Abstract:
:Extracellular vesicles (EVs) are secreted nanosized particles with many biological functions and pathological associations. The inability to image EVs in fixed tissues has been a major limitation to understanding their role in healthy and diseased tissue microenvironments. Here, we show that crosslinking mammalian tissues with formaldehyde results in significant EV loss, which can be prevented by additional fixation with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) for visualization of EVs in a range of normal and cancer tissues.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Gupta MP,Tandalam S,Ostrager S,Lever AS,Fung AR,Hurley DD,Alegre GB,Espinal JE,Remmel HL,Mukherjee S,Levine BM,Robins RP,Molina H,Dill BD,Kenific CM,Tuschl T,Lyden D,D'Amico DJ,Pena JTGdoi
10.1038/s41592-019-0623-4subject
Has Abstractpub_date
2019-12-01 00:00:00pages
1269-1273issue
12eissn
1548-7091issn
1548-7105pii
10.1038/s41592-019-0623-4journal_volume
16pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract::We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4396
更新日期:2017-10-01 00:00:00
abstract::Chromosome segregation requires both compaction and disentanglement of sister chromatids. We describe SisterC, a chromosome conformation capture assay that distinguishes interactions between and along identical sister chromatids. SisterC employs 5-bromo-2'-deoxyuridine (BrdU) incorporation during S-phase to label newl...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-0930-9
更新日期:2020-10-01 00:00:00
abstract::We have developed a versatile, potent technique for imaging cells in culture and in vivo by expressing a metabolically biotinylated cell-surface receptor and visualizing it with labeled streptavidin moieties. The recombinant reporter protein, which incorporates a biotin acceptor peptide (BAP) between an N-terminal sig...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth875
更新日期:2006-05-01 00:00:00
abstract::The analysis of synthetic genetic interaction networks can reveal how biological systems achieve a high level of complexity with a limited repertoire of components. Studies in yeast and bacteria have taken advantage of collections of deletion strains to construct matrices of quantitative interaction profiles and infer...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1581
更新日期:2011-04-01 00:00:00
abstract::We report a simple and generic method for the direct transfer of protein complexes separated by native gel electrophoresis to electron microscopy grids. After transfer, sufficient material remains in the gel for identification and characterization by mass spectrometry. The method should facilitate higher-throughput si...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1840
更新日期:2012-01-08 00:00:00
abstract::Sequencing of RNA 3' ends has uncovered numerous sites that do not correspond to the termination sites of known transcripts. Through their 3' untranslated regions, protein-coding RNAs interact with RNA-binding proteins and microRNAs, which regulate many properties, including RNA stability and subcellular localization....
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0114-z
更新日期:2018-10-01 00:00:00
abstract::Glial cells have been identified as key signaling components in the brain; however, methods to investigate their structure and function in vivo have been lacking. Here, we describe a new, highly selective approach for labeling astrocytes in intact rodent neocortex that allows in vivo imaging using two-photon microscop...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth706
更新日期:2004-10-01 00:00:00
abstract::The quality of genetically encoded calcium indicators (GECIs) has improved dramatically in recent years, but high-performing ratiometric indicators are still rare. Here we describe a series of fluorescence resonance energy transfer (FRET)-based calcium biosensors with a reduced number of calcium binding sites per sens...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2773
更新日期:2014-02-01 00:00:00
abstract::Many protein interactions are mediated by small linear motifs interacting specifically with defined families of globular domains. Quantifying the specificity of a motif requires measuring and comparing its binding affinities to all its putative target domains. To this end, we developed the high-throughput holdup assay...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3438
更新日期:2015-08-01 00:00:00
abstract::High spatial and temporal resolution of conditional gene expression is typically difficult to achieve in whole tissues or organisms. We synthesized two reversibly inhibited, photoactivatable ('caged') doxycycline derivatives with different membrane permeabilities for precise spatial and temporal light-controlled activ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1340
更新日期:2009-07-01 00:00:00
abstract::Plants have evolved a unique system in which the plant hormone auxin directly induces rapid degradation of the AUX/IAA family of transcription repressors by a specific form of the SCF E3 ubiquitin ligase. Other eukaryotes lack the auxin response but share the SCF degradation pathway, allowing us to transplant the auxi...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1401
更新日期:2009-12-01 00:00:00
abstract::The complexity of the angiogenic cascade limits cellular approaches to studying angiogenic endothelial cells (ECs). In turn, in vivo assays do not allow the analysis of the distinct cellular behavior of ECs during angiogenesis. Here we show that ECs can be grafted as spheroids into a matrix to give rise to a complex t...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1198
更新日期:2008-05-01 00:00:00
abstract::The implementation of efficient technologies for the production of recombinant mammalian proteins remains an outstanding challenge in many structural and functional genomics programs. We have developed a new method for rapid identification of soluble protein expression in E. coli, based on a separation of soluble prot...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth767
更新日期:2005-07-01 00:00:00
abstract::The complexities of tumor genomes are rapidly being uncovered, but how they are regulated into functional proteomes remains poorly understood. Standard proteomics workflows use databases of known proteins, but these databases do not capture the uniqueness of the cancer transcriptome, with its point mutations, unusual ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3138
更新日期:2014-11-01 00:00:00
abstract::We developed a caged GABA (gamma-aminobutyric acid), which, when combined with an appropriate caged glutamate, allows bimodal control of neuronal membrane potential with subcellular resolution using optically independent two-photon uncaging of each neurotransmitter. We used two-color, two-photon uncaging to fire and b...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1413
更新日期:2010-02-01 00:00:00
abstract::We discuss unique features of lens-free computational imaging tools and report some of their emerging results for wide-field on-chip microscopy, such as the achievement of a numerical aperture (NA) of ∼0.8-0.9 across a field of view (FOV) of more than 20 mm(2) or an NA of ∼0.1 across a FOV of ∼18 cm(2), which correspo...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2114
更新日期:2012-09-01 00:00:00
abstract::Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4178
更新日期:2017-02-13 00:00:00
abstract::We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algo...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1681
更新日期:2011-09-04 00:00:00
abstract::A label-free microscopy technique based on electrochemical impedance offers a new way of studying electrochemical processes in single cells. ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/nmeth0311-202
更新日期:2011-03-01 00:00:00
abstract::To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wire...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3536
更新日期:2015-10-01 00:00:00
abstract::Targeted quantification of DNA methylation allows for interrogation of the most informative loci across many samples quickly and cost-effectively. Here we report improved bisulfite padlock probes (BSPPs) with a design algorithm to generate efficient padlock probes, a library-free protocol that dramatically reduces sam...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1871
更新日期:2012-02-05 00:00:00
abstract::The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be cova...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3899
更新日期:2016-08-01 00:00:00
abstract::Live-cell single mRNA imaging is a powerful tool but has been restricted in higher eukaryotes to artificial cell lines and reporter genes. We describe an approach that enables live-cell imaging of single endogenous labeled mRNA molecules transcribed in primary mammalian cells and tissue. We generated a knock-in mouse ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1551
更新日期:2011-02-01 00:00:00
abstract::We describe a protein quantification method called neutron encoding that exploits the subtle mass differences caused by nuclear binding energy variation in stable isotopes. These mass differences are synthetically encoded into amino acids and incorporated into yeast and mouse proteins via metabolic labeling. Mass spec...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2378
更新日期:2013-04-01 00:00:00
abstract::We demonstrate tracking of protein structural changes with time-resolved wide-angle X-ray scattering (TR-WAXS) with nanosecond time resolution. We investigated the tertiary and quaternary conformational changes of human hemoglobin under nearly physiological conditions triggered by laser-induced ligand photolysis. We a...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1255
更新日期:2008-10-01 00:00:00
abstract::Biomolecular dynamics and stability are predominantly investigated in vitro and extrapolated to explain function in the living cell. We present fast relaxation imaging (FreI), which combines fluorescence microscopy and temperature jumps to probe biomolecular dynamics and stability inside a single living cell with high...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1435
更新日期:2010-04-01 00:00:00
abstract::In the originally published paper, the "before" image for the afatinib condition in Fig. 6c was incorrect. Instead of an image displaying a GBM-3 neoplastic organoid before afatinib treatment, this panel showed an image from the GBM-2 control (DMSO) group before treatment. This error has now been corrected in the HTML...
journal_title:Nature methods
pub_type: 已发布勘误
doi:10.1038/s41592-018-0118-8
更新日期:2018-09-01 00:00:00
abstract::The Q system is a repressible binary expression system for transgenic manipulations in living organisms. Through protein engineering and in vivo functional tests, we report here variants of the Q-system transcriptional activator, including QF2, for driving strong and ubiquitous expression in all Drosophila tissues. Ou...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3250
更新日期:2015-03-01 00:00:00
abstract::Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-0731-1
更新日期:2020-03-01 00:00:00
abstract::Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via 'mapping' to existing data. However, manual interpretation scales poorly to lar...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0529-1
更新日期:2019-10-01 00:00:00