Primary Deuterium Kinetic Isotope Effects From Product Yields: Rationale, Implementation, and Interpretation.

abstract：:Reviewing the circumstances that have led to the first monoclonal antibody against the disease-associated form of PrP, we consider the availability of PrP knockout mice and recombinant PrP, as well as a reliable conformational screening protocol as being important prerequisites for a successful immunization approach. ...

journal_title：Methods in enzymology

authors： Korth C,Streit P,Oesch B

更新日期：1999-01-01 00:00:00

abstract：:The Gene Expression Omnibus (GEO) repository at the National Center for Biotechnology Information archives and freely distributes high-throughput molecular abundance data, predominantly gene expression data generated by DNA microarray technology. The database has a flexible design that can handle diverse styles of bot...

journal_title：Methods in enzymology

authors： Barrett T,Edgar R

更新日期：2006-01-01 00:00:00

abstract：:RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include ...

journal_title：Methods in enzymology

authors： Wong TN,Pan T

更新日期：2009-01-01 00:00:00

abstract：:Extracellular signals dictate the biological processes of neural stem cells (NSCs) both in vivo and in vitro. The intracellular response elicited by these signals is dependent on the context in which the signal is received, which in turn is decided by previous and concurrent signals impinging on the cell. A synthesis ...

journal_title：Methods in enzymology

authors： Rajan P,Snyder E

更新日期：2006-01-01 00:00:00

abstract：:An optimal tool to unravel the role of a specific player within a cellular network or process requires its spatiotemporally resolved perturbation. Chemically induced dimerization (CID) by the rapamycin system has proven useful to induce protein dimerization or translocation with high spatiotemporal precision. Recently...

journal_title：Methods in enzymology

authors： Schifferer M,Feng S,Stein F,Schultz C

更新日期：2017-01-01 00:00:00

abstract：:This protocol describes Coomassie brilliant blue staining, one of the most common methods of detecting proteins in polyacrylamide gels (PAGE). ...

journal_title：Methods in enzymology

authors： Brunelle JL,Green R

更新日期：2014-01-01 00:00:00

abstract：:The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of p...

journal_title：Methods in enzymology

authors： Dunn WB

更新日期：2011-01-01 00:00:00

abstract：:Current methodologies available to quantify changes in mitochondrial turnover are limited to pulse-chase assays or specific assays that quantify mitophagy. Accordingly, new tools that can assess mitochondrial turnover are needed for the study of cellular, subcellular, and spatial parameters of mitochondrial turnover a...

journal_title：Methods in enzymology

authors： Trudeau KM,Gottlieb RA,Shirihai OS

更新日期：2014-01-01 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：:Chloroplast genomes of land plants and algae contain generally between 100 and 150 genes. These genes are involved in plastid gene expression and photosynthesis and in various other tasks. The function of some chloroplast genes is still unknown and some of them appear to be essential for growth and survival. Repressib...

journal_title：Methods in enzymology

authors： Ramundo S,Rochaix JD

更新日期：2015-01-01 00:00:00

abstract：:The yeast Saccharomyces cerevisiae is an ideal model system for examining fundamental nitrogen oxide biochemistry. The utility of this model system lies in both the similarities and the differences between yeast and mammalian cells. The similarities between the two systems, with regards to many of the fundamental bioc...

journal_title：Methods in enzymology

authors： Shinyashiki M,Lopez BE,Rodriguez CE,Fukuto JM

更新日期：2005-01-01 00:00:00

abstract：:The study of model organisms in pure culture has provided detailed information about the physiology and biochemistry of nitrification and related processes. Metagenomic sequencing of environmental samples is providing information to what extent this understanding also applies to natural microbial communities. Here, we...

journal_title：Methods in enzymology

authors： Müller S,Strous M

更新日期：2011-01-01 00:00:00

abstract：:The gasdermin (GSDM) family consists of gasdermin A (GSDMA), B (GSDMB), C (GSDMC), D (GSDMD), E or DNFA5 (GSDME), and DFNB59 in human. Expressed in the skin, gastrointestinal tract, and various immune cells, GSDMs mediate homeostasis and inflammation upon activation by caspases and unknown proteases. In particular, GS...

journal_title：Methods in enzymology

authors： Xia S,Ruan J,Wu H

更新日期：2019-01-01 00:00:00

abstract：:Plots of free energy versus temperature are commonly called stability curves or Gibbs-Helmholtz curves, and they have proven to be extremely useful in protein folding and ligand-binding studies. Curvature in a Gibbs-Helmholtz or stability plot is indicative of a heat capacity change, and some of their primary uses in ...

journal_title：Methods in enzymology

authors： LiCata VJ,Liu CC

更新日期：2011-01-01 00:00:00

abstract：:This chapter outlines the approaches and techniques that can be used to analyze the regulation of antibiotic production in streptomycetes. It describes how to isolate antibiotic nonproducing and overproducing mutants by UV, nitrosoguanidine (NTG), transposon, and insertion mutagenesis, and then how to use those mutant...

journal_title：Methods in enzymology

authors： Bibb M,Hesketh A

更新日期：2009-01-01 00:00:00

abstract：:Lymphocytes proliferate in response to several stimuli. In many situations, a rapid lymphocyte expansion, or the identification of a slow dividing cell subpopulation may be of great interest. Thus, it is necessary to perform reliable assays to study and compare lymphocyte subsets proliferation. For this purpose, carbo...

journal_title：Methods in enzymology

authors： Terrén I,Orrantia A,Vitallé J,Zenarruzabeitia O,Borrego F

更新日期：2020-01-01 00:00:00

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：:Adiponectin is a circulating bioactive hormone secreted by adipocytes as oligomers ranging in size from 90 kDa trimers and 180 kDa hexamers to larger high molecular weight oligomers that may reach 18- or 36-mers in size. While total circulating adiponectin levels correlate well with metabolic health, it is the relativ...

journal_title：Methods in enzymology

authors： Rutkowski JM,Scherer PE

更新日期：2014-01-01 00:00:00

abstract：:Guanine nucleotide exchange factors (GEFs) are essential regulators of the spatiotemporal conditions of small GTP-binding protein (SMG) activation. Their cellular activities combine the biochemical stimulation of GDP/GTP exchange, which leads to the active conformation of the SMG, to the detection of upstream signals ...

journal_title：Methods in enzymology

authors： Zeeh JC,Antonny B,Cherfils J,Zeghouf M

更新日期：2008-01-01 00:00:00

abstract：:Rab7, a member of the Rab family of small G proteins, has been shown to regulate late endocytic traffic and lysosome biogenesis, but the exact roles and the mode of actions of Rab7 are still undetermined. Accumulating evidence suggests that each Rab protein has multiple target proteins and works together with them to ...

journal_title：Methods in enzymology

authors： Mizuno K,Sakane A,Sasaki T

更新日期：2005-01-01 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：:Paraquat (PQ) is a prototypical redox cycling agent commonly used experimentally to generate reactive oxygen species and oxidative stress. Recently, PQ has also come under investigation as a potential environmental neurotoxin associated with increased risk for neurodegenerative disease developing after chronic exposur...

journal_title：Methods in enzymology

authors： Drechsel DA,Patel M

更新日期：2009-01-01 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：: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：:Aliphatic carbon-halogen (C-X) bonds are prevalent in modern pharmaceuticals and bioactive natural products. Three distinct chemical strategies are known in Nature to generate these structural motifs. The first is via the nucleophilic substitution at a prefunctionalized electrophilic carbon center with a halide anion ...

journal_title：Methods in enzymology

authors： Liu X

更新日期：2018-01-01 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：:Anomalous small angle X-ray scattering (ASAXS) exploits contrast variation methods to highlight the scattering from one elemental component in a multielement sample, such as one ion species in an ion-DNA system. The ASAXS method has been applied to measure ions condensed around short nucleic acid duplexes. This chapte...

journal_title：Methods in enzymology

authors： Pabit SA,Finkelstein KD,Pollack L

更新日期：2009-01-01 00:00:00

abstract：:Yeast cells in an isogenic population do not all display the same phenotypes. To study such variation within a population of cells, we need to perform measurements on each individual cell instead of measurements that average out the behavior of a cell over the entire population. Here, we provide the basic concepts and...

journal_title：Methods in enzymology

authors： Youk H,Raj A,van Oudenaarden A

更新日期：2010-01-01 00:00:00

abstract：:Ubiquitination is a prevalent protein modification catalyzed by E1, E2, and E3 enzymes that activate, conjugate, and ligate, respectively, the ubiquitin protein to substrate protein. In order to establish a mutualistic or parasitic relationship with their eukaryotic hosts, many microorganisms hijack different aspects ...

journal_title：Methods in enzymology

authors： Qiu J,Luo ZQ

更新日期：2019-01-01 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