Tracking the structural dynamics of proteins in solution using time-resolved wide-angle X-ray scattering.

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

authors： Hernandez VH,Bortolozzi M,Pertegato V,Beltramello M,Giarin M,Zaccolo M,Pantano S,Mammano F

更新日期：2007-04-01 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

authors： Raman R,Raguram S,Venkataraman G,Paulson JC,Sasisekharan R

更新日期：2005-11-01 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

authors： Dai Q,Moshitch-Moshkovitz S,Han D,Kol N,Amariglio N,Rechavi G,Dominissini D,He C

更新日期：2017-07-01 00:00:00

abstract：:Current extracellular multisite recordings suffer from low signal-to-noise ratio, limiting the monitoring to action potentials, and preclude detection of subthreshold synaptic potentials. Here we report an approach to induce Aplysia californica neurons to actively engulf protruding microelectrodes, providing 'in-cell ...

journal_title：Nature methods

authors： Hai A,Shappir J,Spira ME

更新日期：2010-03-01 00:00:00

abstract：:We present DeNovoGear software for analyzing de novo mutations from familial and somatic tissue sequencing data. DeNovoGear uses likelihood-based error modeling to reduce the false positive rate of mutation discovery in exome analysis and fragment information to identify the parental origin of germ-line mutations. We ...

journal_title：Nature methods

authors： Ramu A,Noordam MJ,Schwartz RS,Wuster A,Hurles ME,Cartwright RA,Conrad DF

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

authors： Albert TJ,Dailidiene D,Dailide G,Norton JE,Kalia A,Richmond TA,Molla M,Singh J,Green RD,Berg DE

更新日期：2005-12-01 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

authors： Lotfollahi M,Wolf FA,Theis FJ

更新日期：2019-08-01 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：: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

authors： Chen F,Pruett-Miller SM,Huang Y,Gjoka M,Duda K,Taunton J,Collingwood TN,Frodin M,Davis GD

更新日期：2011-07-17 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：: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：:Transcription activator-like effector (TALE) proteins have gained broad appeal as a platform for targeted DNA recognition, largely owing to their simple rules for design. These rules relate the base specified by a single TALE repeat to the identity of two key residues (the repeat variable diresidue, or RVD) and enable...

journal_title：Nature methods

authors： Miller JC,Zhang L,Xia DF,Campo JJ,Ankoudinova IV,Guschin DY,Babiarz JE,Meng X,Hinkley SJ,Lam SC,Paschon DE,Vincent AI,Dulay GP,Barlow KA,Shivak DA,Leung E,Kim JD,Amora R,Urnov FD,Gregory PD,Rebar EJ

更新日期：2015-05-01 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：: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：:CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome pro...

journal_title：Nature methods

authors： Datlinger P,Rendeiro AF,Schmidl C,Krausgruber T,Traxler P,Klughammer J,Schuster LC,Kuchler A,Alpar D,Bock C

更新日期：2017-03-01 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：:Spontaneous and sensory-evoked activity propagates across varying spatial scales in the mammalian cortex, but technical challenges have limited conceptual links between the function of local neuronal circuits and brain-wide network dynamics. We present a method for simultaneous cellular-resolution two-photon calcium i...

journal_title：Nature methods

authors： Barson D,Hamodi AS,Shen X,Lur G,Constable RT,Cardin JA,Crair MC,Higley MJ

更新日期：2020-01-01 00:00:00

abstract：:Monomeric (m)Eos2 is an engineered photoactivatable fluorescent protein widely used for super-resolution microscopy. We show that mEos2 forms oligomers at high concentrations and forms aggregates when labeling membrane proteins, limiting its application as a fusion partner. We solved the crystal structure of tetrameri...

journal_title：Nature methods

authors： Zhang M,Chang H,Zhang Y,Yu J,Wu L,Ji W,Chen J,Liu B,Lu J,Liu Y,Zhang J,Xu P,Xu T

更新日期：2012-05-13 00:00:00

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：:High-speed, large-scale three-dimensional (3D) imaging of neuronal activity poses a major challenge in neuroscience. Here we demonstrate simultaneous functional imaging of neuronal activity at single-neuron resolution in an entire Caenorhabditis elegans and in larval zebrafish brain. Our technique captures the dynamic...

journal_title：Nature methods

authors： Prevedel R,Yoon YG,Hoffmann M,Pak N,Wetzstein G,Kato S,Schrödel T,Raskar R,Zimmer M,Boyden ES,Vaziri A

更新日期：2014-07-01 00:00:00

abstract：:An outstanding challenge of epigenome-wide association studies (EWASs) performed in complex tissues is the identification of the specific cell type(s) responsible for the observed differential DNA methylation. Here we present a statistical algorithm called CellDMC ( https://github.com/sjczheng/EpiDISH ), which can ide...

journal_title：Nature methods

authors： Zheng SC,Breeze CE,Beck S,Teschendorff AE

更新日期：2018-12-01 00:00:00

abstract：:We combined rapid microfluidic mixing with single-molecule fluorescence resonance energy transfer to study the folding kinetics of the intrinsically disordered human protein α-synuclein. The time-resolution of 0.2 ms revealed initial collapse of the unfolded protein induced by binding with lipid mimics and subsequent ...

journal_title：Nature methods

authors： Gambin Y,VanDelinder V,Ferreon AC,Lemke EA,Groisman A,Deniz AA

更新日期：2011-03-01 00:00:00

abstract：:Counting molecules in complexes is challenging, even with super-resolution microscopy. Here, we use the programmable and specific binding of dye-labeled DNA probes to count integer numbers of targets. This method, called quantitative points accumulation in nanoscale topography (qPAINT), works independently of dye phot...

journal_title：Nature methods

authors： Jungmann R,Avendaño MS,Dai M,Woehrstein JB,Agasti SS,Feiger Z,Rodal A,Yin P

更新日期：2016-05-01 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：:We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art met...

journal_title：Nature methods

authors： Wang B,Zhu J,Pierson E,Ramazzotti D,Batzoglou S

更新日期：2017-04-01 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

authors： Taouatas N,Drugan MM,Heck AJ,Mohammed S

更新日期：2008-05-01 00:00:00

abstract：:Researchers designed an enzyme to carry out the Diels-Alder reaction, an activity not found in nature. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2010-09-01 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 have developed hydrogel-based virtual microfluidics as a simple and robust alternative to complex engineered microfluidic systems for the compartmentalization of nucleic acid amplification reactions. We applied in-gel digital multiple displacement amplification (dMDA) to purified DNA templates, cultured bacterial c...

journal_title：Nature methods

authors： Xu L,Brito IL,Alm EJ,Blainey PC

更新日期：2016-09-01 00:00:00

abstract：:The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A variety of mass spectrometry-based approaches allow characterization of cellular protein assemblies under near-physiological conditions and subsequent assignmen...

journal_title：Nature methods

authors： Köcher T,Superti-Furga G

更新日期：2007-10-01 00:00:00