Abstract:
:Genome editing using the Cas9 endonuclease of Streptococcus pyogenes has demonstrated unprecedented efficacy and facility in a wide variety of biological systems. In zebrafish, specifically, studies have shown that Cas9 can be directed to user-defined genomic target sites via synthetic guide RNAs, enabling random or homology-directed sequence alterations, long-range chromosomal deletions, simultaneous disruption of multiple genes, and targeted integration of several kilobases of DNA. Altogether, these methods are opening new doors for the engineering of knock-outs, conditional alleles, tagged proteins, reporter lines, and disease models. In addition, the ease and high efficiency of generating Cas9-mediated gene knock-outs provides great promise for high-throughput functional genomics studies in zebrafish. In this chapter, we briefly review the origin of CRISPR/Cas technology and discuss current Cas9-based genome-editing applications in zebrafish with particular emphasis on their designs and implementations.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Gonzales AP,Yeh JRdoi
10.1016/B978-0-12-801185-0.00018-0subject
Has Abstractpub_date
2014-01-01 00:00:00pages
377-413eissn
0076-6879issn
1557-7988pii
B978-0-12-801185-0.00018-0journal_volume
546pub_type
杂志文章,评审abstract::Pathogen-host interactions are mediated in part by secreted microbial proteins capable of exploiting host cells for their survival. Several of these manipulations involve, but are not limited to, suppression of defense responses, alterations in host vesicular trafficking, and manipulation of gene expression. The deliv...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-397925-4.00007-9
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abstract::Sequence analysis of synthetic peptides using Edman chemistry can be very useful for the elucidation of certain types of synthetic problems, such as residue deletions and the presence of common stable derivatives, and for following the progress of the synthesis itself. However, it can also be a relatively poor techniq...
journal_title:Methods in enzymology
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doi:10.1016/s0076-6879(97)89056-8
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abstract::Antibodies are excellent binding proteins that have found numerous applications in biological research, biotechnology, and medicine. Characterization of their ligand binding properties has long been, and continues to be, the focus of many researchers. Antibodies are also perfect test systems which can be used for the ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-405539-1.00005-1
更新日期:2013-01-01 00:00:00
abstract::Complex I is the major entry point in the bacterial and mitochondrial respiratory chain. Structural knowledge of the enzyme is still limited because of its large size and complicated architecture. Only the structure of the hydrophilic domain of a bacterial Complex I has been solved to high resolution by X-ray crystall...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)04401-7
更新日期:2009-01-01 00:00:00
abstract::Cells belonging to the monocyte/macrophage lineage are in general highly resistant to peroxynitrite. Resistance is not dependent on the scavenging of peroxynitrite itself, or of other secondary reactive species, but is rather associated with the prompt activation of a survival signaling leading to the prevention of to...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)01205-6
更新日期:2008-01-01 00:00:00
abstract::Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA[uracil-54,C5]-MTases). In eukaryotes and many bacteria, the methyl donor for this reaction is generally S-adenosyl-L-methionine (S-AdoMet). However, in other bacteria, like ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)25004-9
更新日期:2007-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-420119-4.00013-6
更新日期:2014-01-01 00:00:00
abstract::The RNA degradosome is a bacterial protein machine devoted to RNA degradation and processing. In Escherichia coli, it is typically composed of the endoribonuclease RNase E, which also serves as a scaffold for the other components: the exoribonuclease PNPase, the RNA helicase RhlB, and enolase. The variable presence of...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)02206-4
更新日期:2008-01-01 00:00:00
abstract::In the yeast Saccharomyces cerevisiae, autophagy contributes to the sustaining of cell viability under starvation conditions, possibly through the supply of amino acids that is generated as a result of the degradation of cytosolic materials. Therefore, cellular viability is one of the best indexes for monitoring the c...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)03202-3
更新日期:2008-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-388448-0.00024-3
更新日期:2012-01-01 00:00:00
abstract::Acidic organelles and vesicles, such as endosomes, lysosomes, autophagosomes, trans-Golgi network, and synaptic vesicles, are known to play important roles in a broad range of cellular events. To facilitate studying these multifunctional systems, we describe here an acid-brightening fluorescent protein (abFP), which f...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.04.013
更新日期:2020-01-01 00:00:00
abstract::Because polysaccharides have very complicated chemical structures constructed by a great diversity of monosaccharide residues and glycosidic linkages, enzymatic approaches have been identified as powerful tools to precisely synthesize polysaccharides as the reactions progress in highly controlled regio- and stereoarra...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.06.009
更新日期:2019-01-01 00:00:00
abstract::Microscopy is a simple, direct technique for examining the morphology of cells and their organelles. Embedding cells in agarose and then in paraffin as 'cell blocks' allows for them to be processed in the same manner that tissue specimens are processed for histology. This method is advantageous because numerous sectio...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-420067-8.00018-0
更新日期:2013-01-01 00:00:00
abstract::The procedures described in this chapter have enabled us to identify and characterize monoclonal antibodies and their respective anti-idiotypes. We have developed several different types of immunoassays which afford greater flexibility to the investigator, depending on the type of antibodies desired and the availabili...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(89)78005-8
更新日期:1989-01-01 00:00:00
abstract::Galectins are a family of animal lectins with affinity for beta-galactosides. By using recombinant proteins, a number of galectins have been shown to interact with cell-surface and extracellular matrix glycoconjugates through lectin-carbohydrate interactions. Through this action, they can affect a variety of cellular ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(06)17018-4
更新日期:2006-01-01 00:00:00
abstract::Stable isotope tracers are widely used to quantify metabolic rates, and yet a limited number of studies have considered the impact of analytical error on estimates of flux. For example, when estimating the contribution of de novo lipogenesis, one typically measures a minimum of four isotope ratios, i.e., the precursor...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2015.06.021
更新日期:2015-01-01 00:00:00
abstract::Accurate diagnosis of attentional disorders such as attention-deficit hyperactivity disorder (ADHD) is imperative because there are multiple negative psychosocial sequelae related to undiagnosed and untreated ADHD. Early and accurate detection can lead to effective intervention and prevention of negative sequelae. Unf...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)67014-2
更新日期:2009-01-01 00:00:00
abstract::We describe methods for expressing and isolating formin proteins from a wide range of species and comparing quantitatively their effects on actin assembly. We first developed these procedures for purification of S. cerevisiae formins Bni1 and Bnr1 but have extended them to mammalian formins, including mouse mDia1 and ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)06016-2
更新日期:2006-01-01 00:00:00
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journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)08032-3
更新日期:2006-01-01 00:00:00
abstract::Anomalous small angle X-ray scattering (ASAXS) exploits contrast variation methods to highlight the scattering from one elemental component in a multielement sample, such as one ion species in an ion-DNA system. The ASAXS method has been applied to measure ions condensed around short nucleic acid duplexes. This chapte...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)69019-4
更新日期:2009-01-01 00:00:00
abstract::The identification and isolation of the soluble catalytic domains of adenylyl cyclase have provided investigators with useful reagents for the study of these enzymes. They have permitted detailed mechanistic investigation of the actions of forskolin, Gs alpha, and the inhibitory G protein, Gi alpha. They have served a...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(02)45012-4
更新日期:2002-01-01 00:00:00
abstract::Receptor ensemble docking (RED) is an effective strategy to account for receptor flexibility in the course of a docking-based virtual screening campaign. Such an approach can be applied when multiple crystal structures of a receptor have been solved, but it can also be applied when only a single crystal structure is a...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-407865-9.00014-5
更新日期:2013-01-01 00:00:00
abstract::Considering that HIV-1 accumulates and replicates actively within lymphoid tissues, any strategy that will decrease viral stores in these tissues might be beneficial to the infected host. Follicular dendritic cells (FDC), B lymphocytes, antigen-presenting cells like macrophages, and activated CD4(+) T cells are abunda...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)91019-7
更新日期:2005-01-01 00:00:00
abstract::The combination of PCR amplification and chemiluminescent detection of PCR products provides a highly sensitive system for the quantitation of DNA and RNA. The broad dynamic range of the chemiluminescent detection assay simplifies the selection of cycling and concentration parameters critical to harnessing the quantit...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/s0076-6879(00)05507-5
更新日期:2000-01-01 00:00:00
abstract::The kinetics of biomolecular systems can be quantified by calculating the stochastic rate constants that govern the biomolecular state vs time trajectories (i.e., state trajectories) of individual biomolecules. To do so, the experimental signal vs time trajectories (i.e., signal trajectories) obtained from observing i...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.08.021
更新日期:2016-01-01 00:00:00
abstract::Glycoproteins are a major class of glycoconjugates displaying a variety of mutual interactions between glycan and protein moieties that ultimately affect molecular organization. Modulation of the pendant glycan structures is important in tuning the functions of glycoproteins. Here we discuss structural aspects and som...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)78018-6
更新日期:2010-01-01 00:00:00
abstract::Although many players of the DNA damage response and DNA repair have been identified in several systems their biochemical role is still poorly understood. The use of the Xenopus laevis egg extract cell-free system allowed biochemical dissection of DNA replication and cell cycle events in a complex biological context. ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2017.03.018
更新日期:2017-01-01 00:00:00
abstract::Physical, chemical, and biological processes commonly discriminate among stable isotopes. Therefore, the stable isotope compositions of biomass, growth substrates, and products often carry the isotopic fingerprints of the processes that shape them. Therefore, measuring isotope fractionation by enzymes and cultures of ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-385112-3.00014-7
更新日期:2011-01-01 00:00:00
abstract::Graphene oxide (GO) and reduced graphene oxide (rGO) were demonstrated in the past decade as biocompatible carbon-based materials that could be efficiently used in bioelectrochemical systems (BESs). Specifically, for redox enzyme encapsulation in order to improve electron communication between enzymes and electrodes. ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.05.008
更新日期:2018-01-01 00:00:00
abstract::Pulsed electron double resonance technique, also known as double electron-electron resonance, jointly with site-directed spin labeling (SDSL) have been used extensively for studying structures and structural change. During the last decades, significant enhancements have been made by optimization of the experimental pr...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.05.027
更新日期:2015-01-01 00:00:00