Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry.

abstract：:Precise investigation and manipulation of gene function often require modulation in a controlled and dynamic manner. In this chapter, we describe the methods to apply HIT systems for drug inducible transcriptional activation or simultaneous activation and genome editing in human cells. Together with those for editing,...

journal_title：Methods in enzymology

authors： Zhao C,Wei S,Wang Y

更新日期：2019-01-01 00:00:00

abstract：:Microfluidic devices have very broad applications in biological assays from simple chemotaxis assays to much more complicated 3D bioreactors. In this chapter, we describe the design and methods for performing chemotaxis assays using simple microfluidic chemotaxis chambers. With these devices, using real-time video mic...

journal_title：Methods in enzymology

authors： Sai J,Rogers M,Hockemeyer K,Wikswo JP,Richmond A

更新日期：2016-01-01 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

authors： Kinz-Thompson CD,Bailey NA,Gonzalez RL Jr

更新日期：2016-01-01 00:00:00

abstract：:Sulfate-reducing prokaryotes (SRPs) exploit sulfate as an electron acceptor for anaerobic respiration and exclusively catalyze this essential step of the world's sulfur cycle. Because SRPs are found in many prokaryotic phyla and are often closely related to non-SRPs, 16S rRNA gene-based analyses are inadequate to iden...

journal_title：Methods in enzymology

authors： Wagner M,Loy A,Klein M,Lee N,Ramsing NB,Stahl DA,Friedrich MW

更新日期：2005-01-01 00:00:00

abstract：:G-protein-coupled receptors (GPCRs) form a superfamily of membrane proteins that play a crucial role in mediating physiological processes as well as pathogenesis of many critical diseases. They are one of the most successful drug targets, accounting for more than 30% of prescription drugs on the market today. Three-di...

journal_title：Methods in enzymology

authors： Vaidehi N,Pease JE,Horuk R

更新日期：2009-01-01 00:00:00

abstract：:We have developed two screening systems for isolating inhibitors that target bacterial two-component signal transduction: (1) a differential growth assay using a temperature-sensitive yycF mutant (CNM2000) of Bacillus subtilis, which is supersensitive to histidine kinase inhibitors, and (2) a high-throughput genetic s...

journal_title：Methods in enzymology

authors： Okada A,Gotoh Y,Watanabe T,Furuta E,Yamamoto K,Utsumi R

更新日期：2007-01-01 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：:Gene therapy vectors based on murine retroviruses have now been in clinical trials for over 20 years. During that time, a variety of novel vector pseudotypes were developed in an effort to improve gene transfer. Lentiviral vectors are now in clinical trials and a similar evolution of vector technology is anticipated. ...

journal_title：Methods in enzymology

authors： Leath A,Cornetta K

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：: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：:kappaB-Ras1 and kappaB-Ras2 are two small proteins that display similarity at the amino acid level to Ras-like small GTPases. Although little is known about the function of the kappaB-Ras proteins, they have been shown to interfere with activation of transcription factor NF-kappaB. They accomplish this by binding to I...

journal_title：Methods in enzymology

authors： Huxford T,Ghosh G

更新日期：2006-01-01 00:00:00

abstract：:Staphylococcus aureus ribonuclease III (Sa-RNase III) belongs to the enzyme family known to process double-stranded RNAs consisting of two turns of the RNA helix. Although the enzyme is thought to play a role in ribosomal RNA processing and gene regulation, the deletion of the rnc gene in S. aureus does not affect cel...

journal_title：Methods in enzymology

authors： Chevalier C,Huntzinger E,Fechter P,Boisset S,Vandenesch F,Romby P,Geissmann T

更新日期：2008-01-01 00:00:00

abstract：:Dimethylsulfoniopropionate (DMSP) demethylase is a tetrahydrofolate-dependent enzyme that initiates the DMSP demethylation pathway in marine bacteria. This enzyme is important for understanding of organic sulfur flux from the oceans because it directs the sulfur from DMSP away from dimethylsulfide. This enzyme has bee...

journal_title：Methods in enzymology

authors： Reisch CR

更新日期：2018-01-01 00:00:00

abstract：:Aging that involves contact with dying yeast cells is one of the differential processes between sparkling and still wine production. The release of the products of autolysis during this aging step is fundamental for the quality of sparkling wines made by the traditional method. These cells undergo an autolysis process...

journal_title：Methods in enzymology

authors： Cebollero E,Rejas MT,González R

更新日期：2008-01-01 00:00:00

abstract：:Vitamin K-dependent carboxylation, an essential posttranslational modification catalyzed by gamma-glutamyl carboxylase, is required for the biological functions of proteins that control blood coagulation, vascular calcification, bone metabolism, and other important physiological processes. Concomitant with carboxylati...

journal_title：Methods in enzymology

authors： Tie JK,Stafford DW

更新日期：2017-01-01 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：:It has become increasingly clear that large RNA molecules, especially long noncoding RNAs, function in almost all gene regulatory processes (Cech & Steitz, 2014). Many large RNAs appear to be structural scaffolds for assembly of important RNA/protein complexes. However, the structures of most large cellular RNA molecu...

journal_title：Methods in enzymology

authors： Lin Y,May GE,Joel McManus C

更新日期：2015-01-01 00:00:00

abstract：:In recent years, sphingolipid metabolites ceramide, sphingosine, and sphingosine-1-phosphate have emerged as important second messengers in addition to their role as precursors of biomembrane components. The investigation of these sphingolipid metabolites requires the development of new, more sensitive methods for ass...

journal_title：Methods in enzymology

authors： Spassieva S,Bielawski J,Anelli V,Obeid LM

更新日期：2007-01-01 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：:Live cell microscopy using fluorescent proteins and small fluorescent probes is a well-established and essential tool for cell biology; however, there is a considerable need for noninvasive techniques able to study tissue and cell dynamics without the need to introduce chemical or genetically encoded probes. Coherent ...

journal_title：Methods in enzymology

authors： Pope I,Langbein W,Borri P,Watson P

更新日期：2012-01-01 00:00:00

abstract：:A synthetic ligand regulable system for gene transfer and expression has been developed in our laboratory based on mechanistic studies of steriod hormone receptor and transcriptional regulation. This gene switch system possesses most of the important features that are required for application of the system in biologic...

journal_title：Methods in enzymology

authors： Ye X,Schillinger K,Burcin MM,Tsai SY,O'Malley BW

更新日期：2002-01-01 00:00:00

abstract：:Nanotechnology offers a new platform for therapeutic delivery of antiretrovirals to the central nervous system (CNS) where human immunodeficiency virus (HIV-1) is sequestered in patients with HIV-1-associated neurological disorders (HAND). HAND is a spectrum of neurocognitive disorders that continue to persist in HIV-...

journal_title：Methods in enzymology

authors： Mahajan SD,Law WC,Aalinkeel R,Reynolds J,Nair BB,Yong KT,Roy I,Prasad PN,Schwartz SA

更新日期：2012-01-01 00:00:00

abstract：:Human embryonic stem cells (hESCs) are derived from preimplantation embryos. Approximately 60% of human embryos are blocked during in vitro development. Although statistics are inconclusive, experience demonstrates that hESCs are more effectively derived from high-quality embryos. In this way, optimal human embryo cul...

journal_title：Methods in enzymology

authors： Mercader A,Valbuena D,Simón C

更新日期：2006-01-01 00:00:00

abstract：:The combined use of rotating-frame relaxation methods, temperature-dependent measurements of line shapes and magnetization transfer experiments allows in favorable cases the examination in some detail of exchange processes that occur on the millisecond time scale. It is possible to determine not only the rate constant...

journal_title：Methods in enzymology

authors： Lane AN,Lefèvre JF

更新日期：1994-01-01 00:00:00

abstract：:Numerous aspects of the immune system operate on the basis of complex regulatory networks that are amenable to mathematical and computational modeling. Several modeling frameworks have recently been applied to simulating the immune system, including systems of ordinary differential equations, delay differential equati...

journal_title：Methods in enzymology

authors： Kim PS,Levy D,Lee PP

更新日期：2009-01-01 00:00:00

abstract：:Dynamin I is a large GTPase enzyme required in membrane constriction and fission during multiple forms of endocytosis. The first method described here is for the rapid purification of native dynamin from peripheral membrane extracts of sheep brain using ammonium sulfate precipitation and affinity purification on recom...

journal_title：Methods in enzymology

authors： Quan A,Robinson PJ

更新日期：2005-01-01 00:00:00

abstract：:The three-dimensional (3D) organization of the genome is important for chromatin regulation. This organization is nonrandom and appears to be tightly correlated with or regulated by chromatin state and scaffolding proteins. To understand how specific DNA and chromatin elements contribute to the functional organization...

journal_title：Methods in enzymology

authors： Harr JC,Reddy KL

更新日期：2016-01-01 00:00:00

abstract：:Specific recognition of mRNA 5' cap by eukaryotic initiation factor eIF4E is a rate-limiting step in the translation initiation. Structural determination of the eIF4E-cap complexes, as well as complexes of eIF4E with other proteins regulating its activity, requires complementary experiments that allow for energetic an...

journal_title：Methods in enzymology

authors： Niedzwiecka A,Stepinski J,Antosiewicz JM,Darzynkiewicz E,Stolarski R

更新日期：2007-01-01 00:00:00

abstract：:We have described procedures for collecting, processing, and analyzing kinetic data obtained by photobleaching microscopy of GFP-tagged chromatin proteins in nuclei of cultured living cells. These procedures are useful for characterizing the in vivo binding of chromatin proteins to their natural template--unperturbed,...

journal_title：Methods in enzymology

authors： Phair RD,Gorski SA,Misteli T

更新日期：2004-01-01 00:00:00

abstract：:Monte Carlo simulations of neighbor exclusion models have been used to demonstrate the importance of collecting and fitting data over a wide range of saturation. Low saturation data are important for good estimates of the affinity K of a drug or protein for the lattice site. High saturation data are important for dist...

journal_title：Methods in enzymology

authors： Correia JJ,Chaires JB

更新日期：1994-01-01 00:00:00