Showing papers in "Biophysical Journal in 2008"

TL;DR: This work describes how spatially structured illumination microscopy can be applied in three dimensions to double the axial as well as the lateral resolution, with true optical sectioning, and has produced the first light microscopy images of the synaptonemal complex in which the lateral elements are clearly resolved.

TL;DR: This work demonstrates that the mechanical and biochemical properties of an aNSC microenvironment can be tuned to regulate the self-renewal and differentiation of aN SCs.

TL;DR: The phasor approach has the potential to simplify the way data are analyzed in FLIM, paving the way for the analysis of large data sets and, in general, making the FLIM technique accessible to the nonexpert in spectroscopy and data analysis.

TL;DR: An enzymatic oxygen scavenging system for improved dye stability in single-molecule experiments and it is found that biological reducing agents increase both the frequency and duration of blinking events of Cy5, an effect that scales with reducing potential.

TL;DR: Experimental and computational advances in improving the resolution and reliability of traction force microscopy are reported and fibroblast traction is reconstructed for the first time with a spatial resolution of approximately 1 microm.

TL;DR: An improved method for determining lipid areas helps to reconcile long-standing differences in the values of lipid areas obtained from stand-alone x-ray and neutron scattering experiments and poses new challenges for molecular dynamics simulations.

TL;DR: The relationship between the distribution in membranes, bulk partitioning to cyclohexane, and several amino acid hydrophobicity scales is discussed and the results give detailed insight in the molecular basis of the preferred location and orientation of each side chain.

TL;DR: The voltage-driven translocation dynamics of individual DNA molecules through solid-state nanopores in the diameter range 2.7-5 nm are investigated, finding a transition in the fraction of ion current blocked by DNA, from a length-independent regime for short DNA molecules to a regime where the longer the DNA, the more current is blocked.

TL;DR: It is shown that alignment of collagen perpendicular to the tumor-explant boundary promotes local invasion of both human and mouse mammary epithelial cells, which supports the conclusion that Rho-mediated matrix alignment is an early step in the invasion process, preceding and subsequently facilitating 3D migration.

TL;DR: It is demonstrated, on examples of several common fluorescent dyes, that sFCS can be used to measure D with high precision without a need for a standard, and the correct value of D can be determined in the presence of weak photobleaching, and when the measurement volume size is modified, indicating the robustness of the method.

TL;DR: It is concluded that extracellular stiffness near that of native myocardium significantly enhances neonatal rat ventricular myocytes maturation and appears to involve RhoA kinase.

TL;DR: A technique based on moment-analysis for the measurement of the average number of molecules and brightness in each pixel in fluorescence microscopy images is described, which reveals binding dynamics at the focal adhesions with pixel resolution and provides a picture of the binding and unbinding process.

TL;DR: A revision to the CHARMM ether force field is shown to reproduce experimentally observed conformational populations of dimethoxyethane and low molecular weight PEG behaves as an ideal chain.

TL;DR: It is shown that bleb nucleation depends on pressure, membrane-cortex adhesion energy, and membrane tension, and is tested experimentally to find that retracting blebs are fivefold more rigid than expanding blebs, an increase entirely explained by the properties of the newly formed cortical actin mesh.

TL;DR: It is theoretically confirmed that the intermolecular coordination and hydrogen bonds between Pchlide a and methanol molecules can be strengthened in the electronically excited state of PchLide a.

TL;DR: Simulation of Ala(5) in water finds that most current force fields do overpopulate the alpha-region, with quantitative results depending on the choice of Karplus relation and on the peptide termini, while experiments on short peptides open the way toward the systematic improvement of current simulation models.

TL;DR: This group contribution method is demonstrated to be capable of estimating Delta(r)G'(o) and Delta(f)G (o) for the majority of the biochemical compounds and reactions found in the iJR904 and iAF1260 genome-scale metabolic models of Escherichia coli and in the Kyoto Encyclopedia of Genes and Genomes and University of Minnesota Biocatalysis and Biodegradation Database.

TL;DR: This work finds that cells can detect and respond to substrate strains created by the traction stresses of a neighboring cell, and that this response is dependent on matrix stiffness, and indicates that cells have the ability to communicate mechanically through their matrix.

TL;DR: The mathematical basis of the phenomenon is explained, it is related to spatial segregation of Rho GTPases, and it is shown how it can account for spatial amplification and maintenance of polarity, as well as sensitivity to new stimuli typical in polarization of eukaryotic cells.

TL;DR: It is shown that shallow rodlike inclusions are more effective in membrane shaping than are lipids having a high propensity for curvature, and the ability of an inclusion to bend membranes by an effective spontaneous curvature is characterized.

TL;DR: A ten-microsecond simulation of an incipient downhill-folding WW domain mutant along with measurement of a molecular time and activated folding time of 1.5 microseconds and 13.3 microseconds is reported.

TL;DR: Investigation of the effect of the three-dimensional microstructure of collagen-glycosaminoglycan scaffolds on the migratory behavior of individual mouse fibroblasts shows that the fibroblast migration, characterized by motile fraction as well as locomotion speed, decreases as scaffold pore size increases across a range from 90 to 150 mum.

TL;DR: X-ray diffuse scattering was measured from oriented stacks and unilamellar vesicles of dioleoylphosphatidylcholine lipid bilayers to obtain the temperature dependence of the structure and of the material properties, and interactions between bilayers were found to be nearly independent of temperature.

TL;DR: A point model of the cardiac myofilament is developed to simulate a wide variety of experimental muscle characterizations including Force-Ca relations and twitches under isometric, isosarcometric, isotonic, and auxotonic conditions and demonstrates that the feedback effects of force on Ca binding to troponin can modify the cytosolic Ca transient.

TL;DR: In this article, the temperature dependence of line tension between liquid domains and of fluctuation correlation lengths in lipid membranes was quantitatively evaluated to obtain a critical exponent, nu = 1.2 +/- 0.2.

TL;DR: The results suggest that cellular contractility can be sensitively regulated by tuning the (local) activity of molecular motors and the cross-linker density and binding affinity.

TL;DR: The results suggest that the stress-strain behavior of collagen fibrils is dictated by global characteristic dimensions as well as internal structure.

TL;DR: A statistical theory is developed to facilitate direct comparison of experimental prepore formation kinetics with the (single event) preporation times derived from the simulations, which also allows us to extract an effective number of lipids involved in each pore formation event.

TL;DR: Using MUM and MUMLA, the full 3D trajectories of QD-labeled antibody molecules undergoing endocytosis in live cells from the plasma membrane to the sorting endosome deep inside the cell are reported for the first time.

TL;DR: A computational study of membrane bending by BAR domains at four levels of resolution, described by 1), all-atom molecular dynamics; 2), residue-based coarse-graining (resolving single amino acids and lipid molecules); 3), shape- based coarse- graining (Resolving overall protein and membrane shapes); and 4), a continuum elastic membrane model.