Detection of quantum well induced single degenerate-transition-dipoles in ZnO nanorods

Quantifying and characterising atomic defects in nanocrystals is difficult and low-throughput using the existing methods such as high resolution transmission electron microscopy (HRTEM). In this article, using a defocused wide-field optical imaging technique, we demonstrate that a single ultrahigh-piezoelectric ZnO nanorod contains a single defect site. We model the observed dipole-emission patterns from optical imaging with a multi-dimensional dipole and find that the experimentally observed dipole pattern and model-calculated patterns are in excellent agreement. This agreement suggests the presence of vertically oriented degenerate-transition-dipoles in vertically aligned ZnO nanorods. The HRTEM of the ZnO nanorod shows the presence of a stacking fault, which generates a localised quantum well induced degenerate-transition-dipole. Finally, we elucidate that defocused wide-field imaging can be widely used to characterise defects in nanomaterials to answer many difficult questions concerning the performance of low-dimensional devices, such as in energy harvesting, advanced metal-oxide-semiconductor storage, and nanoelectromechanical and nanophotonic devices.

Framework for morphometric classification of cells in imaging flow cytometry

Imaging flow cytometry is an emerging technology that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy. It allows high-throughput imaging of cells with good spatial resolution, while they are in flow. This paper proposes a general framework for the processing/classification of cells imaged using imaging flow cytometer. Each cell is localized by finding an accurate cell contour. Then, features reflecting cell size, circularity and complexity are extracted for the classification using SVM. Unlike the conventional iterative, semi-automatic segmentation algorithms such as active contour, we propose a noniterative, fully automatic graph-based cell localization. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using custom fabricated cost-effective microfluidics-based imaging flow cytometer. The proposed system is a significant development in the direction of building a cost-effective cell analysis platform that would facilitate affordable mass screening camps looking cellular morphology for disease diagnosis. Lay description In this article, we propose a novel framework for processing the raw data generated using microfluidics based imaging flow cytometers. Microfluidics microscopy or microfluidics based imaging flow cytometry (mIFC) is a recent microscopy paradigm, that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy, which allows us imaging cells while they are in flow. In comparison to the conventional slide-based imaging systems, mIFC is a nascent technology enabling high throughput imaging of cells and is yet to take the form of a clinical diagnostic tool. The proposed framework process the raw data generated by the mIFC systems. The framework incorporates several steps: beginning from pre-processing of the raw video frames to enhance the contents of the cell, localising the cell by a novel, fully automatic, non-iterative graph based algorithm, extraction of different quantitative morphological parameters and subsequent classification of cells. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using cost-effective microfluidics based imaging flow cytometer. The cell lines of HL60, K562 and MOLT were obtained from ATCC (American Type Culture Collection) and are separately cultured in the lab. Thus, each culture contains cells from its own category alone and thereby provides the ground truth. Each cell is localised by finding a closed cell contour by defining a directed, weighted graph from the Canny edge images of the cell such that the closed contour lies along the shortest weighted path surrounding the centroid of the cell from a starting point on a good curve segment to an immediate endpoint. Once the cell is localised, morphological features reflecting size, shape and complexity of the cells are extracted and used to develop a support vector machine based classification system. We could classify the cell-lines with good accuracy and the results were quite consistent across different cross validation experiments. We hope that imaging flow cytometers equipped with the proposed framework for image processing would enable cost-effective, automated and reliable disease screening in over-loaded facilities, which cannot afford to hire skilled personnel in large numbers. Such platforms would potentially facilitate screening camps in low income group countries; thereby transforming the current health care paradigms by enabling rapid, automated diagnosis for diseases like cancer.

Insights into the Structural Dynamics of Nucleocytoplasmic Transport of tRNA by Exportin-t

Exportin-t (Xpot) transports mature 5'- and 3'-end processed tRNA from the nucleus to the cytoplasm by associating with a small G-protein Ran (RAs-related nuclear protein), in the nucleus. The release of tRNA in cytoplasm involves RanGTP hydrolysis. Despite the availability of crystal structures of nuclear and cytosolic forms of Xpot, the molecular details regarding the sequential events leading to tRNA release and subsequent conformational changes occurring in Xpot remain unknown. We have performed a combination of classical all-atom and accelerated molecular dynamics simulations on a set of complexes involving Xpot to study a range of features including conformational flexibility of free and cargo-bound Xpot and functionally critical contacts between Xpot and its cargo. The systems investigated include free Xpot and its different complexes, bound either to Ran (GTP/GDP) or tRNA or both. This approach provided a statistically reliable estimate of structural dynamics of Xpot after cargo release. The mechanistic basis for Xpot opening after cargo release has been explained in terms of dynamic structural hinges, about which neighboring region could be displaced to facilitate the nuclear to cytosolic state transition. Post-RanGTP hydrolysis, a cascade of events including local conformational change in RanGTP and loss of critical contacts at Xpot/tRNA interface suggest factors responsible for eventual release of tRNA. The level of flexibility in different Xpot complexes varied depending on the arrangement of individual HEAT repeats. Current study provides one of the most comprehensive and robust analysis carried out on this protein using molecular dynamics schemes.

Quantitative RNA-seq analysis of the campylobacter jejuni transcriptome

Campylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community. © 2011 SGM.

Probabilistic Modeling of Rosette Formation

英文摘要: Rosetting, or forming a cell aggregate between a single target nucleated cell and a number of red blood cells (RBCs), is a simple assay for cell adhesion-mediated by specific receptor-ligand interaction. For example, rosette formation between sheep RBC and human lymphocytes has been used to differentiate T cells from B cells. Rosetting assay is commonly used to determine the interaction of Fc gamma-receptors (Fc gamma R) expressed on inflammatory cells and IgG-coated on RBCs. Despite its wide use in measuring cell adhesion, the biophysical parameters of rosette formation have not been well characterized. Here we developed a probabilistic model to describe the distribution of rosette sizes, which is Poissonian. The average rosette size is predicted to be proportional to the apparent two-dimensional binding affinity of the interacting receptor-ligand pair and their site densities. The model has been supported by experiments of rosettes mediated by four molecular interactions: Fc gamma RIII interacting with IgG, T cell receptor and coreceptor CD8 interacting with antigen peptide presented by major histocompatibility molecule, P-selectin interacting with P-selectin glycoprotein ligand 1 (PSGL-1), and L-selectin interacting with PSGL-1. The latter two are structurally similar and are different from the former two. Fitting the model to data enabled us to evaluate the apparent effective two-dimensional binding affinity of the interacting molecular pairs: 7.19x10(-5) mu m(4) for Fc gamma RIII-IgG interaction, 4.66x10(-3) mu m(4) for P-selectin-PSGL-1 interaction, and 0.94x10(-3) mu m(4) for L-selectin-PSGL-1 interaction. These results elucidate the biophysical mechanism of rosette formation and enable it to become a semiquantitative assay that relates the rosette size to the effective affinity for receptor-ligand binding.

Herramientas y métodos para la caracterización de la sostenibilidad socio, productivo, ambiental en áreas representativas de la cuenca del río Carcarañá, en el sur de la provincia de Santa Fe

Resumen: El presente trabajo aborda la caracterización socio-ambiental de un tramo de la cuenca del Río Carcarañá que atraviesa el sur de la Provincia de Santa Fe, en Argentina. El sector de interés ha sido especialmente afectado por el desarrollo de la agricultura extensiva que, si bien ha sido un elemento determinante del crecimiento económico y de la expansión tanto de las áreas de uso agropecuario, como del medio urbano y recreacional hacia el rural, ha sido sometido a un uso extensivo que requiere analizar la vulnerabilidad ambiental de la cuenca por pérdida de bienes y servicios ecosistémicos, evaluar el soporte ambiental, el uso de los recursos y la sostenibilidad ambiental. Para lograr este objetivo se propone el empleo de La metodologia multimodal, para generar un marco de evaluaciones tanto sociales como biofísicas y energéticas y además bosquejar modelos empíricos y/o teóricos que permitan interpretar la dinámica de los diferentes contaminantes en la cuenca, así como las preocupaciones de la población con relación a estos temas.

Low Spring Constant Regulates P-Selectin-Psgl-1 Bond Rupture

Forced dissociation of selectin-ligand bonds is crucial to such biological processes as leukocyte recruitment, thrombosis formation, and tumor metastasis. Although the bond rupture has been well known at high loading rate r(f) (>= 10(2) pN/s), defined as the product of spring constant k and retract velocity v, how the low r(f) (< 10(2) pN/s) or the low k regulates the bond dissociation remains unclear. Here an optical trap assay was used to quantify the bond rupture at r(f) <= 20 pN/s with low k (similar to 10(-3)-10(-2) pN/nm) when P-selectin and P-selectin glycoprotein ligand 1 (PSGL-1) were respectively coupled onto two glass microbeads. Our data indicated that the bond rupture force f retained the similar values when r(f) increased up to 20 pN/s. It was also found that f varied with different combinations of k and v even at the same r(f). The most probable force, f

Stability Of Adhesion Clusters And Cell Reorientation Under Lateral Cyclic Tension

This work is motivated by experimental observations that cells on stretched substrate exhibit different responses to static and dynamic loads. A model of focal adhesion that can consider the mechanics of stress fiber, adhesion bonds, and substrate was developed at the molecular level by treating the focal adhesion as an adhesion cluster. The stability of the cluster under dynamic load was studied by applying cyclic external strain on the substrate. We show that a threshold value of external strain amplitude exists beyond which the adhesion cluster disrupts quickly. In addition, our results show that the adhesion cluster is prone to losing stability under high-frequency loading, because the receptors and ligands cannot get enough contact time to form bonds due to the high-speed deformation of the substrate. At the same time, the viscoelastic stress fiber becomes rigid at high frequency, which leads to significant deformation of the bonds. Furthermore, we find that the stiffness and relaxation time of stress fibers play important roles in the stability of the adhesion cluster. The essence of this work is to connect the dynamics of the adhesion bonds (molecular level) with the cell's behavior during reorientation (cell level) through the mechanics of stress fiber. The predictions of the cluster model are consistent with experimental observations.

Development Of Biosensor Based On Imaging Ellipsometry

The concept of biosensor based on imaging ellipsometry was proposed ten years ago. Its principle and the methodology as well as some solutions to problems which have to be faced during the development are mentioned. Its properties of phase sensitive, high throughput and fast sampling, as well as label-free, sensitivity better than 1 ng/ml for Immunoglobulin G, and real-time analysis for protein interaction process, etc. provide a potential for applications in biomedicine field. The recent biosensing development with total internal reflection imaging ellipsometry is presented also. [GRAPHICS] An example of 48 protein arrays in matrix. (C) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two-Dimensional Kinetics Of Beta(2)-Integrin And Icam-1 Bindings Between Neutrophils And Melanoma Cells In A Shear Flow

Cell adhesion, mediated by specific receptor-ligand interactions, plays an important role in biological processes such as tumor metastasis and inflammatory cascade. For example, interactions between beta(2)-integrin ( lymphocyte function-associated antigen-1 and/or Mac-1) on polymorphonuclear neutrophils (PMNs) and ICAM-1 on melanoma cells initiate the bindings of melanoma cells to PMNs within the tumor microenvironment in blood flow, which in turn activate PMN-melanoma cell aggregation in a near-wall region of the vascular endothelium, therefore enhancing subsequent extravasation of melanoma cells in the microcirculations. Kinetics of integrin-ligand bindings in a shear flow is the determinant of such a process, which has not been well understood. In the present study, interactions of PMNs with WM9 melanoma cells were investigated to quantify the kinetics of beta(2)-integrin and ICAM-1 bindings using a cone-plate viscometer that generates a linear shear flow combined with a two-color flow cytometry technique. Aggregation fractions exhibited a transition phase where it first increased before 60 s and then decreased with shear durations. Melanoma-PMN aggregation was also found to be inversely correlated with the shear rate. A previously developed probabilistic model was modified to predict the time dependence of aggregation fractions at different shear rates and medium viscosities. Kinetic parameters of beta(2)-integrin and ICAM-1 bindings were obtained by individual or global fittings, which were comparable to respectively published values. These findings provide new quantitative understanding of the biophysical basis of leukocyte-tumor cell interactions mediated by specific receptor-ligand interactions under shear flow conditions.

PICES Press, Vol. 6, No. 1, January 1998

Highlights of PICES VI The state of the eastern North Pacific in the first half of 1997 The state of the western North Pacific in the first half of 1997 The status of the Bering Sea in the first eight month of 1997 Organization of fisheries, environmental and ocean science in Canada Richard James Beamish PICES-GLOBEC Climate Change and Carrying Capacity Program Epipelagic fish production in the open Subarctic Pacific: bottom up or self-regulating control? Activity Report of SCOR Working Group 105 Establishment of Marine Information Research Center: new strategy on oceanographic data management in Japan Bering Sea Ecosystem Biophysical Metadatabase: a collaborative research tool for fisheries-oceanography and ecosystem investigations

Adenylate Cyclase Toxin Promotes Internalisation of Integrins and Raft Components and Decreases Macrophage Adhesion Capacity

10 p.

Two Nuclear Localization Signals in USP1 Mediate Nuclear Import of the USP1/UAF1 Complex

9 p. : il.

Uncovering Ecosystem Service Bundles through Social Preferences

11 p.

An automatic imaging spectroscopic ellipsometer for characterization of nano-film pattern on solid substrate

In order to characterize the physical and spatial properties of nano-film pattern on solid substrates, an automatic imaging spectroscopic ellipsometer (ISE) based on a polarizer - compensator - specimen - analyzer configuration in the visible region is presented. It can provide the spectroscopic ellipsometric parameters psi (x, y, lambda) and Delta (x, y, lambda) of a large area specimen with a lateral resolution in the order of some microns. A SiO2 stepped layers pattern is used to demonstrate the function of the ISE which shows potential application in thin film devices' such as high-throughput bio-chips.