High-throughput ballistic injection nanorheology to measure cell mechanics.

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：: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：:Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions ...

journal_title：Nature protocols

authors： Jeffries CM,Graewert MA,Blanchet CE,Langley DB,Whitten AE,Svergun DI

更新日期：2016-11-01 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：: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：:The pig has emerged as an important large animal model in biomedical and pharmaceutical research. We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in pigs by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection of a plasmid encoding ...

journal_title：Nature protocols

authors： Ivics Z,Garrels W,Mátés L,Yau TY,Bashir S,Zidek V,Landa V,Geurts A,Pravenec M,Rülicke T,Kues WA,Izsvák Z

更新日期：2014-04-01 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：:Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers thr...

journal_title：Nature protocols

authors： Wittkop T,Emig D,Truss A,Albrecht M,Böcker S,Baumbach J

更新日期：2011-03-01 00:00:00

abstract：:This protocol describes a cell-free system for studying vertebrate centromere and kinetochore formation. We reconstitute tandem arrays of centromere protein A (CENP-A) nucleosomes as a substrate for centromere and kinetochore assembly. These chromatin substrates are immobilized on magnetic beads and then incubated in ...

journal_title：Nature protocols

authors： Guse A,Fuller CJ,Straight AF

更新日期：2012-10-01 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

abstract：:The ability to isolate and analyze rare circulating tumor cells (CTCs) has the potential to further our understanding of cancer metastasis and enhance the care of cancer patients. In this protocol, we describe the procedure for isolating rare CTCs from blood samples by using tumor antigen-independent microfluidic CTC-...

journal_title：Nature protocols

authors： Karabacak NM,Spuhler PS,Fachin F,Lim EJ,Pai V,Ozkumur E,Martel JM,Kojic N,Smith K,Chen PI,Yang J,Hwang H,Morgan B,Trautwein J,Barber TA,Stott SL,Maheswaran S,Kapur R,Haber DA,Toner M

更新日期：2014-03-01 00:00:00

abstract：:The development of single-molecule switching (SMS) fluorescence microscopy (also called single-molecule localization microscopy) over the last decade has enabled researchers to image cell biological structures at unprecedented resolution. Using two opposing objectives in a so-called 4Pi geometry doubles the available ...

journal_title：Nature protocols

authors： Wang J,Allgeyer ES,Sirinakis G,Zhang Y,Hu K,Lessard MD,Li Y,Diekmann R,Phillips MA,Dobbie IM,Ries J,Booth MJ,Bewersdorf J

更新日期：2020-12-16 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：:This protocol describes a method for the extraction of DNA from elephant ivory. These techniques are being used to assign geographic origin to poached ivory by comparing the ivory genotype to a geographic-based gene frequency map, developed separately. The method has three components: ivory pulverization, decalcificat...

journal_title：Nature protocols

authors： Mailand C,Wasser SK

更新日期：2007-01-01 00:00:00

abstract：:Single-cell gene expression analysis has contributed to a better understanding of the transcriptional heterogeneity in a variety of model systems, including those used in research in developmental, cancer and stem cell biology. Nowadays, technological advances facilitate the generation of large gene expression data se...

journal_title：Nature protocols

authors： Durruthy-Durruthy R,Gottlieb A,Heller S

更新日期：2015-03-01 00:00:00

abstract：:This protocol outlines steps for optimizing the transfection of adherent primary mammalian cells using the readily available off-the-shelf cationic polymer, 25-kDa branched polyethylenimine (bPEI25). Transfection efficiency of cationic polymers varies among cell lines and is highly dependent on the conditions and envi...

journal_title：Nature protocols

authors： Hsu CY,Uludağ H

更新日期：2012-04-19 00:00:00

abstract：:The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specif...

journal_title：Nature protocols

authors： Mulvey CM,Breckels LM,Geladaki A,Britovšek NK,Nightingale DJH,Christoforou A,Elzek M,Deery MJ,Gatto L,Lilley KS

更新日期：2017-06-01 00:00:00

abstract：:The analysis of large microbiome data sets holds great promise for the delineation of the biological and metabolic functioning of living organisms and their role in the environment. In the midst of this genomic puzzle, viruses, especially those that infect microbial communities, represent a major reservoir of genetic ...

journal_title：Nature protocols

authors： Paez-Espino D,Pavlopoulos GA,Ivanova NN,Kyrpides NC

更新日期：2017-08-01 00:00:00

abstract：:We present a protocol for visualizing and quantifying single mRNA molecules in mammalian (mouse and human) tissues. In the approach described here, sets of about 50 short oligonucleotides, each labeled with a single fluorophore, are hybridized to target mRNAs in tissue sections. Each set binds to a single mRNA molecul...

journal_title：Nature protocols

authors： Lyubimova A,Itzkovitz S,Junker JP,Fan ZP,Wu X,van Oudenaarden A

更新日期：2013-09-01 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：: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：: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：:A protocol for ester condensation between equimolar amounts of carboxylic acids and alcohols catalyzed by bulky diarylammonium pentafluorobenzenesulfonate is described. We also present procedures for the synthesis of N-(2,6-diisopropylphenyl)-N-mesitylammonium pentafluorobenzenesulfonate. The present ester condensatio...

journal_title：Nature protocols

authors： Sakakura A,Nakagawa S,Ishihara K

更新日期：2007-01-01 00:00:00

abstract：:The research community is in a race to understand the molecular mechanisms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, to repurpose currently available antiviral drugs and to develop new therapies and vaccines against coronavirus disease 2019 (COVID-19). One major challenge in achieving ...

journal_title：Nature protocols

authors： Gurumurthy CB,Quadros RM,Richardson GP,Poluektova LY,Mansour SL,Ohtsuka M

更新日期：2020-12-01 00:00:00

abstract：:Here, we provide comprehensive, highly efficient protocols for Agrobacterium tumefaciens-mediated transformation of a wide range of rice genotypes. Methods that use either immature embryos (japonica and indica rice) or calli (japonica cultivars and the indica cultivar, Kasalath) as a starting material for inoculation ...

journal_title：Nature protocols

authors： Hiei Y,Komari T

更新日期：2008-01-01 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：:The synthesis of an azobenzene amino acid (aa) for use as a photo-inducible conformational switch in polypeptides is described. The compound can be easily incorporated into an aa sequence by solid-phase peptide synthesis using standard 9-fluorenylmethoxycarbonyl methods. A reversible conformational change of the pepti...

journal_title：Nature protocols

authors： Aemissegger A,Hilvert D

更新日期：2007-01-01 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：: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：:In the past decade, Drosophila has emerged as an ideal model organism for studying the genetic components of sleep as well as its regulation and functions. In fruit flies, sleep can be conveniently estimated by measuring the locomotor activity of the flies using techniques and instruments adapted from the field of cir...

journal_title：Nature protocols

authors： Gilestro GF

更新日期：2012-04-26 00:00:00