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- Bioinformatics (2)
- Mass spectrometry (2)
- Metaproteomics (2)
- Steel slag (2)
- Transmission function (2)
- X-ray photoelectron spectroscopy (2)
- Air-coupled ultrasound (1)
- Alveolar-capillary barrier (1)
- Benchmarking (1)
- Calibration-free analysis (1)
Organisationseinheit der BAM
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Im Rahmen eines von der Kulturstiftung des Bundes und der Kulturstiftung der Länder geförderten
Projektes zum Erhalt naturkundlicher Nasssammlungen wurden 1) der Zustand der Sammlungen bewertet
(Profiling; Analyse der Vergällungsmittel), 2) über Workshops Expertenwissen in das Projekt gebracht,
3) neue archivbeständige Materialien und Managementmaßnahmen eingeführt (Borosilikat-Gläser und -
Röhrchen, Augenwatte, Tefloneinlagen, Japanpapier, archivbeständige Kleber und Papier, Etikettenaufbewahrung;
digitales Dichtemessgerät, Alcomon-Indikator, Kontrollintervalle), 4) Erhaltungsmaßnahmen
zur langfristigen Konservierung in großem Umfange durchgeführt (Messen der Alkoholkonzentration,
Umsetzen von Präparaten in geeignetere Gefäße, Wiederverschluss von Schaugläsern) und 5) Erfahrungen
und Diskussionsergebnisse zusammengestellt, nicht ohne auf Wissenslücken und wünschenswerte
Forschungsaspekte hinzuweisen. Das Projekt profitierte besonders von der Expertise aus den Materialwissenschaften
und der Papierrestaurierung. Das Museum für Naturkunde Berlin kooperierte eng mit
dem Berliner Medizinhistorischen Museum der Charité, der Zoologischen Staatssammlung München und
dem Forschungsinstitut Senckenberg in Frankfurt. Letzteres Museum führte ein eigenes, themenverwandtes
KUR-Projekt Restauration der Sammlungen 'Vergleichende Anatomie, Embryologie und Histologie'
des Naturmuseums Senckenberg durch.
This guideline was drafted following and complementing the norm ISO 22232-2:2020(E) to include air-coupled ultrasonic transducers. This document specifies the characteristics of probes used for non-destructive air-coupled ultrasonic testing with center frequencies above 20 kHz, with focusing or without focusing means.
We report the results of a Versailles Project on Advanced Materials and Standards interlaboratory study on the intensity scale calibration of x-ray photoelectron spectrometers using low-density polyethylene (LDPE) as an alternative material to gold, silver, and copper. An improved set of LDPE reference spectra, corrected for different instrument geometries using a quartz-monochromated Al Kα x-ray source, was developed using data provided by participants in this study. Using
these new reference spectra, a transmission function was calculated for each dataset that participants provided. When compared to a similar calibration procedure using the NPL reference spectra for gold, the LDPE intensity calibration method achieves an absolute offset of ∼3.0% and a systematic deviation of ±6.5% on average across all participants. For spectra recorded at high pass energies (≥90 eV), values of absolute offset and systematic deviation are ∼5.8% and ±5.7%, respectively, whereas for spectra collected at lower pass energies (<90 eV), values of absolute offset and systematic deviation are ∼4.9% and ±8.8%, respectively; low pass energy spectra perform worse than the global average, in terms of systematic deviations, due to diminished count rates and signal-to-noise ratio. Differences in absolute offset are attributed to the surface roughness of the LDPE induced by sample preparation. We further assess the usability of LDPE as a secondary reference material and comment on its performance in the presence of issues such as variable dark noise, x-ray warm up times, inaccuracy at low count rates, and underlying spectrometer problems. In response to participant feedback and the results of the study, we provide an updated LDPE intensity calibration protocol to address the issues highlighted in the interlaboratory study. We also comment on the lack of implementation of a consistent and traceable intensity calibration method across the community of x-ray photoelectron spectroscopy (XPS) users and, therefore, propose a route to achieving this with the assistance of instrument manufacturers, metrology laboratories, and experts leading to an international standard for XPS intensity scale calibration.
The lead authors failed to name two collaborators as co-authors. The authors listed should include:
Miss Claudia L. Compean-Gonzalez (ORCID:
0000-0002-2367-8450) and Dr. Giacomo Ceccone (ORCID:
0000-0003-4637-0771).
These co-authors participated in VAMAS project A27, provided data that were analyzed and presented in this publication (and supporting information), and reviewed the manuscript before submission.
Drug and gene delivery via nanoparticles across biological barriers such as the alveolar-capillary barrier of the lung constitutes an interesting and increasingly relevant field in nanomedicine. Nevertheless, potential hazardous effects of nanoparticles (NPs) as well as their cellular and systemic fate should be thoroughly examined. Hence, this study was designed to evaluate the effects of amorphous silica NPs (Sicastar) and (poly)organosiloxane NPs (AmOrSil) on the viability and the inflammatory response as well as on the cellular uptake mechanisms and fate in cells of the alveolar barrier. For this purpose, the alveolar epithelial cell line (NCI H441) and microvascular endothelial cell line (ISO-HAS-1) were used in an experimental set up resembling the alveolar-capillary barrier of the lung. In terms of IL-8 and sICAM Sicastar resulted in harmful effects at higher concentrations (60 µg/ml) in conventional monocultures but not in the coculture, whereas AmOrSil showed no significant effects. Immunofluorescence counterstaining of endosomal structures in NP-incubated cells showed no evidence for a clathrin- or caveolae-mediated uptake mechanism. However, NPs were enclosed in flotillin-1 and -2 marked vesicles in both cell types. Flotillins appear to play a role in cellular uptake or trafficking mechanisms of NPs and are discussed as indicators for clathrin- or caveolae-independent uptake mechanisms. In addition, we examined the transport of NPs across this in vitro model of the alveolar-capillary barrier forming a tight barrier with a transepithelial electrical resistance of 560 ± 8 Ω cm². H441 in coculture with endothelial cells took up much less NPs compared to monocultures. Moreover, coculturing prevented the transport of NP from the epithelial compartment to the endothelial layer on the bottom of the filter insert. This supports the relevance of coculture models, which favour a differentiated and polarised epithelial layer as in vitro test systems for nanoparticle uptake.
The lack of traceability to meter of X-ray Computed Tomography (CT) measurements still hinders a more extensive acceptance of CT in coordinate metrology and industry. To ensure traceable, reliable, and accurate measurements, the determination of the task-specific measurement uncertainty is necessary. The German guideline VDI/VDE 2630 part 2.1 describes a procedure to determine the measurement uncertainty for CT experimentally by conducting several repeated measurements with a calibrated test specimen. However, this experimental procedure is cost and effort intensive. Therefore, the simulation of dimensional measurement tasks conducted with X-ray computed tomography can close these drawbacks. Additionally, recent developments towards a resource and cost-efficient production (“smart factory”) motivate the need for a corresponding numerical model of a CT system (“digital twin”) as well. As there is no standardized procedure to determine the measurement uncertainty of a CT system by simulation at the moment, the project series CTSimU was initiated, aiming at this gap. Concretely, the goal is the development of a procedure to determine the measurement uncertainty numerically by radiographic simulation. The first project (2019-2022), "Radiographic Computed Tomography Simulation for Measurement Uncertainty Evaluation - CTSimU" developed a framework to qualify a radiographic simulation software concerning the correct simulation of physical laws and functionalities. The most important outcome was a draft for a new guideline VDI/VDE 2630 part 2.2, which is currently under discussion in the VDI/VDE committee. The follow-up project CTSimU2 "Realistic Simulation of real CT systems with a basic-qualified Simulation Software" will deal with building and characterizing a digital replica of a specific real-world CT system. The two main targets of this project will be a toolbox including methods and procedures to configure a realistic CT system simulation and to develop tests to check if this replica is sufficient enough. The result will be a draft for a follow-up VDI/VDE guideline proposing standardized procedures to determine a CT system's corresponding characteristics and test the simulation (copy) of a real-world CT system which we call a "digital twin".
To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.
Laser-induced breakdown spectroscopy (LIBS) is a fast and versatile technique for (semi) quantitative element analysis of solids, liquids, gases, and particulate matter. The LIBS method is used for optical sensing in various branches of industrial production. In the contribution we review some of our recent results on LIBS analysis of slags from secondary metallurgy in industrial steel making. Major oxides in steel slags are measured at-line and after homogenization using a calibration-free (CF) method. Two approaches for CF analysis based on the Boltzmann plot method and on the calculation of synthetic spectra are compared for the analysis of quaternary oxides. We also present the research in cooperation with our industrial partners in the process-analytical chemistry network PAC.