High-throughput identification of proteins with AMPylation using self-assembled human protein (NAPPA) microarrays.

abstract：:Optogenetic tools provide users the ability to photocontrol the activity of cells. Commonly, activation is achieved by expression of proteins from photosynthetic organisms, for example, microbial opsins (e.g., ChR2). Alternatively, a sister approach, synthetic optogenetics, enables photocontrol over proteins of mammal...

journal_title：Nature protocols

authors： Carmi I,De Battista M,Maddalena L,Carroll EC,Kienzler MA,Berlin S

更新日期：2019-03-01 00:00:00

abstract：:In recent years, many mouse models have been developed to mark and trace the fate of adult cell populations using fluorescent proteins. High-resolution visualization of such fluorescent markers in their physiological setting is thus an important aspect of adult stem cell research. Here we describe a protocol to produc...

journal_title：Nature protocols

authors： Snippert HJ,Schepers AG,Delconte G,Siersema PD,Clevers H

更新日期：2011-07-28 00:00:00

abstract：:N-Succinimidyl 3-(di-tert-butyl[(18)F]fluorosilyl)benzoate ([(18)F]SiFB) is a highly reactive prosthetic group for radiolabeling of proteins for use in positron emission tomography (PET). It is similar to N-succinimidyl-4-[(18)F]fluorobenzoate ([(18)F]SFB), the 'gold-standard' prosthetic group for protein (18)F-labeli...

journal_title：Nature protocols

authors： Kostikov AP,Chin J,Orchowski K,Schirrmacher E,Niedermoser S,Jurkschat K,Iovkova-Berends L,Wängler C,Wängler B,Schirrmacher R

更新日期：2012-11-01 00:00:00

abstract：:The human stomach contains two primary domains: the corpus, which contains the fundic epithelium, and the antrum. Each of these domains has distinct cell types and functions, and therefore each presents with unique disease pathologies. Here, we detail two protocols to differentiate human pluripotent stem cells (hPSCs)...

journal_title：Nature protocols

authors： Broda TR,McCracken KW,Wells JM

更新日期：2019-01-01 00:00:00

abstract：:Methods development in chromatography is a time-consuming, trial-and-error process that requires laborious experimentation. We describe a high-throughput screening (HTS) protocol for the rapid identification of chromatographic steps for protein purification from cell-free expression broths. Broths containing the prote...

journal_title：Nature protocols

authors： Rege K,Heng M

更新日期：2010-03-01 00:00:00

abstract：:The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually perform...

journal_title：Nature protocols

authors： Ben-David U,Mayshar Y,Benvenisty N

更新日期：2013-05-01 00:00:00

abstract：:Genetically encoded fluorescent proteins (FPs) are highly utilized in cell biology research to study proteins of interest or signal processes using biosensors. To perform well in specific applications, these FPs require a multitude of tailored properties. It is for this reason that they need to be optimized by using m...

journal_title：Nature protocols

authors： Bindels DS,Postma M,Haarbosch L,van Weeren L,Gadella TWJ Jr

更新日期：2020-02-01 00:00:00

abstract：:We describe the use of a microfabricated cell culture substrate, consisting of a uniform array of closely spaced, vertical, elastomeric microposts, to study the effects of substrate rigidity on cell function. Elastomeric micropost substrates are micromolded from silicon masters comprised of microposts of different hei...

journal_title：Nature protocols

authors： Yang MT,Fu J,Wang YK,Desai RA,Chen CS

更新日期：2011-02-01 00:00:00

abstract：:This protocol describes a directed evolution method for in vitro mutagenesis and recombination of polynucleotide sequences. The staggered extension process (StEP) is essentially a modified PCR that uses highly abbreviated annealing and extension steps to generate staggered DNA fragments and promote crossover events al...

journal_title：Nature protocols

authors： Zhao H,Zha W

更新日期：2006-01-01 00:00:00

abstract：:In most organisms, one crossover (CO) event inhibits the chances of another nearby event. The term used to describe this phenomenon is 'CO interference'. Here, we describe a protocol for quickly generating large data sets that are amenable to CO interference analysis in the flowering plant, Arabidopsis thaliana. We em...

journal_title：Nature protocols

authors： Berchowitz LE,Copenhaver GP

更新日期：2008-01-01 00:00:00

abstract：:The elucidation of protein-protein interaction networks is a crucial task in the postgenomic era. In this protocol, we describe our approach to discover protein-protein interactions using the surface plasmon resonance technique coupled to mass spectrometry (MS). A peptide or a protein is immobilized on a sensor chip a...

journal_title：Nature protocols

authors： Madeira A,Ohman E,Nilsson A,Sjögren B,Andrén PE,Svenningsson P

更新日期：2009-01-01 00:00:00

abstract：:Gene tagging with fluorescent proteins is essential for investigations of the dynamic properties of cellular proteins. CRISPR-Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and allows functionality and physiological expression of the fusion protein. ...

journal_title：Nature protocols

authors： Koch B,Nijmeijer B,Kueblbeck M,Cai Y,Walther N,Ellenberg J

更新日期：2018-06-01 00:00:00

abstract：:Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP...

journal_title：Nature protocols

authors： Toby TK,Fornelli L,Srzentić K,DeHart CJ,Levitsky J,Friedewald J,Kelleher NL

更新日期：2019-01-01 00:00:00

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：:The unprecedented increase in the throughput of DNA sequencing driven by next-generation technologies now allows efficient analysis of the complete protein-coding regions of genomes (exomes) for multiple samples in a single sequencing run. However, sample preparation and targeted enrichment of multiple samples has bec...

journal_title：Nature protocols

authors： Harakalova M,Mokry M,Hrdlickova B,Renkens I,Duran K,van Roekel H,Lansu N,van Roosmalen M,de Bruijn E,Nijman IJ,Kloosterman WP,Cuppen E

更新日期：2011-11-03 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：: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：:Targeted nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), have provided researchers with the ability to manipulate nearly any genomic sequence in hu...

journal_title：Nature protocols

authors： Liu J,Gaj T,Yang Y,Wang N,Shui S,Kim S,Kanchiswamy CN,Kim JS,Barbas CF 3rd

更新日期：2015-11-01 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：:Establishing a small animal model that accurately recapitulates hepatotropic pathogens, including hepatitis C virus (HCV) infection and immunopathogenesis, is essential for the study of hepatitis virus-induced liver disease and for therapeutics development. This protocol describes our recently developed humanized mous...

journal_title：Nature protocols

authors： Bility MT,Zhang L,Washburn ML,Curtis TA,Kovalev GI,Su L

更新日期：2012-09-01 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：:This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled micros...

journal_title：Nature protocols

authors： Kong L,Zhang P,Wang G,Yu J,Setlow P,Li YQ

更新日期：2011-05-01 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：:The Golgi apparatus undergoes extensive disassembly during mitosis and reassembly in post-mitotic daughter cells. This process has been mimicked in vitro by treating Golgi membranes with mitotic and interphase cytosol. To determine the minimal machinery that controls the morphological change, we have developed a defin...

journal_title：Nature protocols

authors： Tang D,Xiang Y,Wang Y

更新日期：2010-04-01 00:00:00

abstract：:In situ mRNA hybridization is one of the most powerful techniques for analyzing patterns of gene expression. However, its usefulness is limited in complex plant tissues by the need to fix, embed and section samples before localizing the desired mRNA. Here we present a robust whole-mount in situ hybridization method th...

journal_title：Nature protocols

authors： Rozier F,Mirabet V,Vernoux T,Das P

更新日期：2014-10-01 00:00:00

abstract：:Carbohydrate microarrays have received considerable attention as an advanced technology for the rapid analysis of carbohydrate-protein interactions. This protocol provides detailed procedures for the preparation of carbohydrate microarrays by immobilizing hydrazide-conjugated carbohydrates on epoxide-derivatized glass...

journal_title：Nature protocols

authors： Park S,Lee MR,Shin I

更新日期：2007-01-01 00:00:00

abstract：:The fabrication of 3D tissues retaining the original functions of tissues/organs in vitro is crucial for optimal tissue engineering and regenerative medicine. The fabrication of 3D tissues also contributes to the establishment of in vitro tissue/organ models for drug screening. Our laboratory has developed a fabricati...

journal_title：Nature protocols

authors： Haraguchi Y,Shimizu T,Sasagawa T,Sekine H,Sakaguchi K,Kikuchi T,Sekine W,Sekiya S,Yamato M,Umezu M,Okano T

更新日期：2012-04-05 00:00:00

abstract：:Growing evidence indicates that RNA G-quadruplexes have important roles in various processes such as transcription, translation, regulation of telomere length, and formation of telomeric heterochromatin. Investigation of RNA G-quadruplex structures associated with biological events is therefore essential to understand...

journal_title：Nature protocols

authors： Bao HL,Xu Y

更新日期：2018-04-01 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：:Mass spectrometry imaging (MSI) enables label-free spatial mapping of hundreds of biomolecules in tissue sections. This capability provides valuable information on tissue heterogeneity that is difficult to obtain using population-averaged assays. Despite substantial developments in both instrumentation and methodology...

journal_title：Nature protocols

authors： Yin R,Burnum-Johnson KE,Sun X,Dey SK,Laskin J

更新日期：2019-12-01 00:00:00