A Bayesian approach to tracking in single molecule fluorescence microscopy

Using fluorescence microscopy with single molecule sensitivity it is now possible to follow the movement of individual fluorophore tagged molecules such as proteins and lipids in the cell membrane with nanometer precision. These experiments are important as they allow many key biological processes on the cell membrane and in the cell, such as transcription, translation and DNA replication, to be studied at new levels of detail. Computerized microscopes generate sequences of images (in the order of tens to hundreds) of the molecules diffusing and one of the challenges is to track these molecules to obtain reliable statistics such as speed distributions, diffusion patterns, intracellular positioning, etc. The data set is challenging because the molecules are tagged with a single or small number of fluorophores, which makes it difficult to distinguish them from the background, the fluorophore bleaches irreversibly over time, the number of tagged molecules are unknown and there is occasional loss of signal from the tagged molecules. All these factors make accurate tracking over long trajectories difficult. Also the experiments are technically difficulty to conduct and thus there is a pressing need to develop better algorithms to extract the maximum information from the data. For this purpose we propose a Bayesian approach and apply our technique to synthetic and a real experimental data set.

A simple bioconjugate attachment protocol for use in single molecule force spectroscopy experiments based on mixed self-assembled monolayers.

Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin.

Biofunctionalization of PET/SiO2 surfaces for single molecule experiments and medical applications

PET/SiO2 layers were chemically modified to maintain immobilization of functional single molecules. GFP molecules provide an ideal system due to their stability and intrinsic fluorescence. GFP in vivo biotinylated within its NH2-terminal region and attached on the substrate via the biotinstreptavidin bond was further investigated with confocal microscopy, atomic force microscopy (AFM) and spectroscopic ellipsometry (SE). AFM revealed monolayered donut-like structures representing assemblies of biotinstreptavidinbiotinGFP immobilized onto PET/SiO2 surfaces via mPEG. In particular, regions with an approximate height of 12 nm, which approaches the molecular dimensions of the above complex given by molecular modeling, could be detected. The dimensions of the donut-like structures suggest a close-to-each-other positioning of the GFP molecules - which, however, retain their functionality, as evidenced by confocal microscopy. © 2011 World Scientific Publishing Company.

Measurement of the Interaction Between Recombinant I-domain from Integrin alpha 2 beta 1 and a Triple Helical Collagen Peptide with the GFOGER Binding Motif Using Molecular Force Spectroscopy.

The role of the collagen-platelet interaction is of crucial importance to the haemostatic response during both injury and pathogenesis of the blood vessel wall. Of particular interest is the high affinity interaction of the platelet transmembrane receptor, alpha 2 beta 1, responsible for firm attachment of platelets to collagen at and around injury sites. We employ single molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) to study the interaction of the I-domain from integrin alpha 2 beta 1 with a synthetic collagen related triple-helical peptide containing the high-affinity integrin-binding GFOGER motif, and a control peptide lacking this sequence, referred to as GPP. By utilising synthetic peptides in this manner we are able to study at the molecular level subtleties that would otherwise be lost when considering cell-to-collagen matrix interactions using ensemble techniques. We demonstrate for the first time the complexity of this interaction as illustrated by the complex multi-peaked force spectra and confirm specificity using control blocking experiments. In addition we observe specific interaction of the GPP peptide sequence with the I-domain. We propose a model to explain these observations.

Nanotubes complexed with DNA and proteins for resistive-pulse sensing

We use a resistive-pulse technique to analyze molecular hybrids of single-wall carbon nanotubes (SWNTs) wrapped in either single-stranded DNA or protein. Electric fields confined in a glass capillary nanopore allow us to probe the physical size and surface properties of molecular hybrids at the single-molecule level. We find that the translocation duration of a macromolecular hybrid is determined by its hydrodynamic size and solution mobility. The event current reveals the effects of ion exclusion by the rod-shaped hybrids and possible effects due to temporary polarization of the SWNT core. Our results pave the way to direct sensing of small DNA or protein molecules in a large unmodified solid-state nanopore by using nanofilaments as carriers. © 2013 American Chemical Society.

Theoretical simulation studies of pulsed field magnetisation of (RE)BCO bulk superconductors

The magnetisation of bulk high temperature superconductors (HTS), such as RE-Ba-Cu-O [(RE)BCO, where RE is a rare earth element or Y], by a practical technique is essential for their application in high field, permanent magnet-like devices. Research to-date into the pulsed field magnetisation (PFM) of these materials, however, has been limited generally to experimental techniques, with relatively little progress in the development of theoretical models. This is because not only is a multi-physics approach needed to take account of the heating of the samples but also the high electric fields generated are well above the regime in which there are reliable experimental results. This paper describes a framework of theoretical simulation using the finite element method (FEM) that is applicable to both single- and multi-pulse magnetisation processes of (RE)BCO bulk superconductors. The model incorporates the heat equation and provides a convenient way of determining the distribution of trapped field, current density and temperature change within a bulk superconductor at each stage of the magnetisation process. An example of the single-pulse magnetisation of a (RE)BCO bulk is described. Potentially, the model may serve as a cost-effective tool for the optimisation of the bulk geometry and the magnetisation profile in multi-pulse magnetisation processes. © 2010 IOP Publishing Ltd.

Mechanism And Selectivity In The Epoxidation Of Ethylene Over Silver: The Results Of Single Crystal Measurements

The silver-catalysed oxidation of ethylene has been examined on the (III) face of a single crystal by a combination of electron spectroscopy and kinetic measurements at pressures of up to 50 Torr. The necessary and sufficient conditions for ethylene oxide formation are established, reaction intermediates are identified, kinetic isotope effects are observed and the role of Cs in modifying reaction selectivity is examined. It is shown that surface alkali exhibits opposite effects on the reactions which lead to the further oxidation of ethylene oxide and on the direct combustion of ethylene. © 1984.

Patterning and detailed study of human hNT astrocytes on parylene-C/silicon dioxide substrates to the single cell level.

It is estimated that the adult human brain contains 100 billion neurons with 5-10 times as many astrocytes. Although it has been generally considered that the astrocyte is a simple supportive cell to the neuron, recent research has revealed new functionality of the astrocyte in the form of information transfer to neurons of the brain. In our previous work we developed a protocol to pattern the hNT neuron (derived from the human teratocarcinoma cell line (hNT)) on parylene-C/SiO(2) substrates. In this work, we report how we have managed to pattern hNT astrocytes, on parylene-C/SiO(2) substrates to single cell resolution. This article disseminates the nanofabrication and cell culturing steps necessary for the patterning of such cells. In addition, it reports the necessary strip lengths and strip width dimensions of parylene-C that encourage high degrees of cellular coverage and single cell isolation for this cell type. The significance in patterning the hNT astrocyte on silicon chip is that it will help enable single cell and network studies into the undiscovered functionality of this interesting cell, thus, contributing to closer pathological studies of the human brain.

Performance of single mode laser components using 2D photonic lattice reflectors

This paper will report studies of the placement of 2D photonic gratings on either side of the ridge in a Fabry Perot laser device in order to cause single mode emission. Using this approach, side mode suppression ratios of up to 30 dB are achieved, the emission remaining single mode even under 10 Gb/s large signal modulation. It is found that the use of the grating not only causes spectrally dependent reflection but in addition can lead to transverse mode fluctuations. The action of the grating has been studied not just in terms of its edge emission where conversion of the transverse modes is achieved, but also through measurement of the vertical emission from the structure where strong filtering action is observed.

Superconducting properties of Gd-Ba-Cu-O single grains processed from a new, Ba-rich precursor compound

Gd-Ba-Cu-O (GdBCO) single grains have been previously melt-processed successfully in air using a generic Mg-Nd-Ba-Cu-O (Mg-NdBCO) seed crystal. Previous research has revealed that the addition of a small amount of BaO 2 to the precursor powders prior to melt processing can suppress the formation of Gd/Ba solid solution, and lead to a significant improvement in superconducting properties of the single grains. Research into the effects of a higher Ba content on single grain growth, however, has been limited by the relatively small grain size in the earlier studies. This has been addressed by developing Ba-rich precursor compounds Gd-163 and Gd-143, fabricated specifically to enable the presence of greater concentrations of Ba during the melt process. In this study, we propose a new processing route for the fabrication of high performance GdBCO single grain bulk superconductors in air by enriching the precursor powder with these new Ba rich compounds. The influence of the addition of the new compounds on the microstructures and superconducting properties of GdBCO single grains is reported. © 2008 IOP Publishing Ltd.

A single-rate context-dependent learning process underlies rapid adaptation to familiar object dynamics.

Motor learning has been extensively studied using dynamic (force-field) perturbations. These induce movement errors that result in adaptive changes to the motor commands. Several state-space models have been developed to explain how trial-by-trial errors drive the progressive adaptation observed in such studies. These models have been applied to adaptation involving novel dynamics, which typically occurs over tens to hundreds of trials, and which appears to be mediated by a dual-rate adaptation process. In contrast, when manipulating objects with familiar dynamics, subjects adapt rapidly within a few trials. Here, we apply state-space models to familiar dynamics, asking whether adaptation is mediated by a single-rate or dual-rate process. Previously, we reported a task in which subjects rotate an object with known dynamics. By presenting the object at different visual orientations, adaptation was shown to be context-specific, with limited generalization to novel orientations. Here we show that a multiple-context state-space model, with a generalization function tuned to visual object orientation, can reproduce the time-course of adaptation and de-adaptation as well as the observed context-dependent behavior. In contrast to the dual-rate process associated with novel dynamics, we show that a single-rate process mediates adaptation to familiar object dynamics. The model predicts that during exposure to the object across multiple orientations, there will be a degree of independence for adaptation and de-adaptation within each context, and that the states associated with all contexts will slowly de-adapt during exposure in one particular context. We confirm these predictions in two new experiments. Results of the current study thus highlight similarities and differences in the processes engaged during exposure to novel versus familiar dynamics. In both cases, adaptation is mediated by multiple context-specific representations. In the case of familiar object dynamics, however, the representations can be engaged based on visual context, and are updated by a single-rate process.