Analysis of protein glycosylation by mass spectrometry.

abstract：:Positron emission tomography (PET) is a sensitive and noninvasive imaging method that is widely used to explore molecular events in living subjects. PET can precisely and quantitatively evaluate cellular apoptosis, which has a crucial role in various physiological and pathological processes. In this protocol, we descr...

journal_title：Nature protocols

authors： Wang Z,Wang F,Hida N,Kiesewetter DO,Tian J,Niu G,Chen X

更新日期：2015-05-01 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：:The Strep-tag II is an eight-residue minimal peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) that exhibits intrinsic affinity toward streptavidin and can be fused to recombinant proteins in various fashions. We describe a protocol that enables quick and mild purification of corresponding Strep-tag II fusion protein...

journal_title：Nature protocols

authors： Schmidt TG,Skerra A

更新日期：2007-01-01 00:00:00

abstract：:Forebrain γ-aminobutyric acid (GABA) interneurons have crucial roles in high-order brain function via modulating network activities and plasticity, and they are implicated in many psychiatric disorders. Availability of enriched functional human forebrain GABA interneurons, especially those from people affected by GABA...

journal_title：Nature protocols

authors： Liu Y,Liu H,Sauvey C,Yao L,Zarnowska ED,Zhang SC

更新日期：2013-09-01 00:00:00

abstract：:Hi-C is a powerful method that provides pairwise information on genomic regions in spatial proximity in the nucleus. Hi-C requires millions of cells as input and, as genome organization varies from cell to cell, a limitation of Hi-C is that it only provides a population average of genome conformations. We developed si...

journal_title：Nature protocols

authors： Nagano T,Lubling Y,Yaffe E,Wingett SW,Dean W,Tanay A,Fraser P

更新日期：2015-12-01 00:00:00

abstract：:The glycocalyx comprises glycosylated proteins and lipids and fcorms the outermost layer of cells. It is involved in fundamental inter- and intracellular processes, including non-self-cell and self-cell recognition, cell signaling, cellular structure maintenance, and immune protection. Characterization of the glycocal...

journal_title：Nature protocols

authors： Li Q,Xie Y,Wong M,Barboza M,Lebrilla CB

更新日期：2020-08-01 00:00:00

abstract：:A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uch...

journal_title：Nature protocols

authors： Källberg M,Wang H,Wang S,Peng J,Wang Z,Lu H,Xu J

更新日期：2012-07-19 00:00:00

abstract：:Many techniques have been developed for studying inducible gene expression, but all of them are multicomponent systems consisting of cis-acting elements at the DNA or RNA level, trans-acting regulator proteins and/or small molecules as inducers. RNA thermometers are the only known single-component regulators of gene e...

journal_title：Nature protocols

authors： Neupert J,Bock R

更新日期：2009-01-01 00:00:00

abstract：:Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA...

journal_title：Nature protocols

authors： van Rooden EJ,Florea BI,Deng H,Baggelaar MP,van Esbroeck ACM,Zhou J,Overkleeft HS,van der Stelt M

更新日期：2018-04-01 00:00:00

abstract：:Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows t...

journal_title：Nature protocols

authors： Takahashi H,Lassmann T,Murata M,Carninci P

更新日期：2012-02-23 00:00:00

abstract：:Several noncanonical initial nucleotides (NCINs) have been found to cap RNAs and possibly regulate RNA stability, transcription and translation. NAD+ is one of the NCINs that has recently been discovered to cap RNAs in a wide range of species. Identification of the NAD+-capped RNAs (NAD-RNAs) could help to unveil the ...

journal_title：Nature protocols

authors： Shao X,Zhang H,Yang Z,Zhong H,Xia Y,Cai Z

更新日期：2020-09-01 00:00:00

abstract：:Cyclodepsipeptides are cyclic peptides in which at least one amide link on the backbone is replaced with an ester link. These natural products present a high structural diversity that corresponds to a broad range of biological activities. Therefore, they are very promising pharmaceutical candidates. Most of the cyclod...

journal_title：Nature protocols

authors： Pelay-Gimeno M,Albericio F,Tulla-Puche J

更新日期：2016-10-01 00:00:00

abstract：:Using siRNAs to genetically manipulate immune cells is important to both basic immunological studies and therapeutic applications. However, siRNA delivery is challenging because primary immune cells are often sensitive to the delivery materials and generate immune responses. We have recently developed an amphiphilic d...

journal_title：Nature protocols

authors： Chen J,Ellert-Miklaszewska A,Garofalo S,Dey AK,Tang J,Jiang Y,Clément F,Marche PN,Liu X,Kaminska B,Santoni A,Limatola C,Rossi JJ,Zhou J,Peng L

更新日期：2021-01-01 00:00:00

abstract：:We describe a protocol for the insertion of ultrashort single-walled carbon nanotubes (SWCNTs) to form nanopores in a Montal-Mueller lipid bilayer. The SWCNTs are designed to bind to a specific analyte of interest; binding will result in the reduction of current in single-channel recording experiments. The first stage...

journal_title：Nature protocols

authors： Liu L,Xie J,Li T,Wu HC

更新日期：2015-11-01 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：:Dynamic interplay between intracellular organelles requires a particular functional apposition of membrane structures. The organelles involved come into close contact, but do not fuse, thereby giving rise to notable microdomains; these microdomains allow rapid communication between the organelles. Plasma membrane-asso...

journal_title：Nature protocols

authors： Suski JM,Lebiedzinska M,Wojtala A,Duszynski J,Giorgi C,Pinton P,Wieckowski MR

更新日期：2014-02-01 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：:We describe a simple and versatile scheme to prepare a series of poly(ethylene glycol)-based bidentate ligands that permit strong interactions with colloidal semiconductor nanocrystals (quantum dots, QDs) and gold nanoparticles (AuNPs) alike and promote their dispersion in aqueous solutions. These ligands are synthesi...

journal_title：Nature protocols

authors： Mei BC,Susumu K,Medintz IL,Mattoussi H

更新日期：2009-01-01 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：: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 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：:RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially expressed genes across different conditions (e.g., tissues, perturbations) while opt...

journal_title：Nature protocols

authors： Anders S,McCarthy DJ,Chen Y,Okoniewski M,Smyth GK,Huber W,Robinson MD

更新日期：2013-09-01 00:00:00

abstract：:A big challenge in proteomics is the identification of cell-type-specific proteomes in vivo. This protocol describes how to label, purify and identify cell-type-specific proteomes in living mice. To make this possible, we created a Cre-recombinase-inducible mouse line expressing a mutant methionyl-tRNA synthetase (L27...

journal_title：Nature protocols

authors： Alvarez-Castelao B,Schanzenbächer CT,Langer JD,Schuman EM

更新日期：2019-02-01 00:00:00

abstract：:At present, several assays that use radioisotope labeling to quantify the degradation of long-lived proteins have been developed to measure autophagic flux. Here, we describe a nonradioactive pulse-chase protocol using L-azidohomoalanine (AHA) labeling to quantify long-lived protein degradation during autophagy. AHA i...

journal_title：Nature protocols

authors： Wang J,Zhang J,Lee YM,Ng S,Shi Y,Hua ZC,Lin Q,Shen HM

更新日期：2017-12-01 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：:The forced swim test (FST) is one of the most commonly used animal models for assessing antidepressant-like behavior. This protocol details using the FST in rats, which takes place over 48 h and is followed by the video analysis of the behavior. The swim test involves the scoring of active (swimming and climbing) or p...

journal_title：Nature protocols

authors： Slattery DA,Cryan JF

更新日期：2012-05-03 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：: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 protein called 'small ubiquitin-like modifier' (SUMO) is post-translationally linked to target proteins at the ɛ-amino group of lysine residues. This 'SUMOylation' alters the behavior of the target protein, a change that is utilized to regulate diverse cellular processes. Understanding the target-specific conseque...

journal_title：Nature protocols

authors： Tammsalu T,Matic I,Jaffray EG,Ibrahim AF,Tatham MH,Hay RT

更新日期：2015-09-01 00:00:00

abstract：:The analysis of highly hydrophobic proteins is still an analytical challenge. Using a recombinant gamma-aminobutyric acid A (GABAA)-receptor subunit as a model protein, we developed a gel-based proteomic approach for high MS/MS-peptide sequence coverage identification. Protein samples were separated by multi-dimension...

journal_title：Nature protocols

authors： Kang SU,Fuchs K,Sieghart W,Pollak A,Csaszar E,Lubec G

更新日期：2009-01-01 00:00:00