LambdaN-GFP: an RNA reporter system for live-cell imaging.

abstract：:We have developed a versatile, potent technique for imaging cells in culture and in vivo by expressing a metabolically biotinylated cell-surface receptor and visualizing it with labeled streptavidin moieties. The recombinant reporter protein, which incorporates a biotin acceptor peptide (BAP) between an N-terminal sig...

journal_title：Nature methods

authors： Tannous BA,Grimm J,Perry KF,Chen JW,Weissleder R,Breakefield XO

更新日期：2006-05-01 00:00:00

abstract：:Stable in vivo mapping and modulation of the same neurons and brain circuits over extended periods is critical to both neuroscience and medicine. Current electrical implants offer single-neuron spatiotemporal resolution but are limited by such factors as relative shear motion and chronic immune responses during long-t...

journal_title：Nature methods

authors： Fu TM,Hong G,Zhou T,Schuhmann TG,Viveros RD,Lieber CM

更新日期：2016-10-01 00:00:00

abstract：:The complexity of the angiogenic cascade limits cellular approaches to studying angiogenic endothelial cells (ECs). In turn, in vivo assays do not allow the analysis of the distinct cellular behavior of ECs during angiogenesis. Here we show that ECs can be grafted as spheroids into a matrix to give rise to a complex t...

journal_title：Nature methods

authors： Alajati A,Laib AM,Weber H,Boos AM,Bartol A,Ikenberg K,Korff T,Zentgraf H,Obodozie C,Graeser R,Christian S,Finkenzeller G,Stark GB,Héroult M,Augustin HG

更新日期：2008-05-01 00:00:00

abstract：:Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets...

journal_title：Nature methods

authors： Kim J,Bhinge AA,Morgan XC,Iyer VR

更新日期：2005-01-01 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

authors： van den Bedem H,Bhabha G,Yang K,Wright PE,Fraser JS

更新日期：2013-09-01 00:00:00

abstract：:We describe a statistical analysis methodology designed to minimize the impact of off-target activities upon large-scale RNA interference (RNAi) screens in mammalian cells. Application of this approach enhances reconfirmation rates and facilitates the experimental validation of new gene activities through the probabil...

journal_title：Nature methods

authors： König R,Chiang CY,Tu BP,Yan SF,DeJesus PD,Romero A,Bergauer T,Orth A,Krueger U,Zhou Y,Chanda SK

更新日期：2007-10-01 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

authors： Matsumura H,Tada M,Otsuji T,Yasuchika K,Nakatsuji N,Surani A,Tada T

更新日期：2007-01-01 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

authors： Ebbinghaus S,Dhar A,McDonald JD,Gruebele M

更新日期：2010-04-01 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：:Quantitative measurements of cell-generated forces have heretofore required that cells be cultured on two-dimensional substrates. We describe a technique to quantitatively measure three-dimensional traction forces exerted by cells fully encapsulated in well-defined elastic hydrogel matrices. Using this approach we mea...

journal_title：Nature methods

authors： Legant WR,Miller JS,Blakely BL,Cohen DM,Genin GM,Chen CS

更新日期：2010-12-01 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

authors： Kukura P,Ewers H,Müller C,Renn A,Helenius A,Sandoghdar V

更新日期：2009-12-01 00:00:00

abstract：:Spatiotemporal activity patterns in three-dimensionally organized cellular networks are fundamental to the function of the nervous system. Despite advances in functional imaging of cell populations, a method to resolve local network activity in three dimensions has been lacking. Here we introduce a three-dimensional (...

journal_title：Nature methods

authors： Göbel W,Kampa BM,Helmchen F

更新日期：2007-01-01 00:00:00

abstract：:A robust method for simultaneous visualization of all four cell cycle phases in living cells is highly desirable. We developed an intensiometric reporter of the transition from S to G2 phase and engineered a far-red fluorescent protein, mMaroon1, to visualize chromatin condensation in mitosis. We combined these new re...

journal_title：Nature methods

authors： Bajar BT,Lam AJ,Badiee RK,Oh YH,Chu J,Zhou XX,Kim N,Kim BB,Chung M,Yablonovitch AL,Cruz BF,Kulalert K,Tao JJ,Meyer T,Su XD,Lin MZ

更新日期：2016-12-01 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

authors： Greenbaum A,Luo W,Su TW,Göröcs Z,Xue L,Isikman SO,Coskun AF,Mudanyali O,Ozcan A

更新日期：2012-09-01 00:00:00

abstract：:Single-cell RNA sequencing (scRNA-seq) is a rich resource of cellular heterogeneity, opening new avenues in the study of complex tissues. We introduce Cell Population Mapping (CPM), a deconvolution algorithm in which reference scRNA-seq profiles are leveraged to infer the composition of cell types and states from bulk...

journal_title：Nature methods

authors： Frishberg A,Peshes-Yaloz N,Cohn O,Rosentul D,Steuerman Y,Valadarsky L,Yankovitz G,Mandelboim M,Iraqi FA,Amit I,Mayo L,Bacharach E,Gat-Viks I

更新日期：2019-04-01 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

authors： Martinez-Sanchez A,Kochovski Z,Laugks U,Meyer Zum Alten Borgloh J,Chakraborty S,Pfeffer S,Baumeister W,Lučić V

更新日期：2020-02-01 00:00:00

abstract：:A label-free microscopy technique based on electrochemical impedance offers a new way of studying electrochemical processes in single cells. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2011-03-01 00:00:00

abstract：:Electron cryotomography is currently the only method capable of visualizing cells in three dimensions at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information, data processing is very labor intensive and the results are often limited...

journal_title：Nature methods

authors： Chen M,Bell JM,Shi X,Sun SY,Wang Z,Ludtke SJ

更新日期：2019-11-01 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

authors： Gessulat S,Schmidt T,Zolg DP,Samaras P,Schnatbaum K,Zerweck J,Knaute T,Rechenberger J,Delanghe B,Huhmer A,Reimer U,Ehrlich HC,Aiche S,Kuster B,Wilhelm M

更新日期：2019-06-01 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

authors： Hirsch SM,Sundaramoorthy S,Davies T,Zhuravlev Y,Waters JC,Shirasu-Hiza M,Dumont J,Canman JC

更新日期：2018-11-01 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

authors： Lippert C,Listgarten J,Liu Y,Kadie CM,Davidson RI,Heckerman D

更新日期：2011-09-04 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

authors： Gauchier M,van Mierlo G,Vermeulen M,Déjardin J

更新日期：2020-04-01 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：: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

authors： Knispel RW,Kofler C,Boicu M,Baumeister W,Nickell S

更新日期：2012-01-08 00:00:00

abstract：:We present functional ultrasound (fUS), a method for imaging transient changes in blood volume in the whole brain at better spatiotemporal resolution than with other functional brain imaging modalities. fUS uses plane-wave illumination at high frame rate and can measure blood volumes in smaller vessels than previous u...

journal_title：Nature methods

authors： Macé E,Montaldo G,Cohen I,Baulac M,Fink M,Tanter M

更新日期：2011-07-03 00:00:00

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 re...

journal_title：Nature methods

authors： Collins RT,Linker C,Lewis J

更新日期：2010-03-01 00:00:00

abstract：:Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high. Here we report th...

journal_title：Nature methods

authors： Radivojac P,Clark WT,Oron TR,Schnoes AM,Wittkop T,Sokolov A,Graim K,Funk C,Verspoor K,Ben-Hur A,Pandey G,Yunes JM,Talwalkar AS,Repo S,Souza ML,Piovesan D,Casadio R,Wang Z,Cheng J,Fang H,Gough J,Koskinen P,Törö

更新日期：2013-03-01 00:00:00

abstract：:We have used a mass spectrometry-based proteomic approach to compile an atlas of the thermal stability of 48,000 proteins across 13 species ranging from archaea to humans and covering melting temperatures of 30-90 °C. Protein sequence, composition and size affect thermal stability in prokaryotes and eukaryotic protein...

journal_title：Nature methods

authors： Jarzab A,Kurzawa N,Hopf T,Moerch M,Zecha J,Leijten N,Bian Y,Musiol E,Maschberger M,Stoehr G,Becher I,Daly C,Samaras P,Mergner J,Spanier B,Angelov A,Werner T,Bantscheff M,Wilhelm M,Klingenspor M,Lemeer S,Liebl W

更新日期：2020-05-01 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

authors： Chen F,Wassie AT,Cote AJ,Sinha A,Alon S,Asano S,Daugharthy ER,Chang JB,Marblestone A,Church GM,Raj A,Boyden ES

更新日期：2016-08-01 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

authors： Keller PJ,Schmidt AD,Santella A,Khairy K,Bao Z,Wittbrodt J,Stelzer EH

更新日期：2010-08-01 00:00:00