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 consequence, robust and automatable methods to measure the position of individual loci within the nuclear volume in populations of cells are necessary to support quantitative analysis of nuclear position. Here, we describe a three-dimensional membrane reconstruction approach that uses fluorescently tagged nuclear envelope or endoplasmic reticulum membrane marker proteins to precisely map the nuclear volume. This approach is robust to a variety of nuclear shapes, providing greater biological accuracy than alternative methods that enforce nuclear circularity, while also describing nuclear position in all three dimensions. By combining this method with established approaches to reconstruct the position of diffraction-limited chromatin markers-in this case, lac Operator arrays bound by lacI-GFP-the distribution of loci positions within the nuclear volume with respect to the nuclear periphery can be quantitatively obtained. This stand-alone image analysis pipeline should be of broad practical utility for individuals interested in various aspects of chromatin biology, while also providing, to our knowledge, a new conceptual framework for investigators who study organelle shape.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Zhao Y,Schreiner SM,Koo PK,Colombi P,King MC,Mochrie SGdoi
10.1016/j.bpj.2016.05.036subject
Has Abstractpub_date
2016-07-12 00:00:00pages
19-24issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(16)30361-7journal_volume
111pub_type
杂志文章abstract::39K nuclear magnetic resonance (NMR) spectra were readily obtained, in vivo, from rat muscle, kidney, and brain in 5-10 min with signal-to-noise ratios of approximately 20:1. Quantitation of the K+ signal was achieved by reference to an external standard of KCl/dysprosium nitrate as well as by reference to the proton ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83332-5
更新日期:1987-02-01 00:00:00
abstract::Giant vesicles formed of 1,2-dipalmitoylphosphatidylcholine (DPPC) and sterols (cholesterol or ergosterol) in water and water/ethanol solutions have been used to examine the effect of sterol composition and ethanol concentration on the area compressibility modulus (K(a)), overall mechanical behavior, vesicle morpholog...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.057943
更新日期:2005-10-01 00:00:00
abstract::Photoreverse reactions of octopus rhodopsin (Rh) from acid-metarhodopsin (Acid-Meta), which is the final product of the photoreaction of Rh, to Rh were studied by the time-resolved transient absorption and transient grating methods. The time course of the absorption signal showed a rapid change within 500 ns followed ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.101741
更新日期:2007-05-15 00:00:00
abstract::The p7 protein from hepatitis C virus is critical for the assembly and secretion of infectious virus, making it an attractive drug target. It is thought to be a viroporin with a demonstrated ion channel activity when reconstituted into planar lipid bilayers. Electron microscopy experiments suggest that p7 oligomers co...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2008.10.004
更新日期:2009-01-01 00:00:00
abstract::Many studies of specific protein-nucleic acid binding use short oligonucleotides or restriction fragments, in part to minimize the potential for nonspecific binding of the protein. However, when the specificity ratio is low, multiple nonspecifically bound proteins may occupy the region of DNA corresponding to one spec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75847-X
更新日期:2001-10-01 00:00:00
abstract::The pKa values of ionizable groups that lie between the active site region of bacteriorhodopsin (bR) and the extracellular surface of the protein are reported. Glu-204 is found to have an elevated pKa in the resting state of bR, suggesting that it corresponds to the proton-releasing group in bR. Its elevated pKa is pr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79320-7
更新日期:1996-09-01 00:00:00
abstract::We introduce here a novel Monte Carlo simulation method for studying the interactions of hydrophobic peptides with lipid membranes. Each of the peptide's amino acids is represented as two interaction sites: one corresponding to the backbone alpha-carbon and the other to the side chain, with the membrane represented as...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74765-1
更新日期:2003-12-01 00:00:00
abstract::We present a theoretical and experimental analysis of the effects of nonlinear flow in a cone-plate viscometer. The analysis predicts that flow in the viscometer is a function of two parameters, the Reynolds number and the cone angle. Nonlinear flow occurs at high shear rates and causes spatial variations in wall shea...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76233-9
更新日期:2001-06-01 00:00:00
abstract::An understanding of the structure-dynamics relationship is essential for understanding how a protein works. Prior research has shown that the activity of a protein correlates with intradomain dynamics occurring at picosecond to millisecond timescales. However, the correlation between interdomain dynamics and the funct...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.06.010
更新日期:2020-07-21 00:00:00
abstract::Reverberating spontaneous synchronized brain activity is believed to play an important role in neural information processing. Whether and how external stimuli can influence this spontaneous activity is poorly understood. Because periodic synchronized network activity is also prominent in in vitro neuronal cultures, we...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.112730
更新日期:2008-06-01 00:00:00
abstract::Cartilage has a limited capacity for self-repair and focal damage can eventually lead to complete degradation of the tissue. Early diagnosis of degenerative changes in cartilage is therefore essential. Contrast agent-based computed tomography and magnetic resonance imaging provide promising tools for this purpose. How...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.04.041
更新日期:2014-07-15 00:00:00
abstract::The four-way DNA (Holliday) junction is an important postulated intermediate in the process of genetic recombination. Earlier studies have suggested that the junction exists in two alternative conformations, depending upon the salt concentration present. At high salt concentrations the junction folds into a stacked X ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(94)80765-9
更新日期:1994-01-01 00:00:00
abstract::An attempt was made to confirm previous reports of resonant-like dielectric absorption of plasmid DNA in aqueous solutions at 1-10 GHz. The dielectric properties of the sample were measured using an automatic network analyzer with two different techniques. One technique used an open-ended coaxial probe immersed in the...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83231-9
更新日期:1987-09-01 00:00:00
abstract::We studied the photocurrents of a cyanobacterial rhodopsin Gloeobacter violaceus (GR) in Xenopus laevis oocytes and HEK-293 cells. This protein is a light-driven proton pump with striking similarities to marine proteorhodopsins, including the D121-H87 cluster of the retinal Schiff base counterion and a glutamate at po...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.08.031
更新日期:2013-11-05 00:00:00
abstract::A detailed treatment is provided of the various free-energy terms that contribute to the transfer of a polyalanine alpha-helix from the aqueous phase into lipid bilayers. In agreement with previous work, the hydrophobic effect is found to provide the major driving force for helix insertion. However, an opposing effect...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79744-8
更新日期:1996-04-01 00:00:00
abstract::The orientational ordering of beta-carotene and crocetin embedded in lamellar model membranes has been investigated by angle-resolved resonance Raman scattering at a temperature well above the phase transition of the lipid chains. It is shown that the ordering of the carotenoids is dependent on the chemical compositio...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84269-1
更新日期:1984-06-01 00:00:00
abstract::A new Fourier series representation of supercoiled DNA is employed in Langevin dynamics simulations to study large-scale configurational motions of intermediate-length chains. The polymer is modeled as an ideal elastic rod subject to long-range van der Waals' interactions. The van der Waals' term prevents the self-con...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78205-5
更新日期:1997-10-01 00:00:00
abstract::Under the assumption that vesicles are the anatomic correlate of quantal release, the forces governing the movement of synaptic vesicles inside neurons are analyzed. Semiquantitative calculations are presented to show that a diffuse layer field penetrates a few Debye lengths into the axoplasm. This field binds tightly...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(73)85973-9
更新日期:1973-02-01 00:00:00
abstract::Elastin-derived peptides are released from the extracellular matrix remodeling by numerous proteases and seem to regulate many biological processes, notably cancer progression. The canonical elastin peptide is VGVAPG, which harbors the XGXXPG consensus pattern, allowing interaction with the elastin receptor complex lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.04.019
更新日期:2020-06-02 00:00:00
abstract::We investigate the microsecond-timescale kinetics of the RNA hairpin ga*cUUCGguc. The fluorescent nucleotide 2-aminopurine (a*) reports mainly on base stacking. Ten kinetic traces and the temperature denaturation curve are globally fitted to four-state models of the free-energy surface. In the best-fitting sequential ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.06.035
更新日期:2009-09-02 00:00:00
abstract::4',6-diamidino-2-phenylindole (DAPI), netropsin, and pentamidine are minor groove binders that have terminal -C(NH2)2+ groups. The hydration changes that accompany their binding to the minor groove of the (AATT)2 sequence have been studied using the osmotic stress technique with fluorescence spectroscopy. The affinity...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.097451
更新日期:2007-02-01 00:00:00
abstract::The yolk granule is the most abundant membrane-bound organelle present in sea urchin eggs and embryos. The major protein component of this organelle, toposome, accounts for approximately 50% of the total yolk protein and has been shown to be localized to the embryonic cell surface. Extensive characterization in severa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.089979
更新日期:2006-12-15 00:00:00
abstract::This study aims to define the role of E-cadherin (Ecad) engagement in cell-cell contact during membrane-cortex interaction. As a tool, we used a hydrodynamic membrane tube extrusion technique to characterize the mechanical interaction between the plasma membrane and the underlying cortical cytoskeleton. Cells were anc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.11.059
更新日期:2009-03-18 00:00:00
abstract::Employing nonequilibrium molecular dynamics simulations, a comprehensive computational study of the photoinduced conformational dynamics of a photoswitchable bicyclic azobenzene octapeptide is presented. The calculation of time-dependent probability distributions along various global and local reaction coordinates rev...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.084996
更新日期:2006-08-15 00:00:00
abstract::It is shown that if x(t) is the solution of a second order differential equation, with real negative characteristic roots (not necessarily distinct), which exhibits an extremum at t = T, then T|x(T)|/|A| [UNK] 1/e where A is the area under the x(t) curve. This result is compared to a special case previously derived by...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(61)86910-5
更新日期:1961-09-01 00:00:00
abstract::Potassium accumulation associated with outward membrane potassium current was investigated experimentally in myelinated fibers and analyzed in terms of two models-three-compartment and diffusion in an unstirred layer. In the myelinated fibers, as in squid giant axons, the three-compartment model satisfactorily describ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85028-4
更新日期:1980-12-01 00:00:00
abstract::High speed cinemicrographs were made of sea urchin sperm at temperatures varying from 22 to 6 degrees C. Apparatus, combining a television camera and a video digitizer, was constructed to scan individual flagellar images and to digitize the flagellar waveforms. With appropriate smoothing and averaging procedures, the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83931-X
更新日期:1985-03-01 00:00:00
abstract::Helix-coil transitions in polyalanine molecules of length 10 are studied by multi-canonical Monte Carlo simulations. The solvation effects are included by either a distance-dependent dielectric permittivity or by a term that is proportional to the solvent-accessible surface area of the peptide. We found a strong depen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75668-3
更新日期:2002-06-01 00:00:00
abstract::Stochastic effects in gene expression may result in different physiological states of individual cells, with consequences for pathogen survival and artificial gene network design. We studied the contributions of a regulatory factor to gene expression noise in four basic mechanisms of negative gene expression control: ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2008.09.052
更新日期:2009-01-01 00:00:00
abstract::A recently completed model of Ca concentration and movements in the cardiac cell diadic cleft space predicts that removal or neutralization of inner sarcolemmal (SL) leaflet anionic Ca-binding sites at the sarcolemmal border of this space will greatly diminish Na/Ca exchange-mediated Ca efflux. The present study tests...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79792-8
更新日期:1996-05-01 00:00:00