Measurement of mechanical tractions exerted by cells in three-dimensional matrices.

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 measured traction forces for several cell types in various contexts and revealed patterns of force generation attributable to morphologically distinct regions of cells as they extend into the surrounding matrix.

journal_name

Nat Methods

journal_title

Nature methods

authors

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

doi

10.1038/nmeth.1531

subject

Has Abstract

pub_date

2010-12-01 00:00:00

pages

969-71

issue

12

eissn

1548-7091

issn

1548-7105

pii

nmeth.1531

journal_volume

7

pub_type

杂志文章
  • Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.2558

    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

  • Enhanced antibody validation.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,杂志文章

    doi:10.1038/s41592-018-0248-z

    authors: Doerr A

    更新日期:2018-12-01 00:00:00

  • An in vivo multiplexed small-molecule screening platform.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.3992

    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

  • Designer receptors for every body.

    abstract::Using a directed evolution approach, researchers demonstrate a way of creating 'designer' receptors that are specifically activated by a ligand with no other biological activity in the cell. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth0507-382b

    authors: Kaganman I

    更新日期:2007-05-01 00:00:00

  • Varying label density allows artifact-free analysis of membrane-protein nanoclusters.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.3897

    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

  • Neutron-encoded mass signatures for multiplexed proteome quantification.

    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

    authors: Hebert AS,Merrill AE,Bailey DJ,Still AJ,Westphall MS,Strieter ER,Pagliarini DJ,Coon JJ

    更新日期:2013-04-01 00:00:00

  • Three-dimensional biomaterials for the study of human pluripotent stem cells.

    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

    authors: Kraehenbuehl TP,Langer R,Ferreira LS

    更新日期:2011-08-30 00:00:00

  • Improved and expanded Q-system reagents for genetic manipulations.

    abstract::The Q system is a repressible binary expression system for transgenic manipulations in living organisms. Through protein engineering and in vivo functional tests, we report here variants of the Q-system transcriptional activator, including QF2, for driving strong and ubiquitous expression in all Drosophila tissues. Ou...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.3250

    authors: Riabinina O,Luginbuhl D,Marr E,Liu S,Wu MN,Luo L,Potter CJ

    更新日期:2015-03-01 00:00:00

  • FRETting for a more detailed interactome.

    abstract::A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth0207-112b

    authors: Kaganman I

    更新日期:2007-02-01 00:00:00

  • Protein folding stability and dynamics imaged in a living cell.

    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

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

    更新日期:2010-04-01 00:00:00

  • In-cell recordings by extracellular microelectrodes.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.1420

    authors: Hai A,Shappir J,Spira ME

    更新日期:2010-03-01 00:00:00

  • Identification of differentially methylated cell types in epigenome-wide association studies.

    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

    pub_type: 杂志文章

    doi:10.1038/s41592-018-0213-x

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

    更新日期:2018-12-01 00:00:00

  • Nm-seq maps 2'-O-methylation sites in human mRNA with base precision.

    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

    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

  • A transgenic mouse for in vivo detection of endogenous labeled mRNA.

    abstract::Live-cell single mRNA imaging is a powerful tool but has been restricted in higher eukaryotes to artificial cell lines and reporter genes. We describe an approach that enables live-cell imaging of single endogenous labeled mRNA molecules transcribed in primary mammalian cells and tissue. We generated a knock-in mouse ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.1551

    authors: Lionnet T,Czaplinski K,Darzacq X,Shav-Tal Y,Wells AL,Chao JA,Park HY,de Turris V,Lopez-Jones M,Singer RH

    更新日期:2011-02-01 00:00:00

  • Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis.

    abstract::Generation of complex libraries of defined nucleic acid sequences can greatly aid the functional analysis of protein and gene function. Previously, such studies relied either on individually synthesized oligonucleotides or on cellular nucleic acids as the starting material. As each method has disadvantages, we have de...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth724

    authors: Cleary MA,Kilian K,Wang Y,Bradshaw J,Cavet G,Ge W,Kulkarni A,Paddison PJ,Chang K,Sheth N,Leproust E,Coffey EM,Burchard J,McCombie WR,Linsley P,Hannon GJ

    更新日期:2004-12-01 00:00:00

  • Multiomics sequencing goes spatial.

    abstract::Microfluidic channels provide a means to deliver barcodes encoding spatial information to a tissue, which allows co-profiling of gene expression and proteins of interest in a spatially resolved manner. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/s41592-020-01043-w

    authors: Tang L

    更新日期:2021-01-01 00:00:00

  • Quantifying small numbers of antibodies with a 'near-universal' protein-DNA chimera.

    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

    authors: Burbulis I,Yamaguchi K,Yu R,Resnekov O,Brent R

    更新日期:2007-12-01 00:00:00

  • Glycomics: an integrated systems approach to structure-function relationships of glycans.

    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

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

    更新日期:2005-11-01 00:00:00

  • Lost in presumption: stochastic reactions in spatial models.

    abstract::Physical modeling is increasingly important for generating insights into intracellular processes. We describe situations in which combined spatial and stochastic aspects of chemical reactions are needed to capture the relevant dynamics of biochemical systems. ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2253

    authors: Mahmutovic A,Fange D,Berg OG,Elf J

    更新日期:2012-12-01 00:00:00

  • Anna Moroni.

    abstract:: ...

    journal_title:Nature methods

    pub_type: 评论,新闻

    doi:10.1038/s41592-018-0192-y

    authors: Marx V

    更新日期:2018-11-01 00:00:00

  • PyClone: statistical inference of clonal population structure in cancer.

    abstract::We introduce PyClone, a statistical model for inference of clonal population structures in cancers. PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced ...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2883

    authors: Roth A,Khattra J,Yap D,Wan A,Laks E,Biele J,Ha G,Aparicio S,Bouchard-Côté A,Shah SP

    更新日期:2014-04-01 00:00:00

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

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth.1255

    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

  • Tracking transmitter-gated P2X cation channel activation in vitro and in vivo.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth1144

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

    更新日期:2008-01-01 00:00:00

  • Chemically defined generation of human cardiomyocytes.

    abstract::Existing methods for human induced pluripotent stem cell (hiPSC) cardiac differentiation are efficient but require complex, undefined medium constituents that hinder further elucidation of the molecular mechanisms of cardiomyogenesis. Using hiPSCs derived under chemically defined conditions on synthetic matrices, we s...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.2999

    authors: Burridge PW,Matsa E,Shukla P,Lin ZC,Churko JM,Ebert AD,Lan F,Diecke S,Huber B,Mordwinkin NM,Plews JR,Abilez OJ,Cui B,Gold JD,Wu JC

    更新日期:2014-08-01 00:00:00

  • RESA identifies mRNA-regulatory sequences at high resolution.

    abstract::Gene expression is extensively regulated at the levels of mRNA stability, localization and translation. However, decoding functional RNA-regulatory features remains a limitation to understanding post-transcriptional regulation in vivo. Here, we developed RNA-element selection assay (RESA), a method that selects RNA el...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4121

    authors: Yartseva V,Takacs CM,Vejnar CE,Lee MT,Giraldez AJ

    更新日期:2017-02-01 00:00:00

  • Mapping DNA-protein interactions in large genomes by sequence tag analysis of genomic enrichment.

    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

    pub_type: 杂志文章

    doi:10.1038/nmeth726

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

    更新日期:2005-01-01 00:00:00

  • Independence and reproducibility across microarray platforms.

    abstract::Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth757

    authors: Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J

    更新日期:2005-05-01 00:00:00

  • Post-translational selective intracellular silencing of acetylated proteins with de novo selected intrabodies.

    abstract::The ability to selectively interfere with post-translationally modified proteins would have many biological and therapeutic applications. However, post-translational modifications cannot be selectively targeted by nucleic-acid-based interference approaches. Here we describe post-translational intracellular silencing a...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4144

    authors: Chirichella M,Lisi S,Fantini M,Goracci M,Calvello M,Brandi R,Arisi I,D'Onofrio M,Di Primio C,Cattaneo A

    更新日期:2017-03-01 00:00:00

  • Blotting protein complexes from native gels to electron microscopy grids.

    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

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

    更新日期:2012-01-08 00:00:00

  • In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain.

    abstract::High-resolution optical imaging is critical to understanding brain function. We demonstrate that three-photon microscopy at 1,300-nm excitation enables functional imaging of GCaMP6s-labeled neurons beyond the depth limit of two-photon microscopy. We record spontaneous activity from up to 150 neurons in the hippocampal...

    journal_title:Nature methods

    pub_type: 杂志文章

    doi:10.1038/nmeth.4183

    authors: Ouzounov DG,Wang T,Wang M,Feng DD,Horton NG,Cruz-Hernández JC,Cheng YT,Reimer J,Tolias AS,Nishimura N,Xu C

    更新日期:2017-04-01 00:00:00