A bright and photostable photoconvertible fluorescent protein.

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

authors： Biteen JS,Thompson MA,Tselentis NK,Bowman GR,Shapiro L,Moerner WE

更新日期：2008-11-01 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

authors： Cammarata M,Levantino M,Schotte F,Anfinrud PA,Ewald F,Choi J,Cupane A,Wulff M,Ihee H

更新日期：2008-10-01 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

authors： Grüner BM,Schulze CJ,Yang D,Ogasawara D,Dix MM,Rogers ZN,Chuang CH,McFarland CD,Chiou SH,Brown JM,Cravatt BF,Bogyo M,Winslow MM

更新日期：2016-10-01 00:00:00

abstract：:Accurate identification of cell subsets in complex populations is key to discovering novelty in multidimensional single-cell experiments. We present X-shift (http://web.stanford.edu/~samusik/vortex/), an algorithm that processes data sets using fast k-nearest-neighbor estimation of cell event density and arranges popu...

journal_title：Nature methods

authors： Samusik N,Good Z,Spitzer MH,Davis KL,Nolan GP

更新日期：2016-06-01 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

authors： Landgraf D,Okumus B,Chien P,Baker TA,Paulsson J

更新日期：2012-04-08 00:00:00

abstract：:We present an easy-to-use integrated software suite, DIA-NN, that exploits deep neural networks and new quantification and signal correction strategies for the processing of data-independent acquisition (DIA) proteomics experiments. DIA-NN improves the identification and quantification performance in conventional DIA ...

journal_title：Nature methods

authors： Demichev V,Messner CB,Vernardis SI,Lilley KS,Ralser M

更新日期：2020-01-01 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

authors： Selega A,Sirocchi C,Iosub I,Granneman S,Sanguinetti G

更新日期：2017-01-01 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

authors： Gauthier NP,Soufi B,Walkowicz WE,Pedicord VA,Mavrakis KJ,Macek B,Gin DY,Sander C,Miller ML

更新日期：2013-08-01 00:00:00

abstract：:Here we integrated multiphoton laser scanning microscopy and the registration of second harmonic generation images of collagen fibers to overcome difficulties in tracking stromal cell-matrix interactions for several days in live mice. We show that the matrix-modifying hormone relaxin increased tumor-associated fibrobl...

journal_title：Nature methods

authors： Perentes JY,McKee TD,Ley CD,Mathiew H,Dawson M,Padera TP,Munn LL,Jain RK,Boucher Y

更新日期：2009-02-01 00:00:00

abstract：:Time resolution of current single-molecule fluorescence techniques is limited to milliseconds because of dye blinking and bleaching. Here we introduce a photoprotection strategy that affords microsecond resolution by combining efficient triplet quenching by oxygen and Trolox with minimized bleaching via the oxygen rad...

journal_title：Nature methods

authors： Campos LA,Liu J,Wang X,Ramanathan R,English DS,Muñoz V

更新日期：2011-02-01 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

authors： Newman AM,Liu CL,Green MR,Gentles AJ,Feng W,Xu Y,Hoang CD,Diehn M,Alizadeh AA

更新日期：2015-05-01 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

authors： Alberti C,Manzenreither RA,Sowemimo I,Burkard TR,Wang J,Mahofsky K,Ameres SL,Cochella L

更新日期：2018-04-01 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

authors： Robertson G,Schein J,Chiu R,Corbett R,Field M,Jackman SD,Mungall K,Lee S,Okada HM,Qian JQ,Griffith M,Raymond A,Thiessen N,Cezard T,Butterfield YS,Newsome R,Chan SK,She R,Varhol R,Kamoh B,Prabhu AL,Tam A,Zhao Y

更新日期：2010-11-01 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

authors： Toettcher JE,Gong D,Lim WA,Weiner OD

更新日期：2011-09-11 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

authors： Zhang F,Wang LP,Boyden ES,Deisseroth K

更新日期：2006-10-01 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

authors： Lever J,Zhao EY,Grewal J,Jones MR,Jones SJM

更新日期：2019-06-01 00:00:00

abstract：:Cryogenic electron microscopy (cryo-EM) maps are now at the point where resolvability of individual atoms can be achieved. However, resolvability is not necessarily uniform throughout the map. We introduce a quantitative parameter to characterize the resolvability of individual atoms in cryo-EM maps, the map Q-score. ...

journal_title：Nature methods

authors： Pintilie G,Zhang K,Su Z,Li S,Schmid MF,Chiu W

更新日期：2020-03-01 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

authors： Nimmerjahn A,Kirchhoff F,Kerr JN,Helmchen F

更新日期：2004-10-01 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

authors： Chavez A,Scheiman J,Vora S,Pruitt BW,Tuttle M,P R Iyer E,Lin S,Kiani S,Guzman CD,Wiegand DJ,Ter-Ovanesyan D,Braff JL,Davidsohn N,Housden BE,Perrimon N,Weiss R,Aach J,Collins JJ,Church GM

更新日期：2015-04-01 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

authors： Hayworth KJ,Peale D,Januszewski M,Knott GW,Lu Z,Xu CS,Hess HF

更新日期：2020-01-01 00:00:00

abstract：:Ribonucleoproteins (RNPs) are key regulators of cellular function. We established an efficient approach, crosslinking of segmentally isotope-labeled RNA and tandem mass spectrometry (CLIR-MS/MS), to localize protein-RNA interactions simultaneously at amino acid and nucleotide resolution. The approach was tested on pol...

journal_title：Nature methods

authors： Dorn G,Leitner A,Boudet J,Campagne S,von Schroetter C,Moursy A,Aebersold R,Allain FH

更新日期：2017-05-01 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

authors： Richler E,Chaumont S,Shigetomi E,Sagasti A,Khakh BS

更新日期：2008-01-01 00:00:00

abstract：:Methods for genomic analysis at single-cell resolution enable new understanding of complex biological phenomena. Single-cell techniques, ranging from flow cytometry and microfluidics to PCR and sequencing, are used to understand the cellular composition of complex tissues, find new microbial species and perform genome...

journal_title：Nature methods

authors： Kalisky T,Quake SR

更新日期：2011-04-01 00:00:00

abstract：:Despite the vital role of mechanical forces in biology, it still remains a challenge to image cellular force with sub-100-nm resolution. Here, we present tension points accumulation for imaging in nanoscale topography (tPAINT), integrating molecular tension probes with the DNA points accumulation for imaging in nanosc...

journal_title：Nature methods

authors： Brockman JM,Su H,Blanchard AT,Duan Y,Meyer T,Quach ME,Glazier R,Bazrafshan A,Bender RL,Kellner AV,Ogasawara H,Ma R,Schueder F,Petrich BG,Jungmann R,Li R,Mattheyses AL,Ke Y,Salaita K

更新日期：2020-10-01 00:00:00

abstract：:Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to defi...

journal_title：Nature methods

authors： Chen Y,McElvain LE,Tolpygo AS,Ferrante D,Friedman B,Mitra PP,Karten HJ,Freund Y,Kleinfeld D

更新日期：2019-04-01 00:00:00

abstract：: ...

journal_title：Nature methods

authors： Doerr A

更新日期：2018-11-01 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

authors： Kraehenbuehl TP,Langer R,Ferreira LS

更新日期：2011-08-30 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

authors： Berlin S,Carroll EC,Newman ZL,Okada HO,Quinn CM,Kallman B,Rockwell NC,Martin SS,Lagarias JC,Isacoff EY

更新日期：2015-09-01 00:00:00

abstract：:Macromolecular crowding in cells influences processes such as folding, association and diffusion of proteins and polynucleic acids. Direct spatiotemporal readout of crowding would be a powerful approach for unraveling the structure of the cytoplasm and determining the impact of excluded volume on protein function in l...

journal_title：Nature methods

authors： Boersma AJ,Zuhorn IS,Poolman B

更新日期：2015-03-01 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

authors： Sims PA,Greenleaf WJ,Duan H,Xie XS

更新日期：2011-06-12 00:00:00