19 Works

Dataset for: Image-based screen capturing misfolding status of Niemann-Pick type C1 identifies potential candidates for chaperone drugs

Kenji Ohgane, Ryuta Shioi, Fumika Karaki, Hiromasa Yoshioka, Tomomi Noguchi-Yachide, Minoru Ishikawa, Kosuke Dodo, Mikiko Sodeoka & Yuichi Hashimoto
Niemann-Pick disease type C is a rare, fatal neurodegenerative disorder characterized by massive intracellular accumulation of cholesterol. In most cases, loss-of-function mutations in NPC1 gene that encodes for a lysosomal cholesterol transporter NPC1 are responsible for the disease, and more than half of the mutations are considered to interfere with biogenesis or folding of the protein. Previously we have identified a series of oxysterol derivatives and phenanthridine-6-one derivatives as pharmacological chaperones, small molecules that rescue...

Verifiability of genus-level classification under quantification and parsimony theories: a case study of follicucullid radiolarians

Yifan Xiao, Noritoshi Suzuki, Weihong He, Michael Benton, Tinglu Yang & Chenyang Cai
The classical taxonomy of fossil invertebrates is based on subjective judgments of morphology, which can cause confusion since there are no codified standards for the classification of genera. Here, we explore the validity of the genus taxonomy of 75 species and morphospecies of the Follicucullidae, a Late Paleozoic family of radiolarians, using a new method, Hayashi’s quantification theory II (HQT-II), a general multivariate statistical method for categorical datasets relevant to discriminant analysis. We identify a...

Data from: Cough reflex sensitivity and urge-to-cough deterioration in dementia with Lewy bodies

Takae Ebihara, Peijun Gui, Chika Ooyama, Koichi Kozaki & Satoru Ebihara
Cough, an important respiratory symptom, predominantly involves the brainstem, and the urge-to-cough is modulated by the cerebral cortex. Lewy body disease is associated with decreased cough reflex sensitivity and central respiratory chemosensitivity. Additionally, the insula, associated with the urge-to-cough, shows decreased activation and atrophy in dementia with Lewy bodies (DLB). We investigated the relationships between cognition and cough reflex and the urge-to-cough and compared the differences in responses of patients with DLB and other dementia...

Tracking long-distance migration of marine fishes using compound-specific stable isotope analysis of amino acids

Jun Matsubayashi, Yutaka Osada, Kazuaki Tadokoro, Yoshiyuki Abe, Atsushi Yamaguchi, Kotaro Shirai, Kentaro Honda, Chisato Yoshikawa, Nanako Ogawa, Naohiko Ohkouchi, Naoto Ishikawa, Toshi Nagata, Hiroomi Miyamoto, Shigeto Nishino & Ichiro Tayasu
The long-distance migrations by marine fishes are difficult to track by field observation. Here, we propose a new method to track such migrations using stable nitrogen isotopic composition at the base of the food web (δ15NBase), which allows for direct comparison of isotope ratios between proxy organisms of the isoscape and the target migratory animal. We initially constructed a δ15NBase isoscape in the North Pacific by bulk and compound-specific isotope analyses of copepods (n =...

Data from: Florivory defence: are phenolic compounds distributed differently within perianths?

Michio Oguro, Saya Nakano, Tomoyuki Itagaki & Satoki Sakai
Plants might allocate chemical defenses unequally within attractive units of flowers including petals, sepals, and bracts because of variations in the probability of florivory. Based on the optimal defense theory, which predicts that plants allocate higher chemical defenses to tissues with higher probabilities of herbivore attack, we predicted that distal parts and sepals would have higher chemical defense allocations than proximal parts and petals. To test this prediction, we compared total phenolics and condensed tannins...

Testing trait plasticity over the range of spectral composition of sunlight in forb species differing in shade tolerance

Qing-Wei Wang, T. Matthew Robson, Marta Pieristè, Michio Oguro, Riichi Oguchi, Yoshinori Murai & Hiroko Kurokawa
Although sunlight is essential for plant growth and development, the relative importance of each spectral region in shaping functional traits is poorly understood, particularly in dynamic light environments such as forest ecosystems. We examined responses of 25 functional traits from groups of 11 shade-intolerant and 12 understorey shade-tolerant forb species grown outdoors under five filter treatments differing in spectral transmittance: (1) transmitting c 95% of solar radiation; (2) attenuating ultraviolet-B (UV-B); (3) attenuating all UV;...

Museomics for reconstructing historical floristic exchanges: Divergence of Stone Oaks across Wallacea

Joeri Strijk, Hoang Thi Bin Thi Bin, Ferry Slik, Rahayu Sukri, Yoshihisa Suyama, Shuichiro Tagane, Jan Wieringa, Tetsukazu Yahara & Damien Hinsinger
Natural history collections and tropical tree diversity are treasure troves of biological and evolutionary information, but its accessibility is impeded by several properties. DNA in historical specimens generally occurs in a highly fragmented state, complicating the recovery of high-grade genetic material for scientific studies. Our understanding of hyperdiverse, wide-spread tree assemblages suffers from patchy information on distributions, phenology and paucity of diagnostic characters. This prohibits rapid identification and the strengthening of taxonomic frameworks and in...

Genetic diversity and the origin of commercial plantation of Indonesian teak on Java Island

Eko Prasetyo, Widiyatno Widiyatno, Sapto Indrioko, Mohammad Na'iem, Tetsuya Matsui, Ayumi Matsuo, Yoshihisa Suyama & Yoshihiko Tsumura
Teak (Tectona grandis) has been widely planted in 70 tropical countries because of the utility and value of its wood. This species was introduced to Indonesia more than 100 years ago, and large plantations - covering 1.2 million ha – can be found on Java Island. However, little information currently exists about the genetic diversity and origin of these trees. We collected plant materials from three regions across Java Island (east, central, and west), and...

Refugia during the last glacial period and the origin of the disjunct distribution of the insular plant Microtropis japonica (Celastraceae)

Takayuki Yamada, Goro Kokubugata, Shinji Fujii, Chien-Fan Chen, Akira Asakawa, Takuro Ito & Masayuki Maki
Aim: While many phylogeographical studies have focused on continental refugia, the function of islands as refugia has been long overlooked. In this study, we examined the biogeographic history of Microtropis japonica and its insular distribution to elucidate the hidden status of islands on the range expansion of plants. Location: Two disjunct island areas of Japan (the Izu and Ryukyu Islands) and their adjacent areas (the Japanese mainlands Honshu and Kyushu, and Taiwan). Taxon: Microtropis japonica...

Raw data used in A unified framework for herbivore-to-producer biomass ratio reveals the relative influence of four ecological factor

Jotaro Urabe, Takehiro Kazama, Masato Yamamichi, Kotaro Tokita, Xuwang Yin, Izumi Katano, Hideyuki Doi, Takehito YOSHIDA & Nelson Hairston
The biomass ratio of herbivores to primary producers reflects the structure of a community. Four primary factors have been proposed to affect this ratio, including production rate, defense traits and nutrient contents of producers, and predation by carnivores. However, identifying the joint effects of these factors across natural communities has been elusive, in part because of the lack of a framework for examining their effects simultaneously. Here, we develop a framework based on Lotka-Volterra equations...

Raw data used in: Variations in effects of ectosymbiotic microbes on the growth rates among different species and genotypes of Daphnia fed different algal diets

Xuan Zhang, Hajime Ohtsuki, Wataru Makino, Yasuhiko Kato, Hajime Watanabe & Jotaro Urabe
Several recent studies have shown that ectosymbiotic bacterial microbiota, including gut microbes, affect the growth and reproduction of Daphnia, a key organism in lake ecosystems. However, these studies examined specific species, such as the model organism, D. magna, and used green algae as food. It is unclear if symbiotic bacteria affect fitness in other Daphnia species common in lakes and ponds in Japan. In this study, we examined the growth rates of sterilized individuals of...

Alu-Mediated MEN1 Gene Deletion and Loss of Heterozygosity in a Patient with Multiple Endocrine Neoplasia Type 1

Satoshi Yoshiji, Yorihiro Iwasaki, Kanako Iwasaki, Sachiko Honjo, Koichi Hirano, Katsuhiko Ono, Yuto Yamazaki, Hironobu Sasano & Akihiro Hamasaki
Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disorder caused by mutations of the tumor suppressor gene MEN1. Most of the germline MEN1 gene mutations have been small mutations, and the whole gene deletion is rarely observed. In the present study, we revealed Alu retrotransposon-mediated de novo germline deletion of the whole MEN1 gene and somatic copy-neutral loss of heterozygosity (LOH) in a patient with MEN1. The patient is a 39-year-old woman who...

Data from: Estimating fish population abundance by integrating quantitative data on environmental DNA and hydrodynamic modeling

Keiichi Fukaya, Hiroaki Murakami, Seokjin Yoon, Kenji Minami, Yutaka Osada, Satoshi Yamamoto, Reiji Masuda, Akihide Kasai, Kazushi Miyashita, Toshifumi Minamoto & Michio Kondoh
Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of...

Data from: Ancient drainage networks mediated a large-scale genetic introgression in the East Asian freshwater snails

Osamu Miura, Urabe Misako, Hideaki Mori & Satoshi Chiba
Biogeography and genetic variation of freshwater organisms are influenced not only by current freshwater connections but also by past drainage networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but geological evidence showed that a large freshwater drainage had intermittently appeared in this area between the late Pliocene and Pleistocene. Here we demonstrated that this paleodrainage greatly affected the genetic variation of the East Asian freshwater snails, Semisulcospira spp. We found that...

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: 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: 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...

Accumulation of deleterious mutations in landlocked threespine stickleback populations

Jun Kitano, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Tomoyuki Kokita & Seiichi Mori
Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared to the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole genome resequencing data,...

Neuronal octopamine signaling regulates mating-induced germline stem cell increase in female Drosophila melanogaster

Ryusuke Niwa, Yuto Yoshinari, Tomotsune Ameku, Shu Kondo, Hiromu Tanimoto, Takayuki Kuraishi & Yuko Shimada-Niwa
Stem cells fuel the development and maintenance of tissues. Many studies have addressed how local signals from neighboring niche cells regulate stem cell identity and their proliferative potential. However, the regulation of stem cells by tissue-extrinsic signals in response to environmental cues remains poorly understood. Here we report that efferent octopaminergic neurons projecting to the ovary are essential for germline stem cell (GSC) increase in response to mating in female Drosophila. The neuronal activity of...

Registration Year

  • 2020

Resource Types

  • Dataset


  • Tohoku University
  • University of Tokyo
  • University of Tsukuba
  • Kyoto University
  • Forestry and Forest Products Research Institute
  • National Museum of Nature and Science
  • Hokkaido University
  • Toho University
  • National Institute of Genetics
  • China University of Geosciences