The Thing Metabolome Repository family (XMRs): comparable untargeted metabolome databases for analyzing sample-specific unknown metabolites.

The identification of unknown chemicals has emerged as a significant issue in untargeted metabolome analysis owing to the limited availability of purified standards for identification; this is a major bottleneck for the accumulation of reusable metabolome data in systems biology. Public resources for discovering and prioritizing the unknowns that should be subject to practical identification, as well as further detailed study of spending costs and the risks of misprediction, are lacking. As such a resource, we released databases, Food-, Plant- and Thing-Metabolome Repository (http://metabolites.in/foods, http://metabolites.in/plants, and http://metabolites.in/things, referred to as XMRs) in which the sample-specific localization of unknowns detected by liquid chromatography-mass spectrometry in a wide variety of samples can be examined, helping to discover and prioritize the unknowns. A set of application programming interfaces for the XMRs facilitates the use of metabolome data for large-scale analysis and data mining. Several applications of XMRs, including integrated metabolome and genome analyses, are presented. Expanding the concept of XMRs will accelerate the identification of unknowns and increase the discovery of new knowledge.

Surface plasmon resonance sensor using a polarization-maintaining fiber on a hetero-core optical fiber structure with gold thin film.

This study experimentally demonstrated the effects of two polarization-maintaining fibers (PMFs) as a sensing region instead of conventional single-mode fiber (SMF) using Au-coated hetero-core optical fiber surface plasmon resonance (SPR) sensor. We experimentally observed that the SPR resonant wavelength is shifted toward longer wavelength with refractive index (RI) increasing from 1.332 to 1.396. A PMF sensor exhibits the broad SPR spectra, resulting in a higher sensitivity with a 1.5-fold change in the light intensity at 850 nm relative to RI, compared with the SMF case. Discussions most likely responsible for this effect are given by the lower angular distribution peak in the hetero-core region of PMFs.

Development of two-dimensional qualitative visualization method for isoflavones secreted from soybean roots using sheets with immobilized bovine serum albumin.

A visualization method for the qualitative evaluation of soybean isoflavones secreted from soybean roots by transferring them onto a sheet with immobilized bovine serum albumin (BSA) was developed. BSA was chemically bonded onto a glass microfiber filter. The fluorescence quenching resulting from the interaction of BSA with soybean isoflavones such as daidzein and daidzin was utilized. Fluorescence images before and after soybean roots were placed in contact with the sheets with immobilized BSA were taken with an electron-multiplying charge-coupled device camera. The fluorescence quenching in the images was visualized and analyzed. Soybean isoflavones were extracted from the sheets for quantitative analysis, and the correlation coefficient between the quenched fluorescence intensity per sheet and the total amount of soybean isoflavones was 0.78 (p < 0.01), indicating a high correlation. The quenched fluorescence intensity was lower in pumpkin roots, which do not secrete soybean isoflavone. It was found from analyzed images that soybean isoflavone is secreted in larger amounts from the basal region of the taproot and the tips of the lateral roots of soybean.

Quick response hydrogen LSPR sensor based on a hetero-core fiber structure with palladium nanoparticles.

A novel fiber optic localized surface plasmon resonance (LSPR) hydrogen sensor has been developed based on the hetero-core structured with palladium nanoparticles (PdNPs) onto a cylindrical cladding surface. In a light-intensity-based experiment with an LED operating at 850 nm, it has been observed that a transmitted loss change of 0.23 dB was induced with response and recovery times of 1.5 and 3.2 s for 4% hydrogen which are the fastest response times among optical fiber hydrogen sensors. The proposed sensor resolved the inevitable trade-off issue between sensitivity and response time which existed in the previously reported SPR sensors, with keeping the response time below 2.0 s even in a high sensitivity region of interest.

Localized surface plasmon sensor based on gold island films using a hetero-core structured optical fiber.

This paper reports the effect of applying an Au island film to the hetero-core structured optical fiber, which is fabricated by annealing thin Au films with thicknesses of 3 and 5 nm and its sensing performance for the refractive index changes. We experimentally observe that novel localized surface plasmon resonance spectra for 1.333 RIU appear in the visible-to-near-infrared region, depending on the shape of Au islands. The absorbance and spectral sensitivity for a given refractive index region of the tested solvents were obtained to be 4.81 AU/RIU and 517 nm/RIU, respectively, in the range of 1.333-1.384 RIU in the case of 5 nm thick Au film annealed at 900°C.

A hydrogen curing effect on surface plasmon resonance fiber optic hydrogen sensors using an annealed Au/Ta2O5/Pd multi-layers film.

In this paper, a response time of the surface plasmon resonance fiber optic hydrogen sensor has successfully improved with keeping sensor sensitivity high by means of hydrogen curing (immersing) process of annealed Au/Ta2O5/ Pd multi-layers film. The hydrogen curing effect on the response time and sensitivity has been experimentally revealed by changing the annealing temperatures of 400, 600, 800°C and through observing the optical loss change in the H2 curing process. When the 25-nm Au/60-nm Ta2O5/10-nm Pd multi-layers film annealed at 600°C is cured with 4% H2/N2 mixture, it is found that a lot of nano-sized cracks were produced on the Pd surface. After H2 curing process, the response time is improved to be 8 s, which is two times faster than previous reported one in the case of the 25-nm Au/60-nm Ta2O5/3-nm Pd multi-layers film with keeping the sensor sensitivity of 0.27 dB for 4% hydrogen adding. Discussions most likely responsible for this effect are given by introducing the α-ß transition Pd structure in the H2 curing process.