254 Works

Data from: HSP90 as a global genetic modifier for male genital morphology in Drosophila melanogaster

Kazuo H. Takahashi, Motoyuki Ishimori & Hiroyoshi Iwata
The molecular chaperone protein HSP90 has been proposed to modulate genotype-phenotype relationship in a broad range of organisms. To understand the genetic modifier effect of HSP90, genetic variations under the influence of HSP90 need to be identified on a genome-wide scale. Here, we show that HSP90 functions as a genetic modifier of genital morphology in Drosophila melanogaster. We identified a large number of single-nucleotide polymorphisms (SNPs) with an HSP90-dependent effect by using genome wide association...

Data from: Genotype-aggregated planting improves yield in Jerusalem artichoke (Helianthus tuberosus) due to self/non-self discrimination

Yuya Fukano, Wei Guo, Koji Noshita, Shoko Hashida & Shotaka Kamikawa
Accumulating evidence indicates that plants are capable of self/non-self and kin/stranger discrimination. Plants increase biomass of and resource allocation to roots when they encounter roots of conspecific non-self neighbors, but not when they encounter self roots. Root proliferation usually occurs at the expense of reproductive investment. Therefore, if clonal crops are capable of self/non-self discrimination, spatially aggregated planting with seedlings of the same genotype may decrease root proliferation and produce a higher yield than planting...

Data from: Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae)

Sarah A. Unruh, Michael R. McKain, Yung-I Lee, Tomohisa Yukawa, Melissa K. McCormick, Richard P. Shefferson, Ann Smithson, James H. Leebens-Mack & J. Chris Pires
Premise of Study: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated ten transcriptomes and incorporated existing RNA-seq data to infer a multi-locus nuclear phylogeny of the Cypripedioideae and to determine if a whole genome duplication event (WGD) correlated to the large genome size of this subfamily....

Data from: Determining the minimum number of protein-protein interactions required to support known protein complexes

Natsu Nakajima, Morihiro Hayashida, Jesper Jansson, Osamu Maruyama & Tatsuya Akutsu
The prediction of protein complexes from protein-protein interactions (PPIs) is a well-studied problem in bioinformatics. However, the currently available PPI data is not enough to describe all known protein complexes. In this paper, we express the problem of determining the minimum number of (additional) required protein-protein interactions as a graph theoretic problem under the constraint that each complex constitutes a connected component in a PPI network. For this problem, we develop two computational methods: one...

Data from: Biogeographical network analysis of cretaceous terrestrial tetrapods: a phylogeny-based approach

Tai Kubo
Network methods are widely used to represent and analyse biogeography. It is difficult, however, to convert occurrence data of fossil vertebrates to a biogeographical network, as most species were known from a single locality. A new method for creating a biogeographical network that can incorporate phylogenetic information is proposed in this study, which increases the number of edges in the network of fossil vertebrates and enables the application of various network methods. Using ancestral state...

Contrasting effects of land-use changes on herbivory and pollination networks

Naoto Shinohara, Kei Uchida & Takehito Yoshida
Land-use changes, one of the greatest threats to global biodiversity, can cause under-appreciated effects on ecosystems by altering the structures of interspecific interaction networks. These effects have typically been explored by evaluating interaction networks composed of a single type of interaction. Therefore, it remains unclear whether the different types of interaction networks sharing the same species respond to the same land-use changes in a similar manner. To compare the responses of herbivory and pollination networks...

Data from: A new method of Bayesian causal inference in non-stationary environments

Shuji Shinohara, Pegio-Yukio Gunji, Tatsuji Takahashi, Kouta Suzuki, Ung-Il Chung, Yoshihiro Nakajima, Nobuhito Manome, Shunji Mitsuyoshi & Hiroshi Okamoto
Bayesian inference is the process of narrowing down the hypotheses (causes) to the one that best explains the observational data (effects). To accurately estimate a cause, a considerable amount of data is required to be observed for as long as possible. However, the object of inference is not always constant. In this case, a method such as exponential moving average (EMA) with a discounting rate is used to improve the ability to respond to a...

Data from: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies

John Chiang, Michael Herman, Kei Yoshimura & Inez Fung
This archive contain the isoGSM2 model output used in the publication Chiang, J. C. H., M. J. Herman, K. Yoshimura, and I. Y. Fung: Enriched East Asian oxygen isotope of precipitation indicates reduced summer seasonality in regional climate and westerlies. In press for Proceedings of the National Academy of Sciences, April 2020

The genetic basis of scale-loss phenotype in the rapid radiation of Takifugu fishes

Kiyoshi Kikuchi, Kim Dong, Wataru Kai, Sho Hosoya, Mana Sato, Aoi Nozawa, Miwa Kuroyanagi, Yuka Jo, Satoshi Tasumi, Hiroaki Suetake & Yuzuru Suzuki
The genetic basis of scale-loss in Takifugu pufferfishes Abstract Rapid radiation associated with phenotypic divergence and convergence provides an opportunity to study the genetic mechanisms of evolution. Here we investigate the genus Takifugu that has undergone explosive radiation relatively recently and contains a subset of closely-related species with a scale-loss phenotype. By using observations during development and genetic mapping approaches, we show that the scale-loss phenotype of two Takifugu species, T. pardalis Temminck & Schlegel...

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...

The supplementary datasets of the study of free moment Induced by oblique transverse tarsal joint: investigation by constructive approach

Tsung-Yuan Chen, Kawakami Takahiro, Naomichi Ogihara & Koh Hosoda
The human foot provides numerous functions that let humans deal with various environments. Recently, study of the structure of the human foot and adjustment of an appropriate reaction force and vertical free moment during bipedal locomotion has gained attention. However, little is known about the mechanical (morphological) contribution of the foot structure to the reaction force and free moment. It is difficult to conduct a comparative experiment to investigate the contribution systematically by using conventional...

Comprehensive comparative morphology and developmental staging of final instar larvae toward metamorphosis in the insect order Odonata

Genta Okude, Takema Fukatsu & Ryo Futahashi
The order Odonata (dragonflies and damselflies) is among the most ancestral groups of winged insects with drastic morphological changes upon metamorphosis, and thus important for understanding evo-devo aspects of insects. However, basic developmental descriptions of Odonata have been scarce. In an attempt to establish the foundation of developmental and experimental biology of Odonata, we present an unprecedentedly comprehensive survey of dragonflies and damselflies, in total 158 larvae representing 49 species and 14 families, wherein morphological...

GPS tracks and behaviour detection of chick-rearing streaked shearwaters at Funakoshi Oshima Island, Japan, 2018 & 2019

Aran Garrod, Sei Yamamoto, Kentaro Sakamoto & Katsufumi Sato
The study of seabird behaviour has largely relied on animal-borne tags to gather information, requiring interpretation to estimate at-sea behaviours. Details of shallow-diving birds’ foraging are less known than deep-diving species due to difficulty in identifying shallow dives from biologging devices. Development of smaller video loggers allow a direct view of these birds’ behaviours, at the cost of short battery life. However, recordings from video loggers combined with relatively low power usage accelerometers give a...

Sperm competition risk affects ejaculate strategy in terms of sperm number but not sperm size in squid

Yoko Iwata, Noriyosi Sato, Noritaka Hirohashi, Yoshiro Watanabe, Warwick Sauer & Paul Shaw
In polygamous species, the mode of sperm storage in females influences evolution of sperm quantitative and qualitative traits because it provides the arena for sperm competition, cryptic female choice and fertilization processes. In this study, we compared ejaculate traits of two squid species, Heterololigo bleekeri and Loligo reynaudii. Both species show dimorphic sperm traits associated with alternative reproductive tactics where consort and sneaker males transfer sperm to different storage sites within a female (on the...

Data from: Metabolic proxy for cephalopods: Stable carbon isotope values recorded in different biogenic carbonates

Ming-Tsung Chung, Ching-Yi Chen, Jen-Chieh Shiao, Kotaro Shirai & Chia-Hui Wang
1. Measuring the metabolic rate of marine animals in their natural environment is challenging, impeding our understanding of their physiological ecology. Recently, a novel metabolic proxy, namely the δ13C values of biogenic carbonates (otoliths), was experimentally validated in teleost fishes. Cephalopods possess several types of biogenic carbonates, such as statolith, cuttlebone, and other internal and external shells, which are all potential metabolic recorders, but few have been evaluated. 2. To test the feasibility of the...

Modelled fluvial flood hazard maps in Vietnam for the period 2070-2100

L. Hawker, J. Neal, K.N. Pham, Y. Hirabayashi & D. Yamazaki
This dataset contains fluvial flood maps of the present day 1 in 20 year return period, and corresponding flood extents for 3 SSP (Shared Socioeconomic Pathway)/RCP(Representative Concentration Pathway) scenarios for the future (2070-2100). Change in flood return periods are estimated using CMIP6 projections and subsequently used to extract flood maps from a global flood model.

Mass cytometry immunophenotyping data of two-week-old mouse pups' spleens depleted of maternal cells

Flore Castellan
The maternal cells transferred into the fetus during gestation persist long after birth in the progeny. These maternal cells have been hypothesized to promote the maturation of the fetal immune system in utero but there are still significant gaps in our knowledge of their potential roles after birth. To provide insights into these maternal cells' postnatal functional roles, we set up a transgenic mouse model to specifically eliminate maternal cells in the neonates by diphtheria...

Data from: Effectiveness of signs of activity as relative abundance indices for wild boar

Daishi Higashide, Takeo Kuriyama, Shun Takagi, Yoshihiro Nakashima, Keita Fukasawa, Gota Yajima, Minoru Kasada & Mayumi Yokoyama
Population growth in wild boars and feral pigs (Sus scrofa) has negative environmental and economic implications worldwide. Accordingly, it is necessary to monitor population trends for appropriate management. Despite the potential for bias, relative abundance indices based on signs of activity have the potential to be practical, low-cost monitoring tools for data collection at a local scale and over large areas. However, few studies have examined the effectiveness of specific signs as measures of relative...

Data from: Phylogeny of gracillariid leaf-mining moths: evolution of larval behaviour inferred from phylogenomic and Sanger data

Xuankun Li, Ryan St Laurent, Chandra Earl, Camiel Doorenweerd, Erik Van Nieukerken, Don Davis, Atsushi Kawakita, Shigeki Kobayashi, Andreas Zwick, Carlos Lopez-Vaamonde, Issei Ohshima & Akito Kawahara
Gracillariidae is the most taxonomically diverse cosmopolitan leaf-mining moth family, consisting of nearly 2000 named species in 105 described genera, classified into eight extant subfamilies. The majority of gracillariid species are internal plant feeders as larvae, creating mines and galls in plant tissue. Despite their diversity and ecological adaptations, their phylogenetic relationships, especially at the subfamily level, remain largely uncertain. Genomic data (83 taxa and 589 loci) were integrated with Sanger data (130 taxa and...

Rotary catalysis of bovine mitochondrial F1-ATPase studied by single-molecule experiments

Ryohei Kobayashi, Hiroshi Ueno, Chun-Biu Li & Hiroyuki Noji
The reaction scheme of rotary catalysis and the torque generation mechanism of bovine mitochondrial F1 (bMF1) were studied in single-molecule experiments. Under ATP-saturated concentrations, high-speed imaging of single 40 nm gold bead attached to the γ subunit of bMF1 showed two types of intervening pauses during the rotation that were discriminated by short dwell and long dwell. Using ATPgS as a slowly hydrolyzing ATP derivative as well as using a functional mutant bE188D with slowed...

Areal (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots

Junji Takabayashi, Kyohei Fukuda, Masayoshi Uefune, Hidehiro Fukaki, Yasuo Yamauchi, Ikuko Hara-Nishimura, Rika Ozawa, Kenji Matsui, Kazunori Okada, Ryozo Imai, Kenshi Takahashi, Shinichi Enami, Rene Wurst & Junji Takabayashi
One of the characteristic aspects of odour sensing in humans is the activation of olfactory receptors in a slightly different manner to different enantiomers. Here, we focused on whether plants showed enantiomer-specific responses similar to that in humans. We exposed Arabidopsis seedlings to methanol (control) and (+)- or (−)-borneol, and found that only (+)-borneol reduced the root length. Furthermore, the root-tip width was more increased upon (+)-borneol exposure than upon (−)-borneol exposure. In addition, root-hair...

Data and scripts from: Exploratory analysis of multi-trait coadaptations in the light of population history

Reiichiro Nakamichi, Shuichi Kitada & Hirohisa Kishino
During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to...

Dataset from: Lung evolution in vertebrates and the water-to-land transition

Camila Cupello, Tatsuya Hirasawa, Norifumi Tatsumi, Yoshitaka Yabumoto, Pierre Gueriau, Sumio Isogai, Ryoko Matsumoto, Toshiro Saruwatari, Andrew King, Masato Hoshino, Kentaro Uesugi, Masataka Okabe & Paulo M Brito
A crucial evolutionary change in vertebrate history was the Palaeozoic (Devonian ~400 million years ago) water-to-land transition, allowed by key morphological and physiological modifications including the acquisition of lungs. Nonetheless, the origin and early evolution of vertebrate lungs remain highly controversial, particularly whether the ancestral state was paired or unpaired. Due to the rarity of fossil soft tissue preservation, lung evolution can only be traced based on the extant phylogenetic bracket. Here we investigate, for...

EnKF Analyses and Forecasts of Hurricane Harvey (2017)

Y. Zhang, S.B. Sieron, Y. Lu, X. Chen, R.G. Nystrom, M. Minamide, M. Chan, C.M. Hartman, Z. Yao, J.H. Ruppert, A. Okazaki, S.J. Greybush & E.E. Clothiaux
Ensemble-based data assimilation of radar observations across inner-core regions of tropical cyclones (TCs) in tandem with satellite all-sky infrared radiances across the TC domain improves TC track and intensity forecasts. This study further investigates potential enhancements in TC track, intensity, and rainfall forecasts via assimilation of all-sky microwave radiances using Hurricane Harvey (2017) as an example. Assimilating GPM constellation all-sky microwave radiances in addition to GOES-16 all-sky infrared radiances reduces the forecast errors in the...

Additional file 1 of Effects of let-7a microRNA and C–C chemokine receptor type 7 expression on cellular function and prognosis in esophageal squamous cell carcinoma

Masahiro Yura, Kazumasa Fukuda, Satoru Matsuda, Tomoyuki Irino, Rieko Nakamura, Hirofumi Kawakubo, Hiroya Takeuchi & Yuko Kitagawa
Additional file 1: Table S1. Quantitative RT-PCR analysis.

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  • University of Tokyo
  • Tohoku University
  • Hokkaido University
  • Kyoto University
  • National Institute for Environmental Studies
  • National Institute of Advanced Industrial Science and Technology
  • Chiba Institute of Technology
  • Kyushu University
  • Keio University
  • The University of Tokyo