48 Works

Data from: Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi

Pamela Gan, Kyoko Ikeda, Hiroki Irieda, Mari Narusaka, Richard J. O'Connell, Yoshihiro Narusaka, Yoshitaka Takano, Yasuyuki Kubo & Ken Shirasu
Hemibiotrophic fungal plant pathogens represent a group of agronomically significant disease-causing agents that grow first on living tissue and then cause host death in later, necrotrophic growth. Among these, Colletotrichum spp. are devastating pathogens of many crops. Identifying expanded classes of genes in the genomes of phytopathogenic Colletotrichum, especially those associated with specific stages of hemibiotrophy, can provide insights on how these pathogens infect a large number of hosts. The genomes of C. orbiculare, which...

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...

Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.

Brenda Andrews
Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments — endocytic patch, actin patch,...

sj-jpg-2-jhs-10.1177_17531934221126864 - Supplemental material for Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly

Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge & Naoki Morimoto
Supplemental material, sj-jpg-2-jhs-10.1177_17531934221126864 for Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly by Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge and Naoki Morimoto in Journal of Hand Surgery (European Volume)

sj-jpg-2-jhs-10.1177_17531934221126864 - Supplemental material for Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly

Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge & Naoki Morimoto
Supplemental material, sj-jpg-2-jhs-10.1177_17531934221126864 for Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly by Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge and Naoki Morimoto in Journal of Hand Surgery (European Volume)

Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates

Keita Sato, Takahiro Yamashita, Keiichi Kojima, Kazumi Sakai, Yuki Matsutani, Masataka Yanagawa, Yumiko Yamano, Akimori Wada, Naoyuki Iwabe, Hideyo Ohuchi & Yoshinori Shichida
Pinopsin is the opsin most closely related to vertebrate visual pigments on the phylogenetic tree. This opsin has been discovered among many vertebrates, except mammals and teleosts, and was thought to exclusively function in their brain for extraocular photoreception. Here, we show the possibility that pinopsin also contributes to scotopic vision in some vertebrate species. Pinopsin is distributed in the retina of non-teleost fishes and frogs, especially in their rod photoreceptor cells, in addition to...

Maternal gut microbiota in pregnancy dictates offspring metabolic phenotype

Ikuo Kimura, Junki Miyamoto, Ryuji Ohue-Kitano, Keita Watanabe, Takahiro Yamada, Masayoshi Onuki, Ryo Aoki, Yosuke Isobe, Daiji Kashihara, Daisuke Inoue, Akihiko Inaba, Yuta Takamura, Satsuki Taira, Shunsuke Kumaki, Masaki Watanabe, Masato Ito, Fumiyuki Nakagawa, Junichiro Irie, Hiroki Kakuta, Masakazu Shinohara, Ken Iwatsuki, Gozoh Tsujimoto, Hiroaki Ohno, Makoto Arita, Hiroshi Ito … & Koji Hase
Antibiotics and dietary habits can affect the gut microbial community, influencing disease susceptibility. Although the influence of microbiota on the postnatal environment has been well documented, much less is known regarding the impact of gut microbiota at the embryonic stage. Here, we show that maternal microbiota shapes the metabolic system of offspring. During pregnancy, short-chain fatty acids produced by the maternal microbiota dictate the differentiation of neural, intestinal, and pancreatic cells through embryonic GPR41 and...

Data from: Division of functional roles for termite gut protists revealed by single-cell transcriptomes

Yuki Nishimura, Masato Otagiri, Masahiro Yuki, Michiru Shimizu, Jun-Ichi Inoue, Shigeharu Moriya & Moriya Ohkuma
The microbiome in the hindgut of wood-feeding termites comprises various species of bacteria, archaea, and protists. This gut community is indispensable for the termite, which thrives solely on recalcitrant and nitrogen-poor wood. However, the difficulty in culturing these microorganisms has hindered our understanding of the function of each species in the gut. Although protists predominate in the termite gut microbiome and play a major role in wood digestion, very few culture-independent studies have explored the...

Data from: Reproductive interference hampers species coexistence despite conspecific sperm precedence

Suzuki Noriyuki & Ryosuke Iritani
Negative interspecific mating interactions, known as reproductive interference, can hamper species coexistence in a local patch and promote niche partitioning or geographical segregation of closely related species. Conspecific sperm precedence (CSP), which occurs when females that have mated with both conspecific and heterospecific males preferentially use conspecific sperm for fertilization, might contribute to species coexistence by mitigating the costs of interspecific mating and hybridization. We discussed whether two species exhibiting CSP can coexist in a...

Data from: Niclosamide activates the NLRP3 inflammasome by intracellular acidification and mitochondrial inhibition

Uyen Thi Tran & Toshimori Kitami
The NLRP3 inflammasome is unique among pattern recognition receptors in using changes in cellular physiology as a mechanism for sensing host danger. To dissect the physiological network controlling inflammasome activation, we screened for small-molecule activators and suppressors of IL-1β release in macrophages. Here we identified niclosamide, a mitochondrial uncoupler, as an activator of NLRP3 inflammasome. We find that niclosamide inhibits mitochondria and induces intracellular acidification, both of which are necessary for inflammasome activation. Intracellular acidification,...

Data For: The developing bird pelvis passes through ancestral Archosaurian and Dinosaurian conditions

Christopher Griffin, João Botelho, Michael Hanson, Matteo Fabbri, Daniel Smith-Paredes, Ryan Carney, Mark Norell, Shiro Egawa, Stephen Gatesy, Timothy Rowe, Ruth Elsey, Sterling Nesbitt & Bhart-Anjan Bhullar
Living birds (Aves) have bodies dramatically modified from the ancestral reptilian condition. The avian pelvis in particular experienced dramatic changes during the transition from early archosaurs to living birds. This stepwise transformation is well documented by an excellent fossil record; however, the ontogenetic alterations that underly it are less well-understood. We used embryological imaging techniques to examine the morphogenesis of avian pelvic tissues in three dimensions, allowing direct comparison with the fossil record. Many ancestral...

Additional file 1 of Visualization of clonal expansion after massive depletion of cells carrying the bovine leukemia virus (BLV) integration sites during the course of disease progression in a BLV naturally-infected cow: a case report

Susumu Saito, Kazuyoshi Hosomichi, Meripet Polat Yamanaka, Tetsuya Mizutani, Shin-nosuke Takeshima & Yoko Aida
Additional file 1. Probes for NGS and PCR primers.

Additional file 2 of Visualization of clonal expansion after massive depletion of cells carrying the bovine leukemia virus (BLV) integration sites during the course of disease progression in a BLV naturally-infected cow: a case report

Susumu Saito, Kazuyoshi Hosomichi, Meripet Polat Yamanaka, Tetsuya Mizutani, Shin-nosuke Takeshima & Yoko Aida
Additional file 2: Figure S1. Visualization of paired-end short read sequences of Stages I, II, and III mapped to the BLV reference FLK-BLV sequence (NCBI accession number EF600696). Horizontal lines in the schematic structure of the biotinylated probe targeting region at the top indicate biotinylated probes used in this study.

Data from: Insecticide applications to soil contribute to development of Burkholderia mediating insecticide resistance in stinkbugs

Kanako Tago, Yoshitomo Kikuchi, Shinji Nakaoka, Chie Katsuyama, Masahito Hayatsu & Sinji Nakaoka
Some soil Burkholderia strains are capable of degrading the organophosphorus insecticide, fenitrothion, and establish symbiosis with stinkbugs, making the host insects fenitrothion-resistant. However, the ecology of the symbiotic degrading Burkholderia adapting to fenitrothion in the free-living environment is unknown. We hypothesized that fenitrothion applications affect the dynamics of fenitrothion-degrading Burkholderia, thereby controlling the transmission of symbiotic degrading Burkholderia from the soil to stinkbugs. We investigated changes in the density and diversity of culturable Burkholderia (i.e....

Data from: Heterogeneous genetic makeup of the Japanese house mouse (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

Takashi Kuwayama, Mitsuo Nunome, Gohta Kinoshita, Kuniya Abe & Hitoshi Suzuki
In this study, phylogenetic analysis of relatively long sequences of mitochondrial DNA (4225 bp) in the Japanese house mouse Mus musculus provides the first evidence that both southern Asian subspecies of Mus musculus castaneus (CAS) and northern Asian subspecies of Mus musculus musculus (MUS) arrived in Japan through rapid population expansion events, from Southern China ~4000 years ago and the Korean Peninsula ~2000 years ago, respectively. Nuclear DNA haplotype structure analyses targeting a chromosome region...

Whole-organ analysis of TGF-beta-mediated remodelling of the tumour microenvironment by tissue clearing

Shimpei I. Kubota
Tissue clearing is one of the most powerful strategies for a comprehensive analysis of disease progression. Here, we established an integrated pipeline that combines tissue clearing, 3D imaging, and machine learning and applied to a mouse tumour model of experimental lung metastasis using human lung adenocarcinoma A549 cells. This pipeline provided the spatial information of the tumour microenvironment. We further explored the role of transforming growth factor-beta (TGF-beta) in cancer metastasis. TGF-beta-stimulated cancer cells enhanced...

Data from: Gut bacterial and fungal communities in ground-dwelling beetles are associated with host food habit and habitat

Rina Kudo, Hayato Masuya, Rikiya Endoh, Taisei Kikuchi & Hiroshi Ikeda
Beetles (Coleoptera) have the highest species diversity among all orders, and they have diverse food habits. Gut microbes may have contributed to this diversification of food habits. Here, we identified the pattern of the relationship between ground-dwelling beetles and their gut microbial communities (bacteria and fungi) in the field. We collected 46 beetle species of five families from secondary deciduous forests and grasslands in Japan and extracted microbial DNA from whole guts for amplicon sequencing....

Data assimilation using high-frequency radar for tsunami early warning: A case study of the 2022 Tonga volcanic tsunami

Yuchen Wang, Kentaro Imai, Iyan E. Mulia, Keisuke Ariyoshi, Narumi Takahashi, Kenichi Sasaki, Hitoshi Kaneko & Yoshiaki Sato
Tide gauge data in Japan of the 2022 Tonga volcanic tsunami

Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly

Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge & Naoki Morimoto
This study systematically and comprehensively analysed 129 thumb polydactylies in 122 patients using a duplicating range concept based on the level of skin and skeletal bifurcation. Numerical levels were defined along the longitudinal axis of the ulnar thumb duplicate from distal to proximal: level 0 (thumb tip) to level 6 (carpometacarpal joint). The relationships between duplication range and morphological parameters were evaluated. Nail asymmetry was associated with skin bifurcation levels 0 to 2. Proximal phalangeal...

sj-jpg-1-jhs-10.1177_17531934221126864 - Supplemental material for Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly

Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge & Naoki Morimoto
Supplemental material, sj-jpg-1-jhs-10.1177_17531934221126864 for Use of the duplication range concept for understanding morphology and predicting prognosis in thumb polydactyly by Susumu Saito, Aiko Makino, Hiroki Yamanaka, Itaru Tsuge and Naoki Morimoto in Journal of Hand Surgery (European Volume)

Microheliella maris possesses the most gene-rich mitochondiral genome in Diaphoretikes

Yazaki Euki, Akinori Yabuki, Yuki Nishimura, Takashi Shiratori, Tetsuo Hashimoto & Yuji Inagaki
The mitochondrial genomes are very diverse, but their evolutionary history is unclear due to the lack of efforts to sequence that of protists (unicellular eukaryotes), which cover a major part of the eukaryotic tree. Cryptista comprises cryptophytes, goniomonads, kathablepharids, and Palpitomonas bilix, and their mitochondrial genomes (mt-genomes) are characterized by various gene contents, particularly the presence/absence of an ancestral (bacterial) system for the cytochrome c maturation system. To shed light on mt-genome evolution in Cryptista,...

Species interactions and diversity: a unified framework using Hill numbers

William Godsoe, Rua Murray & Ryosuke Iritani
Biodiversity describes the variety of organisms on planet earth. Ecologists have long hoped for a synthesis between analyses of biodiversity and analyses of biotic interactions among species, such as predation, competition, and mutualism. However, it is often unclear how to connect details of these interactions with complex modern analyses of biodiversity. To resolve this gap, we propose a unification of models of biotic interactions and measurements of diversity. We show that analyses of biodiversity obscure...

Data from: Evolutionary and dispersal history of Eurasian wild mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

Hitoshi Suzuki, Mitsuo Nunome, Ghota Kinotshita, K. P. Aplin, Peter Vogel, Alexey P. Kryukov, Mei-Lei Jin, Sang-Hoon Han, Ibnu Maryanto, Kimiyuki Tsuchiya, Hidetoshi Ikeda, T. Shiroishi, Hiromichi Yonekawa & Kazuo Moriwaki
We examined sequence variation of mitochondrial DNA control region and cytochrome b gene of the house mouse (Mus musculus sensu lato) drawn from ca. 200 localities, with 290 new samples drawn primarily from previously unsampled portions of their Eurasian distribution and with the objective of further clarifying evolutionary episodes of this species before and after the onset of human-mediated long-distance dispersals. Phylogenetic analysis of the expanded data detected five equally distinct clades, with geographic ranges...

Dataset associated with 'Quantification of Ebola virus replication kinetics in vitro'

Laura Liao, Jonathan Carruthers, Sophie J. Smither, , Simon A. Weller, Diane Williamson, Thomas R. Laws, Isabel Garcia-Dorival, Julian Hiscox, Benjamin P. Holder, Catherine Beauchemin, Alan S. Perelson, MARTIN LOPEZ-GARCIA, Grant Lythe, John Barr & carmen molina-parís
This dataset is associated with ‘Quantification of Ebola virus replication kinetics in vitro’. In the paper, a mathematical model is developed to describe the replication of Ebola virus in Vero cells. The model is parametrised using measurements of total and infectious extracellular virus at three different multiplicities of infection. The results provide insights into the distribution of time an infected cell spends in the eclipse phase (the period between infection and the start of virus...

Data assimilation using high-frequency radar for tsunami early warning: A case study of the 2022 Tonga volcanic tsunami

Yuchen Wang, Kentaro Imai, Iyan E. Mulia, Keisuke Ariyoshi, Narumi Takahashi, Kenichi Sasaki, Hitoshi Kaneko & Yoshiaki Sato
Tide gauge data in Japan of the 2022 Tonga volcanic tsunami

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