Inhibitors of LAMP used to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease in Akoya pearl oysters, and additives to reduce the effect of the inhibitors.

Black-spot shell disease is an unresolved disease that decreases pearl quality and threatens pearl oyster survival. In previous studies, the bacterium Tenacibaculum sp. strain Pbs-1 was isolated from diseased Akoya pearl oysters Pinctada fucata, and a rapid, specific, and sensitive loop-mediated isothermal amplification (LAMP) assay for detecting this pathogen was established. This technology has considerable potential for routine diagnosis of strain Pbs-1 in oyster hatcheries and/or pearl farms; therefore, it is vital to identify substances in environmental samples that might inhibit LAMP and to find additives that can reduce the inhibition. In this study, we investigated the effects of six chemicals or proteins, otherwise known as conventional PCR inhibitors, on LAMP, using the DNA of strain Pbs-1 as template: humic acid, urea, iron (III) chloride hexahydrate, melanin, myoglobin, and Ethylenediamine-N,N,N',N'-tetraacetic acid, disodium salt, dihydrate (EDTA; pH 6.5). Next, to reduce the effects of identified inhibitors, we tested the addition of bovine serum albumin (BSA) or T4 gene 32 protein (gp32) to the LAMP assay. When 50 ng of DNA template was used, 4 ng/µL of humic acid, 0.05% melanin, and 10 mM of EDTA (pH 6.5) inhibited the LAMP reaction, whereas myoglobin, urea, and FeCl3 had no effect. When 50 pg of DNA template was used, 4 ng/µL of humic acid, 0.05% melanin, 4 µg/µL of myoglobin, 10 µg/µL of urea, and 10 mM of EDTA inhibited the LAMP reaction. Thus, it was shown that the gene-amplification inhibitory effect of melanin, humic acid, and urea could be reduced by adding BSA or gp32 to the LAMP reaction mixture. This technique could be applied as part of a protocol to prevent mass mortalities of pearl oysters; moreover, the results enhance our knowledge about substances that inhibit LAMP and methods to reduce the inhibition, which have rarely been reported.

Superficial Thoracic Artery Perforator Flap for Volume Replacement Oncoplastic Breast-conserving Surgery.

Lateral chest wall perforator flaps, such as the lateral intercostal artery perforator flap, lateral thoracic artery perforator flap, and thoracodorsal artery perforator flap, have been used for volume replacement oncoplastic breast-conserving surgery (VR-OPBCS) in the lateral and central breast. However, there are cases in which these perforators are missing or too thin, making it difficult to raise a flap for partial breast reconstruction. A 58-year-old woman underwent VR-OPBCS for breast cancer in the lower quadrant of the right breast. Preoperative imaging studies did not identify lateral thoracic artery perforator or thoracodorsal artery perforator but identified a well-developed superficial thoracic artery perforator (STAP). A flap based on the STAP was dissected, and partial breast reconstruction was performed. The flap survived with no complications. No deformity of the lower breast or displacement of the nipple-areola complex was observed 8 months after the completion of postoperative radiotherapy. The STAP flap can be used as an alternative to VR-OPBCS when other lateral chest wall perforator flaps are unavailable.

Simultaneous Electrochemical Detection of Multiple Bacterial Species Using Metal-Organic Nanohybrids.

Organic metallic nanohybrids (NHs), in which many small metal nanoparticles are encapsulated within a conductive polymer matrix, are useful as sensitive electrochemical labels because the constituents produce characteristic oxidation current responses. Gold NHs, consisting of gold nanoparticles and poly(m-toluidine), and copper NHs, consisting of copper nanoparticles and polyaniline, did not interfere with each other in terms of the electrochemical signals obtained on the same electrode. Antibodies were introduced into these NHs to function as electrochemical labels for targeting specific bacteria. Electrochemical measurements using screen-printed electrodes dry-fixed with NH-labeled bacterial cells enabled the estimation of bacterial species and number within minutes, based on the distinct current response of the labels. Our proposed method achieved simultaneous detection of enterohemorrhagic Escherichia coli and Staphylococcus aureus in a real sample. These NHs will be powerful tools as electrochemical labels and are expected to be useful for rapid testing in food and drug-related manufacturing sites.

Gargoyles: An Open Source Graph-Based Molecular Optimization Method Based on Deep Reinforcement Learning.

Automatic optimization methods for compounds in the vast compound space are important for drug discovery and material design. Several machine learning-based molecular generative models for drug discovery have been proposed, but most of these methods generate compounds from scratch and are not suitable for exploring and optimizing user-defined compounds. In this study, we developed a compound optimization method based on molecular graphs using deep reinforcement learning. This method searches for compounds on a fragment-by-fragment basis and at high density by generating fragments to be added atom by atom. Experimental results confirmed that the quantum electrodynamics (QED), the optimization target set in this study, was enhanced by searching around the starting compound. As a use case, we successfully enhanced the activity of a compound by targeting dopamine receptor D2 (DRD2). This means that the generated compounds are not structurally dissimilar from the starting compounds, as well as increasing their activity, indicating that this method is suitable for optimizing molecules from a given compound. The source code is available at https://github.com/sekijima-lab/GARGOYLES.

Purification and Characterization of the Lecithin-Dependent Thermolabile Hemolysin Vhe1 from the Vibrio sp. Strain MA3 Associated with Mass Mortality of Pearl Oyster (Pinctada fucata).

In a previous study, we isolated a Vibrio sp. strain MA3 and its virulence factor, a hemolysin encoded by vhe1. This strain is associated with mass mortalities of the pearl oyster Pinctada fucata. In the present study, the vhe1 gene from strain MA3 was cloned and its encoded product was purified and characterized. Our results show that the vhe1 gene encodes a protein of 417 amino acids with an estimated molecular mass of 47.2 kDa and a pI of 5.14. The deduced protein, Vhe1, was found to contain the conserved amino acid sequence (GDSL motif) of the hydrolase/esterase superfamily and five conserved blocks characteristic of SGNH hydrolases. A BLAST homology search indicated that Vhe1 belongs the lecithin-dependent hemolysin/thermolabile hemolysin (LDH/TLH) family. In activity analyses, the optimal temperature for both the hemolytic and phospholipase activities of Vhe1 was 50 °C. Vhe1 hemolytic activity and phospholipase activity were highest at pH 8.5 and pH 8.0, respectively. However, both enzymatic activities sharply decreased at high temperature (> 50 °C) and pH < 7.0. Compared with previously reported hemolysins, Vhe1 appeared to be more thermal- and pH-labile. Both its hemolytic activity and phospholipase activity were significantly inhibited by CuCl2, CdCl2, ZnCl2, and NiCl2, and slightly inhibited by MnCl2 and CoCl2. Vhe1 showed higher phospholipase activity toward medium-chain fatty acids (C8-C12) than toward shorter- and longer-chain fatty acids. These results accumulate knowledge about the LDH/TLH of V. alginolyticus, which detailed characterization has not been reported, and contribute to solving of the mass mortality of pearl oyster.

Hes1 marks peri-condensation mesenchymal cells that generate both chondrocytes and perichondrial cells in early bone development.

Bone development starts with condensations of undifferentiated mesenchymal cells that set a framework for future bones within the primordium. In the endochondral pathway, mesenchymal cells inside the condensation differentiate into chondrocytes and perichondrial cells in a SOX9-dependent mechanism. However, the identity of mesenchymal cells outside the condensation and how they participate in developing bones remain undefined. Here we show that mesenchymal cells surrounding the condensation contribute to both cartilage and perichondrium, robustly generating chondrocytes, osteoblasts, and marrow stromal cells in developing bones. Single-cell RNA-seq analysis of Prrx1-cre-marked limb bud mesenchymal cells at E11.5 reveals that Notch effector Hes1 is expressed in a mutually exclusive manner with Sox9 that is expressed in pre-cartilaginous condensations. Analysis of a Notch signaling reporter CBF1:H2B-Venus reveals that peri-condensation mesenchymal cells are active for Notch signaling. In vivo lineage-tracing analysis using Hes1-creER identifies that Hes1+ early mesenchymal cells surrounding the SOX9+ condensation at E10.5 contribute to both cartilage and perichondrium at E13.5, subsequently becoming growth plate chondrocytes, osteoblasts of trabecular and cortical bones, and marrow stromal cells in postnatal bones. In contrast, Hes1+ cells in the perichondrium at E12.5 or E14.5 do not generate chondrocytes within cartilage, contributing to osteoblasts and marrow stromal cells only through the perichondrial route. Therefore, Hes1+ peri-condensation mesenchymal cells give rise to cells of the skeletal lineage through cartilage-dependent and independent pathways, supporting the theory that early mesenchymal cells outside the condensation also play important roles in early bone development.

Synthesis of α-Aminophosphonates by Umpolung-Enabled Cu-Catalyzed Regioselective Hydroamination.

A copper-catalyzed regioselective hydroamination of α,ß-unsaturated phosphonates has been developed to form corresponding α-aminophosphonates of interest in medicinal chemistry. The introduction of an umpolung, electrophilic amination strategy with the hydroxylamine derivative is the key to achieving the α-amination regioselectivity, which is otherwise difficult under the conventional nucleophilic hydroamination conditions with the parent amine. Asymmetric synthesis with a chiral bisphosphine ligand and application to a related silylamination reaction are also described.

Development and evaluation of a rapid, specific, and sensitive loop-mediated isothermal amplification assay to detect Tenacibaculum sp. strain pbs-1 associated with black-spot shell disease in Akoya pearl oysters.

Black-spot shell disease decreases pearl quality and threatens pearl oyster survival. Establishment of a rapid, specific, and sensitive assay to detect Tenacibaculum sp. strain Pbs-1 associated with black-spot shell disease is of commercial importance. We developed a rapid, specific, and highly sensitive loop-mediated isothermal amplification (LAMP) assay to detect Tenacibaculum sp. Pbs-1 in Akoya pearl oysters Pinctada fucata. A set of five specific primers (two inner, two outer, and a loop) were designed based on the 16S-23S internal spacer region of strain Pbs-1. The optimum reaction temperature was 63 °C, and concentrations of the inner and loop primers were 1.4 and 1.0 µM, respectively. The LAMP product can be detected using agarose gel electrophoresis, and the color change in the reaction tube can be detected visually (by the naked eye) following the addition of malachite green. Our assay proved to be specific for strain Pbs-1, with no cross-reactivity with five other species of Tenacibaculum. The detection limit of the LAMP assay at 35 min is 50 pg, and at 60 min it is 5 fg. We evaluated the LAMP assay using diseased and healthy pearl oysters. The results demonstrate the suitability and simplicity of this test for rapid field diagnosis of strain Pbs-1.

Eukaryotic Communities in Aquatic Mesocosms with and without Calcined Dolomite Investigated Using 18S rRNA Amplicon-Based Metagenomics.

We report the 18S rRNA gene amplicon data from aquatic mesocosms with and without calcined dolomite. Intramacronucleata and Eumetazoa were present in roughly the same amounts in the water phase in both mesocosms. Chlorophyceae and several groups were detected as the major eukaryotes in the microbes attached to the calcined dolomite surface.

[A CASE OF REPEATED DRUG-INDUCED LUNG DISEASES DUE TO MULTIPLE HERBAL MEDICINES CONTAINING COMMON INGREDIENTS].

We present a rare case of repetitive lung disease caused by various herbal medicines containing common ingredients. In June 201X-2, an 81-year-old man with chronic sinusitis was treated with Shini-seihai-to. One month later, the patient experienced liver dysfunction, and pulmonary opacity was observed on a chest radiograph; this condition improved following the discontinuation of Shini-seihai-to. In October 201X-2, the patient developed fever and dyspnea after treatment with Saiko-keishi-to, which was administered to treat irritable bowel syndrome, and was diagnosed with pneumonia. His condition did not improve with antimicrobial treatment but did improve with systemic corticosteroids. Following discharge from the hospital, the patient took both Shini-seihai-to and Hochu-ekki-to. He developed a fever two days later, which improved after discontinuing the medicines. The patient developed a cough after taking Sairei-to in February 201X and was subsequently admitted to our hospital with respiratory failure; pulmonary opacity was observed on a chest computed tomography scan. On the basis of clinical course, lymphocytosis in bronchoalveolar lavage fluid, and drug-induced lymphocyte stimulation tests, we diagnosed the patient with Sairei-to-induced lung disease. The patient's condition improved after discontinuing Sairei-to. We conclude that common ingredients in different herbal medicines may cause drug-induced lung injury. Therefore, we recommend that scrupulous attention should be paid to Chinese herbal medicine use in patients with a history of lung injury induced by herbal medicines.

Size resolved characteristics of urban and suburban bacterial bioaerosols in Japan as assessed by 16S rRNA amplicon sequencing.

To study the size-resolved characteristics of airborne bacterial community composition, diversity, and abundance, outdoor aerosol samples were analysed by 16S rRNA gene-targeted quantitative PCR and amplicon sequencing with Illumina MiSeq. The samples were collected using size-resolved samplers between August and October 2016, at a suburban site in Toyama City and an urban site in Yokohama City, Japan. The bacterial communities were found to be dominated by Actinobacteria, Firmicutes, and Proteobacteria. At the genus level, we found a high abundance of human skin-associated bacteria, such as Propionibacterium, Staphylococcus, and Corynebacterium, in the urban site. Whereas, a high abundance of bacteria associated with soil and plants, such as Methylobacterium and Sphingomonas, was observed in the suburban site. Furthermore, our data revealed a shift in the bacterial community structure, diversity, and abundance of total bacteria at a threshold of 1.1-µm diameter. Interestingly, we observed that Legionella spp., the causal agents of legionellosis in humans, were mainly detected in > 2.1 µm coarse particles. Our data indicate that local environmental factors including built environments could influence the outdoor airborne bacterial community at each site. These results provide a basis for understanding the size-resolved properties of bacterial community composition, diversity, and abundance in outdoor aerosol samples and their potential influence on human health.

Molecular Identification, Characterization, and Expression Analysis of a Metallothionein Gene from Septifer virgatus.

This study provides a preliminary characterization of a metallothionein (MT) gene in Septifer virgatus and highlights its potential use in biomonitoring. The full-length SvMT cDNA and the complete sequence of the SvMT gene were identified using reverse transcriptase PCR coupled with the rapid amplification of cDNA ends and the primer walking method. The SvMT cDNA encodes a protein of 72 amino acids having nine classical Cys-X-Cys motifs. Moreover, the deduced amino acids contained the conserved motif (Cys-x-Cys-x(3)-Cys-Thr-Gly-x(3)-Cys-x-Cys-x(3)-Cys-x-Cys-Lys) of MT family 2. Its molecular mass and isoelectric point were estimated to be 7.01 kDa and 7.00, respectively. BLAST-based searching indicated that SvMT shared 81.0% amino acid sequence identity with Mytilus edulis MT-20-II. The SvMT gene has three coding exons and two introns. After exposure to 1 mg/L cadmium chloride, the expression of SvMT increased 15-fold by 3 days (d), with a maximum expression of 27-fold by 5 d compared with the pre-exposure level. After exposure to 2 mg/L zinc chloride, the expression of SvMT increased 2.5-fold by 3 d and 4.7-fold by 5 d compared with the pre-exposure level. A significant increase in the expression level of SvMT mRNA was observed after the exposure of S. virgatus to the combination of 0.003 mg/L cadmium chloride and 0.2 mg/L zinc chloride compared with the pre-exposure level. Our work indicates that the SvMT gene is associated with stress responses and could be a potential biomarker for marine pollution.

Heat health risk assessment in Philippine cities using remotely sensed data and social-ecological indicators.

More than half of the world's population currently live in urban areas and are particularly at risk from the combined effects of the urban heat island phenomenon and heat increases due to climate change. Here, by using remotely sensed surface temperature data and social-ecological indicators, focusing on the hot dry season, and applying the risk framework of the Intergovernmental Panel on Climate Change, we assessed the current heat health risk in 139 Philippine cities, which account for about 40% of the country's total population. The cities at high or very high risk are found in Metro Manila, where levels of heat hazard and exposure are high. The most vulnerable cities are, however, found mainly outside the national capital region, where sensitivity is higher and capacity to cope and adapt is lower. Cities with high levels of heat vulnerability and exposure must be prioritized for adaptation. Our results will contribute to risk profiling in the Philippines and to the understanding of city-level heat health risks in developing regions of the Asia-Pacific.

Transition-metal-free Intramolecular C-H amination of sulfamate esters and N-alkylsulfamides.

The transition-metal-free intramolecular C-H amination of sulfamate esters using iodine oxidants, tert-butyl hypoiodite (t-BuOI) and N-iodosuccinimide (NIS) is reported. A method using NIS was also successfully applied to the oxidative cyclization of N-alkylsulfamides.

Scenario-based land abandonment projections: Method, application and implications.

Land abandonment, e.g. agricultural land abandonment, can result in various social and ecological impacts. It would thus be helpful if the extent and spatial pattern of future land abandonment could be projected. However, the trajectory of future land abandonment generally depends on various factors, including biophysical conditions and future changes in socioeconomic indicators in the area. In this study, we developed a general framework for a scenario-based land abandonment projection, featuring a coupled regional economic and spatially explicit land change modeling approach. We applied this framework in selected municipalities in Fukushima Prefecture, Japan, under two socioeconomic development scenarios (2014-2050): low population and economic growth (LL scenario) and high population and economic growth (HH scenario). The case study results, which are also visualized through a set of hot spot maps, revealed that agricultural land abandonment would be more intense under the HH scenario due to the much higher future decline in farmer population driven by the shift in people's employment and main source of livelihood. Under the LL scenario, residential and urban land abandonment would be more profound because of the much higher future decline in total population. In general, our results provide insights into some plausible future socioeconomic changes, their interplay and their consequent land abandonment in the case study area, which would be useful in the context of forward-looking adaptive development planning. The proposed framework can be applied to other case study areas.

Airborne Microbial Communities at High-Altitude and Suburban Sites in Toyama, Japan Suggest a New Perspective for Bioprospecting.

Airborne microorganisms, especially those at high altitude, are exposed to hostile conditions, including ultraviolet (UV) radiation, desiccation, and low temperatures. This study was conducted to compare the composition and abundance of airborne microorganisms at a high-altitude site, Mt. Jodo [2,839 m above mean sea level (AMSL)] and a suburban site (23 m AMSL) in Toyama, Japan. To our knowledge, this is the first study to investigate microbial communities in air samples collected simultaneously at two sites in relatively close proximity, from low and high altitude. Air samples were collected over a period of 3 years during 2009-2011. We then examined the bacterial and eukaryotic communities and estimated the abundance of bacteria and fungi with real-time TaqMan PCR. The airborne bacterial and eukaryotic communities differed between high-altitude and suburban sites on each sampling day. Backward trajectory analysis of air masses that arrived at high-altitude and suburban sites on each sampling day displayed almost the same paths. The bacterial communities were dominated by Actinobacteria, Firmicutes, and Proteobacteria, while the eukaryotic communities included Ascomycota, Basidiomycota, and Streptophyta. We also predicted some application of such microbial communities. The airborne bacterial and fungal abundance at the high-altitude site was about two times lower than that at the suburban site. These results showed that each airborne microbial communities have locality even if they are collected close location.

Proteinase K is an activator for the male-dependent spermiogenesis pathway in Caenorhabditis elegans: Its application to pharmacological dissection of spermiogenesis.

Caenorhabditis elegans spermiogenesis involves spermatid activation into spermatozoa. Activation occurs through either SPE-8 class-dependent or class-independent pathways. Pronase (Pron) activates the SPE-8 class-dependent pathway, whereas no in vitro tools are available to stimulate the SPE-8 class-independent pathway. Thus, whether there is a functional relationship between these two pathways is currently unclear. In this study, we found that proteinase K (ProK) can activate the SPE-8 class-independent pathway. In vitro spermiogenesis assays using Pron and ProK suggested that SPE-8 class proteins act in the hermaphrodite- and male-dependent spermiogenesis pathways and that some spermatid proteins presumably working downstream of spermiogenesis pathways, including MAP kinases, are preferentially involved in the SPE-8 class-dependent pathway. We screened a library of chemicals, and a compound that we named DDI-1 inhibited both Pron- and ProK-induced spermiogenesis. To our surprise, several DDI-1 analogues that are structurally similar to DDI-1 blocked Pron, but not ProK, induced spermiogenesis. Although the mechanism by which DDI-1 blocks spermiogenesis is yet unknown, we have begun to address this issue by selecting two DDI-1-resistant mutants. Collectively, our data support a model in which C. elegans male and hermaphrodite spermiogenesis each has its own distinct, parallel pathway.

A review of quality of life (QOL) assessments and indicators: Towards a "QOL-Climate" assessment framework.

Quality of life (QOL), although a complex and amorphous concept, is a term that warrants attention, especially in discussions on issues that touch on the impacts of climate change and variability. Based on the principles of RepOrting standards for Systematic Evidence Synthesis, we present a systematic review aimed at gaining insights into the conceptualization and methodological construct of previous studies regarding QOL and QOL-related indexes. We find that (i) QOL assessments vary in terms of conceptual foundations, dimensions, indicators, and units of analysis, (ii) social indicators are consistently used across assessments, (iii) most assessments consider indicators that pertain to the livability of the environment, and (iv) QOL can be based on objective indicators and/or subjective well-being, and on a composite index or unaggregated dimensions and indicators. However, we also find that QOL assessments remain poorly connected with climate-related issues, an important research gap. Our proposed "QOL-Climate" assessment framework, designed to capture the social-ecological impacts of climate change and variability, can potentially help fill this gap.

Electronic and Thermoelectric Properties of Layered Oxychalcogenides (BiO)Cu Ch ( Ch = S, Se, Te).

We study the new details of electronic and thermoelectric properties of polycrystalline layered oxychalcogenide systems of (BiO)Cu Ch ( Ch = Se, Te) prepared by using a solid-state reaction. The systems were characterized by using photoemission (PE) spectroscopy and four-probe temperature-dependent electrical resistivity ρ( T). PE spectra are explained by calculating the electronic properties using the generalized-gradient approximation method. PE spectra and ρ( T) show that (BiO)CuSe system is a semiconductor, while (BiO)CuTe system exhibits the metallic behavior that induces the high thermoelectric performance. The calculation of electronic properties of (BiO)Cu Ch ( Ch = S, Se, Te) confirms that the metallic behavior of (BiO)CuTe system is mainly induced by Te 5p states at Fermi energy level, while the indirect bandgaps of 0.68 and 0.40 eV are obtained for (BiO)CuS and (BiO)CuSe systems, respectively. It is also shown that the local symmetry distortion at Cu site strongly stimulates Cu 3d-t2g to be partially hybridized with Ch p orbitals. This study presents the essential properties of the inorganic systems for novel functional device applications.