A versatile technology for cellular glycomics using lectin microarray.

abstract：:The binding of the chemokine [C-X-C motif] ligand 12 (CXCL12 or stromal cell-derived factor 1alpha [SDF-1alpha]) constitutively produced by bone marrow stromal cells and osteoblasts, to the CXC receptor (CXCR) 4, a transmembrane chemokine receptor expressed on hematopoietic stem and progenitor cells (HSPCs), has emerg...

journal_title：Methods in enzymology

authors： Rettig MP,Ramirez P,Nervi B,DiPersio JF

更新日期：2009-01-01 00:00:00

abstract：:The ability to examine gene regulation in living cells has been greatly enabled by the development of chromatin immunoprecipitation (ChIP) methodology. ChIP captures a snapshot of protein-DNA interactions in vivo and has been used to study interactions in bacteria, yeast, and mammalian cell culture. ChIP conditions va...

journal_title：Methods in enzymology

authors： Davis SE,Mooney RA,Kanin EI,Grass J,Landick R,Ansari AZ

更新日期：2011-01-01 00:00:00

abstract：:Antibody unfolding and aggregation have been gaining increasing concern as the need for pharmaceutical antibodies with high quality has increased. Assays for continuous application of severe stress to antibodies, which are typically employed to evaluate tolerance to aggregation or to understand the mechanism of aggreg...

journal_title：Methods in enzymology

authors： Imamura H,Honda S

更新日期：2019-01-01 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：:Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes ma...

journal_title：Methods in enzymology

authors： Armengaud J

更新日期：2017-01-01 00:00:00

abstract：:Protein kinase C (PKC), a family of serine/threonine kinases, plays an important role in apoptosis. Several members of the PKC family act as substrates for caspases. In addition, PKCs can also regulate caspase activation and cell death by apoptosis. The cleavage of PKCs separates the regulatory domain from the catalyt...

journal_title：Methods in enzymology

authors： Basu A,Persaud SD,Sivaprasad U

更新日期：2008-01-01 00:00:00

abstract：:In this chapter we have discussed the methodology used to identify and characterize three intermediates in protein transport from the ER that represent stages of transport vesicle budding, targeting, and fusion. The intermediates are obtained using a variety of transport inhibitors: low-temperature incubations, additi...

journal_title：Methods in enzymology

authors： Rexach MF,Schekman RW

更新日期：1992-01-01 00:00:00

abstract：:Granzyme B (GrB) is the primary molecular mediator of apoptosis by cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells. It is a unique mammalian aspartic acid-cleaving serine protease. On T cell receptor activation, GrB is released from the CTL cytoplasmic granules by exocytosis, enters the target cells and, ...

journal_title：Methods in enzymology

authors： Shi L,Yang X,Froelich CJ,Greenberg AH

更新日期：2000-01-01 00:00:00

abstract：:The aminocoumarin antibiotics novobiocin, clorobiocin and coumermycin A(1) are formed by different Streptomyces strains and are potent inhibitors of bacterial gyrase. Their biosynthetic gene clusters have been analyzed in detail by genetic and biochemical investigations. Heterologous expression of these gene clusters ...

journal_title：Methods in enzymology

authors： Heide L

更新日期：2009-01-01 00:00:00

abstract：:To maintain cellular homeostasis, the levels of transmembrane receptors found on the plasma membrane must be tightly regulated. Endocytosis of activated receptors and the eventual degradation of these transmembrane proteins in the lysosome serve a vital role in maintaining the plasma membrane receptor levels as well a...

journal_title：Methods in enzymology

authors： Davies BA,Carney DS,Horazdovsky BF

更新日期：2005-01-01 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：: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：:Enzymology is approaching an era where many problems can benefit from computational studies. While ample challenges remain in quantitatively predicting behavior for many enzyme systems, the insights that often come from computations are an important asset for the enzymology community. Here we provide a primer for enzy...

journal_title：Methods in enzymology

authors： Roston D,Cui Q

更新日期：2016-01-01 00:00:00

abstract：:High-content screening (HCS), a combination of fluorescence microscopic imaging and automated image analysis, has become a frequently applied tool to study test compound effects in cellular disease-modeling systems. This chapter describes the measurement of G protein-coupled receptor (GPCR) internalization in the HCS ...

journal_title：Methods in enzymology

authors： Haasen D,Schnapp A,Valler MJ,Heilker R

更新日期：2006-01-01 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：: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：: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：:Concomitant with the rapid development in biomedical knowledge, including the methods of molecular biology and proteomics, and the manufacture of ever more precise optical instruments, powerful lasers, and sophisticated microcomputing hardware and software, laser microdissection systems have emerged which are now ente...

journal_title：Methods in enzymology

authors： Willenberg HS,Walters R,Bornstein SR

更新日期：2002-01-01 00:00:00

abstract：:ClpB belongs to the Hsp100 family of ring-forming heat-shock proteins involved in degradation of unfolded/misfolded proteins and in reactivation of protein aggregates. ClpB monomers reversibly associate to form the hexameric molecular chaperone that, together with the DnaK system, has the ability to disaggregate stres...

journal_title：Methods in enzymology

authors： Alfonso C,del Castillo U,Martín I,Muga A,Rivas G

更新日期：2015-01-01 00:00:00

abstract：:The reverse dot-blot method is a simple and rapid diagnostic procedure that allows screening of sample for a variety of mutations/polymorphisms in a single hybridization reaction. Several methods of immobilizing the oligonucleotide probes are discussed. The reverse dot-blot method has several unique properties that ar...

journal_title：Methods in enzymology

authors： Kawasaki E,Saiki R,Erlich H

更新日期：1993-01-01 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：:The exodus of the alarmin high mobility group box 1 (HMGB1) from the nucleus constitutes a crucial cellular danger signal and manifests as a sequential process in which HMGB1 first exits the nucleus into the cytoplasm and then is secreted or passively released through the permeabilized plasma membrane. Extracellular H...

journal_title：Methods in enzymology

authors： Zhao L,Liu P,Kepp O,Kroemer G

更新日期：2019-01-01 00:00:00

abstract：:ADP-ribosylation factor domain protein 1 (ARD1) is a multifunctional protein that belongs to the family of 20-kDa ARF proteins. The ARD1 gene encodes a 64-kDa protein with a structure comprising an 18-kDa ADP-ribosylation factor (ARF) domain at the C-terminus (amino acids 403-574), and a 46-kDa N-terminal domain (amin...

journal_title：Methods in enzymology

authors： Vichi A,Moss J,Vaughan M

更新日期：2005-01-01 00:00:00

abstract：:Determination of the three-dimensional structures of the globins led to the problem of determining how the ligands bound to the heme. In many of these structures there was no clear path from the solvent to the ligand-binding site. Even in those structures that appeared to have one or more tunnels from the exterior to ...

journal_title：Methods in enzymology

authors： Golden SD,Olsen KW

更新日期：2008-01-01 00:00:00

abstract：:Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is benefic...

journal_title：Methods in enzymology

authors： Imhof P

更新日期：2016-01-01 00:00:00

abstract：:Polyacrylamide gel electrophoresis under native conditions (native PAGE) is a well-established and versatile method for probing nucleic acid conformation and nucleic acid-protein interactions. Native PAGE has been used to measure RNA folding equilibria and kinetics under a wide variety of conditions. Advantages of thi...

journal_title：Methods in enzymology

authors： Woodson SA,Koculi E

更新日期：2009-01-01 00:00:00

abstract：:In eukaryotes, determination of the subcellular location of a novel protein encoded in genomic or transcriptomic data provides useful clues as to its possible function. However, experimental localization studies are expensive and time-consuming. As a result, accurate in silico prediction of subcellular localization fr...

journal_title：Methods in enzymology

authors： Gaston D,Tsaousis AD,Roger AJ

更新日期：2009-01-01 00:00:00

abstract：:Over the past 19 years, we have developed a novel myxoma virus-derived anti-inflammatory serine protease inhibitor, termed a serpin, as a new class of immunomodulatory therapeutic. This review will describe the initial identification of viral serpins with anti-inflammatory potential, beginning with preclinical analysi...

journal_title：Methods in enzymology

authors： Chen H,Zheng D,Davids J,Bartee MY,Dai E,Liu L,Petrov L,Macaulay C,Thoburn R,Sobel E,Moyer R,McFadden G,Lucas A

更新日期：2011-01-01 00:00:00

abstract：:Neutron reflectometry (NR) is uniquely positioned in structural biology, because of its ability to characterize biomolecular interfacial architectures like lipid membranes and membrane-associated proteins nondestructively and in their native environment. Mimicking biological processes, samples can be manipulated and t...

journal_title：Methods in enzymology

authors： Heinrich F

更新日期：2016-01-01 00:00:00

abstract：:Sedimentation velocity experiments measure the transport of molecules in solution under centrifugal force. Here, we describe a method for monitoring the sedimentation of very large biological molecular assemblies using the interference optical systems of the analytical ultracentrifuge. The mass, partial-specific volum...

journal_title：Methods in enzymology

authors： Rogge RA,Hansen JC

更新日期：2015-01-01 00:00:00