180 research outputs found

    Elucidation of the pre-nucleation phase directing metal-organic framework formation

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    Metal-organic framework (MOF) crystallization is governed by molecular assembly processes in the pre-nucleation stage. Yet, unravelling these pre-nucleation pathways and rationalizing their impact on crystal formation poses a great challenge since probing molecular-scale assemblies and macroscopic particles simultaneously is very complex. Herein, we present a multimodal, integrated approach to monitor MOF nucleation across multiple length scales by combining in situ optical spectroscopy, mass spectrometry, and molecular simulations. This approach allows tracing initial metal-organic complexes in solution and their assembly into oligomeric nuclei and simultaneously probing particle formation. During Co-ZIF-67 nucleation, a metal-organic pool forms with a variety of complexes caused by ligand exchange and symmetry reduction reactions. We discriminate complexes capable of initiating nucleation from growth species required for oligomerization into frameworks. Co4-nuclei are observed, which grow into particles following autocatalytic kinetics. The geometric and compositional variability of metal-organic pool species clarifies long-debated amorphous zeolitic imidazolate framework (ZIF)-particle nucleation and non-classic pathways of MOF crystallization

    Assessment of Kinome-wide Activity Remodeling Upon Picornavirus Infection

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    Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus (EMCV)). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of EMCV. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions

    Imaging Mass Spectrometry: Hype or Hope?

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    Imaging mass spectrometry is currently receiving a significant amount of attention in the mass spectrometric community. It offers the potential of direct examination of biomolecular patterns from cells and tissue. This makes it a seemingly ideal tool for biomedical diagnostics and molecular histology. It is able to generate beautiful molecular images from a large variety of surfaces, ranging from cancer tissue sections to polished cross sections from old-master paintings. What are the parameters that define and control the implications, challenges, opportunities, and (im)possibilities associated with the application of imaging MS to biomedical tissue studies. Is this just another technological hype or does it really offer the hope to gain new insights in molecular processes in living tissue? In this critical insight this question is addressed through the discussion of a number of aspects of MS imaging technology and sample preparation that strongly determine the outcome of imaging MS experiments

    Multi order correction algorithms to remove image distortions from mass spectrometry imaging datasets

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    Time-of-flight secondary ion mass spectrometry imaging is a rapidly evolving technology. Its main application is the study of the distribution of small molecules on biological tissues. The sequential image acquisition process remains susceptible to measurement distortions that can render imaging data less analytically useful. Most of these artifacts show a repetitive nature from tile to tile. Here we statistically describe these distortions and derive two different algorithms to correct them. Both, a generalized linear model approach and the linear discriminant analysis approach are able to increase image quality for negative and positive ion mode datasets. Additionally, performing simulation studies with repetitive and non-repetitive tiling error we show that both algorithms are only removing repetitive distortions. It is further shown that the spectral component of the dataset is not altered by the use of these correction methods. Both algorithms presented in this work greatly increase the image quality and improve the analytical usefulness of distorted images dramatically

    MALDI imaging mass spectrometry for direct tissue analysis: a new frontier for molecular histology

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    Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for investigating the distribution of proteins and small molecules within biological systems through the in situ analysis of tissue sections. MALDI-IMS can determine the distribution of hundreds of unknown compounds in a single measurement and enables the acquisition of cellular expression profiles while maintaining the cellular and molecular integrity. In recent years, a great many advances in the practice of imaging mass spectrometry have taken place, making the technique more sensitive, robust, and ultimately useful. In this review, we focus on the current state of the art of MALDI-IMS, describe basic technological developments for MALDI-IMS of animal and human tissues, and discuss some recent applications in basic research and in clinical settings

    Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics

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    Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis
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