Automated three-dimensional tracing of neurons in confocal and brightfield images.

Automated three-dimensional (3-D) image analysis methods are presented for tracing of dye-injected neurons imaged by fluorescence confocal microscopy and HRP-stained neurons imaged by transmitted-light brightfield microscopy. An improved algorithm for adaptive 3-D skeletonization of noisy images enables the tracing. This algorithm operates by performing connectivity testing over large N x N x N voxel neighborhoods exploiting the sparseness of the structures of interest, robust surface detection that improves upon classical vacant neighbor schemes, improved handling of process ends or tips based on shape collapse prevention, and thickness-adaptive thinning. The confocal image stacks were skeletonized directly. The brightfield stacks required 3-D deconvolution. The results of skeletonization were analyzed to extract a graph representation. Topological and metric analyses can be carried out using this representation. A semiautomatic method was developed for reconnection of dendritic fragments that are disconnected due to insufficient dye penetration, an imaging deficiency, or skeletonization errors.     

Resolving rotational motions of nano-objects in engineered environments and live cells with gold nanorods and differential interference contrast microscopy

Gold nanorods are excellent orientation probes due to their anisotropic optical properties. Their dynamic rotational motion in the 3D space can be disclosed with Nomarski-type differential interference contrast (DIC) microscopy. We demonstrate that by using the combination of gold nanorod probes and DIC microscopy, we are able to resolve rotational motions of nano-cargos transported by motor proteins at video rate not only on engineered surfaces but also on cytoskeleton tracks in live cells.     

Enhanced feature analysis using wavelets for scanning probe microscopy images of surfaces

In this work we develop wavelet theory for the analysis of surface topography images obtained by scanning probe microscopy (SPM) such as atomic force microscopy (AFM). Wavelet transformation is localized in space and frequency, which can offer an advantage for analyzing information on surface morphology and topography. Wavelet transformation is an ideal tool to detect trends, discontinuities, and short periodicities on a surface. Additionally, wavelets can be used to remove artifacts and noise from scanning microscopy images. In terms of 3-D image analysis, discrete wavelet transform can capture patterns at all relevant frequency scales, thus providing a level of image analysis that is not possible otherwise. It is also possible to use the methodology for analyzing surface structures at the molecular level. The results demonstrate superior capabilities of wavelet approach to scanning probe microscopy image analysis compared to traditional analysis techniques.     

Robust automated three-dimensional segmentation of secondary ion mass spectrometry image sets

Three-dimensional (3-D) element distributions generated by scanning secondary ion mass spectrometry (SIMS) are usually noisy and blurred and contain objects which do not usually have sharp edges or may have noise induced boundaries. Additionally, there are local intensity differences due to sensitivity differences of the channelplate. As a result, traditional segmentation techniques become difficult and yield rather poor results. We present a novel methodology which combines a restoration process (using a combination of channelplate sensitivity compensation with a 3-D de-noising technique based on the wavelet transform) with a fuzzy logic 3-D gray level segmentation which can be used to successfully segment 3-D SIMS image sets. The restoration algorithm removes the artifacts produced by the channelplate inhomogeneities as well as noise aberrations from the image sets and the gray level thresholding algorithm segments their features. The algorithm is designed for minimal user interaction to achieve a high automation level. The methodology is discussed and experimental results using real 3-D images are presented.     

Tethered particle motion as a diagnostic of DNA tether length

The tethered particle motion (TPM) technique involves an analysis of the Brownian motion of a bead tethered to a slide by a single DNA molecule. We describe an improved experimental protocol with which to form the tethers, an algorithm for analyzing bead motion visualized using differential interference contrast microscopy, and a physical model with which we have successfully simulated such DNA tethers. Both experiment and theory show that the statistics of the bead motion are quite different from those of a free semiflexible polymer. Our experimental data for chain extension versus tether length fit our model over a range of tether lengths from 109 to 3477 base pairs, using a value for the DNA persistence length that is consistent with those obtained under similar solution conditions by other methods. Moreover, we present the first experimental determination of the full probability distribution function of bead displacements and find excellent agreement with our theoretical prediction. Our results show that TPM is a useful tool for monitoring large conformational changes such as DNA looping.     

Arrays of mobile tethered vesicles on supported lipid bilayers

We report a new system of laterally mobile, arrayed vesicles that are encoded with DNA to control tethering to fluid-supported phospholipid bilayers. The motion of individual fluorescently labeled vesicles, specifically bound, are easily visualized by fluorescence video microscopy and observed to collide reversibly on the surface. This system is an ideal model for studying interactions involving membranes, in particular integral membrane proteins.     

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

In order to investigate the structures and properties of cyclic peptide nanotubes of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-], cyclo[(-D: -Phe-L: -Ala)( n = 4)-] was synthesized and self-assembled to nanotubes, and its structure and morphology of the nanotube were characterized by mass spectrometry (MS), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). On the basis of these experimental results, the structures of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-] were characterized by molecular dynamics. In addition, the motion behaviors of H(2)O molecules in nanotubes were investigated by molecular dynamics using a COMPASS force field. Experimental results show that cyclo[(-D: -Phe-L: -Ala)( n = 4)-] peptides self-assemble into nanotube bundles. Molecular modeling results indicate that cyclic peptide nanotubes with n = 3, 4, 5 and 6 are very stable; these nanotubes have internal diameters of 5.9 A, 8.1 A, 10.8 A and 13.1 A and outer diameters of 18.2 A, 21.7 A, 23.4 A and 25.9 A respectively. Modeling results demonstrate that H(2)O molecules move in cooperation in single nanotube and they diffuse in one dimension, but they did not diffuse unilaterally due to the antiparallel ring stacking arrangement.     

Methods of stretching DNA molecules using flow fields

Using fluorescence microscopy, we compare the degree of adsorption and stretching of DNA onto surfaces achieved by published stretching methods that use fluid flow: molecular combing, spin-stretching, and air-blowing. Molecular combing uses a receding meniscus to stretch out and deposit the DNA onto a hydrophobic surface. In spin-stretching, we find that the effect of radial hydrodynamic flow created by the centrifugal force of the rotating disk is minimal and that the DNA is stretched out on a hydrophobic substrate by the moving meniscus. In air-blowing, a jet of gas pushes liquid across a substrate, depositing stretched DNA molecules along the way. In our study, DNA molecules either combed or spin-stretched onto hydrophobic surfaces stretch to a greater degree than those that are air-blown; fewer are deposited at pH 8.0 than at lower pH, apparently because at pH 8.0 DNA adhesion occurs primarily only at the DNA extremities and so avoids trapped regions of incompletely stretched DNA, with the side effect that more molecules avoid adhesion altogether. We find by high-speed video microscopy that there is complex droplet deformation and motion during air-blowing, which complicates the deposition and stretching process, leading to radial alignment. Our results are a first step toward understanding and optimizing the various proposed methods of DNA stretching and anchoring onto surfaces, which is important in studying their interactions with proteins.     

Automatic alignment of infrared video frames for equipment leak detection

Petroleum refining and petrochemical industries start using infrared (IR) cameras to detect volatile organic compounds (VOC) leaking out of process equipment. However, further quantitative processing of these video image data or automatic recognition of VOC plumes are hindered by unaligned video frames owing to the slight vibrations of the camera. An automatic method is developed to align the IR video frames as a preprocessing procedure for other possible video processing methods. The alignment method is based on a two-dimensional spatial Fourier transform. The accuracy can reach fractional pixels in estimation of translational shift and 1-2° for rotational shift. Temporal Fourier transform of actual industrial tests of IR videos is performed with both unaligned and aligned video frames. The results indicate that only after the alignment of the video frames, the camera motion interferences on VOC plume identification can be eliminated or minimized, and the VOC plume can be identified through investigating the characteristic flickering frequency power in the temporal Fourier transform. This alignment method provides a useful tool for IR or other optical video image data preprocessing purposes.     

Colloidal dynamics near a particle-covered surface

How the diffusive dynamics of colloidal spheres changes in the vicinity of a particle-coated surface is of importance for industrial challenges such as fouling and sedimentation as well as for fundamental studies into confinement effects. We addressed this question by studying colloidal dynamics in a partially coated surface layer, using video microscopy. Particle mean squared displacement (MSD) functions were measured as a function of a (local) effective volume fraction (EVF), which was varied by making use of gravity settling. Comparison of MSDs at the bare and coated surfaces for EVF of 0.2-0.4 revealed that at the latter surface the motion amplitudes are strongly reduced, accompanied by a sharp transition from diffusive to nearly caged motion. This clearly indicates that the surface-attached particles cannot be taken into account via volume fraction and that their immobility has a distinct effect. For EVF > 0.45, the caging becomes dominated by the suspended particles, making the dynamics at the bare and coated surfaces similar.     

Observation and analysis of single DNA nano-kinetics by pin-fiber video scope

The nano-kinetic movement of a single DNA molecule was observed and analyzed by a newly developed video-microscope system with an optical fiber, called a pin-fiber video scope. A single lambda-DNA molecule was put in focus using fiber-illumination, and the stretching and shrinking motion was measured. The molecule's kinetics were analyzed by numerical calculations and are discussed. A photocleavage phenomenon of DNA molecules was also visualized by the pin-fiber video scope. The new video-microscope system has the potential to observe and analyze the nano-kinetics of a single molecule.     

Denaturation mapping of Saccharomyces cerevisiae

Optical mapping of DNA provides large-scale genomic information that can be used to assemble contigs from next-generation sequencing, and to detect rearrangements between single cells. A recent optical mapping technique called denaturation mapping has the advantage of using physical principles rather than the action of enzymes to probe genomic structure. Denaturation mapping uses fluorescence microscopy to image the pattern of partial melting along a DNA molecule extended in a channel of cross-section 120 nm at the heart of a nanofluidic device. We used denaturation mapping to locate single DNA molecules on the yeast genome (12.1 Mbp) by comparing images to a computationally predicted map for the entire genome sequence. By locating 84 molecules we assembled an optical map of the yeast genome with > 50% coverage.     

Electrochemical investigation of the interaction of 2,4-D and double stranded DNA using pencil graphite electrodes

2,4-dichlorophenoxyacetic acid (2,4-D) is an auxinic herbicide used to control broadleaf weeds. It is also a threatening factor for not only aquatic life but also human health due to its genotoxicity and endocrine disruptive property. Herein, the interaction between 2,4-D and double stranded DNA was investigated by using single-use pencil graphite electrodes (PGE) in combination with electrochemical techniques. The detection mechanism was based on the monitoring of the changes at the guanine oxidation signal obtained before/after surface-confined interaction of 2,4-D and DNA at the surface of PGE. The electrochemical characterization of the interaction was studied by using microscopic and electrochemical techniques. The response obtained by interaction in the presence of another herbicide, glyphosate, which is widely used with 2,4-D for weed control, was compared to the one occurred in the presence of 2,4-D. Electrochemical monitoring of the interaction between the herbicide whose active molecule was 2,4-D and DNA was also investigated. The detection (LOD) and quantification limits (LOQ) for 2,4-D and the herbicide could be obtained in the linear concentration ranges of 30–70 µg/mL and 10–30 µg/mL, respectively and LOD and LOQ values were found to be 2.85 and 9.50 µg/mL for both 2,4-D and the herbicide. The sensitivity of the biosensor was calculated as 0.087 µA.mL / µg.cm² .This is the first study in literature by means of not only voltammetric detection of 2,4-D and DNA interaction but also the herbicide-DNA interaction at the surface of PGE based on the changes at the guanine signal.     

Fabrication of 3-D gel microarrays directly with raw polymerase chain reaction products by heat-directed polymerization

In this study, a new method for fabricating 3-D polyacrylamide gel microarrays was presented. In the method, a 3-D gel microarray was successfully fabricated by directly heating the slides with arrayed prepolymer at 80 degrees C for 2 min. The prepolymer on the microarray only contained 40% v/v raw/unpurified PCR products, 1.4% ammonium persulfate (APS), 6% acrylamide, and 20% glycerol and the balance H2O but no TEMED. The heat could induce the free radicals from APS to initiate polymerization of the 3-D gel and allow the incorporation of raw PCR products into the 3-D gel. The immobilized DNA on the gel microarray had the specificity of hybridization and the ability to distinguish base mismatch. It has been demonstrated that SNP genotyping of both the 194072 loci and the 252944 loci in the beta2 subunit gene of gamma-aminobutyric acid A receptor (GABRB2) gene was successfully performed by using the 3-D gel microarray. This method is efficient, simple, rapid, and easy to control in preparing a 3-D gel microarray, which would be widely used for various purposes in laboratory research and clinic application.     

Nonrigid registration of CLSM images of physical sections with discontinuous deformations

When biological specimens are cut into physical sections for three-dimensional (3D) imaging by confocal laser scanning microscopy, the slices may get distorted or ruptured. For subsequent 3D reconstruction, images from different physical sections need to be spatially aligned by optimization of a function composed of a data fidelity term evaluating similarity between the reference and target images, and a regularization term enforcing transformation smoothness. A regularization term evaluating the total variation (TV), which enables the registration algorithm to account for discontinuities in slice deformation (ruptures), while enforcing smoothness on continuously deformed regions, was proposed previously. The function with TV regularization was optimized using a graph-cut (GC) based iterative solution. However, GC may generate visible registration artifacts, which impair the 3D reconstruction. We present an alternative, multilabel TV optimization algorithm, which in the examined samples prevents the artifacts produced by GC. The algorithm is slower than GC but can be sped up several times when implemented in a multiprocessor computing environment. For image pairs with uneven brightness distribution, we introduce a reformulation of the TV-based registration, in which intensity-based data terms are replaced by comparison of salient features in the reference and target images quantified by local image entropies.     

Determination of potential landscapes using video microscopy

Colloidal particles are used to characterize microscopic potential landscapes, which are defined on a sample surface and arise in ensembles of particles. The positions of the particles are recorded using video microscopy. Analysis of the positions, which the particles occupy during their Brownian motion, yields the exact shape of the surface potential, in which the particles move. The underlying principle of our measurements is well-known from measurements using total internal reflection microscopy; in contrast to these measurements, our scheme can be expanded to measurements of inter-particle interactions. As an example, we demonstrate the measurement of interactions between two magnetic particles, sedimenting towards a potential barrier in a tilted geometry.     

Atomic force microscopy and transmission electron microscopy of cellulose from Micrasterias denticulata; evidence for a chiral helical microfibril twist

Atomic force microscopy (AFM), tapping mode atomic force microscopy (TM-AFM) and transmission electron microscopy (TEM) have been used to image the cell wall, ultrathin sections of whole cells and cellulose microfibrils prepared from the green alga Micrasterias denticulata. Measurements of the microfibril dimensions are in agreement with earlier observations carried out by electron microscopy. Images at the molecular level of the surface of the microfibrils were obtained with AFM and show regular periodicities along the microfibril axis that correspond to the fibre and glucose repeat distances of cellulose. Twisted regions visible at intervals along the microfibrils dried down onto substrates were noted to be right-handed in over 100 observations by TEM, AFM and TM-AFM. This revised version was published online in August 2006 with corrections to the Cover Date.     

Modeling and simulation of IEF in 2-D microgeometries

A 2-D finite-volume model is developed to simulate nonlinear IEF in complex microgeometries. This mathematical model is formulated based on the mass conservation and ionic dissociation relations of amphoteric macromolecules, charge conservation, and the electroneutrality condition. Based on the 2-D model, three different separation cases are studied: an IPG in a planar channel, an ampholyte-based pH gradient in a planar channel, and an ampholyte-based pH gradient in a contraction-expansion channel. In the IPG case, cacodylic acid (pK(1) = 6.21) and Tris (pK(1) = 8.3) are used as the acid and base, respectively, to validate the 2-D IEF model. In the ampholyte-based pH gradient cases, IEF is performed in the pH range, 6.21-8.3 using 10 ampholytes in the planar channel and 20 ampholytes in the contraction-expansion channel. The numerical results reveal different focusing efficiencies and resolution in the narrow and wide sections of the contraction-expansion channel. To explain this, the expressions for separation resolution and peak concentrations of separands in the contraction-expansion channel are presented in terms of the channel shape factor. In a 2-D planar channel, a focused band remains straight all the time. However, in a contraction-expansion channel, initially straight bands take on a crescent profile as they pass through the trapezoidal sections joining the contraction and expansion sections.     

An image analysis strategy to study cell adhesion

A semi-automated in situ technique has been developed for the study of the extent and kinetics of cell adhesion at the individual cell level. Our investigation involves the static sedimentation of glutaraldehyde-fixed human erythrocytes suspended in 10 mM NaCl or 10 mM NaCl containing 2% (v/v) 1-propanol onto flat, horizontal, and transparent surfaces. The surfaces used are glass, poly(ethylene terephthalate), polystyrene, and fluorinated ethylene propylene. An inverted microscope is utilized for observations. Brownian motion is used as the distinguishing criterion between adherent and non-adherent cells. The extent of adhesion is expressed as the percentage of adherent cells. Two digital image processing techniques, image averaging and image subtraction, are presented for automation of the methodology. Although all non-adherent cells undergo Brownian motion, they exhibit this behavior to varying degrees. Factors under consideration are the liquid medium's surface tension (γ_LV) and the solid substrate surface tension (γ_SV). Preliminary results reveal that, in general, variations of γ_SV and γ_LV have a statistically significant effect on the extent of adhesion at the 99% and 96% confidence levels, respectively. A time depepdence for the adhesion of populations of cells is observed. However, individual cells either instantly or gradually adhere. Image subtraction generally overestimates the number of adherent cells due to the difficulty in detection of minute oscillations. The deviation between the adhesion percentage obtained from visual observations of the monitor and image subtraction is less than 10%.     

Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks – Influence of the DNA Sequence and Substrate

DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF₂ as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7–2.3×10⁻¹⁶ cm². The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.