Influence of DNA extraction kits on freshwater fungal DNA metabarcoding

[Background] Environmental DNA (eDNA) metabarcoding is a common technique for efficient biodiversity monitoring, especially of microbes. Recently, the usefulness of aquatic eDNA in monitoring the diversity of both terrestrial and aquatic fungi has been suggested. In eDNA studies, different experimental factors, such as DNA extraction kits or methods, can affect the subsequent analyses and the results of DNA metabarcoding. However, few methodological studies have been carried out on eDNA of fungi, and little is known about how experimental procedures can affect the results of biodiversity analysis. In this study, we focused on the effect of DNA extraction method on fungal DNA metabarcoding using freshwater samples obtained from rivers and lakes. [Methods] DNA was extracted from freshwater samples using the DNeasy PowerSoil kit, which is mainly used to extractmicrobial DNA from soil, and the DNeasy Blood & Tissue kit, which is commonly used for eDNA studies on animals. We then compared PCR inhibition and fungal DNA metabarcoding results; i.e., operational taxonomic unit (OTU) number and composition of the extracted samples. [Results] No PCR inhibition was detected in any of the samples, and no significant differences in the number of OTUs and OTU compositions were detected between the samples processed using different kits. These results indicate that both DNA extraction kits may provide similar diversity results for the river and lake samples evaluated in this study. Therefore, it may be possible to evaluate the diversity of fungi using a unified experimental method, even with samples obtained for diversity studies on other taxa such as those of animals

Conceptual Design of 3-D FDTD Dedicated Computer With Dataflow Architecture for High Performance Microwave Simulation

For practical use of microwave simulations in industry applications such as high frequency product design, this paper presents a conceptual design of 3-D finite difference time domain (FDTD) dedicated computer with dataflow architecture as one of the portable high performance computing technologies. A basic concept of the dataflow architecture for the FDTD dedicated computer itself was presented already in 2003 for 2-D microwave simulations. Detail design of 3-D FDTD dataflow machine is considered in this paper

Factorizing a String into Squares in Linear Time

A square factorization of a string w is a factorization of w in which each factor is a square. Dumitran et al. [SPIRE 2015, pp. 54-66] showed how to find a square factorization of a given string of length n in O(n log n) time, and they posed a question whether it can be done in O(n) time. In this paper, we answer their question positively, showing an O(n)-time algorithm for square factorization in the standard word RAM model with machine word size omega = Omega(log n). We also show an O(n + (n log^2 n) / omega)-time (respectively, O(n log n)-time) algorithm to find a square factorization which contains the maximum (respectively, minimum) number of squares

Evaluation of host effects on ectomycorrhizal fungal community compositions in a forested landscape in northern Japan

Electronic supplementary material is available online at https://doi.org/10.6084/m9.figshare.c.4853145.Community compositions of ectomycorrhizal (ECM) fungi are similar within the same host taxa. However, careful interpretation is required to determine whether the combination of ECM fungi and plants is explained by the host preference for ECM fungi, or by the influence of neighbouring heterospecific hosts. In the present study, we aimed to evaluate the effects of host species on the ECM community compositions in a forested landscape (approx. 10 km) where monodominant forest stands of six ECM host species belonging to three families were patchily distributed. A total of 180 ECM operational taxonomic units (OTUs) were detected with DNA metabarcoding. Quantitative multivariate analyses revealed that the ECM community compositions were primarily structured by host species and families, regardless of the soil environments and spatial arrangements of the sampling plots. In addition, 38 ECM OTUs were only detected from particular host tree species. Furthermore, the neighbouring plots harboured similar fungal compositions, although the host species were different. The relative effect of the spatial factors on the ECM compositions was weaker than that of host species. Our results suggest that the host preference for ECM fungi is the primary determinant of ECM fungal compositions in the forested landscape

Demonstration of periodic nanostructure formation with less ablation by double-pulse laser irradiation on titanium

By pairing femtosecond laser pulses (duration ∼40 fs and central wavelength ∼810 nm) at an appropriate time interval, a laser-induced periodic surface structure (LIPSS) is formed with much less ablation than one formed with a single pulse. On a titanium plate, a pair of laser pulses with fluences of 70 and 140 mJ/cm² and a rather large time interval (>10 ps) creates a LIPSS with an interspace of 600 nm, the same as that formed by a single pulse of 210 mJ/cm², while the double pulse ablates only 4 nm, a quarter of the ablation depth of a single pulse

New readout and data-acquisition system in an electron-tracking Compton camera for MeV gamma-ray astronomy (SMILE-II)

For MeV gamma-ray astronomy, we have developed an electron-tracking Compton camera (ETCC) as a MeV gamma-ray telescope capable of rejecting the radiation background and attaining the high sensitivity of near 1 mCrab in space. Our ETCC comprises a gaseous time-projection chamber (TPC) with a micro pattern gas detector for tracking recoil electrons and a position-sensitive scintillation camera for detecting scattered gamma rays. After the success of a first balloon experiment in 2006 with a small ETCC (using a 10$\times$10$\times$15 cm$^3$ TPC) for measuring diffuse cosmic and atmospheric sub-MeV gamma rays (Sub-MeV gamma-ray Imaging Loaded-on-balloon Experiment I; SMILE-I), a (30 cm)$^{3}$ medium-sized ETCC was developed to measure MeV gamma-ray spectra from celestial sources, such as the Crab Nebula, with single-day balloon flights (SMILE-II). To achieve this goal, a 100-times-larger detection area compared with that of SMILE-I is required without changing the weight or power consumption of the detector system. In addition, the event rate is also expected to dramatically increase during observation. Here, we describe both the concept and the performance of the new data-acquisition system with this (30 cm)$^{3}$ ETCC to manage 100 times more data while satisfying the severe restrictions regarding the weight and power consumption imposed by a balloon-borne observation. In particular, to improve the detection efficiency of the fine tracks in the TPC from $\sim$10\% to $\sim$100\%, we introduce a new data-handling algorithm in the TPC. Therefore, for efficient management of such large amounts of data, we developed a data-acquisition system with parallel data flow.Comment: 11 pages, 24 figure

Administration of oxygen ultra-fine bubbles improves nerve dysfunction in a rat sciatic nerve crush injury model

Ultra-fine bubbles (<200 nm in diameter) have several unique properties and have been tested in various medical fields. The purpose of this study was to investigate the effects of oxygen ultra-fine bubbles (OUBs) on a sciatic nerve crush injury (SNC) model rats. Rats were intraperitoneally injected with 1.5 mL saline, OUBs diluted in saline, or nitrogen ultra-fine bubbles (NUBs) diluted in saline three times per week for 4 weeks in four groups: (1) control, (sham operation + saline); (2) SNC, (crush + saline); (3) SNC+OUB, (crush + OUB-saline); (4) SNC+NUB, (crush + NUB-saline). The effects of the OUBs on dorsal root ganglion (DRG) neurons and Schwann cells (SCs) were examined by serial dilution of OUB medium in vitro. Sciatic functional index, paw withdrawal thresholds, nerve conduction velocity, and myelinated axons were significantly decreased in the SNC group compared to the control group; these parameters were significantly improved in the SNC+OUB group, although NUB treatment did not affect these parameters. In vitro, OUBs significantly promoted neurite outgrowth in DRG neurons by activating AKT signaling and SC proliferation by activating ERK1/2 and JNK/c-JUN signaling. OUBs may improve nerve dysfunction in SNC rats by promoting neurite outgrowth in DRG neurons and SC proliferation.Matsuoka H., Ebina K., Tanaka H., et al. Administration of oxygen ultra-fine bubbles improves nerve dysfunction in a rat sciatic nerve crush injury model. International Journal of Molecular Sciences 19, 1395 (2018); https://doi.org/10.3390/ijms19051395