Abstract:
:Video-based particle tracking monitors the microscopic movement of labeled biomolecules and fluorescent probes within a complex cellular environment. Information gained from this technique enables us to extract the dynamic behavior of biomolecules and the local mechanical properties inside the cell from a tracked particle's mean-square displacement (MSD). However, MSD measurements are highly susceptible to static error introduced by noise in the image acquisition process that leads to an incorrect positioning of the particle. Static error can mask the subtle effects from the local microenvironment on the MSD and potentially generate misleading conclusions about the biophysical properties of cells. An approach that greatly increases the accuracy of MSD measurements is presented herein by combining experimental data with Monte Carlo simulations to eliminate the inherent static error. This practical method of static error correction greatly advances particle-tracking techniques.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Wu PH,Arce SH,Burney PR,Tseng Ydoi
10.1016/j.bpj.2009.03.029subject
Has Abstractpub_date
2009-06-17 00:00:00pages
5103-11issue
12eissn
0006-3495issn
1542-0086pii
S0006-3495(09)00770-Xjournal_volume
96pub_type
杂志文章abstract::Thymine dimers were irradiated in aqueous solution with (60)Co gamma-rays in N(2) or O(2). Thymine and unidentified non-UV-absorbing products appeared. The thymine was identified by spectrophotometry, chromatography, and ability to support the growth of Escherichia coli 15 T(-). Residual dimer was determined by a UV-r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(68)86491-4
更新日期:1968-03-01 00:00:00
abstract::T cell receptor phosphorylation by Lck is an essential step in T cell activation. It is known that the conformational states of Lck control enzymatic activity; however, the underlying principles of how Lck finds its substrate over the plasma membrane remain elusive. Here, single-particle tracking is paired with photoa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.01.041
更新日期:2020-03-24 00:00:00
abstract::We present a molecular model of a chromatophore vesicle from Rhodobacter sphaeroides. These vesicles are ideal benchmark systems for molecular and systemic simulations, because they have been well studied, they are small, and they are naturally separated from their cellular environment. To set up a photosynthetic chai...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.067561
更新日期:2006-08-01 00:00:00
abstract::Amyloid diseases are traditionally characterized by the appearance of inter- and intracellular fibrillar protein deposits, termed amyloid. Historically, these deposits have been thought to be the etiology of the disease. However, recent evidence suggests that small oligomers of the amyloidogenic protein/peptide are th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.05.035
更新日期:2009-08-05 00:00:00
abstract::Cardiac contraction and relaxation dynamics result from a set of simultaneously interacting Ca(2+) regulatory mechanisms. In this study, cardiocyte Ca(2+) dynamics were modeled using a set of six differential equations that were based on theories, equations, and parameters described in previous studies. Among the uniq...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76276-X
更新日期:2000-07-01 00:00:00
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
更新日期:2017-08-08 00:00:00
abstract::Laser Raman spectroscopy has been used detect structural changes in troponin C induced by Ca2+ binding. Addition of Ca2+ - Mg2+ sites produces perturbations in the amide III region of the spectrum indicative of increased alpha-helical content, and in regions of the spectrum corresponding to carboxylate, thiol, and phe...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85099-5
更新日期:1980-05-01 00:00:00
abstract::Leukocyte capture and rolling on the vascular endothelium is mediated principally by the selectin family of cell adhesion receptors. In a parallel plate flow chamber, neutrophil rolling on purified selectins or a selectin-ligand substrate was resolved by high speed videomicroscopy as a series of ratchet-like steps wit...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77169-9
更新日期:1999-12-01 00:00:00
abstract::A mathematical model is formulated for the development of a population of cells in which the individual members may grow and divide or die. A given cell is characterized by its age and volume, and these parameters are assumed to determine the rate of volume growth and the probability per unit time of division or death...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(67)86592-5
更新日期:1967-07-01 00:00:00
abstract::The effects of rigor and cycling cross-bridges on distributions of calcium (Ca) bound within sarcomeres of rabbit psoas muscle fibers were compared using electron probe x-ray microanalysis. Calcium in the overlap region of rigor fibers, after correction for that bound to thick filaments, was significantly higher than ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.093757
更新日期:2007-01-15 00:00:00
abstract::The relationship between calcium current and transmitter release was studied in squid giant synapse. It was found that the voltage-dependent calcium current triggers the release of synaptic transmitter in direct proportion to its magnitude and duration. Transmitter release occurs with a delay of approximately 200 mus ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(81)84899-0
更新日期:1981-03-01 00:00:00
abstract::Current analyses of protein sequence/structure relationships have focused on expected similarity relationships for structurally similar proteins. To survey and explore the basis of these relationships, we present a general sequence/structure map that covers all combinations of similarity/dissimilarity relationships an...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(02)75287-9
更新日期:2002-11-01 00:00:00
abstract::A study on clonal growth in Chinese hamster ovary (CHO) cells was conducted after exposure to optical trapping wavelengths using Nd:YAG (1064 nm) and tunable titanium-sapphire (700-990 nm) laser microbeam optical traps. The nuclei of cells were exposed to optical trapping forces at various wavelengths, power densities...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79716-3
更新日期:1996-03-01 00:00:00
abstract::Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresol...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.04.035
更新日期:2011-06-08 00:00:00
abstract::beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81288-8
更新日期:1993-12-01 00:00:00
abstract::Molecular dynamics simulations of wild-type bacteriorhodopsin (bR) and of its D85N, D85T, D212N, and Y57F mutants have been carried out to investigate possible differences in the photoproducts of these proteins. For each mutant, a series of 50 molecular dynamics simulations of the photoisomerization and subsequent rel...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78781-2
更新日期:1997-03-01 00:00:00
abstract::We present direct quasielastic neutron scattering measurements, in vivo, of macromolecular dynamics in Escherichia coli. The experiments were performed on a wide range of timescales to cover the large panel of internal and self-diffusion motions. Three major internal processes were extracted at physiological temperatu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.124420
更新日期:2008-07-01 00:00:00
abstract::Many aspects of chromatin biology are influenced by the nuclear compartment in which a locus resides, from transcriptional regulation to DNA repair. Further, the dynamic and variable localization of a particular locus across cell populations and over time makes analysis of a large number of cells critical. As a conseq...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.05.036
更新日期:2016-07-12 00:00:00
abstract::An alternative theoretical approach to enzyme kinetics that is particularly applicable to single-molecule enzymology is presented. The theory, originated by Van Slyke and Cullen in 1914, develops enzyme kinetics from a "time perspective" rather than the traditional "rate perspective" and emphasizes the nonequilibrium ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.131771
更新日期:2008-07-01 00:00:00
abstract::The thermal transitions of fibrillar collagen are investigated with second-harmonic generation polarization anisotropy microscopy. Second-harmonic generation images and polarization anisotropy profiles of corneal stroma heated in the 35-80°C range are analyzed by means of a theoretical model that is suitable to probe ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.07.055
更新日期:2012-09-19 00:00:00
abstract::A recent theory for the long time dynamics of flexible chain molecules is applied for the first time to a peptide of biological importance, the neurotransmitter met-enkephalin. The dynamics of met-enkephalin is considerably more complicated than that of the previously studied glycine oligomers; met-enkephalin contains...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77185-7
更新日期:1999-01-01 00:00:00
abstract::A new electrophoresis model of charged components in a spherical phospholipid vesicle is proposed. In the new model the effective local tangential electric field is a result of the uniform external electric field modified by the electric field of redistributed charges. The modification is calculated on the basis of th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(97)78699-5
更新日期:1997-02-01 00:00:00
abstract::Amperometry recording reveals the exocytosis of catecholamine from individual vesicles as a sequential process, typically beginning slowly with a prespike foot, accelerating sharply to initiate a spike, reaching a peak, and then decaying. This complex sequence reflects the interplay between diffusion, flux through a f...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.06.001
更新日期:2020-07-07 00:00:00
abstract::Sharing of positive or negative regulators between multiple targets is frequently observed in cellular signaling cascades. For instance, phosphatase sharing between multiple kinases is ubiquitous within the MAPK pathway. Here we investigate how such phosphatase sharing could shape robustness and evolvability of the ph...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.10.037
更新日期:2018-01-09 00:00:00
abstract::Intercellular channels formed of members of the gene family of connexins (Cxs) vary from being substantially cation selective to being anion selective. We took advantage of the ability of Cx46 to function as an unopposed hemichannel to examine the basis of Cx charge selectivity. Previously we showed Cx46 hemichannels ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76539-8
更新日期:2000-12-01 00:00:00
abstract::The cell membrane having a transport system is inferred to be flexible when its function is being activated. For the brush border membrane vesicles prepared from rat small intestine, which have the co-transport system of Na+ and glucose, the membrane elasticity was measured as a function of the d-glucose concentration...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(88)83130-8
更新日期:1988-04-01 00:00:00
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
更新日期:2018-04-10 00:00:00
abstract::Experimental approaches such as fiber diffraction and cryo-electron microscopy reconstruction have defined regulatory positions of tropomyosin on actin but have not, as yet, succeeded at determining key atomic-level contacts between these proteins or fully substantiated the dynamics of their interactions at a structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.05.017
更新日期:2020-07-07 00:00:00
abstract::It has recently been observed in situ in mice that insulin takes approximately 10 min to be transported 20 microm into the t-tubule networks of skeletal muscle fibers. The mechanisms for this slow transport are unknown. It has been suggested that the biochemical composition of the t-tubular space that may include larg...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.107888
更新日期:2007-11-01 00:00:00
abstract::Many organisms are able to survive subzero temperatures at which bodily fluids would normally be expected to freeze. These organisms have adapted to these lower temperatures by synthesizing antifreeze proteins (AFPs), capable of binding to ice, which make further growth of ice energetically unfavorable. To date, the s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75821-3
更新日期:2001-09-01 00:00:00