Tools for investigating peptide-protein interactions: peptide incorporation of environment-sensitive fluorophores via on-resin derivatization.

abstract：:Isolation of monoclonal antibodies is an important technique for understanding the specificities and characteristics of antibodies that underlie the humoral immune response to a given antigen. Here we describe a technique for isolating monoclonal antibodies from human peripheral blood mononuclear cells. The protocol i...

journal_title：Nature protocols

authors： Huang J,Doria-Rose NA,Longo NS,Laub L,Lin CL,Turk E,Kang BH,Migueles SA,Bailer RT,Mascola JR,Connors M

更新日期：2013-10-01 00:00:00

abstract：:This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcr...

journal_title：Nature protocols

authors： Marchal C,Sasaki T,Vera D,Wilson K,Sima J,Rivera-Mulia JC,Trevilla-García C,Nogues C,Nafie E,Gilbert DM

更新日期：2018-05-01 00:00:00

abstract：:Cognitive computing is revolutionizing the way big data are processed and integrated, with artificial intelligence (AI) natural language processing (NLP) platforms helping researchers to efficiently search and digest the vast scientific literature. Most available platforms have been developed for biomedical researcher...

journal_title：Nature protocols

authors： Majumder EL,Billings EM,Benton HP,Martin RL,Palermo A,Guijas C,Rinschen MM,Domingo-Almenara X,Montenegro-Burke JR,Tagtow BA,Plumb RS,Siuzdak G

更新日期：2021-01-22 00:00:00

abstract：:Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine ...

journal_title：Nature protocols

authors： Zhang HB,Scheuring CF,Zhang M,Zhang Y,Wu CC,Dong JJ,Li Y

更新日期：2012-02-16 00:00:00

abstract：:Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have b...

journal_title：Nature protocols

authors： Tulkens J,De Wever O,Hendrix A

更新日期：2020-01-01 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：:Aptamers are single-stranded DNA or RNA molecules that can bind target molecules with high affinity and specificity. The conformation of an aptamer usually changes upon binding to its target analyte, and this property has been used in a wide variety of sensing applications, including detection based on fluorescence in...

journal_title：Nature protocols

authors： Liu J,Lu Y

更新日期：2006-01-01 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 scototaxis (dark/light preference) protocol is a behavioral model for fish that is being validated to assess the antianxiety effects of pharmacological agents and the behavioral effects of toxic substances, and to investigate the (epi)genetic bases of anxiety-related behavior. Briefly, a fish is placed in a centra...

journal_title：Nature protocols

authors： Maximino C,Marques de Brito T,Dias CA,Gouveia A Jr,Morato S

更新日期：2010-02-01 00:00:00

abstract：:Spectroscopic techniques such as Fourier-transform infrared (FTIR) spectroscopy are used to study interactions of light with biological materials. This interaction forms the basis of many analytical assays used in disease screening/diagnosis, microbiological studies, and forensic/environmental investigations. Advantag...

journal_title：Nature protocols

authors： Morais CLM,Paraskevaidi M,Cui L,Fullwood NJ,Isabelle M,Lima KMG,Martin-Hirsch PL,Sreedhar H,Trevisan J,Walsh MJ,Zhang D,Zhu YG,Martin FL

更新日期：2019-05-01 00:00:00

abstract：:Recombineering is an efficient method of in vivo genetic engineering applicable to chromosomal as well as episomal replicons in Escherichia coli. This method circumvents the need for most standard in vitro cloning techniques. Recombineering allows construction of DNA molecules with precise junctions without constraint...

journal_title：Nature protocols

authors： Sharan SK,Thomason LC,Kuznetsov SG,Court DL

更新日期：2009-01-01 00:00:00

abstract：:Here we describe a protocol for the production of frozen competent yeast cells that can be transformed with high efficiency using the lithium acetate/single-stranded carrier DNA/PEG method. This protocol allows the production of highly competent yeast cells that can be frozen and used at a later date and is especially...

journal_title：Nature protocols

authors： Gietz RD,Schiestl RH

更新日期：2007-01-01 00:00:00

abstract：:Fast, high-resolution mapping of heterogeneous interfaces with a wide elastic modulus range is a major goal of atomic force microscopy (AFM). This goal becomes more challenging when the nanomechanical mapping involves biomolecules in their native environment. Over the years, several AFM-based methods have been develop...

journal_title：Nature protocols

authors： Benaglia S,Gisbert VG,Perrino AP,Amo CA,Garcia R

更新日期：2018-12-01 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：:Laser-mediated gene transfection into mammalian cells has recently emerged as a powerful alternative to more traditional transfection techniques. In particular, the use of a femtosecond-pulsed laser operating in the near-infrared (NIR) region has been proven to provide single-cell selectivity, localized delivery, low ...

journal_title：Nature protocols

authors： Antkowiak M,Torres-Mapa ML,Stevenson DJ,Dholakia K,Gunn-Moore FJ

更新日期：2013-06-01 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：:The adeno-associated virus (AAV) is one of the most promising viral vectors for human gene therapy. As with any potential therapeutic system, a thorough understanding of it at the in vitro and in vivo levels is required. Over the years, numerous methods have been developed to better characterize AAV vectors. These met...

journal_title：Nature protocols

authors： Grieger JC,Choi VW,Samulski RJ

更新日期：2006-01-01 00:00:00

abstract：:Analysis of the sequence and nature of protein N termini has many applications. Defining the termini of proteins for proteome annotation in the Human Proteome Project is of increasing importance. Terminomics analysis of protease cleavage sites in degradomics for substrate discovery is a key new application. Here we de...

journal_title：Nature protocols

authors： Kleifeld O,Doucet A,Prudova A,auf dem Keller U,Gioia M,Kizhakkedathu JN,Overall CM

更新日期：2011-09-22 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：:Studies on colonic cells in the lamina propria (LP) of mice are important for understanding the cellular and immune responses in the gut, especially in inflammatory bowel diseases (such as morbus crohn and colitis ulcerosa). This protocol details a method to isolate LP cells and characterize freshly isolated cells by ...

journal_title：Nature protocols

authors： Weigmann B,Tubbe I,Seidel D,Nicolaev A,Becker C,Neurath MF

更新日期：2007-01-01 00:00:00

abstract：:An optimized procedure for the efficient preparation of 2-heptyl-3-hydroxy-4(1H)-quinolone (Pseudomonas quinolone signal or PQS) and a diverse range of structurally related 2-alkyl-4-quinolones with biological activity is presented. The two-step synthesis begins with the formation of α-chloro ketones by the coupling o...

journal_title：Nature protocols

authors： Hodgkinson JT,Galloway WR,Welch M,Spring DR

更新日期：2012-05-24 00:00:00

abstract：:This protocol describes pulsed-field gel electrophoresis (PFGE), a method developed for separation of large DNA molecules. Whereas standard DNA gel electrophoresis commonly resolves fragments up to approximately 50 kb in size, PFGE fractionates DNA molecules up to 10 Mb. The mechanism driving these separations exploit...

journal_title：Nature protocols

authors： Herschleb J,Ananiev G,Schwartz DC

更新日期：2007-01-01 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：:Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and p...

journal_title：Nature protocols

authors： Butler HJ,Ashton L,Bird B,Cinque G,Curtis K,Dorney J,Esmonde-White K,Fullwood NJ,Gardner B,Martin-Hirsch PL,Walsh MJ,McAinsh MR,Stone N,Martin FL

更新日期：2016-04-01 00:00:00

abstract：:Methods for installing natural and unnatural amino acids and their modifications into proteins in a benign and precise manner are highly sought-after in protein science. Here we describe a protocol for 'post-translational mutagenesis' that enables the programmed installation of protein side chains through the use of r...

journal_title：Nature protocols

authors： Wright TH,Davis BG

更新日期：2017-10-01 00:00:00

abstract：:This protocol describes an efficient method to site-specifically label cell-surface or purified proteins with chemical probes in two steps: probe incorporation mediated by enzymes (PRIME) followed by chelation-assisted copper-catalyzed azide-alkyne cycloaddition (CuAAC). In the PRIME step, Escherichia coli lipoic acid...

journal_title：Nature protocols

authors： Uttamapinant C,Sanchez MI,Liu DS,Yao JZ,Ting AY

更新日期：2013-08-01 00:00:00

abstract：:In cell affinity chromatography, type-specific cell separation is based on the interaction between cell-surface receptors and an immobilized ligand on a stationary matrix. This protocol describes the preparation of monolithic polyacrylamide and polydimethylacrylamide cryogel affinity matrices that can be used as a gen...

journal_title：Nature protocols

authors： Kumar A,Srivastava A

更新日期：2010-11-01 00:00:00

abstract：:Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long read...

journal_title：Nature protocols

authors： Yue JX,Liti G

更新日期：2018-06-01 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：: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