A real-time fluorometric method for the simultaneous detection of cell death type and rate.

abstract：:This protocol describes a methodology for imaging the sequestration of infected erythrocytes of the rodent malaria parasite Plasmodium berghei in the bodies of live mice or in dissected organs, using a transgenic parasite that expresses luciferase. Real-time imaging of infected erythrocytes is performed by measuring b...

journal_title：Nature protocols

authors： Franke-Fayard B,Waters AP,Janse CJ

更新日期：2006-01-01 00:00:00

abstract：:Hepatic stellate cells (HSCs) have been identified as the main fibrogenic cell type in the liver. Hence, efforts to understand hepatic fibrogenesis and to develop treatment strategies have focused on this cell type. HSC isolation, originally developed in rats, has subsequently been adapted to mice, thus allowing the s...

journal_title：Nature protocols

authors： Mederacke I,Dapito DH,Affò S,Uchinami H,Schwabe RF

更新日期：2015-02-01 00:00:00

abstract：:The partial reduction of electron-deficient pyrroles using either Birch (Li/NH(3)) or ammonia-free (Li/di-tert-butyl biphenyl) conditions allows formation of pyrroline compounds in good yield and, when combined with a reductive alkylation or similar approach, leads to highly functionalized, synthetically useful compou...

journal_title：Nature protocols

authors： Donohoe TJ,Thomas RE

更新日期：2007-01-01 00:00:00

abstract：:Hypochlorous acid (HOCl) is a critical member of the reactive oxygen species (ROS) produced by immune cells to fight infections. On the other hand, HOCl in homeostasis causes oxidative damage to biomolecules and is linked to many diseases, including inflammatory, neurodegenerative, and cardiovascular diseases. Herein,...

journal_title：Nature protocols

authors： Zhu H,Zhang Z,Long S,Du J,Fan J,Peng X

更新日期：2018-10-01 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：:Targeted nucleases, including zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9), have provided researchers with the ability to manipulate nearly any genomic sequence in hu...

journal_title：Nature protocols

authors： Liu J,Gaj T,Yang Y,Wang N,Shui S,Kim S,Kanchiswamy CN,Kim JS,Barbas CF 3rd

更新日期：2015-11-01 00:00:00

abstract：:Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, w...

journal_title：Nature protocols

authors： Banerjee J,Hanson AJ,Muhonen WW,Shabb JB,Mallik S

更新日期：2010-01-01 00:00:00

abstract：:Interactions of proteins with DNA mediate many critical nuclear functions. Chromatin immunoprecipitation (ChIP) is a robust technique for studying protein-DNA interactions. Current ChIP assays, however, either require large cell numbers, which prevent their application to rare cell samples or small-tissue biopsies, or...

journal_title：Nature protocols

authors： Dahl JA,Collas P

更新日期：2008-01-01 00:00:00

abstract：:We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detecti...

journal_title：Nature protocols

authors： Royer LA,Lemon WC,Chhetri RK,Keller PJ

更新日期：2018-11-01 00:00:00

abstract：:Biominerals serve as critical structures of living systems and play important roles in biochemical processes. Understanding their crystallization mechanisms is therefore central to many areas of biology, biogeoscience, and biochemistry. Some biominerals, such as bone and dentin, are hierarchical nanocomposite structur...

journal_title：Nature protocols

authors： Zhang X,He Y,Liu J,Bowden ME,Kovarik L,Mao SX,Wang C,De Yoreo JJ,Rosso KM

更新日期：2018-09-01 00:00:00

abstract：:The Buccal Micronucleus Cytome (BMCyt) assay is a minimally invasive method for studying DNA damage, chromosomal instability, cell death and the regenerative potential of human buccal mucosal tissue. This method is increasingly used in molecular epidemiological studies for investigating the impact of nutrition, lifest...

journal_title：Nature protocols

authors： Thomas P,Holland N,Bolognesi C,Kirsch-Volders M,Bonassi S,Zeiger E,Knasmueller S,Fenech M

更新日期：2009-01-01 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：: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：: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：:Overexpression screens can be used to explore gene function in Drosophila melanogaster, but to demonstrate their full potential, comprehensive and systematic collections of fly strains are required. Here we provide a protocol for high-throughput cloning of Drosophila open-reading frames (ORFs) that are regulated by up...

journal_title：Nature protocols

authors： Bischof J,Sheils EM,Björklund M,Basler K

更新日期：2014-07-01 00:00:00

abstract：:With the advent of massively parallel sequencing, considerable work has gone into adapting chromosome conformation capture (3C) techniques to study chromosomal architecture at a genome-wide scale. We recently demonstrated that the inactive murine X chromosome adopts a bipartite structure using a novel 3C protocol, ter...

journal_title：Nature protocols

authors： Ramani V,Cusanovich DA,Hause RJ,Ma W,Qiu R,Deng X,Blau CA,Disteche CM,Noble WS,Shendure J,Duan Z

更新日期：2016-11-01 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：:Brachypodium distachyon is emerging as a new model system for bridging research into temperate cereal crops, such as wheat and barley, and for promoting research in novel biomass grasses. Here, we provide an adapter ligation PCR protocol that allows the large-scale characterization of T-DNA insertions into the genome ...

journal_title：Nature protocols

authors： Thole V,Alves SC,Worland B,Bevan MW,Vain P

更新日期：2009-01-01 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：:Because RNA-protein interactions have a central role in a wide array of biological processes, methods that enable a quantitative assessment of these interactions in a high-throughput manner are in great demand. Recently, we developed the high-throughput sequencing-RNA affinity profiling (HiTS-RAP) assay that couples s...

journal_title：Nature protocols

authors： Ozer A,Tome JM,Friedman RC,Gheba D,Schroth GP,Lis JT

更新日期：2015-08-01 00:00:00

abstract：:ErmineJ is software for the analysis of functionally interesting patterns in large gene lists drawn from gene expression profiling data or other high-throughput genomics studies. It can be used by biologists with no bioinformatics background to conduct sophisticated analyses of gene sets with multiple methods. It allo...

journal_title：Nature protocols

authors： Gillis J,Mistry M,Pavlidis P

更新日期：2010-06-01 00:00:00

abstract：:Although differences in protein staining intensity can often be visualized by difference gel electrophoresis, abundant proteins can obscure less abundant proteins, and quantification of post-translational modifications is difficult. We present a protocol for quantifying changes in the abundance of a specific protein o...

journal_title：Nature protocols

authors： Asara JM,Zhang X,Zheng B,Maroney LA,Christofk HR,Wu N,Cantley LC

更新日期：2006-01-01 00:00:00

abstract：:The genomic instability of stem cells in culture, caused by their routine in vitro propagation or by their genetic manipulation, is deleterious both for their clinical application and for their use in basic research. Frequent evaluation of the genomic integrity of stem cells is thus required, and it is usually perform...

journal_title：Nature protocols

authors： Ben-David U,Mayshar Y,Benvenisty N

更新日期：2013-05-01 00:00:00

abstract：:Iterative saturation mutagenesis (ISM) is a new and efficient method for the directed evolution of functional enzymes. It reduces the necessary molecular biological work and the screening effort drastically. It is based on a Cartesian view of the protein structure, performing iterative cycles of saturation mutagenesis...

journal_title：Nature protocols

authors： Reetz MT,Carballeira JD

更新日期：2007-01-01 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：: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：: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：:The increasing multi-resistance of pathogenic bacteria requires the development of novel classes of antibiotics. Antimicrobial host defense peptides represent one promising class. Here we describe a protocol for screening large numbers of peptides against any microbe of interest. Peptides synthesized on a cellulose su...

journal_title：Nature protocols

authors： Hilpert K,Hancock RE

更新日期：2007-01-01 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：:In most organisms, one crossover (CO) event inhibits the chances of another nearby event. The term used to describe this phenomenon is 'CO interference'. Here, we describe a protocol for quickly generating large data sets that are amenable to CO interference analysis in the flowering plant, Arabidopsis thaliana. We em...

journal_title：Nature protocols

authors： Berchowitz LE,Copenhaver GP

更新日期：2008-01-01 00:00:00