon, MB) with a seven base-pair stem (dT24-stem7, dT18-stem7), as well as with DNA oligonucleotides (dT38, dT24) without a defined secondary structure. All oligonucleotides were end-labeled with a Cy3-fluorophore and a BHQ2-quencher. In the case of DNA oligonucleotides without a secondary structure, an almost complete quenching of their strong fluorescence (with about 5% residual intensity) was observed upon the binding of G5P. This implies an exact alignment of the ends of the DNA strand(s) in the saturated complex. The interaction of the DNA hairpins with G5P led to the unzipping of the base-paired stem, as revealed by fluorescence measurements, fluorescence microfluidic mixing experiments, and electrophoretic mobility shift assay data. Importantly, the disruption of ssDNA’s secondary structure agrees with the behavior of other single-stranded DNA-binding proteins (SBPs). In addition, substantial protein-induced fluorescence enhancement (PIFE) of the Cy3-fluorescence was observed.
An isotopic effect of normal (H2O) vs. heavy water (D2O) is well known to fundamentally affect structure and chemical properties of proteins, for instance. Here we correlate results from small angle X-ray and neutron scattering (SAXS, SANS) with high-resolution scanning transmission electron microscopy to track the evolution of CdS nanoparticle size and crystallinity from aqeuous solution in presence of the organic ligand ethylenediaminetetraacetate (EDTA) at room temperature in both H2O and D2O. We provide evidence via SANS experiments that exchanging H2O by D2O impacts nanoparticle formation by changing the equilibria and dynamics of EDTA clusters in solution as investigated by nuclear magnetic resonance. The colloidal stability of the CdS nanoparticles, covered by a layer of [Cd(EDTA)]2- complexes, is significantly reduced in D2O despite the strong stabilizing effect of EDTA in suspensions of normal water. Hence, conclusions about nanoparticle formation mechanisms from D2O solutions can bare limited transferability to reactions in normal water due to isotopic effects, which thus need to be discussed for contrast match experiments.
In this study, the wavefield radiated from a building to its surroundings is identified and extracted from M4.6 earthquake recordings collected by sensors installed in a building and on the nearby athletic field in Matera (Italy) using a new approach for soil-structure interaction assessment. The proposed approach for earthquake data analysis combines in an innovative way two methods already used in seismology and engineering seismology: deconvolution and polarization analysis. The approach enables the identification, reconstruction, and characterization of the wavefield radiated from a vibrating building into its surroundings, and the estimation of the amount of energy associated with it. The approach consists of four steps: estimation of the resonant frequencies of the building, deconvolution of the earthquake recordings from a building and its surroundings, identification of the seismic phases, reconstruction of the signal transmitted from the building to its surroundings, and estimation of its energy, and polarization analysis. Analysis of recordings of the M4.6 event highlighted that the motion related to the wavefield radiated from the building to the ground was mostly linearly polarized in the radial and transverse planes, while a clear ellipticity was observed only in the horizontal plane. The wavefield radiated from the building might be dominated by unconventionally polarized surface waves, i.e., quasi-Rayleigh waves or a combination of quasi-Rayleigh and quasi-Love waves. The results indicated that the energy transmitted from the analyzed vibrating building to its surroundings was significant and decreased the ground motion shaking due to the out-of-phase motion.
This presentation summarizes recent developments within the scope of the national pre-standardization project “ZfPStatik”, which aims to prepare a guideline about NDT-supported structural analyses. The focus is on the purposeful and explicit utilization of geometrical tendon and reinforcement bar positions measured on-site in reliability analysis — shown by means of a prestressed concrete bridge as case study.
Per- and polyfluoroalkyl substances (PFAS) are a large, ever-growing and widely used class of chemicals. Due to the strength of the C-F bond, they do not decompose but accumulate in the environment posing a risk for nature and humans alike. While the use of some PFAS, like perfluorooctanoic acid (PFOA) is already regulated in the EU, new ‘precursor’ substances are used to replace them. However, these precursors may be equally harmful to the environment.
In recent years, many ‘hot spot’ sites with high PFAS contaminations in soil have been distinguished, but no German-wide background values have been determined yet. Knowing these background values is crucial to understand the degree of PFAS contamination, underpinning future regulatory decisions.
Due to the complexity and variety of different PFAS compounds, one needs to apply a broad spectrum of different techniques to capture most of the PFAS content in one sample.
In the framework of this project, 600 soil samples are taken at different sites all over Germany. The concentration of 30 PFAS - 13 carboxylic acids (C4-C18), 5 sulfonic acids (C4-C10) and 12 precursor substances) - is determined in these soil samples using three different sample preparation approaches: 1) ultrasonic extraction of the soil samples with Methanol; 2) preparation of eluates to test the leaching behaviour of the PFAS and 3) TOP assays following the method published by Houtz & Sedlak.
Targeted LC-MS/MS is used to determine PFAS concentration after all three preparation steps.
For the TOP-assay, the concentration of all 30 PFAS is compared prior to and after the oxidation reaction.
Besides the ‘classic’ TOP-Assay, two other TOP-Assay approaches, the dTOP Assay and the photoTOP-Assay, are tested and the results of all three approaches are compared. First, all three TOP-Assay approaches will be tested on a reference soil spiked with a solution including all 30 PFAS measured in the project. Later, soil samples taken in the frame of the priorly described project will be tested.
This poster will focus on the results of the experiments comparing the three different TOP Assay approaches in spiked reference soil. Additionally, some of the results of the other sample preparation methods, extraction and eluate preparation will be presented.
Experimentally informed multiscale creep modelling of additive manufactured Ni-based superalloys
(2023)
Excellent creep resistance at elevated temperatures, i.e. T / T_m> 0.5, due to γ-γ’ microstructure is one of the main properties of nickel-based superalloys. Due to its great importance for industrial applications, a remarkable amount of research has been devoted to understanding the underlying deformation mechanism in a wide spectrum of temperature and loading conditions. Additive manufactured (AM) nickel-based superalloys while being governed by similar γ-γ’ microstructure, exhibit AM-process specific microstructural characteristics, such as columnar grains, strong crystallographic texture (typically <001> fiber texture parallel to build direction) and compositional inhomogeneity, which in turn leads to anisotropic creep response in both stationary and tertiary phases.
Despite the deep insights achieved recently on the correlation between process parameters and the resulting microstructure, the anisotropic creep behavior and corresponding deformation mechanism of these materials are insufficiently understood so far. One reason for this is the lack of capable material models that can link the microstructure to the mechanical behavior. To overcome this challenge, a multiscale microstructure-based approach has been applied by coupling crystal plasticity (CP) and polycrystal model which enables the inclusion of different deformation mechanisms and microstructural characteristics such as crystallographic texture and grain morphology. The method has been applied to experimental data for AM-manufactured INCONEL-738LC (IN738). The effect of different slip systems, texture, and morphology on creep anisotropy at 850°C has been investigated. Results suggest a strong correlation between superlattice extrinsic stacking fault (SESF) and microtwinning and observed creep anisotropy.
HR-CS-GFMAS a new screening tool for per- and polyfluoroalkyl substances (PFAS) in the environment
(2023)
Per- and polyfluorinated alkyl substances (PFASs) are a large group of anthropogenic contaminates. Concerning are especially their persistent, bioaccumulative and toxic properties. Mostly, target-based approaches (e.g., LC-MS/MS) are utilized for the analysis of PFASs in the environment. But these approaches are limited to the availability of analytical grade standards and therefore drastically underestimate the total PFAS burden. Analytical approaches based on total fluorine for PFAS sum parameter analysis become increasingly important to indicate realistic PFAS pollution levels.
PFAS sum parameters display the proportion of organically bound fluorine that can either be extracted (EOF) or adsorbed to activated carbon (AOF). For the instrumental analysis of such sum parameters, a fluorine selective detector is needed. Besides combustion ion chromatography (CIC), high resolution-continuum source-graphite furnace molecular absorption spectrometry (HR-CS-GFMAS) is a sensitive and highly selective tool for fluorine determination. The method is based on the in situ formation of diatomic gallium-mono fluoride (GaF) in a graphite furnace at a temperature of 1550°C. The molecular absorption of GaF can be detected at its most sensitive wavelength at 211.248 nm providing limits of quantification in the low µg F L-1 range.
Here, we present a comparison of total fluorine analysis methods – AOF vs. EOF and HR-CS-GFMAS vs. CIC. Therefore, surface water samples from the Spree River in Berlin, Germany were analyzed at 10 locations for total fluorine (TF), AOF and EOF. The AOF made up 0.14–0.81% of TF and the EOF 0.04–0.28% of TF while AOF concentrations were systematically higher. For the instrumental comparison, HR-CS-GFMAS was the more sensitive and precise method for fluorine analysis compared to CIC.
Photoluminescence Quantum Yields of Luminescent Nanocrystals and Particles in the UV/vis/NIR/SWIR
(2023)
The rational design of functional luminescent materials such as semiconductor quantum dots and lanthanide-based upconversion nanoparticles, all photophysical and mechanistic studies, and the comparison of different emitters require accurate and quantitative photoluminescence measurements. Particularly the reliable determination of the key performance parameter photoluminescence quantum yield (f), the number of emitted per absorbed photons, and the brightness are of special importance for luminescence applications in the life and material sciences and nano(bio)photonics.[1] In this context, examples for absolute measurements of the photoluminescence quantum yields of UV/vis/NIR/SWIR emissive semiconductor quantum dots and rods, made from different materials, and spectrally shifting lanthanide upconversion nanocrystals with different surface chemistries in transparent matrices are presented including excitation wavelength and power density dependent studies utilizing integration sphere spectroscopy.[2,3] In addition, procedures for the absolute determination of the photoluminescence quantum yields of scattering dispersions of larger size quantum rods and differently sized inorganic particles have been developed as well as procedures for the characterization of solid luminescent nanomaterials such as different perovskites and YAG:Cer converter materials.[4] Thereby, challenges and pitfalls of f measurements in different wavelength regions including the SWIR and material-specific effects related to certain emitter classes are addressed, achievable uncertainties are quantified, and relative and absolute measurements of photoluminescence quantum yield measurements are compared to underline limitations of the former approach. Finally, a set of novel UV/vis/NIR quantum yield standards is presented including their certification with a complete uncertainty budget.[5]
Glimpses of the Future ✨: Advancing X-ray Scattering in an Automated Materials Research Laboratory
(2023)
In our (dramatically understaffed) X-ray scattering laboratory, developing a systematic, holistic methodology1 let us provide scattering and diffraction information for more than 2100 samples for 200+ projects led by 120+ collaborators. Combined with automated data correction pipelines, and our analysis and simulation software, this led to more than 40 papers2 in the last 5 years with just over 2 full-time staff members.
This year, our new, modular synthesis platform has made more than 1000 additional samples for us to analyse and catalogue. By virtue of the automation, the synthesis of these samples is automatically documented in excruciating detail, preparing them for upload and exploitation in large-scale materials databases. Having developed these proof-of-concepts, we find that materials research itself is changed dramatically by automating dull tasks in a laboratory.
This talk is intended to spark ideas and invite collaborations by providing an overview of: 1) the current improvements in our wide-range X-ray scattering laboratory methodology, 2) Introduce some of our open-source analysis and simulation software, touching on scattering, diffraction and PDF, and 3) introducing our open, modular robotic platform for systematic sample preparation. Finally, the remaining bottlenecks and points of attention across all three are highlighted.
The second talk for the Swiss Society for Crystallography (SSCr) workshop on SAXS will highlight the data processing challenges, holistic experimental workflow developments, and the pitfalls. In particular, the following items will be addressed:
- The importance of data processing and estimating uncertainty
- A universal correction pipeline – away with the headaches, at least for this step!
- Experiment planning part 2, some tips and advice to improve your corrected data.
- Sample preparation, background selection, some tips and advice to improve your corrected data.
- Automate for your mental well-being; electronic logbooks, measurement catalogs and workflow management software
- Life on the edge: several pitfalls to avoid…
This talk for the Swiss Society for Crystallography (SSCr) workshop on SAXS will introduce scattering from various angles, focusing in particular on:
- Information content of X-ray scattering experiments, three entry points…
- An introduction to Fourier Transforms
- Sample criteria, compatibility, and selection
- Key indicators of a measurement – where is the information?
- Key indicators of measurement quality
- Experiment planning, the basics
Reliability assessment of existing concrete bridges with geometrical NDT results - Case studies
(2023)
The results of and the validity in reliability assessment of existing bridges essentially depend on the information available about the considered system. Information about the actual condition as well as structural and material characteristics can be observed on-site to refine the computation models used in assessment. Non-destructive testing (NDT) methods for concrete structures are capable of reconstructing missing, questioned, or inconsistent as-built plans. This contribution summarizes recent developments within the scope of the national pre-standardization project “ZfPStatik”, which aims to prepare a guideline about NDT-supported structural analyses. The focus is on the purposeful and explicit utilization of geometrical tendon and reinforcement bar positions (measured on-site using the ultrasound echo and ground penetrating radar (GPR) techniques) in probabilistic reliability analyses — shown by means of real case studies. The well-established first order reliability method is applied to different concrete bridges, which are typical for the German road bridge stock, to demonstrate the utility of incorporating quality-evaluated NDT-results in terms of changes in structural reliability.
In our (dramatically understaffed) X-ray scattering laboratory, developing a systematic, holistic methodology let us provide scattering and diffraction information for more than 2100 samples for 200+ projects led by 120+ collaborators. Combined with automated data correction pipelines, and our analysis and simulation software, this led to more than 40 papers in the last 5 years with just over 2 full-time staff members.
This year, our new, modular synthesis platform has made more than 1000 additional samples for us to analyse and catalogue. By virtue of the automation, the synthesis of these samples is automatically documented in excruciating detail, preparing them for upload and exploitation in large-scale materials databases.
This talk is intended to spark ideas and invite collaborations by providing an overview of: 1) the current improvements in our wide-range X-ray scattering laboratory methodology, and 2) introducing our open, modular robotic platform for systematic sample preparation.
Introduction: The influence of copper, iron and zinc concentrations on the formation of ß-amyloid plaques and neurofibrillary tangles in Alzheimer’s disease (AD) is widely discussed in the community. The results from human and animal studies so far are mixed with some studies showing a correlation and others not. From a number of studies, it is known that disease state and isotopic composition of essential elements can be coupled.
Aim: The aim of the study was to identify changes in element content and isotopic composition in two transgenic mouse models used in AD research compared to their genetic WT relatives and to establish whether element content and isotopic signature between different laboratories is comparable.
Methods: ß-amyloid (5xFAD) and tau overexpressing (L66) mice together with their matching wild-types were bred at dedicated facilities in accordance with the European Communities Council Directive (63/2010/EU). Serum and brain were sampled after sacrifice and the samples distributed among the participants of the study. The tissues were acid digested for total element determination and high-precision isotope ratio determination. Element content was determined by either sector-field or quadrupole-based inductively coupled plasma mass spectrometry (ICPMS). For the determination of isotope ratios multi-collector ICPMS was used.
Results: Total copper content was significantly higher for L66 and their matched WT compared to 5xFAD and WT. Brains of L66 mice contained more Fe in brain than their WT, Zn and Cu were not significantly different between L66 and WT. Whereas 5xFAD mice had a slightly lower Cu and slightly higher Zn concentration in brain compared to WT. The isotopic signature in brain of L66 mice for Fe was different from their controls, whereas Zn isotope ratios were influenced in 5xFAD mice compared to their WT . The Cu isotopic ratio did not seem to be influenced in either strain. In serum, the shifts were less pronounced.
Conclusion: Even though neither Tau-protein nor amyloid precursor protein are known to be metal-dependent / -containing proteins, the overexpression of both influences the Fe, Cu and Zn metabolism in brain and to some extent also in serum as can be seen not only using total element determination but probably more clearly studying the isotopic signature of Fe, Cu and Zn.
Hierarchically porous, high‐surface‐area silica materials are excellent candidates for multiple applications like catalysis and environmental remediation. Shaping these materials with additive manufacturing (AM) techniques, like robocasting, could enable their use with the benefit of on‐demand, customized shaping and maximizing performance. Herein, ordered mesoporous silica COK‐12 slurries were robocasted into monoliths, containing different ratios of uncalcined COK‐12 and sodium bentonite (0–25 wt.%). The rheology of the mixed slurries is characterized by lower flow indexes (0.69 vs. 0.32) and higher yield stresses (96 vs. 259 Pa) compared to pure COK‐12 ones. Monoliths were printed in woodpile structures and calcined at 600°C. Micro‐CT measurements showed a linear shrinkage of 25% after calcination. Mechanical characterization showed increased uniaxial strength (0.20 ± 0.07 to 1.0 ± 0.3 MPa) with increasing binder/solids ratio from 13 to 25%. The amorphous, mesoporous structure of COK‐12 was retained. The structures exhibited open porosities of 52 ± 4% and showed higher specific mesopore volumes, and increased average mesopore size (6 vs. 8 nm) compared to COK‐12. Small‐angle x‐ray scattering analysis revealed an increased lattice parameter (10.3 vs. 11.0 nm) and reduced wall thickness (3.1 nm vs. 4.1 nm) of the COK‐12 in the monoliths. These properties indicate suitability for their application as porous supports and adsorbents.
Due to the extremely high specific surface area of nanoparticles and corresponding potential for adsorption, the results of surface analysis can be highly dependent on the history of the particles, particularly regarding sample preparation and storage. The sample preparation method has, therefore, the potential to have a significant influence on the results. This report describes an interlaboratory comparison (ILC) with the aim of assessing which sample preparation methods for ToF-SIMS analysis of nanoparticles provided the most intra- and interlaboratory consistency and the least amount of sample contamination. The BAM reference material BAM-P110 (TiO2 nanoparticles with a mean Feret diameter of 19 nm) was used as a sample representing typical nanoparticles. A total of 11 participants returned ToF-SIMS data,in positive and (optionally) negative polarity, using sample preparation methods of “stick-and-go” as well as optionally “drop-dry” and “spin-coat.” The results showed that the largest sources of variation within the entire data set were caused by adventitious hydrocarbon contamination or insufficient sample coverage, with the spin-coating protocol applied in this ILC showing a tendency toward insufficient sample coverage; the sample preparation method or the participant had a lesser influence on results.
The performance of second generation ICP-TOFMS, equipped with a micro-channel plate (MCP) enabling multi-isotope detection, in terms of isotope ratio precision and instrumental isotopic fractionation (IIF) for (multi-)isotope ratio analysis was thoroughly assessed for B, Sr and Pb. Experimental isotope ratio precision of 0.14 % for 11B/10B intensity ratio, 0.15 % for 87Sr/86Sr intensity ratio and 0.07% for 208Pb/206Pb intensity ratio were obtained at high signal levels ($500 mg L−1) which is comparable to first generation ICP-TOFMS. The long-term stability of isotope ratios, measured over several hours and expressed as repeatability, is between 0.05 % and 1.8 % for B, Sr and Pb. The observed IIF per mass unit is negative for B (i.e., −11 % for 11B/10B) which is in accordance with measurements using sector field (MC) ICP-MS. But the observed IIF per mass unit is positive for Sr (i.e., 2 % for 87Sr/86Sr) and Pb (i.e., 4.5 % for 208Pb/206Pb) which is not in accordance with measurements using sector field (MC) ICP-MS. Furthermore, different IIFs per mass unit were observed for different isotope pairs of the same isotopic system (i.e., Sr, Pb) and adjacent isotopic systems (i.e., Pb vs. Tl). This and the observations from three-isotope plots for Sr and Pb show that ion formation, ion extraction, ion transmission, ion separation and ion detection in second generation ICP-TOFMS is subject to IIF that does not follow the known mass dependent fractionation laws and is possibly caused by mass independent fractionation and/or multiple (contradictory) fractionation processes with varying contributions. The non-mass dependent IIF behavior observed for second generation ICP TOFMS has profound consequences for the IIF correction of isotope raw data, including application of multi-isotope dilution mass spectrometry (IDMS) using ICP-TOFMS. Hence, only IIF correction models that correct also for mass independent fractionation are applicable to calculate reliable isotope ratios using second generation ICP-TOFMS. In the present study, reliable d11B values, and absolute B, Sr and Pb isotope ratios could be determined using the SSB approach in single-element solutions as well as in a mixture of B, Sr and Pb, where the isotopes were measured simultaneously.
In-situ monitoring of water dependent DNA and protein radiation damage by near-ambient-pressure XPS
(2023)
X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS experiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. Our results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.
Many metallic materials gain better mechanical properties through controlled heat treatments. For example, in age-hardenable aluminium alloys, the strengthening mechanism is based on the controlled formation of nanometre-sized precipitates, which represent obstacles to dislocation movement and consequently increase the strength. Precise tuning of the material microstructure is thus crucial for optimal mechanical behaviour under service condition of a component. Therefore, analysis of the microstructure, especially the precipitates, is essential to determine the optimum parameters for the interplay of material and heat treatment. Transmission electron microscopy (TEM) is utilized to identify precipitate types and orientations in the first step. Dark-field imaging (DF-TEM) is often used to image the precipitates and thereafter quantify their relevant dimensions. Often, these evaluations are still performed by manual image analysis, which is very time-consuming and to some extent also poses reproducibility problems.
Our work aims at a semantic representation of an automatable digital approach for this material specific characterization method under adaption of FAIR data practices. Based on DF-TEM images of different precipitation states of a wrought aluminium alloy, the modularizable, digital workflow of quantitative analysis of precipitate dimensions is described. The integration of this workflow into a data pipeline concept will also be discussed. Using ontologies, the raw image data, their respective contextual information, and the resulting output data of the quantitative image analysis can be linked in a triplestore. Publishing the digital workflow and the ontologies will ensure data reproducibility. In addition, the semantic structure enables data sharing and reuse for other applications and purposes, demonstrating interoperability.
We report about a joint project aiming at the digitalization of a lab course in materials testing. The undergraduate students were asked to prepare samples of a precipitation hardened aluminum alloy and characterize them using hardness and tensile tests. In a first step, we developed the frames for the digital labor notebook using eLabFTW. The primary data and the relevant metadata of each run were saved in a central database and made available for analysis and report issues. The whole set of results produced in a course was made available in the database. This database can be improved and serve as an open repository for data on this specific alloy.
The logical frame for the joint project was provided by the PMD Core Ontology (PMDco), a mid-level ontology that enables the representation and description of processes and process chains in an MSE-specific manner, ensuring full traceability of generated data. For the digitalization of this lab course, the tensile test ontology (TTO) was applied which is designed as a module of the PMDco using strongly related semantic concepts.