Isochron-based phase response analysis of circadian rhythms.

Abstract:

:Circadian rhythms possess the ability to robustly entrain to the environmental cycles. This ability relies on the phase synchronization of circadian rhythm gene regulation to different environmental cues, of which light is the most obvious and important. The elucidation of the mechanism of circadian entrainment requires an understanding of circadian phase behavior. This article presents two phase analyses of oscillatory systems for infinitesimal and finite perturbations based on isochrons as a phase metric of a limit cycle. The phase response curve of circadian rhythm can be computed from the results of the analyses. The application to a mechanistic Drosophila circadian rhythm model gives experimentally testable hypotheses for the control mechanisms of circadian phase responses and evidence for the role of phase and period modulations in circadian photic entrainment.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Gunawan R,Doyle FJ 3rd

doi

10.1529/biophysj.105.078006

subject

Has Abstract

pub_date

2006-09-15 00:00:00

pages

2131-41

issue

6

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(06)71928-2

journal_volume

91

pub_type

杂志文章
  • Reversal of the surface charge asymmetry in purple membrane due to single amino acid substitutions.

    abstract::Twenty-seven mutant bacteriorhodopsin's were screened to determine the PKa for reversal of the permanent electric dipole moment. The photoelectric response of an aqueous purple-membrane suspension was used to determine the direction of the purple-membrane dipole moment as a function of pH. The pK(a) for the dipole rev...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79802-8

    authors: Hsu KC,Rayfield GW,Needleman R

    更新日期:1996-05-01 00:00:00

  • Quantitative Analysis of Spatial Distributions of All tRNA Genes in Budding Yeast.

    abstract::In the budding yeast nucleus, transfer RNA (tRNA) genes are considered to localize in the vicinity of the nucleolus; however, the use of Hi-C and fluorescent repressor-operator system techniques has clearly indicated that the tRNA genes are distributed not only around the nucleolus but also at other nuclear locations....

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2019.12.029

    authors: Tokuda N

    更新日期:2020-05-05 00:00:00

  • Farnesyltransferase--new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism.

    abstract::Despite the enormous interest that has been devoted to the study of farnesyltransferase, many questions concerning its catalytic mechanism remain unanswered. In particular, several doubts exist on the structure of the active-site zinc coordination sphere, more precisely on the nature of the fourth ligand, which is dis...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.048207

    authors: Sousa SF,Fernandes PA,Ramos MJ

    更新日期:2005-01-01 00:00:00

  • Bacteriorhodopsin/amphipol complexes: structural and functional properties.

    abstract::The membrane protein bacteriorhodopsin (BR) can be kept soluble in its native state for months in the absence of detergent by amphipol (APol) A8-35, an amphiphilic polymer. After an actinic flash, A8-35-complexed BR undergoes a complete photocycle, with kinetics intermediate between that in detergent solution and that...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.121848

    authors: Gohon Y,Dahmane T,Ruigrok RW,Schuck P,Charvolin D,Rappaport F,Timmins P,Engelman DM,Tribet C,Popot JL,Ebel C

    更新日期:2008-05-01 00:00:00

  • New ordered metastable phases between the gel and subgel phases in hydrated phospholipids.

    abstract::Formation of low-temperature ordered gel phases in several fully hydrated phosphatidylethanolamines (PEs) and phosphatidylcholines (PCs) with saturated chains as well as in dipalmitoylphosphatidylglycerol (DPPG) was observed by synchrotron x-ray diffraction, microcalorimetry, and densitometry. The diffraction patterns...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(01)76157-7

    authors: Tenchov B,Koynova R,Rapp G

    更新日期:2001-04-01 00:00:00

  • Molecular origin of the L-type Ca2+ current of skeletal muscle myotubes selectively deficient in dihydropyridine receptor beta1a subunit.

    abstract::The origin of Ibetanull, the Ca2+ current of myotubes from mice lacking the skeletal dihydropyridine receptor (DHPR) beta1a subunit, was investigated. The density of Ibetanull was similar to that of Idys, the Ca2+ current of myotubes from dysgenic mice lacking the skeletal DHPR alpha1S subunit (-0.6 +/- 0.1 and -0.7 +...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(98)77507-1

    authors: Strube C,Beurg M,Sukhareva M,Ahern CA,Powell JA,Powers PA,Gregg RG,Coronado R

    更新日期:1998-07-01 00:00:00

  • A Thermodynamic Model for Genome Packaging in Hepatitis B Virus.

    abstract::Understanding the fundamentals of genome packaging in viral capsids is important for finding effective antiviral strategies and for utilizing benign viral particles for gene therapy. While the structure of encapsidated genomic materials has been routinely characterized with experimental techniques such as cryo-electro...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2015.08.021

    authors: Kim J,Wu J

    更新日期:2015-10-20 00:00:00

  • Free energies of molecular bound states in lipid bilayers: lethal concentrations of antimicrobial peptides.

    abstract::The lipid matrix, or the lipid bilayer, of cell membranes is a natural binding site for amphipathic molecules, including antimicrobial peptides, pore-forming proteins, and many drugs. The unique property of pore-forming antimicrobial peptides is that they exhibit a threshold concentration (called the lethal concentrat...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.01.030

    authors: Huang HW

    更新日期:2009-04-22 00:00:00

  • Novel chelate-induced magnetic alignment of biological membranes.

    abstract::A phospholipid chelate complexed with ytterbium (DMPE-DTPA:Yb3+) is shown to be readily incorporated into a model membrane system, which may then be aligned in a magnetic field such that the average bilayer normal lies along the field. This so-called positively ordered smectic phase, whose lipids consist of less than ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(98)77659-3

    authors: Prosser RS,Volkov VB,Shiyanovskaya IV

    更新日期:1998-11-01 00:00:00

  • Role of Inverse-Cone-Shape Lipids in Temperature-Controlled Self-Reproduction of Binary Vesicles.

    abstract::We investigate a temperature-driven recursive division of binary giant unilamellar vesicles (GUVs). During the heating step of the heating-cooling cycle, the spherical mother vesicle deforms to a budded limiting shape using up the excess area produced by the chain melting of the lipids and then splits off into two dau...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2016.02.028

    authors: Jimbo T,Sakuma Y,Urakami N,Ziherl P,Imai M

    更新日期:2016-04-12 00:00:00

  • Osmotic pressure and packaging structure of caged DNA.

    abstract::We present a theoretical model for aqueous solutions of double-stranded (ds) DNA with explicit consideration of electrostatic interactions, excluded-volume effects, van der Waals attractions, and salt ions. With reasonable parameters estimated from the DNA structure and experimental data for electrolytes, we are able ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.112508

    authors: Li Z,Wu J,Wang ZG

    更新日期:2008-02-01 00:00:00

  • Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise.

    abstract::Genetically identical cells exhibit diverse phenotypes even when experiencing the same environment. This phenomenon in part originates from cell-to-cell variability (noise) in protein expression. Although various kinetic schemes of stochastic transcription initiation are known to affect gene expression noise, how post...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.02.010

    authors: Kim S,Jacobs-Wagner C

    更新日期:2018-04-10 00:00:00

  • Solvation, water permeation, and ionic selectivity of a putative model for the pore region of the voltage-gated sodium channel.

    abstract::This paper describes a molecular dynamics and molecular mechanics study of the solvation and selectivity of the narrow pore and vestibule region of a model-built structure for the voltage-gated sodium channel. The particular structure used was one proposed by Guy and Durell. However, many of the features we saw would ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79438-9

    authors: Singh C,Sankararamakrishnan R,Subramaniam S,Jakobsson E

    更新日期:1996-11-01 00:00:00

  • Magnetoreception through cryptochrome may involve superoxide.

    abstract::In the last decades, it has been demonstrated that many animal species orient in the Earth magnetic field. One of the best-studied examples is the use of the geomagnetic field by migratory birds for orientation and navigation. However, the biophysical mechanism underlying animal magnetoreception is still not understoo...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.03.048

    authors: Solov'yov IA,Schulten K

    更新日期:2009-06-17 00:00:00

  • Molecular probes: what is the range of their interaction with the environment?

    abstract::We performed pressure-tuning hole-burning experiments on a modified cytochrome c protein in a glycerol/buffer glass. The shift and the broadening of the holes were investigated for various frequencies within the inhomogeneous band. On the basis of a simple model, we were able to estimate the interaction range between ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(04)74124-7

    authors: Lesch H,Schlichter J,Friedrich J,Vanderkooi JM

    更新日期:2004-01-01 00:00:00

  • The Influence of Crowding Conditions on the Thermodynamic Feasibility of Metabolic Pathways.

    abstract::Intracellular reactions are carried out in a crowded medium where the macromolecules occupy ∼40% of the total volume. This decrease in the available volume affects the activity of the reactants. Scaled particle theory is used for the estimation of the activity coefficients of the metabolites, and thereby for the asses...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2015.09.030

    authors: Angeles-Martinez L,Theodoropoulos C

    更新日期:2015-12-01 00:00:00

  • Equilibrium and kinetics of DNA overstretching modeled with a quartic energy landscape.

    abstract::It is well known that the dsDNA molecule undergoes a phase transition from B-DNA into an overstretched state at high forces. For some time, the structure of the overstretched state remained unknown and highly debated, but recent advances in experimental techniques have presented evidence of more than one possible phas...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2014.09.014

    authors: Argudo D,Purohit PK

    更新日期:2014-11-04 00:00:00

  • Non-bias-limited tracking of spherical particles, enabling nanometer resolution at low magnification.

    abstract::We present a three-dimensional tracking routine for nondiffraction-limited particles, which significantly reduces pixel bias. Our technique allows for increased resolution compared to that of previous methods, especially at low magnification or at high signal/noise ratio. This enables tracking with nanometer accuracy ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.03.073

    authors: van Loenhout MT,Kerssemakers JW,De Vlaminck I,Dekker C

    更新日期:2012-05-16 00:00:00

  • Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains.

    abstract::Segmentation of the Drosophila melanogaster embryo results from the dynamic establishment of spatial mRNA and protein patterns. Here, we exploit recent temporal mRNA and protein expression measurements on the full surface of the blastoderm to calibrate a dynamical model of the gap gene network on the entire embryo cor...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2011.05.060

    authors: Bieler J,Pozzorini C,Naef F

    更新日期:2011-07-20 00:00:00

  • Effects of bath resistance on action potentials in the squid giant axon: myocardial implications.

    abstract::This study presents a simplified version of the quasi-one-dimensional theory (Wu, J., E. A. Johnson, and J. M. Kootsey. 1996. A quasi-one-dimensional theory for anisotropic propagation of excitation in cardiac muscle. Biophys. J. 71:2427-2439) with two components of the extracellular current, along and perpendicular t...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(97)78265-1

    authors: Wu J,Wikswo JP Jr

    更新日期:1997-11-01 00:00:00

  • Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching.

    abstract::Phytochromes sense red/far-red light and control many biological processes in plants, fungi, and bacteria. Although the crystal structures of dark- and light-adapted states have been determined, the molecular mechanisms underlying photoactivation remain elusive. Here, we demonstrate that the conserved tongue region of...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2019.11.025

    authors: Gustavsson E,Isaksson L,Persson C,Mayzel M,Brath U,Vrhovac L,Ihalainen JA,Karlsson BG,Orekhov V,Westenhoff S

    更新日期:2020-01-21 00:00:00

  • Na-K-2Cl Cotransporter and Store-Operated Ca2+ Entry in Pacemaking by Interstitial Cells of Cajal.

    abstract::Pacemaker depolarization in interstitial cells of Cajal (ICCs) is believed to be induced by Ca2+ transients and activation of anoctamin-1 (Ano1) channels in the plasma membrane. However, block of store-operated calcium entry (SOCE) or the Na-K-2Cl cotransporter (NKCC1) terminates pacemaker activity in ICC, indicating ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2019.07.020

    authors: Youm JB,Zheng H,Koh SD,Sanders KM

    更新日期:2019-08-20 00:00:00

  • Spin States of divalent iron in anhydrohemoglobin.

    abstract::Mössbauer spectra of anhydrohemoglobin establish the existence of two ferrous iron spin states in anhydrohemoglobin. Magnetic susceptibility measurements show that anhydrohemoglobin is paramagnetic and has an effective magnetic moment per iron atom of 3.5+/-0.1mu(B) at low temperatures. In conjunction with the suscept...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(67)86614-1

    authors: Grant RW,Cape JA,Gonser U,Topol LE,Saltman P

    更新日期:1967-11-01 00:00:00

  • Fibrin assembly. Lateral aggregation and the role of the two pairs of fibrinopeptides.

    abstract::The structural basis of the wide variability of the physical properties of fibrin clots and the process of assembly of the clot were investigated by electron microscopy of fibers formed under various ionic conditions. In addition, highly specific proteolytic enzymes from different snake venoms were used to remove sele...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(86)83552-4

    authors: Weisel JW

    更新日期:1986-12-01 00:00:00

  • Interspike interval fluctuations in the crayfish stretch receptor.

    abstract::Trains of nerve impulses from the crayfish stretch receptor under steady conditions are found to be extremely regular with a standard deviation of S = 0.7 x 10(-2)tau when tau, the mean interval, is in the 15 to 80 msec range. Such a small fluctuation increases the problems of film recording, accurate measurement of i...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(66)86651-1

    authors: Firth DR

    更新日期:1966-03-01 00:00:00

  • Molecular restraints in the permeation pathway of ion channels.

    abstract::Ion channels assist and control the diffusion of ions through biological membranes. The conduction process depends on the structural characteristics of these nanopores, among which are the hydrophobicity and the afforded diameter of the conduction pathway. In this contribution, we use full atomistic free-energy molecu...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.087437

    authors: Treptow W,Tarek M

    更新日期:2006-08-01 00:00:00

  • Binding of alkaline cations to the double-helical form of gramicidin.

    abstract::Gramicidin is a polypeptide antibiotic that forms monovalent cation-specific channels in membrane environments. In organic solvents and in lipids containing unsaturated fatty acid chains, it forms a double-helical "pore" structure, in which two monomers are intertwined. This form of gramicidin can bind two cations ins...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79213-5

    authors: Chen Y,Wallace BA

    更新日期:1996-07-01 00:00:00

  • Hsp70 Inhibits Aggregation of IAPP by Binding to the Heterogeneous Prenucleation Oligomers.

    abstract::Molecular chaperone Hsp70 plays important roles in the pathology of amyloid diseases by inhibiting aberrant aggregation of proteins. However, the biophysical mechanism of the interaction of Hsp70 with the intrinsically disordered proteins (IDPs) is unclear. Here, we report that Hsp70 inhibits aggregation of islet amyl...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2020.12.019

    authors: Chilukoti N,Sil TB,Sahoo B,Deepa S,Cherakara S,Maddheshiya M,Garai K

    更新日期:2021-01-06 00:00:00

  • Two mechanisms by which fluorescent oxonols indicate membrane potential in human red blood cells.

    abstract::Optical potentiometric indicators have been used to monitor the transmembrane electrical potential (Em) of many cells and organelles. A better understanding of the mechanisms of dye response is needed for the design of dyes with improved responses and for unambiguous interpretation of experimental results. This paper ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(90)82603-5

    authors: Pratap PR,Novak TS,Freedman JC

    更新日期:1990-04-01 00:00:00

  • Mechanism for Triggered Waves in Atrial Myocytes.

    abstract::Excitation-contraction coupling in atrial cells is mediated by calcium (Ca) signaling between L-type Ca channels and Ryanodine receptors that occurs mainly at the cell boundary. This unique architecture dictates essential aspects of Ca signaling under both normal and diseased conditions. In this study we apply laser s...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.06.026

    authors: Shiferaw Y,Aistrup GL,Wasserstrom JA

    更新日期:2017-08-08 00:00:00