Abstract:
:We present a method to robustly discriminate clustered from randomly distributed molecules detected with techniques based on single-molecule localization microscopy, such as PALM and STORM. The approach is based on deliberate variation of labeling density, such as titration of fluorescent antibody, combined with quantitative cluster analysis, and it thereby circumvents the problem of cluster artifacts generated by overcounting of blinking fluorophores. The method was used to analyze nanocluster formation in resting and activated immune cells.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Baumgart F,Arnold AM,Leskovar K,Staszek K,Fölser M,Weghuber J,Stockinger H,Schütz GJdoi
10.1038/nmeth.3897subject
Has Abstractpub_date
2016-08-01 00:00:00pages
661-4issue
8eissn
1548-7091issn
1548-7105pii
nmeth.3897journal_volume
13pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract::Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA-element selection assay (RESA), a method that selects RNA el...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4121
更新日期:2017-02-01 00:00:00
abstract::A new system for lineage ablation is based on transgenic expression of a diphtheria toxin receptor (DTR) in mouse cells and application of diphtheria toxin (DT). To streamline this approach, we generated Cre-inducible DTR transgenic mice (iDTR) in which Cre-mediated excision of a STOP cassette renders cells sensitive ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth762
更新日期:2005-06-01 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 comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information dens...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth807
更新日期:2005-11-01 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::An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s) responsible for the observed differential DNA methylation. Here we present a statistical algorithm called CellDMC ( https://github.com/sjczheng/EpiDISH ), which can ide...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0213-x
更新日期:2018-12-01 00:00:00
abstract::The normalization of RNA-seq data is essential for accurate downstream inference, but the assumptions upon which most normalization methods are based are not applicable in the single-cell setting. Consequently, applying existing normalization methods to single-cell RNA-seq data introduces artifacts that bias downstrea...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4263
更新日期:2017-06-01 00:00:00
abstract::New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth747
更新日期:2005-04-01 00:00:00
abstract::Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium i...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0625-2
更新日期:2020-01-01 00:00:00
abstract::Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2879
更新日期:2014-04-01 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::Zinc-finger nucleases (ZFNs) have enabled highly efficient gene targeting in multiple cell types and organisms. Here we describe methods for using simple ssDNA oligonucleotides in tandem with ZFNs to efficiently produce human cell lines with three distinct genetic outcomes: (i) targeted point mutation, (ii) targeted g...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1653
更新日期:2011-07-17 00:00:00
abstract::An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...
journal_title:Nature methods
pub_type: 已发布勘误
doi:10.1038/s41592-019-0588-3
更新日期:2019-10-01 00:00:00
abstract::We report attainment of subdiffraction resolution using stimulated emission depletion (STED) microscopy with GFP-labeled samples. The approximately 70 nm lateral resolution attained in this study is demonstrated by imaging GFP-labeled viruses and the endoplasmic reticulum (ER) of a mammalian cell. Our results mark the...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth922
更新日期:2006-09-01 00:00:00
abstract::Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2253
更新日期:2012-12-01 00:00:00
abstract::The RNA-guided nuclease Cas9 can be reengineered as a programmable transcription factor. However, modest levels of gene activation have limited potential applications. We describe an improved transcriptional regulator obtained through the rational design of a tripartite activator, VP64-p65-Rta (VPR), fused to nuclease...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3312
更新日期:2015-04-01 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::Single-molecule localization microscopy is a powerful tool for visualizing subcellular structures, interactions and protein functions in biological research. However, inhomogeneous refractive indices inside cells and tissues distort the fluorescent signal emitted from single-molecule probes, which rapidly degrades res...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-0816-x
更新日期:2020-05-01 00:00:00
abstract::Phenotype-based small-molecule screening is a powerful method to identify molecules that regulate cellular functions. However, such screens are generally performed in vitro under conditions that do not necessarily model complex physiological conditions or disease states. Here, we use molecular cell barcoding to enable...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3992
更新日期:2016-10-01 00:00:00
abstract::The self-renewal and differentiation of human pluripotent stem cells (hPSCs) have typically been studied in flat, two-dimensional (2D) environments. In this Perspective, we argue that 3D model systems may be needed in addition, as they mimic the natural 3D tissue organization more closely. We survey methods that have ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1671
更新日期:2011-08-30 00:00:00
abstract::Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameri...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2021
更新日期:2012-05-13 00:00:00
abstract::Database searching is an essential element of large-scale proteomics. Because these methods are widely used, it is important to understand the rationale of the algorithms. Most algorithms are based on concepts first developed in SEQUEST and PeptideSearch. Four basic approaches are used to determine a match between a s...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth725
更新日期:2004-12-01 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::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::Next-generation sequencing technology is a powerful tool for transcriptome analysis. However, under certain conditions, only a small amount of material is available, which requires more sensitive techniques that can preferably be used at the single-cell level. Here we describe a single-cell digital gene expression pro...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1315
更新日期:2009-05-01 00:00:00
abstract::The commonly used, monomeric EYFP enabled imaging of intracellular protein structures beyond the optical resolution limit ('super-resolution' imaging) in living cells. By combining photoinduced activation of single EYFP fusions and time-lapse imaging, we obtained sub-40 nm resolution images of the filamentous superstr...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1258
更新日期:2008-11-01 00:00:00
abstract::Counting molecules in complexes is challenging, even with super-resolution microscopy. Here, we use the programmable and specific binding of dye-labeled DNA probes to count integer numbers of targets. This method, called quantitative points accumulation in nanoscale topography (qPAINT), works independently of dye phot...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3804
更新日期:2016-05-01 00:00:00
abstract::Circuit mapping requires knowledge of both structural and functional connectivity between cells. Although optical tools have been made to assess either the morphology and projections of neurons or their activity and functional connections, few probes integrate this information. We have generated a family of photoactiv...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3480
更新日期:2015-09-01 00:00:00
abstract::Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2999
更新日期:2014-08-01 00:00:00
abstract::Small molecules are known to stabilize membrane proteins and to modulate their function and oligomeric state, but such interactions are often hard to precisely define. Here we develop and apply a high-resolution, Orbitrap mass spectrometry-based method for analyzing intact membrane protein-ligand complexes. Using this...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3771
更新日期:2016-04-01 00:00:00