FLIRT: fast local infrared thermogenetics for subcellular control of protein function.

abstract：:We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scala...

journal_title：Nature methods

authors： Steemers FJ,Chang W,Lee G,Barker DL,Shen R,Gunderson KL

更新日期：2006-01-01 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：: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：:Methods for visualizing protein or nucleic acid motifs have traditionally relied upon residue frequencies to graphically scale character heights. We describe the pLogo, a motif visualization in which residue heights are scaled relative to their statistical significance. A pLogo generation tool is publicly available at...

journal_title：Nature methods

authors： O'Shea JP,Chou MF,Quader SA,Ryan JK,Church GM,Schwartz D

更新日期：2013-12-01 00:00:00

abstract：:Thermodynamic stability is fundamental to the biology of proteins. Information on protein stability is essential for studying protein structure and folding and can also be used indirectly to monitor protein-ligand or protein-protein interactions. While clearly valuable, the experimental determination of a protein's st...

journal_title：Nature methods

authors： Park C,Marqusee S

更新日期：2005-03-01 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

authors： Doerr A

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：:Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been cha...

journal_title：Nature methods

authors： Gisselbrecht SS,Barrera LA,Porsch M,Aboukhalil A,Estep PW 3rd,Vedenko A,Palagi A,Kim Y,Zhu X,Busser BW,Gamble CE,Iagovitina A,Singhania A,Michelson AM,Bulyk ML

更新日期：2013-08-01 00:00:00

abstract：:To enhance the repertoire of molecular tools for studying malaria parasite biology, we adapted a ligand-regulatable FKBP protein destabilization domain (ddFKBP) for use in P. falciparum. We destabilized the reporter yellow fluorescent protein (YFP) and the P. falciparum protease falcipain-2 in a ligand-reversible mann...

journal_title：Nature methods

authors： Armstrong CM,Goldberg DE

更新日期：2007-12-01 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

authors： Shults MD,Janes KA,Lauffenburger DA,Imperiali B

更新日期：2005-04-01 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

authors： Mali P,Esvelt KM,Church GM

更新日期：2013-10-01 00:00:00

abstract：:RNAs are ideal for the design of gene switches that can monitor and program cellular behavior because of their high modularity and predictable structure-function relationship. We have assembled an expression platform with an embedded modular ribozyme scaffold that correlates self-cleavage activity of designer ribozyme...

journal_title：Nature methods

authors： Ausländer S,Stücheli P,Rehm C,Ausländer D,Hartig JS,Fussenegger M

更新日期：2014-11-01 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

authors： Nishimura K,Fukagawa T,Takisawa H,Kakimoto T,Kanemaki M

更新日期：2009-12-01 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

authors： Schrödel T,Prevedel R,Aumayr K,Zimmer M,Vaziri A

更新日期：2013-10-01 00:00:00

abstract：:We present a method to robustly discriminate clustered from randomly distributed molecules detected with techniques based on single-molecule localization microscopy, such as PALM and STORM. The approach is based on deliberate variation of labeling density, such as titration of fluorescent antibody, combined with quant...

journal_title：Nature methods

authors： Baumgart F,Arnold AM,Leskovar K,Staszek K,Fölser M,Weghuber J,Stockinger H,Schütz GJ

更新日期：2016-08-01 00:00:00

abstract：:Fluorescence microscopy is a powerful quantitative tool for exploring regulatory networks in single cells. However, the number of molecular species that can be measured simultaneously is limited by the spectral overlap between fluorophores. Here we demonstrate a simple but general strategy to drastically increase the ...

journal_title：Nature methods

authors： Lubeck E,Cai L

更新日期：2012-06-03 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

authors： Gu H,Bock C,Mikkelsen TS,Jäger N,Smith ZD,Tomazou E,Gnirke A,Lander ES,Meissner A

更新日期：2010-02-01 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：: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： Fiolka R

更新日期：2019-10-01 00:00:00

abstract：:Firefly luciferase is the most widely used optical reporter for noninvasive bioluminescence imaging (BLI) in rodents. BLI relies on the ability of the injected luciferase substrate D-luciferin to access luciferase-expressing cells and tissues within the animal. Here we show that injection of mice with a synthetic luci...

journal_title：Nature methods

authors： Evans MS,Chaurette JP,Adams ST Jr,Reddy GR,Paley MA,Aronin N,Prescher JA,Miller SC

更新日期：2014-04-01 00:00:00

abstract：:To enable the detection of expression signatures specific to individual cells, we developed PLAYR (proximity ligation assay for RNA), a method for highly multiplexed transcript quantification by flow and mass cytometry that is compatible with standard antibody staining. When used with mass cytometry, PLAYR allowed for...

journal_title：Nature methods

authors： Frei AP,Bava FA,Zunder ER,Hsieh EW,Chen SY,Nolan GP,Gherardini PF

更新日期：2016-03-01 00:00:00

abstract：:We established a conditional site-specific recombination system based on dimerizable Cre recombinase-mediated recombination in the apicomplexan parasite Toxoplasma gondii. Using a new single-vector strategy that allows ligand-dependent, efficient removal of a gene of interest, we generated three knockouts of apicomple...

journal_title：Nature methods

authors： Andenmatten N,Egarter S,Jackson AJ,Jullien N,Herman JP,Meissner M

更新日期：2013-02-01 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：:We achieve simultaneous two-photon excitation of three chromophores with distinct absorption spectra using synchronized pulses from a femtosecond laser and an optical parametric oscillator. The two beams generate separate multiphoton processes, and their spatiotemporal overlap provides an additional two-photon excitat...

journal_title：Nature methods

authors： Mahou P,Zimmerley M,Loulier K,Matho KS,Labroille G,Morin X,Supatto W,Livet J,Débarre D,Beaurepaire E

更新日期：2012-07-08 00:00:00

abstract：:Measuring complete gene expression profiles for a large number of experiments is costly. We propose an approach in which a small subset of probes is selected based on a preliminary set of full expression profiles. In subsequent experiments, only the subset is measured, and the missing values are inputed. We developed ...

journal_title：Nature methods

authors： Donner Y,Feng T,Benoist C,Koller D

更新日期：2012-11-01 00:00:00

abstract：:We developed a general approach that allows unnatural amino acids with diverse physicochemical and biological properties to be genetically encoded in mammalian cells. A mutant Escherichia coli aminoacyl-tRNA synthetase (aaRS) is first evolved in yeast to selectively aminoacylate its tRNA with the unnatural amino acid ...

journal_title：Nature methods

authors： Liu W,Brock A,Chen S,Chen S,Schultz PG

更新日期：2007-03-01 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：:Our Patterning on Topography (PoT) printing technique enables fibronectin, laminin and other proteins to be applied to biomaterial surfaces in complex geometries that are inaccessible using traditional soft lithography techniques. Engineering combinatorial surfaces that integrate topographical and biochemical micropat...

journal_title：Nature methods

authors： Sun Y,Jallerat Q,Szymanski JM,Feinberg AW

更新日期：2015-02-01 00:00:00

abstract：:Chromosome segregation requires both compaction and disentanglement of sister chromatids. We describe SisterC, a chromosome conformation capture assay that distinguishes interactions between and along identical sister chromatids. SisterC employs 5-bromo-2'-deoxyuridine (BrdU) incorporation during S-phase to label newl...

journal_title：Nature methods

authors： Oomen ME,Hedger AK,Watts JK,Dekker J

更新日期：2020-10-01 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

authors： Clément V,Marino D,Cudalbu C,Hamou MF,Mlynarik V,de Tribolet N,Dietrich PY,Gruetter R,Hegi ME,Radovanovic I

更新日期：2010-03-01 00:00:00