Characterization of bacterial spore germination using phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers.

abstract：:Mitophagy is a cellular process that selectively removes damaged, old or dysfunctional mitochondria. Defective mitophagy is thought to contribute to normal aging and to various neurodegenerative and cardiovascular diseases. Previous methods used to detect mitophagy in vivo were cumbersome, insensitive and difficult to...

journal_title：Nature protocols

authors： Sun N,Malide D,Liu J,Rovira II,Combs CA,Finkel T

更新日期：2017-08-01 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：:The accurate knowledge of receptor kinetics is crucial to our understanding of cell signal transduction in general and neural function in particular. The classical technique of probing membrane receptors on a millisecond scale involves placing a recording micropipette with a membrane patch in front of a double-barrel ...

journal_title：Nature protocols

authors： Sylantyev S,Rusakov DA

更新日期：2013-01-01 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：:Methods for installing natural and unnatural amino acids and their modifications into proteins in a benign and precise manner are highly sought-after in protein science. Here we describe a protocol for 'post-translational mutagenesis' that enables the programmed installation of protein side chains through the use of r...

journal_title：Nature protocols

authors： Wright TH,Davis BG

更新日期：2017-10-01 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：:Apoptosis is a critical factor in AIDS and other viral illnesses, cerebral and myocardial ischemia, autoimmune and neurodegenerative states, organ and bone marrow transplant rejection, and tumor response to chemotherapy and radiation. Improved methods to identify sites of apoptosis are increasing our understanding of ...

journal_title：Nature protocols

authors： Blankenberg FG,Vanderheyden JL,Strauss HW,Tait JF

更新日期：2006-01-01 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：:The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, sub...

journal_title：Nature protocols

authors： Kumar P,Henikoff S,Ng PC

更新日期：2009-01-01 00:00:00

abstract：:Protein ubiquitination is a versatile protein modification that regulates virtually all cellular processes. This versatility originates from polyubiquitin chains, which can be linked in eight distinct ways. The combinatorial complexity of eight linkage types in homotypic (one chain type per polymer) and heterotypic (m...

journal_title：Nature protocols

authors： Hospenthal MK,Mevissen TET,Komander D

更新日期：2015-02-01 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：:This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of shor...

journal_title：Nature protocols

authors： Gansauge MT,Meyer M

更新日期：2013-04-01 00:00:00

abstract：:Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long read...

journal_title：Nature protocols

authors： Yue JX,Liti G

更新日期：2018-06-01 00:00:00

abstract：:In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASs) of multiple cohorts need to be combined in a meta-analysis in order to obtain enough power. This requires all cohorts to have the same single-nucleotide polymorphisms (SNPs) in their GWASs. To this e...

journal_title：Nature protocols

authors： van Leeuwen EM,Kanterakis A,Deelen P,Kattenberg MV,Genome of the Netherlands Consortium.,Slagboom PE,de Bakker PI,Wijmenga C,Swertz MA,Boomsma DI,van Duijn CM,Karssen LC,Hottenga JJ

更新日期：2015-09-01 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：:Live single-cell mass spectrometry (live MS) provides a mass spectrum that shows thousands of metabolite peaks from a single live plant cell within minutes. By using an optical microscope, a cell is chosen for analysis and a metal-coated nanospray microcapillary tip is used to remove the cell's contents. After adding ...

journal_title：Nature protocols

authors： Fujii T,Matsuda S,Tejedor ML,Esaki T,Sakane I,Mizuno H,Tsuyama N,Masujima T

更新日期：2015-09-01 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：:Discovery of biomarker patterns using proteomic techniques requires examination of large numbers of patient and control samples, followed by data mining of the molecular read-outs (e.g., mass spectra). Adequate signal processing and statistical analysis are critical for successful extraction of markers from these data...

journal_title：Nature protocols

authors： Villanueva J,Philip J,DeNoyer L,Tempst P

更新日期：2007-01-01 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：:This protocol describes the principles and methods used for the preparation of cryopreserved cell stocks. Following these procedures will ensure the availability of reproducible cultures for use within a single laboratory at different times and for different collaborating laboratories. Although the basic principle is ...

journal_title：Nature protocols

authors： Stacey GN,Masters JR

更新日期：2008-01-01 00:00:00

abstract：:The terminal monosaccharide of cell surface glycoconjugates is typically a sialic acid (SA), and aberrant sialylation is involved in several diseases. Several methodological approaches in sample preparation and subsequent analysis using mass spectrometry (MS) have enabled the identification of glycosylation sites and ...

journal_title：Nature protocols

authors： Palmisano G,Lendal SE,Engholm-Keller K,Leth-Larsen R,Parker BL,Larsen MR

更新日期：2010-12-01 00:00:00

abstract：:The telomeric repeat amplification protocol (TRAP) is a two-step process for analyzing telomerase activity in cell or tissue extracts. Recent modifications of this sensitive assay include elimination of radioactivity by using a fluorescently labeled primer instead of a radiolabeled primer. In addition, the TRAP assay ...

journal_title：Nature protocols

authors： Herbert BS,Hochreiter AE,Wright WE,Shay JW

更新日期：2006-01-01 00:00:00

abstract：:Microfluidic mixing in combination with single-molecule spectroscopy allows the investigation of complex biomolecular processes under non-equilibrium conditions. Here we present a protocol for building, installing and operating microfluidic mixing devices optimized for this purpose. The mixer is fabricated by replica ...

journal_title：Nature protocols

authors： Wunderlich B,Nettels D,Benke S,Clark J,Weidner S,Hofmann H,Pfeil SH,Schuler B

更新日期：2013-08-01 00:00:00

abstract：:Glycoproteins are involved in diverse biological processes ranging from extracellular contact and recognition to intracellular signaling. Crystal structures of glycoproteins would yield tremendous insight into these processes. But glycoprotein structural analysis has been hindered by difficulties in expressing milligr...

journal_title：Nature protocols

authors： Lee JE,Fusco ML,Saphire EO

更新日期：2009-01-01 00:00:00

abstract：:The plant cell wall is a chemically complex structure composed mostly of polysaccharides. Detailed analyses of these cell wall polysaccharides are essential for our understanding of plant development and for our use of plant biomass (largely wall material) in the food, agriculture, fabric, timber, biofuel and biocompo...

journal_title：Nature protocols

authors： Pettolino FA,Walsh C,Fincher GB,Bacic A

更新日期：2012-09-01 00:00:00

abstract：:The adeno-associated virus (AAV) is one of the most promising viral vectors for human gene therapy. As with any potential therapeutic system, a thorough understanding of it at the in vitro and in vivo levels is required. Over the years, numerous methods have been developed to better characterize AAV vectors. These met...

journal_title：Nature protocols

authors： Grieger JC,Choi VW,Samulski RJ

更新日期：2006-01-01 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：:Generation of precisely patterned neural cells from human pluripotent stem cells (hPSCs) is instrumental in developing disease models and stem cell therapies. Here, we provide a detailed 16-d protocol for obtaining high-purity ventral midbrain (VM) dopamine (DA) progenitors for intracerebral transplantation into anima...

journal_title：Nature protocols

authors： Nolbrant S,Heuer A,Parmar M,Kirkeby A

更新日期：2017-09-01 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：:Desorption electrospray ionization (DESI) allows the direct analysis of ordinary objects or pre-processed samples under ambient conditions. Among other applications, DESI is used to identify and record spatial distributions of lipids and drug molecules in biological tissue sections. This technique does not require sam...

journal_title：Nature protocols

authors： Wiseman JM,Ifa DR,Venter A,Cooks RG

更新日期：2008-01-01 00:00:00