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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.
Surface-functionalized polymer beads encoded with molecular luminophores and nanocrystalline emitters such as semiconductor nanocrystals, often referred to as quantum dots (QDs), or magnetic nanoparticles are broadly used in the life sciences as reporters and carrier beads. Many of these applications require a profound knowledge of the chemical nature and total number of their surface functional groups (FGs), that control bead charge, colloidal stability, hydrophobicity, and the interaction with the environment and biological systems. For bioanalytical applications, also the
number of groups accessible for the subsequent functionalization with, e.g., biomolecules or targeting ligands is relevant. In this study, we explore the influence of QD encoding on the amount of carboxylic acid (COOH) surface FGs of 2 μm polystyrene microparticles (PSMPs). This is done for frequently employed oleic acid and oleylamine stabilized, luminescent core/shell CdSe QDs and two commonly used encoding procedures. This included QD addition during bead formation by a thermally induced polymerization reaction and a post synthetic swelling procedure. The accessible number of COOH groups on the surface of QD-encoded and pristine beads was quantified by two colorimetric assays, utilizing differently sized reporters and electrostatic and covalent interactions. The results were compared to the total number of FGs obtained by a conductometric titration and Fourier transform infrared spectroscopy (FTIR). In addition, a comparison of the impact of QD and dye encoding on the bead surface chemistry was performed. Our results demonstrate the influence of QD encoding and the QD-encoding strategy on the number of surface FG that is ascribed to an interaction of the QDs with the carboxylic acid groups on the bead surface. These findings are of considerable relevance for applications of nanoparticle-encoded beads and safe-by-design concepts for nanomaterials.
Outer membrane lipopolysaccharides (LPS) play a crucial role in determining attachment behavior and pathogenicity of bacteria. The aim of this study was to develop a simple procedure for anchoring bacterial lipopolysaccharides to polystyrene (PS) microparticles as a model system for in situ attachment studies. By using a swellcapture methodology, commercially available LPS of Pseudomonas aeruginosa (strain ATCC 27316 serotype 10.22) was anchored onto PS microparticles in a proof-of-concept study. A detailed chemical and morphological characterization has proven the success of LPS incorporation. It was shown that the coverage and structure of the LPS film was concentration dependent. The procedure can easily be adapted to LPS of other bacterial strains to generate a synthetic model toolkit for attachment studies.
Growth factors are a class of proteins that play a role in the proliferation (the increase in the number of cells resulting from cell division) and differentiation (when a cell undergoes changes in gene expression becoming a more specific type of cell) of cells. They can have both positive (accelerating the normal healing process) and negative effects (causing cancer) on disease progression and have potential applications in gene therapy and wound healing. However, their short half-life, low stability, and susceptibility to degradation by enzymes at body temperature make them easily degradable in vivo. To improve their effectiveness and stability, growth factors require carriers for delivery that protect them from heat, pH changes, and proteolysis. These carriers should also be able to deliver the growth factors to their intended destination. This review focuses on the current scientific literature concerning the physicochemical properties (such as biocompatibility, high affinity for binding growth factors, improved bioactivity and stability of the growth factors, protection from heat, pH changes or appropriate electric charge for growth factor attachment via electrostatic interactions) of macroions, growth factors, and macroion-growth factor assemblies, as well as their potential uses in medicine (e.g., diabetic wound healing, tissue regeneration, and cancer therapy).
Specific attention is given to three types of growth factors: vascular endothelial growth factors, human fibroblast growth factors, and neurotrophins, as well as selected biocompatible synthetic macroions (obtained through standard polymerization techniques) and polysaccharides (natural macroions composed of repeating monomeric units of monosaccharides). Understanding the mechanisms by which growth factors bind to potential carriers could lead to more effective delivery methods for these proteins, which are of significant interest in the diagnosis and treatment of neurodegenerative and civilization diseases, as well as in the healing of chronic wounds.
A new concept for the ecotoxicological assessment of plastics under consideration of aging processes
(2023)
Microplastics are widely distributed in aquatic and terrestrial environments, but up to now less is known about (eco)toxicological impacts under realistic conditions. Research so far has focused mainly on impacts on organisms by fresh, single‐origin plastic fragments or beads. However, plastics found in the environment are complex in composition, this means different polymer types and sources, with and without additives and in all stages of age, and therefore, in a more or less advanced stage of degradation. For oxidized degradation products that might be released from plastic materials during aging, there is a lack of information on potentially adverse effects on aquatic biota. The latter is of particular interest as oxidized degradation products might become more water soluble due to higher polarity and are more bioavailable, therefore. The present study focused on plastic leachates of polystyrene (PS) and polylactic acid (PLA), which were derived from alternating stress by hydrolysis and ultraviolet (UV) radiation—representing a realistic scenario in the environment. Test specimens of PS, PLA, or a PLA/PS layer (each 50%) were alternately exposed to UV radiation for 5 days followed by hydrolysis for 2 days, for several weeks alternating. Ecotoxicological effects of the storage water (artificial freshwater) of the test specimens and additionally, in a second experimental setup, the effects of five potential polymer degradation products were detected by 72 h algae growth inhibition tests with Desmodesmus subspicatus. Results clearly indicate inhibitory effects on algae growth by contaminants in the storage water of stressed plastics with increasing growth inhibition of proceeding hydrolysis and UV stress times. Different polymers caused variable inhibitions of algae growth with stronger inhibitions by PS and less effects by PLA and the mixed layer of both. Moreover, not microplastic particles but the resulting dissolved degradation products after aging caused the ecotoxicological effects—with strong effects by the oxidized degradation products. The existing data highlight the relevance of plastic aging as a framework for microplastic ecotoxicity evaluation and allow a proof of concept.
A fast method for microplastic detection is thermal extraction desorption‐gas chromatography/mass spectrometry (TED‐GC/MS), which uses polymer‐specific thermal decomposition products as marker compounds to determine polymer mass contents in environmental samples. So far, matrix impacts of different environmental matrices on TED‐GC/MS performance had not yet been assessed systematically. Therefore, three solid freshwater matrices representing different aquatic bodies with varying organic matter contents were spiked with a total of eight polymers. Additionally, for the first time, the two biodegradable polymers polybutylene adipate terephthalate (PBAT) and polylactide (PLA) were analysed using TED‐GC/MS. The methodological focus of this work was on detectability, quality of signal formation as well as realisation of quantification procedures and determination of the limit of detection (LOD) values. Overall, TED‐GC/MS allowed the unambiguous detection of the environmentally most relevant polymers analysed, even at low mass contents: 0.02 wt% for polystyrene (PS), 0.04 wt% for the tyre component styrene butadiene rubber (SBR) and 0.2 wt% for polypropylene (PP), polyethylene (PE) and PBAT. Further, all obtained LOD values were increased in all matrices compared to the neat polymer without matrix. The LOD of the standard polymers were increased similarly (PS: 0.21–0.34 μg, SBR: 0.27–0.38 μg, PP: 0.32–0.36 μg, PMMA: 0.64–1.30 μg, PET: 0.90–1.37 μg, PE: 3.80–6.99 μg) and their decompositions by radical scission processes were not significantly influenced by the matrices. In contrast, matrixspecific LOD increases of both biodegradable polymers PBAT (LOD: 1.41–7.18 μg) and PLA (0.84–20.46 μg) were observed, probably due to their hetero‐functional character and interactions with the matrices. In conclusion, the TED‐GC/MS performance is not solely determined by the type of the polymers but also by the composition of the matrix.
Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations
(2023)
Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells and their organelles, the study of linear energy transfer (LET), the relative biological effectiveness (RBE), ion beam cancer therapy, microbeam radiation therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed.
Microplastic particles with sizes between 1 to 1000 μm are widely distributed worldwide. Origin, transport pathways and fate are poorly known, as sampling, sample preparation and detection methods are major challenges. In addition, reference materials that mimic environmental particles are lacking. Most challenging is the yield of MP particle production and the need for resource-intensive grinding with liquid nitrogen. In this paper, a machine is designed to produce aged microplastic particles as reference material candidates with high yield. The machine is based on ultraviolet aging of a thin foil and mechanical fragmentation using clean air. An example of aging and fragmentation of high density polyethylene with additional physical and chemical characterization of shape, size, aging state by carbonyl index and density is presented.
Showcasing research from the Federal Institute for Material Research and Testing Berlin and Fraunhofer Institute for Celltherapy and Immunology Branch Bioanalytics and Bioprocesses Potsdam.
Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine.
We aimed to increase the possible undisturbed exposure time during bio-SAXS measurements of single-stranded DNA-binding proteins. Therefore small angle X-ray scattering was performed on Gene-V Protein (G5P/GVP), which is involved in DNA repair processes. To achieve this, irradiations were performed in presence and absence of the hydroxyl-radical scavenger and osmolyte Ectoine, which showed efficient radiation protection and prevented protein aggregation, thus allows for a non-disturbing way to improve structure-determination of biomolecules.
This study reflects typical consumer textile washing behaviour while taking into account existing standards in the household appliance and garment industries. Two garments were washed repeatedly with artificial dirt and detergent 30 times. The collected washing water was separated using fractional filtration. Textile physical tests were used to follow property changes of the garments, the microplastic release is determined using thermoextraction/desorbtion–gas chromatography/mass spectrometry and the total organic carbon was measured as a sum parameter for the organic bonded carbon. This article shows the importance of a reality‐based approach when investigating microplastics of textile origin in the laundry care process. Deposits of detergent and dirt on the textiles were detected. The total mass of sieve residues was much higher than the release of synthetic polymers. The cotton content of the garments causes a much higher fibre release than synthetic fibres. Both will lead to false results by purely gravimetric analysis because nonpolymer fibres will be included microplastic mass. The results cannot be generalised only by the main polymer type, knowledge of the textile construction must be included for final evaluation.