Showing papers in "IEEE Transactions on Nanobioscience in 2006"

An efficient semi-unsupervised gene selection method via spectral biclustering

Abstract: Gene selection is an important issue in microarray data processing. In this paper, we propose an efficient method for selecting relevant genes. First, we use spectral biclustering to obtain the best two eigenvectors for class partition. Then gene combinations are selected based on the similarity between the genes and the best eigenvectors. We demonstrate our semi-unsupervised gene selection method using two microarray cancer data sets, i.e., the lymphoma and the liver cancer data sets, where our method is able to identify a single gene or a two-gene combinations which can lead to predictions with very high accuracy.

Dielectrophoresis of DNA: time- and frequency-dependent collections on microelectrodes

Abstract: This paper reports measurements that characterize the collection of DNA onto interdigitated microelectrodes by high-frequency dielectrophoresis. Measurements of time-dependent collection of 12 kilobase pair plasmid DNA onto microelectrodes by dielectrophoresis show significant reduction in the response as the frequency increases from 100 kHz to 20 MHz. Collection time profiles are quantitatively measured using fluorescence microscopy over the range 100 kHz to 5 MHz and are represented in terms of two parameters: the initial dielectrophoretic collection rate, and the initial to steady-state collection transition. Measured values for both parameters are consistent with trends in the frequency-dependent real part of the effective polarizability measured for the same plasmid DNA using dielectric spectroscopy. The experimentally measured parameters are qualitatively compared with trends predicted by theory that takes into account dielectrophoretic particle movement and diffusion. The differences between experiment and theory are discussed with suggested improvements to theoretical models, for example, including the effects of electrohydrodynamically driven fluid motion

Principles and Design of a Novel Magnetic Force Mechanical Conditioning Bioreactor for Tissue Engineering, Stem Cell Conditioning, and Dynamic In Vitro Screening

Abstract: Mechanical conditioning of cells and tissue constructs in bioreactors is an important factor in determining the properties of tissue being produced. Mechanical conditioning within a bioreactor environment, however, has proven difficult. This paper presents the theoretical basis, design, and initial results of a mechanical conditioning system for cell and tissue culture which is based on biocompatible magnetic micro- and nanoparticles acting as a remote stress mechanism without invasion of the sterile bioreactor environment

Mechanical analysis of chorion softening in prehatching stages of zebrafish embryos

Abstract: During early development, the chorion envelope of the zebrafish embryo undergoes a thinning process called "chorion softening," which has so far only been characterized chemically. In this study, a micromechanical force sensing system was used to characterize and quantitate mechanical modifications of the zebrafish embryo chorion during early development. Quantitative relationships between applied forces and chorion structural deformations were established at various embryonic stages. The measured penetration force into the chorion at the blastula stage was 1.3-fold greater than those at the prehatching stage. Furthermore, chorion elastic modulus values were determined by using a biomembrane elastic model. The elastic modulus of the chorion at the blastula stage was 1.66-fold greater than that at the prehatching stage, thus indicating that the chorion envelope become mechanically "softened" at the prehatching stage. The experimental results quantitatively describe "chorion softening," which is most likely due to proteolytic activities at the prehatching stage. Gradual chorion softening during embryonic development was also artificially achieved by treating blastula chorion with pronase, a proteolytic enzyme. The forces required to penetrate the pronase-treated chorion were similar to those at the prehatching stage. This similarity suggests that "chorion softening" may be induced by the release of protease from the embryos, and the chemical nature of the process involves proteolytic fragmentation of the ZP2 protein.

Quantum Dot as a Drug Tracer In Vivo

Abstract: Quantum dots (QDs) have been applied to a wide range of biological studies by taking advantage of their fluorescence properties. There is almost no method to trace small molecules including medicine. Here, we used QDs for fluorescent tracers for medicine and analyzed their kinetics and dynamics. We conjugated QDs with captopril, anti-hypertensive medicine, by an exchange reaction while retaining the medicinal properties. We investigated the medicinal effect of QD-conjugated captopril (QD-cap) in vitro and in vivo. We also evaluated the concentration and the distribution of the QD-cap in the blood and the organs with their fluorescence. We demonstrate that the QD-cap inhibits the activity of ACE in vitro. The QD-cap reduced the blood pressure of hypertensive model rats. The concentration of the QD-cap in the blood was measured by using the standard curve of the fluorescence intensity. The blood concentration of the QD-cap decrease exponentially and QD-cap has approximately the same half-life as that of captopril. In addition, the fluorescence of the QDs revealed that QD-cap accumulates in the liver, lungs, and spleen. We succeeded in analyzing the dynamics and kinetics of small molecules using fluorescence of QDs

Rule generation for protein secondary structure prediction with support vector machines and decision tree

Abstract: Support vector machines (SVMs) have shown strong generalization ability in a number of application areas, including protein structure prediction. However, the poor comprehensibility hinders the success of the SVM for protein structure prediction. The explanation of how a decision made is important for accepting the machine learning technology, especially for applications such as bioinformatics. The reasonable interpretation is not only useful to guide the "wet experiments," but also the extracted rules are helpful to integrate computational intelligence with symbolic AI systems for advanced deduction. On the other hand, a decision tree has good comprehensibility. In this paper, a novel approach to rule generation for protein secondary structure prediction by integrating merits of both the SVM and decision tree is presented. This approach combines the SVM with decision tree into a new algorithm called SVM_DT, which proceeds in three steps. This algorithm first trains an SVM. Then, a new training set is generated through careful selection from the output of the SVM. Finally, the obtained training set is used to train a decision tree learning system and to extract the corresponding rule sets. The results of the experiments of protein secondary structure prediction on RS126 data set show that the comprehensibility of SVM_DT is much better than that of the SVM. Moreover, the generalization ability of SVM_DT is better than that of C4.5 decision trees and is similar to that of the SVM. Hence, SVM_DT can be used not only for prediction, but also for guiding biological experiments

Grid-Enabled High-Throughput In Silico Screening Against Influenza A Neuraminidase

Abstract: Encouraged by the success of the first EGEE biomedical data challenge against malaria (WISDOM) , the second data challenge battling avian flu was kicked off in April 2006 to identify new drugs for the potential variants of the influenza A virus. Mobilizing thousands of CPUs on the Grid, the six-week-long high-throughput screening activity has fulfilled over 100 CPU years of computing power and produced around 600 gigabytes of results on the Grid for further biological analysis and testing. In the paper, we demonstrate the impact of a worldwide Grid infrastructure to efficiently deploy large-scale virtual screening to speed up the drug design process. Lessons learned through the data challenge activity are also discussed

Nano- and Microscale Holes Modulate Cell-Substrate Adhesion, Cytoskeletal Organization, and $-\beta 1$ Integrin Localization in Sv40 Human Corneal Epithelial Cells

Abstract: Human corneal epithelial cells (HCECs) interface with a basement membrane in vivo that possesses complex nanoscale topographic features. We report that synthetic substrates patterned with nano- and microscale holes differentially modulate the proliferation, shape and adhesion of SV40 human corneal epithelial cells (SV40-HCECs) as a function of feature size: 1) Cell proliferation was inhibited on nanoscale features (features size less than 800 nm in pitch) compared to microscale features or planar substrates in identical culture conditions. 2)Cells on nanoscale holes had a stellate morphology compared to those on microscale features that were more evenly spread. 3) Cells adhered more to nanoscale features than to microscale features when exposed to shear stress in a laminar flow chamber. Transmission electron microscopy showed that cells cultured on the 400 nm pitch patterns had longer and more numerous filopodia and retraction fibers than cells cultured on the 1600 nm pitch patterns. Immunogold labeling of -beta1 integrins revealed that these receptors were localized at the cell periphery and in the aforementioned cytoskeletal elements. Our findings indicate that surface discontinuities and the activation of mechanochemical cell signaling mechanisms may contribute to the observed responses exhibited by SV40-HCECs cultured on nano- and microscale topography

The effects of colloidal nanotopography on initial fibroblast adhesion and morphology

Abstract: Colloidal lithography offers a simple, inexpensive method of producing irregular nanotopographies, a pattern not easily attainable utilizing conventional serial writing processes. Colloids with 20- or 50-nm diameter were utilized to produce such an irregular topography and were characterized by calculating the percentage area coverage of particles. Interparticle and nearest neighbor spacing were also assessed for the individual colloids in the pattern. Two-way analysis of variance (ANOVA) indicated significant differences between the number of fibroblasts adhering to planar, 20-, and 50-nm-diameter colloidal topographies, the number of fibroblasts adhering to the substrates at the time intervals studied, namely 20 min, 1 h, and 3 h and significant interaction between time and topography on fibroblast adhesion (P<0.01). Tukey tests were utilized for sensitive identification of the differences between the sample means and compounded ANOVA results. Cytoskeletal and general cell morphology were investigated on planar and colloidal substrates, and indicated cells in contact with irregular nanotopographies exhibit many peripheral protrusions while such protrusions are absent in cells on planar control surfaces. These protrusions are rich in microtubules on 20-nm-diameter colloidal surfaces while microfilaments are prevalent on 50-nm-diameter surfaces. Moreover, by 3 h, cells on the colloidal substrates initiate cell-cell adhesions, also absent in controls

Using Carbon Nanotubes to Absorb Low-Concentration Hydrogen Sulfide in Fluid

Abstract: Hydrogen sulfide is a colorless and flammable gas under room temperature. Usually hydrogen sulfide is considered to be toxic; however, the recent research revealed that hydrogen sulfide in the cardiovascular system plays the role of a vascular dilator. The physiological role of hydrogen sulfide depends on its in vivo level. As such, the measurement of hydrogen sulfide with nano-quantity resolution becomes an important subject. Existing methods generally require bulky samples and are invasive and offline. It will be significantly helpful to measure hydrogen sulfide with a small amount of tissue in a noninvasive method The first attempt was to take a blood or serum sample with a trace amount to examine the interaction between hydrogen sulfide and carbon nanotube. The carbon nanotube is chosen because of a known fact that hydrogen sulfide can be adsorbed by activated carbon. The carbon nanotube is an excellent activated carbon in this regard. Fluorescence intensity of the carbon nanotube with and without immersion of it in a hydrogen sulfide medium was examined in the study. It was found that the intensities increase as the concentrations of hydrogen sulfide increase. Furthermore, the concentration of 10 muM hydrogen sulfide in water was successfully measured

All-Optical Switching in Pharaonis Phoborhodopsin Protein Molecules

Abstract: Low-power all-optical switching with pharaonis phoborhodopsin (ppR) protein is demonstrated based on nonlinear excited-state absorption at different wavelengths. A modulating pulsed 532-nm laser beam is shown to switch the transmission of a continuous-wave signal light beam at: 1) 390 nm; 2) 500 nm; 3) 560 nm; and 4) 600 nm, respectively. Simulations based on the rate equation approach considering all seven states in the ppR photocycle are in good agreement with experimental results. It is shown that the switching characteristics at 560 and 600 nm, respectively, can exhibit negative to positive switching. The switching characteristics at 500 nm can be inverted by increasing the signal beam intensity. The profile of switched signal beam is also sensitive to the modulating pulse frequency and signal beam intensity and wavelength. The switching characteristics are also shown to be sensitive to the lifetimes of ppRM and ppRO intermediates. The results show the applicability of ppR as a low-power wavelength tunable all-optical switch

A mathematical formulation of DNA computation

Abstract: DNA computation is to use DNA molecules for information storing and processing. The task is accomplished by encoding and interpreting DNA molecules in suspended solutions before and after the complementary binding reactions. DNA computation is attractive, due to its fast parallel information processing, remarkable energy efficiency, and high storing capacity. Challenges currently faced by DNA computation are: 1) lack of theoretical computational models for applications and 2) high error rate for implementation. This paper attempts to address these problems from mathematical modeling and genetic coding aspects. The first part of this paper presents a mathematical formulation of DNA computation. The model may serve as a theoretical framework for DNA computation. In the second part, a genetic code based DNA computation approach is presented to reduce error rate for implementation, which has been a major concern for DNA computation. The method provides a promising alternative to reduce error rate for DNA computation

Peptide Coated Quantum Dots for Biological Applications

Abstract: Quantum dots (QDOTs) have been widely recognized by the scientific community and the biotechnology industry, as witnessed by the exponential growth of this field in the past several years. We describe the synthesis and characterization of visible and near infrared QDots-a critical step for engineering organic molecules like proteins and peptides for building nanocomposite materials with multifunctional properties suitable for biological applications

Effects of cellular fine structure on scattered light pattern

Abstract: Biological cells are complex in both morphological and biochemical structure. The effects of cellular fine structure on light scattered from cells are studied by employing a three-dimensional code named AETHER which solves the full set of Maxwell equations by using the finite-difference time-domain method. It is shown that changes in cellular fine structure can cause significant changes in the scattered light pattern over particular scattering angles. These changes potentially provide the possibility for distinguishability of cellular intrastructures. The effects that features of different intrastructure have on scattered light are discussed from the viewpoint of diagnosing cellular fine structure. Finally, we discuss scattered light patterns for lymphocyte-like cells and basophil-like cells.

Nanofabrication of polymer surfaces utilizing colloidal lithography and ion etching

Abstract: In this paper, we utilize colloidal lithography based on electrostatic self-assembly of polystyrene colloidal particles onto a polymer surface as a nanoscale mask. The pattern is then transferred to the surface by ion beam etching. Each particle acts as an individual mask, resulting in an array of identical structure. Ion beam exposure etches away the unmasked surface between the particles, so the particle mask pattern can be transferred into the polymer surface. This method allows to nanofabricate bulk polymeric surfaces with systematic variation in relief, structure sizes, and aspect ratios. It is a fast, simple, and reliable method to fabricated different polymeric surfaces even on large area samples (>1 cm2). The structural variation is achieved by use of different conditions during the self-assembly of the mask (e.g., different particles sizes) or different ion etching conditions during the pattern transfer (e.g., ion energy, ion flux, ion incident angle, etching time, gas environment)

LPC cepstral distortion measure for protein sequence comparison

Abstract: Protein sequence comparison is the most powerful tool for the inference of novel protein structure and function. This type of inference is commonly based on the similar sequence-similar structure-similar function paradigm, and derived by sequence similarity searching on databases of protein sequences. As entire genomes have been being determined at a rapid rate, computational methods for comparing protein sequences will be more essential for probing the complexity of molecular machines. In this paper we introduce a pattern-comparison algorithm, which is based on the mathematical concepts of linear predictive coding (LPC) and LPC cepstral distortion measure, for computing similarities/dissimilarities between protein sequences. Experimental results on a real data set of functionally related and functionally nonrelated protein sequences have shown the effectiveness of the proposed approach on both accuracy and computational efficiency.

Synthesizing Biofunctionalized Nanoparticles to Image Cell Signaling Pathways

Abstract: This minireview outlines the synthetic efforts, from our research group, to produce nanomaterials for use as imaging agents to study cell signaling pathways. An overview of our approach to the synthesis and biofunctionalization of metal, semiconductor, and ceramic nanomaterials is presented. The probes investigated include coinage metals, Cd-based, Gedeg, naturally occurring fluorescent (NOF) minerals, and Ln-based nanoparticles which were synthesized from novel metal alkoxide, amide, and alkyl precursors. We illustrate the applications of some of these materials as imaging probes to detect signaling pathway components and cellular responses to signals (apoptosis and degranulation) in inflammatory and cancer cells

Computational modeling of a new fluorescent biosensor for caspase proteolytic activity improves dynamic range

Abstract: The class of fluorescence resonance energy transfer (FRET) protein biosensors that are useful for measuring protease activity is composed of a tandem fusion of yellow fluorescent protein (YFP), a cleavage recognition sequence, and cyan fluorescent protein (CFP). The dynamic range of these FRET-based protein biosensors is often weak, but applications such as high throughput drug screening require stronger dynamic ranges. Using the biosensor for the caspase-3 protease as an example, here we showed a computational approach to improve the FRET dynamic range based on the atomic structure of caspase-3 bound to its inhibitor. This result was verified from our experiments where the FRET dynamic range improved by at least 60% on average in both in vitro and in vivo contexts. In concept, the same strategy can be applied to improve dynamic range of other FRET-based protein biosensors for protease activity where there exist solved atomic structures for protein complexes

Forming Microstructured Alkanethiol Self-Assembled Monolayers on Gold by Laser Ablation

Abstract: A process to form microstructured alkanethiol self-assembled monolayers (SAMs) on gold is described. It is well known that alkanethiols spontaneously form homogenous SAMs on gold surfaces. By means of laser ablation, the exposed areas of alkanethiol monolayers can be removed from the gold surface. Free gold is obtained which can react further with second and third thiols. By this technique, structured alkanethiol SAMs are obtained reliably and easily. In a rather narrow window of pulse intensities, in our example 120 MW/cm2plusmn10% from a frequency-doubled Nd :YVO4 laser with 6-ns pulsewidth operating at a repetition rate of 20 kHz, ablation of alkanethiol monolayers is obtained without causing any damage to the gold substrate. Examples are presented where lines down to 10 mum in width were laser ablated into an SAM formed either from a hydrophilic or a hydrophobic alkanethiol and filled with a monolayer of a second alkanethiol of opposite hydrophilicity. The patterned structures were examined by optical and fluorescence microscopy as well as by lateral force microscopy. The presented method enables the preparation of microstructured SAMs on gold and probably on a wide variety of other substrates

Adaptive Brownian dynamics Simulation for estimating potential mean force in ion channel permeation

Abstract: Ion channels are biological nanotubes formed by large protein molecules in the cell membrane. This paper presents a novel multiparticle simulation methodology, which we call adaptive controlled Brownian dynamics, for estimating the force experienced by a permeating ion at each discrete position along the ion-conducting pathway. The profile of this force, commonly known as the potential of mean force, results from the electrostatic interactions between the ions in the conduit and all the charges carried by atoms forming the channel the protein, as well as the induced charges on the protein wall. The current across the channel is solely determined by the potential of mean force encountered by the permeant ions. The simulation algorithm yields consistent estimates of this profile. The algorithm operates on an angstrom unit spatial scale and femtosecond time scale. Numerical simulations on the gramicidin ion channel show that the algorithm yields the potential of mean force profile that accurately reproduces experimental observations.

Acoustic activation of targeted liquid perfluorocarbon nanoparticles does not compromise endothelial integrity

Abstract: Perfluorocarbon nanoparticles consisting essentially of liquid perfluoro-octyl bromide (PFOB) core surrounded by a lipid monolayer can serve as highly specific site-targeted contrast and therapeutic agents after binding to cellular biomarkers. Based on previous findings that ultrasound applied at 2 MHz and 1.9 mechanical index (MI) for a 5-min duration dramatically enhances the cellular interaction of targeted PFOB nanoparticles with melanoma cells in vitro without inducing apoptosis or other harmful effects to cells that are targeted, we sought to define mechanisms of interaction and the safety profile of ultrasound used in conjunction with liquid perfluorocarbon nanoparticles for targeted drug delivery, as compared with conventional microbubble ultrasound contrast agents under identical insonification conditions. Cell-culture inserts were used to grow a confluent monolayer of human umbilical vein endothelial cells. Definity in conjunction with continuous wave ultrasound (2.25 MHz for 1 and 5 min) increased the permeability of monolayer by four to six times above the normal, decreased transendothelial electrical resistance (a sign of reduced membrane integrity), and decreased cell viability by /spl sim/50%. Histological evaluation demonstrated extensive disruptions of cell monolayers. Nanoparticles (both nontargeted and targeted) elicited no changes in these different measures under similar insonification conditions and did not disrupt cell monolayers. We hypothesize that ultrasound facilitates drug transport from the perfluorocarbon nanoparticles not by cavitation-induced effects on cell membrane but rather by direct interaction with the nanoparticles that stimulate lipid exchange and drug delivery.

Hybridization-ligation versus parallel overlap assembly: an experimental comparison of initial pool generation for direct-proportional length-based DNA computing

Abstract: Previously, direct-proportional length-based DNA computing (DPLB-DNAC) for solving weighted graph problems has been reported. The proposed DPLB-DNAC has been successfully applied to solve the shortest path problem, which is an instance of weighted graph problems. The design and development of DPLB-DNAC is important in order to extend the capability of DNA computing for solving numerical optimization problem. According to DPLB-DNAC, after the initial pool generation, the initial solution is subjected to amplification by polymerase chain reaction and, finally, the output of the computation is visualized by gel electrophoresis. In this paper, however, we give more attention to the initial pool generation of DPLB-DNAC. For this purpose, two kinds of initial pool generation methods, which are generally used for solving weighted graph problems, are evaluated. Those methods are hybridization-ligation and parallel overlap assembly (POA). It is found that for DPLB-DNAC, POA is better than that of the hybridization-ligation method, in terms of population size, generation time, material usage, and efficiency, as supported by the results of actual experiments.

Peptide-directed binding of quantum dots to integrins in human fibroblast

Abstract: There is currently a major international effort aimed at integrating semiconductor nanostructures with biological structures. This paper reports the use of peptide sequences with certain motifs like artinine-glycine-aspartic acid (RGD) and leucine-aspartic acid-valine (LDV) to functionalize zinc sulfide (ZnS)-capped cadmiun selenide (CdSe) quantum dots, so that the quantum dot-peptide complexes selectively bind to integrins on HT1080 human fibrosarcoma cells membrane. In this way, an interface between semiconductor nanocrystals and subcellular components was achieved, and the distribution pattern of RGD and LDV receptors on HT1080 cell membranes is revealed. These findings point the way to using a wide class of peptide-functionalized semiconductor quantum dots for the study of cellular processes involving integrins

Tissue and Species Differences in the Application of Quantum Dots as Probes for Biomolecular Targets in the Inner Ear and Kidney

Abstract: Quantum dots (QDs) are useful biological probes because of the increased photostability and quantum efficiency they offer over organic fluorophores. However, toxicity concerns arise because the QD core is composed of cadmium and selenium, metals known to be unsafe for humans and animals. We investigated the feasibility of quantum dots as biological labels for imaging studies of inner ear and kidney, tissues that share a polarized epithelial arrangement and drug susceptibility. We found that methods for labeling the actin cytoskeleton of monolayers of cultured amphibian kidney cells (Xenopus A6) with 565 nm QD conjugates were not feasible with large Xenopus inner ear organs. We then compared the uptake of 565 nm cationic peptide-targeted and nontargeted QDs in live kidney cell lines (amphibian, A6 and XLK-WG; human, HEK-293). Results showed that targeted QDs are internalized by all three kidney cell lines, and that nontargeted CdSe nanocrystals are sequestered only by human kidney cells. CellTracker Red CMTPX confirmed the membrane integrity and viability of HEK-293 cells that internalized QDs. Our results demonstrate species and tissue differences in QD uptake and labeling, and underscore the need for long-term studies of QD toxicity and fate in cells

Detecting Single Quantum Dot Motion With Nanometer Resolution for Applications in Cell Biology

Abstract: Quantum dots (QDs), semiconductor particles of nanometer dimension, have emerged as excellent fluorescent analogs in tracer experiments with single molecule sensitivity for bioassays. Cell imaging greatly benefits from the remarkable optical and physical properties of these inorganic nanocrystals: QDs are much brighter and exhibit a higher resistance to photobleaching than traditional fluorophores, and their narrow emission spectrum and flexible surface chemistry make them particularly suitable for multiplex imaging. Here, we have demonstrated the achievement of a nanometer spatial resolution on the position of a single QD in a simple optomechanical instrument using a high-sensitivity low-noise detector, an intensified CCD camera. Furthermore, nanometer variations in the amplitude of a QD's sinusoidal oscillations could be quantitatively distinguished after fast Fourier transform (FFT) based data processing. As confirmed by experiments where QDs were attached to the surface of bovine aortic endothelial cells, this method can be exploited in biology to assess molecular and subcellular contributions to responses such as motility, intracellular trafficking, and mechanotransduction, with high resolution and minimal disturbance to cells

Quantum Dot Probes for Monitoring Dynamic Cellular Response: Reporters of T Cell Activation

Abstract: Antibody-conjugated quantum dots (QDs) have been used to map the expression dynamics of the cytokine receptor interleukin-2 receptor-alpha (IL-2Ralpha) following Jurkat T cell activation. Maximal receptor expression was observed 48 h after activation, followed by a sharp decrease consistent with IL-2R internalization subsequent to IL-2 engagement. Verification of T cell activation and specificity of QD labeling were demonstrated using fluorescence microscopy, ELISA, and FACS analyses. These antibody conjugates provide a versatile means to rapidly determine cell state and interrogate membrane associated proteins involved in cell signaling pathways. Ultimately, incorporation with a microfluidic platform capable of simultaneously monitoring several cell signaling pathways will aid in toxin detection and discrimination

Whole-Cell Sensing for a Harmful Bloom-Forming Microscopic Alga by Measuring Antibody&#8211;Antigen Forces

Abstract: Aureococcus anophagefferens, a harmful bloom-forming alga responsible for brown tides in estuaries of the Middle Atlantic U.S., has been investigated by atomic force microscopy for the first time, using probes functionalized with a monoclonal antibody specific for the alga. The rupture force between a single monoclonal antibody and the surface of A. anophagefferens was experimentally found to be 246 plusmn 11 pN at the load rate of 12 nN/s. Force histograms for A. anophagefferens and other similarly-sized algae are presented and analyzed. The results illustrate the effects of load rates, and demonstrate that force-distance measurements can be used to build biosensors with high signal-to-noise ratios for A. anophagefferens. The methods described in this paper can be used, in principle, to construct sensors with single-cell resolution for arbitrary cells for which monoclonal antibodies are available

Light-Induced In Situ Patterning of DNA-Tagged Biomolecules and Nanoparticles

Abstract: We present an in situ method for the selective manipulation of DNA-tagged nano-objects such as vesicles or gold colloids in aqueous solution, at neutral pH. The method makes use of the photosensitizer concept found in photodynamic therapy. Here, single-stranded DNA is immobilized onto a surface via the biotin/streptavidin linkage. If the streptavidin is fluorescently labeled, reactive species will be created during laser-induced photobleaching of the label. These reactive species can then completely or partly suppress the DNA hybridization and cause the removal of the streptavidin. The technique thereby enables a dynamic on-off control over surface density of immobilized DNA-tagged nano-objects. Furthermore, combining this in situ manipulation of DNA with prepatterning of single-stranded DNA in the micro and later in the nano range provides a means for the dynamic patterning required for applications in biosensing and nanotechnology

All-Optical Switching in Plant Blue Light Photoreceptor Phototropin

Abstract: We theoretically analyze all-optical switching in the recently characterized LOV2 domain from Avena sativa (oat) phot1 phototropin, a blue-light plant photoreceptor, based on nonlinear intensity-induced excited-state absorption. The transmission of a cw probe laser beam at 660 nm corresponding to the peak absorption of the first excited L-state, through the LOV2 sample, is switched by a pulsed pump laser beam at 442 nm that corresponds to the maximum initial D state absorption. The switching characteristics have been analyzed using the rate equation approach, considering all the three intermediate states and transitions in the LOV2 photocycle. It is shown that for a given pump pulse intensity, there is an optimum pump pulsewidth for which the switching contrast is maximum. It is shown that the probe laser beam can be completely switched off (100% modulation) by the pump laser beam at 50 kW/cm2 for a concentration of 1 mM with sample thickness of 5.5 mm. The switching characteristics are sensitive to various parameters such as concentration, rate constant of L-state, peak pump intensity and pump pulse width. At typical values, the switch-off and switch-on time is 1.6 and 22.3 mus, respectively. The switching characteristics have also been used to design all-optical not and the universal nor and nand logic gates

The state of the art of nanobioscience in Japan

Abstract: This paper reviews a part of the state of the art of nanobioscience in Japan. The importance of combination and integration of interdisciplinary principles is emphasized for the development of nanobioscience. Biomagnetics, biomechanics, nanomachining, self-replicating cell model, neuronal network, drug delivery system, and tissue engineering are discussed