Abstract:
:To trace cell lineages in a developing vertebrate and to observe, in vivo, how behaviors of individual cells are affected by the genes they express, we created a zebrafish line containing a transgene called mosaic analysis in zebrafish (MAZe), built around a self-excising hsp70:Cre cassette. Heat shock triggers Cre recombinase-mediated recombination in a random subset of cells, bringing the transcriptional activator Gal4:VP16 under control of the EF1alpha promoter. Gal4-VP16 then activates expression of a fluorescent protein from an upstream activating sequence (UAS) promoter. Marked clones of cells expressing any desired gene product can be generated by crossing MAZe fish with other lines containing UAS-driven transgenes. The number of clones induced, and their time of origin, could be varied by adjusting heat-shock timing and duration. As an alternative to heat shock, we introduced Cre under a tissue-specific promoter in MAZe fish to generate clones in a designated tissue.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Collins RT,Linker C,Lewis Jdoi
10.1038/nmeth.1423subject
Has Abstractpub_date
2010-03-01 00:00:00pages
219-23issue
3eissn
1548-7091issn
1548-7105pii
nmeth.1423journal_volume
7pub_type
杂志文章相关文献
NATURE METHODS文献大全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::Structure probing coupled with high-throughput sequencing could revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite recent technological advances, intrinsic noise and high sequence coverage requirements greatly limit the applicability of these techniques. Here we desc...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4068
更新日期:2017-01-01 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::We discuss the advantages and challenges of the open-source strategy in biological image analysis and argue that its full impact will not be realized without better support and recognition of software engineers' contributions to the biological sciences and more support of this development model from funders and instit...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2082
更新日期:2012-06-28 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::FLIRT (fast local infrared thermogenetics) is a microscopy-based technology to locally and reversibly manipulate protein function while simultaneously monitoring the effects in vivo. FLIRT locally inactivates fast-acting temperature-sensitive mutant proteins. We demonstrate that FLIRT can control temperature-sensitive...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-018-0168-y
更新日期:2018-11-01 00:00:00
abstract::The biomedical application of human embryonic stem (hES) cells will increasingly depend on the availability of technologies for highly controlled genetic modification. In mouse genetics, conditional mutagenesis using site-specific recombinases has become an invaluable tool for gain- and loss-of-function studies. Here ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth884
更新日期:2006-06-01 00:00:00
abstract::Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/nmeth0910-671
更新日期:2010-09-01 00:00:00
abstract::We developed genetically encoded RNA probes for characterizing localization and dynamics of mitochondrial RNA (mtRNA) in single living cells. The probes consist of two RNA-binding domains of PUMILIO1, each connected with split fragments of a fluorescent protein capable of reconstituting upon binding to a target RNA. W...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1030
更新日期:2007-05-01 00:00:00
abstract:: ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/s41592-019-0343-9
更新日期:2019-03-01 00:00:00
abstract::We developed a multiplex sequencing-by-synthesis method combining terminal phosphate-labeled fluorogenic nucleotides (TPLFNs) and resealable polydimethylsiloxane (PDMS) microreactors. In the presence of phosphatase, primer extension by DNA polymerase using nonfluorescent TPLFNs generates fluorophores, which are confin...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1629
更新日期:2011-06-12 00:00:00
abstract::Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA interactions in vivo by analyzing purified cellular RNA, without protein purification or cross-linking. An RNA-binding protein of interest is fused to an enzyme...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3651
更新日期:2015-12-01 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::In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0426-7
更新日期:2019-06-01 00:00:00
abstract::High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamic...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2964
更新日期:2014-07-01 00:00:00
abstract::Tumor-initiating cells with stem cell properties are believed to sustain the growth of gliomas, but proposed markers such as CD133 cannot be used to identify these cells with sufficient specificity. We report an alternative isolation method purely based on phenotypic qualities of glioma-initiating cells (GICs), avoidi...
journal_title:Nature methods
pub_type: 杂志文章,收录出版
doi:10.1038/nmeth.1430
更新日期:2010-03-01 00:00:00
abstract::We report a technique to selectively and continuously label the proteomes of individual cell types in coculture, named cell type-specific labeling using amino acid precursors (CTAP). Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on supplemented e...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2529
更新日期:2013-08-01 00:00:00
abstract::The dynamic reshaping of tissues during morphogenesis results from a combination of individual cell behaviors and collective cell rearrangements. However, a comprehensive framework to unambiguously measure and link cell behavior to tissue morphogenesis is lacking. Here we introduce such a kinematic framework, bridging...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1327
更新日期:2009-06-01 00:00:00
abstract::Epistasis analysis, which reports on the extent to which the function of one gene depends on the presence of a second, is a powerful tool for studying the functional organization of the cell. Systematic genome-wide studies of epistasis, however, have been limited, with the majority of data being collected in the buddi...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1098
更新日期:2007-10-01 00:00:00
abstract::We introduce a nonintrusive method exploiting single-cell variability after cell division to validate protein localization. We found that Clp proteases, widely reported to form biologically relevant foci, were uniformly distributed in Escherichia coli cells, and that many commonly used fluorescent proteins caused seve...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1955
更新日期:2012-04-08 00:00:00
abstract::Optical studies have revealed that, after binding, virions move laterally on the plasma membrane, but the complexity of the cellular environment and the drawbacks of fluorescence microscopy have prevented access to the molecular dynamics of early virus-host couplings, which are important for cell infection. Here we pr...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1395
更新日期:2009-12-01 00:00:00
abstract::We report an atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) setup with a lateral resolution of 1.4 μm, a mass resolution greater than 100,000, and accuracy below ±2 p.p.m. We achieved this by coupling a focusing objective with a numerical aperture (NA) of ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4071
更新日期:2017-01-01 00:00:00
abstract::We have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial c...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3955
更新日期:2016-09-01 00:00:00
abstract::Using a directed evolution approach, researchers demonstrate a way of creating 'designer' receptors that are specifically activated by a ligand with no other biological activity in the cell. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth0507-382b
更新日期:2007-05-01 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::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::Tumors from individuals with cancer are frequently genetically profiled for information about the driving forces behind the disease. We present the CancerMine resource, a text-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. All data are available online ( ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0422-y
更新日期:2019-06-01 00:00:00
abstract::Researchers show that to reliably establish protein interaction networks from microarray data it is necessary to measure saturation binding curves for each arrayed protein and its potential binding partners. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1206-966
更新日期:2006-12-01 00:00:00
abstract::Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR-RfxCas13d can effectively discrimin...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-01011-4
更新日期:2021-01-01 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