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.

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.

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.

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.

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.

Scanning gate microscopy of current-annealed single layer graphene

We have used scanning gate microscopy to explore the local conductivity of a current-annealed graphene flake. A map of the local neutrality point (NP) after annealing at low current density exhibits micron-sized inhomogeneities. Broadening of the local e-h transition is also correlated with the inhomogeneity of the NP. Annealing at higher current density reduces the NP inhomogeneity, but we still observe some asymmetry in the e-h conduction. We attribute this to a hole-doped domain close to one of the metal contacts combined with underlying striations in the local NP. © 2010 American Institute of Physics.