Modeling of spatial intracellular signaling events in neurons.

abstract：:Fluorescence live-cell RNA imaging to monitor the intracellular localization and dynamics of the target RNA is a challenging subject. One of the difficulties to achieve this is to establish a precise method to enable a fluorescent labeling to the target RNA in living cells. Technologies to reduce the background fluore...

journal_title：Methods in enzymology

authors： Yoshimura H,Ozawa T

更新日期：2016-01-01 00:00:00

abstract：:This chapter discusses experimental methods and protocols for the purification and preliminary characterization of DNA polymerases that are specialized for the replicative bypass (translesion DNA synthesis) of base or other types of DNA damage that typically arrest high-fidelity DNA synthesis, with particular emphasis...

journal_title：Methods in enzymology

authors： Fischhaber PL,McDaniel LD,Friedberg EC

更新日期：2006-01-01 00:00:00

abstract：:In human, rat, and mice, a UGT1 complex locus provides for developmental-, inducer-, and cell-specific synthesis of a family of chemical-detoxifying isozymes, UDP-glucuronosyltransferases, which prevent toxicities, mutagenesis, and/or carcinogenesis. Between 10 and 14 first exons with individual promoter elements are ...

journal_title：Methods in enzymology

authors： Owens IS,Basu NK,Banerjee R

更新日期：2005-01-01 00:00:00

abstract：:ADP-ribosylation is a protein post-translational modification that is critically involved in a wide array of biological processes connected to cell stress responses. Enzymes known as poly-ADP-ribose polymerases (PARPs) catalyze the addition of the ADP-ribose units to amino acids with various side chain chemistries. In...

journal_title：Methods in enzymology

authors： Li P,Zhen Y,Yu Y

更新日期：2019-01-01 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

authors： Mauri P,Dehò G

更新日期：2008-01-01 00:00:00

abstract：:T lymphocytes express on their surface a heterodimeric αβ receptor, called the T cell receptor (TCR), which recognizes foreign antigens. Unlike antibodies, the recognition requires both an antigenic peptide epitope and a protein encoded by the major histocompatibility complex (MHC). In contrast to conventional antibod...

journal_title：Methods in enzymology

authors： Stone JD,Chervin AS,Aggen DH,Kranz DM

更新日期：2012-01-01 00:00:00

abstract：:Tubulin is known to form high-affinity complexes with certain G proteins. The formation of such complexes allows tubulin to activate Galpha and fosters a system whereby elements of the cytoskeleton can influence G-protein signaling. This article describes the interaction between tubulin and G proteins and discusses me...

journal_title：Methods in enzymology

authors： Rasenick MM,Donati RJ,Popova JS,Yu JZ

更新日期：2004-01-01 00:00:00

abstract：:The breaking of RNA strands by 2'-O-transphosphorylation is a ubiquitous reaction in biology, and enzymes that catalyze this reaction play key roles in RNA metabolism. The mechanisms of 2'-O-transphosphorylation in solution are relatively well studied, but complex and can involve different transition states depending ...

journal_title：Methods in enzymology

authors： Harris ME,York DM,Piccirilli JA,Anderson VE

更新日期：2017-01-01 00:00:00

abstract：:Ion channels open and close in response to diverse stimuli, and the molecular events underlying these processes are extensively modulated by ligands of both endogenous and exogenous origin. In the past decade, high-resolution structures of several channel types have been solved, providing unprecedented details of the ...

journal_title：Methods in enzymology

authors： Chakrapani S

更新日期：2015-01-01 00:00:00

abstract：:Interactions between chemokines and glycosaminoglycans (GAGs) are crucial for the physiological and pathophysiological activities of chemokines. GAGs are therefore commonly designated as chemokine coreceptors which are deeply involved in the chemokine-signaling network. Studying the interaction of chemokines with GAGs...

journal_title：Methods in enzymology

authors： Kitic N,Gschwandtner M,Derler R,Gerlza T,Kungl AJ

更新日期：2016-01-01 00:00:00

abstract：:Silica biomorphs and silica gardens are canonical examples of precipitation phenomena yielding self-assembled nanocrystalline composite materials with outstanding properties in terms of morphology and texture. Both types of structures form spontaneously in alkaline environments and rely on simple, and essentially simi...

journal_title：Methods in enzymology

authors： Kellermeier M,Glaab F,Melero-García E,García-Ruiz JM

更新日期：2013-01-01 00:00:00

abstract：:Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor (TF)-target gene interactions that regulate gene expression, with gene regulatory networks (GRNs) representing a temporal and spatial manifestation of a portion of the GRG, essential for the specification of gene expression. Thus...

journal_title：Methods in enzymology

authors： Yang F,Ouma WZ,Li W,Doseff AI,Grotewold E

更新日期：2016-01-01 00:00:00

abstract：:Prior to the development of 3D reconstruction, images were interpreted in terms of models made from simple units like ping-pong balls. Generally, people eye-balled the images and with other knowledge about its structure, such as the number of subunits, proposed models to account for the images. How was one to know if ...

journal_title：Methods in enzymology

authors： Derosier D

更新日期：2010-01-01 00:00:00

abstract：:Hematopoietic stem cells (HSCs) primarily reside in bone marrow, are defined by their ability to maintain blood homeostasis, and replenish themselves through self-renewal. Although HSC purification schemes vary from laboratory to laboratory, the resulting cell populations are similar, if not the same. This chapter wil...

journal_title：Methods in enzymology

authors： Lin KK,Goodell MA

更新日期：2006-01-01 00:00:00

abstract：:Genetic modifier screens offer a powerful, indeed a uniquely powerful tool for the analysis and identification of elements capable of modulating specific cellular functions in development. Here, we describe the methodology that allowed us to explore the genetic circuitry that affects a Notch mutant phenotype caused by...

journal_title：Methods in enzymology

authors： Hori K,Sen A,Artavanis-Tsakonas S

更新日期：2014-01-01 00:00:00

abstract：:The Duffy blood group antigen is a serpentine protein with seven transmembrane domains that is not coupled to G-proteins or other known intracellular effectors. In addition to erythrocytes, it is also expressed in endothelial cells and neurons. In recent years the Duffy antigen has received much attention because of i...

journal_title：Methods in enzymology

authors： Rot A,Horuk R

更新日期：2009-01-01 00:00:00

abstract：:Precisely imaging and tracking dynamic biological processes in live cells are crucial for both fundamental research in life sciences and biomedical applications. Nonfluorescent nanoparticles are emerging as important optical probes in live-cell imaging because of their excellent photostability, large optical cross sec...

journal_title：Methods in enzymology

authors： Wang G,Fang N

更新日期：2012-01-01 00:00:00

abstract：:Many methods have been developed for the cloning of PCR products. These methods include blunt-end cloning, TA cloning, and using restriction sites incorporated into the PCR primers. The restrictionless cloning technique allows efficient directional cloning of PCR products into any cloning site within a vector regardle...

journal_title：Methods in enzymology

authors： Algire MA

更新日期：2013-01-01 00:00:00

abstract：:Chromatin plays a vital role in regulating cellular processes that occur on the DNA. Modulation of chromatin structure is conducted through interactions with binding factors that direct critical actions such as posttranslational modifications, nucleosome remodeling, and incorporation of histone variants. Specific fact...

journal_title：Methods in enzymology

authors： Winkler DD,Luger K,Hieb AR

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

authors： Wang N,Wang L

更新日期：2020-01-01 00:00:00

abstract：:Cellular signaling and regulatory cascades often rely on post-translational modification of proteins, particularly phosphorylation, to quickly and effectively relay signals from a variety of inputs. Numerous kinases, the effectors of phosphorylation, and kinase networks have been implicated in human diseases. Until re...

journal_title：Methods in enzymology

authors： Mohler K,Rinehart J

更新日期：2019-01-01 00:00:00

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：: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：:We describe here the methods we have used to generate selective peptide inhibitors and activators of PKC-mediated signaling. These approaches should be applicable to any signaling event that is dependent on protein-protein interaction. Furthermore, targeting downstream enzymes in signal transduction has been notorious...

journal_title：Methods in enzymology

authors： Schechtman D,Mochly-Rosen D

更新日期：2002-01-01 00:00:00

abstract：:It is widely acknowledged that mitochondria are highly active structures that rapidly respond to cellular and environmental perturbations by changing their shape, number, and distribution. Mitochondrial remodeling is a key component of diverse biological processes, ranging from cell cycle progression to autophagy. In ...

journal_title：Methods in enzymology

authors： Marchi S,Bonora M,Patergnani S,Giorgi C,Pinton P

更新日期：2017-01-01 00:00:00

abstract：:Constitutively activating mutations of the TSHR are the major cause for nonautoimmune hyperthyroidism, which is based on ligand independent, permanent receptor activation. Several reports have highlighted the difficulties to determine whether a TSHR mutation is constitutively active or not especially for borderline ca...

journal_title：Methods in enzymology

authors： Mueller S,Jaeschke H,Paschke R

更新日期：2010-01-01 00:00:00

abstract：:The RNA-guided, sequence-specific endonuclease Cas9 has been widely adopted as genome engineering tool due to its efficiency and ease of use. Derived from the microbial CRISPR (clustered regularly interspaced short palindromic repeat) type II adaptive immune system, Cas9 has now been successfully engineered for genome...

journal_title：Methods in enzymology

authors： Trevino AE,Zhang F

更新日期：2014-01-01 00:00:00

abstract：:RNA modifications, with over one hundred known so far, are commonly proposed to fine-tune the structure and function of RNA. While modifications in rRNA and tRNA are used to modulate RNA folding and decoding properties, little is known about the function of internal modifications in mRNA/lncRNA, which includes N(6)-me...

journal_title：Methods in enzymology

authors： Liu N,Pan T

更新日期：2015-01-01 00:00:00

abstract：:The group IVA phospholipase A2, commonly called cytosolic phospholipase A2α (cPLA2α), is a widely expressed enzyme that hydrolyzes membrane phospholipid to produce arachidonic acid and lysophospholipids, which are precursors for a number of bioactive lipid mediators. Arachidonic acid is metabolized through the cycloox...

journal_title：Methods in enzymology

authors： Yun B,Leslie CC

更新日期：2017-01-01 00:00:00

abstract：:Neuroblastoma (NB) is the most common extracranial solid tumor in childhood and the most frequently diagnosed neoplasm during infancy. Despite of aggressive treatment strategies, the 5-year survival rate for metastatic disease is still less than 60% and, consequently, novel therapeutic approaches are needed. For incre...

journal_title：Methods in enzymology

authors： Di Paolo D,Loi M,Pastorino F,Brignole C,Marimpietri D,Becherini P,Caffa I,Zorzoli A,Longhi R,Gagliani C,Tacchetti C,Corti A,Allen TM,Ponzoni M,Pagnan G

更新日期：2009-01-01 00:00:00