Koutarou D Kimura

Koutarou D Kimura
Nagoya City University | NCU · Graduate School of Natural Sciences

PhD

About

65
Publications
7,001
Reads
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6,525
Citations
Additional affiliations
April 2018 - present
Nagoya City University
Position
  • Professor
January 2009 - March 2018
Osaka University
Position
  • Professor (Associate)
March 2003 - December 2008
National Institute of Genetics
Position
  • Professor (Assistant)

Publications

Publications (65)
Article
Full-text available
Many neuronal groups such as dopamine-releasing (dopaminergic) neurons are functionally divergent, although the details of such divergence are not well understood. Dopamine in the nematode Caenorhabditis elegans modulates various neural functions and is released from four left-right pairs of neurons. The terminal identities of these dopaminergic ne...
Article
Full-text available
Animal behavior is the final and integrated output of brain activity. Thus, recording and analyzing behavior is critical to understand the underlying brain function. While recording animal behavior has become easier than ever with the development of compact and inexpensive devices, detailed behavioral data analysis requires sufficient prior knowled...
Article
The brain performs various functions by coordinating and integrating activities of its units, called nerve cells or "neurons". Therefore, the mechanisms underlying brain functions should be explored by analyzing neuronal activities in the entire brain [i.e. whole brain activities (WBAs)]. Because the brain consists of a very large number of neurons...
Article
Full-text available
Despite recent improvements in microscope technologies, segmenting and tracking cells in three-dimensional time-lapse images (3D + T images) to extract their dynamic positions and activities remains a considerable bottleneck in the field. We developed a deep learning-based software pipeline, 3DeeCellTracker, by integrating multiple existing and new...
Article
Recent advancements in 3D microscopy have enabled scientists to monitor signals of multiple cells in various animals/organs. However, segmenting and tracking the moving cells in three-dimensional time-lapse images (3D + T images), to extract their dynamic positions and activities, remains a considerable bottleneck in the field. We developed a deep...
Preprint
Animals' sensory systems adjust their responsiveness to environmental stimuli that vary greatly in their intensity. Here we report the neural mechanism of experience-dependent sensory adjustment, especially gain control, in the ASH nociceptive neurons in Caenorhabditis elegans. Using calcium imaging under gradual changes in stimulus intensity, we f...
Article
Full-text available
Since the variables inherent to various diseases cannot be controlled directly in humans, behavioral dysfunctions have been examined in model organisms, leading to better understanding their underlying mechanisms. However, because the spatial and temporal scales of animal locomotion vary widely among species, conventional statistical analyses canno...
Preprint
Electricity is widely utilized as environmental stimulus to sense the world by many animal species. Despite its importance, however, molecular and physiological mechanisms for responding to electrical stimulus have been far less understood compared to other sensory stimuli. Here we report novel behavioral responses to electrical stimulus of the nem...
Article
Full-text available
Olfactory behavior is among the most fundamental animal behaviors both in the wild and in the laboratory. To elucidate the neural mechanisms underlying olfactory behavior, it is critical to measure neural responses to odorant concentration changes resembling those that animals actually sense during olfactory behavior. However, reproducing the dynam...
Preprint
Full-text available
Since the variables inherent to various diseases cannot be controlled directly in humans, behavioral dysfunctions have been examined in model organisms, leading to better understanding their underlying mechanisms. However, because the spatial and temporal scales of animal locomotion vary widely among species, conventional statistical analyses canno...
Article
Full-text available
A comparative analysis of animal behavior (e.g., male vs. female groups) has been widely used to elucidate behavior specific to one group since pre-Darwinian times. However, big data generated by new sensing technologies, e.g., GPS, makes it difficult for them to contrast group differences manually. This study introduces DeepHL, a deep learning-ass...
Article
Full-text available
The limited per-pixel bandwidth of most microscopy methods requires compromises between field of view, sampling density and imaging speed. This limitation constrains studies involving complex motion or fast cellular signaling, and presents a major bottleneck for high-throughput structural imaging. Here, we combine high-speed intensified camera tech...
Article
Recent advances in robotics and measurement technologies have enabled biologists to record the trajectories created by animal movements. In this paper, we convert time series of animal trajectories into sequences of finite symbols, and then propose a machine learning method for gaining biological insight from the trajectory data in the form of symb...
Preprint
Animal behavior is the final and integrated output of the brain activity. Thus, recording and analyzing behavior is critical to understand the underlying brain function. While recording animal behavior has become easier than ever with the development of compact and inexpensive devices, detailed behavioral data analysis requires sufficient previous...
Article
Animals process sensory information from the environment to make behavioral decisions. Although environmental information may be ambiguous or gradually changing, animals can still choose one behavioral option among several through perceptual decision-making. Perceptual decision-making has been intensively studied in primates and rodents, and neural...
Preprint
Full-text available
The brain is a complex system that operates based on coordinated neuronal activities. Brain-wide cellular calcium imaging techniques have quickly advanced in recent years and become powerful tools for understanding the neuronal activities of small animal models. The whole brain imaging generally requires to extract the neuronal activities from thre...
Article
Odor is the most fundamental chemical stimulus that delivers information regarding food, mating partners, enemies, and danger in the surrounding environment. Research on odor response in animals is widespread, although studies on experimental systems in which the gradient of odor concentration is quantitatively measured has been quite limited. Here...
Data
Detailed results of statistical tests in this study are shown. DOI: http://dx.doi.org/10.7554/eLife.21629.027
Data
Plasmids used in this study are shown. DOI: http://dx.doi.org/10.7554/eLife.21629.028
Data
Strains used in this study are shown. DOI: http://dx.doi.org/10.7554/eLife.21629.029
Article
Full-text available
Brains regulate behavioral responses with distinct timings. Here we investigate the cellular and molecular mechanisms underlying the timing of decision-making during olfactory navigation in Caenorhabditis elegans. We find that, based on subtle changes in odor concentrations, the animals appear to choose the appropriate migratory direction from mult...
Chapter
Introduction Optogenetics emerged from the discovery of light-activated ion channels and ion pumps (Nagel et al., 2002; Nagel et al., 2003; Zhang et al., 2007), which have revolutionized our ways of controlling neural activities non-invasively and with high spatiotemporal precision. For optogenetics, as its name indicates, the combination of two te...
Article
An animal's behavior is modulated by learning; however, the behavioral component modulated by learning and the mechanisms of this modulation have not been fully understood. We show here that two types of neural signalings are required for the modulation of different behavioral components in non-associative odor learning in the nematode Caenorhabdit...
Article
We present a new and simple optogenetic system for the behavioral analysis of small animals. This system includes a strong LED ring array, a high-resolution CCD camera, and the improved channelrhodopsin ChRGR. We used the system for behavioral analysis with the nematode Caenorhabditis elegans as a model, and we found that it can stimulate ChRGR exp...
Article
Full-text available
Although a large proportion of molecules expressed in the nervous system are conserved from invertebrate to vertebrate, functional properties of such molecules are less characterized. Here, we show that highly conserved hydrolase AHO-3 acts as a novel regulator of starvation-induced thermotactic plasticity in Caenorhabditis elegans. As wild-type an...
Article
A Caenorhabditis elegans insulin-like signaling pathway regulates development, metabolism, and longevity. We detected abundant DAF-2 insulin-like receptor protein mainly in the nervous system, consistent with the assignment of DAF-2 pathway regulation of longevity to the nervous system. DAF-2 abundance in the nervous system is dependent on food int...
Article
Although a large proportion of molecules expressed in the nervous system are conserved from invertebrate to vertebrate, functional properties of such molecules are less characterized. Here, we show that highly conserved hydrolase AHO-3 acts as a novel regulator of starvation-induced thermotactic plasticity in Caenorhabditis elegans. As wild-type an...
Article
Defecation behavior in Caenorhabditis elegans is driven by an endogenous ultradian clock in the intestine. Its periods are positively regulated by FLR-1, an ion channel of the epithelial sodium channel/degenerin superfamily, and FLR-4, a protein kinase with a hydrophobic domain at the carboxyl terminus. FLR-1 has many putative phosphorylation sites...
Article
Full-text available
The enhancement of sensory responses after prior exposure to a stimulus is a fundamental mechanism of neural function in animals. Its molecular basis, however, has not been studied in as much depth as the reduction of sensory responses, such as adaptation or habituation. We report here that the avoidance behavior of the nematode Caenorhabditis eleg...
Article
The intestine plays an essential role in organism-wide regulatory networks in both vertebrates and invertebrates. In Caenorhabditis elegans, class 1 flr genes (flr-1, flr-3 and flr-4) act in the intestine and control growth rates and defecation cycle periods, while class 2 flr genes (flr-2, flr-5, flr-6 and flr-7) are characterized by mutations tha...
Article
Full-text available
Temperature is an unavoidable environmental cue that affects the metabolism and behavior of any creature on Earth, yet how animals perceive temperature is poorly understood. The nematode Caenorhabditis elegans "memorizes" temperatures, and this stored information modifies its subsequent migration along a temperature gradient. We show that the olfac...
Article
Full-text available
Caenorhabditis elegans exhibits a food-associated behavior that is modulated by the past cultivation temperature. Mutations in INS-1, the homolog of human insulin, caused the defect in this integrative behavior. Mutations in DAF-2/insulin receptor and AGE-1/phosphatidylinositol 3 (PI-3)-kinase partially suppressed the defect of ins-1 mutants, and a...
Article
Full-text available
Molecular and pharmacological studies in vitro suggest that protein kinase C (PKC) family members play important roles in intracellular signal transduction. Nevertheless, the in vivo roles of PKC are poorly understood. We show here that nPKC-epsilon/eta TTX-4 in the nematode Caenorhabditis elegans is required for the regulation of signal transducti...
Article
Full-text available
Animals modify behavioral outputs in response to environmental changes. C. elegans exhibits thermotaxis, where well-fed animals show attraction to their cultivation temperature on a thermal gradient without food. We show here that feeding-state-dependent modulation of thermotaxis is a powerful behavioral paradigm for elucidating the mechanism under...
Article
Full-text available
The defecation behavior of the nematode Caenorhabditis elegans is controlled by a 45-s ultradian rhythm. An essential component of the clock that regulates the rhythm is the inositol trisphosphate receptor in the intestine, but other components remain to be discovered. Here, we show that the flr-4 gene, whose mutants exhibit very short defecation c...
Article
The mechanism of temperature sensation is far less understood than the sensory response to other environmental stimuli such as light, odor, and taste. Thermotaxis behavior in C. elegans requires the ability to discriminate temperature differences as small as approximately 0.05 degrees C and to memorize the previously cultivated temperature. The AFD...
Article
Full-text available
The pharyngeal muscles of Caenorhabditis elegans are composed of the corpus, isthmus and terminal bulb from anterior to posterior. These components are excited in a coordinated fashion to facilitate proper feeding through pumping and peristalsis. We analysed the spatiotemporal pattern of intracellular calcium dynamics in the pharyngeal muscles duri...
Article
An insulinlike signaling pathway controlsCaenorhabditis elegans aging, metabolism, and development. Mutations in the daf-2 insulin receptor–like gene or the downstream age-1 phosphoinositide 3-kinase gene extend adult life-span by two- to threefold. To identify tissues where this pathway regulates aging and metabolism, we restored daf-2pathway sign...
Article
Full-text available
We have previously shown that sustained phosphatidylinositol (PI)-3 kinase activity is necessary for neurite outgrowth of PC12 cells induced by nerve growth factor (NGF). Microinjection of a constitutively active mutant of PI-3 kinase induced process formation suggesting that PI-3 kinase is indeed involved in the neurite outgrowth. However, the pro...
Article
We have explored the levels of phosphatidylinositol-3 kinase protein during culture of rat 3Y1 cells. Confluent cell cultures exhibited a higher level of phosphatidylinositol-3 kinase compared with that of growing cells. After replating of the cells on fresh dishes, the level of phosphatidylinositol-3 kinase returned to that of growing cells within...
Article
Full-text available
A C. elegans neurosecretory signaling system regulates whether animals enter the reproductive life cycle or arrest development at the long-lived dauer diapause stage. daf-2, a key gene in the genetic pathway that mediates this endocrine signaling, encodes an insulin receptor family member. Decreases in DAF-2 signaling induce metabolic and developme...
Article
We have purified a protein that binds phosphatidylinositol 3,4,5-trisphosphate [PtdIns(3,4,5)P3] using beads bearing a PtdIns(3,4,5)P3 analogue. This protein, with a molecular mass of 43 kDa, was termed PtdIns(3,4,5)P3-binding protein. The partial amino acid sequences were determined and a full-length cDNA encoding the protein was isolated from bov...
Article
We have found a factor that induces neurite outgrowth of rat PC12 cells in the culture supernatant of the cell line MLE-15A2. This factor was designated as MDDF. The factor was sensitive to protease, dithiothreitol, and high-temperature treatments. The apparent molecular mass was 80 kDa on Superdex 200 gel filtration. No significant tyrosine phosph...
Article
Full-text available
Effects of p110, the catalytic subunit of PI-3 kinase, on induction of TPA response element-driven promoter by EGF was examined. The induction was enhanced by co-expression of the wild type of p110. The truncated p110 mutants containing the binding site for p85 but missing the catalytic activity repressed the induction. A mutant with no binding act...
Article
Full-text available
Overexpression of a TPA-insensitive PKC member, an atypical protein kinase C (aPKClambda), results in an enhancement of the transcriptional activation of TPA response element (TRE) in cells stimulated with epidermal growth factor (EGF) or platelet-derived growth factor (PDGF). EGF or PDGF also caused a transient increase in the in vivo phosphorylat...
Article
Homochiral 1-O-acyl and 1-O-acyl derivatives of myo-inositol 3,4,5-trisphosphate were designed and synthesized as novel analogues of phosphatidyl-myo-inositol 3,4,5-trisphosphate. 1-O-Octadecyl and 1-O-stearoyl analogues inhibited the synthesis of phosphatidyl-myo-inositol 3,4-bisphosphate from phosphatidyl-myo-inositol 3,4,5-trisphosphate catalyze...
Article
A DNA fragment coding for a part of a putative phosphatidylinositol 3 kinase was cloned from Schizosaccharomyces pombe by cross-hybridization with Saccharomyces cerevisiae VPS34 gene, a yeast homologue of mammalian PI-3 kinase. The clone contained an open reading frame of 797 amino acids but lacked the initiation codon, ATG. The predicted amino aci...
Article
Full-text available
The effects of wortmannin (WT), an inhibitor of phosphatidylinositol (PI) 3-kinase, on differentiation of PC12 cells were analyzed. WT inhibited PI 3-kinase activity of PC12 cells at a concentration of 10(-7) M in vivo and in vitro. Transient inhibition of PI 3-kinase activity at the time of nerve growth factor stimulation had no effect on activati...
Article
Full-text available
The surface engagement of high affinity immunoglobulin E receptor (Fc epsilon RI) of rat basophilic leukemia 2H3 (RBL-2H3) cells induced histamine secretion and leukotriene release following activation of the tyrosine kinase Lyn together with phosphatidylinositol 3-kinase (PI3-kinase). Wortmannin inhibited the activity of partially purified PI3-kin...
Article
Full-text available
The surface engagement of high affinity immunoglobulin E receptor (Fc epsilon RI) of rat basophilic leukemia 2H3 (RBL-2H3) cells induced histamine secretion and leukotriene release following activation of the tyrosine kinase Lyn together with phosphatidylinositol 3-kinase (PI3-kinase). Wortmannin inhibited the activity of partially purified PI3-kin...

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