Abstract:
:We describe a simple method for efficiently labeling cell-surface sialic acid-containing glycans on living animal cells. The method uses mild periodate oxidation to generate an aldehyde on sialic acids, followed by aniline-catalyzed oxime ligation with a suitable tag. Aniline catalysis dramatically accelerates oxime ligation, allowing use of low concentrations of aminooxy-biotin at neutral pH to label the majority of cell-surface sialylated glycoproteins while maintaining high cell viability.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Zeng Y,Ramya TN,Dirksen A,Dawson PE,Paulson JCdoi
10.1038/nmeth.1305subject
Has Abstractpub_date
2009-03-01 00:00:00pages
207-9issue
3eissn
1548-7091issn
1548-7105pii
nmeth.1305journal_volume
6pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract::Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2646
更新日期:2013-12-01 00:00:00
abstract::Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-01043-w
更新日期:2021-01-01 00:00:00
abstract::Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have activity against related off-target sequences. To better understand TALEN specificity, we profiled 30 unique TALENs with different target sites, array length and domain sequences for their abil...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2845
更新日期:2014-04-01 00:00:00
abstract::We present a noninvasive approach to track activation of ATP-gated P2X receptors and potentially other transmitter-gated cation channels that show calcium fluxes. We genetically engineered rat P2X receptors to carry calcium sensors near the channel pore and tested this as a reporter for P2X(2) receptor opening. The me...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1144
更新日期:2008-01-01 00:00:00
abstract::The measurement of lifespan pervades aging research. Because lifespan results from complex interactions between genetic, environmental and stochastic factors, it varies widely even among isogenic individuals. The actions of molecular mechanisms on lifespan are therefore visible only through their statistical effects o...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2475
更新日期:2013-07-01 00:00:00
abstract::Measuring complete gene expression profiles for a large number of experiments is costly. We propose an approach in which a small subset of probes is selected based on a preliminary set of full expression profiles. In subsequent experiments, only the subset is measured, and the missing values are inputed. We developed ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2207
更新日期:2012-11-01 00:00:00
abstract::Infrared fluorescent proteins (IFPs) provide an additional color to GFP and its homologs in protein labeling. Drawing on structural analysis of the dimer interface, we identified a bacteriophytochrome in the sequence database that is monomeric in truncated form and engineered it into a naturally monomeric IFP (mIFP). ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3447
更新日期:2015-08-01 00:00:00
abstract::Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3330
更新日期:2015-05-01 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::Engineering precise genetic changes in a genome is powerful way to study gene function, and several recent papers describe new applications of gene-editing tools. Working with researchers at Sangamo BioSciences, Howard Hughes Medical Institute investigator Barbara Meyer and her colleagues at the University of Californ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/nmeth.1683
更新日期:2011-09-01 00:00:00
abstract::It remains particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here we present a strategy for isolating complexes at endogenous levels from GFP-tagged transgenic cell lines. Using cross-linking mass spectrometry, we extracted distance restraints that...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3617
更新日期:2015-12-01 00:00:00
abstract::Small interfering RNAs (siRNAs) have been widely exploited for sequence-specific gene knockdown, predominantly to investigate gene function in cultured vertebrate cells, and also hold promise as therapeutic agents. Because not all siRNAs that are cognate to a given target mRNA are equally effective, computational tool...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth911
更新日期:2006-09-01 00:00:00
abstract::Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolon...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1062
更新日期:2007-07-01 00:00:00
abstract::The self-reconstructing properties of Bessel beams provide healing benefits in highly scattering media. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1110-876
更新日期:2010-11-01 00:00:00
abstract::A 'paired-end ditag' (PET) strategy for pinpointing protein binding sites can reveal a wealth of information about transcription factors and other DNA-binding proteins. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth0506-341
更新日期:2006-05-01 00:00:00
abstract::Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2069
更新日期:2012-06-03 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::We achieve simultaneous two-photon excitation of three chromophores with distinct absorption spectra using synchronized pulses from a femtosecond laser and an optical parametric oscillator. The two beams generate separate multiphoton processes, and their spatiotemporal overlap provides an additional two-photon excitat...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2098
更新日期:2012-07-08 00:00:00
abstract::Single-cell transcriptomics provides an opportunity to characterize cell-type-specific transcriptional networks, intercellular signaling pathways and cellular diversity with unprecedented resolution by profiling thousands of cells in a single experiment. However, owing to the unique statistical properties of scRNA-seq...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0372-4
更新日期:2019-05-01 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::We must reliably map the interactomes of cellular macromolecular complexes in order to fully explore and understand biological systems. However, there are no methods to accurately predict how to capture a given macromolecular complex with its physiological binding partners. Here, we present a screening method that com...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3395
更新日期:2015-06-01 00:00:00
abstract::The ability to apply precise inputs to signaling species in live cells would be transformative for interrogating and understanding complex cell-signaling systems. Here we report an 'optogenetic' method for applying custom signaling inputs using feedback control of a light-gated protein-protein interaction. We applied ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1700
更新日期:2011-09-11 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::Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the hippocampus of freely moving ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0008-0
更新日期:2018-06-01 00:00:00
abstract::Thermodynamic stability is fundamental to the biology of proteins. Information on protein stability is essential for studying protein structure and folding and can also be used indirectly to monitor protein-ligand or protein-protein interactions. While clearly valuable, the experimental determination of a protein's st...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth740
更新日期:2005-03-01 00:00:00
abstract::MicroRNAs (miRNAs) play an essential role in the post-transcriptional regulation of animal development and physiology. However, in vivo studies aimed at linking miRNA function to the biology of distinct cell types within complex tissues remain challenging, partly because in vivo miRNA-profiling methods lack cellular r...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4610
更新日期:2018-04-01 00:00:00
abstract::t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0308-4
更新日期:2019-03-01 00:00:00
abstract::Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrho...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth936
更新日期:2006-10-01 00:00:00
abstract:: ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/s41592-018-0283-9
更新日期:2019-01-01 00:00:00
abstract::We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art met...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4207
更新日期:2017-04-01 00:00:00