Analytische Chemie
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Fungal pigments such as melanin and carotenoids are distinctive markers of animal and plant pathogenic fungi as well as their environmental relatives. These complex pigments play important roles in pathogenicity and stress tolerance while also being useful as biomarkers. Accordingly, it is important to be able to identify in situ the pigments in black fungi, a group of clinical and environmental importance. In this study, wild-type and genetically modified strains of Knufia petricola A95 and wild fungal cells attached to ancient rock were investigated for their spectroscopic and microscopic Raman features and morphological appearance. Knockout mutants of melanin synthesis genes pks1 (polyketide synthase), sdh1 (scytalone dehydratase), and both pks1 and the carotenoid synthesis gene phd1 (phytoene desaturase) were studied We applied two different Raman microscopes using two lasers, with 633 nm and 488 nm wavelengths. We analyzed and compared Raman spectra between the measured reference substances and the mutant and wild-type strains. In the wild strain WT:A95, the peaks close to melanin peals were found at 1353 cm−1 and 1611 cm−1. There are no characteristic melanin peaks at 1580–1600 cm−1 and around 1350 cm−1 at the spectrum of the Δpks1/Δphd1 mutant and the Δsdh1 mutant. The Δpks1 mutant spectrum has the peaks at the beta-carotene v2 C-C in-plane stretch at 1155 cm−1 and v3 C-CH3 deformation at 1005 cm−1. The peaks of carotenoids and melanin were found in all mutants and the wild strain, except the Δpks1/Δphd1 mutant. Raman spectra allow for discrimination between the various pigments. Hence, interactions between natural fungal melanin, as well as other protective pigments, and complex environmental matrices can be characterized on a range of spatial and temporal scales.
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. Furthermore, first data about the degradation of single-stranded DNA binding-proteins (G5P / GV5 and hmtSSB) under vacuum and NAP-XPS conditions are presented.
We give an overview about recent work concerning ionizing radiation damage to Oligonucleotides, plasmid DNA, DNA binding proteins (G5P), and DNA-protein complexes.
We focus on combining new experimental setups with Geant4/TOPAS particle scattering simulations to understand the effets of ionizing radiation.
Radiation biophysics
(2023)
A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.
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.
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.
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.
With femtosecond-laser direct writing (fs-LDW) maturing in all aspects as a manufacturing technology, a toolset for quality assurance must be developed. In this work we introduce a first of its kind test artifact. Test artifacts are standardized 3D models with specific geometric features to evaluate the performance of writing parameters. Test artifacts are already common in other 3D additive manufacturing technologies e.g. selective laser melting. The test artifact introduced in this work was developed in particular to accommodate the high geometrical resolution of fs-LDW structures and the limited possibilities to examine the resulting structure. Geometric accuracy, surface adhesion as well as confocal Raman spectroscopy results were considered when evaluating the design of the test artifact. We will explain the individual features and design considerations of our fs-LDW test artifact. The difference between two slicers, Cura and 3DPoli, and the implications on measured feature sizes and the general shape is quantified. The measured geometries are used to derive a general design guide for a specific combination of photoresists, laser power and scanning speed and to analyze the geometric accuracy of a structure produced using these guidelines. The shown test artifact is publicly available as STL file on GitHub (https://github.com/BAMresearch/2PP-TestArtifact) and in the supplement.
Im Verbundprojekt RUSEKU wurde die Probenahme von Wasserproben entscheidend weiterentwickelt. Wichtig ist hierbei zu gewährleisten, dass genügend Merkmalsträger in jeder Probe untersucht werden. Es muss daher eine für den Probenahmeort repräsentative Beprobung hinsichtlich des Wasservolumens in Abhängigkeit der Partikelanzahl gewährleistet sein.
Das Hauptaugenmerk lag im vorliegenden Projekt auf einer praxisnahen Beprobungsstrategie. Es wurden verschiedene Konzepte ausprobiert.
• Grundsätzlich hat sich gezeigt, dass eine Stichprobe eine Momentaufnahme des MP-Massengehaltes zeigt. Es wird eine hohe Statistik, also eine Vielzahl an Messungen am gleichen Probenahmeort, benötigt, um eine valide Aussage über den MP-Gehalt zu machen.
• Es zeigt sich, dass eine integrale Probenahme über mehrere Wochen mit dem SK routinemäßig möglich ist. Die erfassten MP-Massen sind reproduzierbar und robust.
• Die DFZ ist für Stichproben geeignet. Partikel < 50 µm werden eventuell unterschätzt
• Die fraktionierte Filtration kann für Stich- und Mischproben direkt im Feld genutzt werden. Fraktionen von 10 und 5 µm werden später im Labor Vakuum filtriert. Es erfolgt eine Fraktionierung der Probe mit Siebmaschenweiten von 1000, 500, 100, 50, 10 und 5 µm.
• Die fraktionierte Filtration kann auch anschließend an die Beprobung mit dem SK zur Anwendung kommen. Wird die mit dem SK gewonnene Wasserprobe fraktioniert filtriert, kann neben einem MP-Gesamtgehalt auch eine Einschätzung über die Partikelgrößen gewonnen werden.
• Für Wässer mit geringen Partikelzahlen wurde ein Messfiltertiegel entwickelt. Dieser hat eine Maschenweite von 6 µm. Seine Anwendung kann mögliche Verluste beim Transferieren vom Probenahmetool zum Messgefäß und mögliche Kontaminationen reduzieren.
Die Optimierung der Probenahmestrategie wurde durch Modellversuche und Simulationen unterstützt. Modellversuche zum Sinkverhalten und Simulationen von MP in realen Gewässern verdeutlichten das komplexe Verhalten der Partikel. Es konnte gezeigt werden, dass Partikel ab einer bestimmten Größe (und kleiner) bei genügend starker Turbulenz sich in der Wassersäule unabhängig von ihrer Dichte verhalten und so auch MP mit kleiner Dichte (z.B. PE) in der gesamten Wassersäule zu finden sind. Es konnte mit dem TEM die Existenz von NP gezeigt werden.
Ein wesentlicher Aspekt des RUSEKU Projektes war die Beprobung realer Kompartimente. Beprobt wurde neben Oberflächengewässern, das urbane Abwassersystem der Stadt Kaiserslautern, Waschmaschinenabwasser und Flaschenwasser.
• In Oberflächengewässern wurde hauptsächlich PE gefunden. Je nach Probe und Gewässer konnten auch PP, PS, PET, PA, SBR und Acrylate nachgewiesen werden.
• Im urbanen Abwassersystem der Stadt Kaiserslautern konnte an allen Probenahmestandorten MP nachgewiesen werden. Es wurde hauptsächlich PE, neben geringeren Mengen an PP, PS und SBR gefunden. Nach einem Regenereignis war der SBR Anteil deutlich erhöht.
• Die Beprobung eines realen Wäschepostens, bestehend aus T-Shirts und Hemden mit PA/CO oder PES/CO Mischgewebe, zeigte einen PA- und PES-Austrag im Waschwasser. Der überwiegende Teil der detektierten Fasern ist aber auf Baumwolle zurückzuführen. Reine gravimetrische Messungen zur Detektion von MP führen zu einer starken Überschätzung.
• In Flaschenwasser (PET-Flaschen) konnte MP detektiert werden. PET wurde nur im stillen Mineralwasser, nicht in Mineralwasser mit Kohlensäure gefunden werden. Teilweise wurde auch das MP-Material des Verschlusses im Wasser detektiert.
• Für Luftproben konnte ein Aufbau zur größenselektiven Beprobung getestet werden.
Neben der Probenahme hat das Projekt auch gezeigt, dass die TED-GC/MS geeignet für die MP-Detektion im Routinebetrieb ist. Die TED-GC/MS konnte weiter optimiert werden. Es wurden MP-Massen bestimmt.
Im Projekt wurden erste realitätsnahe Referenzmaterialien für die MP Detektion hergestellt. Die Herstellung von realitätsnahen Polymeren in ausreichender Homogenität und Menge hat sich als große Herausforderung herausgestellt.