Bogomol'nyi Decomposition for Vesicles of Arbitrary Genus

We apply the Bogomol'nyi technique, which is usually invoked in the study of solitons or models with topological invariants, to the case of elastic energy of vesicles. We show that spontaneous bending contribution caused by any deformation from metastable bending shapes falls in two distinct topological sets: shapes of spherical topology and shapes of non-spherical topology experience respectively a deviatoric bending contribution a la Fischer and a mean curvature bending contribution a la Helfrich. In other words, topology may be considered to describe bending phenomena. Besides, we calculate the bending energy per genus and the bending closure energy regardless of the shape of the vesicle. As an illustration we briefly consider geometrical frustration phenomena experienced by magnetically coated vesicles.Comment: 8 pages, 1 figure; LaTeX2e + IOPar

Self-Dual Bending Theory for Vesicles

We present a self-dual bending theory that may enable a better understanding of highly nonlinear global behavior observed in biological vesicles. Adopting this topological approach for spherical vesicles of revolution allows us to describe them as frustrated sine-Gordon kinks. Finally, to illustrate an application of our results, we consider a spherical vesicle globally distorted by two polar latex beads.Comment: 10 pages, 3 figures, LaTeX2e+IOPar

Toolbox for analyzing finite two-state trajectories

In many experiments, the aim is to deduce an underlying multi-substate on-off kinetic scheme (KS) from the statistical properties of a two-state trajectory. However, the mapping of a KS into a two-state trajectory leads to the loss of information about the KS, and so, in many cases, more than one KS can be associated with the data. We recently showed that the optimal way to solve this problem is to use canonical forms of reduced dimensions (RD). RD forms are on-off networks with connections only between substates of different states, where the connections can have non-exponential waiting time probability density functions (WT-PDFs). In theory, only a single RD form can be associated with the data. To utilize RD forms in the analysis of the data, a RD form should be associated with the data. Here, we give a toolbox for building a RD form from a finite two-state trajectory. The methods in the toolbox are based on known statistical methods in data analysis, combined with statistical methods and numerical algorithms designed specifically for the current problem. Our toolbox is self-contained - it builds a mechanism based only on the information it extracts from the data, and its implementation on the data is fast (analyzing a 10^6 cycle trajectory from a thirty-parameter mechanism takes a couple of hours on a PC with a 2.66 GHz processor). The toolbox is automated and is freely available for academic research upon electronic request

High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins

Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding/unbinding events and conformational changes under biologically relevant conditions without ensemble averaging. However, single-spot smFRET measurements in solution are slow. Here, we detail a high-throughput smFRET approach that extends the traditional single-spot confocal geometry to a multispot one. The excitation spots are optically conjugated to two custom silicon single photon avalanche diode (SPAD) arrays. Two-color excitation is implemented using a periodic acceptor excitation (PAX), allowing distinguishing between singly- and doubly-labeled molecules. We demonstrate the ability of this setup to rapidly and accurately determine FRET efficiencies and population stoichiometries by pooling the data collected independently from the multiple spots. We also show how the high throughput of this approach can be used o increase the temporal resolution of single-molecule FRET population characterization from minutes to seconds. Combined with microfluidics, this high-throughput approach will enable simple real-time kinetic studies as well as powerful molecular screening applications

APM_GUI: analyzing particle movement on the cell membrane and determining confinement

<p>Abstract</p> <p>Background</p> <p>Single-particle tracking is a powerful tool for tracking individual particles with high precision. It provides useful information that allows the study of diffusion properties as well as the dynamics of movement. Changes in particle movement behavior, such as transitions between Brownian motion and temporary confinement, can reveal interesting biophysical interactions. Although useful applications exist to determine the paths of individual particles, only a few software implementations are available to analyze these data, and these implementations are generally not user-friendly and do not have a graphical interface,.</p> <p>Results</p> <p>Here, we present APM_GUI (Analyzing Particle Movement), which is a MatLab-implemented application with a Graphical User Interface. This user-friendly application detects confined movement considering non-random confinement when a particle remains in a region longer than a Brownian diffusant would remain. In addition, APM_GUI exports the results, which allows users to analyze this information using software that they are familiar with.</p> <p>Conclusions</p> <p>APM_GUI provides an open-source tool that quantifies diffusion coefficients and determines whether trajectories have non-random confinements. It also offers a simple and user-friendly tool that can be used by individuals without programming skills.</p

Decreased MCM2-6 in Drosophila S2 cells does not generate significant DNA damage or cause a marked increase in sensitivity to replication interference.

A reduction in the level of some MCM proteins in human cancer cells (MCM5 in U20S cells or MCM3 in Hela cells) causes a rapid increase in the level of DNA damage under normal conditions of cell proliferation and a loss of viability when the cells are subjected to replication interference. Here we show that Drosophila S2 cells do not appear to show the same degree of sensitivity to MCM2-6 reduction. Under normal cell growth conditions a reduction of >95% in the levels of MCM3, 5, and 6 causes no significant short term alteration in the parameters of DNA replication or increase in DNA damage. MCM depleted cells challenged with HU do show a decrease in the density of replication forks compared to cells with normal levels of MCM proteins, but this produces no consistent change in the levels of DNA damage observed. In contrast a comparable reduction of MCM7 levels has marked effects on viability, replication parameters and DNA damage in the absence of HU treatment

Comparison of Two Cameras based on Single Photon Avalanche Diodes (SPADs) for Fluorescence Lifetime Imaging Application with Picosecond Resolution

We report on a comparative study of two time-resolved cameras based on digital Single Photon Avalanche Diodes (SPADs) for Fluorescen ce Lifetime Imaging applications. In contrast to standard imagers such as cameras, SPAD imagers provide intensity as well as direct access to the fluorescence decay temporal profile, from which lifetime contrast can be extracted. Intensity images provide physicians with anatomical information to localize cancerous tissue; lifetime maps on the other hand provide metabolic information on tissues and can help detect the presence and location of metastatic cells [1,2,3]. With a timing resolution better than 100ps in a compact setup, the SPAD camera represents an innovative solution to explore subnanosecond fluorescence mechanisms

Phase ordering and shape deformation of two-phase membranes

Within a coupled-field Ginzburg-Landau model we study analytically phase separation and accompanying shape deformation on a two-phase elastic membrane in simple geometries such as cylinders, spheres and tori. Using an exact periodic domain wall solution we solve for the shape and phase ordering field, and estimate the degree of deformation of the membrane. The results are pertinent to a preferential phase separation in regions of differing curvature on a variety of vesicles.Comment: 4 pages, submitted to PR

High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins

Single-molecule Förster resonance energy transfer (smFRET) is a powerful technique for nanometer-scale studies of single molecules. Solution-based smFRET, in particular, can be used to study equilibrium intra- and intermolecular conformations, binding/unbinding events and conformational changes under biologically relevant conditions without ensemble averaging. However, single-spot smFRET measurements in solution are slow. Here, we detail a high-throughput smFRET approach that extends the traditional single-spot confocal geometry to a multispot one. The excitation spots are optically conjugated to two custom silicon single photon avalanche diode (SPAD) arrays. Two-color excitation is implemented using a periodic acceptor excitation (PAX), allowing distinguishing between singly- and doubly-labeled molecules. We demonstrate the ability of this setup to rapidly and accurately determine FRET efficiencies and population stoichiometries by pooling the data collected independently from the multiple spots. We also show how the high throughput of this approach can be used o increase the temporal resolution of single-molecule FRET population characterization from minutes to seconds. Combined with microfluidics, this high-throughput approach will enable simple real-time kinetic studies as well as powerful molecular screening applications

Synthesis and Spectral Studies of CdTe–Dendrimer Conjugates

In order to couple high cellular uptake and target specificity of dendrimer molecule with excellent optical properties of semiconductor nanoparticles, the interaction of cysteine-capped CdTe quantum dots with dendrimer was investigated through spectroscopic techniques. NH2-terminated dendrimer molecule quenched the photoluminescence of CdTe quantum dots. The binding constants and binding capacity were calculated, and the nature of binding was found to be noncovalent. Significant decrease in luminescence intensity of CdTe quantum dots owing to noncovalent binding with dendrimer limits further utilization of these nanoassemblies. Hence, an attempt is made, for the first time, to synthesize stable, highly luminescent, covalently linked CdTe–Dendrimer conjugate in aqueous medium using glutaric dialdehyde (G) linker. Conjugate has been characterized through Fourier transform infrared spectroscopy and transmission electron microscopy. In this strategy, photoluminescence quantum efficiency of CdTe quantum dots with narrow emission bandwidths remained unaffected after formation of the conjugate