Generating high-purity cardiac and endothelial derivatives from patterned mesoderm using human pluripotent stem cells.

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：:Mass spectrometry (MS)-based proteomics has become the preferred tool for the analysis of protein phosphorylation. To be successful at such an endeavor, there is a requirement for an efficient enrichment of phosphopeptides. This is necessary because of the substoichiometric nature of phosphorylation at a given site an...

journal_title：Nature protocols

authors： Zhou H,Ye M,Dong J,Corradini E,Cristobal A,Heck AJ,Zou H,Mohammed S

更新日期：2013-03-01 00:00:00

abstract：:The mouse embryo hindbrain is a robust and adaptable model for studying sprouting angiogenesis. It permits the spatiotemporal analysis of organ vascularization in normal mice and in mouse strains with genetic mutations that result in late embryonic or perinatal lethality. Unlike postnatal models such as retinal angiog...

journal_title：Nature protocols

authors： Fantin A,Vieira JM,Plein A,Maden CH,Ruhrberg C

更新日期：2013-02-01 00:00:00

abstract：:Cell migration through 3D extracellular matrices (ECMs) is crucial to the normal development of tissues and organs and in disease processes, yet adequate analytical tools to characterize 3D migration are lacking. The motility of eukaryotic cells on 2D substrates in the absence of gradients has long been described usin...

journal_title：Nature protocols

authors： Wu PH,Giri A,Wirtz D

更新日期：2015-03-01 00:00:00

abstract：:Characterization of the cellular participants in tissue immune responses is crucial to understanding infection, cancer, autoimmunity, allergy, graft rejection and other immunological processes. Previous reports indicate that leukocytes in lung vasculature fail to be completely removed by perfusion. Several studies sug...

journal_title：Nature protocols

authors： Anderson KG,Mayer-Barber K,Sung H,Beura L,James BR,Taylor JJ,Qunaj L,Griffith TS,Vezys V,Barber DL,Masopust D

更新日期：2014-01-01 00:00:00

abstract：:High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular...

journal_title：Nature protocols

authors： Hejátko J,Blilou I,Brewer PB,Friml J,Scheres B,Benková E

更新日期：2006-01-01 00:00:00

abstract：:The tracking of cell fate, shape and migration is an essential component in the study of the development of multicellular organisms. Here we report a protocol that uses the protein Kaede, which is fluorescent green after synthesis but can be photoconverted red by violet or UV light. We have used Kaede along with confo...

journal_title：Nature protocols

authors： Hatta K,Tsujii H,Omura T

更新日期：2006-01-01 00:00:00

abstract：:The CRISPR-Cas9 genome-editing tool and the availability of whole-genome sequences from plant species have revolutionized our ability to introduce targeted mutations into important crop plants, both to explore genetic changes and to introduce new functionalities. Here, we describe protocols adapting the CRISPR-Cas9 sy...

journal_title：Nature protocols

authors： Osakabe Y,Liang Z,Ren C,Nishitani C,Osakabe K,Wada M,Komori S,Malnoy M,Velasco R,Poli M,Jung MH,Koo OJ,Viola R,Nagamangala Kanchiswamy C

更新日期：2018-12-01 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：:An important goal of the analysis of sequenced genomes of microbial pathogens is to improve the therapy of infectious diseases. In this context, a major challenge is to detect genomic-level evolutionary changes that increase microbial virulence. TimeZone, a genome analysis software package, is designed to detect footp...

journal_title：Nature protocols

authors： Chattopadhyay S,Paul S,Dykhuizen DE,Sokurenko EV

更新日期：2013-04-01 00:00:00

abstract：:The pollen tube is an excellent single-cell model system for studying cellular processes in plant cell biology. This protocol describes a detailed step-by-step procedure with optimized conditions for introducing various fluorescent reporter proteins into lily, tobacco and Arabidopsis pollen grains by means of biolisti...

journal_title：Nature protocols

authors： Wang H,Jiang L

更新日期：2011-04-01 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：:Embryonic stem cells (ESCs) constitute a tool of great potential in neurobiology, enabling the directed differentiation of specific neural cell types. We have shown recently that neurons of the cerebral cortex can be generated from mouse ESCs cultured in a chemically defined medium that contains no morphogen, but in t...

journal_title：Nature protocols

authors： Gaspard N,Bouschet T,Herpoel A,Naeije G,van den Ameele J,Vanderhaeghen P

更新日期：2009-01-01 00:00:00

abstract：:A fluorescence-based microarray technique that does not require target DNA labeling is detailed. This 'label-free' approach utilizes a cationic, water-soluble conjugated polymer PFBT (poly[9,9'-bis(6''-(N,N,N-trimethylammonium)hexyl)fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide]), and neutral PNA (peptide nuc...

journal_title：Nature protocols

authors： Sun C,Gaylord BS,Hong JW,Liu B,Bazan GC

更新日期：2007-01-01 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：:A mechanistic understanding of HIV-1 latency depends on a model system that recapitulates the in vivo condition of latently infected, resting CD4(+) T lymphocytes. Latency seems to be established after activated CD4(+) T cells, the principal targets of HIV-1 infection, become productively infected and survive long eno...

journal_title：Nature protocols

authors： Kim M,Hosmane NN,Bullen CK,Capoferri A,Yang HC,Siliciano JD,Siliciano RF

更新日期：2014-12-01 00:00:00

abstract：:The world is on the cusp of a post-antibiotic era, but researchers and medical doctors have found a way forward-by looking back at how infections were treated before the advent of antibiotics, namely using phage therapy. Although bacteriophages (phages) continue to lack drug approval in Western medicine, an increasing...

journal_title：Nature protocols

authors： Luong T,Salabarria AC,Edwards RA,Roach DR

更新日期：2020-09-01 00:00:00

abstract：:Protein digestion using a dedicated protease represents a key element in a typical mass spectrometry (MS)-based shotgun proteomics experiment. Up to now, digestion has been predominantly performed with trypsin, mainly because of its high specificity, widespread availability and ease of use. Lately, it has become appar...

journal_title：Nature protocols

authors： Giansanti P,Tsiatsiani L,Low TY,Heck AJ

更新日期：2016-05-01 00:00:00

abstract：:Reactive oxygen species (ROS) are continuously produced in the cell as a consequence of aerobic metabolism, and are controlled by several antioxidant mechanisms. An accurate measurement of ROS is essential to evaluate the redox status of the cell, or the effects of molecules with the pro-oxidant or antioxidant activit...

journal_title：Nature protocols

authors： Cossarizza A,Ferraresi R,Troiano L,Roat E,Gibellini L,Bertoncelli L,Nasi M,Pinti M

更新日期：2009-01-01 00:00:00

abstract：:This protocol measures externalization of aminophospholipids (APLs) to the outside of the plasma membrane using mass spectrometry (MS). APL externalization occurs in numerous events, and it is relevant for transplant medicine, immunity and cancer. In this protocol, externalized APLs are chemically modified by using a ...

journal_title：Nature protocols

authors： Thomas CP,Clark SR,Hammond VJ,Aldrovandi M,Collins PW,O'Donnell VB

更新日期：2014-01-01 00:00:00

abstract：:Postembryonic development is an important process of organismal maturation after embryonic growth. Despite key progress in recent years in understanding embryonic development via fluorescence time-lapse microscopy, comparatively less live-cell imaging of postembryonic development has been done. Here we describe a prot...

journal_title：Nature protocols

authors： Chai Y,Li W,Feng G,Yang Y,Wang X,Ou G

更新日期：2012-12-01 00:00:00

abstract：:Carbon-based dots (CDs) and their functionalized (nano)composites have recently attracted attention due to their seemingly easy preparation and numerous potential applications, ranging from those in the biomedical field (i.e., imaging and drug delivery) to those in (opto)electronics (i.e., solar cells and LEDs). This ...

journal_title：Nature protocols

authors： Ðorđević L,Arcudi F,Prato M

更新日期：2019-10-01 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：:Determining enantiomeric excess (e.e.) in chiral compounds is key to development of chiral catalyst auxiliaries and chiral drugs. Here we describe a sensitive and robust fluorescence-based assay for determining e.e. in mixtures of enantiomers of 1,2- and 1,3-diols, chiral amines, amino alcohols, and amino-acid esters....

journal_title：Nature protocols

authors： Shcherbakova EG,James TD,Anzenbacher P Jr

更新日期：2020-07-01 00:00:00

abstract：:High-throughput ballistic injection nanorheology is a method for the quantitative study of cell mechanics. Cell mechanics are measured by ballistic injection of submicron particles into the cytoplasm of living cells and tracking the spontaneous displacement of the particles at high spatial resolution. The trajectories...

journal_title：Nature protocols

authors： Wu PH,Hale CM,Chen WC,Lee JS,Tseng Y,Wirtz D

更新日期：2012-01-05 00:00:00

abstract：:Cell-to-cell chemical signaling plays multiple roles in coordinating the activity of the functional elements of an organism, with these elements ranging from a three-neuron reflex circuit to the entire animal. In recent years, single-cell mass spectrometry (MS) has enabled the discovery of cell-to-cell signaling molec...

journal_title：Nature protocols

authors： Rubakhin SS,Sweedler JV

更新日期：2007-01-01 00:00:00

abstract：:Prediction of protein-protein interactions at the structural level on the proteome scale is important because it allows prediction of protein function, helps drug discovery and takes steps toward genome-wide structural systems biology. We provide a protocol (termed PRISM, protein interactions by structural matching) f...

journal_title：Nature protocols

authors： Tuncbag N,Gursoy A,Nussinov R,Keskin O

更新日期：2011-08-11 00:00:00

abstract：:PatternLab for proteomics is an integrated computational environment that unifies several previously published modules for the analysis of shotgun proteomic data. The contained modules allow for formatting of sequence databases, peptide spectrum matching, statistical filtering and data organization, extracting quantit...

journal_title：Nature protocols

authors： Carvalho PC,Lima DB,Leprevost FV,Santos MD,Fischer JS,Aquino PF,Moresco JJ,Yates JR 3rd,Barbosa VC

更新日期：2016-01-01 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

abstract：:In this protocol, we describe the preparation of nanoscale iron oxide-based materials and their use in the catalysis of different hydrogenation reactions. Pyrolysis of a Fe(OAc)2-phenanthroline complex on carbon at 800 °C under argon atmosphere results in the formation of nanoscale Fe2O3 particles surrounded by nitrog...

journal_title：Nature protocols

authors： Jagadeesh RV,Stemmler T,Surkus AE,Junge H,Junge K,Beller M

更新日期：2015-04-01 00:00:00