Directed differentiation of human pluripotent cells to neural crest stem cells.

abstract：:Proteins are continually produced and degraded, to avoid the accumulation of old or damaged molecules and to maintain the efficiency of physiological processes. Despite its importance, protein turnover has been difficult to measure in vivo. Previous approaches to evaluating turnover in vivo have required custom labeli...

journal_title：Nature protocols

authors： Alevra M,Mandad S,Ischebeck T,Urlaub H,Rizzoli SO,Fornasiero EF

更新日期：2019-12-01 00:00:00

abstract：:We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro-siRNAs for prokaryotic siRNAs. We present a detailed protocol d...

journal_title：Nature protocols

authors： Huang L,Lieberman J

更新日期：2013-12-01 00:00:00

abstract：:Chromatin and transcriptional processes are among the most intensively studied fields of biology today. The introduction of chromatin immunoprecipitations (ChIP) represents a major advancement in this area. This powerful method allows researchers to probe specific protein-DNA interactions in vivo and to estimate the d...

journal_title：Nature protocols

authors： Nelson JD,Denisenko O,Bomsztyk K

更新日期：2006-01-01 00:00:00

abstract：:This protocol describes a general method for the preparation of RNAs in which the reactivity or hydrogen-bonding properties of the molecule are modified in a photoreversible fashion by use of a caging strategy. A single caged adenosine, modified at the 2' position as a nitro-benzyl ether, can be incorporated into shor...

journal_title：Nature protocols

authors： Chaulk SG,MacMillan AM

更新日期：2007-01-01 00:00:00

abstract：:Conventional gene expression studies analyze multiple cells simultaneously or single cells, for which the exact in vivo or in situ position is unknown. Although cellular heterogeneity can be discerned when analyzing single cells, any spatially defined attributes that underpin the heterogeneous nature of the cells cann...

journal_title：Nature protocols

authors： Chen J,Suo S,Tam PP,Han JJ,Peng G,Jing N

更新日期：2017-03-01 00:00:00

abstract：:Post-translational modifications alter protein structure, affecting activity, stability, localization and/or binding partners. Antibodies that specifically recognize post-translationally modified proteins have a number of uses including immunocytochemistry and immunoprecipitation of the modified protein to purify prot...

journal_title：Nature protocols

authors： Arur S,Schedl T

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：: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：:An important area of proteomics involves the need for quantification, whether relative or absolute. Many methods now exist for relative quantification, but to support biomarker proteomics and systems biology, absolute quantification rather than relative quantification is required. Absolute quantification usually invol...

journal_title：Nature protocols

authors： Pratt JM,Simpson DM,Doherty MK,Rivers J,Gaskell SJ,Beynon RJ

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：:This protocol describes an optimized method for direct in vitro monitoring of homo- and heterotypic axon-axon interactions involved in the developmental assembly of neural circuits. The assay exploits a classical example of heterotypic axonal interactions by modeling the sequential extension of spinal motor and somato...

journal_title：Nature protocols

authors： Wang L,Marquardt T

更新日期：2012-01-26 00:00:00

abstract：:Pseudo-afferent cervical lymph-duct cannulation in a sheep model allows large amounts of lymph cells to be collected under physiological conditions, carrying immune signaling information from the head tissues, including oro-nasal mucosae. Importantly, large quantities of dendritic cells (DCs) of several subtypes are o...

journal_title：Nature protocols

authors： Schwartz-Cornil I,Epardaud M,Bonneau M

更新日期：2006-01-01 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：: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：: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：: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：: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：: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：: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：:This protocol is used to produce stably transformed tobacco (Nicotiana tabacum) NT1 cell lines, using Agrobacterium tumefaciens-mediated DNA delivery of a binary vector containing a gene encoding hepatitis B surface antigen and a gene encoding the kanamycin selection marker. The NT1 cultures, at the appropriate stage ...

journal_title：Nature protocols

authors： Mayo KJ,Gonzales BJ,Mason HS

更新日期：2006-01-01 00:00:00

abstract：:Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA-protein complexes. The high reactivity and lack of base specificity of the hydroxyl radical makes it an excellent probe for high-resolution footprinting of DNA-protein complexes; this technique can provide structural detail th...

journal_title：Nature protocols

authors： Jain SS,Tullius TD

更新日期：2008-01-01 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：: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：:Stabilized α-helices and nonpeptidic helix mimetics have emerged as powerful molecular scaffolds for the discovery of protein-protein interaction inhibitors. Protein-protein interactions often involve large contact areas, which are often difficult for small molecules to target with high specificity. The hypothesis beh...

journal_title：Nature protocols

authors： Patgiri A,Menzenski MZ,Mahon AB,Arora PS

更新日期：2010-11-01 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：:High-throughput sequencing of the variable domains of immune receptors (antibodies and T cell receptors (TCRs)) is of key importance in the understanding of adaptive immune responses in health and disease. However, the sequencing of both immune receptor chains (VH+VL or TCRβ/δ+TCRα/γ) at the single-cell level for typi...

journal_title：Nature protocols

authors： McDaniel JR,DeKosky BJ,Tanno H,Ellington AD,Georgiou G

更新日期：2016-03-01 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：: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：:Electrochemically active bacteria (EAB) have the ability to transfer electrons to electron acceptors located outside the cell, and they are widely present in diverse environments. In spite of their important roles in geochemical cycles, environmental remediation and electricity generation, so far, only a limited numbe...

journal_title：Nature protocols

authors： Yuan SJ,Li WW,Cheng YY,He H,Chen JJ,Tong ZH,Lin ZQ,Zhang F,Sheng GP,Yu HQ

更新日期：2014-01-01 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