Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil((R)) DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin((R)) Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity

Discovery of New Eunicellins from an Indonesian Octocoral Cladiella sp.

Two new 11-hydroxyeunicellin diterpenoids, cladieunicellin F (1) and (–)-solenopodin C (2), were isolated from an Indonesian octocoral Cladiella sp. The structures of eunicellins 1 and 2 were established by spectroscopic methods, and eunicellin 2 was found to be an enantiomer of the known eunicellin solenopodin C (3). Eunicellin 2 displayed inhibitory effects on the generation of superoxide anion and the release of elastase by human neutrophils. The previously reported structures of two eunicellin-based compounds, cladielloides A and B, are corrected in this study

Gapped Electronic Structure of Epitaxial Stanene on InSb(111)

Stanene (single-layer grey tin), with an electronic structure akin to that of graphene but exhibiting a much larger spin-orbit gap, offers a promising platform for room-temperature electronics based on the quantum spin Hall (QSH) effect. This material has received much theoretical attention, but a suitable substrate for stanene growth that results in an overall gapped electronic structure has been elusive; a sizable gap is necessary for room-temperature applications. Here, we report a study of stanene epitaxially grown on the (111)B-face of indium antimonide (InSb). Angle-resolved photoemission spectroscopy (ARPES) measurements reveal a gap of 0.44 eV, in agreement with our first-principles calculations. The results indicate that stanene on InSb(111) is a strong contender for electronic QSH applications.Comment: 15 pages, 4 figure

Investigation of Novel Noncontacting Measurement Method by the Design of Loop-Type Probe and Reconstruction of Radiation Modeling

Because the ICs’ application frequency and speed become higher and trends of system packaging and device under test request higher reliability, a novel technology combining noncontacting measurement method and reconstructing radiation model was proposed to solve signal deliveries in system packages or PCBs. In this study, a novel noncontacting method for the ICs’ measurements was investigated by the design of loop-type near-field probe and reconstructed the radiation model to substitute the traditional measurement methods, such as using probes and SMA connectors. A near-field probe was used to receive the coupling signal. The assessing circuit modeling could be completed by some synthesized theorems. According to the study’s results, frequency responses of reconstruction model developed by theorems, radiation measurements, and simulated by EM methods were highly curve fitting

The patatin-containing phospholipase A pPLAIIα modulates oxylipin formation and water loss in Arabidopsis thaliana

The patatin-related phospholipase A (pPLA) hydrolyzes membrane glycerolipids to produce monoacyl compounds and free fatty acids. Phospholipids are cleaved by pPLAIIα at the sn-1 and sn-2 positions, and galactolipids, including those containing oxophytodienoic acids, can also serve as substrates. Ablation of pPLAIIα decreased lysophosphatidylcholine and lysophosphatidylethanolamine levels, but increased free linolenic acid. pPLAIIα-deficient plants displayed a higher level of jasmonic acid and methyl jasmonate, as well as the oxylipin-biosynthetic intermediates 13-hydroperoxylinolenic acid and 12-oxophytodienoic acid than wild-type plants. The expression of genes involved in oxylipin production was also higher in the pPLAIIα-deficient mutant than in wild-type plants. The mutant plants lost water faster than wild type plants did. The stomata of wild type and mutant plants responded similarly to abscisic acid. In response to desiccation, the mutant and wild type leaves produced abscisic acid at the same rate, but after 4 h of desiccation, the jasmonic acid level was much higher in mutant than wild-type leaves. These results indicate that pPLAIIα negatively regulates oxylipin production and suggest a role in the removal of oxidatively modified fatty acids from membranes

The potential impact of primary headache disorders on stroke risk

Distribution of PHDs. (DOC 55 kb

Elemental topological Dirac semimetal: {\alpha}-Sn on InSb(111)

Three-dimensional (3D) topological Dirac semimetals (TDSs) are rare but important as a versatile platform for exploring exotic electronic properties and topological phase transitions. A quintessential feature of TDSs is 3D Dirac fermions associated with bulk electronic states near the Fermi level. Using angle-resolved photoemission spectroscopy (ARPES), we have observed such bulk Dirac cones in epitaxially-grown {\alpha}-Sn films on InSb(111), the first such TDS system realized in an elemental form. First-principles calculations confirm that epitaxial strain is key to the formation of the TDS phase. A phase diagram is established that connects the 3D TDS phase through a singular point of a zero-gap semimetal phase to a topological insulator (TI) phase. The nature of the Dirac cone crosses over from 3D to 2D as the film thickness is reduced

Natural Product Chemistry of Gorgonian Corals of Genus Junceella—Part II

The structures, names, bioactivities, and references of 81 new secondary metabolites obtained from gorgonian corals belonging to the genus Junceella are described in this review. All compounds mentioned in this review were obtained from sea whip gorgonian corals Junceella fragilis and Junceella juncea, collected from the tropical and subtropical Indo-Pacific Ocean

Magnetic anisotropy reversal driven by structural symmetry-breaking in monolayer {\alpha}-RuCl3

Layered {\alpha}-RuCl3 is a promising material to potentially realize the long-sought Kitaev quantum spin liquid with fractionalized excitations. While evidence of this exotic state has been reported under a modest in-plane magnetic field, such behavior is largely inconsistent with theoretical expectations of Kitaev phases emerging only in out-of-plane fields. These predicted field-induced states have been mostly out of reach due to the strong easy-plane anisotropy of bulk crystals, however. We use a combination of tunneling spectroscopy, magnetotransport, electron diffraction, and ab initio calculations to study the layer-dependent magnons, anisotropy, structure, and exchange coupling in atomically thin samples. Due to structural distortions, the sign of the average off-diagonal exchange changes in monolayer {\alpha}-RuCl3, leading to a reversal of magnetic anisotropy to easy-axis. Our work provides a new avenue to tune the magnetic interactions in {\alpha}-RuCl3 and allows theoretically predicted quantum spin liquid phases for out-of-plane fields to be more experimentally accessible

In Vitro Response of Retinal Pigment Epithelial Cells Exposed to Chitosan Materials Prepared with Different Cross-Linkers

The interaction between cells and biopolymers is the evaluation indicator of the biocompatibility of materials. The purpose of this work was to examine the responses of retinal pigment epithelial (RPE) cells to genipin (GP) or glutaraldehyde (GTA) cross-linked chitosan by means of cell viability assays, cytokine expression analyses, and apoptosis assays. Evaluations of non-cross-linked chitosan were conducted simultaneously for comparison. Both GP and GTA treated samples with the same extent of cross-linking (around 80%) were prepared by varying cross-linking time. Our results showed that GP cross-linking was carried out by either radical polymerization of the monomers or SN2 nucleophilic substitution reaction involving the replacement of the ester group on the monomer with a secondary amide linkage. On the other hand, GTA could react with free amino groups of chitosan, leading to the formation of either the Schiff bases or the Michael-type adducts with terminal aldehydes. The biocompatibility of non-cross-linked chitosan membranes was demonstrated by the absence of any signs of toxicity or inflammation reaction. The present study showed that the ARPE-19 cells exposed to GTA cross-linked chitosan membranes had significantly higher cytotoxicity, interleukin-6 levels, and number of TUNEL-positive nuclei than did those exposed to GP treated samples. In addition, the materials modified with GTA trigger apoptosis at an early stage and may induce toxicity in the RPE cells later. The findings suggest that while the chitosan molecules bridged by GP are satisfactorily cytocompatible, the counterparts treated by GTA do not seem to be tolerated. In terms of material safety, the GP cross-linked chitosan may be compatible with human RPE cells and may have a potential application as delivery carriers in the treatment of posterior segment diseases