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_name
Nat Methodsjournal_title
Nature methodsauthors
Kaganman Idoi
10.1038/nmeth0507-382bsubject
Has Abstractpub_date
2007-05-01 00:00:00pages
382-3issue
5eissn
1548-7091issn
1548-7105journal_volume
4pub_type
杂志文章相关文献
NATURE METHODS文献大全abstract::Focused-ion-beam scanning electron microscopy (FIB-SEM) has become an essential tool for studying neural tissue at resolutions below 10 nm × 10 nm × 10 nm, producing data sets optimized for automatic connectome tracing. We present a technical advance, ultrathick sectioning, which reliably subdivides embedded tissue sa...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3292
更新日期:2015-04-01 00:00:00
abstract::Protein function often depends on the exchange between conformational substates. Allosteric ligand binding or distal mutations can stabilize specific active-site conformations and consequently alter protein function. Observing alternative conformations at low levels of electron density, in addition to comparison of in...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2592
更新日期:2013-09-01 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::We show that nanoscopy based on the principle called RESOLFT (reversible saturable optical fluorescence transitions) or nonlinear structured illumination can be effectively parallelized using two incoherently superimposed orthogonal standing light waves. The intensity minima of the resulting pattern act as 'doughnuts'...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2556
更新日期:2013-08-01 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 have developed a single-plasmid system for the efficient bacterial expression of mutant proteins containing unnatural amino acids at specific sites designated by amber nonsense codons. In this system, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus jannaschii tyrosyl-tR...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth864
更新日期:2006-04-01 00:00:00
abstract::To engineer a stem cell genome, we developed a technology for targeted elimination of chromosomes from mouse embryonic stem (ES)-somatic hybrid cells. Here we demonstrate the use of a universal chromosome elimination cassette (CEC) for elimination of a single embryonic stem cell (ESC)-derived chromosome 11 or 12, and ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth973
更新日期:2007-01-01 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
abstract::Accurately modeling cellular response to perturbations is a central goal of computational biology. While such modeling has been based on statistical, mechanistic and machine learning models in specific settings, no generalization of predictions to phenomena absent from training data (out-of-sample) has yet been demons...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0494-8
更新日期:2019-08-01 00:00:00
abstract::The stable expansion of tissue-specific stem cells in vitro has contributed to research on several organs. Alveolar epithelial type II (AT2) cells function as tissue stem cells in the lung, but robust models for studying human AT2 cells are lacking. Here we report a method for the efficient generation and long-term ex...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4448
更新日期:2017-11-01 00:00:00
abstract::By combining activity-based proteomics and metabolomics, researchers have developed a new systems biology strategy for characterizing enzymes in the context of metabolic networks. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth0107-8b
更新日期:2007-01-01 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::Drug-inducible systems allowing the control of gene expression in mammalian cells are invaluable tools for genetic research, and could also fulfill essential roles in gene- and cell-based therapy. Currently available systems, however, often have limited in vivo functionality because of leakiness, insufficient levels o...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth846
更新日期:2006-02-01 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::RNA-guided Cas9 nucleases derived from clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems have dramatically transformed our ability to edit the genomes of diverse organisms. We believe tools and techniques based on Cas9, a single unifying factor capable of colocalizing RNA, DNA and protein,...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth.2649
更新日期:2013-10-01 00:00:00
abstract::X-ray free-electron lasers (XFELs) offer opportunities beyond classic X-ray crystallography, particularly for proteins that are difficult to crystallize. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3070
更新日期:2014-09-01 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::Understanding how cells maintain genome integrity when challenged with DNA double-strand breaks (DSBs) is of major importance, particularly since the discovery of multiple links of DSBs with genome instability and cancer-predisposition disorders. Ionizing radiation is the agent of choice to produce DSBs in cells; howe...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.f.206
更新日期:2008-03-01 00:00:00
abstract::We introduce a method for sequencing peptides by mass spectrometry using a metalloendopeptidase that cleaves proteins at the amino side of lysine (Lys-N). When analyzed by electron transfer dissociation (ETD)-based mass spectrometric sequencing, Lys-N-digested peptides that contain a single lysine residue produce spec...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1204
更新日期:2008-05-01 00:00:00
abstract::Bisulfite sequencing measures absolute levels of DNA methylation at single-nucleotide resolution, providing a robust platform for molecular diagnostics. We optimized bisulfite sequencing for genome-scale analysis of clinical samples: here we outline how restriction digestion targets bisulfite sequencing to hotspots of...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1414
更新日期:2010-02-01 00:00:00
abstract::Optimism about biomedicine is challenged by the increasingly complex ethical, legal and social issues it raises. Reporting of scientific methods is no longer sufficient to address the complex relationship between science and society. To promote 'ethical reproducibility', we call for transparent reporting of research e...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2564
更新日期:2013-09-01 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::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::Genetically encoded unnatural amino acids provide powerful strategies for modulating the molecular functions of proteins in mammalian cells. However, this approach has not been coupled to genome-wide measurements, because efficient incorporation of unnatural amino acids is limited to transient expression settings that...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3701
更新日期:2016-02-01 00:00:00
abstract::A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth0207-112b
更新日期:2007-02-01 00:00:00
abstract::We demonstrate gas cluster ion beam scanning electron microscopy (SEM), in which wide-area ion milling is performed on a series of thick tissue sections. This three-dimensional electron microscopy technique acquires datasets with <10 nm isotropic resolution of each section, and these can then be stitched together to s...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-019-0641-2
更新日期:2020-01-01 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 describe Trans-ABySS, a de novo short-read transcriptome assembly and analysis pipeline that addresses variation in local read densities by assembling read substrings with varying stringencies and then merging the resulting contigs before analysis. Analyzing 7.4 gigabases of 50-base-pair paired-end Illumina reads f...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1517
更新日期:2010-11-01 00:00:00
abstract::We developed a quantitative PCR method featuring a reusable single-cell cDNA library immobilized on beads for measuring the expression of multiple genes in a single cell. We used this method to analyze multiple cDNA targets (from several copies to several hundred thousand copies) with an experimental error of 15.9% or...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1338
更新日期:2009-07-01 00:00:00
abstract::Understanding how chromatin is regulated is essential to fully grasp genome biology, and establishing the locus-specific protein composition is a major step toward this goal. Here we explain why the isolation and analysis of a specific chromatin segment are technically challenging, independently of the method. We then...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/s41592-020-0765-4
更新日期:2020-04-01 00:00:00