Spectroscopic Investigation of Increased Fluorescent Intensity of Fluorescent Dyes When Adsorbed onto Polystyrene Microparticles.

Microplastics as environmental pollutants are increasingly a source of alarm. The characterization of microplastics will be necessary to discriminate microplastics from other types of particles. To discriminate specific microplastics, plastic-adsorbable fluorescent dyes are used, the stained microplastics are separated from the dye-microplastic mixture by filtration, and the type of fluorescent staining of the microplastics is analyzed by fluorescent microscopy.

Nanoscale observation of PM2.5 incorporated into mammalian cells using scanning electron-assisted dielectric microscope.

PM2.5 has been correlated with risk factors for various diseases and infections. It promotes tissue injury by direct effects of particle components.

MicroRNA biomarkers for chemical hazard screening identified by RNA deep sequencing analysis in mouse embryonic stem cells.

We investigated the responses of microRNAs (miRNAs) using mouse embryonic stem cells (mESCs) exposed to nine chemicals (bis(2-ethylhexyl)phthalate, p-cresol, p-dichlorobenzene, phenol, pyrocatecol, chloroform, tri-n-butyl phosphate, trichloroethylene, and benzene), which are listed as "Class I Designated Chemical Substances" from the Japan Pollutant Release and Transfer Register. Using deep sequencing analysis (RNA-seq), several miRNAs were identified that show a substantial response to general chemical toxicity (i.e.

384-Channel electrochemical sensor array chips based on hybridization-triggered switching for simultaneous oligonucleotide detection.

We investigated the feasibility of simultaneous detection of multiple environmentally- and biomedically-relevant RNA biomarker target sequences on a single newly fabricated 384-ch sensor array chip aiming at practical application. The individual sensor is composed of a photolithographically-fabricated Au/Cr-based electrode modified with peptide nucleic acid (PNA) probes. The sensor array chips showed sequence-specific responses upon hybridization of the probes with target sequences complementary to the probes in contrast to mismatch versions.

Effect of methyl p-hydroxybenzoate on the culture of mammalian cell.

Several chemicals, such as methyl p-hydroxybenzoate (MHB), have been widely used as preservatives in the water baths of CO incubators used for mammalian cell culture, and they are not considered to produce any biological effects. However, no detailed analyses of the effects of these compounds on cultured cells have been reported. In this study, we thus examined whether MHB in the incubator water bath affects cell viability or genome-wide gene expression in mouse embryonic stem cells under control conditions [using only dimethyl sulfoxide (DMSO) in the culture medium] and under chemical-treated conditions using benzene and chloroform; conditions that simulate a cell-based toxicity assay.

Identification of RNA biomarkers for chemical safety screening in mouse embryonic stem cells using RNA deep sequencing analysis.

Although it is not yet possible to replace in vivo animal testing completely, the need for a more efficient method for toxicity testing, such as an in vitro cell-based assay, has been widely acknowledged. Previous studies have focused on mRNAs as biomarkers; however, recent studies have revealed that non-coding RNAs (ncRNAs) are also efficient novel biomarkers for toxicity testing. Here, we used deep sequencing analysis (RNA-seq) to identify novel RNA biomarkers, including ncRNAs, that exhibited a substantial response to general chemical toxicity from nine chemicals, and to benzene toxicity specifically.

Rapid monitoring of RNA degradation activity in vivo for mammalian cells.

We have developed a rapid fluorescence assay based on fluorescence resonance energy transfer (FRET) for the monitoring of RNA degradation activity in mammalian cells. In this technique, double-stranded RNA (dsRNA) fluorescent probes are used. The dsRNA fluorescent probes consist of a 5' fluorophore-labeled strand hybridized to a 3' quencher-labeled strand, and the fluorescent dye is quenched by a quencher dye.

Multi-stage Mass Spectrometry of Poly(vinyl pyrrolidone) and Its Vinyl Succinimide Copolymer Formed upon Exposure to Sodium Hypochlorite.

The degradation routes of poly(vinyl pyrrolidone) (PVP) exposed to sodium hypochlorite (bleach) have been previously investigated using chemical analyses such as infrared spectroscopy. So far, no reports have proposed mass spectrometry (MS) as an alternative tool despite its capability to provide molecular and structural information using its single stage electrospray (ESI) or matrix assisted laser desorption ionization (MALDI) and multi stage (MS ) configurations, respectively. The present study thus reports on the characterization of PVP after its exposure to bleach by high resolution MALDI spiralTOF-MS and Kendrick mass defect analysis providing clues as to the formation of a vinyl pyrrolidone/vinyl succinimide copolymeric degradation product.

An Evaluation of Sensor Performance for Harmful Compounds by Using Photo-Induced Electron Transfer from Photosynthetic Membranes to Electrodes.

Rapid, simple, and low-cost screening procedures are necessary for the detection of harmful compounds in the effluent that flows out of point sources such as industrial outfall. The present study investigated the effects on a novel sensor of harmful compounds such as KCN, phenol, and herbicides such as 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), 2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine (atrazine), and 2-N-tert-butyl-4-N-ethyl-6-methylsulfanyl-1,3,5-triazine-2,4-diamine (terbutryn). The sensor employed an electrode system that incorporated the photocurrent of intra-cytoplasmic membranes (so-called chromatophores) prepared from photosynthetic bacteria and linked using carbon paste electrodes.

Genome-wide gene expression analysis of mouse embryonic stem cells exposed to p-dichlorobenzene.

Because of the limitations of whole animal testing approaches for toxicological assessment, new cell-based assay systems have been widely studied. In this study, we focused on two biological products for toxicological assessment: mouse embryonic stem cells (mESCs) and long noncoding RNAs (lncRNAs). mESCs possess the abilities of self-renewal and differentiation into multiple cell types.

Effect of the sp(2)/sp(3) Ratio in a Hybrid Nanocarbon Thin Film Electrode for Anodic Stripping Voltammetry Fabricated by Unbalanced Magnetron Sputtering Equipment.

The effect of the sp(2)/sp(3) ratio in an unbalanced magnetron sputtered nanocarbon film electrode was studied for determining Cd(2+) and Pb(2+) by anodic stripping voltammetry (ASV). The signal-to-noise ratio in the ASV measurement improved as the sp(3) concentration in the carbon film increased because the noise current decreased with the increasing sp(3) concentration. The detection limits with a carbon film containing 50% sp(3) were 0.

Photocatalytic degradation of the antiviral drug Tamiflu by UV-A/TiO2: Kinetics and mechanisms.

The photocatalytic degradation of the antiviral drug Tamiflu (oseltamivir phosphate, OP) by TiO2 - P25, ST-01 and ATO was investigated in aqueous solution under ultraviolet (UV-A) irradiation. The photocatalysis of OP is well described by pseudo-first-order kinetics with r2>98.0% for all cases.

Development of cytotoxicity-sensitive human cells using overexpression of long non-coding RNAs.

Biosensors using live cells are analytical devices that have the advantage of being highly sensitive for their targets. Although attention has primarily focused on reporter gene assays using functional promoters, cell viability assays are still efficient. We focus on long non-coding RNAs (lncRNAs) that are involved in the molecular mechanisms associated with responses to cellular stresses as a new biological material.

Long non-coding RNAs as surrogate indicators for chemical stress responses in human-induced pluripotent stem cells.

In this study, we focused on two biological products as ideal tools for toxicological assessment: long non-coding RNAs (lncRNAs) and human-induced pluripotent stem cells (hiPSCs). lncRNAs are an important class of pervasive non-protein-coding transcripts involved in the molecular mechanisms associated with responses to cellular stresses. hiPSCs possess the capabilities of self-renewal and differentiation into multiple cell types, and they are free of the ethical issues associated with human embryonic stem cells.

Creation of artificial luciferases for bioassays.

The present study demonstrates the creation of artificial luciferases (ALuc) for bioassays, inspired by a sequence alignment of copepod luciferases. Extraction of the consensus amino acids from the alignment enabled us to generate a series of ALucs with unique optical properties and sequential identities that are clearly different from those of any existing copepod luciferase. For example, some ALucs exhibited heat stability, dramatically prolonged optical intensities, broad full width at half-maximum, and strong optical intensities.

Identification of short-lived long non-coding RNAs as surrogate indicators for chemical stress response.

Abiotic and biotic stressors in human cells are often a result of sudden and/or frequent changes in environmental factors. The molecular response to stress involves elaborate modulation of gene expression and is of homeostatic, ecological, and evolutionary importance. Although attention has primarily focused on signaling pathways and protein networks, long non-coding RNAs (ncRNAs) are increasingly involved in the molecular mechanisms associated with responses to cellular stresses.

Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes.

Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer.

The RNA degradation pathway regulates the function of GAS5 a non-coding RNA in mammalian cells.

Studies of various mRNAs have revealed that changes in the abundance of transcripts, through mRNA degradation, act as a critical step in the control of various biological pathways. Similarly, the regulation of non-coding RNA (ncRNA) levels is also considered to be important for their biological functions; however, far less is known about the mechanisms and biological importance of ncRNA turnover for the regulation of ncRNA functions. The growth arrest-specific 5 (GAS5) ncRNA accumulates during growth arrest induced by serum starvation and its transcript is degraded by the well characterized nonsense-mediated RNA decay (NMD) pathway.

Bioluminescent capsules for live-cell imaging.

A bioluminescent capsule was designed for illuminating cell signaling and protein localization. The capsule consists of four components, namely, a secretion peptide (SP), a luciferase body, a cargo protein (or peptide), and a membrane-localization signal (MLS). Any functional proteins sandwiched between the luciferase body and MLS may be cartable to the plasma membrane (PM), where the capsule waits for outer signals and quickly releases the embedded luciferase in response to the signals.

Characterization of the Lactobacillus casei group based on the profiling of ribosomal proteins coded in S10-spc-alpha operons as observed by MALDI-TOF MS.

The taxonomy of the members of the Lactobacillus casei group is complicated because of their phylogenetic similarity and controversial nomenclatural status. In this study, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of ribosomal proteins coded in the S10-spc-alpha operon, termed S10-GERMS, was applied in order to classify 33 sample strains belonging to the L. casei group.

Evolution of bioluminescence in marine planktonic copepods.

Copepods are the dominant taxa in zooplankton communities of the ocean worldwide. Although bioluminescence of certain copepods has been known for more than a 100 years, there is very limited information about the structure and evolutionary history of copepod luciferase genes. Here, we report the cDNA sequences of 11 copepod luciferases isolated from the superfamily Augaptiloidea in the order Calanoida.

A bioluminescent probe for salivary cortisol.

Cortisol is a classical biomarker for the stress levels of human beings. We fabricated highly sensitive bioluminescent probes for salivary cortisol. The following strategies were contrived in the molecular design.

Phylogenetic analysis of Rhodococcus erythropolis based on the variation of ribosomal proteins as observed by matrix-assisted laser desorption ionization-mass spectrometry without using genome information.

Rhodococcus erythropolis strains characterized as antibiotic producers can be classified into three groups according to their antibiotic spectrum and growth compatibility. Due to their high genotypic similarity, the taxonomic relationship of these strains has not been elucidated. In this study, ribosomal protein profiling using matrix-assisted laser desorption ionization-mass spectrometry (MALDI-MS) was employed to classify twenty-one strains of R.

Affinity capillary electrophoresis with magnetic beads for multiplex quantitative analysis of bacterial 16S rRNA.

We have developed a novel method for microbial community analysis of bacterial 16S rRNAs based on affinity capillary electrophoresis using 16S rRNA-conjugated magnetic beads. We called this method magnetic beads affinity capillary electrophoresis (MB-ACE) which can be used for sequential and quantitative analysis of 16S rRNA. In this method, RNA extracted from a microbial community is biotin-modified and mixed with streptavidin-modified paramagnetic beads.

Variable-pitch dispensing workstation and its application to the preparation of microsensor arrays.

We have developed an 8-ch capillary-based dispensing workstation with a variable capillary pitch mechanism. The capillary intervals can be varied from 1 to 9 mm to dispense different solutions simultaneously at an arbitrary dispensing pitch, allowing direct dispensing from microplates to integrated analytical systems. To evaluate the precision of its dispensing performance, droplets of Rhodamine G dye were dispensed onto glass slides and the values of the optical volume were analyzed.