TY - JOUR A1 - Kuhring, M. A1 - Doellinger, J. A1 - Nitsche, A. A1 - Muth, Thilo A1 - Renard, B. Y. T1 - TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples N2 - Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to noniterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted, and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt. KW - Bioinformatics KW - Mass spectrometry KW - Microbial proteomics KW - Strain identification KW - MS/MS PY - 2020 DO - https://doi.org/10.1021/acs.jproteome.9b00714 VL - 19 IS - 6 SP - 2501 EP - 2510 PB - ACS AN - OPUS4-50942 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Faßbender, Sebastian A1 - Rodiouchkina, K. A1 - Vanhaecke, F. A1 - Meermann, Björn T1 - Method development for on-line species-specific sulfur isotopic analysis by means of capillary electrophoresis/multicollector ICP-mass spectrometry N2 - In this work, a method for species-specific isotopic analysis of sulfur via capillary electrophoresis hyphenated on-line with multicollector ICP-MS (CE/MC-ICP-MS) was developed. Correction for the mass bias caused by instrumental mass discrimination was realized via external correction with multiple-injection sample-standard bracketing. By comparing the isotope ratio measurement results obtained using the newly developed on-line CE/MC-ICP-MS method with those obtained via traditional MC-ICP-MS measurement after analyte/matrix separation by anion exchange chromatography for isotopic reference materials and an in-house bracketing standard, the most suitable data evaluation method could be identified. The repeatability for the sulfate-δ34S value (calculated from 18 measurements of a standard conducted over seven measurement sessions) was 0.57‰ (2SD) and thereby only twice that obtained with off-line measurements (0.30‰, n = 68). As a proof of concept for analysis of samples with a real matrix, the determination of the sulfur isotopic composition of naturally present sulfate was performed for different river systems. The CE/MC-ICP-MS results thus obtained agreed with the corresponding off-line MC-ICP-MS results within the 2SD ranges, and the repeatability of consecutive δ34S measurements (n = 3) was between 0.3‰ and 1.3‰ (2SD). Finally, the isotopic analysis of two different S-species in a river water sample spiked with 2-pyridinesulfonic acid (PSA) was also accomplished. KW - River water sulfate KW - Environmental speciation KW - Sulfur isotopes KW - On-line CE/MC-ICP-MS KW - Multiple-injection sample-standard bracketing PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-509549 DO - https://doi.org/10.1007/s00216-020-02781-8 SN - 1618-2642 VL - 412 IS - 23 SP - 5637 EP - 5646 PB - Springer CY - Berlin, Heidelberg AN - OPUS4-50954 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Maiwald, Michael T1 - The internet of things in the lab and in process - The digital transformation challenges for the laboratory 4.0 T1 - Das Internet of Things in Labor und Prozess - Herausforderungen des digitalen Wandels für das Labor 4.0 N2 - It is a fact that much of the time spent on analytical laboratory instrumentation these days goes into system maintenance. Digital transformation could give us more time again for creativity and our actual laboratory work – if we shape it the right way. N2 - Fakt ist: Einen Großteil der Zeit, der an analytischen Laborgeräten verbracht wird, nimmt heute die Systempflege in Anspruch. Der digitale Wandel kann uns endlich wieder mehr Zeit für Kreativität und die eigentliche Laborarbeit geben – wenn wir ihn richtig gestalten. KW - Lab of the Future KW - Digitalisation KW - Automation KW - Data Analysis KW - Instrument Communication KW - Labor der Zukunft KW - Digitale Transformation KW - Automatisierung KW - Gerätekommunikation PY - 2020 IS - 4 SP - 1 EP - 3 PB - Lumitos AG CY - Darmstadt AN - OPUS4-50618 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Zhang, Zhiyang A1 - Li, Y. A1 - Frisch, J. A1 - Bär, M. A1 - Rappich, J. A1 - Kneipp, Janina T1 - In situ surface-enhanced Raman scattering shows ligand-enhanced hot electron harvesting on silver, gold, and copper nanoparticles N2 - Hot carriers (electrons and holes) generated from the decay of localized surface plasmon resonances can take a major role in catalytic reactions on metal nanoparticles. By obtaining surface enhanced Raman scattering (SERS) spectra of p-aminothiophenol as product of the reduction of p-nitrothiophenol by hot electrons, different catalytic activity is revealed here for nanoparticles of silver, gold, and copper. As a main finding, a series of different ligands, comprising halide and non-halide species, are found to enhance product formation in the reduction reaction on nanoparticles of all three metals. A comparison with the standard electrode potentials of the metals with and without the ligands and SERS data obtained at different electrode potential indicate that the higher catalytic activity can be associated with a higher Fermi level, thereby resulting in an improved efficiency of hot carrier generation. The concept of such a ligand-enhanced hot electron reduction provides a way to make light-to-chemical energy conversion more efficient due to improved electron harvesting. KW - Ligands KW - Hot electrons KW - SERS KW - p-Nitrothiophenol KW - p-Aminothiophenol PY - 2020 DO - https://doi.org/10.1016/j.jcat.2020.01.006 VL - 383 SP - 153 EP - 159 PB - Elsevier Inc. CY - Amsterdam, NL AN - OPUS4-50626 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ebel, Kenny A1 - Bald, Ilko T1 - Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA N2 - The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A4), d(A8), d(A12), d(A16), and d(A20)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A4) to d(A16), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A20), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA20 sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy. KW - DNA origami KW - DNA radiation damage KW - DNA strand breaks KW - Low-energy electrons KW - Sequence dependence PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-503563 DO - https://doi.org/10.3390/ijms21010111 VL - 21 IS - 1 SP - 1 EP - 11 PB - MDPI CY - Basel, Switzerland AN - OPUS4-50356 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schmidt, C. A1 - Schierack, P. A1 - Gerber, U. A1 - Schröder, C. A1 - Choi, Youngeun A1 - Bald, Ilko A1 - Lehmann, W. A1 - Rödiger, S. T1 - Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures N2 - One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10–15 μm in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH–biotin bond was temperature-sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 °C. When oligonucleotides were bis-biotinylated, all SA/SAH–biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability. KW - Biopolymers Probes KW - Hybridization KW - Fluorescence KW - Genetics PY - 2020 DO - https://doi.org/10.1021/acs.langmuir.9b02339 VL - 36 IS - 2 SP - 628 EP - 636 PB - American Chemical Society Publication CY - Washington AN - OPUS4-50357 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - von der Au, Marcus A1 - Borovinskaya, O. A1 - Flamigni, L. A1 - Kuhlmeier, K. A1 - Büchel, C. A1 - Meermann, Björn T1 - Single cell-inductively coupled plasma-time of flight-mass spectrometry approach for ecotoxicological testing N2 - Diatoms play a key role in assessing the eco-toxicology of metals and are already part of several national and international guidelines and regulations. Data on metal uptake and its correlation with a natural metal composition of the diatoms are mostly lacking on a cellular basis - mainly due to the lack of a suitable method on both the preparation and detection side. Therefore, within this work a fully automated approach based on the on-line coupling of a high performance liquid chromatograph (HPLC) and an inductively coupled plasma-time of flight-mass spectrometer (ICP-ToF-MS) was applied to analyze single cells of the alga Cyclotella meneghiniana multi-elementally in order to provide a deeper insight into the metal composition and its response to environmental stress. Multi-elemental analysis in single diatoms also enables assessment of combined toxicity of a set of metals. A set of four fingerprint elements, characteristically for diatoms (Mg, P, Si, Fe), were identified and hence the investigation of environmental stress onto the cells was enabled by performing incubation experiments with environmentally relevant toxic elements. It could be shown at moderate environmental stress caused by increasing the metal concentration in the medium (zinc) that the fingerprint element concentrations remained stable and thus the suitability of the selected elements for algae tracing was demonstrated. With regard to further ecotoxicological assessments, a multivariate approach was successfully applied allowing for cell classification upon different incubation concentration levels. This multivariate approach also facilitated an effective identification of three different diatom species (Cyclotella meneghiniana, Thalassiosira weissflogii and Thalassiosira pseudonana). KW - ICP-TOF-MS KW - Ecotoxicological Testing KW - Diatoms PY - 2020 DO - https://doi.org/10.1016/j.algal.2020.101964 VL - 49 SP - 101964 PB - Elsevier B.V. AN - OPUS4-50875 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Marques, T. S. A1 - Schürmann, Robin A1 - Ebel, Kenny A1 - Heck, C. A1 - Smialek, M. A1 - Eden, Sam A1 - Mason, N. A1 - Bald, Ilko T1 - Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses-A 5-Bromouracil case study N2 - Laser illuminated gold nanoparticles (AuNPs) efficiently absorb light and heat up the surrounding medium, leading to versatile applications ranging from plasmonic catalysis to cancer photothermal therapy. Therefore, an in-depth understanding of the thermal, optical, and electron induced reaction pathways is required. Here, the electrophilic DNA nucleobase analog 5-Bromouracil (BrU) has been used as a model compound to study its decomposition in the vicinity of AuNPs illuminated with intense ns laser pulses under various conditions. The plasmonic response of the AuNPs and the concentration of BrU and resulting photoproducts have been tracked by ultraviolet and visible (UV–Vis) spectroscopy as a function of the irradiation time. A kinetic model has been developed to determine the reaction rates of two parallel fragmentation pathways of BrU, and their dependency on laser fluence and adsorption on the AuNP have been evaluated. In addition, the size and the electric field enhancement of the decomposed AuNPs have been determined by atomic force microscopy and finite domain time difference calculations, respectively. A minor influence of the direct photoreaction and a strong effect of the heating of the AuNPs have been revealed. However, due to the size reduction of the irradiated AuNPs, a trade-off between laser fluence and plasmonic response of the AuNPs has been observed. Hence, the decomposition of the AuNPs might be limiting the achievable temperatures under irradiation with several laser pulses. These findings need to be considered for an efficient design of catalytic plasmonic systems. KW - Kinetics KW - Gold nanoparticles KW - 5-Bromouracil PY - 2020 DO - https://doi.org/10.1063/1.5137898 VL - 152 IS - 12 SP - 24712 EP - 24712 PB - AIP Publishing AN - OPUS4-50787 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kepsutlu, B. A1 - Wycisk, V. A1 - Achazi, K. A1 - Kapishnikov, S. A1 - Perez-Berna, A.J. A1 - Guttmann, P. A1 - Cossmer, Antje A1 - Pereiro, E. A1 - Ewers, H. A1 - Ballauff, M. A1 - Schneider, G. A1 - McNally, J.G. T1 - Cells Undergo Major Changes in the Quantity of Cytoplasmic Organelles after Uptake of Gold Nanoparticles with Biologically Relevant Surface Coatings N2 - Here, we use cryo soft X-ray tomography (cryo-SXT), which delivers 3D ultrastructural volumes of intact cells without chemical fixation or staining, to gain insight about nanoparticle uptake for nanomedicine. We initially used dendritic polyglycerol sulfate (dPGS) with potential diagnostic and therapeutic applications in inflammation. Although dPGS-coated gold nanoparticle (dPGS-AuNP) uptake followed a conventional endocytic/degradative pathway in human lung epithelial cell lines (A549), with cryo-SXT, we detected ∼5% of dPGS-AuNPs in the cytoplasm, a level undetectable by confocal light microscopy. We also observed ∼5% of dPGS-AuNPs in a rarely identified subcellular site, namely, lipid droplets, which are important for cellular energy metabolism. Finally, we also found substantial changes in the quantity of cytoplasmic organelles upon dPGS-AuNP uptake over the 1–6 h incubation period; the number of small vesicles and mitochondria significantly increased, and the number of multivesicular bodies and the number and volume of lipid droplets significantly decreased. Although nearly all organelle numbers at 6 h were still significantly different from controls, most appeared to be returning to normal levels. To test for generality, we also examined cells after uptake of gold nanoparticles coated with a different agent, polyethylenimine (PEI), used for nucleic acid delivery. PEI nanoparticles did not enter lipid droplets, but they induced similar, albeit less pronounced, changes in the quantity of cytoplasmic organelles. We confirmed these changes in organelle quantities for both nanoparticle coatings by confocal fluorescence microscopy. We suggest this cytoplasmic remodeling could reflect a more common cellular response to coated gold nanoparticle uptake. KW - Cellular trafficking KW - Confocal laser scanning microscopy KW - Cytoplasmic remodeling KW - Dendritic polyglycerol sulfate KW - Polyethylenimine KW - 3D ultrastructural analysis KW - Cryo-soft X-ray tomography PY - 2020 DO - https://doi.org/10.1021/acsnano.9b09264 VL - 14 IS - 2 SP - 2248 EP - 2264 AN - OPUS4-50464 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schulze-Makuch, D. A1 - Haque, S. A1 - Beckles, D. A1 - Schmitt-Kopplin, P. A1 - Harir, M. A1 - Schneider, Beate A1 - Stumpp, C. A1 - Wagner, D. T1 - A chemical and microbial characterization of selected mud volcanoes in Trinidad reveals pathogens introduced by surface water and rain water N2 - Terrestrial mud volcanoes are unique structures driven by tectonic pressure and fluids from the deep subsurface. These structures are mainly found in active tectonic zones, such as the area near the Los Bajos Fault in Trinidad. Here we report a chemical and microbiological characterization of three mud volcanoes, which included analyses of multiple liquid and solid samples from the mud volcanoes. Our study confirms previous suggestions that at least some of the mud volcano fluids are a mixture of deeper salt-rich water and surficial/precipitation water. No apparent water quality differences were found between sampling sites north and south of a major geological fault line. Microbiological analyses revealed diverse communities, both aerobic and anaerobic, including sulfate reducers, methanogens, carbon dioxide fixing and denitrifying bacteria. Several identified species were halophilic and likely derived from the deeper salt-rich subsurface water, while we also cultivated pathogenic species from the Vibrionaceae, Enterobacteriaceae, Shewanellaceae, and Clostridiaceae. These microorganisms were likely introduced into the mud volcano fluids both from surface water or shallow ground-water, and perhaps to a more minor degree by rain water. The identified pathogens are a major health concern that needs to be addressed. KW - Water stable isotope analysis KW - Mud volcanoe fluids KW - Metabolomics PY - 2020 DO - https://doi.org/10.1016/j.scitotenv.2019.136087 VL - 707 SP - 136087 PB - Elsevier B.V. AN - OPUS4-50499 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -