Abstract：
:Many techniques have been developed for studying inducible gene expression, but all of them are multicomponent systems consisting of cis-acting elements at the DNA or RNA level, trans-acting regulator proteins and/or small molecules as inducers. RNA thermometers are the only known single-component regulators of gene expression. They consist of a temperature-sensitive secondary structure in the 5' untranslated region of the mRNA, which contains the ribosome-binding site. The ribosome-binding site can be masked or unmasked by a simple temperature shift, thereby repressing or inducing translation. Recently, we and others have designed synthetic RNA thermometers that are considerably simpler than naturally occurring thermometers and can be exploited as convenient on/off switches of gene expression. In this protocol, we describe the construction and use of synthetic RNA thermometers. We provide guidelines for the in silico design of thermometer-controlled mRNA leaders and for their experimental testing and optimization; the entire procedure can be completed in 2-3 weeks.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Neupert J,Bock Rdoi
10.1038/nprot.2009.112subject
Has Abstractpub_date
2009-01-01 00:00:00pages
1262-73issue
9eissn
1754-2189issn
1750-2799pii
nprot.2009.112journal_volume
4pub_type
杂志文章相关文献
Nature Protocols文献大全abstract：:The pig has emerged as an important large animal model in biomedical and pharmaceutical research. We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in pigs by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection of a plasmid encoding ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2014.010
更新日期：2014-04-01 00:00:00
abstract：:Single-cell gene expression analysis has contributed to a better understanding of the transcriptional heterogeneity in a variety of model systems, including those used in research in developmental, cancer and stem cell biology. Nowadays, technological advances facilitate the generation of large gene expression data se...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.022
更新日期：2015-03-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2009.117
更新日期：2009-01-01 00:00:00
abstract：:Among the different developed solid-state nanopores, nanopores constructed in a monolayer of molybdenum disulfide (MoS2) stand out as powerful devices for single-molecule analysis or osmotic power generation. Because the ionic current through a nanopore is inversely proportional to the thickness of the pore, ultrathin...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0131-0
更新日期：2019-04-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2012.005
更新日期：2012-02-23 00:00:00
abstract：:Protein phosphorylation plays important roles in various aspects of cellular events. Visualization of site-specific phosphorylation in cells is of great importance not only to analyze spatial and temporal distribution but also to investigate biological function. Now, site- and phosphorylation state-specific antibodies...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.374
更新日期：2007-01-01 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
pub_type： 杂志文章
doi：10.1038/s41596-020-0379-4
更新日期：2020-10-01 00:00:00
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
pub_type： 杂志文章
doi：10.1038/s41596-018-0104-8
更新日期：2019-02-01 00:00:00
abstract：:Association studies can focus on candidate gene(s), a particular genomic region, or adopt a genome-wide association approach, each of which has implications for marker selection. The strategy for marker selection will affect the statistical power of the study to detect a disease association and is a crucial element of...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2009.38
更新日期：2009-01-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2018.025
更新日期：2018-06-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2006.239
更新日期：2006-01-01 00:00:00
abstract：:By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, we discuss how to use data obtained in affinity purification-mass spectrometry (AP-MS) experiments to generate meaningf...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2014.164
更新日期：2014-11-01 00:00:00
abstract：:Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0265-0
更新日期：2020-02-01 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
pub_type： 杂志文章
doi：10.1038/s41596-020-00418-9
更新日期：2021-01-01 00:00:00
abstract：:Here we present a protocol for labeling aliphatic carboxylic acids with the positron-emitting radionuclide 11C (t(1/2) = 20.4 min) at the carboxyl position using [11C]carbon monoxide via photoinitiated free radical-mediated carbonylation. A solution of an alkyl iodide in a homogenous binary organic solvent-water mixtu...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.112
更新日期：2006-01-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2016.126
更新日期：2016-11-01 00:00:00
abstract：:The scototaxis (dark/light preference) protocol is a behavioral model for fish that is being validated to assess the antianxiety effects of pharmacological agents and the behavioral effects of toxic substances, and to investigate the (epi)genetic bases of anxiety-related behavior. Briefly, a fish is placed in a centra...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2009.225
更新日期：2010-02-01 00:00:00
abstract：:This protocol describes pulsed-field gel electrophoresis (PFGE), a method developed for separation of large DNA molecules. Whereas standard DNA gel electrophoresis commonly resolves fragments up to approximately 50 kb in size, PFGE fractionates DNA molecules up to 10 Mb. The mechanism driving these separations exploit...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.94
更新日期：2007-01-01 00:00:00
abstract：:Small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS) are techniques used to extract structural parameters and determine the overall structures and shapes of biological macromolecules, complexes and assemblies in solution. The scattering intensities measured from a sample contain contributions ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.113
更新日期：2016-11-01 00:00:00
abstract：:Postembryonic development is an important process of organismal maturation after embryonic growth. Despite key progress in recent years in understanding embryonic development via fluorescence time-lapse microscopy, comparatively less live-cell imaging of postembryonic development has been done. Here we describe a prot...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2012.128
更新日期：2012-12-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2008.227
更新日期：2009-01-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2013.015
更新日期：2013-02-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2015.008
更新日期：2015-02-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2010.78
更新日期：2010-06-01 00:00:00
abstract：:This protocol is an extension to: Nat. Protoc. 6, 870-895 (2014); doi:10.1038/nprot.2011.328; published online 02 June 2011Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early- and late-replicating regions differ in terms of mutation rates, transcr...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2017.148
更新日期：2018-05-01 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
pub_type： 杂志文章
doi：10.1038/nprot.2015.018
更新日期：2015-02-01 00:00:00
abstract：:Establishing a small animal model that accurately recapitulates hepatotropic pathogens, including hepatitis C virus (HCV) infection and immunopathogenesis, is essential for the study of hepatitis virus-induced liver disease and for therapeutics development. This protocol describes our recently developed humanized mous...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2012.083
更新日期：2012-09-01 00:00:00
abstract：:The direct detection of drug-protein interactions in living cells is a major challenge in drug discovery research. Recently, we introduced an approach termed thermal proteome profiling (TPP), which enables the monitoring of changes in protein thermal stability across the proteome using quantitative mass spectrometry. ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.101
更新日期：2015-10-01 00:00:00
abstract：:Herein we describe a protocol that uses hollow-fiber flow field-flow fractionation (FFF) coupled with multiangle light scattering (MALS) for hydrodynamic size-based separation and characterization of complex protein aggregates. The fractionation method, which requires 1.5 h to run, was successfully modified from the a...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.009
更新日期：2015-01-01 00:00:00
abstract：:Most currently available colorectal cancer (CRC) mouse models are not suitable for studying progression toward the metastatic stage. Recently, establishment of tumor organoid lines, either from murine CRC models or patients, and the possibility of engineering them with genome-editing technologies, have provided a larg...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2017.137
更新日期：2018-02-01 00:00:00
