Hydrodynamic size-based separation and characterization of protein aggregates from total cell lysates.

abstract：:Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and p...

journal_title：Nature protocols

authors： Butler HJ,Ashton L,Bird B,Cinque G,Curtis K,Dorney J,Esmonde-White K,Fullwood NJ,Gardner B,Martin-Hirsch PL,Walsh MJ,McAinsh MR,Stone N,Martin FL

更新日期：2016-04-01 00:00:00

abstract：:Although lung transplant is a life-saving therapy for some patients, primary graft dysfunction (PGD) is a leading cause of mortality and morbidity soon after a transplant. Ischemia reperfusion injury is known to be one of the most critical factors in PGD development. PGD is by definition an acute lung injury syndrome ...

journal_title：Nature protocols

authors： Mariscal A,Caldarone L,Tikkanen J,Nakajima D,Chen M,Yeung J,Cypel M,Liu M,Keshavjee S

更新日期：2018-08-01 00:00:00

abstract：:Human embryonic stem (hES) cells are self-renewing, pluripotent cells that are valuable research tools and hold promise for use in regenerative medicine. Most hES cell lines are derived from cryopreserved human embryos that were created during in vitro fertilization (IVF) and are in excess of clinical need. Embryos th...

journal_title：Nature protocols

authors： Lerou PH,Yabuuchi A,Huo H,Miller JD,Boyer LF,Schlaeger TM,Daley GQ

更新日期：2008-01-01 00:00:00

abstract：:We describe a protocol for easy isolation and culture of human umbilical vein endothelial cells (HUVECs) to supply every researcher with a method that can be applied in cell biology laboratories with minimum equipment. Endothelial cells (ECs) are isolated from umbilical vein vascular wall by a collagenase treatment, t...

journal_title：Nature protocols

authors： Baudin B,Bruneel A,Bosselut N,Vaubourdolle M

更新日期：2007-01-01 00:00:00

abstract：:This protocol details a method for obtaining a considerable number of human mast cells from peripheral blood cells from normal donors without using stem cell mobilization treatment. By using the magnetic cell sorting system, 10(4)-10(5) cells are retrieved in the CD34+ fraction when 100 ml of blood is drawn from a hea...

journal_title：Nature protocols

authors： Saito H,Kato A,Matsumoto K,Okayama Y

更新日期：2006-01-01 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：:Reversible thiol oxidation of cysteine residues occurs in many intracellular catalytic and signaling processes. Here we describe an optimized protocol, which can be completed in ∼5 d, to unambiguously identify specific cysteine residues that are transiently and reversibly oxidized by comparing two complex biological s...

journal_title：Nature protocols

authors： García-Santamarina S,Boronat S,Domènech A,Ayté J,Molina H,Hidalgo E

更新日期：2014-05-01 00:00:00

abstract：:The mouse embryo hindbrain is a robust and adaptable model for studying sprouting angiogenesis. It permits the spatiotemporal analysis of organ vascularization in normal mice and in mouse strains with genetic mutations that result in late embryonic or perinatal lethality. Unlike postnatal models such as retinal angiog...

journal_title：Nature protocols

authors： Fantin A,Vieira JM,Plein A,Maden CH,Ruhrberg C

更新日期：2013-02-01 00:00:00

abstract：:One of the challenges for modern neuroscience is to understand the rules of concerted neuronal function in vivo. This question can be addressed using noninvasive high-resolution imaging techniques like two-photon microscopy. This protocol describes a versatile approach for in vivo two-photon calcium imaging of neural ...

journal_title：Nature protocols

authors： Garaschuk O,Milos RI,Konnerth A

更新日期：2006-01-01 00:00:00

abstract：:Optogenetic tools provide users the ability to photocontrol the activity of cells. Commonly, activation is achieved by expression of proteins from photosynthetic organisms, for example, microbial opsins (e.g., ChR2). Alternatively, a sister approach, synthetic optogenetics, enables photocontrol over proteins of mammal...

journal_title：Nature protocols

authors： Carmi I,De Battista M,Maddalena L,Carroll EC,Kienzler MA,Berlin S

更新日期：2019-03-01 00:00:00

abstract：:Cap-analysis gene expression (CAGE) provides accurate high-throughput measurement of RNA expression. CAGE allows mapping of all the initiation sites of both capped coding and noncoding RNAs. In addition, transcriptional start sites within promoters are characterized at single-nucleotide resolution. The latter allows t...

journal_title：Nature protocols

authors： Takahashi H,Lassmann T,Murata M,Carninci P

更新日期：2012-02-23 00:00:00

abstract：:This protocol describes a method combining phase-contrast and fluorescence microscopy, Raman spectroscopy and optical tweezers to characterize the germination of single bacterial spores. The characterization consists of the following steps: (i) loading heat-activated dormant spores into a temperature-controlled micros...

journal_title：Nature protocols

authors： Kong L,Zhang P,Wang G,Yu J,Setlow P,Li YQ

更新日期：2011-05-01 00:00:00

abstract：:Activity-based protein profiling (ABPP) has emerged as a valuable chemical proteomics method to guide the therapeutic development of covalent drugs by assessing their on-target engagement and off-target activity. We recently used ABPP to determine the serine hydrolase interaction landscape of the experimental drug BIA...

journal_title：Nature protocols

authors： van Rooden EJ,Florea BI,Deng H,Baggelaar MP,van Esbroeck ACM,Zhou J,Overkleeft HS,van der Stelt M

更新日期：2018-04-01 00:00:00

abstract：:The use of anisotropic NMR data, such as residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), has emerged as a powerful technique for structural characterization of organic small molecules. RDCs typically report the relative orientations of different 1H-13C bonds; RCSAs report the relati...

journal_title：Nature protocols

authors： Liu Y,Navarro-Vázquez A,Gil RR,Griesinger C,Martin GE,Williamson RT

更新日期：2019-01-01 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 explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription...

journal_title：Nature protocols

authors： Defrance M,Janky R,Sand O,van Helden J

更新日期：2008-01-01 00:00:00

abstract：:Raman and Fourier transform IR (FTIR) microspectroscopic images of biological material (tissue sections) contain detailed information about their chemical composition. The challenge lies in identifying changes in chemical composition, as well as locating and assigning these changes to different conditions (pathology, ...

journal_title：Nature protocols

authors： Felten J,Hall H,Jaumot J,Tauler R,de Juan A,Gorzsás A

更新日期：2015-02-01 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：: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：: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：:Neurotransmitter release is triggered by membrane depolarization, Ca(2+) influx and Ca(2+) sensing by the release machinery, causing synaptic vesicle (SV) fusion with the plasma membrane. Interlinked is a complex membrane cycle in which vesicles are tethered to the release site, primed, fused and recycled. As many of ...

journal_title：Nature protocols

authors： Burgalossi A,Jung S,Man KN,Nair R,Jockusch WJ,Wojcik SM,Brose N,Rhee JS

更新日期：2012-06-21 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：:The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of suffici...

journal_title：Nature protocols

authors： Pechkova E,Nicolini C

更新日期：2017-12-01 00:00:00

abstract：:Metabolic labeling of glycans with a bioorthogonal chemical reporter such as the azide enables their visualization in cells and organisms as well as the enrichment of specific glycoprotein types for proteomic analysis. This process involves two steps. Azido sugars are fed to cells or organisms and integrated by the gl...

journal_title：Nature protocols

authors： Laughlin ST,Bertozzi CR

更新日期：2007-01-01 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：: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：: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：: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：:As proteins within cells are spatially organized according to their role, knowledge about protein localization gives insight into protein function. Here, we describe the LOPIT technique (localization of organelle proteins by isotope tagging) developed for the simultaneous and confident determination of the steady-stat...

journal_title：Nature protocols

authors： Sadowski PG,Dunkley TP,Shadforth IP,Dupree P,Bessant C,Griffin JL,Lilley KS

更新日期：2006-01-01 00:00:00

abstract：:Detailed biochemical analysis of unmanipulated germinal center (GC) B cells has not been achieved. Previously, we designed and used a simple, economical and new magnetic bead separation scheme for the purification of 'untouched' mature GC and non-GC B cells from the spleens of immunized mice and reported the first bio...

journal_title：Nature protocols

authors： Cato MH,Yau IW,Rickert RC

更新日期：2011-06-09 00:00:00