404 Works

Data from: MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

Masaki Miya, Yukuto Sato, Tsukasa Fukunaga, Tetsuya Sado, Jan Y. Poulsen, Keiichi Sato, Toshifumi Minamoto, Satoshi Yamamoto, Hiroki Yamanaka, Hitoshi Araki, Michio Kondoh & Wataru Iwasaki
We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163–185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility...

Data from: Characteristics of pneumonia deaths after earthquake and tsunami: an ecological study of 5.7 million subjects in 131 municipalities, Japan

Yosuke Shibata, Toshiyuki Ojima, Yasutake Tomata, Eisaku Okada, Mieko Nakamura, Miyuki Kawado & Shuji Hashimoto
Objective: On 11 March 2011, the Great East Japan Earthquake struck off Japan. Although some studies showed that the earthquake increased the risk of pneumonia death, no study reported whether and how much tsunami increased the risk. We examined the risk for pneumonia death after the earthquake/tsunami. Design: This is an ecological study. Setting: Data on population and pneumonia deaths obtained from the Vital Statistics 2010 and 2012, National Census 2010 and Basic Resident Register...

Data from: Effects of light environment during growth on the expression of cone opsin genes and behavioral spectral sensitivities in guppies (Poecilia reticulata)

Yusuke Sakai, Hajime Ohtsuki, Satoshi Kasagi, Shoji Kawamura & Masakado Kawata
Background: The visual system is important for animals for mate choice, food acquisition, and predator avoidance. Animals possessing a visual system can sense particular wavelengths of light emanating from objects and their surroundings and perceive their environments by processing information contained in these visual perceptions of light. Visual perception in individuals varies with the absorption spectra of visual pigments and the expression levels of opsin genes, which may be altered according to the light environments....

Data from: Genetic basis for variation in salinity tolerance between stickleback ecotypes

Makoto Kusakabe, Asano Ishikawa, Mark Ravinet, Kohta Yoshida, Takashi Makino, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Adaptation to different salinities can drive and maintain divergence between populations of aquatic organisms. Anadromous and stream ecotypes of threespine stickleback (Gasterosteus aculeatus) are an excellent model to explore the genetic mechanisms underlying osmoregulation divergence. Using a parapatric pair of anadromous and stream stickleback ecotypes, we employed an integrated genomic approach to identify candidate genes important for adaptation to different salinity environments. Quantitative trait loci (QTL) mapping of plasma sodium concentrations under a seawater challenge...

Data from: Adaptive genetic divergence along narrow environmental gradients in four stream insects

Kozo Watanabe, So Kazama, Tatsuo Omura & Michael T. Monaghan
A central question linking ecology with evolutionary biology is how environmental heterogeneity can drive adaptive genetic divergence among populations. We examined adaptive divergence of four stream insects from six adjacent catchments in Japan by combining field measures of habitat and resource components with genome scans of non-neutral Amplified Fragment Length Polymorphism (AFLP) loci. Neutral genetic variation was used to measure gene flow and non-neutral genetic variation was used to test for adaptive divergence. We identified...

Data from: Long-term stasis and short-term divergence in the phenotypes of microsnails on oceanic islands

Shinichiro Wada, Yuichi Kameda & Satoshi Chiba
Phenotypic divergence is often unrelated to genotypic divergence. An extreme example is rapid phenotypic differentiation despite genetic similarity. Another extreme is morphological stasis despite substantial genetic divergence. These opposite patterns have been viewed as reflecting opposite properties of the lineages. In this study, phenotypic radiation accompanied by both rapid divergence and long-term conservatism is documented in the inferred molecular phylogeny of the micro land snails Cavernacmella (Assimineidae) on the Ogasawara Islands. The populations of Cavernacmella...

Data from: Palaeobiogeography and evolutionary patterns of the larger foraminifer Borelis de Montfort (Borelidae)

Davide Bassi, Juan Carlos Braga, Giovanni Di Domenico, Johannes Pignatti, Sigal Abramovich, Pamela Hallock, Janine Koenen, Zoltan Kovacs, Martin R. Langer, Giulio Pavia & Yasufumi Iryu
The palaeobiogeography of the alveolinoid Borelis species reveals the evolutionary patterns leading to the two extant representatives, which occur in shallow-water tropical carbonate, coral reef-related settings. Type material and new material of fossil Borelis species, along with Recent specimens were studied to assess their taxonomic status, species circumscriptions (based on proloculus size, occurrence of Y-shaped septula, and the index of elongation), palaeobiogeography and evolutionary dynamics. The species dealt with here are known from exclusively fossil...

γ-radiation effects on metal oxide particles and their wetted surfaces

John McGrady, Shinichi Yamashita, Atsushi Kimura, Sho Kano, Huilong Yang, Zhengang Duan, Takumi Saito & Hiroaki Abe
Typical metal oxide corrosion products of structural materials have been irradiated with γ-rays in ultra-pure water to investigate the effect of radiation on the surface oxide and the nature of adsorbed water. Analysis techniques including thermal gravimetric analysis, differential thermal analysis, diffuse reflectance infrared Fourier transform spectroscopy, and X-ray photoelectron spectroscopy before and after γ-irradiation were employed to investigate surface structural effects and adsorbed water behaviour. The production of H2 in the oxide nanoparticle mixtures...

Data from: Human−geographic effects on variations in the population genetics of Sinotaia quadrata (Gastropoda: Viviparidae) that historically migrated from continental East Asia to Japan

Bin Ye, Takumi Saito, Takahiro Hirano, Zhengzhong Dong, Van Tu Do & Satoshi Chiba
Background: Anthropogenic factors potentially affect observed biogeographical patterns in genetic variations of populations, but the effects of ancient human activities on the original patterns that were created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear if S. quadrata in Japan was introduced from China, and how different human uses and varying geographic patterns affect the genetic structure of...

Data from: An intermediate type of medusa from the early Cambrian Kuanchuanpu Formation, South China

Xing Wang, Jean Vannier, Xiaoguang Yang, Shin Kubota, Qiang Ou, Xiaoyong Yao, Kentaro Uesugi, Osamu Sasaki, Tsuyoshi Komiya & Jian Han
The tetraradial or pentaradial fossil embryos and related hatched individuals from the early Cambrian Kuanchuanpu Formation are of great interest for understanding the early evolution of medusozoans. The phylogenetic and evolutionary significance of their external and internal characters (e.g. manubrium, tentacles, septa and claustra) is still controversial. Here we describe a new pentamerous medusozoan, Hanagyroia orientalis gen. et sp. nov., characterized by five well-developed perradial oral lips around a remarkably large manubrium, a conspicuous equatorial...

Data from: Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis

Yuji Inagaki, Chihiro Sarai, Goro Tanifuji, Takuro Nakayama, Ryoma Kamikawa, Tazuya Takahashi, Hideaki Miyashita, Ken-Ichiro Ishida, Mitsunori Iwataki, Euki Yazaki & Eriko Matsuo
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggested that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet...

Data from: Amadori-glycated phosphatidylethanolamine enhances the physical stability and selective targeting ability of liposomes

Taiki Miyazawa, Reina Kamiyoshihara, Naoki Shimizu, Takahiro Harigae, Yurika Otoki, Junya Ito, Shunji Kato, Teruo Miyazawa & Kiyotaka Nakagawa
Liposomes consisting of 100% phosphatidylcholine exhibit poor membrane fusion, cellular uptake and selective targeting capacities. To overcome these limitations, we used Amadori-glycated phosphatidylethanolamine, which is universally present in animals and commonly consumed in foods. We found that liposomes containing Amadori-glycated phosphatidylethanolamine exhibited significantly reduced negative membrane potential and demonstrated high cellular uptake.

Data from: Balanced genetic diversity improves population fitness

Yuma Takahashi, Ryoya Tanaka, Daisuke Yamamoto, Noriyuki Suzuki, Masakado Kawata & Suzuki Noriyuki
Although genetic diversity within a population is suggested to improve population-level fitness and productivity, the existence of these effects is controversial because empirical evidence for an ecological effect of genetic diversity and the underlying mechanisms is scarce and incomplete. Here, we show that the natural single-gene behavioural polymorphism (Rover and sitter) in Drosophila melanogaster has a positive effect on population fitness. Our simple numerical model predicted that the fitness of a polymorphic population would be...

Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application

Yoko Masuda, Yutaka Shiratori, Hirotomo Ohba, Takanori Ishida, Ryo Takano, Sakura Satoh, Weishou Shen, Nan Gao, Hideomi Itoh & Keishi Senoo
Anaeromyxobacter and Geobacter, iron-reducing bacteria belonging to Deltaproteobacteria, are newly discovered nitrogen-fixing bacteria predominant in paddy soils. We hypothesized that adding ferric iron oxide as an electron acceptor for respiration of the iron-reducing bacteria could enhance the nitrogen-fixing activity of Anaeromyxobacter and Geobacter in paddy soils. In the soil microcosm study, soil nitrogen-fixing activity significantly increased after adding ferrihydrite or Fe2O3, ferric iron oxides, to the soil. In these soils, gene transcripts of nifD from...

Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application

Yoko Masuda, Yutaka Shiratori, Hirotomo Ohba, Takanori Ishida, Ryo Takano, Sakura Satoh, Weishou Shen, Nan Gao, Hideomi Itoh & Keishi Senoo
Anaeromyxobacter and Geobacter, iron-reducing bacteria belonging to Deltaproteobacteria, are newly discovered nitrogen-fixing bacteria predominant in paddy soils. We hypothesized that adding ferric iron oxide as an electron acceptor for respiration of the iron-reducing bacteria could enhance the nitrogen-fixing activity of Anaeromyxobacter and Geobacter in paddy soils. In the soil microcosm study, soil nitrogen-fixing activity significantly increased after adding ferrihydrite or Fe2O3, ferric iron oxides, to the soil. In these soils, gene transcripts of nifD from...

Data from: Intraspecific variations in leaf traits, productivity, and resource use efficiencies in the dominant species of subalpine evergreen coniferous and deciduous broad-leaved forests along the altitudinal gradient

Kouki Hikosaka, Hiroko Kurokawa, Takahisa Arai, Sakino Takayanagi, Hiroshi Tanaka, Soichiro Nagano & Tohru Nakashizuka
Many studies have reported intraspecific variations in leaf functional traits, but their contribution to plant performance and ecosystem function are poorly understood. We studied altitudinal gradients of intraspecific variations in leaf traits, productivity, and resource use efficiency in the dominant species of subalpine evergreen coniferous and deciduous broad-leaved forests in Japan. We addressed three hypotheses, which are exclusive to each other. 1) Leaf traits vary along the leaf economics spectrum (LES). Plants that grow at...

Data from: A shady phytoplankton paradox: when phytoplankton increases under low light

Masato Yamamichi, Takehiro Kazama, Kotaro Tokita, Izumi Katano, Hideyuki Doi, Takehito Yoshida, Nelson Hairston, Jotaro Urabe & Nelson G. Hairston
Light is a fundamental driver of ecosystem dynamics, affecting the rate of photosynthesis and primary production. In spite of its importance, less is known about its community-scale effects on aquatic ecosystems compared with those of nutrient loading. Understanding light limitation is also important for ecosystem management, as human activities have been rapidly altering light availability to aquatic ecosystems. Here we show that decreasing light can paradoxically increase phytoplankton abundance in shallow lakes. Our results, based...

Data from: Invasive invertebrates associated with highly duplicated gene content

Takashi Makino & Masakado Kawata
Invasions of alien species have led to serious problems, including the destruction of native ecosystems. In general, invasive species adapt to novel various environments rapidly, suggesting that they have high genetic diversity that could directly influences environmental adaptability. However, we do not yet know how genomic architecture generates genetic diversity that leads to invasive species. Recent studies showed that the proportion of duplicated genes (PD) in whole animal genomes correlated with environmental variability within habitat....

How co-distribution of two related azaleas (Rhododendron) developed in the Japanese archipelago: Insights from evolutionary and demographic analyses

Watanabe Yoichi, Etsuo Ono, Koichi Uehara, Yoshihiro Tsunamoto, Ayumi Matsuo & Yoshihisa Suyama
Plants growing in similar climates with extensively overlapping distributions may exhibit similar phylogeographic patterns, due to similarities in range shifts during past climatic oscillations. We tested and exploited this expectation in a comparison of the evolutionary and demographic histories of two related and co-distributed species endemic to Japan – Rhododendron pentaphyllum and R. quinquefolium. Genetic variation in sequences of noncoding chloroplast DNA regions and hundreds of nuclear single nucleotide polymorphisms were used to investigate 191...

Therapeutic effect of a novel curcumin derivative GT863 on a mouse model of amyotrophic lateral sclerosis

Hajime Kato, Hiroyasu Sato, Michiaki Okuda, Jun Wu, Shingo Koyama, Yasuhiko Izumi, Tomonori Waku, Mitsuyoshi Iino, Masashi Aoki, Shigeki Arawaka, Yasuyuki Ohta, Kenichi Ishizawa, Kanan Kawasaki, Yasuomi Urano, Tomohiro Miyasaka, Noriko Noguchi, Toshiaki Kume, Akinori Akaike, Hachiro Sugimoto & Takeo Kato
The present study investigated the therapeutic effects of the curcumin derivative 3-[(1E)-2-(1H-indol-6-yl)ethenyl]-5-[(1E)-2-[2-methoxy-4-(2-pyridylmethoxy)phenyl]ethenyl]-1H-pyrazole (GT863) in amyotrophic lateral sclerosis (ALS). The inhibitory effect of GT863 on superoxide dismutase 1 (SOD1) aggregation was evaluated in cell-free assays. GT863 interfered with the conformational changes of the SOD1 protein and later, oligomeric aggregation. Furthermore, its antioxidant, anti-inflammatory, and neuroprotective effects were evaluated in cell-free and cultured cell assays. GT863 inhibited H2O2− and glutamate-induced cytotoxicity and activated an antioxidant responsive element...

Data from: Organic farming and associated management practices benefit multiple wildlife taxa: a large-scale field study in rice paddy landscapes

Naoki Katayama, Yutaka Osada, Miyuki Mashiko, Yuki G. Baba, Koichi Tanaka, Yoshinobu Kusumoto, Satoru Okubo, Hiroaki Ikeda & Yosihiro Natuhara
1. Organic farming has potential for the conservation of global biodiversity and associated ecosystem services. Despite this, knowledge of the effects of organic farming systems on farmland biodiversity is limited in Asia, the worldwide leader in rice production. 2. We conducted the first national-scale study to investigate the effects of three different rice farming systems (conventional, low-input, and organic) and specific management practices (e.g. herbicide and insecticide applications, crop rotation, and levee-vegetation management) on species...

Dataset and R code from: Positive and negative effects of land abandonment on butterfly communities revealed by a hierarchical sampling design across climatic regions

Keita Fukasawa, Naoki Sugimoto, Akio Asahara, Minoru Kasada, Misako Matsuba & Tadashi Miyashita
Land abandonment may decrease biodiversity but also provides an opportunity for rewilding. It is therefore necessary to identify areas that may benefit from traditional land management practices and those that may benefit from a lack of human intervention. In this study, we conducted comparative field surveys of butterfly occurrence in abandoned and inhabited settlements in 18 regions of diverse climatic zones in Japan to test the hypotheses that species-specific responses to land abandonment correlate with...

Genetic basis for the evolution of pelvic-fin brooding, a new mode of reproduction, in a Sulawesian fish

Javier Montenegro, Shingo Fujimoto, Satoshi Ansai, Atsushi Nagano, Masahiro Sato, Yusuke Maeda, Rieko Fujitani, Kawilarang Masengi, Ryosuke Kimura, Jun Kitano & Kazunori Yamahira
Modes of reproduction in animals are diverse, with different modes having evolved independently in multiple lineages across a variety of taxa. However, an understanding of the genomic change driving the transition between different modes of reproduction is limited. Several ricefishes (Adrianichthyidae) on the island of Sulawesi have a unique mode of reproduction called “pelvic-fin brooding,” wherein females carry externally fertilized eggs until hatching using their pelvic fins. Phylogenomic analysis demonstrated pelvic-fin brooders to have evolved...

Data from: Terrigenous subsidies in lakes support zooplankton production mainly via a green food chain and not the brown food chain

Jotaro Urabe, Fumiya Hirama, Hideyuki Doi, Takehiro Kazama, Takumi Noguchi, Tyler H. Tappenbeck, Izumi Katano, Masato Yamamichi, Takehito Yoshida & James J. Elser
Terrestrial organic matter (t-OM) has been recognized as an important cross-boundary subsidy to aquatic ecosystems. However, recent evidence has shown that t-OM contributes little to promote secondary production in lakes because it is low quality food for aquatic consumers. To resolve this conflict, we performed a field experiment using leaf litter as t-OM. In the experiment, we monitored zooplankton biomass in enclosures with and without addition of leaf litter under shaded and unshaded conditions and...

Anolis homolechis gene annotation

Shunsuke Kanamori, Luis M. Díaz, Antonio Cádiz, Katsushi Yamaguchi, Shuji Shigenobu & Masakado Kawata
The result of gene annotation for Anolis homolechis genome using BRAKER2.

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  • Tohoku University
  • National Institute for Basic Biology
  • Chinese Academy of Medical Sciences & Peking Union Medical College
  • Capital Medical University
  • University of Melbourne
  • Shanghai Jiao Tong University
  • Chinese Academy of Sciences
  • Southern Medical University
  • Washington University in St. Louis
  • Nanjing Medical University