Abstract:
:Circadian clocks are present in most cells and are essential for maintenance of daily rhythms in physiology, mood, and cognition. Thus, not only neurons of the central circadian pacemaker but also many other peripheral tissues possess the same functional and self-sustained circadian clocks. Surprisingly, however, their properties vary widely within the human population. In recent years, this clock variance has been studied extensively both in health and in disease using robust lentivirus-based reporter technologies to probe circadian function in human peripheral cells as proxies for those in neurologically and physiologically relevant but inaccessible tissues. The same procedures can be used to investigate other conserved signal transduction cascades affecting multiple aspects of human physiology, behavior, and disease. Accessing gene expression variation within human populations via these powerful in vitro cell-based technologies could provide important insights into basic phenotypic diversity or to better interpret patterns of gene expression variation in disease.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Gaspar L,Brown SAdoi
10.1016/bs.mie.2014.10.023subject
Has Abstractpub_date
2015-01-01 00:00:00pages
231-56eissn
0076-6879issn
1557-7988pii
S0076-6879(14)00024-Xjournal_volume
552pub_type
杂志文章,评审abstract::Endothelial cell adhesion and migration is fundamental to a number of physiologic processes, including vascular development and angiogenesis. It has been investigated in a variety of contexts, including tumorigenesis, wound healing, tissue engineering, and biomaterial design. The chemical and mechanical extracellular ...
journal_title:Methods in enzymology
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doi:10.1016/S0076-6879(08)02003-X
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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
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doi:10.1016/S0076-6879(09)69019-4
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abstract::Neurofilament biology is important to understanding structural properties of axons, such as establishment of axonal diameter by radial growth. In order to study the function of neurofilaments, a series of genetically modified mice have been generated. Here, we describe a brief history of genetic modifications used to ...
journal_title:Methods in enzymology
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doi:10.1016/bs.mie.2015.07.027
更新日期:2016-01-01 00:00:00
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doi:10.1016/bs.mie.2017.12.006
更新日期:2018-01-01 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
pub_type: 杂志文章
doi:10.1016/B978-0-12-407865-9.00004-2
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abstract::Throughout the history of single-particle electron microscopy (EM), automated technologies have seen varying degrees of emphasis and development, usually depending upon the contemporary demands of the field. We are currently faced with increasingly sophisticated devices for specimen preparation, vast increases in the ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)83015-0
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abstract::Phospholipase A(2)s (PLA(2)s) are a superfamily of enzymes involved in production of a wide variety of lipid mediators, including arachidonic acid, lysophospholipids, platelet activation factor, and eicosanoids. Fluorescence-based, real-time cellular activity assays for PLA(2)s have been developed as a tool for studyi...
journal_title:Methods in enzymology
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doi:10.1016/S0076-6879(07)34002-0
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abstract::Advances in chemical synthesis and characterization of nucleic acids allows for atom-specific modification of complex RNAs, such as present in RNA editing substrates. By preparing substrates for ADARs by chemical synthesis, it is possible to subtly alter the structure of the edited nucleotide. Evaluating the effect th...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)24017-0
更新日期:2007-01-01 00:00:00
abstract::Antimicrosomal antibodies in inflammatory liver diseases all seem to be directed against members of the cytochrome P450 family of proteins. These autoantigens seem to be genetically polymorphic, the autoantibodies are inhibitory, and the autoepitopes are generally conserved among species. Anti-P450 autoantibodies shar...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/0076-6879(91)06092-h
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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
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)07002-3
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abstract::Coat protein complex II (COPII) vesicle-mediated protein export from the endoplasmic reticulum (ER) can be controlled by linear, independent motifs embedded within the cargo. ER export motifs directly interact with selective components of COPII vesicles and enhance cargo recruitment onto COPII vesicles. Moreover, ER e...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-391862-8.00010-7
更新日期:2013-01-01 00:00:00
abstract::Considering that HIV-1 accumulates and replicates actively within lymphoid tissues, any strategy that will decrease viral stores in these tissues might be beneficial to the infected host. Follicular dendritic cells (FDC), B lymphocytes, antigen-presenting cells like macrophages, and activated CD4(+) T cells are abunda...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(05)91019-7
更新日期:2005-01-01 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
pub_type: 杂志文章
doi:10.1016/bs.mie.2018.04.002
更新日期:2018-01-01 00:00:00
abstract::Glycoproteins are a major class of glycoconjugates displaying a variety of mutual interactions between glycan and protein moieties that ultimately affect molecular organization. Modulation of the pendant glycan structures is important in tuning the functions of glycoproteins. Here we discuss structural aspects and som...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(10)78018-6
更新日期:2010-01-01 00:00:00
abstract::Hybrid proteins or chimeras are generated by recombination of protein fragments. In the course of evolution, this mechanism has led to major diversification of protein folds and their functionalities. Similarly, protein engineers have taken advantage of this attractive strategy to build new proteins. Methods that use ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/B978-0-12-394292-0.00018-7
更新日期:2013-01-01 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
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.10.035
更新日期:2017-01-01 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
pub_type: 杂志文章
doi:10.1016/B978-0-12-391940-3.00011-1
更新日期:2012-01-01 00:00:00
abstract::Rarely is any solution simply solute and water. In vivo, solutes, such as proteins and nucleic acids, swim in a sea of water, salts, ions, small molecules, and lipids, not to mention other macromolecules. In vitro, virtually all solutions contain a mixture of aqueous solvents, or "cosolvents" [i.e., solvent(s) in addi...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/S0076-6879(07)28022-X
更新日期:2007-01-01 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
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(08)03408-3
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abstract::Death receptors are a subgroup of the tumor necrosis factor receptor superfamily (TNFRSF) and mediate activation of what is widely known as the "extrinsic" apoptosis pathway. TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) is one of the most recent death receptor ligands identified. The TRAIL receptor ...
journal_title:Methods in enzymology
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doi:10.1016/S0076-6879(08)01618-2
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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
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doi:10.1016/S0076-6879(05)03059-4
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abstract::The history of free radical biochemistry is briefly reviewed in respect to major trend shifts from the focus on radiation damage toward enzymology of radical production and removal and ultimately the role of radicals, hydroperoxides, and related fast reacting compounds in metabolic regulation. Selected aspects of the ...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(10)73001-9
更新日期:2010-01-01 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
pub_type: 杂志文章
doi:10.1016/bs.mie.2015.05.007
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abstract::Structural approaches have provided insight into the mechanisms of circadian clock oscillators. This review focuses upon the myriad structural methods that have been applied to the molecular architecture of cyanobacterial circadian proteins, their interactions with each other, and the mechanism of the KaiABC posttrans...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/bs.mie.2014.10.004
更新日期:2015-01-01 00:00:00
abstract::Since its major launch into academia in the mid-1990s, spotted DNA microarray technology has expanded and matured into an important mainstream tool for genomic-scale gene expression studies across many species with many applications. Based on the principles of enzymatic nucleic acid labeling and DNA hybridization, the...
journal_title:Methods in enzymology
pub_type: 杂志文章,评审
doi:10.1016/S0076-6879(06)10007-5
更新日期:2006-01-01 00:00:00
abstract::In principle, the long emission lifetimes of lanthanide chelates should enable their ultrasensitive detection in biological systems by time-resolved optical microscopy. However, most lanthanide-imaging systems cannot achieve sensitivities that exceed those of conventional fluorescence microscopes, since they are limit...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2020.04.030
更新日期:2020-01-01 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
pub_type: 杂志文章
doi:10.1016/S0076-6879(04)92019-8
更新日期:2005-01-01 00:00:00
abstract::Virtually all eukaryotic cell functions and signaling pathways are regulated by protein phosphorylation. The Rad53 kinase plays crucial roles in the DNA damage response in Saccharomyces cerevisiae and is widely used as a surrogate marker for DNA damage checkpoint activation by diverse genotoxic agents. Most currently ...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2016.09.032
更新日期:2017-01-01 00:00:00
abstract::This protocol describes the expression and analysis of membrane proteins produced in yeast, as illustrated with Yarrowia lipolytica and Pichia pastoris. Step by step, we explain how to generate a yeast strain expressing the membrane protein of interest, how to prepare a membrane protein sample from yeast, and how to a...
journal_title:Methods in enzymology
pub_type: 杂志文章
doi:10.1016/bs.mie.2014.12.010
更新日期:2015-01-01 00:00:00
abstract::Significant progress has been made in discovering and cloning a host of proteins, including a range of glycoproteins. The availability of their predicted amino acid sequences provides useful information, including potential N-linked glycosylation sites. However, only a limited number of protein structures have been so...
journal_title:Methods in enzymology
pub_type: 杂志文章
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更新日期:2006-01-01 00:00:00