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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.
The precipitation of struvite, a magnesium ammonium phosphate hexahydrate (MgNH₄PO₄ · 6H₂O) mineral, from wastewater is a promising method for recovering phosphorous. While this process is commonly used in engineered environments, our understanding of the underlying mechanisms responsible for the formation of struvite crystals remains limited. Specifically, indirect evidence suggests the involvement of an amorphous precursor and the occurrence of multi-step processes in struvite formation, which would indicate non-classical paths of nucleation and crystallization. In this study, we use synchrotron-based in situ x-ray scattering complemented by cryogenic transmission electron microscopy to obtain new insights from the earliest stages of struvite formation. The holistic scattering data captured the structure of an entire assembly in a time-resolved manner. The structural features comprise the aqueous medium, the growing struvite crystals, and any potential heterogeneities or complex entities. By analysing the scattering data, we found that the onset of crystallization causes a perturbation in the structure of the surrounding aqueous medium. This perturbation is characterized by the occurrence and evolution of Ornstein-Zernike fluctuations on a scale of about 1 nm, suggesting a non-classical nature of the system. We interpret this phenomenon as a liquid-liquid phase separation, which gives rise to the formation of the amorphous precursor phase preceding actual crystal growth of struvite. Our microscopy results confirm that the formation of Mg-struvite includes a short-lived amorphous phase, lasting >10 s.
Graphene oxide (GO) has emerged as a promising biomaterial as it is easily and cheaply synthesized, strong, cytocompatible, osteoinductive, and has a well-characterized aqueous degradation pathway. It is also a great substrate for functionalization with biomolecules such as proteins, peptides, and small molecules that can enhance or add bioactivity. Covalent chemical linkages as opposed to typical noncovalent association methods are preferable so that the biomolecules do not quickly diffuse away or face replacement by other proteins, which is critical in long time scale applications like bone regeneration. However, covalent chemistry tends to carry a drawback of harsh reaction conditions that can damage the structure, conformation, and therefore function of a delicate biomolecule like a protein. Here, the Mitsunobu reaction is introduced as a novel method of covalently attaching proteins to graphene oxide. It features gentle reaction conditions and has the added benefit of utilizing the plentiful basal plane alcohol functionalities on graphene oxide, allowing for high yield protein functionalization. The amino acid Glycine (G), the protein bovine serum albumin (BSA), and the small molecule SVAK-12 are utilized to create the three Mitsunobu Graphene (MG) materials G-MG, BSA-MG, and SVAK-MG that demonstrate the wide applicability of this functionalization method.
The capabilities of National Metrology Institutes (NMIsthose which are members of the Comité Consultatif pour la Quantité de Matière (CCQM)of the CIPM) and selected outside "expert" laboratories to quantitate (C4H9)3Sn+ (TBT) in a prepared marine sediment were assessed. This exercise was sanctioned by the 7th CCQM meeting, April 46, 2001, as an activity of the Inorganic Analysis Working Group and was jointly piloted by the Institute for National Measurement Standards of the National Research Council of Canada (NRC) and the Laboratory of the Government Chemist (LGC), UK. A total of 11 laboratories submitted results (7 NMIs, and 4 external labs). Two external laboratories utilized a standard calibration approach based on a natural abundance TBT standard, whereas all NMIs relied upon isotope dilution mass spectrometry for quantitation. For this purpose, a species specific 117Sn-enriched TBT standard was supplied by the LGC. No sample preparation methodology was prescribed by the piloting laboratories and, by consequence, a variety of approaches was adopted by the participants, including mechanical shaking, sonication, accelerated solvent extraction, microwave assisted extraction and heating in combination with Grignard derivatization, ethylation and direct sampling. Detection techniques included ICPMS (with GC and HPLC sample introduction), GCMS, GCAED and GCFPD. Recovery of TBT from a control standard (NRCC CRM PACS-2 marine sediment) averaged 93.5±2.4% (n=14). Results for the pilot material averaged 0.680±0.015 µmol kg1 (n=14; 80.7±1.8 µg kg1) with a median value of 0.676 µmol kg1. Overall, performance was substantially better than state-of-the-art expectations and the satisfactory agreement amongst participants permitted scheduling of a follow-up Key comparison for TBT (K-28), a Pilot intercomparison for DBT (P-43), and certification of the test sediment for TBT content and its release as a new Certified Reference Material (HIPA-1) with a TBT content of 0.679±0.089 µmol kg1 (expanded uncertainty, k=2, as Sn) (80.5±10.6 µg kg1). Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00216-003-2016-9.
The calcitic prisms of Pinna nobilis (Pinnidae, Linnaeus 1758) are shown to be perfect examples of a mesocrystalline material. Based on their ultrastructure and on the occurrence of an amorphous transient precursor during the early stages of prism formation, we provide evidence for the pathway of mesocrystallisation proposed by Seto et al. (2012), which proceeds not by self-organized oriented attachment of crystalline nano-bricks but by aggregation of initially amorphous nanogranules which later transform by epitaxial nucleation to a three-dimensional array of well aligned nanocrystals. We further fathom the role of a liquid amorphous calcium carbonate in biomineralisation processes and provide strong evidence for the occurrence of PILP-like intermediates during prism formation. We develop a new scenario of prism formation based on the presented findings presented findings and discuss the implications of a speculative liquid amorphous calcium carbonate (LACC) intermediate in vivo.
