abstract：:The shape of the genome is thought to play an important part in the coordination of transcription and other DNA-metabolic processes. Chromosome conformation capture (3C) technology allows us to analyze the folding of chromatin in the native cellular state at a resolution beyond that provided by current microscopy tech...

journal_title：Nature methods

authors： Simonis M,Kooren J,de Laat W

更新日期：2007-11-01 00:00:00

abstract：:We describe a statistical analysis methodology designed to minimize the impact of off-target activities upon large-scale RNA interference (RNAi) screens in mammalian cells. Application of this approach enhances reconfirmation rates and facilitates the experimental validation of new gene activities through the probabil...

journal_title：Nature methods

authors： König R,Chiang CY,Tu BP,Yan SF,DeJesus PD,Romero A,Bergauer T,Orth A,Krueger U,Zhou Y,Chanda SK

更新日期：2007-10-01 00:00:00

abstract：:Epistasis analysis, which reports on the extent to which the function of one gene depends on the presence of a second, is a powerful tool for studying the functional organization of the cell. Systematic genome-wide studies of epistasis, however, have been limited, with the majority of data being collected in the buddi...

journal_title：Nature methods

authors： Roguev A,Wiren M,Weissman JS,Krogan NJ

更新日期：2007-10-01 00:00:00

abstract：:The study of protein-protein interactions by mass spectrometry is an increasingly important part of post-genomics strategies to understand protein function. A variety of mass spectrometry-based approaches allow characterization of cellular protein assemblies under near-physiological conditions and subsequent assignmen...

journal_title：Nature methods

authors： Köcher T,Superti-Furga G

更新日期：2007-10-01 00:00:00

abstract：:We describe a GFP-based RNA reporter system (lambdaN-GFP) to visualize RNA molecules in live mammalian cells. It consists of GFP fused to an arginine-rich peptide derived from the phage lambda N protein, lambdaN22, which binds a unique minimal RNA motif and can be used to tag any RNA molecule. LambdaN-GFP uses a small...

journal_title：Nature methods

authors： Daigle N,Ellenberg J

更新日期：2007-08-01 00:00:00

abstract：:Fluorescent proteins have become extremely popular tools for in vivo imaging and especially for the study of localization, motility and interaction of proteins in living cells. Here we report TagRFP, a monomeric red fluorescent protein, which is characterized by high brightness, complete chromophore maturation, prolon...

journal_title：Nature methods

authors： Merzlyak EM,Goedhart J,Shcherbo D,Bulina ME,Shcheglov AS,Fradkov AF,Gaintzeva A,Lukyanov KA,Lukyanov S,Gadella TW,Chudakov DM

更新日期：2007-07-01 00:00:00

abstract：:Glycosylation, which represents the most complex posttranslational modification (PTM) event during protein maturation, has a vital role in biological processes. Glycan biosynthesis is orchestrated by numerous glycosyltransferases, each displaying different selectivities for multiple reaction sites. The precise specifi...

journal_title：Nature methods

authors： Ito H,Kameyama A,Sato T,Sukegawa M,Ishida HK,Narimatsu H

更新日期：2007-07-01 00:00:00

abstract：:We developed genetically encoded RNA probes for characterizing localization and dynamics of mitochondrial RNA (mtRNA) in single living cells. The probes consist of two RNA-binding domains of PUMILIO1, each connected with split fragments of a fluorescent protein capable of reconstituting upon binding to a target RNA. W...

journal_title：Nature methods

authors： Ozawa T,Natori Y,Sato M,Umezawa Y

更新日期：2007-05-01 00:00:00

abstract：:Using a directed evolution approach, researchers demonstrate a way of creating 'designer' receptors that are specifically activated by a ligand with no other biological activity in the cell. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2007-05-01 00:00:00

abstract：:Gap junction channels assembled from connexin protein subunits mediate intercellular transfer of ions and metabolites. Impaired channel function is implicated in several hereditary human diseases. In particular, defective permeation of cAMP or inositol-1,4,5-trisphosphate (InsP(3)) through connexin channels is associa...

journal_title：Nature methods

authors： Hernandez VH,Bortolozzi M,Pertegato V,Beltramello M,Giarin M,Zaccolo M,Pantano S,Mammano F

更新日期：2007-04-01 00:00:00

abstract：:We developed a general approach that allows unnatural amino acids with diverse physicochemical and biological properties to be genetically encoded in mammalian cells. A mutant Escherichia coli aminoacyl-tRNA synthetase (aaRS) is first evolved in yeast to selectively aminoacylate its tRNA with the unnatural amino acid ...

journal_title：Nature methods

authors： Liu W,Brock A,Chen S,Chen S,Schultz PG

更新日期：2007-03-01 00:00:00

abstract：:A quantitative high-throughput FRET-based method of screening fluorescent protein fusion libraries brings the promise of more detailed interactome maps. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2007-02-01 00:00:00

abstract：:We developed a highly sensitive parallel allele-specific sequencing (PASS) assay to simultaneously analyze a large number of viral genomes and detect minor drug-resistant populations at approximately 0.1-0.01% levels. Using this assay on samples from individuals infected with human immunodeficiency viruses (HIV), we s...

journal_title：Nature methods

authors： Cai F,Chen H,Hicks CB,Bartlett JA,Zhu J,Gao F

更新日期：2007-02-01 00:00:00

abstract：:Spatiotemporal activity patterns in three-dimensionally organized cellular networks are fundamental to the function of the nervous system. Despite advances in functional imaging of cell populations, a method to resolve local network activity in three dimensions has been lacking. Here we introduce a three-dimensional (...

journal_title：Nature methods

authors： Göbel W,Kampa BM,Helmchen F

更新日期：2007-01-01 00:00:00

abstract：:To engineer a stem cell genome, we developed a technology for targeted elimination of chromosomes from mouse embryonic stem (ES)-somatic hybrid cells. Here we demonstrate the use of a universal chromosome elimination cassette (CEC) for elimination of a single embryonic stem cell (ESC)-derived chromosome 11 or 12, and ...

journal_title：Nature methods

authors： Matsumura H,Tada M,Otsuji T,Yasuchika K,Nakatsuji N,Surani A,Tada T

更新日期：2007-01-01 00:00:00

abstract：:By combining activity-based proteomics and metabolomics, researchers have developed a new systems biology strategy for characterizing enzymes in the context of metabolic networks. ...

journal_title：Nature methods

authors： Doerr A

更新日期：2007-01-01 00:00:00

abstract：:Researchers show that to reliably establish protein interaction networks from microarray data it is necessary to measure saturation binding curves for each arrayed protein and its potential binding partners. ...

journal_title：Nature methods

authors： Rusk N

更新日期：2006-12-01 00:00:00

abstract：:An uncharged CoA precursor that can enter the cell is used for covalent, site-specific labeling of proteins inside living cells. ...

journal_title：Nature methods

authors： Kaganman I

更新日期：2006-11-01 00:00:00

abstract：:Electrically excitable cells are important in the normal functioning and in the pathophysiology of many biological processes. These cells are typically embedded in dense, heterogeneous tissues, rendering them difficult to target selectively with conventional electrical stimulation methods. The algal protein Channelrho...

journal_title：Nature methods

authors： Zhang F,Wang LP,Boyden ES,Deisseroth K

更新日期：2006-10-01 00:00:00

abstract：:Small interfering RNAs (siRNAs) have been widely exploited for sequence-specific gene knockdown, predominantly to investigate gene function in cultured vertebrate cells, and also hold promise as therapeutic agents. Because not all siRNAs that are cognate to a given target mRNA are equally effective, computational tool...

journal_title：Nature methods

authors： Pei Y,Tuschl T

更新日期：2006-09-01 00:00:00

abstract：:Deciphering global signaling networks is of great importance for the detailed understanding of cellular signaling processes controlling many important biological functions. Among signaling processes, tyrosine phosphorylation has a central role. At present, adequate techniques for the global characterization of the tyr...

journal_title：Nature methods

authors： Dierck K,Machida K,Voigt A,Thimm J,Horstmann M,Fiedler W,Mayer BJ,Nollau P

更新日期：2006-09-01 00:00:00

abstract：:We report attainment of subdiffraction resolution using stimulated emission depletion (STED) microscopy with GFP-labeled samples. The approximately 70 nm lateral resolution attained in this study is demonstrated by imaging GFP-labeled viruses and the endoplasmic reticulum (ER) of a mammalian cell. Our results mark the...

journal_title：Nature methods

authors： Willig KI,Kellner RR,Medda R,Hein B,Jakobs S,Hell SW

更新日期：2006-09-01 00:00:00

abstract：:We examined cell cycle-dependent changes in the proteome of human cells by systematically measuring protein dynamics in individual living cells. We used time-lapse microscopy to measure the dynamics of a random subset of 20 nuclear proteins, each tagged with yellow fluorescent protein (YFP) at its endogenous chromosom...

journal_title：Nature methods

authors： Sigal A,Milo R,Cohen A,Geva-Zatorsky N,Klein Y,Alaluf I,Swerdlin N,Perzov N,Danon T,Liron Y,Raveh T,Carpenter AE,Lahav G,Alon U

更新日期：2006-07-01 00:00:00

abstract：:The biomedical application of human embryonic stem (hES) cells will increasingly depend on the availability of technologies for highly controlled genetic modification. In mouse genetics, conditional mutagenesis using site-specific recombinases has become an invaluable tool for gain- and loss-of-function studies. Here ...

journal_title：Nature methods

authors： Nolden L,Edenhofer F,Haupt S,Koch P,Wunderlich FT,Siemen H,Brüstle O

更新日期：2006-06-01 00:00:00

abstract：:The successful in vitro evolution of a DNA enzyme based on a ribozyme could offer insights into early evolutionary events and provide guidelines for designing hardier catalytic oligonucleotides. ...

journal_title：Nature methods

authors： Eisenstein M

更新日期：2006-06-01 00:00:00

abstract：:We have developed a versatile, potent technique for imaging cells in culture and in vivo by expressing a metabolically biotinylated cell-surface receptor and visualizing it with labeled streptavidin moieties. The recombinant reporter protein, which incorporates a biotin acceptor peptide (BAP) between an N-terminal sig...

journal_title：Nature methods

authors： Tannous BA,Grimm J,Perry KF,Chen JW,Weissleder R,Breakefield XO

更新日期：2006-05-01 00:00:00

abstract：:A 'paired-end ditag' (PET) strategy for pinpointing protein binding sites can reveal a wealth of information about transcription factors and other DNA-binding proteins. ...

journal_title：Nature methods

authors： Eisenstein M

更新日期：2006-05-01 00:00:00

abstract：:We have developed a single-plasmid system for the efficient bacterial expression of mutant proteins containing unnatural amino acids at specific sites designated by amber nonsense codons. In this system, multiple copies of a gene encoding an amber suppressor tRNA derived from a Methanocaldococcus jannaschii tyrosyl-tR...

journal_title：Nature methods

authors： Ryu Y,Schultz PG

更新日期：2006-04-01 00:00:00

abstract：:Drug-inducible systems allowing the control of gene expression in mammalian cells are invaluable tools for genetic research, and could also fulfill essential roles in gene- and cell-based therapy. Currently available systems, however, often have limited in vivo functionality because of leakiness, insufficient levels o...

journal_title：Nature methods

authors： Szulc J,Wiznerowicz M,Sauvain MO,Trono D,Aebischer P

更新日期：2006-02-01 00:00:00

abstract：:We describe an efficient, accurate and robust whole-genome genotyping (WGG) assay based on a two-color, single-base extension (SBE), single-nucleotide polymorphism (SNP)-scoring step. We report genotyping results for biallelic International HapMap quality control (QC) SNPs using a single probe per locus. We show scala...

journal_title：Nature methods

authors： Steemers FJ,Chang W,Lee G,Barker DL,Shen R,Gunderson KL

更新日期：2006-01-01 00:00:00

abstract：:We developed a microarray hybridization-based method, 'comparative genome sequencing' (CGS), to find mutations in bacterial genomes and used it to study metronidazole resistance in H. pylori. CGS identified mutations in several genes, most likely affecting metronidazole activation, and produced no false positives in a...

journal_title：Nature methods

authors： Albert TJ,Dailidiene D,Dailide G,Norton JE,Kalia A,Richmond TA,Molla M,Singh J,Green RD,Berg DE

更新日期：2005-12-01 00:00:00

abstract：:In comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information dens...

journal_title：Nature methods

authors： Raman R,Raguram S,Venkataraman G,Paulson JC,Sasisekharan R

更新日期：2005-11-01 00:00:00

abstract：:The importance of locating proteins in their context within cells has been heightened recently by the accomplishments in molecular structure and systems biology. Although light microscopy (LM) has been extensively used for mapping protein localization, many studies require the additional resolution of the electron mic...

journal_title：Nature methods

authors： Giepmans BN,Deerinck TJ,Smarr BL,Jones YZ,Ellisman MH

更新日期：2005-10-01 00:00:00

abstract：:Achieving information content of satisfactory breadth and depth remains a formidable challenge for proteomics. This problem is particularly relevant to the study of primary human specimens, such as tumor biopsies, which are heterogeneous and of finite quantity. Here we present a functional proteomics strategy that uni...

journal_title：Nature methods

authors： Jessani N,Niessen S,Wei BQ,Nicolau M,Humphrey M,Ji Y,Han W,Noh DY,Yates JR 3rd,Jeffrey SS,Cravatt BF

更新日期：2005-09-01 00:00:00

abstract：:The implementation of efficient technologies for the production of recombinant mammalian proteins remains an outstanding challenge in many structural and functional genomics programs. We have developed a new method for rapid identification of soluble protein expression in E. coli, based on a separation of soluble prot...

journal_title：Nature methods

authors： Cornvik T,Dahlroth SL,Magnusdottir A,Herman MD,Knaust R,Ekberg M,Nordlund P

更新日期：2005-07-01 00:00:00

abstract：:A new system for lineage ablation is based on transgenic expression of a diphtheria toxin receptor (DTR) in mouse cells and application of diphtheria toxin (DT). To streamline this approach, we generated Cre-inducible DTR transgenic mice (iDTR) in which Cre-mediated excision of a STOP cassette renders cells sensitive ...

journal_title：Nature methods

authors： Buch T,Heppner FL,Tertilt C,Heinen TJ,Kremer M,Wunderlich FT,Jung S,Waisman A

更新日期：2005-06-01 00:00:00

abstract：:Microarrays have been widely used for the analysis of gene expression, but the issue of reproducibility across platforms has yet to be fully resolved. To address this apparent problem, we compared gene expression between two microarray platforms: the short oligonucleotide Affymetrix Mouse Genome 430 2.0 GeneChip and a...

journal_title：Nature methods

authors： Larkin JE,Frank BC,Gavras H,Sultana R,Quackenbush J

更新日期：2005-05-01 00:00:00

abstract：:New methods to quantify protein kinase activities directly from complex cellular mixtures are critical for understanding biological regulatory pathways. Herein, a fluorescence-based chemosensor strategy for the direct measurement of kinase activities in crude mammalian cell lysates is described. We first designed a ne...

journal_title：Nature methods

authors： Shults MD,Janes KA,Lauffenburger DA,Imperiali B

更新日期：2005-04-01 00:00:00

abstract：:Thermodynamic stability is fundamental to the biology of proteins. Information on protein stability is essential for studying protein structure and folding and can also be used indirectly to monitor protein-ligand or protein-protein interactions. While clearly valuable, the experimental determination of a protein's st...

journal_title：Nature methods

authors： Park C,Marqusee S

更新日期：2005-03-01 00:00:00

abstract：:Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets...

journal_title：Nature methods

authors： Kim J,Bhinge AA,Morgan XC,Iyer VR

更新日期：2005-01-01 00:00:00