Reannotation of Genomes by Means of Proteomics Data.

abstract：:Signal transduction by vascular endothelial growth factors (VEGFs) through their cognate VEGF receptor tyrosine kinases follows the consensus scheme for receptor tyrosine kinases. Thus, binding of ligand induces receptor dimerization and activation of the tyrosine kinase through transphosphorylation between receptor m...

journal_title：Methods in enzymology

authors： Li X,Claesson-Welsh L,Shibuya M

更新日期：2008-01-01 00:00:00

abstract：:Inducible expression systems represent the founding technology for the emergence of synthetic biology in mammalian cells. The core molecules in these systems are bacterial regulator proteins that bind to or dissociate from a cognate DNA operator sequence in response to an exogenous stimulus like a small-molecule induc...

journal_title：Methods in enzymology

authors： Karlsson M,Weber W,Fussenegger M

更新日期：2011-01-01 00:00:00

abstract：:This chapter outlines methods that can be applied to determine the levels of lipids in cells and tissues. In particular, the methods focus upon the extraction and analysis of those lipids critical for monitoring signal transduction pathways. The methods address the analysis of the phosphoinositides, the lipid agonists...

journal_title：Methods in enzymology

authors： Wakelam MJ,Pettitt TR,Postle AD

更新日期：2007-01-01 00:00:00

abstract：:Benzylisoquinoline alkaloids (BIAs) constitute a diverse class of plant secondary metabolites that includes the opiate analgesics morphine and codeine. Collectively, BIAs exhibit a myriad of pharmacological activities, including antimicrobial, antitussive, antispasmodic, and anticancer properties. Despite 2500 known B...

journal_title：Methods in enzymology

authors： Pyne ME,Narcross L,Fossati E,Bourgeois L,Burton E,Gold ND,Martin VJ

更新日期：2016-01-01 00:00:00

abstract：:Lysosomes are specialized organelles for protein recycling and as such are involved in the terminal steps of autophagy. However, it has become evident that lysosomes also play an important role in the progression of apoptosis. This latter function seems to be dependent on lysosomal proteases, which need to be released...

journal_title：Methods in enzymology

authors： Ivanova S,Repnik U,Bojic L,Petelin A,Turk V,Turk B

更新日期：2008-01-01 00:00:00

abstract：:Undiluted cytoplasmic extract prepared from unfertilized Xenopus laevis eggs by low-speed centrifugation (CSF extracts) is useful for reconstitution of egg microtubule dynamics and meiosis-II spindle organization, but it suffers limitations for biochemical analysis due to abundant particulates. Here, we describe prepa...

journal_title：Methods in enzymology

authors： Groen AC,Ngyuen PA,Field CM,Ishihara K,Mitchison TJ

更新日期：2014-01-01 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

authors： Robeva R,Penberthy JK

更新日期：2009-01-01 00:00:00

abstract：:Desmoplakin (DP) is an obligate component of desmosomes, where it links the desmosomal cadherin/plakoglobin/plakophilin assembly to intermediate filaments. DP contains a large amino-terminal domain (DPNT) that binds to the cadherin/plakoglobin/plakophilin complex, a central coiled-coil domain that dimerizes the molecu...

journal_title：Methods in enzymology

authors： Choi HJ,Weis WI

更新日期：2016-01-01 00:00:00

abstract：:Antimicrosomal antibodies in inflammatory liver diseases all seem to be directed against members of the cytochrome P450 family of proteins. These autoantigens seem to be genetically polymorphic, the autoantibodies are inhibitory, and the autoepitopes are generally conserved among species. Anti-P450 autoantibodies shar...

journal_title：Methods in enzymology

authors： Manns MP,Johnson EF

更新日期：1991-01-01 00:00:00

abstract：:Model building studies may be used to supplement structurally low resolution experimental data with detailed three-dimensional hypothetical atomic models. Because of the strong relation between structure and function in biological molecules such models may give a consistent, integral view of a wealth of experimental d...

journal_title：Methods in enzymology

authors： von Kitzing E

更新日期：1992-01-01 00:00:00

abstract：:This chapter provides the methodologies employed to study the polymorphism of human apoE. These and other related studies have advanced our understanding of the structure and function of this protein as follows: The complex array of human apoE observed by two-dimensional gel electrophoresis results from genetic variat...

journal_title：Methods in enzymology

authors： Zannis VI

更新日期：1986-01-01 00:00:00

abstract：:Using the expression strategies described here, we have demonstrated a model system whereby the sequential signaling events involved in cell proliferation and subsequent transformation regulated by G alpha 12 can be investigated. The model system presented here can also be used to study the temporal interrelationships...

journal_title：Methods in enzymology

authors： Dermott JM,Dhanasekaran N

更新日期：2002-01-01 00:00:00

abstract：:Ubiquitin-like protein (Ubl) ligation is common to diverse archaea and targets many cellular pathways, including those associated with sulfur mobilization, and also tags proteins as substrates for degradation by the proteasome. Here we highlight protocols to assay proteasome function and Ubl ligation in archaea. A cha...

journal_title：Methods in enzymology

authors： Fu X,Adams Z,Maupin-Furlow J

更新日期：2019-01-01 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

authors： Previs SF,Herath K,Castro-Perez J,Mahsut A,Zhou H,McLaren DG,Shah V,Rohm RJ,Stout SJ,Zhong W,Wang SP,Johns DG,Hubbard BK,Cleary MA,Roddy TP

更新日期：2015-01-01 00:00:00

abstract：:During the past several years, major progress has been accomplished in the production of "designer cellulosomes," artificial enzymatic complexes that were demonstrated to efficiently degrade crystalline cellulose. This progress is part of a global attempt to promote biomass waste solutions and biofuel production. In d...

journal_title：Methods in enzymology

authors： Vazana Y,Moraïs S,Barak Y,Lamed R,Bayer EA

更新日期：2012-01-01 00:00:00

abstract：:The goal of the signal transduction pathways, such as those controlled by Ras, is in large part to ensure highly stringent regulation of the target genes in the nucleus, which are collectively responsible for the signal output, or phenotypes, of the cell. Understanding of the Ras effect ultimately requires the identif...

journal_title：Methods in enzymology

authors： Jo H,Cho YJ,Zhang H,Liang P

更新日期：2001-01-01 00:00:00

abstract：:Epitope tagged alpha 2-AR subtypes have been used to address a variety of cell biological questions, and the strategies used are readily applicable to all GPCR as well as other cell surface proteins. We have provided detailed protocols for successful utilization of the epitope-tagged receptor in the studies of protein...

journal_title：Methods in enzymology

authors： Wozniak M,Saunders C,Schramm N,Keefer JR,Limbird LE

更新日期：2002-01-01 00:00:00

abstract：:The study of hormone secretion by anterior pituitary cells is complicated by the presence of multiple cell types. For unambiguous interpretation of data it is necessary to identify the cells from which measurements are made. We have described a reliable experimental approach involving the identification of cultured ce...

journal_title：Methods in enzymology

authors： Croxton TL,Armstrong WM,Ben-Jonathan N

更新日期：1989-01-01 00:00:00

abstract：:Respiration is widely used for evaluation of the metabolic capabilities or physiological state of the microbial culture. This chapter describes novel approaches for characterization of respiration at a single cell level: (1) flow cytometry-based redox sensing (FCRS) of actively metabolizing microbes; (2) respiration r...

journal_title：Methods in enzymology

authors： Konopka MC,McQuaide S,Ojala DS,Kalyuzhnaya MG,Lidstrom ME

更新日期：2011-01-01 00:00:00

abstract：:To elucidate the molecular mechanisms of vertebrate color vision, it is essential to establish associations between amino acid substitutions and the directions of lambda max shifts of visual pigments. In this way, we can identify critical amino acid changes that may be responsible for lambda max shifts of visual pigme...

journal_title：Methods in enzymology

authors： Yokoyama S

更新日期：2000-01-01 00:00:00

abstract：:Autophagy is a major intracellular catabolic pathway induced in response to amino acid starvation. Recent findings implicate it in diverse physiological/pathophysiological events, such as protein and organelle turnover, development, aging, pathogen infection, cell death, and neurodegeneration. However, experimental me...

journal_title：Methods in enzymology

authors： Shvets E,Elazar Z

更新日期：2009-01-01 00:00:00

abstract：:Although the function of histone deacetylases (HDACs) have primarily been associated with influencing transcription through chromatin remodeling, the capacity of these enzymes to interface with a diverse array of biologic processes by modulating a growing list of nonhistone substrates has gained recent attention. Rece...

journal_title：Methods in enzymology

authors： Kahali S,Sarcar B,Chinnaiyan P

更新日期：2011-01-01 00:00:00

abstract：:The genome integrity of living organisms is constantly threatened by endogenous cellular metabolic processes and environmental agents. To quantify these low, physiologically relevant levels of DNA damage, a single-cell gel electrophoresis (comet) combined with strand-specific fluorescence in situ hybridization (FISH)-...

journal_title：Methods in enzymology

authors： Mondal M,Guo J

更新日期：2017-01-01 00:00:00

abstract：:5-FOA is an extremely useful reagent for the selection of Ura- cells amid a population of Ura+ cells. The selection is effective in transformation and recombination studies where loss of URA3+ is desired. A new plasmid shuffling procedure based on the 5-FOAR selection permits the recovery of conditional lethal mutatio...

journal_title：Methods in enzymology

authors： Boeke JD,Trueheart J,Natsoulis G,Fink GR

更新日期：1987-01-01 00:00:00

abstract：:Critical to the advancement of tumor immunotherapy is the reliable identification of responders and the quantification of the tumor-specific immune response elicited by treatments. In this regard, Enzyme-Linked Immunospot assay (ELISpot) is an ideal monitoring technique due to its high sensitivity, ease of execution a...

journal_title：Methods in enzymology

authors： Negri D,Sestili P,Borghi M,Ciccolella M,Bracci L

更新日期：2020-01-01 00:00:00

abstract：:In this chapter, we motivate the need for photoactivatable NO donor molecules and give a brief survey of the existing chemical tools in the field. We then provide detailed protocols for the synthesis and validation of a near-infrared light-activated NO donor molecule, photoNOD-1, developed in our research group. With ...

journal_title：Methods in enzymology

authors： Zhou EY,Knox HJ,Reinhardt CJ,Partipilo G,Chan J

更新日期：2020-01-01 00:00:00

abstract：:Covalent attachment of lipids appears to be an important mechanism by which many proteins interact with membranes. As we learn more about how lipids and adjacent amino acids participate in addressing proteins to specific membranes within the cell, it should be possible to design more elegant and precise membrane targe...

journal_title：Methods in enzymology

authors： Solski PA,Quilliam LA,Coats SG,Der CJ,Buss JE

更新日期：1995-01-01 00:00:00

abstract：:We describe a method for molecular confinement and single-fluorophore sensitive measurement in aqueous nanodroplets in oil. The sequestration of individual molecules in droplets has become a useful tool in genomics and molecular evolution. Similarly, the use of single fluorophores, or pairs of fluorophores, to study b...

journal_title：Methods in enzymology

authors： Goldner LS,Jofre AM,Tang J

更新日期：2010-01-01 00:00:00

abstract：:Rac binds tightly to lipid membranes through a lipid modification. The influence of the lipid membrane environment on the multiple interactions of Rac has not been well documented. In this chapter, we detail a method to prepare geranyl-geranylated Rac bound to liposomes of defined composition. With this method, one ca...

journal_title：Methods in enzymology

authors： Mesmin B,Antonny B

更新日期：2006-01-01 00:00:00

abstract：:Astrocytes are the most abundant cell type in the brain and are a crucial part of solving its mysteries. Originally assumed to be passive supporting cells, astrocyte's functions are now recognized to include active modulation and information processing at the neural synapse. The full extent of the astrocyte contributi...

journal_title：Methods in enzymology

authors： Preston AN,Cervasio DA,Laughlin ST

更新日期：2019-01-01 00:00:00