Dissecting the mechanisms of the clock in Neurospora.

abstract：:Nonsense-mediated mRNA decay (NMD) is activated by exon-junction complexes (EJCs) that are located downstream of the termination codon of the substrate mRNAs. This situation can be imitated by tethering components of the EJC to the 3' untranslated region (3' UTR) of a reporter mRNA. Here we describe the detailed use o...

journal_title：Methods in enzymology

authors： Gehring NH,Hentze MW,Kulozik AE

更新日期：2008-01-01 00:00:00

abstract：:Isothermal Titration Calorimetry (ITC) provides a sensitive and accurate means by which to study the thermodynamics of RNA folding, RNA binding to small molecules, and RNA-protein interactions. The advent of extremely sensitive instrumentation and the increasing availability of ITC in shared facilities have made it in...

journal_title：Methods in enzymology

authors： Feig AL

更新日期：2009-01-01 00:00:00

abstract：:This chapter outlined the methods used to study intra- and extracellular modifications of apolipoproteins. These and other related studies have shown that several of the apolipoproteins undergo a series of intra- and extracellular modifications as follows: All apolipoproteins studied contain an 18-26 long signal pepti...

journal_title：Methods in enzymology

authors： Zannis VI,Karathanasis SK,Forbes GM,Breslow JL

更新日期：1986-01-01 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

authors： Moseley JB,Maiti S,Goode BL

更新日期：2006-01-01 00:00:00

abstract：:Phosphoinositide-3-kinase (PI3K) signaling has been implicated in a panoply of cellular responses including survival, proliferation, protein synthesis, migration, and vesicular trafficking. In addition, alterations in the enzymatic activity of PI3Ks have been involved in the pathogenesis of multiple diseases, ranging ...

journal_title：Methods in enzymology

authors： Ciraolo E,Gulluni F,Hirsch E

更新日期：2014-01-01 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

authors： Sannino V,Pezzimenti F,Bertora S,Costanzo V

更新日期：2017-01-01 00:00:00

abstract：:PqqE is the first enzyme in the biosynthetic pathway of the redox cofactor pyrroloquinoline quinone (PQQ), catalyzing the formation of a carbon-carbon bond in the precursor peptide PqqA. PqqE is a radical S-adenosyl-l-methionine (SAM) (RS) enzyme, a family of enzymes that use the reductive cleavage of a [4Fe-4S] clust...

journal_title：Methods in enzymology

authors： Zhu W,Martins AM,Klinman JP

更新日期：2018-01-01 00:00:00

abstract：:Protein oxidation is implicated in atherogenesis and other inflammatory conditions. Measuring levels of chlorinated and nitrated proteins in biological matrices serves as a quantitative index of oxidative stress in vivo. One potential mechanism for oxidative stress involves myeloperoxidase, a heme protein expressed by...

journal_title：Methods in enzymology

authors： Shao B,Heinecke JW

更新日期：2008-01-01 00:00:00

abstract：:Nitration and oxidation of tyrosine, tryptophan, and methionine residues in proteins are potential markers of their interaction with peroxynitrite. This chapter describes the procedure for the detection of these nitro-oxidative modifications by tandem mass spectrometry. The peptide YGDLANWMIPGK, shown to contain a nit...

journal_title：Methods in enzymology

authors： Rebrin I,Bregere C,Gallaher TK,Sohal RS

更新日期：2008-01-01 00:00:00

abstract：:Although the use of monoclonal antibodies to characterize the Ia antigen system is still in its infancy, the usefulness of this approach is clearly apparent. Since xenogeneic immunization can be used to generate these antibodies, the chances are good that a greater variety of Ia types and determinants will be detected...

journal_title：Methods in enzymology

authors： Zweig SE,Shevach EM

更新日期：1983-01-01 00:00:00

abstract：:There is now considerable experimental evidence that aberrant activation of Rho family small GTPases promotes uncontrolled proliferation, invasion, and metastatic properties of human cancer cells. Therefore, there is considerable interest in the development of small molecule inhibitors of Rho GTPase function. However,...

journal_title：Methods in enzymology

authors： Onesto C,Shutes A,Picard V,Schweighoffer F,Der CJ

更新日期：2008-01-01 00:00:00

abstract：:Peptides corresponding to the calmodulin-binding domain of MLCK and other target enzymes promise to be useful tools in the study of calmodulin action. Not only will they help to elucidate the molecular interactions of calmodulin with specific target enzymes, but they should also prove to be useful calmodulin antagonis...

journal_title：Methods in enzymology

authors： Blumenthal DK,Krebs EG

更新日期：1987-01-01 00:00:00

abstract：:Osmoregulation is the active control of the cellular water balance and encompasses homeostatic mechanisms crucial for life. The osmoregulatory system in the yeast Saccharomyces cerevisiae is particularly well understood. Key to yeast osmoregulation is the production and accumulation of the compatible solute glycerol, ...

journal_title：Methods in enzymology

authors： Hohmann S,Krantz M,Nordlander B

更新日期：2007-01-01 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

authors： Radermacher M

更新日期：2009-01-01 00:00:00

abstract：:Reliable detection of keratins in tissues is important for investigating their physiological role and for using keratin expression as a biomarker in medical diagnostics. A particular challenge for the detection of keratins by immunofluorescence microscopy or immunohistochemistry relates to the fact that keratin interm...

journal_title：Methods in enzymology

authors： Stumptner C,Gogg-Kamerer M,Viertler C,Denk H,Zatloukal K

更新日期：2016-01-01 00:00:00

abstract：:PYP-phytochrome (Ppr) is a unique photoreceptor that contains a blue light-absorbing photoactive yellow protein (PYP) domain, a red light-absorbing phytochrome domain, and a histidine kinase domain. This chapter describes overexpression of Ppr in a strain of Escherichia coli that allows covalent attachment of substoic...

journal_title：Methods in enzymology

authors： Chung YH,Masuda S,Bauer CE

更新日期：2007-01-01 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：: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：: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

abstract：:One of the greatest advances in molecular genetics has been the application of selectable transposons in molecular biology. After 30 years of use in microbial genetics studies, transposons remain indispensable tools for the generation of null alleles tagged with selectable markers, genetic mapping, manipulation of chr...

journal_title：Methods in enzymology

authors： Maloy SR

更新日期：2007-01-01 00:00:00

abstract：:In the near future, computational tools and methods based on the mathematical modeling of biomedically relevant networks and pathways will be necessary for the design of therapeutic strategies that fight complex multifactorial diseases. Beyond the use of pharmacokinetic and pharmacodynamic approaches, we propose here ...

journal_title：Methods in enzymology

authors： Marin-Sanguino A,Gupta SK,Voit EO,Vera J

更新日期：2011-01-01 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：:Transfer RNA is extensively modified by the actions of a variety of enzymes. The radical S-adenosyl-l-methionine enzyme TYW1 modifies tRNAPhe forming the characteristic tricyclic ring via the condensation of carbons 2 and 3 of pyruvate. This chapter details methods that are required for studies of TYW1. ...

journal_title：Methods in enzymology

authors： Young AP,Bandarian V

更新日期：2018-01-01 00:00:00

abstract：:Embryonic stem cells (ESCs) have the ability to expand indefinitely in vitro and give rise to cells of all three germ layers as well as germ cells. For these reasons, ESCs hold great promise for biomedicine. In order to harness the potential of pluripotent cells, it is necessary to first understand the molecular mecha...

journal_title：Methods in enzymology

authors： Schaniel C,Lee DF,Lemischka IR

更新日期：2010-01-01 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：:Ras proteins are small GTPases that exhibit high-affinity binding to GDP and GTP and hydrolyze bound GTP to GDP. The intrinsic GTPase activity of Ras proteins is accelerated by GTPase activating proteins (GAPs), which act to attenuate GTPase signaling by accelerating the conversion of bound GTP to bound GDP. Tumor-ass...

journal_title：Methods in enzymology

authors： Shutes A,Der CJ

更新日期：2006-01-01 00:00:00

abstract：:This study designed, synthesized, and characterized a number of new heterobifunctional photocleavable cross-linking reagents that may be used to photomodulate the activity of proteins or to prepare caged fluorescent dyes. Biomolecules or fluorophores caged via a thiol group with the BNBASE reagent can be covalently li...

journal_title：Methods in enzymology

authors： Marriott G,Ottl J

更新日期：1998-01-01 00:00:00

abstract：:Microsatellite markers are quickly becoming the molecular marker of choice for studies of parentage and kinship in animals. In this chapter, we review methods and give protocols for screening potential microsatellite markers, as well as protocols for genotyping individuals with useful markers once they have been ident...

journal_title：Methods in enzymology

authors： Webster MS,Reichart L

更新日期：2005-01-01 00:00:00

abstract：:The Ras-regulatory network is a loosely defined composition of numerous Ras family members and effector pathways that couple to critical cell-regulatory processes. Investigators are increasingly turning to RNAi-mediated inhibition of gene expression as an effective tool to help generate authentic portraits of Ras prot...

journal_title：Methods in enzymology

authors： Whitehurst AW,White MA

更新日期：2006-01-01 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