Dynamic Correlation Analysis between Stress-Strain Curve and Polymer Film Structure Using Persistent Homology.

Coarse-grained molecular dynamics (CG-MD) simulations and subsequent persistent homology (PH) analysis were performed to correlate the structure and stress-strain behavior of polymer films. During uniaxial tensile MD simulations, the first principal component of the persistence diagram obtained by principal component analysis (PCA) was in good agreement with the stress-strain curve. This indicates that PH + PCA can identify critical ring structures relevant to the dynamic changes in MD simulations without requiring any prior knowledge.

Quality and Safety Considerations for Therapeutic Products Based on Extracellular Vesicles.

Extracellular vesicles (EVs) serve as an intrinsic system for delivering functional molecules within our body, playing significant roles in diverse physiological phenomena and diseases. Both native and engineered EVs are currently the subject of extensive research as promising therapeutics and drug delivery systems, primarily due to their remarkable attributes, such as targeting capabilities, biocompatibility, and low immunogenicity and mutagenicity. Nevertheless, their clinical application is still a long way off owing to multiple limitations.

Molecular Dynamics Simulation of Adhesion of Additive Molecules in Paint Materials toward Enhancement of Anticorrosion Performance.

Adsorption energies of additive molecules in paint materials on the iron oxide substrate are investigated by molecular dynamics (MD) simulations to find the key feature of adhesion, which is one of the indispensable elements for the corrosion resistance of coated materials. Both edge-on and face-on adsorptions are observed for most additive molecules such as phenylsuccinic acid and benzoic acid. On the other hand, only the edge-on adsorption is observed for the specific molecule having a benzothiazole ring due to the effect of steric conformation.

Urinary extracellular vesicles signature for diagnosis of kidney disease.

Congenital disorders characterized by the quantitative and qualitative reduction in the number of functional nephrons are the primary cause of chronic kidney disease (CKD) in children. We aimed to describe the alteration of urinary extracellular vesicles (uEVs) associated with decreased renal function during childhood. By nanoparticle tracking analysis and quantitative proteomics, we identified differentially expressed proteins in uEVs in bilateral renal hypoplasia, which is characterized by a congenitally reduced number of nephrons.

Distinguishing functional exosomes and other extracellular vesicles as a nucleic acid cargo by the anion-exchange method.

The development of a new large-scale purification protocol is required for research on the reliable bioactivity and drug discovery of extracellular vesicles (EVs). To address this issue, herein, we propose an effective method for preparing high-performance exosomes (EXOs) by using an anion-exchange method. Cytotoxic T-lymphocyte (CTL) EVs from 4 L of culture supernatant through a 220 nm cut-off filter are divided into two populations at a deproteinization rate of over 99.

Photo-reactive oligodeoxynucleotide-embedded nanovesicles (PROsomes) with switchable stability for efficient cellular uptake and gene knockdown.

A photo-responsive nanovesicle is fabricated by polyion complex (PIC) formation between poly(ethylene glycol) (PEG)-block-polypeptides and photo-reactive oligodeoxynucleotides (PROs)/anti-sense oligonucleotides (ASOs). The ultraviolet (UV) light triggers reversible crosslinking between PROs and ASOs in the vesicular membrane, providing the nanovesicle with switchable stability under physiological conditions. The resulting nanovesicle allows efficient cellular internalization, leading to significant UV-triggered gene knockdown in cultured cells.

Optical measurement platform of temperature-dependent interaction between nanoliposomes and a polymer-grafted surface.

In this study, we report an opto-microfluidic platform integrated with dark-field light scattering imaging and fluorescence microspectroscopy to investigate the temperature-dependent behavior of nanoliposomes. This newly developed experimental platform enabled both in situ measurements of the temperature of the sample solution and observation of individual nanoliposomes. As a proof-of-concept, the temperature-dependent interaction between 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC) nanoliposomes and a poly(ethylene glycol) (PEG) grafted surface was investigated using this opto-microfluidic platform.

Effect of the Thermal History on the Crystallinity of Poly (L-lactic Acid) During the Micromolding Process.

The micromolding process using biocompatible thermoplastic polymers is highly attractive as a fabrication process of microdevices in biomedical applications. In this study, we investigated the effect of the thermal history in the micromolding process on the crystallinity of semi-crystalline polymers, such as poly (L-lactic acid) (PLLA), during their crystallization from the amorphous and molten states. In particular, the thermal history in the micromolding process using poly(dimethylsiloxane) replica mold embedded with a thermocouple was recorded.

Extracellular vesicles nanoarray technology: Immobilization of individual extracellular vesicles on nanopatterned polyethylene glycol-lipid conjugate brushes.

Arraying individual extracellular vesicles (EVs) on a chip is expected one of the promising approaches for investigating their inherent properties. In this study, we immobilized individual EVs on a surface using a nanopatterned tethering chip-based versatile platform. A microfluidic device was used to ensure soft, reproducible exposure of the EVs over the whole chip surface.

Subtypes of tumour cell-derived small extracellular vesicles having differently externalized phosphatidylserine.

Phosphatidylserine (PS) has skewed distributions in the plasma membrane and is preferentially located in the inner leaflet of normal cells. Tumour cells, however, expose PS at the outer leaflet of cell surfaces, thereby potentially modulating the bio-signalling of cells. Interestingly, exosomes - or, more properly, small extracellular vesicles (sEVs) - which are secreted from tumour cells, are enriched with externalized PS, have been proposed as being involved in the progression of cancers, and could be used as a marker for tumour diagnostics.

Digital enzyme assay using attoliter droplet array.

Single-molecule digital enzyme assay using micron-sized droplet array is a promising analysis method to quantify biomolecules at extremely low concentrations. However, multiplex digital enzyme assays are still difficult to access because the best buffer conditions can vary largely among enzymes. In addition, the best conditions for flurogenic compounds to retain high quantum efficiency and to avoid leakage into the oil phase can be also very different.

Fabrication and Characterization of a Stabilized Thin Film Ag/AgCl Reference Electrode Modified with Self-Assembled Monolayer of Alkane Thiol Chains for Rapid Biosensing Applications.

The fabrication of miniaturized electrical biosensing devices can enable the rapid on-chip detection of biomarkers such as miRNA molecules, which is highly important in early-stage cancer detection. The challenge in realizing such devices remains in the miniaturization of the reference electrodes, which is an integral part of electrical detection. Here, we report on a novel thin film Ag/AgCl reference electrode (RE) that has been fabricated on top of a Au-sputtered glass surface, which was coated with a self-assembled monolayer (SAM) of 6-mercepto-1-hexanol (MCH).

Microcapillary Chip-Based Extracellular Vesicle Profiling System.

A microcapillary chip-based particle electrophoresis system developed for characterizing extracellular vesicles (EVs) is described. So far, it is technologically difficult to analyze or identify a heterogeneous population of particles ranging from several tens to one hundred nanometers, and hence, there is a growing demand for a new analytical method of nanoparticles among researchers working on extracellular vesicles. The analytical platform presented in this chapter allows detection of individual nanoparticles or nanovesicles of less than 50 nm in diameter and enables the characterization of nanoparticles based on multiple indexes such as concentration, diameter, zeta potential, and surface antigenicity.

Abnormal intrinsic dynamics of dendritic spines in a fragile X syndrome mouse model in vivo.

Dendritic spine generation and elimination play an important role in learning and memory, the dynamics of which have been examined within the neocortex in vivo. Spine turnover has also been detected in the absence of specific learning tasks, and is frequently exaggerated in animal models of autistic spectrum disorder (ASD). The present study aimed to examine whether the baseline rate of spine turnover was activity-dependent.

Flexible Sheet-Type Sensor for Noninvasive Measurement of Cellular Oxygen Metabolism on a Culture Dish.

A novel flexible sensor was developed for the noninvasive oxygen metabolism measurement of cultivated cells and tissues. This device is composed of a transparent double-layered polymer sheet of ethylene-vinyl alcohol (EVOH) and poly(dimethylsiloxane) (PDMS) having an array of microhole structures of 90 μm diameter and 50 μm depth on its surface. All the microhole structures were equipped with a 1-μm-thick optical chemical sensing layer of platinum porphyrin-fluoropolymer on their bottom.

On-chip immunoelectrophoresis of extracellular vesicles released from human breast cancer cells.

Extracellular vesicles (EVs) including exosomes and microvesicles have attracted considerable attention in the fields of cell biology and medicine. For a better understanding of EVs and further exploration of their applications, the development of analytical methods for biological nanovesicles has been required. In particular, considering the heterogeneity of EVs, methods capable of measuring individual vesicles are desired.

Microintaglio Printing for Soft Lithography-Based in Situ Microarrays.

Advances in lithographic approaches to fabricating bio-microarrays have been extensively explored over the last two decades. However, the need for pattern flexibility, a high density, a high resolution, affordability and on-demand fabrication is promoting the development of unconventional routes for microarray fabrication. This review highlights the development and uses of a new molecular lithography approach, called "microintaglio printing technology", for large-scale bio-microarray fabrication using a microreactor array (µRA)-based chip consisting of uniformly-arranged, femtoliter-size µRA molds.

Lab-on-a-brain: implantable micro-optical fluidic devices for neural cell analysis in vivo.

The high-resolution imaging of neural cells in vivo has brought about great progress in neuroscience research. Here, we report a novel experimental platform, where the intact brain of a living mouse can be studied with the aid of a surgically implanted micro-optical fluidic device; acting as an interface between neurons and the outer world. The newly developed device provides the functions required for the long-term and high-resolution observation of the fine structures of neurons by two-photon laser scanning microscopy and the microfluidic delivery of chemicals or drugs directly into the brain.

Temperature-controlled microintaglio printing for high-resolution micropatterning of RNA molecules.

We have developed an advanced microintaglio printing method for fabricating fine and high-density micropatterns and applied it to the microarraying of RNA molecules. The microintaglio printing of RNA reported here is based on the hybridization of RNA with immobilized complementary DNA probes. The hybridization was controlled by switching the RNA conformation via the temperature, and an RNA microarray with a diameter of 1.

Implementation of tetra-poly(ethylene glycol) hydrogel with high mechanical strength into microfluidic device technology.

Hydrogels have several excellent characteristics suitable for biomedical use such as softness, biological inertness and solute permeability. Hence, integrating hydrogels into microfluidic devices is a promising approach for providing additional functions such as biocompatibility and porosity, to microfluidic devices. However, the poor mechanical strength of hydrogels has severely limited device design and fabrication.

Statistical fluctuation in zeta potential distribution of nanoliposomes measured by on-chip microcapillary electrophoresis.

The zeta potential of nanoliposomes with a diameter below 100 nm has been studied by the combined use of on-chip microcapillary electrophoresis (μCE) and sensitive fluorescence imaging. Tracking the electrophoretic migration of individual nanoliposomes has enabled the accurate evaluation of the zeta potential distribution of nanoliposomes and the first observation of its abnormal broadening due to a statistical fluctuation phenomenon specific to the "nanoscale world." The materials used for liposome preparation were phosphocholine as the neutral lipid, phosphatidylserine as the anionic lipid, and cholesterol.

Improvement of a puromycin-linker to extend the selection target varieties in cDNA display method.

cDNA display using a puromycin-linker to covalently bridge a protein and its coding cDNA is a stable and efficient in vitro protein selection method. The optimal design of the often-used puromycin-linker is vital for effective selection. In this report, an improved puromycin-linker containing deoxyinosine bases as cleavage sites, which are recognized by endonuclease V, was introduced to extend the variety of the selection targets to molecules such as RNA.

A topographically optimized substrate with well-ordered lattice micropatterns for enhancing the osteogenic differentiation of murine mesenchymal stem cells.

Although recently a growing number of reports demonstrate that topography or geometry of the substrate also plays an important role in the fate of the stem cells, most of these studies are usually completed by a few distinct patterns such as simple lines, posts, etc. As a result, there is a lack of quantitative analysis of the relationship between topographical variation and the differentiation of stem cells. Here, the effectiveness of topography variation is studied systematically in several microengineered substrates on osteogenic differentiation.

Gel shift selection of translation enhancer sequences using messenger RNA display.

We designed a new approach for selection of translation enhancer sequences that enables efficient protein synthesis in cell-free systems. The selection is based on a gel shift assay of a messenger RNA (mRNA)-protein fusion product that is synthesized in a cell-free translation system using an mRNA display method. A library of randomized 20-nt-long sequences, with all possible combinations of the four nucleotides, upstream of a coding region was screened by successive rounds of screening in which the translation time of the succeeding round was reduced compared with the previous round.

Cell electrophoresis on a chip: what can we know from the changes in electrophoretic mobility?

An overview of both experimental and theoretical studies of cell electrophoresis mobility (EPM) over the past fifty years and the relevance of cell EPM measurement are presented and discussed from the viewpoint of exploring the potential use of cell EPM as an index of the biological condition of cells. Physical measurements of the optical and/or electrical properties of cells have been attracting considerable attention as noninvasive cell-evaluation methods that are essential for the future of cell-based application technologies such as cell-based drug screening and cell therapy. Cell EPM, which can be measured in a noninvasive manner by cell electrophoresis, reflects the electrical and mechanical properties of the cell surface.