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The rigorous coupled-wave analysis (RCWA) is applied to the simulation of 4π-microscopy. To this end, we combine the concept of structured illumination with coherent two-sided light incidence. It is demonstrated how the latter is integrated into the RCWA framework. With these techniques we simulate two coherent counter-propagating converging beams incident upon a sample as in 4π-microscopy.
This paper proposes a modified spatially-constrained similarity measure (mSCSM) method for endosomal structure detection and localization under the bag-of-words (BoW) framework. To our best knowledge, the proposed mSCSM is the first method for fully automatic detection and localization of complex subcellular compartments like endosomes. Essentially, a new similarity score and a novel two-stage output...
Observing the dynamic characteristics of proteins by multi-channel fluorescence microscopy allows studying the interactions between different subcellular structures. We introduce a probabilistic approach for tracking and colocalization analysis of viral proteins in two-channel microscopy image sequences. Our approach is based on particle filters and the Kalman filter, and performs tracking and colocalization...
In this work we set several mathematical tools to study the role of Dynamin and Endophilin in the Clathrin-mediated endocytosis process. Their different dynamics and co-localizations are observed by using TIRF microscopy. We define in particular a novel tracking method in order to track the Clathrin-coated pits and quantify their co-localization with the proteins involved in the process. Thereafter,...
Two-photon (TP) calcium imaging is an important imaging modality in neuroscience, allowing for large-scale recording of neural activity in awake, behaving animals at behavior-relevant timescales. Interpretation of TP data requires the accurate extraction of temporal neural activity traces, which can be accomplished via manual or automated methods. In this work we seek to improve the accuracy of both...
We developed Linear Zero Mode Waveguides (LZMWs) for simultaneous observation of kinesin displacement and ATP hydrolysis cycle under higher concentration of fluorescently labeled ATP than that used in conventional total internal reflection microscopy (TIRFM). Single-molecule fluorescent microscopy is a promising method to analyze correlation between the mechanical displacement and hydrolysis of ATP...
We developed a portable odorant detection system composed of collagen micro-pillars with cells expressing olfactory receptors and a CMOS imaging sensor; the CMOS imaging sensor caught fluorescence signals of Ca2+ increased by odorant molecules. While low sensitiveness of the CMOS imaging sensor was insufficient to detect the fluorescent signal from a single cell, the odorant detection system achieved...
In this study, we investigated the ionic current rectification of glass nanopipettes modified with bovine serum albumin glutaraldehyde (BSA-GA) artificial membrane using solutions with various pHs. Ionic current rectification is a phenomenon that is observed with nanopores as asymmetric I-V curves, where the ionic currents recorded through a nanopore differ at the same magnitude of applied electrical...
Modeling has predicted that intramolecular structural vibrations enables proteins to access functionally important structural change. We show that the vibrational density of states and the isotropic absorption in the terahertz range are only weakly dependent on the protein functional state for several bench marking proteins. At the same time the direction of motions changes dramatically with functional...
Quantitative co-localization analysis with fluorescent microscopy is a common approach to assess the spatial co-ordination of molecules and thus to understand their functions in biological processes. However, the co-localization analysis results might not be consistent due to various imaging conditions and different quantification methods used. We propose a novel method to separate a co-localization...
Nanopore sensing has been widely researched owing to its single molecule sensitivity. In this work, we have demonstrated the potential application of a relatively low-cost single borosilicate nanopore-based sensor for simultaneous detection of multiple charged particles with various diameters.
Charged water interfaces are ubiquitous and responsible for many important processes in nature and modern technologies, such as protein folding, electrochemistry, and photocatalysis. They appear in the form of an electric double layer that can be divided into two sub-layers. One is the so-called Stern layer composed of one to two hardly mobile, hydrogen-bonded, water monolayers next to the charged...
Zinc oxide (ZnO) and Titanium dioxide (TiO2) nanoparticles are some of the widely used nanoparticles (NPs) in commercial industry. Thus the chances for the particles to get run off to the aquatic environment and to there by affect the aquatic life are very high. The present study evaluates the short term toxicity of ZnO NPs and TiO2 NPs on Chlorella pyrenoidosa, which is a fresh water algae and on...
Although the genomes of many animals, from worms to humans, have been sequenced, much of the detailed molecular understanding of the biology of these genes and their proteins is unknown. One of the major problems is that we cannot currently see what a protein does, where it is, and how it moves. Thus, most functional conclusions about a protein are necessarily indirect. The visualization of the structure...
Quanterix and Stratec Biomedical have developed an automated analyzer that enables the measurement of subfemtomolar concentrations of proteins. The development of this technology focusing on the custom optical module and microfluidic disc is outlined below.
N-ethylmaleimide-sensitive factor (NSF) and alpha soluble NSF attachment protein (α-SNAP) disassemble the SNAP receptor (SNARE) complex for recycling of the SNARE proteins. Using single-molecule fluorescence and force spectroscopy, we found that NSF appears to use a "spring-loaded" mechanism.
We demonstrated two-photon excitation of fluorescent proteins by using visible light. The excitation scheme has been applied to simultaneous multicolor imaging of biological cells with improved spatial resolution.
This paper reviews recent works of label-free immune assay using terahertz technologies, which includes a terahertz chemical microscopy. Experimental results of label-free detection of lectin-suger chain reactions were also presented.
Microfluidic technologies have become increasingly effective for diagnostic, physiological, and biochemical applications. The biocompatibility of MEMS devices, which are evolving rapidly in their practicality, has become the paramount property to investigate and optimize through biological and optical testing. Potential applications comprise cell culture, biosensing, immunoisolation, bioparticle sorting,...
Fluorescent fusion proteins of caveolin oligomerize to form plasma membrane pits, called caveolae. Amount of caveolin protein in a pit can be estimated by fluorescence intensity of the pit in microscopy image. In this study an automatic method is introduced for pit recognition, intensity measurement and intensity distribution parameter estimation. Dots are recognised and separated from non-caveolar...
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