Molecular tools for investigating ANME community structure and function.

abstract：:The recalcitrance of the cell wall to enzymatic hydrolysis represents one of the greatest challenges for using biomass to replace the petroleum as a feedstock for fuels and chemicals. Cell walls are complex in architecture and composition, posing a biochemical challenge for the development of efficient enzymes to rele...

journal_title：Methods in enzymology

authors： Whitehead C,Gomez LD,McQueen-Mason SJ

更新日期：2012-01-01 00:00:00

abstract：:Recent advances in functional genomics have enabled genome-wide genetic studies in mammalian cells. These include the establishment of high-throughput transfection and viral propagation methodologies, the production of large-scale cDNA and siRNA libraries, and the development of sensitive assay detection processes and...

journal_title：Methods in enzymology

authors： Rines DR,Tu B,Miraglia L,Welch GL,Zhang J,Hull MV,Orth AP,Chanda SK

更新日期：2006-01-01 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：:Nonnative protein aggregation has been classically treated as an amorphous process occurring by colloidal coagulation kinetics and proceeding to an essentially irreversible endpoint often ascribed to a chaotic tangle of unfolded chains. However, some nonnative aggregates, particularly amyloid fibrils, exhibit ordered ...

journal_title：Methods in enzymology

authors： O'Nuallain B,Thakur AK,Williams AD,Bhattacharyya AM,Chen S,Thiagarajan G,Wetzel R

更新日期：2006-01-01 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：:G-protein-coupled receptors (GPCRs) initiate signaling pathways via trimetric guanine nucleotide-binding proteins. GPCRs are classified based on their ligand-binding properties and molecular phylogenetic analyses. Nonetheless, these later analyses are in most case dependent on multiple sequence alignments, themselves ...

journal_title：Methods in enzymology

authors： Rehman ZU,Mirza MT,Khan A,Xhaard H

更新日期：2013-01-01 00:00:00

abstract：:Nonribosomal peptides are natural products typically of bacterial and fungal origin. These highly complex molecules display a broad spectrum of biological activities, and have been exploited for the development of immunosuppressant, antibiotic, anticancer, and other therapeutic agents. The nonribosomal peptides are as...

journal_title：Methods in enzymology

authors： Wilkinson B,Micklefield J

更新日期：2009-01-01 00:00:00

abstract：:The phenomenon of chemical or conformational exchange in NMR spectroscopy has enabled detailed characterization of time-dependent aspects of biomolecular function, including folding, molecular recognition, allostery, and catalysis, on timescales from microsecond to second. Importantly, NMR methods based on a variety o...

journal_title：Methods in enzymology

authors： Palmer AG 3rd,Koss H

更新日期：2019-01-01 00:00:00

abstract：:Multiple lipid and protein components of the plasma membrane of a living cell are organized, both compositionally and functionally, at different spatial and temporal scales. For instance, Rab protein domains in membranes the clathrin-coated pit, or the immunological synapse are exquisite examples of functional compart...

journal_title：Methods in enzymology

authors： Ghosh S,Saha S,Goswami D,Bilgrami S,Mayor S

更新日期：2012-01-01 00:00:00

abstract：:The microbial production of commodity, fine, and specialty chemicals is a driving force in biotechnology. An essential requirement is to introduce biosynthetic pathways to the target compound(s) into chassis organisms. First suitable enzymes must be selected and characterized, and then genetic pathways must be designe...

journal_title：Methods in enzymology

authors： Robinson CJ,Dunstan MS,Swainston N,Titchmarsh J,Takano E,Scrutton NS,Jervis AJ

更新日期：2018-01-01 00:00:00

abstract：:Although the function of histone deacetylases (HDACs) have primarily been associated with influencing transcription through chromatin remodeling, the capacity of these enzymes to interface with a diverse array of biologic processes by modulating a growing list of nonhistone substrates has gained recent attention. Rece...

journal_title：Methods in enzymology

authors： Kahali S,Sarcar B,Chinnaiyan P

更新日期：2011-01-01 00:00:00

abstract：:We have described a method using polyvalent peptide display on filamentous phage that can be used to identify ligands that bind to G protein beta gamma subunits. Also described is how to construct phage that have known beta gamma binding sequences fused to the coat protein to allow a competition analysis to be perform...

journal_title：Methods in enzymology

authors： Smrcka AV,Scott JK

更新日期：2002-01-01 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：: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：: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 Escherichia coli fumarate and nitrate reductase (FNR) regulator protein is an important transcriptional regulator that controls the expression of a large regulon of more than 100 genes in response to changes in oxygen availability. FNR is active when it acquires a [4Fe-4S](2+) cluster under anaerobic conditions. T...

journal_title：Methods in enzymology

authors： Crack JC,Le Brun NE,Thomson AJ,Green J,Jervis AJ

更新日期：2008-01-01 00:00:00

abstract：:Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21-nt small interfering RNAs (siRNAs) during RNA interference and excises microRNAs (miRNAs) from precursor hairpins. PAZ and PIWI domain (PPD) proteins, also involved in RNAi and miRNA function, are the best-characterized proteins kno...

journal_title：Methods in enzymology

authors： Kolb FA,Zhang H,Jaronczyk K,Tahbaz N,Hobman TC,Filipowicz W

更新日期：2005-01-01 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：:This protocol describes a method for determining the concentration of a nucleic acid sample. ...

journal_title：Methods in enzymology

authors： Kolitz S,Lorsch J

更新日期：2013-01-01 00:00:00

abstract：:Transporters are crucial in a number of cellular functions, including nutrient uptake, cell signaling, and toxin removal. As such, transporters are important drug targets and their malfunction is related to several disease states. Treating transporter-related diseases and developing pharmaceuticals targeting transport...

journal_title：Methods in enzymology

authors： Mulligan C,Mindell JA

更新日期：2017-01-01 00:00:00

abstract：:Endosomes are isolated from rat liver using high-speed centrifugation through sucrose density gradients. They are distinguishable from Golgi elements, with which they coisolate, by their capacity to concentrate internalized protein ligands (viz., insulin and epidermal growth factor (EGF)) in receptor-bound intact form...

journal_title：Methods in enzymology

authors： Posner BI,Bergeron JJ

更新日期：2014-01-01 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：:Formation of 5-methyluridine (ribothymidine) at position 54 of the T-psi loop of tRNA is catalyzed by site-specific tRNA methyltransferases (tRNA[uracil-54,C5]-MTases). In eukaryotes and many bacteria, the methyl donor for this reaction is generally S-adenosyl-L-methionine (S-AdoMet). However, in other bacteria, like ...

journal_title：Methods in enzymology

authors： Urbonavicius J,Brochier-Armanet C,Skouloubris S,Myllykallio H,Grosjean H

更新日期：2007-01-01 00:00:00

abstract：:When isolating ribonucleoprotein (RNP) complexes by an affinity selection approach, tagging the RNA component can prove to be strategically important. This is especially true for purifying single types of snoRNPs, because in most cases the snoRNA is thought to be the only unique component. Here, we present a general s...

journal_title：Methods in enzymology

authors： Piekna-Przybylska D,Liu B,Fournier MJ

更新日期：2007-01-01 00:00:00

abstract：:Histone chaperones-key actors in the dynamic organization of chromatin-interact with the various histone variants to ensure their transfer in and out of chromatin. In vitro chromatin assembly assays and isolation of protein complexes using tagged histone variants provided first clues concerning their binding specifici...

journal_title：Methods in enzymology

authors： Clément C,Vassias I,Ray-Gallet D,Almouzni G

更新日期：2016-01-01 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：:This chapter reviews basic concepts of nonlinear fluorescence upconversion, a technique whose temporal resolution is essentially limited only by the pulse width of the ultrafast laser. Design aspects for upconversion spectrophotofluorometers are discussed, and a recently developed system is described. We discuss appli...

journal_title：Methods in enzymology

authors： Xu J,Knutson JR

更新日期：2008-01-01 00:00:00

abstract：:Proteins are fragile molecules that often require great care during purification to ensure that they remain intact and fully active. Nowadays, many proteins are also purified in small amounts under denaturing conditions by various gel electrophoretic techniques, such that inactive proteins are obtained. But even here,...

journal_title：Methods in enzymology

authors： Deutscher MP

更新日期：2009-01-01 00:00:00

abstract：:Intracellular calcium (Ca2+) is involved in the regulation of a variety of biological functions in cancer cells, including growth inhibition, tumor invasiveness, and drug resistance. To gain insight into the possible role played by Ca2+ in the development of drug resistance in breast cancer, we performed a comparative...

journal_title：Methods in enzymology

authors： DeBernardi MA,Brooker G

更新日期：2006-01-01 00:00:00

abstract：:Two-hybrid systems are one of the most popular, preferred, cost effective, and scalable in vivo genetic approaches for screening protein-protein interactions. A number of variants of yeast and bacterial two-hybrid systems exist, rendering them ideal for modern, flexible proteomics-driven studies. For mapping protein i...

journal_title：Methods in enzymology

authors： Mehla J,Caufield JH,Sakhawalkar N,Uetz P

更新日期：2017-01-01 00:00:00