Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.

abstract：:Reversible thiol oxidation of cysteine residues occurs in many intracellular catalytic and signaling processes. Here we describe an optimized protocol, which can be completed in ∼5 d, to unambiguously identify specific cysteine residues that are transiently and reversibly oxidized by comparing two complex biological s...

journal_title：Nature protocols

authors： García-Santamarina S,Boronat S,Domènech A,Ayté J,Molina H,Hidalgo E

更新日期：2014-05-01 00:00:00

abstract：:Realizing the potential of human embryonic stem cells (hESCs) in research and commercial applications requires generic protocols for culture, expansion and genetic modification that function between multiple lines. Here we describe a feeder-free hESC culture protocol that was tested in 13 independent hESC lines derive...

journal_title：Nature protocols

authors： Braam SR,Denning C,Matsa E,Young LE,Passier R,Mummery CL

更新日期：2008-01-01 00:00:00

abstract：:Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin...

journal_title：Nature protocols

authors： Graf M,Lihter M,Thakur M,Georgiou V,Topolancik J,Ilic BR,Liu K,Feng J,Astier Y,Radenovic A

更新日期：2019-04-01 00:00:00

abstract：:One of the challenges for modern neuroscience is to understand the rules of concerted neuronal function in vivo. This question can be addressed using noninvasive high-resolution imaging techniques like two-photon microscopy. This protocol describes a versatile approach for in vivo two-photon calcium imaging of neural ...

journal_title：Nature protocols

authors： Garaschuk O,Milos RI,Konnerth A

更新日期：2006-01-01 00:00:00

abstract：:Live-imaging technology has markedly advanced in the field of neural injury and axon degeneration; however, studies are still predominantly performed in in vitro settings such as cultured neuronal cells or in model organisms such as Caenorhabditis elegans in which axons lack glial wrappings. We recently developed a ne...

journal_title：Nature protocols

authors： Fang Y,Soares L,Bonini NM

更新日期：2013-04-01 00:00:00

abstract：:'Adult' or 'somatic' stem cells harbor an intrinsic ability to regenerate tissues. Heterogeneity of such stem cells along the gastrointestinal tract yields the known segmental specificity of this organ and may contribute to the pathology of certain enteric conditions. Here we detail technology for the generation of 'l...

journal_title：Nature protocols

authors： Duleba M,Yamamoto Y,Neupane R,Rao W,Xie J,Qi Y,Liew AA,Niroula S,Zhang Y,Mahalingam R,Wang S,Goller K,Ajani JA,Vincent M,Ho KY,Hou JK,Hyams JS,Sylvester FA,Crum CP,McKeon F,Xian W

更新日期：2020-05-01 00:00:00

abstract：:The increasing multi-resistance of pathogenic bacteria requires the development of novel classes of antibiotics. Antimicrobial host defense peptides represent one promising class. Here we describe a protocol for screening large numbers of peptides against any microbe of interest. Peptides synthesized on a cellulose su...

journal_title：Nature protocols

authors： Hilpert K,Hancock RE

更新日期：2007-01-01 00:00:00

abstract：:This protocol describes the synthesis of oligo(poly(ethylene glycol) fumarate) (OPF; 1-35 kDa; a polymer useful for tissue engineering applications) by a one-pot reaction of poly(ethylene glycol) (PEG) and fumaryl chloride. The procedure involves three parts: dichloromethane and PEG are first dried; the reaction step ...

journal_title：Nature protocols

authors： Kinard LA,Kasper FK,Mikos AG

更新日期：2012-05-31 00:00:00

abstract：:Here, we describe a simple protocol for the design and construction of a laser-guided direct writing (LGDW) system able to micropattern the self-assembly of liver sinusoid-like structures with micrometer resolution in vitro. To the best of our knowledge, LGDW is the only technique able to pattern cells "on the fly" wi...

journal_title：Nature protocols

authors： Nahmias Y,Odde DJ

更新日期：2006-01-01 00:00:00

abstract：:Fluorescent microspheres are commonly used to assess bone blood supply in large animals, but the technique is not widely used in smaller mammals, as traditional methods such as reference blood sampling, ventilation and catheterization are not easily applied. This protocol describes a viable alternative for measuring b...

journal_title：Nature protocols

authors： Serrat MA

更新日期：2009-01-01 00:00:00

abstract：:Adult stem cell-based organoid technology is a versatile tool for the generation and long-term maintenance of near-native 3D epithelial tissues in vitro. The generation of cancer organoids from primary patient material enables a range of therapeutic agents to be tested in the resulting organoid cultures. Patient-deriv...

journal_title：Nature protocols

authors： Driehuis E,Kretzschmar K,Clevers H

更新日期：2020-10-01 00:00:00

abstract：:More than 400,000 people each year suffer adverse effects following bites from venomous snakes. However, snake venom is also a rich source of bioactive molecules with known or potential therapeutic applications. Manually 'milking' snakes is the most common method to obtain venom. Safer alternative methods to produce v...

journal_title：Nature protocols

authors： Puschhof J,Post Y,Beumer J,Kerkkamp HM,Bittenbinder M,Vonk FJ,Casewell NR,Richardson MK,Clevers H

更新日期：2021-01-27 00:00:00

abstract：:Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by im...

journal_title：Nature protocols

authors： Susaki EA,Tainaka K,Perrin D,Yukinaga H,Kuno A,Ueda HR

更新日期：2015-11-01 00:00:00

abstract：:The systematic mapping of protein interactions by bait-prey techniques, including affinity purification-mass spectrometry or the yeast two-hybrid system, contributes a unique and relevant perspective on the comprehensive picture of cellular machines. We describe here a protocol for statistical analysis of node-and-edg...

journal_title：Nature protocols

authors： Chiang T,Scholtens D

更新日期：2009-01-01 00:00:00

abstract：:Biominerals serve as critical structures of living systems and play important roles in biochemical processes. Understanding their crystallization mechanisms is therefore central to many areas of biology, biogeoscience, and biochemistry. Some biominerals, such as bone and dentin, are hierarchical nanocomposite structur...

journal_title：Nature protocols

authors： Zhang X,He Y,Liu J,Bowden ME,Kovarik L,Mao SX,Wang C,De Yoreo JJ,Rosso KM

更新日期：2018-09-01 00:00:00

abstract：:The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA dete...

journal_title：Nature protocols

authors： Nam JM,Jang KJ,Groves JT

更新日期：2007-01-01 00:00:00

abstract：:The partial reduction of electron-deficient pyrroles using either Birch (Li/NH(3)) or ammonia-free (Li/di-tert-butyl biphenyl) conditions allows formation of pyrroline compounds in good yield and, when combined with a reductive alkylation or similar approach, leads to highly functionalized, synthetically useful compou...

journal_title：Nature protocols

authors： Donohoe TJ,Thomas RE

更新日期：2007-01-01 00:00:00

abstract：:A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It...

journal_title：Nature protocols

authors： Ulitsky I,Maron-Katz A,Shavit S,Sagir D,Linhart C,Elkon R,Tanay A,Sharan R,Shiloh Y,Shamir R

更新日期：2010-02-01 00:00:00

abstract：:This protocol describes a method for direct labeling and detection of small RNAs present in total RNA by splinted ligation. The assay uses a small RNA-specific bridge oligonucleotide to form base pairs with the small RNA and a 5'-end-radiolabeled ligation oligonucleotide. The captured small RNA is directly labeled by ...

journal_title：Nature protocols

authors： Maroney PA,Chamnongpol S,Souret F,Nilsen TW

更新日期：2008-01-01 00:00:00

abstract：:In the version of this protocol originally published, the caption for Fig. 3 was erroneously placed with Fig. 4, and that for Fig. 4 was placed with Fig. 3. This error has been corrected in the HTML and PDF versions of the paper. ...

journal_title：Nature protocols

authors： Cruz-Acuña R,Quirós M,Huang S,Siuda D,Spence JR,Nusrat A,García AJ

更新日期：2019-07-01 00:00:00

abstract：:The bimolecular fluorescence complementation (BiFC) assay is a powerful tool for visualizing and identifying protein interactions in living cells. This assay is based on the principle of protein-fragment complementation, using two nonfluorescent fragments derived from fluorescent proteins. When two fragments are broug...

journal_title：Nature protocols

authors： Shyu YJ,Hiatt SM,Duren HM,Ellis RE,Kerppola TK,Hu CD

更新日期：2008-01-01 00:00:00

abstract：:Live single-cell mass spectrometry (live MS) provides a mass spectrum that shows thousands of metabolite peaks from a single live plant cell within minutes. By using an optical microscope, a cell is chosen for analysis and a metal-coated nanospray microcapillary tip is used to remove the cell's contents. After adding ...

journal_title：Nature protocols

authors： Fujii T,Matsuda S,Tejedor ML,Esaki T,Sakane I,Mizuno H,Tsuyama N,Masujima T

更新日期：2015-09-01 00:00:00

abstract：:Mouse embryonic stem cells (mESCs) are key tools for genetic engineering, development of stem cell-based therapies and basic research on pluripotency and early lineage commitment. However, successful derivation of germline-competent embryonic stem cell lines has, until recently, been limited to a small number of inbre...

journal_title：Nature protocols

authors： Czechanski A,Byers C,Greenstein I,Schrode N,Donahue LR,Hadjantonakis AK,Reinholdt LG

更新日期：2014-03-01 00:00:00

abstract：:This protocol represents a novel enzyme-luminescence method to detect dopamine sensitively and rapidly with high temporal resolution. In principle, dopamine is first oxidized with tyramine oxidase to produce H(2)O(2), and then the produced H(2)O(2) reacts with luminol to generate chemiluminescence in the presence of h...

journal_title：Nature protocols

authors： Shinohara H,Wang F,Hossain SM

更新日期：2008-01-01 00:00:00

abstract：:Periodontal disease (PD) is a common dental disease associated with the interaction between dysbiotic oral microbiota and host immunity. It is a prevalent disease, resulting in loss of gingival tissue, periodontal ligament, cementum and alveolar bone. PD is a major form of tooth loss in the adult population. Experimen...

journal_title：Nature protocols

authors： Marchesan J,Girnary MS,Jing L,Miao MZ,Zhang S,Sun L,Morelli T,Schoenfisch MH,Inohara N,Offenbacher S,Jiao Y

更新日期：2018-10-01 00:00:00

abstract：:Limbal stem cells (LSCs) have an important role in the maintenance of the corneal surface epithelium, and autologous cultured limbal epithelial cell transplantations have contributed substantially to the treatment of the visually disabling condition known as LSC deficiency. In this protocol, we describe a method of es...

journal_title：Nature protocols

authors： Mariappan I,Maddileti S,Savy S,Tiwari S,Gaddipati S,Fatima A,Sangwan VS,Balasubramanian D,Vemuganti GK

更新日期：2010-08-01 00:00:00

abstract：:With the advent of massively parallel sequencing, considerable work has gone into adapting chromosome conformation capture (3C) techniques to study chromosomal architecture at a genome-wide scale. We recently demonstrated that the inactive murine X chromosome adopts a bipartite structure using a novel 3C protocol, ter...

journal_title：Nature protocols

authors： Ramani V,Cusanovich DA,Hause RJ,Ma W,Qiu R,Deng X,Blau CA,Disteche CM,Noble WS,Shendure J,Duan Z

更新日期：2016-11-01 00:00:00

abstract：:Differentiation of stem cells to hepatocytes has industrial applications, as well as the potential to develop new therapeutic strategies for liver disease. The protocol described here, sequentially using cytokines that are known to have a role in liver embryonic development, efficiently differentiates rat multipotent ...

journal_title：Nature protocols

authors： Roelandt P,Sancho-Bru P,Pauwelyn K,Verfaillie C

更新日期：2010-07-01 00:00:00

abstract：:This protocol provides a detailed procedure for the chemical synthesis of proteins through native chemical ligation of peptide hydrazides. The two crucial stages of this protocol are (i) the solid-phase synthesis of peptide hydrazides via Fmoc chemistry and (ii) the native chemical ligation of peptide hydrazides throu...

journal_title：Nature protocols

authors： Zheng JS,Tang S,Qi YK,Wang ZP,Liu L

更新日期：2013-12-01 00:00:00

abstract：:Single-cell electroporation allows transfection of plasmid DNA or macromolecules into individual living cells using modified patch electrodes and common electrophysiological equipment. This protocol is optimized for rapid in vivo electroporation of Xenopus laevis tadpole brains with DNA, dextrans, morpholinos and comb...

journal_title：Nature protocols

authors： Bestman JE,Ewald RC,Chiu SL,Cline HT

更新日期：2006-01-01 00:00:00