254 Works

Data from: Aging, mortality, and the fast growth trade-off of Schizosaccharomyces pombe

Hidenori Nakaoka & Yuichi Wakamoto
Replicative aging has been demonstrated in asymmetrically dividing unicellular organisms, seemingly caused by unequal damage partitioning. Although asymmetric segregation and inheritance of potential aging factors also occurs in symmetrically dividing species, it nevertheless remains controversial whether this results in aging. Based on large-scale single-cell lineage data obtained by time-lapse microscopy with a microfluidic device, in this report, we demonstrate the absence of replicative aging in old-pole cell lineages of Schizosaccharomyces pombe cultured under constant favorable...

Data from: Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug

Akihisa Seita, Hidenori Nakaoka, Reiko Okura & Yuichi Wakamoto
Cancer cell populations consist of phenotypically heterogeneous cells. Growing evidence suggests that pre-existing phenotypic differences among cancer cells correlate with differential susceptibility to anticancer drugs and eventually lead to a relapse. Such phenotypic differences can arise not only externally driven by the environmental heterogeneity around individual cells but also internally by the intrinsic fluctuation of cells. However, the quantitative characteristics of intrinsic phenotypic heterogeneity emerging even under constant environments and their relevance to drug susceptibility...

Data from: Inferring fitness landscapes and selection on phenotypic states from single-cell genealogical data

Takashi Nozoe, Edo Kussell & Yuichi Wakamoto
Recent advances in single-cell time-lapse microscopy have revealed non-genetic heterogeneity and temporal fluctuations of cellular phenotypes. While different phenotypic traits such as abundance of growth-related proteins in single cells may have differential effects on the reproductive success of cells, rigorous experimental quantification of this process has remained elusive due to the complexity of single cell physiology within the context of a proliferating population. We introduce and apply a practical empirical method to quantify the fitness...

Data from: Climatic forcing of Quaternary deep-sea benthic communities in the North Pacific Ocean

Moriaki Yasuhara, Gene Hunt, Thomas M. Cronin, Natsumi Hokanishi, Hodaka Kawahata, Akira Tsujimoto & Miho Ishitake
There is a growing evidence that changes in deep-sea benthic ecosystems are modulated by climate changes, but most evidence to date comes from the North Atlantic Ocean. Here we analyze new ostracod and published foraminiferal records for the last 250,000 years on Shatsky Rise in the North Pacific Ocean. Using linear models, we evaluate statistically the ability of environmental drivers (temperature, productivity, and seasonality of productivity) to predict changes in faunal diversity, abundance and composition....

Data from: Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

Maude W. Baldwin, Yasuka Toda, Tomoya Nakagita, Mary J. O'Connell, Kirk C. Klasing, Takumi Misaka, Scott V. Edwards & Stephen D. Liberles
Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies...

Data from: Genetic effects of marine stock enhancement: a case study based on the highly piscivorous Japanese Spanish mackerel

Kaori Nakajima, Shuichi Kitada, Yoko Habara, Shoko Sano, Emi Yokoyama, Takuma Sugaya, Akio Iwamoto, Hirohisa Kishino & Katsuyuki Hamasaki
We used a before–after control–impact design to quantify the genetic effects of the large piscivorous Japanese Spanish mackerel (Scomberomorus niphonius) stock enhancement program on wild populations in the Seto Inland Sea. Samples of 1424 wild and 230 hatchery fish collected from 13 sites around Japan were genotyped using five microsatellite markers. A total of 758 wild and 103 hatchery fish were sequenced for the mitochondrial DNA D-loop region. The population structure of Japanese Spanish mackerel...

Data from: Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan

Shuichi Kitada, Chie Fujikake, Yoshiho Asakura, Hitomi Yuki, Kaori Nakajima, Kelley M. Vargas, Shiori Kawashima, Katsuyuki Hamasaki & Hirohisa Kishino
Marine aquaculture and stock enhancement are major causes of the introduction of alien species. A good example of such an introduction is the Japanese shortneck clam Ruditapes philippinarum, one of the most important fishery resources in the world. To meet the domestic shortage of R. philippinarum caused by depleted catches, clams were imported to Japan from China and the Korean peninsula. The imported clam is an alien species that has a very similar morphology, and...

Data from: Opposite distortions in interval timing perception for visual and auditory stimuli with temporal modulations

Kenichi Yuasa & Yuko Yotsumoto
When an object is presented visually and moves or flickers, the perception of its duration tends to be overestimated. Such an overestimation is called time dilation. Perceived time can also be distorted when a stimulus is presented aurally as an auditory flutter, but the mechanisms and their relationship to visual processing remains unclear. In the present study, we measured interval timing perception while modulating the temporal characteristics of visual and auditory stimuli, and investigated whether...

Data from: A FISH-based chromosome map for the European corn borer yields insights into ancient chromosomal fusions in the silkworm

Yuji Yasukochi, Mizuki Ohno, Fukashi Shibata, Akiya Jouraku, Ryo Nakano, Yukio Ishikawa & Ken Sahara
A significant feature of the genomes of Lepidoptera, butterflies and moths, is the high conservation of chromosome organization. Recent remarkable progress in genome sequencing of Lepidoptera has revealed that syntenic gene order is extensively conserved across phylogenetically distant species. The ancestral karyotype of Lepidoptera is thought to be n = 31; however, that of the most well studied moth, Bombyx mori, is n = 28, and diverse studies suggest that three chromosomal fusion events occurred...

Data from: Timescale- and sensory modality-dependency of the central tendency of time perception

Yuki Murai & Yuko Yotsumoto
When individuals are asked to reproduce intervals of stimuli that are intermixedly presented at various times, longer intervals are often underestimated and shorter intervals overestimated. This phenomenon may be attributed to the central tendency of time perception, and suggests that our brain optimally encodes a stimulus interval based on current stimulus input and prior knowledge of the distribution of stimulus intervals. Two distinct systems are thought to be recruited in the perception of sub- and...

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: Star-shaped trace fossil and Phymatoderma from Neogene deep-sea deposits in central Japan: probable echiuran feeding and fecal traces

Kentaro Izumi & Kazuko Yoshizawa
A co-occurrence of the ichnogenus Phymatoderma and a star-shaped horizontal trace fossil was discovered from Neogene deep-marine deposits (Misaki Formation, central Japan), and is described herein for the first time. Phymatoderma consists of a straight to slightly curved tunnel that shows first- or second-order branches. The tunnels are 5.30–27.25 mm in diameter and are filled with ellipsoidal pellets. The relatively well-preserved star-shaped trace fossil is a large horizontal structure (~18 cm×19 cm) that consists of...

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: Sperm allocation in relation to female size in a semelparous salmonid

Yuya Makiguchi, Masaki Ichimura, Takenori Kitayama, Yuuki Kawabata, Takashi Kitagawa, Takahito Kojima & Trevor E. Pitcher
To maximize reproductive success, males have to adaptively tailor their sperm expenditure in relation to the quality of potential mates because they require time to replenish their sperm supply for subsequent mating opportunities. Therefore, in mating contexts where males must choose among females in a short period of time, as is the case with semelparous species (which die after one intensely competitive short duration breeding season), selection on sperm allocation can be expected to be...

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: Marine protected area restricts demographic connectivity: dissimilarity in a marine environment can function as a biological barrier

Masaaki Sato, Kentaro Honda, Wilfredo H. Uy, Darwin I. Baslot, Tom G. Genovia, Yohei Nakamura, Lawrence Patrick C. Bernardo, Hiroyuki Kurokochi, Allyn Duvin S. Pantallano, Chunlan Lian, Kazuo Nadaoka & Masahiro Nakaoka
The establishment of marine protected areas (MPAs) can often lead to environmental differences between MPAs and fishing zones. To determine the effects on marine dispersal of environmental dissimilarity between an MPA and fishing zone, we examined the abundance and recruitment patterns of two anemonefishes (Amphiprion frenatus and A. perideraion) that inhabit sea anemones in different management zones (i.e., an MPA and two fishing zones) by performing a field survey and a genetic parentage analysis. We...

Data from: A global perspective on the trophic geography of sharks

Christopher Stephen Bird, Ana Veríssimo, Sarah Magozzi, Kátya G. Abrantes, Alex Aguilar, Hassan Al-Reasi, Adam Barnett, Dana M. Bethea, Gérard Biais, Asuncion Borrell, Marc Bouchoucha, Mariah Boyle, Edward J. Brooks, Juerg Brunnschweiler, Paco Bustamante, Aaron Carlisle, Diana Catarino, Stéphane Caut, Yves Cherel, Tiphaine Chouvelon, Diana Churchill, Javier Ciancio, Julien Claes, Ana Colaço, Dean L. Courtney … & Clive N. Trueman
Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits...

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: Ribosomal RNA gene repeats associate with the nuclear pore complex for maintenance after DNA damage

Chihiro Horigome, Eri Unozawa, Takamasa Ooki & Takehiko Kobayashi
The ribosomal RNA genes (rDNA) comprise a highly repetitive gene cluster. The copy number of genes at this locus can readily change and is therefore one of the most unstable regions of the genome. DNA damage in rDNA occurs after binding of the replication fork blocking protein Fob1 in S phase, which triggers unequal sister chromatid recombination. However, the precise mechanisms by which such DNA double-strand breaks (DSBs) are repaired is not well understood. Here,...

Plant community assembly in suburban vacant lots depends on earthmoving legacy, habitat connectivity, and current mowing frequency

Yoichi Tsuzuki, Tomoyo Koyanagi & Tadashi Miyashita
In suburban regions, vacant lots potentially offer significant opportunities for biodiversity conservation. Recently, in Japan, due to an economic recession, some previously developed lands have become vacant. Little is known, however, about the legacy of earlier earthmoving, which involves topsoil removal and ground levelling before residential construction, on plant community composition in such vacant lots. To understand (dis)assembly processes in vacant lots, we studied 24 grasslands in a suburban region in Japan: 12 grasslands that...

Audio files for applying the Wizard of Oz method

Chang Li & Hideyoshi Yanagisawa
This data set consists of audio files used by the users to apply the Wizard of Oz method in the two reported experiments, in which the experimenter simulated an autonomous virtual assistant in the context of interactive task sections. The audio files serve the purpose of duplicating the reported experiments. The experimental protocol, including instructions, are presented in Support Information affilliated to the PLOS ONE manuscript.

Data from: Older males are not only attractive to but also aggressive toward females in Gnatocerus cornutus

Kensuke Okada, Masako Katsuki, Katsuya Kiyose & Yasukazu Okada
In theory, a male should change the allocation of fighting and mating efforts in relation to his age. Thus, the consequences of sexual selection may be complicated by changes in the male resource allocation due to aging. However, previous studies have focused on changes in female mate choice and male-male competition with aging separately, and the impact of aging on the relationship between mate choice and male competition is unknown. Here, we examined how male...

Data from: Adaptive reduction of male gamete number in the selfing plant Arabidopsis thaliana

Takashi Tsuchimatsu, Hiroyuki Kakui, Misako Yamazaki, Cindy Marona, Hiroki Tsutsui, Afif Hedhly, Dazhe Meng, Yutaka Sato, Thomas Städler, Ueli Grossniklaus, Masahiro Kanaoka, Michael Lenhard, Magnus Nordborg & Kentaro Shimizu
The number of male gametes is critical for reproductive success and varies between and within species. The evolutionary reduction of the number of pollen grains encompassing the male gametes is widespread in selfing plants. Here, we employ genome-wide association study (GWAS) to identify underlying loci and to assess the molecular signatures of selection on pollen number-associated loci in the predominantly selfing plant Arabidopsis thaliana. Regions of strong association with pollen number are enriched for signatures...

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...

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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