Transient expression and analysis of fluorescent reporter proteins in plant pollen tubes.

abstract：:The lung epithelium is derived from the endodermal germ layer, which undergoes a complex series of endoderm-mesoderm-mediated signaling events to generate the final arborized network of conducting airways (bronchi, bronchioles) and gas-exchanging units (alveoli). These stages include endoderm induction, anterior-poste...

journal_title：Nature protocols

authors： Miller AJ,Dye BR,Ferrer-Torres D,Hill DR,Overeem AW,Shea LD,Spence JR

更新日期：2019-02-01 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：:This protocol describes a culture system in which inner-ear sensory tissue is produced from mouse embryonic stem (ES) cells under chemically defined conditions. This model is amenable to basic and translational investigations into inner ear biology and regeneration. In this protocol, mouse ES cells are aggregated in 9...

journal_title：Nature protocols

authors： Koehler KR,Hashino E

更新日期：2014-01-01 00:00:00

abstract：:Coimmunoprecipitation (co-IP) analysis is a useful method for studying protein-protein interactions. It currently involves electrophoresis and western blotting, which are not optimized for detecting weak and transient interactions. In this protocol we describe an advanced version of co-IP analysis that uses real-time,...

journal_title：Nature protocols

authors： Lee HW,Ryu JY,Yoo J,Choi B,Kim K,Yoon TY

更新日期：2013-10-01 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：:Systematic complex genetic interaction studies have provided insight into high-order functional redundancies and genetic network wiring of the cell. Here, we describe a method for screening and quantifying trigenic interactions from ordered arrays of yeast strains grown on agar plates as individual colonies. The proto...

journal_title：Nature protocols

authors： Kuzmin E,Rahman M,VanderSluis B,Costanzo M,Myers CL,Andrews BJ,Boone C

更新日期：2021-01-18 00:00:00

abstract：:A procedure for the conversion of a symmetrical ketone to an enantiomerically pure lactam is described. The technique described here involves a ring-expansion reaction of a 4-substituted cyclohexanone accomplished with a chiral 1,3-azidopropanol derivative. The procedure entails first a one-step preparation of (R)-1-p...

journal_title：Nature protocols

authors： Ribelin TP,Aubé J

更新日期：2008-01-01 00:00:00

abstract：:This protocol describes a method for directing the expression of genes of interest into postmitotic neocortical neurons in vivo. Microinjection of a DNA plasmid-amphiphilic molecule mix into the neocortex followed by delivery of an ad hoc electric pulse protocol during the first few days of life in mice allows rapid, ...

journal_title：Nature protocols

authors： De la Rossa A,Jabaudon D

更新日期：2015-01-01 00:00:00

abstract：:Social recognition (SR) enables rodents to distinguish between familiar and novel conspecifics, largely through individual odor cues. SR tasks utilize the tendency for a male to sniff and interact with a novel individual more than a familiar individual. Many paradigms have been used to study the roles of the neuropept...

journal_title：Nature protocols

authors： Macbeth AH,Edds JS,Young WS 3rd

更新日期：2009-01-01 00:00:00

abstract：:MicroRNAs (miRNAs) are short, about 21 nucleotides in length, noncoding, regulatory RNA molecules representing a new layer in post-transcriptional regulation of gene expression. Intensive miRNA research has necessitated the development of effective miRNA detection methods such as northern analyses, quantitative real-t...

journal_title：Nature protocols

authors： Várallyay E,Burgyán J,Havelda Z

更新日期：2008-01-01 00:00:00

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：: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：:Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP...

journal_title：Nature protocols

authors： Toby TK,Fornelli L,Srzentić K,DeHart CJ,Levitsky J,Friedewald J,Kelleher NL

更新日期：2019-01-01 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：: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：:A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uch...

journal_title：Nature protocols

authors： Källberg M,Wang H,Wang S,Peng J,Wang Z,Lu H,Xu J

更新日期：2012-07-19 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：:Recombineering is an efficient method of in vivo genetic engineering applicable to chromosomal as well as episomal replicons in Escherichia coli. This method circumvents the need for most standard in vitro cloning techniques. Recombineering allows construction of DNA molecules with precise junctions without constraint...

journal_title：Nature protocols

authors： Sharan SK,Thomason LC,Kuznetsov SG,Court DL

更新日期：2009-01-01 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：: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：: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：:We report here a high-throughput method for the modification of bacterial artificial chromosomes (BACs) that uses a novel two-plasmid approach. In this protocol, a vector modified in our laboratory to hold an R6Kγ origin of replication and a marker recombination cassette is inserted into a BAC in a single recombinatio...

journal_title：Nature protocols

authors： Gong S,Kus L,Heintz N

更新日期：2010-09-01 00:00:00

abstract：:Rapid evaluation of microbial cell-surface carbohydrates is essential to understanding the mechanisms by which bacteria use glycans to establish pathogenic or symbiotic relationships. Microbial glycan analysis is complicated both by the vast diversity of possible carbohydrate structures and by their dynamic nature. Ba...

journal_title：Nature protocols

authors： Hsu KL,Mahal LK

更新日期：2006-01-01 00:00:00

abstract：:A major challenge in the analysis of gene expression microarray data is to extract meaningful biological knowledge out of the huge volume of raw data. Expander (EXPression ANalyzer and DisplayER) is an integrated software platform for the analysis of gene expression data, which is freely available for academic use. It...

journal_title：Nature protocols

authors： Ulitsky I,Maron-Katz A,Shavit S,Sagir D,Linhart C,Elkon R,Tanay A,Sharan R,Shiloh Y,Shamir R

更新日期：2010-02-01 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：:RNA production using in vivo transcription by Escherichia coli allows preparation of milligram quantities of RNA for biochemical, biophysical and structural investigations. We describe here a generic protocol for the overproduction and purification of recombinant RNA using liquid chromatography. The strategy utilizes ...

journal_title：Nature protocols

authors： Ponchon L,Beauvais G,Nonin-Lecomte S,Dardel F

更新日期：2009-01-01 00:00:00

abstract：:Ex vivo perfusion systems offer a reliable, reproducible method for studying acute physiological responses of an organ to various environmental manipulations. Unlike in vitro culture systems, the cellular organization, compartmentalization and three-dimensional structure of ex vivo-perfused organs are maintained. Thes...

journal_title：Nature protocols

authors： Goeden N,Bonnin A

更新日期：2013-01-01 00:00:00

abstract：:During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dyna...

journal_title：Nature protocols

authors： Cassaignau AM,Launay HM,Karyadi ME,Wang X,Waudby CA,Deckert A,Robertson AL,Christodoulou J,Cabrita LD

更新日期：2016-08-01 00:00:00

abstract：:Cell proliferation may be measured in vivo by quantifying DNA synthesis with isotopically labeled deoxyribonucleotide precursors. Deuterium-labeled glucose is one such precursor which, because it achieves high levels of enrichment for a short period, is well suited to the study of rapidly dividing cells, in contrast t...

journal_title：Nature protocols

authors： Macallan DC,Asquith B,Zhang Y,de Lara C,Ghattas H,Defoiche J,Beverley PC

更新日期：2009-01-01 00:00:00

abstract：:In the past few decades, marine natural products bioprospecting has yielded a considerable number of drug candidates. Two marine natural products have recently been admitted as new drugs: Prialt (also known as ziconotide) as a potent analgesic for severe chronic pain and Yondelis (known also as trabectedin or E-743) a...

journal_title：Nature protocols

authors： Ebada SS,Edrada RA,Lin W,Proksch P

更新日期：2008-01-01 00:00:00