Similar Datasets
Project description:Effect of histone mutation H2A E92K on open reading frames in HEK293T cells
2022-12-24 | GSE221673 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-12-24 | GSE221674 | GEO
Project description:Interactions between biomolecules underlie all cellular processes, and ultimately control cell fate. Perturbation of native interactions through mutation, changes in expression levels, or external stimuli leads to altered cellular physiology and can result in either disease or therapeutic effects. Mapping these interactions and determining how they respond to stimulus is the genesis of many drug development efforts, leading to new therapeutic targets and improvements in human health. However, in the complex environment of the nucleus it is challenging to determine protein-protein interactions due to low abundance, transient or multi-valent binding, and a lack of technologies that are able to interrogate these interactions without disrupting the protein binding surface under study. Here, we describe a method for the traceless incorporation of Ir-photosensitizers into the nuclear microenvironment using engineered split inteins. These Ir-catalysts can activate diazirine warheads via Dexter energy transfer to form reactive carbenes within a ~10 nm radius, cross-linking with proteins within the immediate microenvironment (a process termed uMap) for analysis via quantitative chemoproteomics. Additionally, we show that this nanoscale proximity labeling method can reveal the critical changes in interactomes in the presence of cancer-associated mutations, as well as treatment with small-molecule inhibitors. uMap improves our fundamental understanding of nuclear protein-protein interactions, and in doing so is expected to have a significant impact on the field of epigenetic drug discovery in both academia and industry.
2022-12-19 | MSV000090929 | MassIVE
Project description:We demonstrate beam scanning-stimulated emission depletion microscopy with in vivo labeled cells. A red emitting fluorescent dye is introduced into membrane protein fused to a multifunctional reporter protein (HaloTag, Promega, Madison, WI) in live cells. This approach allows superresolution stimulated emission depletion imaging without the limitations of immunofluorescence-based staining.
| S-EPMC2710050 | biostudies-literature
Project description:HEK293T cells expressing BS2 in different compartments (cytosol, mitochondria, nucleus, nucleolus) were labeled with AC-2. Subsequent enrichment of labeled RNAs, PolyA capture and RNA-seq reveals RNA populations in those compartments.
2024-04-05 | GSE229451 | GEO
Project description:Extracellular vesicles (EVs), including exosomes and microvesicles, are 30-800 nm vesicles that are released by most cell types, as biological packages for intercellular communication. Their importance in cancer and inflammation makes EVs and their cargo promising biomarkers of disease and cell-free therapeutic agents. Emerging high-resolution cytometric methods have created a pressing need for efficient fluorescent labeling procedures to visualize and detect EVs. Suitable labels must be bright enough for one EV to be detected without the generation of label-associated artifacts. To identify a strategy that robustly labels individual EVs, we used nanoFACS, a high-resolution flow cytometric method that utilizes light scattering and fluorescence parameters along with sample enumeration, to evaluate various labels. Specifically, we compared lipid-, protein-, and RNA-based staining methods and developed a robust EV staining strategy, with the amine-reactive fluorescent label, 5-(and-6)-Carboxyfluorescein Diacetate Succinimidyl Ester, and size exclusion chromatography to remove unconjugated label. By combining nanoFACS measurements of light scattering and fluorescence, we evaluated the sensitivity and specificity of EV labeling assays in a manner that has not been described for other EV detection methods. Efficient characterization of EVs by nanoFACS paves the way towards further study of EVs and their roles in health and disease.
| S-EPMC5431945 | biostudies-literature
Project description:Blood oxygen level dependent (BOLD) functional magnetic resonance imaging (fMRI) is the most widely used method for mapping neural activity in the brain. The interpretation of altered BOLD signals is problematic when cerebral blood flow (CBF) or cerebral blood volume change because of aging and/or neurodegenerative diseases. In this study, a recently developed quantitative arterial spin labeling (ASL) approach, bolus-tracking ASL (btASL), was applied to an fMRI experiment in the rat brain. The mean transit time (MTT), capillary transit time (CTT), relative cerebral blood volume of labeled water (rCBV(lw)), relative cerebral blood flow (rCBF), and perfusion coefficient in the forelimb region of the somatosensory cortex were quantified during neuronal activation and in the resting state. The average MTT and CTT were 1.939+/-0.175 and 1.606+/-0.106 secs, respectively, in the resting state. Both times decreased significantly to 1.616+/-0.207 and 1.305+/-0.201 secs, respectively, during activation. The rCBV(lw), rCBF, and perfusion coefficient increased on average by a factor of 1.123+/-0.006, 1.353+/-0.078, and 1.479+/-0.148, respectively, during activation. In contrast to BOLD techniques, btASL yields physiologically relevant indices of the functional hyperemia that accompanies neuronal activation.
| S-EPMC2949184 | biostudies-literature
Project description:Histone modifications play an important role in epigenetic gene regulation and genome integrity. It remains largely unknown, however, how these modifications dynamically change in individual cells. By using fluorescently labeled specific antigen binding fragments (Fabs), we have developed a general method to monitor the distribution and global level of endogenous histone H3 lysine modifications in living cells without disturbing cell growth and embryo development. Fabs produce distinct nuclear patterns that are characteristic of their target modifications. H3K27 trimethylation-specific Fabs, for example, are concentrated on inactive X chromosomes. As Fabs bind their targets transiently, the ratio of bound and free molecules depends on the target concentration, allowing us to measure changes in global modification levels. High-affinity Fabs are suitable for mouse embryo imaging, so we have used them to monitor H3K9 and H3K27 acetylation levels in mouse preimplantation embryos produced by in vitro fertilization and somatic cell nuclear transfer. The data suggest that a high level of H3K27 acetylation is important for normal embryo development. As Fab-based live endogenous modification labeling (FabLEM) is broadly useful for visualizing any modification, it should be a powerful tool for studying cell signaling and diagnosis in the future.
| S-EPMC3159477 | biostudies-literature
Project description:Gluten-containing grains cause adverse health effects in individuals with celiac disease. Fermentation of these grains results in gluten-derived polypeptides with largely uncharacterized sizes and sequences, which may still trigger an immune response. This research used N-terminal labeling mass spectrometry to characterize protein hydrolysates during each stage of bench-scale brewing, including malting, mashing, boiling, fermentation, and aging. Gluten hydrolysates from each brewing step were tracked and the immunotoxic potential was evaluated in silico. The results indicate that proteolysis and precipitation of gliadins occurring during brewing differ by protein region and brewing stage. The termini of gliadins were hydrolyzed throughout the entire brewing process, but the central regions remained relatively stable. Most hydrolysis occurred during malting, and most precipitation occurred during boiling. The addition of yeast yielded new cleavage sites but did not result in complete hydrolysis. Consistent detection of peptides within the clinically important regions of gliadin corroborated the hydrolytic resistance of this region. N-terminal labeling mass spectrometry served as a novel approach to track the fate of gliadin/gluten throughout bench-scale brewing. Consistently identified fragments could serve as improved targets for detection of hydrolyzed gluten in fermented products.
2021-07-23 | PXD023482 | Pride
Project description:Digital holographic microscopy (DHM) is an emerging imaging technique that permits instantaneous capture of a relatively large sample volume. However, large volumes usually come at the expense of lower spatial resolution, and the technique has rarely been used with prokaryotic cells due to their small size and low contrast. In this paper we demonstrate the use of a Mach-Zehnder dual-beam instrument for imaging of labeled and unlabeled bacteria and microalgae. Spatial resolution of 0.3 ?m is achieved, providing a sampling of several pixels across a typical prokaryotic cell. Both cellular motility and morphology are readily recorded. The use of dyes provides both amplitude and phase contrast improvement and is of use to identify cells in dense samples.
| S-EPMC4874365 | biostudies-literature