276 results on '"Jun-ichi Takahashi"'
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2. Genetic differentiation and local adaptation of the Japanese honeybee, Apis cerana japonica
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Takeshi Wakamiya, Takahiro Kamioka, Yuu Ishii, Jun‐ichi Takahashi, Taro Maeda, and Masakado Kawata
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environmental adaptation ,local adaptation ,population branch statistics ,population genetic structure ,whole genome analysis ,Ecology ,QH540-549.5 - Abstract
Abstract We examine the population genetic structure and divergence among the regional populations of the Japanese honeybee, Apis cerana japonica, by re‐sequencing the genomes of 105 individuals from the three main Japanese islands with diverse climates. The genetic structure results indicated that these individuals are distinct from the mainland Chinese A. cerana samples. Furthermore, population structure analyses have identified three genetically distinct geographic regions in Japan: Northern (Tohoku‐Kanto‐Chubu districts), Central (Chugoku district), and Southern (Kyushu district). In some districts, “possible non‐native” individuals, likely introduced from other regions in recent years, were discovered. Then, genome‐wide scans were conducted to detect candidate genes for adaptation by two different approaches. We performed a population branch statistics (PBS) analysis to identify candidate genes for population‐specific divergence. A latent factor mixed model (LFMM) was used to identify genes associated with climatic variables along a geographic gradient. The PBSmax analysis identified 25 candidate genes for population‐specific divergence whereas the LFMM analysis identified 73 candidate genes for adaptation to climatic variables along a geographic gradient. However, no common genes were identified by both methods.
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- 2023
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3. Effects of H2O to Reduction Reaction of Low Nickel Grade Oxide Ore
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Takashi ISEKI, Jun-ichi KOBAYASHI, and Jun-ichi TAKAHASHI
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nickel ,low grade ,oxide ore ,reduction ,pyrometallurgy ,rotary hearth furnace ,Mining engineering. Metallurgy ,TN1-997 ,Materials of engineering and construction. Mechanics of materials ,TA401-492 - Abstract
As pyrometallurgical technologies to smelt nickel metal from the oxide ore, melting reduction process using an electric furnace (Elkem) and semi-melting reduction process using a rotary kiln (Krupp-Renn) with a saprolite ore as a raw material have been established and operated commercially. However, in the future, it is expected that it will be difficult to smelt nickel from the oxide ore because of the decline of nickel grade in the ore and it is necessary to develop a new process adaptable to lower grade ore and difficult processing ore. The authors have conducted fundamental research on the pyrometallurgical reaction of low grade and difficult processing nickel oxide ore smelting by the rotary hearth furnace (RHF). Liquefied gas burner will be supposed from points of cost, reduction of global warming gas and so on in the operation of Ni smelting. On the other hand, it is getting clearer that Fe and Ni metallization degree in liquefied gas burning atmosphere are lower than those in N2 atmosphere. The reason have been guessed effects of H2O generating in liquefied gas combustion. The results about effects of H2O to reduction reaction of low Nickel grade oxide ore is described in this report.
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- 2022
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4. Category theory and organic electronics
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Jun-ichi Takahashi
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Category theory ,Duality ,Quasiconductor ,Immittance ,SCLC ,Negative capacitance ,Physics ,QC1-999 - Abstract
Inorganic semiconductors and conducting polymers are described by band conduction models with delocalized electrons, whereas small-molecule organic compounds are described by hopping conduction between localized molecular orbitals. However, the latter devices can reproduce fully the characteristics of semiconductor devices. Why are they so different and yet so similar? We will try to answer this question using Category theory and considering the meaning of electrical transport in electronic materials. The meaning of the category theory in physics is to consider different mathematical entities under a common mathematical structure.In this paper, the basic idea of category theory is first explained in detail using the example of complex impedance, and then four examples of its application are discussed. The derivation of the Mott-Gurney equation and the negative capacitance in OLED are discussed as examples of solving problems by moving to different categories. After those simple examples of formal rewriting from physical entity to mathematical entity, it is shown that electrical connection and electrical contact lead to direct sums and direct products of conducting states, based on the duality concept. We conclude that small-molecule organic compounds are not a mere branch of semiconductors, but rather equal counterparts of semiconductors in duality that are necessary to clarify the origin of the difference and similarity between organic electronics and semiconductor physics. Finally, by considering the electrical responses of OLEDs and OFETs in the immittance category, we show that they can be described under a common operating dynamic and propose a new operating model for OFETs.
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- 2023
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5. Formation of Amino Acids and Carboxylic Acids in Weakly Reducing Planetary Atmospheres by Solar Energetic Particles from the Young Sun
- Author
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Kensei Kobayashi, Jun-ichi Ise, Ryohei Aoki, Miei Kinoshita, Koki Naito, Takumi Udo, Bhagawati Kunwar, Jun-ichi Takahashi, Hiromi Shibata, Hajime Mita, Hitoshi Fukuda, Yoshiyuki Oguri, Kimitaka Kawamura, Yoko Kebukawa, and Vladimir S. Airapetian
- Subjects
prebiotic synthesis ,cosmic rays ,solar energetic particles ,weakly reducing atmosphere ,early Earth ,amino acids ,Science - Abstract
Life most likely started during the Hadean Eon; however, the environmental conditions which contributed to the complexity of its chemistry are poorly known. A better understanding of various environmental conditions, including global (heliospheric) and local (atmospheric, surface, and oceanic), along with the internal dynamic conditions of the early Earth, are required to understand the onset of abiogenesis. Herein, we examine the contributions of galactic cosmic rays (GCRs) and solar energetic particles (SEPs) associated with superflares from the young Sun to the formation of amino acids and carboxylic acids in weakly reduced gas mixtures representing the early Earth’s atmosphere. We also compare the products with those introduced by lightning events and solar ultraviolet light (UV). In a series of laboratory experiments, we detected and characterized the formation of amino acids and carboxylic acids via proton irradiation of a mixture of carbon dioxide, methane, nitrogen, and water in various mixing ratios. These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture. In the set of experiments with spark discharges (simulation of lightning flashes) performed for the same gas mixture, we found that at least 15% methane was required to detect the formation of amino acids, and no amino acids were detected in experiments via UV irradiation, even when 50% methane was used. Carboxylic acids were formed in non-reducing gas mixtures (0% methane) by proton irradiation and spark discharges. Hence, we suggest that GCRs and SEP events from the young Sun represent the most effective energy sources for the prebiotic formation of biologically important organic compounds from weakly reducing atmospheres. Since the energy flux of space weather, which generated frequent SEPs from the young Sun in the first 600 million years after the birth of the solar system, was expected to be much greater than that of GCRs, we conclude that SEP-driven energetic protons are the most promising energy sources for the prebiotic production of bioorganic compounds in the atmosphere of the Hadean Earth.
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- 2023
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6. Complete mitochondrial DNA sequence of the Japanese endemic catfish Silurus lithophilus (Siluriformes: Siluridae)
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Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
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next-generation sequencing ,catfish ,lake biwa ,silurus lithophilus ,mitochondrial dna ,Genetics ,QH426-470 - Abstract
The Japanese endemic catfish Silurus lithophilus is distributed only in Lake Biwa, Lake Yogo, and their river drainages. There are four species of the genus Silurus in Japan, of which S. lithophilus has a limited distribution. This catfish needs to be collected for DNA data owing to the lack of information related to its conservation. Here, the complete mitochondrial genome of the S. lithophilus from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. lithophilus was identified as a 16,524 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The AT content was 55.89%. The heavy (H)-strand was predicted to have 12 PCGs and 15 tRNA, and 2 rRNA genes, whereas the light (L)-strand was predicted to contain one PCG and seven tRNA genes. The start codons ATG and GTG were found in 13 PCGs. The stop codons TAA, TAG, and AGA were observed in all PCGs, except CytB. All tRNA genes formed typical cloverleaf secondary structures. The molecular phylogenetic relationship, inferred using 13 PCGs (based on the maximum likelihood), was consistent with that reported in previous studies, which predicted a sister relationship between S. lithophilus and S. asotus. The results also clearly indicated that S. lithophilus is a valid species.
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- 2021
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7. A revision of subspecies structure of western honey bee Apis mellifera
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Rustem A. Ilyasov, Myeong-lyeol Lee, Jun-ichi Takahashi, Hyung Wook Kwon, and Alexey G. Nikolenko
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Apis mellifera ,Honey bee ,Subspecies ,Taxonomy ,Biology (General) ,QH301-705.5 - Abstract
The taxonomy of honey bee A. mellifera contains a lot of issues due to the specificity of population structure, features of biology and resolutions of honey bee subspecies discrimination methods. There are a lot of transition zones between ranges of subspecies which led to the gradual changes of characteristics among neighbor subspecies. The modern taxonomic pattern of honey bee Apis mellifera is given in this paper. Thirty-three distinct honey bee subspecies are distributed across all Africa (11 subspecies), Western Asia and the Middle East (9 subspecies), and Europe (13 subspecies). All honey bee subspecies are subdivided into 5 evolutionary lineages: lineage A (10 subspecies) and its sublineage Z (3 subspecies), lineage M (3 subspecies), lineage C (10 subspecies), lineage O (3 subspecies), lineage Y (1 subspecies), lineage C or O (3 subspecies).
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- 2020
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8. Complete mitochondrial DNA sequence of the Eastern Asian catfish Silurus asotus (Siluriformes: Siluridae) from Lake Biwa in Japan
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Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
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next-generation sequencing ,catfish ,lake biwa ,silurus asotus ,mitochondrial dna ,Genetics ,QH426-470 - Abstract
The east Asian catfish Silurus asotus is a common species living in fresh water in Japan. The complete mitochondrial genome of the S. asotus from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. asotus was identified as a 16,515 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The AT content was 56.1%. Start codons ATG and GTG were found in 13 PCGs. Stop codons TAA, TAG, and AGA were observed in 13 PCGs. The heavy (H)-strand was predicted to have 12 PCGs and 14 tRNA and two rRNA genes, while the light (L)-strand was predicted to contain one PCGs and eight tRNA genes. The molecular phylogenetic analysis showed that S. asotus from Lake Biwa is genetically similar to S. asotus from China.
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- 2022
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9. Complete mitochondrial DNA sequence of the yeast Zygosaccharomyces siamensis (Saccharomycetes: Saccharomycetales) from fermented honey of the Apis cerana japonica in Japan
- Author
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Mao Chikano and Jun-ichi Takahashi
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zygosaccharomyces siamensis ,honey ,apis cerana ,yeast ,ume system ,Genetics ,QH426-470 - Abstract
Japanese Apis cerana honey is believed to ferment due to the presence of some yeast. We analyzed the complete mitochondrial genome of Zygosaccharomyces siamensis, a yeast involved in fermenting honey. Zygosaccharomyces siamensis was obtained from the honey collected from A. cerana hives under traditional beekeeping in the forest of the Minabe-Tanabe Ume system in Wakayama Prefecture, Japan. Its mitochondrial genome was identified as a 23,184 bp circular molecule containing 8 protein-coding genes (PCGs), 24 tRNA genes, and 2 rRNA genes. The PCGs contained a common set of genes encoding ATPase subunits (ATP6, ATP8, and ATP9), three subunits of cytochrome C oxidase (COX1, COX2, and COX3), apocytochrome b (CYTB), and ribosome-associated protein (RPS3). In addition, two open-reading frames coding for LAGLIDADG endonucleases were predicted to be about 1100 bps. The average GC content was found to be 48.6%. The heavy strand was predicted to have 7 PCGs, 22 tRNA genes, and 2 rRNA genes, while the light strand was predicted to contain one PCG and two tRNA genes. Molecular phylogenetic analyses of the mitochondrial DNA genes strongly supported the result obtained from the phylogenetic analysis of partial ITS region sequences, grouping the monophyletic species within the genus Zygosaccharomyces. The complete mitochondrial DNA genome of this honey-fermenting yeast will provide useful information for understanding the basis of the honey fermentation process.
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- 2020
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10. Complete mitochondrial DNA sequence of the East Asian minnow, Pungtungia herzi (Actinopterygii: Cypriniformes)
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Teppei Taniwaki, Misaki Hiroshima, Mihiro Imakita, Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
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minnow ,next-generation sequence ,pungtungia herzi ,yodo river ,Genetics ,QH426-470 - Abstract
Some populations of the East Asian minnow Pungtungia herzi Herzenstein, 1892, which are naturally distributed in western Japan, have declined and are considered endangered. However, P. herzi has become a domestic invasive species in eastern Japan. Thus, knowledge of genetic features and phylogenetic relationships of P. herzi is important for conservation of this species and understanding its impact on ecosystems. We analyzed the complete mitochondrial genome using next generation sequencing of the East Asian minnow P. herzi from Yodo River, Osaka Prefecture, Japan. The mitochondrial genome of P. herzi consists of a circular molecule of 16,599 bp that includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region. The heavy (H)-strand was predicted to have 12 PCGs, 14 tRNA, and two rRNA genes, while the light (L)-strand was predicted to contain one PCGs and eight tRNA genes. The average AT content was 57.68%. The genes ATP8 and ATP6, ATP6 and COIII, ND4L and ND4, and ND5 and ND6 shared seven, one, seven, and four nucleotides, respectively. The initiation codons ATG and GTG were found in 12 and one genes, respectively. The termination codons TAA, TAG, incomplete TA–, and single T–– were observed in nine, one, one, and two genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure. The phylogenetic relationships inferred using 13 PCGs (based on the maximum likelihood) were consistent with previous studies that predicted interrelationships of Cypriniformes.
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- 2020
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11. The draft genome sequence of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae)
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Kakeru YOKOI, Hironobu UCHIYAMA, Takeshi WAKAMIYA, Mikio YOSHIYAMA, Jun-Ichi TAKAHASHI, Tetsuro NOMURA, Tsutomu FURUKAWA, Shunsuke YAJIMA, and Kiyoshi KIMURA
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hymenoptera ,apidae ,apis cerana japonica ,genome sequence ,transposable elements ,innate immune genes ,Zoology ,QL1-991 - Abstract
Honey bees are not only important for honey production but also as pollinators of wild and cultivated plants. The Eastern honeybee (Apis cerana) is more resistant to several pathogens than the Western honeybee (Apis mellifera), and the genomes of two strains of the nominotypical subspecies, A. cerana cerana, northern (Korea) and southern (China) strains, have been sequenced. Apis cerana japonica, another subspecies of A. cerana, shows many specific features (e.g. mildness, low honey production and frequently absconds) and it is important to study the molecular biological and genetic aspects of these features. To accelerate the genetic research on A. cerana japonica, we sequenced the genome of this subspecies. The draft genome sequence of A. cerana japonica presented here is of high quality in terms of basic genome status (e.g. N50 is 180 kbp, total length is 211 Mbp, and largest contig length is 1.31 Mbp) and BUSCO results. The gene set of A. cerana japonica was predicted using AUGUSTUS software and the set of genes was annotated using Blastp and InterProScan, and GO terms were added to each gene. The number of genes is higher than in A. mellifera and in the two strains of A. cerana cerana sequenced previously. A small number of transposable elements and repetitive regions were found in A. cerana japonica, which are also in the genomes of A. mellifera and the northern and southern strains of A. cerana cerana. Apis cerana is resistant to several pathogens that seriously damage A. mellifera. We searched for 41 orthologs related to the IMD and Toll pathways, which have key roles in the immune reaction to invading pathogens. Some orthologs were not identified in the genome of the northern strain of A. cerana cerana. This indicates that the Toll and IMD pathways function in the same way as in A. mellifera and Drosophila melanogaster. Use of the draft genome sequence of A. cerana japonica provided herein and those of the other Apis (sub)species may help to accelerate comparative research on the genome of honey bees.
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- 2018
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12. Complete mitochondrial DNA sequence of the Japanese endemic catfish Silurus biwaensis (Siluriformes: Siluridae) from Lake Biwa
- Author
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Yuu Kishimoto, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
next-generation sequencing ,catfish ,lake biwa ,silurus biwaensis ,mitochondrial dna ,Genetics ,QH426-470 - Abstract
The Japanese endemic catfish Silurus biwaensis is distributed only in Lake Biwa and Yodo river drainages. There are four species of the genus Silurus in Japan, of which S. biwaensis has a most limited distribution. This catfish needs to be collected for DNA data owing to the lack of information related to its phylogenetic relationship. Here, the complete mitochondrial genome of the S. biwaensis from Lake Biwa in Japan was analyzed using next-generation sequencing. The mitochondrial genome of S. biwaensis was identified as a 16,531 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The AT content was 55.83%. The heavy (H)-strand was predicted to have 12 PCGs, 14 tRNA, and 2 rRNA genes, whereas the light (L)-strand was predicted to contain one PCG and eight tRNA genes. The start codons ATG, ATC, and GTG were found in 13 PCGs. The stop codons TAA, TAG, and AGA were observed in all PCGs, except CytB and COX3. All tRNA genes formed typical cloverleaf secondary structures. The molecular phylogenetic relationships estimated using 13 PCGs (maximum-likelihood method) indicated that S. biwaensis is genetically distinct from the sympatric species S. asotus and S. lithophilus. This result clearly indicated that S. biwaensis is a valid species.
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- 2021
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13. Analysis of the complete mitochondrial genomes of two dwarf honeybee species, Apis florea and Apis andreniformis (Insecta: Hymenoptera: Apidae), in Thailand
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Jun-ichi Takahashi, Sureerat Deowanish, and Hisashi Okuyama
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mitochondrial dna ,micrapis ,dwarf honey bee ,next generation sequencing ,Genetics ,QH426-470 - Abstract
The dwarf honeybees Apis florea and Apis andreniformis inhabit the bush and forests of continental Asia and north Africa and some islands of Sundaland and the Philippines. We analysed, for the first time, the complete mitochondrial genomes of two dwarf honeybee species from Thailand using next-generation sequencing. Each mitochondrial genome was a circular and approximately 17 kbp molecule that included 13 protein-coding genes (PCGs), 22 tRNA genes, and two ribosomal RNA genes, along with one A + T-rich control region, besides three tRNA-Ser (AGN) repeats. The AT content values of the mitochondrial genomes of A. florea and A. andreniformis were 86.28% and 85.73%, respectively. The 1150 mutation sites in 13 PCGs differing between A. florea and A. andreniformis in Thailand were evenly distributed throughout their mitochondrial genomes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies, which predicted a sister relationship between A. florea and A. andreniformis.
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- 2018
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14. Complete mitochondrial genome sequence of the broad-winged damselfly, Mnais pruinosa Selys, 1853 (Odonata: Calopterygidae)
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Hisashi Okuyama, Takuya Kiyoshi, Jun-Ichi Takahashi, and Yoshitaka Tsubaki
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next generation sequence ,damselfly ,mnais pruinosa ,dark-brown-winged morphs ,saga prefecture ,Genetics ,QH426-470 - Abstract
In this study, we analyzed the complete mitochondrial genome of the Mnais pruinosa Selys, 1853 from Saga Prefecture, Japan. The mitochondrial genome of M. pruinosa was identified as a circular molecule of 15,494 bp, and was found to be similar to that of other damselfly species. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, as well as one A + T-rich control region. The genes ATP8 and ATP6 shared seven nucleotides, ATP6 and COIII shared one nucleotide, ND4 and ND4L shared seven nucleotides, and ND6 and Cytb shared one nucleotide. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one; the termination codons TAA, TAG, incomplete TA, and single T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.18%.
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- 2019
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15. Complete mitochondrial DNA sequence of the paper wasp Polistes riparius (Hymenoptera: Vespidae)
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Kazuhisa Yamasaki, Katsuhiko Sayama, Tomoki Oishi, Kanae Nakahama, Masato Yoshioka, Hisashi Okuyama, and Jun-ichi Takahashi
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next generation sequence ,paper wasp ,polistes riparius ,polistinae ,vespidae ,Genetics ,QH426-470 - Abstract
The paper wasp Polistes riparius is distributed in cold regions of northern East Asia to Russia. P. riparius are characterized by having longer cells than those of the closely related P. chinensis, which has a similar life history, as an adaptation to cold regions. The phylogenetic relationships of paper wasps have recently been studied; however, the genetic diversity and population structure of P. riparius has not been determined. The present study is the first to analyze the complete mitochondrial genome using next generation sequencing of P. riparius collected from Sapporo, Hokkaido Prefecture, Japan. The genome consisted of a closed loop that was 16,383 bp-long and included 13 protein coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.54%. The heavy (H)-strand was predicted to have 12 PCGs and 14 tRNA genes, while the light (L)-strand was predicted to contain one PCGs, eight tRNA genes, and two rRNA genes. All PCGs started with ATG. Stop codons were of two types: TAA for 11 genes (ND1, ND2, ND3, ND4L, ND5, ND6, COXI, COXII, COXIII, COB, ATP6 and ATP8) and TAG for two genes (ND3 and ND4). The molecular phylogenetic relationship based on the maximum likelihood method using 13 PCGs was consistent with some previous studies in which a closely relationship between P. riparius and P. jokahamae.
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- 2020
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16. Complete mitochondrial DNA sequence of the giant water bug Kirkaldyia deyrolli (Hemiptera: Belostomatidae).
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Juiki Nakasako, Hisashi Okuyama, Shinya Ohba, and Jun-ichi Takahashi
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next generation sequencing ,giant water bug ,kirkaldyia deyrolli ,endangered species ,Genetics ,QH426-470 - Abstract
Giant water bugs (genus Kirkaldyia and Lethocerus) are well known species from aquatic habitats throughout the world’s subtropical and tropical areas. Only one species of the Kirkaldyia deyrolli is distributed in Japan. K. deyrolli has been designated as second category rare species according Law for Conservation of Endangered Species of Wild Fauna and Flora in Japan, in 2019. We analyzed, for the first time, the complete mitochondrial genomes of the giant water bug K. deyrolli from Japan using next-generation sequencing. The mitochondrial genome was a circular and 15,579 bp molecule that included 13 protein-coding genes (PCGs), 22 tRNA genes, and two ribosomal RNA genes, along with one AT-rich control region. The AT content value was 69.55%. The heavy strand was predicted to have nine PCGs and 15 tRNA genes, whereas the light strand was predicted to contain four PCGs, seven tRNA genes, and two rRNA genes. Start codons were variable for all PCGs: four ATA, three ATC, four ATG, two ATT genes as the start codon. Stop codons were of two types: TAA for 12 genes and TAG for one gene. Incomplete stop codon T was identified. The molecular phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies, which predicted a sister relationship to the genus Lethocerus.
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- 2020
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17. Complete mitochondrial DNA sequence of the parasitic honey bee mite Varroa destructor (Mesostigmata: Varroidae)
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Reona Harada, Masato Yoshioka, Hisashi Okuyama, Manabu Kato, Stephen J. Martin, and Jun-ichi Takahashi
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varroa disease ,colony collapse ,apiculture ,beekeeping ,honey bee ,Genetics ,QH426-470 - Abstract
Varroa destructor is a parasite mite of the eastern honey bee Apis cerana, which is native to Asia. The European honey bee Apis mellifera was imported to Asia from Europe and the USA for apiculture in the 19th century. In a short period of time, V. destructor parasitized the artificially introduced honey bees. Varroa destructor was estimated to have spread around the world with A. mellifera when it was exported from Asia to locations worldwide about 50 years ago. The mitochondrial DNA of the parasitic honey bee mite V. destructor was analyzed using next-generation sequencing. The complete mitochondrial genome of V. destructor was identified as a 16,476-bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The heavy strand was predicted to have nine PCGs and 13 tRNA genes, whereas the light strand was predicted to contain four PCGs, nine tRNA genes, and two rRNA genes. All PCGs began with ATA as the start codon, except COIII and CytB, which had ATG as the start codon. Stop codons were of two types: TAA for eight genes and TAG for five genes. Molecular phylogenetic analysis revealed that V. destructor from Japan was genetically distant from that of France. A high base substitution rate of 2.82% was also confirmed between the complete mitochondrial DNA sequences of V. destructor from Japan and the USA, suggesting that one Varroa mite strain found in the USA is not from Japan.
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- 2020
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18. Complete mitochondrial DNA sequence of the alien hornet Vespa velutina (Insecta: Hymenoptera) invading Kyushu Island, Japan
- Author
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Ryoichi Takahashi, Hisashi Okuyama, Yûsuke N. Minoshima, and Jun-Ichi Takahashi
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asian hornet ,origin ,genetic distance ,alien species ,kyushu island ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the invasive Asian hornet Vespa velutina from Kyushu Island, Japan. The mitochondrial genome of V. velutina was identified as a circular molecule of 16,388 bp. We predicted that the genome contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with one A + T-rich control region. The average AT content is 81.68%. Molecular phylogenetic analysis using the 13 mitochondrial PCGs from 11 closely related taxa of Vespidae indicated that the V. velutina invading the Japanese Islands of Kyushu and Tsushima have a common origin.
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- 2018
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19. The complete mitochondrial genome of the bumblebee, Bombus hypocrita sapporensis (Insecta: Hymenoptera: Apidae) from Hokkaido Island, Japan
- Author
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Mana Nishimoto, Misuzu Umezawa, Hisashi Okuyama, Norikuni Kumano, Tetsuro Nomura, and Jun-ichi Takahashi
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bumblebee ,illumina sequencing ,subspecies ,bombus hypocrita ,hokkaido ,Genetics ,QH426-470 - Abstract
The complete is mitochondrial genome of the Japanese bumblebee Bombus hypocrita sapporensis from Hokkaido Island, Japan is analysed using next generation sequencing. The mitochondrial genome of B. h. sapporensis was observed to be a circular molecule of 15,835 bp. The average AT content in the B. h. sapporensis mitochondrial genome was 85.53%. It was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The PCGs had ATA, ATG, or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE, trnF, and trnS1. The molecular phylogenetic analysis indicated that the B. h. sapporensis from Hokkaido Island population was most similar to that of the geographically isolated B. h. sapporensis from Rebun Island.
- Published
- 2018
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20. A comparison of complete mitochondrial DNA sequences of Mnais costalis Selys, 1869 (Odonata: Calopterygidae) from three different populations (one allopatric and two sympatric)
- Author
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Hisashi Okuyama, Takuya Kiyoshi, Jun-Ichi Takahashi, and Yoshitaka Tsubaki
- Subjects
next generation sequence ,damselfly ,mnais costalis ,allopatric population ,sympatric population ,Genetics ,QH426-470 - Abstract
In Japan, two closely-related damselflies, Mnais costalis Selys, 1869 (Odonata: Calopterygidae) and M. pruinosa Selys-Longchamps (Odonata: Calopterygidae), 1853, coexist, and they exhibit geographic variations in wing color, body size, and habitat preference. In this study, we analyzed the complete mitochondrial genome of M. costalis from Saga Prefecture, Japan (sympatric populations that exhibit wing color polymorphism), and compared the genome with M. costalis that exhibit monomorphic orange wing color. The mitochondrial genome of M. costalis from Saga Prefecture was identified as a circular molecule of 15,488 bp, similar to that found in other M. costalis populations. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, along with one A + T-rich control region. Among the PCGs, ATP8 and ATP6, ATP6 and COIII, ND4 and ND4L, and ND6 and Cytb shared seven, one, seven, and one nucleotides, respectively. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one, while the termination codons TAA, TAG, TA, and T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.06%. From a phylogenetic analysis, the loss of wing color polymorphism in monomorphic sympatric populations is likely to occur with the coexistence of two Mnais species.
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- 2019
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21. Complete mitochondrial DNA sequence of the three-keeled pond turtle Mauremys reevesii (Reptilia: Testudines)
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Mari Asami, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
three-keeled pond turtle ,reeve’s pond turtle ,alien species ,next-generation sequencing ,extra base ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the three-keeled pond turtle Mauremys reevesii from Japan was analyzed using next-generation sequencing. The mitochondrial genome of M. reevesii was observed to be a circular molecule of 15,528 bp containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The average AT was found to be 61.11%. One extra base was present at the 174th position in the ND3 gene. Molecular phylogenetic analysis revealed that M. reevesii from Japan was few genetically distant from the geographically isolated M. reevesii from South Korea. This turtle might have been exported to Japan from the Korean Peninsula after the Middle Ages.
- Published
- 2019
- Full Text
- View/download PDF
22. Complete mitochondrial DNA sequence of the small hive beetle Aethina tumida (Insecta: Coleoptera) from Hawaii
- Author
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Jun-ichi Takahashi, Hisashi Okuyama, and Stephen J. Martin
- Subjects
next generation sequence ,small hive beetle ,aethina tumida ,hawaii ,beekeeping ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the small hive beetle Aethina tumida, a major honeybee pest that was accidentally transported to the Hawaii Islands, USA. The mitochondrial genome of A. tumida was identified as a 15,198 bp circular molecule containing 13 protein-coding genes, 22 tRNA genes, and two rRNA genes, along with one A + T-rich control region. The average AT content was found to be 76.2%. The heavy strand was predicted to have nine protein-coding and 14 tRNA genes; while the light strand was predicted to contain four protein-coding, eight tRNA, and two rRNA genes. Among the 13 PCGs, the initiation codon ATT was found in five, ATA in three, ATG in four, and TTG in one gene. Six PCGs used TAA as the stop codon, whereas three PCGs used TAG as the stop codon. Incomplete stop codon TA (COIII, ND5, and ND4) and T (COII) were identified. We found that the genetic distance between A. tumida from Hawaii and the beetles’ natural home South Africa, was small, indicating that the Hawaii population may have originated for the South Africa region.
- Published
- 2019
- Full Text
- View/download PDF
23. Complete mitochondrial DNA sequence of the endemic Japanese pond turtle Mauremys japonica (Reptilia: Testudines)
- Author
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Mari Asami, Hisashi Okuyama, and Jun-ichi Takahashi
- Subjects
next generation sequencing ,extra nucleotide ,near threatened species ,pond turtle ,endemic species ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the Japanese pond turtle Mauremys japonica from Japan was analyzed using next-generation sequencing. The mitochondrial genome of M. japonica was identified as a 16,443 bp circular molecule containing 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes, along with 1 A + T-rich control region; the average AT content was 62.82%. One extra base was present at the 174th position in the ND3 gene. The phylogenetic analyses of the complete mitochondrial DNA genes strongly supported the result obtained from the phylogenetic analysis of partial DNA sequences, grouping the monophyletic species within the genus Mauremys.
- Published
- 2019
- Full Text
- View/download PDF
24. The complete mitochondrial genome of the dusky brown-gray–colored honeybee, Apis mellifera (insecta: Hymenoptera: Apidae) of New Zealand
- Author
-
Mito Maeda, Ikumi Nakagawa, Mao Chikano, Hisashi Okuyama, Robert Murray, and Jun-Ichi Takahashi
- Subjects
dusky brown-gray honeybee ,carniolan ,apis mellifera carnica ,new zealand ,subspecies ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the dusky brown-gray–colored honeybee Apis mellifera, collected from North Island, New Zealand. We determined that the mitochondrial genome was a 16,336 bp and predicted 13 protein-coding genes (PCGs), 22 tRNA genes, and two rRNA genes. The start codon ATA was found in two genes, ATG in four genes, ATT in six genes, and ATC in one gene, whereas the termination codon TAA was observed in all PCGs. The non-coding regions of tRNA-Leu and COII were consistent with the C haplotype of A. mellifera carnica. Phylogenetic analysis suggests a close relationship with the European A. mellifera.
- Published
- 2018
- Full Text
- View/download PDF
25. The complete mitochondrial genome of the yellow coloured honeybee Apis mellifera (Insecta: Hymenoptera: Apidae) of New Zealand
- Author
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Ikumi Nakagawa, Mito Maeda, Mao Chikano, Hisashi Okuyama, Robert Murray, and Jun-Ichi Takahashi
- Subjects
western honeybee ,illumina sequencing ,apis mellifera ligustica ,new zealand ,subspecies ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the yellow coloured honeybee Apis mellifera from North Island, New Zealand was analyzed using next-generation sequencing. The mitochondrial genome was a 16,349bp circular molecule and was predicted to contain 13 protein-coding genes (PCGs), 22 tRNA genes and two rRNA genes. The initiation codon ATA was found in two genes, ATG in four genes, ATT in six genes, and ATC in one gene, while the termination codon TAA was observed in all the PCGs. Phylogenetic analysis using the sequence of 23 closely related taxa suggested a sister relationship with the Italian strain A. mellifera ligustica.
- Published
- 2018
- Full Text
- View/download PDF
26. The complete mitochondrial genome of a Buckfast bee, Apis mellifera (Insecta: Hymenoptera: Apidae) in Northern Ireland
- Author
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Hisashi Okuyama, John Hill, Stephen John Martin, and Jun-ichi Takahashi
- Subjects
buckfast bee ,origin ,ireland ,apis mellifera ligustica ,honeybee ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the ‘Buckfast bee’, Apis mellifera, collected from North Ireland, UK. It consisted of a circular molecule of 16,353 bp. The genome contained 13 protein-coding, 22 tRNA, and 2 rRNA genes, along with one A + T-rich control region. The average AT content was 84.9%. The genes ATP8 and ATP6 shared 19 nucleotides. A phylogenetic analysis, suggested that the matriline ‘Buckfast bee’ has remained most closely related to the A. mellifera ligustica race from which it originated in 1917, despite being cross-bred with many other A. mellifera races over the past 100 years.
- Published
- 2018
- Full Text
- View/download PDF
27. Origin of Terrestrial Bioorganic Homochirality and Symmetry Breaking in the Universe
- Author
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Jun-ichi Takahashi and Kensei Kobayashi
- Subjects
bioorganic homochirality ,circularly polarized photon ,spin-polarized lepton ,parity violation in the weak interaction ,Mathematics ,QA1-939 - Abstract
The origin of terrestrial bioorganic homochirality is one of the most important and unresolved problems in the study of chemical evolution prior to the origin of terrestrial life. One hypothesis advocated in the context of astrobiology is that polarized quantum radiation in space, such as circularly polarized photons or spin-polarized leptons, induced asymmetric chemical and physical conditions in the primitive interstellar media (the cosmic scenario). Another advocated hypothesis in the context of symmetry breaking in the universe is that the bioorganic asymmetry is intrinsically derived from the chiral asymmetric properties of elementary particles, that is, parity violation in the weak interaction (the intrinsic scenario). In this paper, the features of these two scenarios are discussed and approaches to validate them are reviewed.
- Published
- 2019
- Full Text
- View/download PDF
28. The complete mitochondrial DNA sequence of endemic honeybee Apis nuluensis (Insecta: Hymenoptera: Apidae) inhabiting Mount Kinabalu in Sabah Province, Borneo Island
- Author
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Jun-Ichi Takahashi, Salim Tingek, and Hisashi Okuyama
- Subjects
endemic species ,illumina sequencing ,borneo ,apis nuluensis ,honeybee ,Genetics ,QH426-470 - Abstract
The cavity-nesting honeybee Apis nuluensis inhabits only the highlands of Mount Kinabalu of Sabah, Borneo Island. The mitochondrial genome is a circular molecule of approximately 1.6 kb that includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content was 84.5%. The start codons ATC, ATG, and ATT were found in one, three, and nine genes, respectively, whereas the stop codon TAA was observed in all genes. The phylogenetic relationship, inferred using 13 PCGs, was consistent with that reported in previous studies that predicted a sister taxon relationship between A. nuluensis and A. cerana.
- Published
- 2017
- Full Text
- View/download PDF
29. The complete mitochondrial genome of the cavity-nesting honeybee, Apis cerana (Insecta: Hymenoptera: Apidae) from Borneo
- Author
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Hisashi Okuyama, Salim Tingek, and Jun-ichi Takahashi
- Subjects
asian honeybee ,illumina sequencing ,genetic distance ,apis cerana ,borneo ,Genetics ,QH426-470 - Abstract
The complete mitochondrial genome of the cavity-nesting honeybee Apis cerana from Sabah on Borneo Island was analyzed using next-generation sequencing. The mitochondrial genome of A. cerana was a circular molecule of 15,884 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. cerana mitochondrial genome was 84.4%. It was predicted to contain 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region.
- Published
- 2017
- Full Text
- View/download PDF
30. Complete mitochondrial DNA sequence of the tropical hornet Vespa affinis (Insecta, Hymenoptera)
- Author
-
Hisashi Okuyama, Stephen J. Martin, and Jun-Ichi Takahashi
- Subjects
hornet ,illumina sequencing ,repetitive sequence ,monogynous ,polygynous ,Genetics ,QH426-470 - Abstract
We analyzed the complete mitochondrial genome of the Asian tropical hornet Vespa affinis from Ishigaki Island, Japan. It consisted of a circular molecule with 19,109 bp, which is larger to other hornet species e.g. V. velutina. We predicted the genome contained 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region. The repetitive sequences were confirmed at multiple positions in the non-coding genes. The initiation codons ATA was found in one, ATG in seven, and ATT in five genes, while the termination codons TAA and TAG were observed 11 and two genes, respectively. The average AT content of the genome was 78.4%.
- Published
- 2017
- Full Text
- View/download PDF
31. Floating Chip Mounting System Driven by Repulsive Force of Permanent Magnets for Multiple On-Site SPR Immunoassay Measurements
- Author
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Emi Tamechika, Tsuneyuki Haga, Jun-ichi Takahashi, Suzuyo Inoue, Michiko Seyama, Tatsuya Tobita, Toru Miura, Yuzuru Iwasaki, and Tsutomu Horiuchi
- Subjects
SPR ,on-site ,portable ,immunoassay ,magnet ,Chemical technology ,TP1-1185 - Abstract
We have developed a measurement chip installation/removal mechanism for a surface plasmon resonance (SPR) immunoassay analysis instrument designed for frequent testing, which requires a rapid and easy technique for changing chips. The key components of the mechanism are refractive index matching gel coated on the rear of the SPR chip and a float that presses the chip down. The refractive index matching gel made it possible to optically couple the chip and the prism of the SPR instrument easily via elastic deformation with no air bubbles. The float has an autonomous attitude control function that keeps the chip parallel in relation to the SPR instrument by employing the repulsive force of permanent magnets between the float and a float guide located in the SPR instrument. This function is realized by balancing the upward elastic force of the gel and the downward force of the float, which experiences a leveling force from the float guide. This system makes it possible to start an SPR measurement immediately after chip installation and to remove the chip immediately after the measurement with a simple and easy method that does not require any fine adjustment. Our sensor chip, which we installed using this mounting system, successfully performed an immunoassay measurement on a model antigen (spiked human-IgG) in a model real sample (non-homogenized milk) that included many kinds of interfering foreign substances without any sample pre-treatment. The ease of the chip installation/removal operation and simple measurement procedure are suitable for frequent on-site agricultural, environmental and medical testing.
- Published
- 2012
- Full Text
- View/download PDF
32. Passive Fluidic Chip Composed of Integrated Vertical Capillary Tubes Developed for On-Site SPR Immunoassay Analysis Targeting Real Samples
- Author
-
Tsuneyuki Haga, Emi Tamechika, Jun-ichi Takahashi, Suzuyo Inoue, Michiko Seyama, Toru Miura, Yuzuru Iwasaki, and Tsutomu Horiuchi
- Subjects
SPR ,immunoassay ,raw sample ,on-site ,passive pump ,microfluidics ,Chemical technology ,TP1-1185 - Abstract
We have successfully developed a surface plasmon resonance (SPR) measurement system for the on-site immunoassay of real samples. The system is composed of a portable SPR instrument (290 mm(W) x 160 mm(D) x 120 mm(H)) and a microfluidic immunoassay chip (16 mm(W) x 16 mm(D) x 4 mm(H)) that needs no external pump system. An integrated vertical capillary tube functions as a large volume (150 μL ) passive pump and a waste reservoir that has sufficient capacity for several refill operations. An immunoassay was carried out that employed the direct injection of a buffer and a test sample in sequence into a microfluidic chip that included 9 antibody bands and 10 reference reagent bands immobilized in the flow channel. By subtracting a reliable averaged reference sensorgram from the antibody, we effectively reduced the influence of the non-specific binding, and then our chip successfully detected the specific binding of spiked IgG in non-homogeneous milk. IgG is a model antigen that is certain not to be present in non-homogeneous milk, and non-homogeneous milk is a model of real sample that includes many interfering foreign substances that induce non-specific binding. The direct injection of a real sample with no pretreatment enabled us to complete the entire immunoassay in several minutes. This ease of operation and short measuring time are acceptable for on-site agricultural, environmentaland medical testing.
- Published
- 2012
- Full Text
- View/download PDF
33. Photostability of Isovaline and its Precursor 5-Ethyl-5-methylhydantoin Exposed to Simulated Space Radiations
- Author
-
Takeo Kaneko, Kensei Kobayashi, Yumiko Obayashi, Yukinori Kawamoto, Jun-ichi Takahashi, and Palash K. Sarker
- Subjects
isovaline ,space radiation ,ultraviolet light ,gamma ray ,photolysis ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Aqueous solutions of isovaline and its precursor molecule, 5-ethyl-5-methylhydantoin, were irradiated with ultraviolet and γ-ray photons, to evaluate their structural stability against space radiation. The degree of photolysis was measured and irradiation products were identified using chiral, reversed-phase and ion-exchange high-performance liquid chromatography. The experimental results show that the degree of photolysis of 5-ethyl-5-methylhydantoin is more significant than that of isovaline under ultraviolet light irradiation, while the results under γ-ray irradiation are the opposite. As the products of isovaline photolysis, aspartic acid, serine, glutamic acid and alanine were dominantly detected.
- Published
- 2012
- Full Text
- View/download PDF
34. Complete mitochondrial genome of the Japanese bumblebee, Bombus hypocrita hypocrita (Insecta: Hymenoptera: Apidae)
- Author
-
Mana Nishimoto, Hisashi Okuyama, Takuya Kiyoshi, Tetsuro Nomura, and Jun-ichi Takahashi
- Subjects
illumina’s next seq 500 ,bumblebee ,genetic diversity ,conservation ,Genetics ,QH426-470 - Abstract
In the present report, we describe the complete mitochondrial genome of the common bumblebee, Bombus hypocrita hypocrita, from the Otome Plateau, in Yamanashi Prefecture, Japan. The mitochondrial genome of B. h. hypocrita is a circular molecule of 15,795 bp. It contains 13 protein-coding, 22 tRNA and two rDNA genes. The protein-coding genes had ATA, ATG or ATT as the initiation codon and were terminated by the typical stop codon TAA, except for ND4 and Cytb. All the tRNA genes typically formed a cloverleaf secondary structure, except for trnE and trnS1.
- Published
- 2017
- Full Text
- View/download PDF
35. The complete mitochondrial genome of the cavity-nesting honeybee, Apis koschevnikovi (Insecta: Hymenoptera: Apidae)
- Author
-
Takeshi Wakamiya, Salim Tingek, Hisashi Okuyama, Takuya Kiyoshi, and Jun-ichi Takahashi
- Subjects
asian honeybee ,illumina sequencing ,conservation ,borneo ,apis koschevnikovi ,Genetics ,QH426-470 - Abstract
In this study, we analyzed the complete mitochondrial genome of the cavity-nesting honeybee, A. koschevnikovi. The mitochondrial genome of A. koschevnikovi was observed to be a circular molecule of 15,278 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. koschevnikovi mitochondrial genome was 84%. It was predicted to contain 13 protein-coding, 24 tRNA and two rRNA genes, along with one A + T-rich control region, besides three tRNA-Met repeats.
- Published
- 2017
- Full Text
- View/download PDF
36. Complete mitochondrial DNA sequence of the invasive hornet Vespa velutina (Insecta, Hymenoptera) found in Japan
- Author
-
Ryoichi Takahashi, Hisashi Okuyama, Takuya Kiyoshi, and Jun-ichi Takahashi
- Subjects
asian hornet ,illumina sequencing ,genetic distance ,alien species ,invasive species ,Genetics ,QH426-470 - Abstract
In this study, we analyzed the complete mitochondrial genome of the invasive Asian hornet Vespa velutina from Japan. The mitochondrial genome of V. velutina was identified as a circular molecule of 16,765 bp, similar to that in other hornet species. It was predicted to contain 13 protein-coding, 20 tRNA, and two rRNA genes, along with one A + T-rich control region. The initiation codons ATC was found in one, ATG in four, ATT in five, and ATA in three genes, while TAA was the termination codon in all these genes. The average AT content of 13 protein-coding was 82%.
- Published
- 2017
- Full Text
- View/download PDF
37. Chirality Emergence in Thin Solid Films of Amino Acids by Polarized Light from Synchrotron Radiation and Free Electron Laser
- Author
-
Mashahiro Adachi, Hajime Mita, Kensei Kobayashi, Takeo Kaneko, Yuko Ueno, Michiko Seyama, Hiroyuki Shinojima, Jun-ichi Takahashi, Masahito Hosaka, and Masahiro Katoh
- Subjects
chirality ,circularly polarized light ,amino acids ,solid films ,synchrotron radiation ,free electron laser ,origin of terrestrial homochirality ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior to the existence of terrestrial life (Cosmic Scenario). To experimentally introduce chiral structure into racemic films of amino acids (alanine, phenylalanine, isovaline, etc.), we irradiated them with linearly polarized light (LPL) from synchrotron radiation and circularly polarized light (CPL) from a free electron laser. After the irradiation, we evaluated optical anisotropy by measuring the circular dichroism (CD) spectra and verified that new Cotton peaks appeared at almost the same peak position as those of the corresponding non-racemic amino acid films. With LPL irradiation, two-dimensional anisotropic structure expressed as linear dichroism and/or linear birefringence was introduced into the racemic films. With CPL irradiation, the signs of the Cotton peaks exhibit symmetrical structure corresponding to the direction of CPL rotation. This indicates that some kinds of chiral structure were introduced into the racemic film. The CD spectra after CPL irradiation suggest the chiral structure should be derived from not only preferential photolysis but also from photolysis-induced molecular structural change. These results suggest that circularly polarized light sources in space could be associated with the origin of terrestrial homochirality; that is, they would be effective asymmetric exciting sources introducing chiral structures into bio-organic molecules or complex organic compounds.
- Published
- 2009
- Full Text
- View/download PDF
38. Distinguishing between raw honey from Japanese and European honey bees using loop-mediated isothermal amplification
- Author
-
Jun-ichi Takahashi, Mito Maeda, Ikumi Nakagawa, Mao Chikano, and Yuri Shinmura
- Subjects
Food Science - Published
- 2022
39. Power Series Template Matching Model for Pitch Perception
- Author
-
Jun-ichi Takahashi
- Abstract
The problem of pitch perception has been the subject of a long debate between place theory and time theory. Here, we propose a Power Series Template (PoST) model to answer the problem of how and why pitch perception comes about. The sensitive measurement of acoustic signals requires efficient Sound Amplification (SA), which inevitably accompanies mode coupling due to the perturbative non-linearities. Under reinforcement learning for Sound Localization (SL) with the second- and third-order modes as default teacher signals, a chain of coincidence is generated. After learning in SL is completed, two power series templates of 2nand 3mare generated, and the 2f1−f2coupling of the elements contained therein fills the blanks of matchable harmonics up to N=10 in the template, providing the well-known harmonic template. When complex tones containing multiple harmonics are input into the trained network, two power series are evoked from each harmonic, and from their intersection, the brain acquires the fundamental of the complex tone as the pitch. Based on this template model, consistent explanations are given for the problems of missing fundamental, pitch shift, pitch and chroma, and resolvability jump without the help of time theory.
- Published
- 2023
40. Genetic diversity analysis of Apis dorsata (hymenoptera: apidae) based on cytochrome C oxidase subunit I gene sequences
- Author
-
Nurdjannah Jane Niode, Aryani Adji, Jimmy Rimbing, Max Tulung, Jun Ichi Takahashi, Rinaldi Idroes, and Trina Ekawati Tallei
- Published
- 2023
41. Composition of Free Amino Acids in Fermented Honey, an Untapped Resource from Japanese Honeybees
- Author
-
Jun-ichi Takahashi
- Subjects
General Medicine - Published
- 2022
42. Pattern analysis of the combustions of various copper concentrate tablets using high-speed microscopy and video-based deep learning
- Author
-
Shungo Natsui, Yuko Goto, Jun-ichi Takahashi, and Hiroshi Nogami
- Subjects
Applied Mathematics ,General Chemical Engineering ,General Chemistry ,Industrial and Manufacturing Engineering - Published
- 2023
43. First Evidence of Presence of Varroa underwoodi Mites on Native Apis cerana Colonies in Primorsky Territory of Russia Based on COX1 Gene
- Author
-
A. G. Nikolenko, Maxim Yu. Proshchalykin, Hyung Wook Kwon, Arkady S. Lelej, R. A. Ilyasov, Jun-ichi Takahashi, and Myeong-lyeol Lee
- Subjects
0106 biological sciences ,0301 basic medicine ,haplotype ,Range (biology) ,Zoology ,Plant Science ,Subspecies ,01 natural sciences ,Intraspecific competition ,cox1 gene ,03 medical and health sciences ,Genus ,Apis cerana ,varroa underwoodi ,biology ,Honey bee ,biology.organism_classification ,Genetic divergence ,010602 entomology ,apis cerana ,030104 developmental biology ,QL1-991 ,Insect Science ,range ,Varroa ,primorsky territory of russia - Abstract
The species of genus Varroa mites parasitize on the honey bees of genus Apis. Unlike the well-studied V. destructor and V. jacobsoni mites, V. underwoodi remain less known. According to English language publications, the proven V. underwoodi distribution area of A. cerana colonies covers Nepal, South Korea, Indonesia, Papua New Guinea, Vietnam and China, but not Russia even though it had been described morphometrically in Russian language publications in Russia's Primorsky Territory. According to Vavilov's law (1920) of a homologous series, all the species of V. underwoodi, V. destructor and V. jacobsoni have the ability to spill over onto new hosts. Thus, V. underwoodi is a potential parasite of A. mellifera that should be carefully studied. In this study, V. underwoodi mites in colonies of honey bee subspecies A. c. ussuriensis native to Russia's Primorsky Territory are first proven using both morphometry and mitochondrial COX1 gene sequencing. The genetic divergence and p-distances between V. underwoodi and other Varroa species ranged from 7 to 10% and from 0.072 to 0.099, respectively, which matched the intraspecific level of differences. Two identical northernmost V. underwoodi samples from Russia's Primorsky Territory and China's Jilin province with GenBank accession number MH205176 were assigned as COX1 haplotype China 1 MH205176. The first discovery of V. underwoodi in the Primorsky Territory in northern Asia outlined the northern border of its range.
- Published
- 2021
44. Phylogenetic Relationships among Honey Bee Subspecies Apis mellifera caucasia and Apis mellifera carpathica Based on the Sequences of the Mitochondrial Genome
- Author
-
J. H. Park, Kil Won Kim, A. G. Nikolenko, Myeong-lyeol Lee, G. Y. Han, Jun-ichi Takahashi, R. A. Ilyasov, and Hyung Wook Kwon
- Subjects
Genetics ,Mitochondrial DNA ,education.field_of_study ,biology ,Haplotype ,Population ,food and beverages ,Honey bee ,Subspecies ,biology.organism_classification ,Carpathica ,Intergenic region ,Gene pool ,education - Abstract
The sequences of the complete mitochondrial genome of the honey bee Apis mellifera L. subspecies Apis mellifera caucasia Pollmann, 1889 (AP018404, 16 341 bp) and Apis mellifera carpathica Foti et al., 1965 (AP018403, 16 336 bp) are sequenced for the first time. Mitochondrial DNA (mtDNA) of both subspecies contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one AT-rich regulatory region. The ratio of transitions to transversions (tr/tv) in complete mtDNA between A. m. caucasia and A. m. carpathica was 2.05, which reflects the formation of adaptations to changing environmental conditions. Genes with the highest GC content—COX1 (24%), COX2 (19.6%), CYTB (19.1%), COX3 (17.2%), and ND1 (17.2%)—can be highly polymorphic and can be used in phylogenetic and population studies of bees. The majority of mtDNA genes of both subspecies are located on the heavy strand (9 protein-coding genes and 14 tRNA genes), while other genes (4 protein-coding genes, 2 rRNA genes, and 8 tRNA genes) are located on the light strand. Cluster analysis of the complete mtDNA sequence and assessment of the structure of the tRNA-Leu(UUR)–COX2 intergenic region with a single Q element 192 bp in length showed that both subspecies A. m. caucasia and A. m. carpathica are representatives of the line C with haplotypes C2 and C2j, respectively. Honey bee subspecies A. m. caucasia and A. m. carpathica can be differentiated from each other by 34 unique SNPs in 11 mtDNA genes and the XbaI restriction marker in the ND5 gene. These genetic markers can contribute to the preservation of purebred gene pools of honey bee subspecies A. m. caucasia and A. m. carpathica within their natural range.
- Published
- 2021
45. Tracing the invasion characteristics of the yellow-legged hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), in Korea using newly detected variable mitochondrial DNA sequences
- Author
-
Yong Soo Choi, Iksoo Kim, Jun-ichi Takahashi, Yong Hun Jo, Min Jee Kim, Jeong Sun Park, Jun Seong Jeong, and Keon Hee Lee
- Subjects
0106 biological sciences ,0301 basic medicine ,Vespa velutina ,Genetic diversity ,Mitochondrial DNA ,education.field_of_study ,Vespidae ,Velutina ,Haplotype ,Population ,Zoology ,Hymenoptera ,Biology ,biology.organism_classification ,01 natural sciences ,010602 entomology ,03 medical and health sciences ,030104 developmental biology ,Insect Science ,education - Abstract
The yellow-legged hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), invaded South Korea in 2003 through Busan metropolitan city, which is located in the southeast region of the country. Previous studies aiming to trace the origin of V. velutina in Korea used a portion of mitochondrial (mt) COI and detected a single haplotype common to the site of origin. However, no subsequent study on invasive dynamics such as additional entry and/or another site of entry has been performed. In this study, segments of mt COI, CytB, and lrRNA were sequenced from 238 individuals collected in 11 Korean and two Japanese localities, but no variation in each gene was observed. Thus, we developed two intergenic spacer (IGS) sequences from the publicly available mt genome of V. velutina, which provided substantially increased variability (i.e., 19 haplotypes with 1.74% maximum sequence divergence in 1,129–1,146-bp-long concatenated sequences). Population genetic analyses using the concatenated sequences unexpectedly provided higher genetic diversity estimates in the northwest and southwest regions, both of which also harbor international cargo ports, than in the southeast region, in which Busan is located. Furthermore, this genetic result was roughly concordant with our questionnaire survey demonstrating that V. velutina was observed in apiaries located in the northwest and southwest regions up to 2012, when there was no reported prevalent distribution of the hornet beyond the southeast region. These results collectively suggest that the northwest and southwest regions of Korea are additional sites of V. velutina entry to the country, independent from the southeast region origin.
- Published
- 2021
46. Genetic Properties and Evolution of Asian Honey Bee Apis cerana ussuriensis from Primorsky Krai, Russia
- Author
-
Myeong-lyeol Lee, Arkady S. Lelej, Hyung Wook Kwon, Jun-ichi Takahashi, J. H. Park, G. Y. Han, Kil Won Kim, R. A. Ilyasov, Maxim Yu. Proshchalykin, and A. G. Nikolenko
- Subjects
0106 biological sciences ,0303 health sciences ,Beekeeping ,Mitochondrial DNA ,biology ,Zoology ,Honey bee ,Subspecies ,biology.organism_classification ,01 natural sciences ,Japonica ,Genetic divergence ,03 medical and health sciences ,Genetic distance ,Genetics ,Apis cerana ,030304 developmental biology ,010606 plant biology & botany - Abstract
Apis cerana ussuriensis Ilyasov et al., 2019 is the northernmost subspecies of the Asian honey bee A. cerana Fabricius, 1793, common in the forests of Primorsky krai and Khabarovsk krai as far as 47°54′ N. Genetic studies of this subspecies are of great interest for science and apiculture, since all its adaptive traits were formed under the influence of the natural environment without human interference. We sequenced and annotated the complete mitochondrial DNA (mtDNA) sequences of bees of subspecies Apis cerana ussuriensis Ilyasov et al., 2019 (GenBank accession number AP018450) from Primorsky krai and Apis cerana koreana Ilyasov et al., 2019 (AP018431) from South Korea, as well as six exons of the nuclear DNA (nDNA) vitellogenin VG E2–E7 gene of bee subspecies A. c. ussuriensis, A. c. koreana, A. c. japonica Radoszkowski, 1887, A. c. cerana, and A. c. indica Fabricius, 1798. Cluster analysis of the mtDNA and the nDNA VG gene sequences showed the division of bees into two groups, the southern subspecies A. c. indica and the northern subspecies A. c. ussuriensis, A. c. koreana, A. c. japonica, and A. c. cerana. On the basis of the genetic divergence, we showed that subspecies A. c. ussuriensis was genetically closer to subspecies A. c. japonica, A. c. koreana, and A. c. cerana than to subspecies A. c. indica. Values of genetic divergence (0.80–8.00%) and Jukes–Cantor genetic distance (0.005–0.100) for mtDNA and nDNA VG gene between subspecies A. c. ussuriensis, A. c. koreana, A. c. japonica, A. c. cerana, and A. c. indica are within the range of intraspecific differences between insect subspecies. The estimated time of the emergence of the A. cerana subspecies is from two to one million years ago.
- Published
- 2021
47. A revision of subspecies structure of western honey bee Apis mellifera
- Author
-
Jun-ichi Takahashi, Hyung Wook Kwon, R. A. Ilyasov, Myeong-lyeol Lee, and A. G. Nikolenko
- Subjects
0106 biological sciences ,0301 basic medicine ,Honey bee ,animal structures ,Population structure ,Zoology ,Review ,Biology ,Subspecies ,01 natural sciences ,03 medical and health sciences ,lcsh:QH301-705.5 ,Taxonomy ,digestive, oral, and skin physiology ,fungi ,food and beverages ,Western asia ,Western honey bee ,030104 developmental biology ,lcsh:Biology (General) ,behavior and behavior mechanisms ,Taxonomy (biology) ,Apis mellifera ,General Agricultural and Biological Sciences ,010606 plant biology & botany - Abstract
The taxonomy of honey bee A. mellifera contains a lot of issues due to the specificity of population structure, features of biology and resolutions of honey bee subspecies discrimination methods. There are a lot of transition zones between ranges of subspecies which led to the gradual changes of characteristics among neighbor subspecies. The modern taxonomic pattern of honey bee Apis mellifera is given in this paper. Thirty-three distinct honey bee subspecies are distributed across all Africa (11 subspecies), Western Asia and the Middle East (9 subspecies), and Europe (13 subspecies). All honey bee subspecies are subdivided into 5 evolutionary lineages: lineage A (10 subspecies) and its sublineage Z (3 subspecies), lineage M (3 subspecies), lineage C (10 subspecies), lineage O (3 subspecies), lineage Y (1 subspecies), lineage C or O (3 subspecies).
- Published
- 2020
48. PIXE
- Author
-
Jun-ichi Takahashi
- Published
- 2022
49. Category Theory and Organic Electronics
- Author
-
Jun-ichi Takahashi
- Subjects
History ,Polymers and Plastics ,General Physics and Astronomy ,Business and International Management ,Industrial and Manufacturing Engineering - Published
- 2022
50. Passive Fluidic Chip Composed of Integrated Vertical Capillary Tubes Developed for On-Site SPR Immunoassay Analysis Targeting Real Samples.
- Author
-
Tsutomu Horiuchi, Toru Miura, Yuzuru Iwasaki, Michiko Seyama, Suzuyo Inoue, Jun-ichi Takahashi, Tsuneyuki Haga, and Emi Tamechika
- Published
- 2012
- Full Text
- View/download PDF
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