Abstract:
:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron microscope. Here we report the application of small nanocrystals (Quantum dots; QDs) to specifically and efficiently label multiple distinct endogenous proteins. QDs are both fluorescent and electron dense, facilitating their use for correlated microscopic analysis. Furthermore, QDs can be discriminated optically by their emission wavelength and physically by size, making them invaluable for multilabeling analysis. We developed pre-embedding labeling criteria using QDs that allows optimization at the light level, before continuing with electron microscopy (EM). We provide examples of double and triple immunolabeling using light, electron and correlated microscopy in rat cells and mouse tissue. We conclude that QDs aid precise high-throughput determination of protein distribution.
journal_name
Nat Methodsjournal_title
Nature methodsauthors
Giepmans BN,Deerinck TJ,Smarr BL,Jones YZ,Ellisman MHdoi
10.1038/nmeth791keywords:
subject
Has Abstractpub_date
2005-10-01 00:00:00pages
743-9issue
10eissn
1548-7091issn
1548-7105pii
nmeth791journal_volume
2pub_type
杂志文章相关文献
NATURE METHODS文献大全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::Quantification of cell-cycle state at a single-cell level is essential to understand fundamental three-dimensional (3D) biological processes such as tissue development and cancer. Analysis of 3D in vivo images, however, is very challenging. Today's best practice, manual annotation of select image events, generates arb...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3363
更新日期:2015-06-01 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::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::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::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::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/s41592-020-0733-z
更新日期:2020-02-01 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::We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unk...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.3337
更新日期:2015-05-01 00:00:00
abstract:: ...
journal_title:Nature methods
pub_type: 社论
doi:10.1038/s41592-018-0257-y
更新日期:2018-12-01 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::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::The shape of the genome is thought to play an important part in the coordination of transcription and other DNA-metabolic processes. Chromosome conformation capture (3C) technology allows us to analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy tech...
journal_title:Nature methods
pub_type: 杂志文章,评审
doi:10.1038/nmeth1114
更新日期:2007-11-01 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::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::MicroRNA depletion by sequestration produces flexible hypomorphs that mimic mutants obtained by microRNA gene targeting. ...
journal_title:Nature methods
pub_type: 评论,杂志文章
doi:10.1038/nmeth1209-873
更新日期:2009-12-01 00:00:00
abstract::Gap junction channels assembled from connexin protein subunits mediate intercellular transfer of ions and metabolites. Impaired channel function is implicated in several hereditary human diseases. In particular, defective permeation of cAMP or inositol-1,4,5-trisphosphate (InsP(3)) through connexin channels is associa...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1031
更新日期:2007-04-01 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::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::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::The ribose of RNA nucleotides can be 2'-O-methylated (Nm). Despite advances in high-throughput detection, the inert chemical nature of Nm still limits sensitivity and precludes mapping in mRNA. We leveraged the differential reactivity of 2'-O-methylated and 2'-hydroxylated nucleosides to periodate oxidation to develop...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.4294
更新日期:2017-07-01 00:00:00
abstract::We present general means to greatly increase the sensitivity of antibody-based assays. Augmentation relies on a 'tadpole' protein-DNA chimera whose protein moiety binds most classes of mammalian antibodies but not avian immunoglobulin Y (IgY). We used this tadpole in affinity capture assays followed by real-time PCR t...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth1127
更新日期:2007-12-01 00:00:00
abstract::Despite the widespread adoption of organoids as biomimetic tissue models, methods to comprehensively analyze cell-type-specific post-translational modification (PTM) signaling networks in organoids are absent. Here, we report multivariate single-cell analysis of such networks in organoids and organoid cocultures. Simu...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/s41592-020-0737-8
更新日期:2020-03-01 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::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::The analysis of structure and dynamics of biomolecules is important for understanding their function. Toward this aim, we introduce a method called 'switchable FRET', which combines single-molecule fluorescence resonance energy transfer (FRET) with reversible photoswitching of fluorophores. Typically, single-molecule ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1502
更新日期:2010-10-01 00:00:00
abstract::Caenorhabditis elegans is an important model organism in biology, but until now no antibiotic selection markers have been successfully demonstrated for this species. We have developed a selection system using puromycin that allows the rapid and easy isolation of large populations of transgenic worms. This approach is ...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1495
更新日期:2010-09-01 00:00:00
abstract::Recent efforts in neuroscience research have been aimed at obtaining detailed anatomical neuronal wiring maps as well as information on how neurons in these networks engage in dynamic activities. Although the entire connectivity map of the nervous system of Caenorhabditis elegans has been known for more than 25 years,...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.2637
更新日期:2013-10-01 00:00:00
abstract::We developed a microarray hybridization-based method, 'comparative genome sequencing' (CGS), to find mutations in bacterial genomes and used it to study metronidazole resistance in H. pylori. CGS identified mutations in several genes, most likely affecting metronidazole activation, and produced no false positives in a...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth805
更新日期:2005-12-01 00:00:00
abstract::Recording light-microscopy images of large, nontransparent specimens, such as developing multicellular organisms, is complicated by decreased contrast resulting from light scattering. Early zebrafish development can be captured by standard light-sheet microscopy, but new imaging strategies are required to obtain high-...
journal_title:Nature methods
pub_type: 杂志文章
doi:10.1038/nmeth.1476
更新日期:2010-08-01 00:00:00