Abstract:
:Electrochemical microsensors for O2, pH, H2S, H2, and N2O are now available commercially, thus it has become a relatively simple task to analyze the microenvironment in stratified microbial communities for several chemical species. In addition, sensors are available for the physical parameters diffusivity and flow, and based on knowledge about both transport processes and microdistribution of chemistry, it becomes possible to calculate the spatial distribution and local rates of transformations, such as aerobic respiration or denitrification. As compared to other advanced techniques, microsensor equipment is inexpensive. For example, it is possible to start working with oxygen microsensors with an investment of only about 5000 dollars. Construction of one's own microsensors is only recommended for the very dedicated user, but the investment here is mainly in terms of man-hours as the equipment is simple and inexpensive. By establishing a microsensor construction facility, it is possible to work with short-lived sensors such as ion-selective microsensors for H+, NO2(-), NO3(-), Ca2+, and CO3(-) based on ion exchangers and with microscale biosensors for NO(x)-, NO2(-), CH4, and volatile fatty acids based on immobilized bacteria.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Revsbech NPdoi
10.1016/S0076-6879(05)97009-2subject
Has Abstractpub_date
2005-01-01 00:00:00pages
147-66eissn
0076-6879issn
1557-7988pii
S0076-6879(05)97009-2journal_volume
397pub_type
杂志文章abstract::Nucleotide excision repair is a multicomponent, multistep enzymatic system that removes a wide spectrum of DNA damage by dual incisions in the damaged strand on both sides of the lesion. The basic steps are damage recognition, dual incisions, resynthesis to replace the excised DNA, and ligation. Each step has been stu...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)08012-8
更新日期:2006-01-01 00:00:00
abstract::We have shown that Rab34/Rah participates in the promotion of macropinosome formation. Here we describe procedures for the analyses of intracellular localization and some functional properties of Rab34. Rab34 lacks a consensus sequence of the fourth motif for GTP/GDP binding and GTPase activities. Indeed, GTPase assay...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)03019-3
更新日期:2005-01-01 00:00:00
abstract::Microbes are now well recognized as major drivers of the biogeochemical cycling that fuels the Earth, and their viruses (phages) are known to be abundant and important in microbial mortality, horizontal gene transfer, and modulating microbial metabolic output. Investigation of environmental phages has been frustrated ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-407863-5.00008-3
更新日期:2013-01-01 00:00:00
abstract::Modular calcium-dependent carbohydrate-recognition domains (CRDs) of mammalian glycan-binding receptors (C-type lectins), engineered to have novel glycan-binding selectivity, have been developed as tools for the study of glycans on cell surfaces. Structure-based specificity swapping between domains can be complemented...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(10)80009-6
更新日期:2010-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)03049-1
更新日期:2005-01-01 00:00:00
abstract::Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were d...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.11.009
更新日期:2017-01-01 00:00:00
abstract::In this chapter, we motivate the need for photoactivatable NO donor molecules and give a brief survey of the existing chemical tools in the field. We then provide detailed protocols for the synthesis and validation of a near-infrared light-activated NO donor molecule, photoNOD-1, developed in our research group. With ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.05.003
更新日期:2020-01-01 00:00:00
abstract::Retinoic acid (RA), the biologically active metabolite of vitamin A, regulates a vast spectrum of biological processes, such as cell differentiation, proliferation, apoptosis, and morphogenesis. microRNAs (miRNAs) play a crucial role in regulating gene expression by binding to messenger RNA (mRNA) which leads to mRNA ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.02.009
更新日期:2020-01-01 00:00:00
abstract::The development of sensors that mimic the natural smell sensing mechanism and selectively recognizes the odorants remains highly challenging. Electrochemical based sensing approaches aiming at monitoring molecular recognition events between surface receptors and analytes in solution or in the gas phase, are one possib...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.04.071
更新日期:2020-01-01 00:00:00
abstract::Integrin adhesion receptors mediate cell-cell and cell-substratum adhesion and provide a continuous link for the bidirectional transmission of mechanical force and biochemical signals across the plasma membrane. Integrin-dependent cellular activities such as adhesion, migration, proliferation, and survival rely upon t...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)26004-5
更新日期:2007-01-01 00:00:00
abstract::Expression of fusion proteins such as MBP fusions can be used as a way to improve the solubility of the expressed protein in E. coli (Fox and Waugh, 2003; Nallamsetty et al., 2005; Nallamsetty and Waugh, 2006) and as a way to introduce an affinity purification tag. The protocol that follows was designed by the authors...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2014.11.004
更新日期:2015-01-01 00:00:00
abstract::Posttranslational modification of circadian clock proteins by phosphorylation is an essential regulatory process in the control of eukaryotic circadian clocks. In the Neurospora circadian clock, the key clock protein FREQUENCY (FRQ) is progressively phosphorylated. The phosphorylation of FRQ is regulated by both kinas...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)93017-6
更新日期:2005-01-01 00:00:00
abstract::Rab38 is a low-molecular-weight G-protein highly expressed in melanocytes of the skin and alveolar type II cells in the lung. A point mutation in the postulated GTP/GDP-interacting domain of Rab38 has been identified as the genetic lesion responsible for oculocutaneous albinism (OCA) in chocolate (cht) mice. Another p...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)38014-2
更新日期:2008-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)07022-9
更新日期:2006-01-01 00:00:00
abstract::Approximately one-third of all newly translated polypeptides interact with the endoplasmic reticulum (ER), an event that is essential to target these nascent proteins to distinct compartments within the cell or to the extracellular milieu. Thus, the ER houses molecular chaperones that augment the folding of this diver...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)70027-6
更新日期:2010-01-01 00:00:00
abstract::RNA and DNA carry out diverse functions in biology including catalysis, splicing, gene regulation, and storage of genetic information. Interest has grown in understanding how nucleic acids perform such sophisticated functions given their limited molecular repertoire. RNA can fold into diverse shapes that often perturb...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-801122-5.00009-X
更新日期:2014-01-01 00:00:00
abstract::The methods described here concern the use specialized glassware to achieve accurate sub-micromolar to low-millimolar dioxygen concentrations specifically for the study of flavoproteins. Since the early 1960s, these methods have been passed through the lineage of flavin enzymologists almost exclusively as an oral trad...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2019.03.005
更新日期:2019-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(09)05213-6
更新日期:2009-01-01 00:00:00
abstract::Crystallographic studies on flavodiiron proteins (FDPs) have revealed that the common sequence core ( approximately 400 residues) that defines this protein family comprises two structural domains. The N-terminal domain (of approximately 250 residues) displays a metallo-beta-lactamase-like-fold, being indeed structural...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(07)37001-8
更新日期:2008-01-01 00:00:00
abstract::Amyloid aggregates are associated with a number of mammalian neurodegenerative diseases. Infectious aggregates of the mammalian prion protein PrP(sc) are hallmarks of transmissible spongiform encephalopathies in humans and cattle (Griffith, 1967; Legname et al., 2004; Prusiner, 1982; Silveira et al., 2004). Likewise, ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(06)12003-0
更新日期:2006-01-01 00:00:00
abstract::We describe a method for molecular confinement and single-fluorophore sensitive measurement in aqueous nanodroplets in oil. The sequestration of individual molecules in droplets has become a useful tool in genomics and molecular evolution. Similarly, the use of single fluorophores, or pairs of fluorophores, to study b...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)72015-2
更新日期:2010-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)04019-X
更新日期:2005-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(08)02216-7
更新日期:2008-01-01 00:00:00
abstract::Nedd8 is a ubiquitin-like molecule that is highly conserved in eukaryotes. Similar to ubiquitin, Nedd8 attaches to target proteins through an enzymatic cascade composed of Nedd8-specific E1 (activating)- and E2 (conjugating)-enzymes. The E1 for Nedd8 is a heterodimer of APP-BP1 and Uba3, while the E2 is Ubc12. The mos...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)98007-5
更新日期:2005-01-01 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
pub_type: 杂志文章
doi:10.1016/0076-6879(87)39079-2
更新日期:1987-01-01 00:00:00
abstract::Membrane fission, which divides membrane surfaces into separate compartments, is essential to diverse cellular processes including membrane trafficking and cell division. Quantitative assays are needed to elucidate the physical mechanisms by which proteins drive membrane fission. Toward this goal, several experimental...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.08.014
更新日期:2018-01-01 00:00:00
abstract::Contemporary high-throughput sequencing methods, notably RNA-Seq, permit the systematic identification and characterization of transcripts whose levels change significantly in response to altered biological states. We have described methods for the application of this methodology to a definition of the transcripts reg...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.09.005
更新日期:2018-01-01 00:00:00
abstract::In polarized epithelial cells, the tight junction has been ascribed several functions including the regulation of the paracellular permeability, an impediment to the diffusion of molecules between the apical and basolateral domains, a site of delivery of transport vesicles for basolateral proteins, and a scaffold for ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)04029-2
更新日期:2005-01-01 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
pub_type: 杂志文章
doi:10.1016/s0076-6879(02)46076-4
更新日期:2002-01-01 00:00:00
abstract::Glycosaminoglycans (GAGs) are long unbranched polysaccharides, most of which are linked to a core protein to form proteoglycans. Depending on the nature of their backbone, one can discern galactosaminoglycans (chondroitin sulfate [CS] and dermatan sulfate [DS]) and glucosaminoglycans (heparan sulfate [HS], heparin, hy...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(06)16005-X
更新日期:2006-01-01 00:00:00