Nishi-Tokyo-shi, Japan
Nishi-Tokyo-shi, Japan

The Tokyo University of Agriculture , abbreviated as Nodai or Tokyo nodai , is a private university which treats agriculture in Japan.The campus is in three places, Setagaya, Atsugi, and Okhotsk . Wikipedia.


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Yoshizaki T.,Toyo University | Kimira Y.,Josai University | Mano H.,Josai University | Ota M.,Toyo University | And 3 more authors.
Journal of Nutritional Science and Vitaminology | Year: 2017

There has been little epidemiological evidence that has comprehensively clarified whether alterations in lifestyle, such as sleep quality and dietary intake, explain changes in the skin condition of healthy young adults. Therefore, the aim of our study was to elucidate the association between skin condition and lifestyle behaviors such as diet and sleep, after statistically controlling confounding factors. The subjects were 54 participants who were aged 20–32 y, and who attended college in the Kanto region (in Japan). Transepidermal water loss (TEWL) was obtained by putting a probe on the skin surface based on the European Society of Contact Dermatitis guidelines for TEWL measurements. Self-administered questionnaires on demographic characteristics, dietary habits, and health status, such as sleep condition, depression, and fatigue, were handed to participants on the day of measurement. We found that lower sleep efficiency was significantly associated with higher TEWL (p=0.023), while other demographic factors, dietary intakes, and eating behaviors were not (p>0.05). This significant association remained unchanged after controlling for confounding variables, such as sex, BMI, and dietary intake. Our findings may have important implications in the development of valuable health strategies that may suggest behavior modifications for young to middle-aged men and women. © 2017, Center for Academic Publications Japan. All rights reserved.


Azuma N.,Hokkaido University | Zaslavskaya N.I.,RAS A.V. Zhirmunsky Institute of Marine Biology | Yamazaki T.,Shellfish Museum of Rankoshi | Nobetsu T.,Shiretoko Nature Foundation | Chiba S.,Tokyo University of Agriculture
Genetica | Year: 2017

We investigated genetic diversity and population structure of the Sitka periwinkle Littorina sitkana along the coastlines of the northwestern Pacific (NWP) to evaluate the possibility of trans-Pacific colonization of this species from the NWP to the northeastern Pacific (NEP) after the Last Glacial Maximum. We sampled L. sitkana from 32 populations in the NWP, and sequenced a region of the mitochondrial cytochrome b oxidase gene for population genetic analyses. The results were compared with those of previous reports from the NEP. The genetic diversity of L. sitkana was much higher in the NWP than in the NEP. Genetic connectivity between the NWP and NEP populations was indicated by an extremely abundant haplotype in the NEP that was also present in eastern Hokkaido and the Kuril Islands. To confirm these results, we compared sequences of the longest intron of the aminopeptidase N gene (APN54) in the nuclear genome in four populations of L. sitkana in the NWP with previous results from the NEP. Again, much higher genetic diversity was found in the NWP than in the NEP and genetic connectivity was supported between the Kuril Islands and the NEP. These results imply postglacial colonization of this species from the NWP to the NEP, probably along the Kuril and Aleutian Island chains. This study is the first report of possible trans-Pacific postglacial colonization of a direct-developing gastropod, inferred from genetic data. © 2017 Springer International Publishing Switzerland


Takeo S.,Tokyo University of Agriculture | Kimura K.,Okayama University | Shirasuna K.,Tokyo University of Agriculture | Kuwayama T.,Tokyo University of Agriculture | Iwata H.,Tokyo University of Agriculture
Reproduction, Fertility and Development | Year: 2017

Maternal age affects the quality of oocytes. The present study examined whether follicular fluid (FF) is a casual factor for age-Associated decline in oocyte quality. First, we measured the concentration of advanced glycation end-products (AGE) in FF derived from young (21-45 months; Young-FF) and aged (≥120 months; Aged-FF) cows and found significantly higher concentrations of AGE in Aged-FF than Young-FF. Second, oocytes were collected from ovaries of young or aged cows and cultured in maturation medium containing 10% FF derived from young or aged cows. Regardless of oocyte origin, Aged-FF accelerated nuclear maturation progression and gap junction closure between oocytes and cumulus cells, increased reactive oxygen species (ROS) content and the rate of abnormal fertilisation of oocytes and decreased blastulation rate compared with Young-FF. Furthermore, supplementation of maturation medium with AGE induced similar age-Associated events in oocytes derived from young cows, in that AGE accelerated the progression of nuclear maturation, increased ROS content in oocytes, increased the rate of abnormal fertilisation and decreased blastulation rate. In conclusion, maternal aging increased the concentration of AGE in FF, and both AGE and Aged-FF accelerated nuclear maturation and reduced the developmental competence of oocytes. © CSIRO 2017.


Shimomura K.,Tokyo University of Agriculture | Shimomura K.,Earth Biochemical Co. | Matsui S.,Tokyo University of Agriculture | Ohsawa K.,Tokyo University of Agriculture | Yajima S.,Tokyo University of Agriculture
Chemoecology | Year: 2017

Callosobruchus seed beetles (Coleoptera: Chrysomelidae: Bruchinae) are pests of stored legumes in tropical and subtropical regions. The cuticular surfaces of female Callosobruchus seed beetles contain a contact sex pheromone, which elicits copulatory behavior in congeneric males. Asymmetric cross-copulatory behavior was observed between C. maculatus and C. rhodesianus despite considerable differences in the structures of their contact sex pheromones. C. maculatus uses dicarboxylic acid, whereas C. rhodesianus uses two ketone compounds in conjunction with similar synergistic cuticular hydrocarbon blends in both cases. Male C. maculatus exhibited copulatory behavior with females of both C. maculatus and C. rhodesianus, but male C. rhodesianus mated only with congeneric females. To establish the reasons for the asymmetric cross-copulatory behavior of C. maculatus, we tried to identify the heterospecific mate-eliciting compounds in the cuticles collected from virgin C. rhodesianus females. The compounds were fractionated using acid-base partitioning and chromatography techniques and then assayed for their ability to elicit male copulatory activity. Gas chromatography–mass spectrometry (GC–MS) analysis of the active acidic fraction revealed the presence of three dicarboxylic acids: 2-methylsuberic acid (2-methyloctanedioic acid) (1), 3-methylsuberic acid (3-methyloctanedioic acid) (2), and nonanedioic acid (3). The synergistic effect was compared using synthetic standards and natural hydrocarbons. When the compounds were combined with the natural hydrocarbons, compounds 1 and 2 elicited significant copulatory activity in male C. maculatus. In contrast, relative to the effect of natural hydrocarbons alone, compound 3 did not exhibit significant copulatory activity when combined with natural hydrocarbons. The results demonstrated that the asymmetric cross-copulatory behavior of C. maculatus is induced by the presence of contact sex pheromone analogs on the cuticular surface of female C. rhodesianus. In combination with previous reports, although a saltational evolution was hypothesized for the contact sex pheromones of C. rhodesianus, this species continues to produce dicarboxylic acids functioning as pheromones that are structurally similar to those secreted by closely related species. © 2017, Springer International Publishing.


Kiyoshi K.,Tokyo University of Agriculture | Kawashima S.,Tokyo University of Agriculture | Nobuki K.,Tokyo University of Agriculture | Kadokura T.,Tokyo University of Agriculture | And 3 more authors.
Applied and Environmental Microbiology | Year: 2017

We have developed butanol-producing consolidated bioprocessing from cellulosic substrates through coculture of cellulolytic clostridia and butanol-producing Clostridium saccharoperbutylacetonicum strain N1-4. However, the butanol fermentation by strain N1-4 (which has an optimal growth temperature of 30°C) is sensitive to the higher cultivation temperature of 37°C; the nature of this deleterious effect remains unclear. Comparison of the intracellular metabolites of strain N1-4 cultivated at 30°C and 37°C revealed decreased levels of multiple primary metabolites (notably including nucleic acids and cofactors) during growth at the higher temperature. Supplementation of the culture medium with 250 mg/liter adenine enhanced both cell growth (with the optical density at 600 nm increasing from 4.3 to 10.2) and butanol production (increasing from 3.9 g/liter to 9.6 g/liter) at 37°C, compared to those obtained without adenine supplementation, such that the supplemented 37°C culture exhibited growth and butanol production approaching those observed at 30°C in the absence of adenine supplementation. These improved properties were based on the maintenance of cell viability. We further showed that adenine supplementation enhanced cell viability during growth at 37°C by maintaining ATP levels and inhibiting spore formation. This work represents the first demonstration (to our knowledge) of the importance of adenine-related metabolism for clostridial butanol production, suggesting a new means of enhancing target pathways based on metabolite levels. © 2017 American Society for Microbiology.


Takahata K.,Tokyo University of Agriculture | Miura H.,Tokyo University of Agriculture
the horticulture journal | Year: 2017

In the tomato (Solanum lycopersicum), the position of the inflorescence on the stem is known to affect the number of days to first anthesis and has commonly been characterized by the leaf-number (ordinal number from the oldest leaf) of the leaf just below the inflorescence (LEAF-BI) only by the appearance after extension of the stem near the inflorescence. Some examples showing that this evaluation was not suitable were observed by the authors. To confirm the reproducibility of the observation, experiments were conducted in which 4 cultivars were sown in a greenhouse 12 times from Oct. 2008 to Aug. 2010. Based on the vertical positional relationship between the base of the first, second, or third inflorescence and the base of the last initiated leaf before inflorescence primordium on the growing point (L-LEAF, the true guide for determining the inflorescence position), the L-LEAFs of 'My Lock' plants in all growth periods and 'House Momotaro', 'Momotaro 8', and 'Super Fast' plants in the non-high-temperature growth periods were always just above the inflorescences, that is, the LEAF-BIs were always the leaves below the L-LEAFs. In contrast, the L-LEAFs of all cultivars except ‘My Lock’ in the high-temperature growth periods were often just below the inflorescence, that is, the LEAF-BIs were often the L-LEAFs. Comparing the leaf-number of LEAF-BI and that of L-LEAF demonstrated that the former often overestimated the inflorescence positon among growth periods and cultivars. In temperature treatments with 'House Momotaro', such a positional switch of the L-LEAF was reproducible. External observation indicated that the stem on the L-LEAF side and the stem on the inflorescence side extended non-uniformly and the position of the L-LEAF was determined by which side extended faster. Collectively, the LEAF-BI is not a leaf identified morphogenetically, and to identify the position of the inflorescence, the leaf-number of L-LEAF, not LEAF-BI, should be used. © 2017, The Japanese Society for Horticultural Science. All rights reserved.


Kudo K.,University of Tokyo | Tsunekawa N.,Nihon University | Ogawa H.,Tokyo University of Agriculture | Endo H.,University of Tokyo
Journal of Poultry Science | Year: 2017

This study aims to understand the relationships among morphological characteristics, their functional roles, and breeder preferences in Japanese native fowls. We analyzed and compared the shapes and sizes of the skeletal forelimb, pectoral girdle, and sternum among six breeds: Chabo, Oh-Shamo, Onagadori, Shokoku, Tosajidori, and Totenko. Because skeletal forelimb, pectoral girdle, and sternum are one of the bases for composing body appearance and for movement of birds such as flapping, we treated those skeletons. All measurements of size were smaller in Chabo than those in other breeds except Tosajidori. The largest measurement values of all parameters were observed in Oh-Shamo. The largest measurement values were observed in all measurements of Oh-Shamo. Short and wide forelimb bones and a short coracoid were observed in Chabo. Oh-Shamo was equipped with a wide sternum and a widely articulated coracoid. Shokoku and Totenko possessed longer bones that constitute the thoracic cavity. We suggest that the small bone size in ornamental fowls contributes toward a cute appearance and that the large bone size of fighting fowls is correlated with their masculinity and aggressiveness. The short forelimb bones, wide articulation, and corpus of forelimb bones in Chabo create a round and soft body silhouette. The observed short coracoid prevents Chabo from dragging its body on the ground while walking. The wide sternum and articulation of the coracoid observed in Oh-Shamo are considered to contribute to the ability to pounce on an opponent by flapping during a fight. The wide sternum of Oh-Shamo is considered to affect its body outline, producing a strong, masculine physical appearance. We also suggest that the characteristics observed in Shokoku and Totenko create a space for the vocal organs, such as clavicle air sacs. We suggest that the observed morphological characteristics underlie the function and breeder preferences of each breed. © 2017, Japan Poultry Science Association.


Ogawa S.,University of Tokyo | Kawahara-Miki R.,Tokyo University of Agriculture | Miyamoto K.,Teikyo University | Yamane H.,Teikyo University | And 3 more authors.
Biochemical and Biophysical Research Communications | Year: 2017

Jasmonic acid (JA) plays central roles in various events in plants, especially defence against pathogens and insects. The basic helix-loop-helix (bHLH) transcription factor MYC2 has attracted attention as a master regulator of JA signalling in dicotyledonous plants. However, how MYC2 functions in monocotyledonous plants, including agriculturally important crops such as cultivated rice, has been poorly understood. To elucidate the comprehensive effects of rice MYC2 (OsMYC2) on the JA-inducible transcriptional modifications, we performed RNA-sequencing by using OsMYC2-knockdown plants (osmyc2RNAi). In osmyc2RNAi, JA-inducible expression of many defence-related genes, for example chitinases and proteinase inhibitors, was compromised. Decrease in JA-dependent activation of the biosynthetic pathways of specialised metabolites, especially defence compounds, was also evident in the osmyc2RNAi line. Furthermore, a substantial change was noted in the expression of distinct types of transcription factors, such as MYB-type factors, likely depicting the importance of OsMYC2 in not only defence responses but also other morphogenetic events. Our findings provide fundamental information to understand the overall functions of MYC2 in JA signalling in monocotyledonous plants, which might yield agricultural benefits. © 2017 Elsevier Inc.


Ishibashi O.,Osaka Prefecture University | Sakuragi K.,Osaka Prefecture University | Fukutomi Y.,Clinical Research Center for Allergy and Rheumatology Sagamihara National Hospital Sagamihara Japan | Kawakami Y.,Japan Institute for Environmental Sciences | And 7 more authors.
Allergy: European Journal of Allergy and Clinical Immunology | Year: 2016

Background: Booklice, belonging to the order Psocoptera, are small household insect pests that are distributed worldwide. Liposcelis bostrychophila, a common home-inhabiting species of booklouse, infests old books, sheets of paper, and stored food. Recent entomological and serological studies demonstrated that L. bostrychophila accounted for the majority of detectable insects in house dust and could be a potent inducer of respiratory allergy. Our recent proteomic analysis identified a potent allergenic protein from L. bostrychophila, designated Lip b 1, and determined its partial amino acid sequences. Methods: Cloning of cDNAs for Lip b 1 was performed by large-scale transcriptome analysis (RNA-seq) and subsequent reverse transcription polymerase chain reaction. The full-length amino acid sequences deduced from Lip b 1 cDNAs were bioinformatically analyzed. The recombinant proteins of glutathione S-transferase (GST)-fused Lip b 1 were analyzed by Western blot and enzyme-linked immunosorbent assay. Results: Lip b 1 cDNAs encoding two types of 254-amino acid proteins were cloned. The clones shared 87% identity, and the deduced molecular weights and isoelectric points were consistent with those determined in our previous study. The two types of Lip b 1 proteins in the GST-fused form were similarly reactive with sera from allergic patients sensitized with L. bostrychophila. Conclusions: Lip b 1 is a novel protein possibly causing booklouse allergy. © 2016 John Wiley & Sons A/S.


Muramatsu Y.,Tokyo University of Agriculture | Greiby I.,University of Tripoli | Mishra D.K.,Purdue University | Dolan K.D.,Michigan State University
Journal of Food Science | Year: 2017

Thermal diffusivity is an important transport property needed in modeling and computations of transient heat transfer in basic food processing operations. In addition, the prediction of nutritional and microbial changes occurring in food during thermal processing requires knowledge of thermal diffusivity of foods. The objectives of this study were to develop a new nonisothermal and nonlinear determination method of thermal diffusivity and to measure the thermal diffusivity of low-moisture foods using that new method. Thermal diffusivities of 5 kinds of low-moisture foods (almond meal, corn meal, wheat flour, chocolate fudge, and peanut butter) were estimated using an inverse technique. Samples were canned and heated at the surface in a water bath at about 70 °C. The 1-dimensional transient heat conduction problem for radial coordinates was solved with a finite-difference model. The thermal diffusivity of each of the 5 samples was determined by the ordinary least squares and sequential estimation methods, respectively. Predicted and observed temperature matched well, with maximum residuals of 0.9 °C. The thermal diffusivity values of the samples ranged from 9.8 × 10−8 to 1.3 × 10−7 m2/s. The advantages of this method are that the device and the estimation method are simple, inexpensive, rapid, and can handle large spatial temperature gradients, such as those experienced during heating of low-moisture foods. The results obtained in this study will be useful in the design of equipment and in calculations for the thermal processing of low-moisture foods. © 2017 Institute of Food Technologists®


Kamioka H.,Tokyo University of Agriculture | Tsutani K.,Health Science University | Origasa H.,University of Toyama | Yoshizaki T.,Toyo University | And 4 more authors.
Nutrition Research | Year: 2017

The objective of this review was to assess the quality of systematic reviews (SRs) based on the Foods with Function Claims (FFC) registered at the Consumer Affairs Agency (CAA) Web site in Japan by AMSTAR checklist. Study design was a prospective SR of SRs based on the FFC registered at the CAA Web site in Japan. We searched the database from 1 April 2015 (starting date) through 27 October 2015 on the CAA Web site. A full quality appraisal of identified articles was made using the combined tool based on the AMSTAR checklist developed to assess the methodological quality of SRs. Each item was scored as “present” (yes), “absent” (no), “unclear or inadequately described” (cannot answer), or “not applicable” (N/A). Forty-nine SRs met inclusion criteria. The quality of the articles was in the poor description category (mean ± SD; 6.2 ± 1.8 points, range; 2-11 points). Especially, there were very poor descriptions and/or implementations regarding the registration (2%), evaluation of publication bias (12%), and appropriate conclusions based on scientific quality of the included studies (27%). As a whole, the quality of SRs based on the FFC was poor in methodology and reporting. To develop SRs of the FFC and healthy foods, it will be important for future research to introduce and use (1) the AMSTAR checklist (ie, a tool to assess the methodological quality of SRs), (2) the PRISMA (ie, a checklist in the general description of SRs) and PRISMA-NMA checklists (ie, a checklist in the specific description of SRs with meta-analysis), (3) many English databases, (4) development of the original checklist for the FFC and healthy foods, and (5) notification documents (including SR) of the FFC in English. © 2017 Elsevier Inc.


Kataoka N.,Tokyo University of Agriculture
Human Genetics | Year: 2017

Pre-mRNA splicing is an essential step for gene expression in higher eukaryotes. Alternative splicing contributes to diversity of the expressed proteins from the limited number of genes. Disruption of splicing regulation often results in hereditary and sporadic diseases called as ‘RNA diseases’. Modulation of splicing by small chemical compounds and nucleic acids has been tried to target aberrant splicing in those diseases. Several RNA diseases and splicing-target therapeutic approaches will be briefly introduced in this review. Accumulating knowledge about molecular mechanism of aberrant splicing and their correction by chemical compounds is important not only for RNA biologists, but also for clinicians who desire therapies for those diseases. © 2017 Springer-Verlag Berlin Heidelberg


Shinohara A.,National Museum of Nature and Science | Kato Y.,Tokyo University of Agriculture
Zootaxa | Year: 2017

Based on a recently collected specimen, we describe the previously unknown female of Acantholyda flaviventris Shinohara, 1991, and give a revised key to the females of the 14 species of the genus distributed in Japan. Copyright © 2017 Magnolia Press.


Yoshikawa T.,Japan Forestry and Forest Products Research Institute | Endo S.,Rikkyo University | Endo S.,Tokyo University of Agriculture
Ornithological Science | Year: 2017

We summarize records of courtship and offspring feeding for 16 resident passerine birds based on long-term observations made by amateur ornithologists in Kanagawa Prefecture, Japan. Courtship feeding was detected in nine passerine spe- cies, including two that had not been previously reported to perform this behavior in Japan. Fledgling feeding and food transport to nests were detected in almost all of the species. Courtship feeding was detected mainly in early spring, but in some species it also occurred in winter. We discuss briefly the implications of the results, as well as possible biases and limitations of citizen-based research. © The Ornithological Society of Japan 2017.


Kakiuchi J.,Tokyo University of Agriculture | Kobata T.,The University of Shimane
Crop Science | Year: 2017

Seed yield in soybeans [Glycine max (L.) Merr.] strongly depends on nitrogen (N) assimilation (NA). The NA in nodulated soybeans is based on two N sources, soil and N fixation. Hence, the controlling NA in soybean to increase seed yield is more difficult than in many other crops that depend on fertilizer. The objective of this study was to establish a quantitative relationship between NA by plants and N applied via fertilizer (NF) to increase soybean seed production. The NA was modelled as a function of NF with two parameters: amount of available soil N (NS) and maximum N assimilation (NAmax), both to be determined experimentally, and one equation to describe fixed N (NFIX), would be maximum under nonfertilizer conditions (NFIXmax). It is assumed that NA is equal to NAmax when NF ≥ NAmax - NS and that, below this threshold, NA decreases in proportion with NFIX + NS. To obtain variable datasets, different rates of N fertilizer were applied to nodulated and non-nodulated isolines under pot and field conditions from full bloom to beginning of maturity. Seed yields were found to be highly dependent on NA regardless of nodulation type or genotype. In non-nodulated isolines, NA - NF was a good estimate of NS. In nodulated soybeans, NFIX could be modelled as a liner function of NF. These results indicate that the relationship between NA and NF with NS and NFIX can be modelled in a simplified way. The relationships between NFIX, NF, and NFIXmax indicate key traits for determining NA for seed production in nodulated soybeans. © Crop Science Society of America | 5585 Guilford Rd., Madison, WI 53711 USA All rights reserved.


Komaki H.,Chiba Institute of Technology | Ichikawa N.,NBRC | Oguchi A.,NBRC | Hamada M.,Chiba Institute of Technology | And 4 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2017

The aim of this study was to reclarify the taxonomic relationship among Streptomyces hygroscopicus subsp. hygroscopicus, Streptomyces endus and Streptomyces sporocinereus. Whole genome shotgun sequencing was performed for the type strains of these three taxa. Average nucleotide identity and digital DNA–DNA hybridization values among the three taxa were greater than the thresholds for bacterial species delineation, indicating that they belong to the same genomospecies. In addition, the phenotypic data previously reported also support the synonymy. Therefore, S. endus and S. sporocinereus should be reclassified as later heterotypic synonyms of S. hygroscopicus subsp. hygroscopicus. © 2017 IUMS.


Masumoto M.,Yokohama Plant Protection Station | Okajima S.,Tokyo University of Agriculture
Zootaxa | Year: 2017

An Oxythrips-like new genus and species, Paroxythrips podocarpi, is described from Podocarpus macrophyllus in Japan. An Australian species, Oxythrips agathidis Morison, that is associated with Agathis is transferred to Paroxythrips. © 2017 Magnolia Press.


Shin H.S.,Tokyo University of Science | Shin H.S.,Korea Food Research Institute | Shin H.S.,Korean University of Science and Technology | Satsu H.,Tokyo University of Science | And 6 more authors.
Nutrients | Year: 2017

Chlorogenic acid (CHA) and caffeic acid (CA) are phenolic compounds found in coffee, which inhibit oxidative stress-induced interleukin (IL)-8 production in intestinal epithelial cells, thereby suppressing serious cellular injury and inflammatory intestinal diseases. Therefore, we investigated the anti-inflammatory mechanism of CHA and CA, both of which inhibited hydrogen peroxide (H2O2)-induced IL-8 transcriptional activity. They also significantly suppressed nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) transcriptional activity, nuclear translocation of the p65 subunit, and phosphorylation of IκB kinase (IKK). Additionally, upstream of IKK, protein kinase D (PKD) was also suppressed. Finally, we found that they scavenged H2O2-induced reactive oxygen species (ROS) and the functional moiety responsible for the anti-inflammatory effects of CHA and CA was the catechol group. Therefore, we conclude that the presence of catechol groups in CHA and CA allows scavenging of intracellular ROS, thereby inhibiting H2O2-induced IL-8 production via suppression of PKD-NF-κB signaling in human intestinal epithelial cells. © 2017 by the authors; licensee MDPI, Basel, Switzerland.


Yamauchi H.,Azabu University | Hayakawa M.,University of Electro - Communications | Asano T.,University of Electro - Communications | Ohtani N.,Azabu University | Ohta M.,Tokyo University of Agriculture
Animals | Year: 2017

Previous studies have provided quantitative data regarding unusual animal behavior prior to earthquakes; however, few studies include long-term, observational data. Our previous study revealed that the milk yields of dairy cows decreased prior to an extremely large earthquake. To clarify whether the milk yields decrease prior to earthquakes, we examined the relationship between earthquakes of various magnitudes and daily milk yields. The observation period was one year. In the results, cross-correlation analyses revealed a significant negative correlation between earthquake occurrence and milk yields approximately three weeks beforehand. Approximately a week and a half beforehand, a positive correlation was revealed, and the correlation gradually receded to zero as the day of the earthquake approached. Future studies that use data from a longer observation period are needed because this study only considered ten earthquakes and therefore does not have strong statistical power. Additionally, we compared the milk yields with the subionospheric very low frequency/low frequency (VLF/LF) propagation data indicating ionospheric perturbations. The results showed that anomalies of VLF/LF propagation data emerged prior to all of the earthquakes following decreases in milk yields; the milk yields decreased earlier than propagation anomalies. We mention how ultralow frequency magnetic fields are a stimulus that could reduce milk yields. This study suggests that dairy cow milk yields decrease prior to earthquakes, and that they might respond to stimuli emerging earlier than ionospheric perturbations. © 2017 by the authors. Licensee MDPI, Basel, Switzerland.


Kaskoyo H.,Lampung University | Mohammed A.,Tokyo University of Agriculture | Inoue M.,Tokyo University of Agriculture
Journal of Sustainable Forestry | Year: 2017

The global to local-level importance of Indonesian forests for the environment and development is now very well documented. However, how to govern these forests to achieve the diverse and, at times, conflicting interests is still an open question. Hutan Kemasyarakatan (HKm) is a community forest (CF) that is being implemented to contribute to local development while creating sufficient incentives for conserving the forest. Previous studies have demonstrated the potential of HKm to conserve forests. This study analyzed the changes in the five major types of capital for HKm farmers. The results indicated HKm to have contributed positively to the improvement of natural, physical, and human capital. In addition to its direct impact, HKm was also found to improve the financial capital of the farmers by avoiding patron–client relationships and side payments between the pre-HKm illegal encroacher farmers (now legal land cultivators) and government officers. Although the results support the possibility of HKm producing a win-win situation between forest conservation and rural development, its future applicability, especially with consideration of population growth and associated increase in demand for cultivation land, needs to be given due emphasis. © 2017 Taylor & Francis.


Iwadate T.,Tokyo University of Agriculture | Nihei K.-I.,Tokyo University of Agriculture
Bioorganic and Medicinal Chemistry Letters | Year: 2017

Sonnerphenolic C (3), which was predicted in a redox product of epirhododendrin (1) isolated from Acer nikoense, was synthesized for the first time via the epimeric separation of benzylidene acetal intermediates as a key step. From a similar synthetic route, 1 was obtained concisely. As a result of their antioxidative evaluation, only 3 revealed potent activity. The redox transformation of 1 into 3 was achieved in the presence of tyrosinase and vitamin C. Moreover, 3 was identified in the decoction of A. nikoense by HPLC analysis with the effective use of synthesized 3. Thus, a novel naturally occurring antioxidant 3 was developed through the sequential flow including redox prediction, chemical synthesis, evaluation of the activity, and identification as the natural product. © 2017 Elsevier Ltd


Nunome M.,Nagoya University | Nakano M.,Nagoya University | Tadano R.,Gifu University | Kawahara-Miki R.,Tokyo University of Agriculture | And 7 more authors.
PLoS ONE | Year: 2017

To assess the genetic diversity of domestic Japanese quail (Coturnixjaponica) populations, and their genetic relationships, we examined mitochondrial DNA (mtDNA) D-loop sequences and microsatellite markers for 19 Japanese quail populations. The populations included nine laboratory lines established in Japan (LWC, Quv, RWN, WE, AWE, AMRP, rb-TKP, NIES-L, and W), six meat-type quail lines reimported from Western countries (JD, JW, Estonia, NIES-Br, NIES-Fr, and NIES-Hn), one commercial population in Japan, and three wild quail populations collected from three Asian areas. The phylogenetic tree of mtDNA D-loop sequences revealed two distinct haplotype groups, Dloop-Group1 and Dloop-Group2. Dloop-Group1 included a dominant haplotype representing most of the quail populations, including wild quail. Dloop-Group2 was composed of minor haplotypes found in several laboratory lines, two meat-type lines, and a few individuals in commercial and wild quail populations. Taking the breeding histories of domestic populations into consideration, these results suggest that domestic quail populations may have derived from two sources, i.e., domestic populations established before and after World War II in Japan. A discriminant analysis of principal components and a Bayesian clustering analysis with microsatellite markers indicated that the domestic populations are clustered into four genetic groups. The two major groups were Microsat-Group1, which contained WE, and four WE-derived laboratory lines (LWC, Quv, RWN, and AWE), and Microsat-Group2 consisting of NIES-L, JD, JW, Estonia, NIES-Br, NIES-Fr, NIES-Hn, W, and commercial and wild populations. The remaining two lines (AMRP and rb-TKP) were each clustered into a separate clade. This hierarchical genetic difference between domestic quail populations is attributed to the genetic background derived from two different genetic sources - the pre-war and post-war populations - which is well supported by their breeding histories. © 2017 Nunome et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Takano E.,Kobe University | Shimura N.,System Instruments Co. | Akiba T.,System Instruments Co. | Kitayama Y.,Kobe University | And 4 more authors.
Microchimica Acta | Year: 2017

The authors describe a pipette type of biosensor for detecting target genes and using a zinc finger protein fused to luciferase (ZF luciferase). The ZF protein binds to a specific DNA sequence, and the target double-stranded (ds) DNA can be detected by monitoring the enzymatic activity of ZF luciferase. A small avidin-immobilized reaction plate is placed on a plastic pipette tip (referred to as Biologi tip). The dsDNA detection procedures are carried out by using a programmable dispensing robot equipped with a photodetector. These procedures include (a) the aspiration of an analyte to capture the biotinylated target dsDNA (a product of a polymerase chain reaction) on the small reaction plate inside the pipette tip, (b) the introduction of ZF luciferase and luciferin into the pipette tip, and (c) migration of the pipette tip to the detection port to measure bioluminescence on the small reaction plate. The emission originating from luciferase activity is observed on the reaction plate containing immobilized biotin-tagged target dsDNA, whereas plates containing non-target or biotinylated single-stranded DNA only do not yield a signal. The intensity of emission increases proportionally to the concentration of dsDNA, and the detection limit of the target dsDNA is as low as 62 pM. An actual genomic DNA sample from Escherichia coli O157 was successfully detected by this automatic analyzer using the Biologi tip equipped with a reaction plate. This indicates that this system has a large potential for practical applications, including in particular point-of-care analyses in hygiene control, food safety testing, and clinical diagnosis. [Figure not available: see fulltext.] © 2017 Springer-Verlag Wien


Sato H.,Tokyo University of Agriculture | Koizumi R.,Tokyo University of Agriculture | Nakazawa Y.,Tokyo University of Agriculture | Yamazaki M.,Tokyo University of Agriculture | And 7 more authors.
Data in Brief | Year: 2017

This data article provides the weights, specific gravities and chemical compositions (moisture, protein, fat, ash, and carbohydrate) of potato tubers, for food processing use, from the Tokachi, Kamikawa and Abashiri areas of Hokkaido, Japan. Potato tubers of four cultivars (‘Toyoshiro’, ‘Kitahime’, ‘Snowden’ and ‘Poroshiri’) were employed in the current study. The weights and specific gravities of potato tubers from each cultivar, harvested from three areas, were measured, and those of near average weight and specific gravity from each group were analyzed for their chemical composition. In this article, weight, specific gravity, and chemical composition data are provided in tables. © 2017


Li X.,Tokyo University of Agriculture | Li X.,Jiangnan University | Shi C.,Jiangnan University | Wang J.,Jiangnan University | And 4 more authors.
Fibers and Polymers | Year: 2017

A simple and practical strategy has been developed for preparing polyaniline(PANi)-doped TiO2/poly(l-lactide) (P@TiP-C) fibers by a combination of coaxial-electrospinning and in-situ polymerization. The TiO2/PLLA composite fibers with TiO2 located on the surface were fabricated by coaxial-electrospinning, with PLLA as the core phase and a dispersion of TiO2 particles, a well-known photocatalyst, in the sheath phase. The aniline monomers were also located in the core phase and in-situ polymerized by ammonium persulfate (APS) after electrospinning. SEM images show that TiO2 particles were located on the surface of PLLA fibers. Photocatalytic degradation tests show that the P@TiP-C fibers exhibit enhanced photocatalytic activity for degradation of methyl orange under visible light, likely due to the synergistic effect of PANi and TiO2. © 2017, The Korean Fiber Society and Springer Science+Business Media Dordrecht.


Yokoyama D.,Kyoto University | Imai N.,Tokyo University of Agriculture | Kitayama K.,Kyoto University
Plant and Soil | Year: 2017

Aims: Soil hydrolysable P can be a main P source for biota in P-limited tropical rain forests. Soil hydrolysable P occurs in various chemical fractions, including, monoester P, diester P, pyrophosphate and phytate, which need enzymatic hydrolysis into orthophosphate before their assimilation into biota. We examined whether P-limited plants and microbes preferentially hydrolyzed specific fraction of soil hydrolysable P and whether those in different successional stages had different abilities to hydrolyze various soil hydrolysable P. Methods: We measured four classes of phosphatase (phosphomonoesterase, PME; phosphodiesterase, PDE; pyrophosphatase, PyP; and phytase, PhT) activities for fine-roots and soils in nitrogen (N) and P fertilized primary and secondary tropical rain forests in Sabah, Malaysia. Results: P fertilization reduced PME, PyP and PhT activities for fine-roots and PME and PyP activities for soils. Fine-roots in primary forests had higher PME and PyP activities whereas those in secondary forests had higher PhT activities. Conclusions: We suggest that P-limited trees and microbes depend more on hydrolysable P degraded by one step of enzymatic reaction (monoester P, pyrophosphate, and phytate) as a P source. We also suggest that trees have different soil-organic-P acquisition strategies in association with their life history strategies. © 2017 Springer International Publishing Switzerland


Htwe A.Z.,Kyushu University | Kanesaki Y.,Tokyo University of Agriculture | Yoshikawa H.,Tokyo University of Agriculture | Tsurumaru H.,Kagoshima University | Yamakawa T.,Kyushu University
Genome Announcements | Year: 2016

We report here the draft genome sequences of Bradyrhizobium elkanii strains BLY3-8 and BLY6-1, which are incompatible with Rj3 genotype soybean cultivars. The genome sequences of these strains will be useful to identify a causal gene for this incompatibility. © 2016 Zaw Htwe et al.


Muller T.,Szent Istvan University | Matsubara H.,Tokyo University of Agriculture | Kubara Y.,Tokyo University of Agriculture | Horvath A.,Tokyo University of Agriculture | And 2 more authors.
Journal of Applied Ichthyology | Year: 2017

The aim of this study was to test the artificial seminal plasma (ASP) as the extender as well as methanol as the cryoprotectant for cryopreservation, and to collect information on the fertilizing capacity of cryopreserved sperm samples. Eggs from Japanese eel, Anguilla japonica, females were control-fertilized with native sperm diluted with ASP and cryopreserved sperm (ASP as extender [in 1:100 ratio] and 10% methanol in v/v final concentration). No statistical differences (p < .05) were among the measured parameters (hatching, survival after 10 days post-hatch, malformation rates) between the two groups, thus this cryopreservation method can be used effectively for artificial propagation of the Japanese eel, Anguilla japonica. © 2017 Blackwell Verlag GmbH.


Endo S.,Rikkyo University | Endo S.,Tokyo University of Agriculture | Ueda K.,Rikkyo University
Ornithological Science | Year: 2016

In most avian species, parents incubate their eggs until they hatch, paying an energetic cost in the process. Incubating individuals are expected to efficiently adjust their investment in incubation according to the thermal demands of their eggs and their partner’s contribution to the process. In this study, the effects of ambient temperature, incubation stage, clutch size, and food provisioning by males on the incubation behavior of females, were investigated in the Bull-headed Shrike Lanius bucephalus. We video recorded behavior at 16 nests throughout the 15-day incubation period and established that only females incubate. During the early stage of incubation (5–7 days after completion of the clutch) female shrikes spent more time incubating, with longer periods on the nest (on-bout duration) and shorter periods off the nest (off-bout duration), than during the late stage (9–11 days after clutch completion). Females with larger clutches spent more time incubating than those with smaller clutches. Ambient temperature did not strongly affect female incubation behavior. Male provisioning was positively correlated with the length of time females spent incubating and their on-bout duration. Male provisioning plays an important role in the greater involvement of females in incubation, thereby ensuring normal embryonic development. © The Ornithological Society of Japan 2016.


Techo S.,Chulalongkorn University | Miyashita M.,Chiba Institute of Technology | Shibata C.,Chiba Institute of Technology | Tanaka N.,Tokyo University of Agriculture | And 3 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2016

A Gram-stain-positive, lactic acid bacterium, strain Ru20-1T, was isolated from a flower (West- Indian jasmine) collected from Kalasin province, Thailand. A polyphasic approach was used to determine the taxonomic position of this strain. Studies of morphological and biochemical characteristics revealed that strain Ru20-1T belonged to the genus Lactobacillus. The strain was heterofermentative, non-spore-forming and rod-shaped. It produced DL-lactic acid. Based on 16S rRNA gene sequence similarity, this strain was closely related to Lactobacillus lindneri LMG 14528T (96.8%), Lactobacillus sanfranciscensis NRIC 1548T (95.4%) and Lactobacillus florum NRIC 0771T (95.2%), respectively. In addition, the pheS gene sequence of strain Ru20-1T was closely related to those of L. sanfranciscensis NRIC 1548T (92.0%), L. lindneri LMG 14528T (89.0%) and L. florum NRIC 0771T(85.0%). Phylogenetic analysis indicated that strain Ru20-1T was clearly separated from closely related species of the genus Lactobacillus. The DNA G+C content of strain Ru20-1T was 47.8 mol %. The cell-wall peptidoglycan type was L-Lys–D-Asp. The major cellular fatty acids were C18: 1w9c, C20: 0, C20: 1w9c and summed feature 7 (unknown 18.846 and/or C19: 1w6c and/or C19: 0 cyclo). On the basis of the data provided, strain Ru20-1T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus ixorae sp. nov. is proposed. The type strain is Ru20-1T (=LMG 29008T=NBRC 111239T=PCU 346T=TISTR 2381T). © 2016 IUMS.


Fujisawa T.,National Institute of Genetics | Narikawa R.,University of Shizuoka | Maeda S.-I.,Nagoya University | Watanabe S.,Tokyo University of Agriculture | And 9 more authors.
Nucleic Acids Research | Year: 2017

The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale update of the database, which coincides with its 20th anniversary. We have expanded the number of cyanobacterial genomic sequences from 39 to 376 species, which consists of 86 complete and 290 draft genomes. We have also optimized the user interface for large genomic data to include the use of semantic web technologies and JBrowse and have extended community-based reannotation resources through the re-annotation of Synechocystis sp. PCC 6803 by the cyanobacterial research community. These updates have markedly improved CyanoBase, providing cyanobacterial genome annotations as references for cyanobacterial research. © The Author(s).


Gorshkova T.,Russian Academy of Sciences | Brutch N.,Ni Vavilov Research Institute Of Plant Industry | Chabbert B.,French National Institute for Agricultural Research | Deyholos M.,University of Alberta | And 6 more authors.
Critical Reviews in Plant Sciences | Year: 2012

Plant fibers are one of the most important renewable resources, used as raw material in the paper industry, and for various textiles and for composites. Fibers are structural components in timber and an energy-rich component of fuel-wood. For the plant itself, fibers are important in establishing plant architecture, as a source of mechanical support, in defence from herbivory, and in some cases as elements with contractile properties, resembling those of muscles. In addition, fibers may store ergastic carbon resources and water. Here, we review various aspects of fiber development such as initiation, elongation, cell wall formation and multinuclearity, discuss open questions and propose directions for further research. Most of the recent progress in fiber formation biology, especially in cell wall structure and chemistry, emerged from studies of only a few model plants including flax, Populus spp., Eucalyptus spp., Arabidopsis thaliana and hemp. Considering the enormous importance of fibers to humanity, it is surprising how little is known about the biology of fiber formation. © 2012 Copyright Taylor and Francis Group, LLC.


Kurihara T.,Seikai National Fisheries Research Institute | Takami H.,Tohoku National Fisheries Research Institute | Kosuge T.,Tokai University | Chiba S.,Tokyo University of Agriculture | And 2 more authors.
Marine Biology | Year: 2011

Increases of low-latitude species in various sea areas and poleward shifts of ranges of many species have been reported and linked to warming environments. To examine the generality of these trends for mollusks, we conducted 7 quadrat surveys during 1978-2006 on Pacific rocky shores in Japan (26.6-45.0°N). Results showed that the dominance of southern species increased on 11 of the 15 shores in a southern, warming sea area but on only 1 of the 6 shores in a northern area with no warming trend. The latitudes of species ranges increased on average but showed large interspecific variations which showed a weak, positive correlation with interspecific taxonomic distance. The differences of these results from the previously reported trends are discussed in relation to the unique current patterns in our study area and the phylogenetic constraints of species-specific responses to a warming environment. © 2011 Springer-Verlag.


Javadi F.,Osaka Prefecture University | Tun Y.T.,Ministry of Agriculture and Irrigation | Kawase M.,Japan National Institute of Agrobiological Science | Guan K.,Xinjiang Institute of Ecology and Geography | Yamaguchi H.,Tokyo University of Agriculture
Annals of Botany | Year: 2011

Background and Aims: The subgenus Ceratotropis in the genus Vigna is widely distributed from the Himalayan highlands to South, Southeast and East Asia. However, the interspecific and geographical relationships of its members are poorly understood. This study investigates the phylogeny and biogeography of the subgenus Ceratotropis using chloroplast DNA sequence data. Methods: Sequence data from four intergenic spacer regions (petA-psbJ, psbD-trnT, trnT-trnE and trnT-trnL) of chloroplast DNA, alone and in combination, were analysed using Bayesian and parsimony methods. Divergence times for major clades were estimated with penalized likelihood. Character evolution was examined by means of parsimony optimization and MacClade. Key Results: Parsimony and Bayesian phylogenetic analyses on the combined data demonstrated well-resolved species relationships in which 18 Vigna species were divided into two major geographical clades: the East AsiaSoutheast Asian clade and the Indian subcontinent clade. Within these two clades, three well-supported eco-geographical groups, temperate and subtropical (the East AsiaSoutheast Asian clade) and tropical (the Indian subcontinent clade), are recognized. The temperate group consists of V. minima, V. nepalensis and V. angularis. The subtropical group comprises the V. nakashimaeV. riukiuensisV. minima subgroup and the V. hirtellaV. exilisV. umbellata subgroup. The tropical group contains two subgroups: the V. trinerviaV. reflexo-pilosaV. trilobata subgroup and the V. mungoV. grandiflora subgroup. An evolutionary rate analysis estimated the divergence time between the East AsiaSoutheast Asia clade and the Indian subcontinent clade as 3·62 ± 0·3 million years, and that between the temperate and subtropical groups as 2·0 ± 0·2 million years. Conclusions: The findings provide an improved understanding of the interspecific relationships, and ecological and geographical phylogenetic structure of the subgenus Ceratotropis. The quaternary diversification of the subgenus Ceratotropis implicates its geographical dispersal in the south-eastern part of Asia involving adaptation to climatic condition after the collision of the Indian subcontinent with the Asian plate. The phylogenetic results indicate that the epigeal germination is plesiomorphic, and the germination type evolved independently multiple times in this subgenus, implying its limited taxonomic utility. © 2011 The Author. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.


Azuma N.,Tokyo University of Agriculture | Miranda R.M.,Austral University of Chile | Goshima S.,Hokkaido University | Abe S.,Hokkaido University
Plankton and Benthos Research | Year: 2011

Genetic population structure of the Neptune whelk (Neptunea arthritica) in northern Japan was estimated from six samples collected from Hokkaido and one sample from Aomori, in northernmost Honshu, using five polymorphic microsatellite DNA loci. Pairwise FST estimates indicated a genetic cline from eastern and northeastern Hokkaido to southern Hokkaido and northernmost Honshu. The individual-based assignment method and analyses of molecular variance suggested three geographic groups within this cline. The observed population structure was most likely influenced by isolation-by-distance with restricted gene flow, as suggested by the significant correlation between genetic and geographic distance for the entire region examined. The inferred restriction of gene flow is likely due to the poor dispersal ability of this species, which has a benthic, sedentary life history and passive dispersal along the coasts. The observed genetic structure of N. arthritica will be useful for conservation and fisheries management of this species. © The Japanese Association of Benthology.


Masumoto M.,Yokohama Plant Protection Station | Okajima S.,Tokyo University of Agriculture
Zootaxa | Year: 2013

Members of Thrips genus-group from Japan are reviewed, and 45 species in seven genera are recognized. Nine species and one genus are newly described: Stenchaetothrips amamiensis sp. n., S. dentatus sp. n., S. pleioblasti sp. n., Thrips nonakai sp. n., T. ogasawarensis sp. n., T. shiranesanus sp. n., T. syringae sp. n., T. typicus sp. n. and Tsutsumiothrips ryukyuensis gen. et sp. n. Moreover, 14 species of two genera are newly recorded from Japan: S. langkawiensis Ng & Mound, S. undatus Wang, Thrips alni Uzel, T. aspinus Mound & Masumoto, T. brevicornis Priesner, T. brunneus Ishida, T. extensicornis Priesner, T. minutissimus Linnaeus, T. pini (Uzel), T. subnudula (Karny), T. sukki Bhatti & Lee, T. treher-nei Priesner, T. urticae Fabricius and T. vitticornis Karny. A previously recorded species, Stenchaetothrips bambusae (Shumsher) is excluded from the Japanese fauna. © 2013 Magnolia Press.


Kamioka H.,Tokyo University of Agriculture | Kawamura Y.,Oyamada Memorial Spa Hospital | Tsutani K.,University of Tokyo | Maeda M.,International University of Health and Welfare | And 5 more authors.
Complementary Therapies in Medicine | Year: 2013

Objective: The purpose of this study was to develop a checklist of items that describes and measures the quality of reports of interventional trials assessing spa therapy. Methods: The Delphi consensus method was used to select the number of items in the checklist. A total of eight individuals participated, including an epidemiologist, a clinical research methodologist, clinical researchers, a medical journalist, and a health fitness programmer. Participants ranked on a 9-point Likert scale whether an item should be included in the checklist. Results: Three rounds of the Delphi method were conducted to achieve consensus. The final checklist contained 19 items, with items related to title, place of implementation (specificity of spa), care provider influence, and additional measures to minimize the potential bias from withdrawals, loss to follow-up, and low treatment adherence. Conclusion: This checklist is simple and quick to complete, and should help clinicians and researchers critically appraise the medical and healthcare literature, reviewers assess the quality of reports included in systematic reviews, and researchers plan interventional trials of spa therapy. © 2013 Elsevier Ltd.


Kosugi S.,Tokyo University of Agriculture | Kiyoshi K.,Tokyo University of Agriculture | Oba T.,Fukuoka Industrial Technology Center | Kusumoto K.,Fukuoka Industrial Technology Center | And 3 more authors.
Journal of Bioscience and Bioengineering | Year: 2014

We isolated 2,4-dinitrophenol (DNP)-resistant sake yeast strains by UV mutagenesis. Among the DNP-resistant mutants, we focused on strains exhibiting high malic acid and low acetic acid production. The improved organic acid composition is unlikely to be under the control of enzyme activities related to malic and acetic acid synthesis pathways. Instead, low mitochondrial activity was observed in DNP-resistant mutants, indicating that the excess pyruvic acid generated during glycolysis is not metabolized in the mitochondria but converted to malic acid in the cytosol. In addition, the NADH/NAD+ ratio of the DNP-resistant strains was higher than that of the parental strain K901. These results suggest that the increased NADH/NAD+ ratio together with the low mitochondrial activity alter the organic acid composition because malic acid synthesis requires NADH, while acetic acid uses NAD+. © 2013 The Society for Biotechnology, Japan.


Saito S.,Kaohsiung Medical University | Saito S.,Nihon University | Saito S.,Saito Laboratory of Cell Technology | Lin Y.-C.,Kaohsiung Medical University | And 5 more authors.
Current Molecular Medicine | Year: 2012

Human amnion-derived cells possess great potential for the repair of human neural disorders, and recent studies have broadened the spectrum for applications because they exhibit the characteristics of multipotent stem cells. These cells express embryonic stem cell markers such as Oct4, Nanog, Sox2, SSEA-3, SSEA-4 and Rex1, and can differentiate into multiple primary germ layers both in vitro and in vivo. Moreover, induced pluripotent stem cells have been generated from amnion-derived cells by virus-mediated delivery of three or four pluripotency-relating transcription factors or by the introduction of only one transcription factor with electroporation. Because human amnion-derived cells are readily available, less likely to contain genetic aberrations and can be reprogrammed earlier and more efficiently than differentiated cells, they can be ideal resources as the donor pluripotent stem cells for therapeutic purposes. We discuss here the highlights of recent studies and potential applications of human amnion-derived multipotent stem cells to stem cell biology as well as to regenerative medicine in the field of aging, heart disease, diabetes and neural disorders. © 2012 Bentham Science Publishers.


Endo A.,Stellenbosch University | Irisawa T.,Tokyo University of Agriculture | Futagawa-Endo Y.,Stellenbosch University | Sonomoto K.,Kyushu University | And 4 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

A fructophilic lactic acid bacterium, designated strain F214-1T, was isolated from a flower of Tropaeolum majus in South Africa. Based on phylogenetic analysis of 16S rRNA gene sequences, the strain formed a subcluster with Fructobacillus ficulneus and Fructobacillus pseudoficulneus and, based on recA gene sequences, the strain formed a subcluster with F. ficulneus. DNA-DNA hybridization studies showed that strain F214-1T was phylogenetically distinct from its closest relatives. Acid was produced from the fermentation of D-glucose, D-fructose and D-mannitol only. D-Fructose was the preferred sole carbon and energy source and was fermented more rapidly than D-glucose. Growth of the strain on D-glucose under anaerobic conditions was very weak but external electron acceptors such as oxygen and pyruvate enhanced growth on D-glucose. Lactic acid and acetic acid were produced from D-glucose in equimolar amounts. Ethanol was produced at very low levels, despite the strain's obligately heterofermentative metabolism. Based on these data, strain F214-1T represents a novel species of fructophilic bacteria in the genus Fructobacillus, for which the name Fructobacillus tropaeoli sp. nov. is proposed. The type strain is F214-1T (=5JCM 16675T =DSM 23246T). © 2011 IUMS.


Sandvik G.K.,University of Oslo | Lifjeld R.,University of Oslo | Hodne K.,University of Oslo | Nagahama Y.,Japan National Institute for Basic Biology | And 4 more authors.
Developmental Dynamics | Year: 2012

Background: Luteinizing hormone (LH) and follicle stimulating hormone (FSH), produced in gonadotrope cells in the adenohypophysis are key regulators of vertebrate reproduction. The differential regulation of these hormones, however, is poorly understood and little is known about gonadotrope embryonic development. We developed a stable transgenic line of medaka with the LH beta subunit gene (lhb) promotor driving green fluorescent protein (gfp) expression to characterize development of LH-producing gonadotropes in whole larvae and histological sections. Additionally, developmental and tissue-specific gene expression was examined. Results: The lhb gene is maternally expressed during early embryogenesis. Transcript levels increase by stage 21 (36 hours post fertilization [hpf]) and then decrease during continued larval development. Examination of the expression of pituitary marker genes show that LH-producing cells are initially localized outside the primordial pituitary, and they were localized to the developing gut tube by 32 hpf. At hatching, lhb-GFP is clearly detected in the gut epithelium and in the anterior digestive tract. lhb-GFP expression later consolidate in the developing pituitary by 2 weeks postfertilization. Conclusions: During embryonic development, lhb is primarily expressed outside the central nervous system and pituitary. The novel expression of lhb in the embryonic gut suggests that LH has a hitherto unidentified developmental function. © 2012 Wiley Periodicals, Inc.


Chiba S.,Tokyo University of Agriculture | Iida T.,Tokyo University of Agriculture | Tomioka A.,Tokyo University of Agriculture | Azuma N.,Hokkaido University | And 2 more authors.
Journal of Experimental Marine Biology and Ecology | Year: 2016

Temperature is a fundamental element determining the distribution patterns of ectotherms, and it is generally recognized that physiological tolerances of ectotherms change according to thermal gradients in their habitats. However, little is known about the variation in cold tolerance of marine invertebrates among local populations of the same species. In this study, three experiments were conducted to demonstrate inter-population variation in the cold tolerance of the intertidal gastropod Littorina brevicula, and to explore factors driving the variation. First, seasonal changes in the freezing temperature (the supercooling point, SCP) and the median lower lethal temperature (LLT50) of snails collected from a single population were examined to identify the cold tolerance strategies of this species. Seasonal fluctuation was clear in only the LLT50 which was lower than the SCP in winter, indicating that cold tolerance strategy of this species was freeze tolerant. Second, the cold tolerance of snails from four populations was compared. These populations were distributed at latitudinally different locations, and the comparisons were performed before winter when their cold tolerance was not required and in winter when their cold tolerance increased. In this experiment, while the cold tolerance of snails collected in winter was higher than that of snails collected before winter in all four populations, there were differences in tolerance among the populations. Furthermore, to estimate their ability of acclimation to cold environments, snails that were collected from the northernmost and southernmost populations in the four populations before winter were acclimated to a constant low temperature in the laboratory for a long period (120-130 days). This long period of acclimation led to an increase in the cold tolerance of both populations, but the latitudinal difference was maintained. Additionally, after imposing the long period of acclimation to snails that were collected at 12 locations before winter, factors that might cause local variation in their cold tolerance were explored. This experiment clearly showed that local variation in cold tolerance was explained by the lowest local air temperature. Our study demonstrated inter-population variation in the cold tolerance of an intertidal mollusc, and that the variation is explained by thermal gradients in winter. © 2016 Elsevier B.V.


Takeuchi J.,University of Shizuoka | Okamoto M.,Tottori University | Okamoto M.,University of California at Riverside | Akiyama T.,Tokyo University of Agriculture | And 13 more authors.
Nature Chemical Biology | Year: 2014

The plant stress hormone abscisic acid (ABA) is critical for several abiotic stress responses. ABA signaling is normally repressed by group-A protein phosphatases 2C (PP2Cs), but stress-induced ABA binds Arabidopsis PYR/PYL/RCAR (PYL) receptors, which then bind and inhibit PP2Cs. X-ray structures of several receptor-ABA complexes revealed a tunnel above ABA's 3′ ring CH that opens at the PP2C binding interface. Here, ABA analogs with sufficiently long 3′ alkyl chains were predicted to traverse this tunnel and block PYL-PP2C interactions. To test this, a series of 3′-alkylsulfanyl ABAs were synthesized with different alkyl chain lengths. Physiological, biochemical and structural analyses revealed that a six-carbon alkyl substitution produced a potent ABA antagonist that was sufficiently active to block multiple stress-induced ABA responses in vivo. This study provides a new approach for the design of ABA analogs, and the results validated structure-based design for this target class. © 2014 Nature America, Inc. All rights reserved.


Masumoto M.,Yokohama Plant Protection Station | Okajima S.,Tokyo University of Agriculture
Zootaxa | Year: 2013

The occurrence in Japan of the daylily thrips, Frankliniella hemerocallis, is confirmed. This thrips probably originated in Asia or Eurasia, because it is highly specific to Hemerocallis [Liliaceae] which is native to these areas. This thrips feeds on leaf, stem and petals rather than pollen. The second instar larva is described, and a key provided to the adults of Frankliniella species recorded from Japan © 2013 Magnolia Press.


Mattarelli P.,University of Bologna | Holzapfel W.,Handong Global University | Franz C.M.A.P.,Max Rubner Institute | Endo A.,Tokyo University of Agriculture | And 5 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2014

Minimal standards for the description of new cultivable strains that represent novel genera and species belonging to the genera Bifidobacterium, Lactobacillus and related genera are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision): the description of novel species should be based on phenotypic, genotypic and ecological characteristics to ensure a rich polyphasic characterization. Concerning genotypic characterization, in addition to DNA G+C content (mol%) data, the description should be based on DNA-DNA hybridization (DDH), 16S rRNA gene sequence similarities and at least two housekeeping gene (e.g. hsp60 and recA) sequence similarities. DDH might not be needed if the 16S rRNA gene sequence similarity to the closest known species is lower than 97 %. This proposal has been endorsed by members of the Subcommittee on the Taxonomy of Bifidobacterium, Lactobacillus and related organisms of the International Committee on the Systematics of Prokaryotes. © 2014 IUMS.


Nakayama S.,Tokyo University of Agriculture | Tabata K.,Tokyo University of Agriculture | Oba T.,Fukuoka Industrial Technology Center | Kusumoto K.,Fukuoka Industrial Technology Center | And 3 more authors.
Journal of Bioscience and Bioengineering | Year: 2012

We characterized a high malic acid production mechanism in sake yeast strain No. 28. No considerable differences in the activity of the enzymes that were involved in malic acid synthesis were observed between strain No. 28 and its parent strain, K1001. However, compared with strain K1001, which actively took up rhodamine 123 during staining, the cells of strain No. 28 were only lightly stained, even when cultured in high glucose concentrations. In addition, malic acid production by the respiratory-deficient strain of K1001 was 2.5-fold higher than that of the wild-type K1001 and wild-type No. 28. The findings of this study demonstrated that the high malic acid production by strain No. 28 is attributed to the suppression of mitochondrial activity. © 2012.


Matsubayashi H.,Universiti Malaysia Sabah | Ahmad A.H.,Universiti Malaysia Sabah | Wakamatsu N.,Tokyo University of Agriculture | Nakazono E.,Tokyo University of Agriculture | And 2 more authors.
Raffles Bulletin of Zoology | Year: 2011

The use of natural-licks by orangutans (Pongo pygmaeus) was investigated with camera traps in the Deramakot production forest, Sabah, Malaysian Borneo. The results showed that 1) Although orangutans were in the top three species at all the natural-licks, visitation frequency differed at the natural licks depending on the surrounding environment; 2) Natural-licks use by orangutans was impacted more by human activity than concentration of the minerals; and 3) Visiting proportion of each orangutan class: flanged male, female with infant, and others, showed that flanged male accounted for 31%; female with infant, 17%; and others, 52%; although we had anticipated a bias toward the flanged male. These results suggest that the natural-licks are key habitats for all classes of orangutans and suitable sites for ground monitoring. Therefore, it is strongly recommended that other production forests adopt protection of natural licks and managed as a monitoring site for orangutan habitat conservation. Furthermore, as orangutans are vulnerable to human activity, it is necessary to manage natural-licks as protected area with buffer zones of reduced human activity. © National University of Singapore.


Brahmi Z.,Tokyo University of Agriculture | Abe N.,Tokyo University of Agriculture | El Omri A.,University of Tsukuba
Food Control | Year: 2013

The chemical composition of Salicornia herbacea L. a food plant belonging to Chenopodiaceae was investigated based on its mineral composition, proteins and carbohydrates contents. The phenolic composition analyzed by high performance liquid chromatography with diode array detection (HPLC-DAD) showed the presence of eight phenolic acids and eight flavonoids. The biological activities of the methanol extract were conducted on the antioxidant activity evaluated using 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging assay and β-carotene-linoleic acid bleaching test. The extract was an efficient radical scavenger (IC50 = 55.3 ± 2.7 μg/mL) and exhibited a moderate inhibition of lipid peroxidation of linoleic acid emulsion. Antibacterial activity determined by disc diffusion method against four Gram negative and two Gram positive bacteria, showed effects against all strains.Cytochrome P450s (CYPs) inhibitory activity studied for the first time was evaluated against three CYP isozymes namely CYP1A2, CYP3A4 and CYP2D6. The extract was a potent inhibitor against CYP2D6 (IC50 = 3.88 ± 0.02 μg/mL). © 2012 Elsevier Ltd.


Yoshida T.,Tokyo University of Agriculture and Technology | Fujiwara W.,Tokyo University of Agriculture and Technology | Enomoto M.,Tokyo University of Agriculture and Technology | Nakayama S.,Tokyo University of Agriculture and Technology | And 5 more authors.
International Archives of Allergy and Immunology | Year: 2013

Background: Our previous study showed that an oral administration of Lactobacillus plantarum NRIC0380 inhibited immunoglobulin E (IgE) production in a murine model, and that orally administered NRIC0380 induced CD4+CD25+ Foxp3+ T, i.e. regulatory T (Treg), cells in the spleen and Peyer's patch of mice. Although it has been reported that Treg cells might suppress the allergic symptoms, the involvement of the cells in the antiallergic activity of lactic acid bacteria has not been clearly demonstrated. We therefore examined in detail the antiallergic activity of Treg cells obtained from mice that had been fed NRIC0380. Methods: Treg cells were obtained from mice that had been fed NRIC0380. The T cell-suppressive effect of the cells was analyzed by coculturing the cells with splenocytes of β-lactoglobulin-immunized mice and β-lactoglobulin. The effects of the Treg cells on the IgE production and cutaneous anaphylaxis reaction were then analyzed by transferring the cells into another mouse. Results: The Treg cells obtained from the mice that had been fed NRIC0380 showed similar T cell-suppressive activity to those cells obtained from the control mice. The Treg cells obtained from the mice fed NRIC0380 significantly inhibited the IgE production and active cutaneous anaphylaxis reaction when transferred into another mouse that was subsequently immunized with the antigen. Furthermore, the Treg cells also significantly suppressed the passive cutaneous anaphylaxis reaction when cotransferred with the IgE antibody into another mouse. Conclusions: The induction of Treg cells by the oral administration of NRIC0380 would be involved in the antiallergic activity of NRIC0380. © 2013 S. Karger AG, Basel.


Yoshikawa C.,Japan Agency for Marine - Earth Science and Technology | Makabe A.,Tokyo University of Agriculture | Yoshida N.,Tokyo Institute of TechnologyYokohama Japan
Geochemistry, Geophysics, Geosystems | Year: 2015

Nitrogen isotopic ratios of nitrate (δ15N- NO3-) were analyzed above 1000 m water depth along 17°S in the subtropical South Pacific during the revisit WOCE P21 cruise in 2009. The δ15N- NO3- and N* values were as high as 17‰ and as low as -18 μmol N L-1, respectively, at depths around 250 m east of 115°W, but were as low as 5‰ and as high as +1 μmol N L-1, respectively, in subsurface waters west of 170°W. The relationships among NO3- concentrations, N* values, δ15N- NO3- values, and oxygen and nitrite concentrations suggest that a few samples east of 90°W were from suboxic and nitrite-accumulated conditions and were possibly affected by in situ water column denitrification. Most of the high-δ15N- NO3- and negative-N* waters were probably generated by mixing between Subantarctic Mode Water from the Southern Ocean and Oxygen Deficit Zone Water from the eastern tropical South Pacific, with remineralization of organic matter occurring during transportation. Moreover, the relationship between δ15N- NO3- and N* values, as well as Trichodesmium abundances and size-specific nitrogen fixation rates at the surface, suggest that the low-δ15N- NO3- and positive-N* subsurface waters between 160°E and 170°W were generated by the input of remineralized particles created by in situ nitrogen fixation, mainly by Trichodesmium spp. Therefore, the δ15N values of sediments in this region are expected to reveal past changes in nitrogen fixation or denitrification rates in the subtropical South Pacific. © 2015. American Geophysical Union.


Freeman M.A.,University of Malaya | Freeman M.A.,University of Stirling | Eydal M.,University of Iceland | Yoshimizu M.,Hokkaido University | And 4 more authors.
Parasites and Vectors | Year: 2011

Background: Epidermal pseudotumours from Hippoglossoides dubius and Acanthogobius flavimanus in Japan and gill lesions in Limanda limanda from the UK have been shown to be caused by phylogenetically related protozoan parasites, known collectively as X-cells. However, the phylogenetic position of the X-cell group is not well supported within any of the existing protozoan phyla and they are currently thought to be members of the Alveolata. Ultrastructural features of X-cells in fish pseudotumours are somewhat limited and no typical environmental stages, such as spores or flagellated cells, have been observed. The life cycles for these parasites have not been demonstrated and it remains unknown how transmission to a new host occurs. In the present study, pseudobranchial pseudotumours from Atlantic cod, Gadus morhua, in Iceland and epidermal pseudotumours from the northern black flounder, Pseudopleuronectes obscurus, in Japan were used in experimental transmission studies to establish whether direct transmission of the parasite is achievable. In addition, X-cells from Atlantic cod were sequenced to confirm whether they are phylogenetically related to other X-cells and epidermal pseudotumours from the northern black flounder were analysed to establish whether the same parasite is responsible for infecting different flatfish species in Japan. Results: Phylogenetic analyses of small subunit ribosomal DNA (SSU rDNA) sequence data from Atlantic cod X-cells show that they are a related parasite that occupies a basal position to the clade containing other X-cell parasites. The X-cell parasite causing epidermal pseudotumours in P. obscurus is the same parasite that causes pseudotumours in H. dubius. Direct, fish to fish, transmission of the X-cell parasites used in this study, via oral feeding or injection, was not achieved. Non-amoeboid X-cells are contained within discrete sac-like structures that are loosely attached to epidermal pseudotumours in flatfish; these X-cells are able to tolerate exposure to seawater. A sensitive nested PCR assay was developed for the sub clinical detection of both parasites and to assist in future life cycle studies. PCR revealed that the parasite in P. obscurus was detectable in non-pseudotumourous areas of fish that had pseudotumours present in other areas of the body. Conclusions: The inability to successfully transmit both parasites in this study suggests that either host detachment combined with a period of independent development or an alternate host is required to complete the life cycle for X-cell parasites. Phylogenetic analyses of SSU rDNA confirm a monophyletic grouping for all sequenced X-cell parasites, but do not robustly support their placement within any established protist phylum. Analysis of SSU rDNA from X-cells in Japanese flatfish reveals that the same parasite can infect more than one species of fish. © 2011 Freeman et al; licensee BioMed Central Ltd.


Kamioka H.,Tokyo University of Agriculture | Tsutani K.,University of Tokyo | Yamada M.,Kyoto University | Park H.,National Center for Geriatrics and Gerontology | And 10 more authors.
Patient Preference and Adherence | Year: 2014

Objective: The objective of this review was to summarize evidence for the effectiveness of music therapy (MT) and to assess the quality of systematic reviews (SRs) based on randomized controlled trials (RCTs). Study design: An SR of SRs based on RCTs. Methods: Studies were eligible if they were RCTs. Studies included were those with at least one treatment group in which MT was applied. We searched the following databases from 1995 to October 1, 2012: MEDLINE via PubMed, CINAHL (Cumulative Index of Nursing and Allied Health Literature), Web of Science, Global Health Library, and Ichushi-Web. We also searched all Cochrane Database and Campbell Systematic Reviews up to October 1, 2012. Based on the International Classification of Diseases, 10th revision, we identified a disease targeted for each article. Results: Twenty-one studies met all inclusion criteria. This study included 16 Cochrane reviews. As a whole, the quality of the articles was very good. Eight studies were about "Mental and behavioural disorders (F00-99)"; there were two studies on "Diseases of the nervous system (G00-99)" and "Diseases of the respiratory system (J00-99)"; and there was one study each for "Endocrine, nutritional and metabolic diseases (E00-90)", "Diseases of the circulatory system (I00-99)", and "Pregnancy, childbirth and the puerperium (O60)". MT treatment improved the following: global and social functioning in schizophrenia and/or serious mental disorders, gait and related activities in Parkinson's disease, depressive symptoms, and sleep quality. Conclusion: This comprehensive summary of SRs demonstrated that MT treatment improved the following: global and social functioning in schizophrenia and/or serious mental disorders, gait and related activities in Parkinson's disease, depressive symptoms, and sleep quality. MT may have the potential for improving other diseases, but there is not enough evidence at present. Most importantly, no specific adverse effect or harmful phenomenon occurred in any of the studies, and MT was well tolerated by almost all patients. © 2014 Kamioka et al.


Masumoto M.,Yokohama Plant Protection Station | Okajima S.,Tokyo University of Agriculture
Zootaxa | Year: 2012

Okajimaella nonakai sp. n. and Paithrips pornthipae sp. n. are described from bamboo in Vietnam as the third and second species respectively in these genera. Also newly recorded from bamboo in Vietnam are O. tubercula Nonaka & Janguvitaya and P. circularis Nonaka & Janguvitaya, Neocorynothrips asiaticus Rhamakrishna & Margabandhu, Takethrips megas Nonaka & Jangvitaya, Watanabeotrips yasuakii Okajima, and Yoshinothrips thailandicus Nonaka & Jangvitaya. As a result, nine species from seven genera are now known from bamboo in Vietnam. Copyright © 2012 · Magnolia Press.


Lin Y.-C.,Kaohsiung Medical University | Murayama Y.,Nihon University | Hashimoto K.,Tokyo University of Agriculture | Nakamura Y.,RIKEN | And 5 more authors.
Stem Cell Research and Therapy | Year: 2014

Because of their pluripotent characteristics, human induced pluripotent stem cells (iPSCs) possess great potential for therapeutic application and for the study of degenerative disorders. These cells are generated from normal somatic cells, multipotent stem cells, or cancer cells. They express embryonic stem cell markers, such as OCT4, SOX2, NANOG, SSEA-3, SSEA-4, and REX1, and can differentiate into all adult tissue types, both in vitro and in vivo. However, some of the pluripotency-promoting factors have been implicated in tumorigenesis. Here, we describe the merits of tumor suppresser genes as reprogramming factors for the generation of iPSCs without tumorigenic activity. The initial step of reprogramming is induction of the exogenous pluripotent factors to generate the oxidative stress that leads to senescence by DNA damage and metabolic stresses, thus inducing the expression of tumor suppressor genes such as p21 CIP1 and p16 INK4a through the activation of p53 to be the pre-induced pluripotent stem cells (pre-iPSCs). The later stage includes overcoming the barrier of reprogramming-induced senescence or cell-cycle arrest by shutting off the function of these tumor suppressor genes, followed by the induction of endogenous stemness genes for the full commitment of iPSCs (full-iPSCs). Thus, the reactive oxygen species (ROS) produced by oxidative stress might be critical for the induction of endogenous reprogramming-factor genes via epigenetic changes or antioxidant reactions. We also discuss the critical role of tumor suppressor genes in the evaluation of the tumorigenicity of human cancer cell-derived pluripotent stem cells, and describe how to overcome their tumorigenic properties for application in stem cell therapy in the field of regenerative medicine. © 2014 Yokoyama et al.; licensee BioMed Central Ltd.


Masumoto M.,Yokohama Plant Protection Station | Ohno S.,Okinawa Prefectural Agricultural Research Center | Ganaha-Kikumura T.,Okinawa Prefectural Agricultural Research Center | Miyagi A.,Okinawa Prefectural Agricultural Research Center | Okajima S.,Tokyo University of Agriculture
Zootaxa | Year: 2012

Three species of the genus Scolothrips Hinds, all predatory on spider mites [Tetranychidae], are recorded here from Japan, with S. rhagebianus Priesner newly recorded from this country. These three species, including S. asura Ramakrishna & Margabandhu and S. takahashii Priesner, are re-described. Copyright © 2012 Magnolia Press.


Noguchi S.,Tokyo University of Agriculture and Technology | Hattori M.,Tokyo University of Agriculture and Technology | Sugiyama H.,Toyo Suisan Kaisha Ltd. | Hanaoka A.,Toyo Suisan Kaisha Ltd. | And 2 more authors.
Bioscience, Biotechnology and Biochemistry | Year: 2012

The anti-inflammatory effect of lactic acid bacteria (LAB) has been reported in several models for autoimmune diseases. It was considered in those studies that IL-10 induced by LAB might have been involved in such anti-inflammatory activity. We therefore examined the IL-10-inducing activity of LAB in detail by using an in vitro culture system of DO11.10 splenocytes. Most strains of LAB tested in this study increased IL-10 production. A further study using one of the tested strains with potent immune-regulatory activity, Lactobacillus plantarum NRIC1832, showed that the enhanced IL-10 was mainly produced by T cells. However, this enhancement required several types of cells other than T cells. NRIC1832 enhanced IL-10 production after short-term exposure to T cells, but this effect diminished after long-term exposure, indicating that the enhancement of IL-10 production by NRIC1832 was temporary, in contrast to the enhancement of IFN-γ production which was still apparent after long-term exposure.


Tousen Y.,National Institute of Health and Nutrition | Abe F.,National Institute of Health and Nutrition | Ishida T.,Meiji Dairies Corporation | Uehara M.,Tokyo University of Agriculture | Ishimi Y.,National Institute of Health and Nutrition
Metabolism: Clinical and Experimental | Year: 2011

Daidzein is metabolized to equol in the gastrointestinal tract by gut microflora. Equol has greater estrogenic activity than genistein and daidzein, with its production shown to be promoted by dietary fiber. It is known that resistant starch (RS) is not absorbed in the proximal intestine and acts as dietary fiber in the colon. In this study, we investigated the combined effects of daidzein and RS intake on equol production, bone mineral density, and intestinal microflora in ovariectomized (OVX) mice. Female mice of the ddY strain, aged 8 weeks, were either sham operated (n = 6) or OVX. The OVX mice were randomly divided into 5 groups: OVX control (n = 6), OVX fed 0.1% daidzein-supplemented diet (OVX + Dz, n = 8), OVX fed 0.1% daidzein- and 12% RS-supplemented diet (OVX + Dz + RS, n = 8), OVX fed 12% RS-supplemented diet (OVX + RS, n = 8), and OVX who received daily subcutaneous administration of 17 β-estradiol (n = 6). After 6 weeks, urinary equol concentration was significantly higher in the OVX + Dz + RS group than in the OVX + Dz group. The bone mineral density of the whole tibia was higher in the OVX + Dz +RS group compared with the OVX + Dz group. The occupation ratios of Bifidobacterium spp in the cecal microflora in groups fed RS were significantly higher than those in the other groups. The present study demonstrated that RS may increase the bioavailability of daidzein. © 2011 Elsevier Inc.


Oshima T.,Nara Institute of Science and Technology | Morimoto T.,Nara Institute of Science and Technology | Morimoto T.,Kao Corporation | Yoshikawa H.,Tokyo University of Agriculture | And 4 more authors.
Nucleic Acids Research | Year: 2011

We identified the sequence-specific starting positions of consecutive miscalls in the mapping of reads obtained from the Illumina Genome Analyser (GA). Detailed analysis of the miscall pattern indicated that the underlying mechanism involves sequence-specific interference of the base elongation process during sequencing. The two major sequence patterns that trigger this sequence-specific error (SSE) are: (i) inverted repeats and (ii) GGC sequences. We speculate that these sequences favor dephasing by inhibiting single-base elongation, by: (i) folding single-stranded DNA and (ii) altering enzyme preference. This phenomenon is a major cause of sequence coverage variability and of the unfavorable bias observed for population-targeted methods such as RNA-seq and ChIP-seq. Moreover, SSE is a potential cause of false single-nucleotide polymorphism (SNP) calls and also significantly hinders de novo assembly. This article highlights the importance of recognizing SSE and its underlying mechanisms in the hope of enhancing the potential usefulness of the Illumina sequencers. © 2011 The Author(s).


Ishikawa R.,Tokyo University of Agriculture | Kim R.,Tokyo University of Agriculture | Uchino S.,Teikyo University | Kida S.,Tokyo University of Agriculture | Kida S.,Japan Science and Technology Agency
Hippocampus | Year: 2014

Adult hippocampal neurogenesis has been suggested to play modulatory roles in learning and memory. Importantly, previous studies have shown that newborn neurons in the adult hippocampus are integrated into the dentate gyrus circuit and are recruited more efficiently into the hippocampal memory trace of mice when they become 3 weeks old. Interestingly, a single high-dose treatment with the N-methyl-d-aspartate receptor antagonist memantine (MEM) has been shown to increase hippocampal neurogenesis dramatically by promoting cell proliferation. In the present study, to understand the impact of increased adult neurogenesis on memory performance, we examined the effects of a single treatment of MEM on hippocampus-dependent memory in mice. Interestingly, mice treated with MEM showed an improvement of hippocampus-dependent spatial and social recognition memories when they were trained and tested at 3-6 weeks, but not at 3 days or 4 months, after treatment with MEM. Importantly, we observed a significant positive correlation between the scores for spatial memory (probe trial in the Morris water maze task) and the number of young mature neurons (3 weeks old) in MEM-treated mice, but not saline-treated mice. We also observed that the young mature neurons generated by treatment with MEM were recruited into the trace of spatial memory similarly to those generated through endogenous neurogenesis. Taken together, our observations suggest that treatment with MEM temporally improves hippocampus-dependent memory formation and that the newborn neurons increased by treatment with MEM contribute to this improvement when they become 3 weeks old. © 2014 Wiley Periodicals, Inc.


Kamioka H.,Tokyo University of Agriculture | Tsutani K.,University of Tokyo | Okuizumi H.,Mimaki Onsen Spa Clinic | Mutoh Y.,University of Tokyo | And 7 more authors.
Journal of Epidemiology | Year: 2010

Background: The objective of this review was to summarize findings on aquatic exercise and balneotherapy and to assess the quality of systematic reviews based on randomized controlled trials. Methods: Studies were eligible if they were systematic reviews based on randomized clinical trials (with or without a meta-analysis) that included at least 1 treatment group that received aquatic exercise or balneotherapy. We searched the following databases: Cochrane Database Systematic Review, MEDLINE, CINAHL, Web of Science, JDream II, and Ichushi-Web for articles published from the year 1990 to August 17, 2008. Results: We found evidence that aquatic exercise had small but statistically significant effects on pain relief and related outcome measures of locomotor diseases (eg, arthritis, rheumatoid diseases, and low back pain). However, long-term effectiveness was unclear. Because evidence was lacking due to the poor methodological quality of balneotherapy studies, we were unable to make any conclusions on the effects of intervention. There were frequent flaws regarding the description of excluded RCTs and the assessment of publication bias in several trials. Two of the present authors independently assessed the quality of articles using the AMSTAR checklist. Conclusions: Aquatic exercise had a small but statistically significant short-term effect on locomotor diseases. However, the effectiveness of balneotherapy in curing disease or improving health remains unclear. © 2009 by the Japan Epidemiological Association.


Tsuda K.,Tokyo University of Agriculture | Kawahara-Miki R.,Tokyo University of Agriculture | Sano S.,Ulvaniac Inc. | Imai M.,Tokyo University of Agriculture | And 3 more authors.
Genomics | Year: 2013

The native Japanese cattle Mishima-Ushi, a designated national natural treasure, are bred on a remote island, which has resulted in the conservation of their genealogy. We examined the genetic characteristics of 8 Mishima-Ushi individuals by using single nucleotide polymorphisms (SNPs), insertions, and deletions obtained by whole-genome sequencing. Mapping analysis with various criteria showed that predicted heterozygous SNPs were more prevalent than predicted homozygous SNPs in the exonic region, especially non-synonymous SNPs. From the identified 6.54. million polymorphisms, we found 400 non-synonymous SNPs in 313 genes specific to each of the 8 Mishima-Ushi individuals. Additionally, 3,170,833 polymorphisms were found between the 8 Mishima-Ushi individuals. Phylogenetic analysis confirmed that the Mishima-Ushi population diverged from another strain of Japanese cattle. This study provides a framework for further genetic studies of Mishima-Ushi and research on the function of SNP-containing genes as well as understanding the genetic relationship between the domestic and native Japanese cattle breeds. © 2013.


Oba T.,Fukuoka Industrial Technology Center | Enaga H.,Fukuoka Industrial Technology Center | Kayama S.,Tokyo University of Agriculture | Tsuiki S.,Kyushu Sangyo University | And 3 more authors.
Bioscience, Biotechnology and Biochemistry | Year: 2011

We characterized high malic acid-producing strains of Saccharomyces cerevisiae isolated from sake mash. We compared the gene expression of these strains with those of the parental strain by DNA microarray, and found that stress response genes, such as HSP12, were commonly upregulated in the high malate-producing strains, whereas thiamine synthesis genes, such as THI4 and SNZ2, were downregulated in these strains.


Mound L.A.,CSIRO | Masumoto M.,Yokohama Plant Protection Station | Okajima S.,Tokyo University of Agriculture
Zootaxa | Year: 2012

An identification key is provided to 10 species recognised in the genus Craspedothrips, including three new species, C. malaysiae from Malaysia, and C. nyanzai, C. poecilus, and C. reticulatus from East Africa. Plesiopsothrips zurstrasseni Bournier et al. is considered a new synonym of C. hargreavesi, and Plesiopsothrips carvalhoi Bournier a new synonym of C. xanthocerus. One oriental species, C. antennalis Karny, is newly recorded from Australia. Little is known of the biology of most species, but C. antennatus and C. xanthocerus are both recorded in association with Hemileia vastatrix on the leaves of Coffea species (Rubiaceae) in Africa, C. minor is recorded from flowers of Cassia (Fabaceae), and C. antennalis is recorded from plants of the family Apocynaceae.


Yanagimachi R.,Hawaii Medical | Cherr G.,University of California at Davis | Matsubara T.,Hokkaido National Fisheries Research Institute | Andoh T.,Hokkaido National Fisheries Research Institute | And 7 more authors.
Biology of Reproduction | Year: 2013

In some animals, such as fish, insects, and cephalopods, the thick egg coat has a narrow canal-a micropyle-through which spermatozoa enter the eggs. In fish, there is no indication that spermatozoa are attracted by eggs from a distance, but once spermatozoa come near the outer opening of the micropyle, they exhibit directed movement toward it, suggesting that a substance exists in this defined region to attract spermatozoa. Since Coomassie Blue (CB) binds preferentially to the micropyle region in flounder, herring, steelhead, and other fish, it probably stains this sperm guidance substance. This substance-a glycoprotein based on lectin staining-is bound tightly to the surface of the chorion, but can be removed readily by protease treatment. Although fertilization in fish (flounder) is possible after removal of this substance, its absence makes fertilization inefficient, as reflected by a drastic reduction in fertilization rate. The sperm "attraction" to the micropyle opening is species specific and is dependent on extracellular Ca2+. Eggs of some insects, including Drosophila, have distinct micropyle caps with CB affinity, which also may prove to assist sperm entry. Our attempts to fertilize fly eggs in vitro were not successful. © 2013 by the Society for the Study of Reproduction, Inc.


Mwacharo J.M.,University of Nottingham | Bjornstad G.,Kenya International Livestock Research Institute | Mobegi V.,Kenya International Livestock Research Institute | Nomura K.,Tokyo University of Agriculture | And 6 more authors.
Molecular Phylogenetics and Evolution | Year: 2011

Chicken were possibly domesticated in South and Southeast Asia. They occur ubiquitously in East Africa where they show extensive phenotypic diversity. They appeared in the region relatively late, with the first undisputed evidence of domestic chicken in Sudan, around ∼700 BC. We reveal through a detailed analysis of mitochondrial DNA D-loop sequence diversity of 512 domestic village chickens, from four East African countries (Kenya, Ethiopia, Sudan, Uganda), the presence of at least five distinct mitochondrial DNA haplogroups. Phylogeographic analyses and inclusion of reference sequences from Asia allow us to address the origin, ways of introduction and dispersion of each haplogroup. The results indicate a likely Indian subcontinent origin for the commonest haplogroup (D) and a maritime introduction for the next commonest one (A) from Southeast and/or East Asia. Recent introgression of commercial haplotypes into the gene pool of village chickens might explain the rare presence of two haplogroups (B and C) while the origin of the last haplogroup (E) remains unclear being currently observed only outside the African continent in the inland Yunnan Province of China. Our findings not only support ancient historical maritime and terrestrial contacts between Asia and East Africa, but also indicate the presence of large maternal genetic diversity in the region which could potentially support genetic improvement programmes. © 2010 Elsevier Inc.


Oba T.,Fukuoka Industrial Technology Center | Kusumoto K.,Fukuoka Industrial Technology Center | Kichise Y.,Kurume National College of Technology | Izumoto E.,Kurume National College of Technology | And 4 more authors.
FEMS Yeast Research | Year: 2014

Research on the relationship between mitochondrial membrane potential and fermentation profile is being intensely pursued because of the potential for developing advanced fermentation technologies. In the present study, we isolated naturally occurring strains of yeast from sake mash that produce high levels of malic acid and demonstrate that variations in mitochondrial membrane potential correlate with malic acid production. To define the underlying biochemical mechanism, we determined the activities of enzymes required for malic acid synthesis and found that pyruvate carboxylase and malate dehydrogenase activities in strains that produce high levels of malic acid were elevated compared with the standard sake strain K901. These results inspired us to hypothesize that decreased mitochondrial membrane potential was responsible for increased malic acid synthesis, and we present data supporting this hypothesis. Thus, the mitochondrial membrane potential of high malic acid producers was lower compared with standard strains. We conclude that mitochondrial membrane potential correlates with malic acid production. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.


Kamada M.,The University of Shimane | Kamada M.,Japan Society for the Promotion of Science | Kitayuguchi J.,Physical Education and Medicine Research Center | Inoue S.,Tokyo Medical University | And 6 more authors.
International Journal of Behavioral Nutrition and Physical Activity | Year: 2013

Background: We aimed to evaluate the effectiveness of a community-wide campaign (CWC) for promoting physical activity in middle-aged and elderly people.Methods: A cluster randomized controlled trial (RCT) with a community as the unit of randomization was performed using a population-based random-sampled evaluation by self-administered questionnaires in the city of Unnan, Shimane Prefecture, Japan. The evaluation sample included 6000 residents aged 40 to 79 years. We randomly allocated nine communities to the intervention group and three to the control group. The intervention was a CWC from 2009 to 2010 to promote physical activity, and it comprised information, education, and support delivery. The primary outcome was a change in engaging in regular aerobic, flexibility, and/or muscle-strengthening activities evaluated at the individual level.Results: In total, 4414 residents aged 40-79 years responded to a self-administered questionnaire (73.6% response rate). Awareness of the CWC was 79% in the intervention group. Awareness and knowledge were significantly different between the intervention and control groups, although there were no significant differences in belief and intention. The 1-year CWC did not significantly promote the recommended level of physical activity (adjusted odds ratio: 0.97; 95% confidence interval: 0.84-1.14).Conclusions: This cluster RCT showed that the CWC did not promote physical activity in 1 year. Significant differences were observed in awareness and knowledge between intervention and control groups as short-term impacts of the campaign.Trial registration: UMIN-CTR UMIN000002683. © 2013 Kamada et al.; licensee BioMed Central Ltd.


Kamioka H.,Tokyo University of Agriculture | Okada S.,Foundation Medicine | Tsutani K.,University of Tokyo | Park H.,National Center for Geriatrics and Gerontology | And 8 more authors.
Complementary Therapies in Medicine | Year: 2014

The objectives of this review were to summarize the evidence from randomized controlled trials (RCTs) on the effects of animal-assisted therapy (AAT). Studies were eligible if they were RCTs. Studies included one treatment group in which AAT was applied. We searched the following databases from 1990 up to October 31, 2012: MEDLINE via PubMed, CINAHL, Web of Science, Ichushi Web, GHL, WPRIM, and PsycINFO. We also searched all Cochrane Database up to October 31, 2012. Eleven RCTs were identified, and seven studies were about "Mental and behavioral disorders". Types of animal intervention were dog, cat, dolphin, bird, cow, rabbit, ferret, and guinea pig. The RCTs conducted have been of relatively low quality. We could not perform meta-analysis because of heterogeneity.In a study environment limited to the people who like animals, AAT may be an effective treatment for mental and behavioral disorders such as depression, schizophrenia, and alcohol/drug addictions, and is based on a holistic approach through interaction with animals in nature.To most effectively assess the potential benefits for AAT, it will be important for further research to utilize and describe (1) RCT methodology when appropriate, (2) reasons for non-participation, (3) intervention dose, (4) adverse effects and withdrawals, and (5) cost. © 2014 Elsevier Ltd.


Endo A.,Stellenbosch University | Endo A.,University of Turku | Irisawa T.,Tokyo University of Agriculture | Futagawa-Endo Y.,Stellenbosch University | And 4 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2012

Lactobacillus kunkeei is an inhabitant of fructose-rich niches and is a potential member of the fructophilic lactic acid bacteria. In the present study, the phylogenetic and biochemical characteristics of the type strain and eight isolates of L. kunkeei, originating from wine, flowers and honey, were studied. The nine isolates, including the type strain, formed a well-defined phylogenetic subcluster based on the analysis of 16S rRNA gene sequences. The subcluster was not closely related to other subclusters in the Lactobacillus phylogenetic group. Biochemically, the eight new isolates showed typical fructophilic characteristics. The eight isolates grew poorly on glucose, but grew well on fructose. Good growth on glucose was only recorded in the presence of electron acceptors. The type strain of L. kunkeei differed from the other isolates only on the basis of poor growth on fructose. Although they belong to a group of obligately heterofermentative lactic acid bacteria, all nine isolates, including the type strain, produced almost equimolar amounts of lactic acid and acetic acid and very little ethanol from glucose. Eight of the isolates can thus be regarded as typical 'obligately' fructophilic lactic acid bacteria. Although the type strain of L. kunkeei was phenotypically slightly different from the other isolates, it possessed several important fructophilic characteristics. On the basis of the evidence gathered in this study, the type strain of L. kunkeei is recognized as a member of the 'obligately' fructophilic lactic acid bacteria. © 2012 IUMS.


Okajima S.,Tokyo University of Agriculture | Masumoto M.,Yokohama Plant Protection Station
Zootaxa | Year: 2014

Azaleothrips, a phlaeothripine genus of fungus-feeding species, is presumably endemic to the Oriental Region between India and Japan. Although only 10 species have been known in this genus until now, a total of 35 species is recorded here, of which 26 are newly described: from Indonesia-A. bali sp.n., A. bulelengi sp.n., A. dentatus sp.n., A. dorsalis sp.n., A. floresi sp.n., A. inflavus sp.n., A. simulans sp.n., A. sulawesicus sp.n., from the Philippines - A. apoensis sp.n., A. bifidius sp.n., A. luzonensis sp.n., A. mindanaoensis sp.n., A. philippinensis sp.n., from Taiwan - A. atayal sp.n., A. formosae sp.n., A. taiwanus sp.n., from Thailand - A. flavicollis sp.n., A. phuketanus sp.n., A. pulcher sp.n., A. toshifumii sp.n., from Vietnam - A. laocai sp.n., A. vietnamensis sp.n., from W. Malaysia - A. malaya sp.n., A. reticulatus sp.n., A. rich-ardi sp.n., A. templeri sp.n. In addition A. magnus Chen, described from Taiwan, is newly synonymized with A. moundi. Azaleothrips laevigatus, described from southern Japan, is newly recorded more widely in Southeast Asia. A key to 33 species is provided, but A. bhattii and A. lineus cannot be recognized because of the poor information in the original de-scriptions. Copyright © 2014 Magnolia Press.


Go J.,K. MIKIMOTO and Co. | Nagai K.,K. MIKIMOTO and Co. | Segawa S.,Tokyo University of Agriculture | Honjo T.,Kagawa University
Nippon Suisan Gakkaishi (Japanese Edition) | Year: 2016

Recently, red tides caused by the dinoflagellate Karenia mikimotoi in pearl-culturing areas such as Ago Bay, Mie Prefecture have raised concerns about their effects on the Akoya pearl oyster Pinctada fucata. We assessed the mortality of juvenile oysters in red tide seawater and investigated the effect of the dinoflagellates on valve movement of mature oysters. Of juvenile oysters, 7.5percent,died after 36 h in seawater with a K. mikimotoi density of 1×104 cells/mL and all oysters died after 24 h with 6×104 cells/mL. Frequency of valve movement of mature oysters rose with increase of cell density, and became significantly higher than that of the control at 3×103 cells/ mL.


PubMed | Tokyo University of Agriculture, Hida Region Livestock Hygiene Service Center, Shirakawa Institute of Animal Genetics and Gifu Prefectural Livestock Research Institute
Type: Journal Article | Journal: Animal science journal = Nihon chikusan Gakkaiho | Year: 2016

Isoleucyl-tRNA synthetase (IARS) c.235G>C (p.V79L) is a causative mutation for a recessive disease called IARS disorder in Japanese black cattle. The disease is involved in weak calf syndrome and is characterized by low birth weight, weakness and poor suckling. The gestation period is often slightly extended, implying that intrauterine growth is retarded. In a previous analysis of 2597 artificial insemination (AI) procedures, we suggested that the IARS mutation might contribute toward an increase in the incidence of prenatal death. In this study, we extended this analysis to better clarify the association between the IARS mutation and prenatal death. The IARS genotypes of 92 animals resulting from crosses between carrier (G/C) G/C were 27 normal (G/G), 55G/C and 10 affected animals (C/C) (expected numbers: 23, 46 and 23, respectively). Compared to the expected numbers, there were significantly fewer affected animals in this population (P<0.05), suggesting that more than half of the affected embryos died prenatally. When the number of AI procedures examined was increased to 11580, the frequency of re-insemination after G/C G/C insemination was significantly higher at 61-140 days (P<0.001). The findings suggested that the homozygous IARS mutation not only causes calf death, but also embryonic or fetal death.


PubMed | Centers for Disease Control and Prevention, Research and Innovation, Iowa State University, Ministry of Health and 10 more.
Type: Journal Article | Journal: PloS one | Year: 2015

The World Health Organization (WHO) initiative to estimate the global burden of foodborne diseases established the Foodborne Diseases Burden Epidemiology Reference Group (FERG) in 2007. In addition to global and regional estimates, the initiative sought to promote actions at a national level. This involved capacity building through national foodborne disease burden studies, and encouragement of the use of burden information in setting evidence-informed policies. To address these objectives a FERG Country Studies Task Force was established and has developed a suite of tools and resources to facilitate national burden of foodborne disease studies. This paper describes the process and lessons learned during the conduct of pilot country studies under the WHO FERG initiative.Pilot country studies were initiated in Albania, Japan and Thailand in 2011 and in Uganda in 2012. A brief description of each study is provided. The major scientific issue is a lack of data, particularly in relation to disease etiology, and attribution of disease burden to foodborne transmission. Situation analysis, knowledge translation, and risk communication to achieve evidence-informed policies require specialist expertise and resources.The FERG global and regional burden estimates will greatly enhance the ability of individual countries to fill data gaps and generate national estimates to support efforts to reduce the burden of foodborne disease.


PubMed | Health Science University, Mimaki Onsen Spa Clinic, Physical Education and Medicine Research Center Unnan, Tokyo University of Agriculture and 3 more.
Type: | Journal: Complementary therapies in medicine | Year: 2016

The objective of this review were to summarize evidence for the effectiveness of Pilates exercise (PE) and to assess the quality of systematic review (SRs) based on randomized controlled trials (RCTs).A systematic review of SRs based on RCTs.Studies were eligible if they were RCTs. Studies included those with one treatment group in which PE was applied. We searched the following databases from 1995 up to August 20, 2014: MEDLINE via PubMed, CINAHL, Web of Science, Global Health Library, and Ichushi-Web. We also searched All Cochrane Database and Campbell Systematic Reviews up to August 20, 2014. Based on the International Classification of Diseases-10 (ICD-10), we identified a disease targeted for each article.Nine studies met all inclusion criteria. As a whole, the quality of the articles was good. Seven studies were about Musculoskeletal system and connective tissue (M5456). There were two studies in Factors influencing health status and contact with health services (Z723). The traits of participants were for females and the comparatively young- and middle-aged. Five SRs for chronic low back pain (CLBP) concluded that there was pain-relief and functional improvement of the intervention in the short term, but two SRs were inconclusive about the effectiveness of PE. There were no adverse events described in any of the studies.Although no SR reported any adverse effect or harm by PE, there was pain-relief and functional improvement attributed to PE in the short term in participants with CLBP. There was also evidence of improved flexibility and dynamic balance, and of enhanced muscular endurance in healthy people in the short term. In addition, there may have been an effect on body composition in the short term.


PubMed | Japan National Institute of Advanced Industrial Science and Technology, Tokyo University of Agriculture and Kasetsart University
Type: | Journal: Applied microbiology and biotechnology | Year: 2016

We investigated the effects of free ammonia (FA) and free nitrous acid (FNA) concentrations on the predominant ammonia-oxidizing bacteria (AOB) and the emission of nitrous oxide (N


PubMed | Tokyo University of Agriculture and Yokohama Plant Protection Station
Type: Journal Article | Journal: Zootaxa | Year: 2014

Azaleothrips, a phlaeothripine genus of fungus-feeding species, is presumably endemic to the Oriental Region between India and Japan. Although only 10 species have been known in this genus until now, a total of 35 species is recorded here, of which 26 are newly described: from Indonesia--A. bali sp.n., A. bulelengi sp.n., A. dentatus sp.n., A. dorsalis sp.n., A. floresi sp.n., A. inflavus sp.n., A. simulans sp.n., A. sulawesicus sp.n., from the Philippines--A. apoensis sp.n., A. bifidius sp.n., A. luzonensis sp.n., A. mindanaoensis sp.n., A. philippinensis sp.n., from Taiwan--A. atayal sp.n., A. formosae sp.n., A. taiwanus sp.n., from Thailand--A. flavicollis sp.n., A. phuketanus sp.n., A. pulcher sp.n., A. toshifumii sp.n., from Vietnam--A. laocai sp.n., A. vietnamensis sp.n., from W. Malaysia--A. malaya sp.n., A. reticulatus sp.n., A. richardi sp.n., A. templeri sp.n. In addition A. magnus Chen, described from Taiwan, is newly synonymized with A. moundi. Azaleothrips laevigatus, described from southern Japan, is newly recorded more widely in Southeast Asia. A key to 33 species is provided, but A. bhattii and A. lineus cannot be recognized because of the poor information in the original descriptions.


PubMed | Shibaura Institute of Technology, Nihon University, Tokyo University of Agriculture, University of Tokyo and 2 more.
Type: Journal Article | Journal: PloS one | Year: 2014

Muscle contraction results from attachment-detachment cycles between myosin heads extending from myosin filaments and actin filaments. It is generally believed that a myosin head first attaches to actin, undergoes conformational changes to produce force and motion in muscle, and then detaches from actin. Despite extensive studies, the molecular mechanism of myosin head conformational changes still remains to be a matter for debate and speculation. The myosin head consists of catalytic (CAD), converter (CVD) and lever arm (LD) domains. To give information about the role of these domains in the myosin head performance, we have examined the effect of three site-directed antibodies to the myosin head on in vitro ATP-dependent actin-myosin sliding and Ca2+-activated contraction of muscle fibers. Antibody 1, attaching to junctional peptide between 50K and 20K heavy chain segments in the CAD, exhibited appreciable effects neither on in vitro actin-myosin sliding nor muscle fiber contraction. Since antibody 1 covers actin-binding sites of the CAD, one interpretation of this result is that rigor actin-myosin linkage is absent or at most a transient intermediate in physiological actin-myosin cycling. Antibody 2, attaching to reactive lysine residue in the CVD, showed a marked inhibitory effect on in vitro actin-myosin sliding without changing actin-activated myosin head (S1) ATPase activity, while it showed no appreciable effect on muscle contraction. Antibody 3, attaching to two peptides of regulatory light chains in the LD, had no significant effect on in vitro actin-myosin sliding, while it reduced force development in muscle fibers without changing MgATPase activity. The above definite differences in the effect of antibodies 2 and 3 between in vitro actin-myosin sliding and muscle contraction can be explained by difference in experimental conditions; in the former, myosin heads are randomly oriented on a glass surface, while in the latter myosin heads are regularly arranged within filament-lattice structures.


PubMed | Mimaki Onsen Spa Clinic, Physical Education and Medicine Research Center Unnan, Foundation Medicine, University of Tokyo and 4 more.
Type: Journal Article | Journal: Complementary therapies in clinical practice | Year: 2014

The purpose of this study was to assess the quality of study reports on spa therapy based on randomized controlled trials by the spa therapy and balneotherapy checklist (SPAC), and to show the relationship between SPAC score and the characteristics of publication. We searched the following databases from 1990 up to September 30, 2013: MEDLINE via PubMed, CINAHL, Web of Science, Ichushi Web, Global Health Library, the Western Pacific Region Index Medicus, PsycINFO, and the Cochrane Database of Systematic Reviews. We used the SPAC to assess the quality of reports on spa therapy and balneotherapy trials (SPAC) that was developed using the Delphi consensus method. Fifty-one studies metall inclusion criteria. Forty studies (78%) were about Diseases of the musculoskeletal system and connective). The total SPAC score (full-mark; 19pts) was 10.82.3pts (meanSD). The items for which a description was lacking (very poor; <50%) in many studies were as follows: locations of spa facility where the data were collected; pH; scale of bathtub; presence of other facility and exposure than bathing (sauna, steam bath, etc.); qualification and experience of care provider; Instructions about daily life and adherence. We clarified that there was no relationship between the publish period, languages, and the impact factor (IF) for the SPAC score. In order to prevent flawed description, SPAC could provide indispensable information for researchers who are going to design a research protocol according to each disease.


PubMed | Tokyo University of Agriculture, Kyushu University and Yamanashi University
Type: Journal Article | Journal: Biology of reproduction | Year: 2016

The germ line reprogramming barrier resets parental epigenetic modifications according to sex, conferring totipotency to mammalian embryos upon fertilization. However, it is not known whether epigenetic errors are committed during germ line reprogramming that are then transmitted to germ cells, and consequently to offspring. We addressed this question in the present study by performing a genome-wide DNA methylation analysis using a target postbisulfite sequencing method in order to identify DNA methylation errors in cloned mouse sperm. The sperm genomes of two somatic cell-cloned mice (CL1 and CL7) contained significantly higher numbers of differentially methylated CpG sites (P = 0.0045 and P = 0.0116). As a result, they had higher numbers of differentially methylated CpG islands. However, there was no evidence that these sites were transmitted to the sperm genome of offspring. These results suggest that DNA methylation errors resulting from embryo cloning are transmitted to the sperm genome by evading the germ line reprogramming barrier.


PubMed | Japan National Institute of Agrobiological Science, Tokyo University of Agriculture and Kasetsart University
Type: | Journal: Frontiers in plant science | Year: 2015

Genus Vigna comprise several domesticated species including cowpea and mungbean, and diverse wild species. We found an introgressive hybrid population derived from two wild species, Vigna umbellata and Vigna exilis, in Ratchaburi district, Thailand. The hybrid was morphologically similar to V. umbellata but habituated in a limestone rock mountain, which is usually dominated by V. exilis. Analyzing simple sequence repeat loci indicated the hybrid has undergone at least one round of backcross by V. umbellata. We found the hybrid acquired vigorous growth from V. umbellata and drought tolerance plus early flowering from V. exilis, and thus has taken over some habitats of V. exilis in limestone karsts. Given the wide crossability of V. umbellata, the hybrid can be a valuable genetic resource to improve drought tolerance of some domesticated species.


PubMed | Tokyo Gakugei University, Tokyo University of Science and Tokyo University of Agriculture
Type: Journal Article | Journal: Bioscience, biotechnology, and biochemistry | Year: 2016

Part of the salt in soy sauce formed no eutectic H2O2NaCl crystals at sub-zero temperatures and remained in a freeze-concentrated product. NMR line width of (23)Na was broader in the concentrated soy sauce than in the material. A broad line width of (23)Na was also observed in an aqueous solution of NaCl and a non-diffusible soy sauce fraction. The data indicate that part of the salt in soy sauce interacted with its non-diffusible fraction and that such bound salt formed no eutectic crystals.


PubMed | Tokyo University of Agriculture, Stellenbosch University, Tokyo Medical University, RIKEN and University of Turku
Type: Journal Article | Journal: Systematic and applied microbiology | Year: 2016

Lactobacillus kunkeei is classified as a sole obligate fructophilic lactic acid bacterium that is found in fructose-rich niches, including the guts of honeybees. The species is differentiated from other lactobacilli based on its poor growth with glucose, enhanced growth in the presence of oxygen and other electron acceptors, and production of high concentrations of acetate from the metabolism of glucose. These characteristics are similar to phylogenetically distant Fructobacillus spp. In the present study, the genomic structure of L. kunkeei was characterized by using 16 different strains, and it had significantly less genes and smaller genomes when compared with other lactobacilli. Functional gene classification revealed that L. kunkeei had lost genes specifically involved in carbohydrate transport and metabolism. The species also lacked most of the genes for respiration, although growth was enhanced in the presence of oxygen. The adhE gene of L. kunkeei, encoding a bifunctional alcohol dehydrogenase (ADH)/aldehyde dehydrogenase (ALDH) protein, lacked the part encoding the ADH domain, which is reported here for the first time in lactic acid bacteria. The deletion resulted in the lack of ADH activity, implying a requirement for electron acceptors in glucose assimilation. These results clearly indicated that L. kunkeei had undergone a specific reductive evolution in order to adapt to fructose-rich environments. The reduction characteristics were similar to those of Fructobacillus spp., but distinct from other lactobacilli with small genomes, such as Lactobacillus gasseri and Lactobacillus vaginalis. Fructose-richness thus induced an environment-specific gene reduction in phylogenetically distant microorganisms.


PubMed | National Institute for Physiological science, Kyoto University and Tokyo University of Agriculture
Type: | Journal: American journal of physiology. Endocrinology and metabolism | Year: 2016

Emergence of thermogenic adipocytes such as brown and beige adipocytes is critical for whole-body energy metabolism. Promoting the emergence of these adipocytes could be a viable strategy in treating obesity and its related diseases. However, little is known regarding the mechanisms that regulate the emergence of these adipocytes in obese adipose tissue. Here, we demonstrated that classically activated macrophages (M1 M) suppress the induction of thermogenic adipocytes in obese adipose tissues of mice. Cold exposure significantly induced the expression levels of uncoupling protein-1 (UCP1), which is a mitochondrial protein unique in thermogenic adipocytes, in C57BL/6 mice fed a normal diet. However, UCP1 induction was significantly suppressed in adipose tissues of C57BL/6 mice fed a high-fat diet, into which M1 M infiltrated. Depletion of M1 M using clodronate liposomes eliminated the suppressive effect and markedly reduced the mRNA level of tumor necrosis factor- (TNF) in the adipose tissues. Importantly, consistent with the observed changes in the expression levels of marker genes for thermogenic adipocytes, combination treatment of clodronate liposomes and cold exposure resulted in metabolic benefits such as lowered body weight and blood glucose level in obese mice. Moreover, intraperitoneal injection of recombinant TNF protein suppressed UCP1 induction in lean adipose tissues of mice. Collectively, our data indicate that infiltrated M1 M suppress the induction of thermogenic adipocytes in obese adipose tissues via TNF. This report suggests that inflammation induced by infiltrated M could cause not only insulin resistance but also reduction of energy expenditure in adipose tissues.


PubMed | Tohoku University, Yamanashi University, Tokyo University of Agriculture, Kyushu University and Hokkaido University
Type: Journal Article | Journal: Animal science journal = Nihon chikusan Gakkaiho | Year: 2016

Nuclear autoantigenic sperm protein (NASP) is associated with DNA replication, cell proliferation, and cell cycle progression through its specific binding to histones. The aim of this study was to examine the roles of NASP in bovine preimplantation embryonic development. Using NASP gene knockdown (KD), we confirmed the reduction of NASP messenger RNA (mRNA) expression during preimplantation development. NASP KD did not affect cleavage but significantly decreased development of embryos into the blastocyst stage. Furthermore, blastocyst hatching was significantly decreased in NASP KD embryos. Cell numbers in the inner cell mass of NASP KD blastocysts were also decreased compared to those of controls. These results suggest that NASP mRNA expression is required for preimplantation development into the blastocyst stage in cattle.


PubMed | Tokyo University of Agriculture, Center for Regenerative MedicineNational Research Institute for Child Health and Development, Fukushima Medical University and Kanagawa University
Type: Journal Article | Journal: Reproduction (Cambridge, England) | Year: 2016

Spatiotemporal expression of transcription factors is crucial for genomic reprogramming. Pou5f1 (Oct4) is an essential transcription factor for reprogramming. A recent study reported that OCT4A, which is crucial for establishment and maintenance of pluripotent cells, is expressed in oocytes, but maternal OCT4A is dispensable for totipotency induction. Whereas another study reported that OCT4B, which is not related to pluripotency, is predominantly expressed instead of OCT4A during early preimplantation phases in mice. To determine the expression states of OCT4 in murine preimplantation embryos, we conducted in-depth expression and functional analyses. We found that pluripotency-related OCT4 mainly localizes to the cytoplasm in early preimplantation phases, with no major nuclear localization until the 8-16-cell stage despite high expression in both oocytes and early embryos. RNA-sequencing analysis using oocytes and early preimplantation embryos could not identify the splice variants creating alternative forms of OCT4 protein. Forced expression of OCT4 in zygotes by the injection of polyadenylated mRNA clearly showed nuclear localization of OCT4 protein around 3-5-fold greater than physiological levels and impaired developmental competency in a dose-dependent manner. Embryos with modest overexpression of OCT4 could develop to the 16-cell stage; however, more than 50% of the embryos were arrested at this stage, similar to the results for OCT4 depletion. In contrast, extensive overexpression of OCT4 resulted in complete arrest at the 2-cell stage accompanied by downregulation of zygotically activated genes and repetitive elements related to the totipotent state. These results demonstrated that OCT4 protein localization was spatiotemporally altered during preimplantation development, and strict control of Oct4 protein levels was essential for proper totipotential reprogramming.


PubMed | Tokyo University of Agriculture, Universiti Malaysia Sabah and Kitasato University
Type: Journal Article | Journal: Mitochondrial DNA. Part A, DNA mapping, sequencing, and analysis | Year: 2016

Here we report the complete mitochondrial genome of the Bornean banteng Bos javanicus lowi (Cetartiodactyla, Bovidae), which was determined using next-generation sequencing. The mitochondrial genome is 16,344bp in length containing 13 protein-coding genes, 21 tRNAs and 2 rRNAs. It shows the typical pattern of bovine mitochondrial arrangement. Phylogenetic tree analysis of complete mtDNA sequences showed that Bornean banteng is more closely related to gaur than to other banteng subspecies. Divergence dating indicated that Bornean banteng and gaur diverged from their common ancestor approximately 5.03 million years ago. These results suggest that Bornean banteng might be a distinct species in need of conservation.


PubMed | Tokyo University of Agriculture, Stellenbosch University, National Institute of Genetics, Tokyo Medical University and University of Turku
Type: | Journal: BMC genomics | Year: 2015

Fructobacillus spp. in fructose-rich niches belong to the family Leuconostocaceae. They were originally classified as Leuconostoc spp., but were later grouped into a novel genus, Fructobacillus, based on their phylogenetic position, morphology and specific biochemical characteristics. The unique characters, so called fructophilic characteristics, had not been reported in the group of lactic acid bacteria, suggesting unique evolution at the genome level. Here we studied four draft genome sequences of Fructobacillus spp. and compared their metabolic properties against those of Leuconostoc spp.Fructobacillus species possess significantly less protein coding sequences in their small genomes. The number of genes was significantly smaller in carbohydrate transport and metabolism. Several other metabolic pathways, including TCA cycle, ubiquinone and other terpenoid-quinone biosynthesis and phosphotransferase systems, were characterized as discriminative pathways between the two genera. The adhE gene for bifunctional acetaldehyde/alcohol dehydrogenase, and genes for subunits of the pyruvate dehydrogenase complex were absent in Fructobacillus spp. The two genera also show different levels of GC contents, which are mainly due to the different GC contents at the third codon position.The present genome characteristics in Fructobacillus spp. suggest reductive evolution that took place to adapt to specific niches.


PubMed | Tokyo University of Agriculture, Japan International Center for Materials Nanoarchitectonics, Ultizyme International Ltd. and Missouri State University
Type: | Journal: Bioelectrochemistry (Amsterdam, Netherlands) | Year: 2016

Several bacterial flavin adenine dinucleotide (FAD)-harboring dehydrogenase complexes comprise three distinct subunits: a catalytic subunit with FAD, a cytochrome c subunit containing three hemes, and a small subunit. Owing to the cytochrome c subunit, these dehydrogenase complexes have the potential to transfer electrons directly to an electrode. Despite various electrochemical applications and engineering studies of FAD-dependent dehydrogenase complexes, the intra/inter-molecular electron transfer pathway has not yet been revealed. In this study, we focused on the conserved Cys-rich region in the catalytic subunits using the catalytic subunit of FAD dependent glucose dehydrogenase complex (FADGDH) as a model, and site-directed mutagenesis and electron paramagnetic resonance (EPR) were performed. By co-expressing a hitch-hiker protein (-subunit) and a catalytic subunit (-subunit), FADGDH complexes were prepared, and the properties of the catalytic subunit of both wild type and mutant FADGDHs were investigated. Substitution of the conserved Cys residues with Ser resulted in the loss of dye-mediated glucose dehydrogenase activity. ICP-AEM and EPR analyses of the wild-type FADGDH catalytic subunit revealed the presence of a 3Fe-4S-type iron-sulfur cluster, whereas none of the Ser-substituted mutants showed the EPR spectrum characteristic for this cluster. The results suggested that three Cys residues in the Cys-rich region constitute an iron-sulfur cluster that may play an important role in the electron transfer from FAD (intra-molecular) to the multi-heme cytochrome c subunit (inter-molecular) electron transfer pathway. These features appear to be conserved in the other three-subunit dehydrogenases having an FAD cofactor.


PubMed | Yamanashi University, Tohoku University, Tokyo University of Agriculture, Okayama University and 2 more.
Type: Journal Article | Journal: Biochemical and biophysical research communications | Year: 2016

An aerobic endosulfan sulfate-degrading bacterium, Rhodococcus koreensis strain S1-1, was isolated from soil to which endosulfan had been applied annually for more than 10 years until 2008. The strain isolated in this work reduced the concentration of endosulfan sulfate (2) from 12.25M to 2.11M during 14d at 30C. Using ultra performance liquid chromatography-electrospray ionization-mass spectroscopy (UPLC-ESI-MS), a new highly water-soluble metabolite possessing six chlorine atoms was found to be endosulfan diol monosulfate (6), derived from 2 by hydrolysis of the cyclic sulfate ester ring. The structure of 6 was elucidated by chemical synthesis of the candidate derivatives and by HR-MS and UPLC-MS analyses. Therefore, it was suggested that the strain S1-1 has a new metabolic pathway of 2. In addition, 6 was expected to be less toxic among the metabolites of 1 because of its higher water-solubility.


Norikoshi R.,Japan National Agriculture and Food Research Organization | Norikoshi R.,Tokyo University of Agriculture | Imanishi H.,Tokyo University of Agriculture | Ichimura K.,Japan National Agriculture and Food Research Organization
Journal of the Japanese Society for Horticultural Science | Year: 2013

The number of epidermal cells, osmotic potential, and carbohydrate and inorganic ion concentrations in petals during development and opening of Tweedia caerulea D. Don flowers was studied. The number of adaxial epidermal cells was greater than that of abaxial epidermal cells at all stages. The increase in cell number stopped at the stage just before flower opening. The size of adaxial and abaxial epidermal cells increased during flower development and opening. The results indicate that petal growth before flower opening depended on cell division and expansion, and petal growth during flower opening was attributable to petal cell expansion. Osmotic potential decreased and fructose, glucose and sucrose concentrations in the petals gradually increased during flower opening. Starch content and total inorganic ion concentration were almost constant during flower opening. Decreased osmotic potential is mainly attributed to increased glucose, fructose and sucrose concentrations. It is concluded that an increase in these sugar concentrations largely contributes to the decrease in osmotic potential. This decrease may facilitate water influx to cells, thereby maintaining pressure potential, which is apparently involved in petal cell expansion associated with flower opening. © JSHS 2013.


Rameshkumar N.,Indian National Institute for Interdisciplinary Science and Technology | Lang E.,Leibniz Institute DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH | Tanaka N.,Tokyo University of Agriculture
Systematic and Applied Microbiology | Year: 2016

Three strains, namely L3B39T, L3D16, and L1E9, were obtained while studying the cultivable rhizosphere bacteria of saline tolerant pokkali rice, at Kerala, India. The novel strains were negative for many plant growth promoting plate assays such as phytohormone and siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase and growth in nitrogen free agar medium but found to utilize malic acid, citrate, D-glucose, L-arabinose, and D-maltose, important components of the plant root exudates, indicating that they are normal plant rhizosphere residents without yet known benefits to the plant. The 16S rRNA gene analysis placed these strains in the genus Vogesella, forming a separate branch independent of the previously described type strains of this genus in all tree making algorithms applied. Vogesella perlucida DS-28T was the type strain with highest 16S rRNA sequence similarity (97.59%). DNA-DNA hybridization values among these novel strains were above 85% andthat with Vogesella perlucida LMG 24214T was below 50%. Phenotypically, the novel strains can be differentiated from Vogesella perlucida LMG 24214T by many characters such as NaCl tolerance, growth temperature, and utilization of L-arabinose, D-maltose, and citrate. These novel strains contain C16:1 ω6c/C16:1 ω7c and C16:0 as major fatty acids, ubiquinone Q-8 as the major respiratory quinone, and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Based on the results obtained from the polyphasic taxonomic approach we conclude that the strains belong to a novel Vogesella species for which the name Vogesella oryzae sp.nov. is proposed. The type strain is L3B39T (= LMG 28272T = DSM 28780T). © 2015 Elsevier GmbH.


Kokubo Y.,Japan National Cardiovascular Center Research Institute | Iso H.,Osaka University | Saito I.,Ehime University | Yamagishi K.,University of Tsukuba | And 4 more authors.
European Journal of Clinical Nutrition | Year: 2011

Background/Objectives:There has been no study with regard to the association between dietary fibers and the incidence of stroke and coronary heart disease (CHD) in Asia. We investigated the association between dietary fiber and the risk of cardiovascular disease (CVD), which we defined as stroke or CHD, in a Japanese population.Subjects/Methods:We studied 86 387 Japanese subjects (age 45-65 years, without CVD or cancer in 1995 as Cohort I and in 1998 as Cohort II) and used a self-administered questionnaire to follow-up the participants until the end of 2004. Dietary fiber intake was estimated from food-frequency questionnaires comprising 138 food items.Results:After 899 141 person-years of follow-up, we documented the incidence of 2553 strokes and 684 cases of CHD. Multivariable-adjusted hazard ratios (95% confidence intervals (CIs)) of CVD for the third to fifth quintiles of total fiber were 0.79 (0.63-0.99), 0.70 (0.54-0.89) and 0.65 (0.48-0.87) in women, respectively, compared with the lowest quintile. Total fiber intake was inversely associated with the incidence of stroke, either cerebral infarction or intracerebral hemorrhage in women. The results for insoluble fiber in women were similar to those for total fiber, whereas those for soluble fiber were weak. An inverse association of total fiber with CVD was observed primarily in non-smokers (P for trend0.045 and 0.001) and not in smokers (probability values for interaction between total fiber and smoking were 0.06 and 0.01 in men and women, respectively).Conclusions:Higher total dietary fiber was associated with reduced risk of CVD in Japanese non-smokers. © 2011 Macmillan Publishers Limited. All rights reserved.


Akiyama S.,Kyoto University | Nesumi A.,Japan National Agriculture and Food Research Organization | Maeda-Yamamoto M.,Japan National Agriculture and Food Research Organization | Uehara M.,Tokyo University of Agriculture | Murakami A.,Kyoto University
BioFactors | Year: 2012

Sunrouge, an anthocyanin-rich tea, has similar levels of catechins as "Yabukita," the most popular green tea cultivar consumed in Japan. Green tea polyphenols (GTPs) have attracted interest due to their potent antioxidative activities combined with a lack of side effects in humans at normal consumption levels. However, we previously reported that high doses (0.5 and 1%) of dietary GTPs can result in deterioration of colitis and failed to prevent colon carcinogenesis in inflamed colons. In the present study, we determined the inhibitory effects of Sunrouge on colitis in dextran sodium sulfate (DSS)-treated and untreated control mice. Five-week-old female ICR mice were administered a single dose of Yabukita or Sunrouge (extracts in 1 mL distilled water) via a stomach tube for 3 weeks. After 1 week of treatment, the mice were divided into four groups (two Yabukita and two Sunrouge groups) and given drinking water with or without 3% DSS for 2 weeks, then they were euthanized. Those treated with DSS developed watery diarrhea and bloody stools, and showed body weight loss, spleen hypertrophy, and shortening of the colon, as well as deteriorations in survival rate, liver function, colon mucosal interleukin-1β level and expression of phase II detoxification enzyme mRNA. Sunrouge improved these DSS-induced symptoms, at least in part, whereas Yabukita showed either no effect or adverse effects in regard to some those parameters. It is suggested that the differences between Yabukita and Sunrouge on DSS-induced colitis might be due to the high levels of anthocyanins found in Sunrouge tea. © 2012 International Union of Biochemistry and Molecular Biology, Inc.


Wakamori K.,Japan Manned Space Systems Corporation | Ichikawa D.,Japan Manned Space Systems Corporation | Niimi R.,Japan Manned Space Systems Corporation | Suzuki M.,Tokyo University of Agriculture
International Geoscience and Remote Sensing Symposium (IGARSS) | Year: 2013

An operational processing and analysis system for rice growth monitoring has been developed at Japan Manned Space Systems Corporation and Tokyo University of Agriculture. The system processes DMC images having capability to multi-temporal observation during the growing season and generates image maps for rice growing status through satellite-derived NDVI-SPAD value. The monitoring was conducted in paddy fields of northern part of Japan. Mapping algorithm was established by correlation NDVI derived from DMC images and ground collected SPAD value. The correlation coefficient between the SPAD value of rice leaf and NDVI showed good agreement and R2 was 0.79. © 2013 IEEE.


Harada K.,National Fisheries University | Maeda T.,National Fisheries University | Hasegawa Y.,National Fisheries University | Tokunaga T.,National Fisheries University | And 2 more authors.
Molecular Medicine Reports | Year: 2010

Fish sauces are fermented seasonings traditionally used throughout Asia, including Japan. Here, we report on the antioxidant activity of 30 fish sauces, among them a puffer fish sauce developed specifically for this study. To determine the antioxidant activity (i.e., the peroxyl radical elimination capacity) of the fish sauces, the oxygen radical absorbance capacity (ORAC) was measured. ORAC values ranged between 104 μmol (flatfish sauce 1) and 103 μmol (sandfish sauce) trolox equivalent (TE)/100 ml of fish sauce. Hydroxyl radical scavenging activity (IC50) was measured using electron spin resonance. IC50 values ranged between 0.081% (puffer fish sauce) and 0.653% (sardine fish sauce 7). Puffer fish sauce had a high ORAC value (8,365 μmol TE/100 ml) and the highest hydroxyl radical scavenging activity (0.081). The relationship between the ORAC and IC 50 values of the 30 fish sauces was determined to be intermediate (r =-0.521, p=0.01).


Sato T.,Nara Women's University | Sato T.,Kyoto University | Watanabe K.,Kyoto University | Kanaiwa M.,Tokyo University of Agriculture | And 3 more authors.
Ecology | Year: 2011

Parasites are ubiquitous in natural systems and ecosystem-level effects should be proportional to the amount of biomass or energy flow altered by the parasites. Here we quantified the extent to which a manipulative parasite altered the flow of energy through a forest-stream ecosystem. In a Japanese headwater stream, camel crickets and grasshoppers (Orthoptera) were 20 times more likely to enter a stream if infected by a nematomorph parasite (Gordionus spp.), corroborating evidence that nematomorphs manipulate their hosts to seek water where the parasites emerge as free-living adults. Endangered Japanese trout (Salvelinus leucomaenis japonicus) readily ate these infected orthopterans, which due to their abundance, accounted for 60% of the annual energy intake of the trout population. Trout grew fastest in the fall, when nematomorphs were driving energy-rich orthopterans into the stream. When infected orthopterans were available, trout did not eat benthic invertebrates in proportion to their abundance, leading to the potential for cascading, indirect effects through the forest-stream ecosystem. These results provide the first quantitative evidence that a manipulative parasite can dramatically alter the flow of energy through and across ecosystems. © 2011 by the Ecological Society of America.


Harms D.W.,University of Nebraska Medical Center | Quadros R.M.,University of Nebraska Medical Center | Seruggia D.,CSIC - National Center for Biotechnology | Seruggia D.,CIBER ISCIII | And 6 more authors.
Current Protocols in Human Genetics | Year: 2014

The availability of techniques to create desired genetic mutations has enabled the laboratory mouse as an extensively used model organism in biomedical research including human genetics. A new addition to this existing technical repertoire is the CRISPR/Cas system. Specifically, this system allows editing of the mouse genome much more quickly than the previously used techniques, and, more importantly, multiple mutations can be created in a single experiment. Here we provide protocols for preparation of CRISPR/Cas reagents and microinjection into one-cell mouse embryos to create knockout or knock-in mouse models. © 2014 by John Wiley & Sons, Inc.


Shirasuna K.,Tokyo University of Agriculture | Matsumoto H.,Obihiro University of Agriculture and Veterinary Medicine | Matsuyama S.,Japan National Agriculture and Food Research Organization | Kimura K.,Okayama University | And 2 more authors.
Reproduction | Year: 2015

When pregnancy is established, interferon tau (IFNT), a well-known pregnancy recognition signal in ruminants, is secreted by embryonic trophoblast cells and acts within the uterus to prepare for pregnancy. IFNT acts as an endocrine factor on the corpus luteum (CL) to induce refractory ability against the luteolytic action of PGF2α. Hypothesising that IFNT may influence not only the uterine environment but also the CL in cows via local or peripheral circulation, we investigated qualitative changes in the CL of pregnant cows during the maternal recognition period (day 16) and the CL of non-pregnant cows. The CL of pregnant animals had a higher number of neutrophils, and the expression of interleukin 8 (IL8) mRNA and its protein was higher as well as compared with the CL of non-pregnant animals. Although IFNT did not affect progesterone (P4) secretion and neutrophil migration directly, it stimulated IL8 mRNA expression on luteal cells (LCs), influencing the neutrophils, resulting in the increased migration of IFNT-activated neutrophils. Moreover, both IFNT-activated neutrophils and IL8 increased P4 secretion from LCs in vitro. Our novel finding was the increase in neutrophils and IL8 within the CL of pregnant cows, suggesting the involvement of IFNT function within the CL toward establishment of pregnancy in cows. The present results suggest that IFNT upregulates neutrophil numbers and function via IL8 on LCs in the CL of early pregnant cows and that both neutrophils and IL8, stimulated by IFNT, are associated with an increase in P4 concentrations during the maternal recognition period in cows. © 2015 Society for Reproduction and Fertility.


Ichikawa D.,Japan Manned Space Systems Corporation | Wakamori K.,Japan Manned Space Systems Corporation | Suzuki M.,Tokyo University of Agriculture
International Geoscience and Remote Sensing Symposium (IGARSS) | Year: 2014

Agriculture fields located in northern part of Japan having vector polygons as paddy, non-paddy and uncultivated attributes were investigated to identify paddy fields using RapidEye satellite images acquired on June 27 and July 28 of 2012. Paddy, other crop and uncultivated fields were selected from the vector polygons and the polygons were extracted from the images. A bimodal histograms of the extracted polygons were created and established identification algorithm for paddy field classification. The algorithm was applied to RapidEye image and created a map for active paddy fields of the area for 2012. © 2014 IEEE.


Takachi R.,Research Center for Cancer Prevention and Screening | Takachi R.,Tohoku University | Inoue M.,Research Center for Cancer Prevention and Screening | Shimazu T.,Research Center for Cancer Prevention and Screening | And 8 more authors.
American Journal of Clinical Nutrition | Year: 2010

Background: Although the influence of salt, per se, on the risk of cancer or cardiovascular disease (CVD) might differ from that of salt-preserved foods, few studies have simultaneously examined the effects of sodium and salted foods on the risk of either cancer or CVD. Objective: We simultaneously examined associations between sodium and salted food consumption and the risk of cancer and CVD. Design: During 1995-1998, a validated food-frequency questionnaire was administered to 77,500 men and women aged 45-74 y. During up to 598,763 person-years of follow-up until the end of 2004, 4476 cases of cancer and 2066 cases of CVD were identified. Results: Higher consumption of sodium was associated with a higher risk of CVD but not with the risk of total cancer: multivariate hazard ratios for the highest compared with lowest quintiles of intake were 1.19 (95% CI: 1.01, 1.40; P for trend: 0.06) for CVD and 1.04 (95% CI: 0.93, 1.16; P for trend: 0.63) for total cancer. Higher consumption of salted fish roe was associated with higher risk of total cancer, and higher consumption of cooking and table salt was associated with higher risk of CVD. Similar results were seen for the risk of gastric or colorectal cancer and stroke. Conclusions: Sodium intake as a whole salt equivalent may not increase the risk of cancer but may increase that of CVD. In contrast, salted food intake may increase the risk of cancer. Our findings support the notion that sodium and salted foods have differential influences on the development of cancer and CVD. © 2010 American Society for Nutrition.


Almuzara M.N.,University of Buenos Aires | Vazquez M.,Hospital Of Ninos Ricardo Gutierrez | Tanaka N.,Tokyo University of Agriculture | Turco M.,Hospital Of Ninos Ricardo Gutierrez | And 6 more authors.
Journal of Clinical Microbiology | Year: 2010

We report the first case of human infection due to Pseudomonas fulva. P. fulva caused acute meningitis following the placement of a drainage system in a 2-year-old female. Additionally, the isolate displayed a VIM-2 carbapenemase in a class 1 integron context. Copyright © 2010, American Society for Microbiology. All Rights Reserved.


Kobayashi M.,Otsuma Women's University | Kobayashi M.,Research Center for Cancer Prevention and Screening | Adachi H.Y.,Research Center for Cancer Prevention and Screening | Ishihara J.,Research Center for Cancer Prevention and Screening | And 2 more authors.
European Journal of Clinical Nutrition | Year: 2011

Background/Objectives:The effect of cooking loss on vitamin intake is an important consideration in dietary and epidemiological studies in Japanese. However, because few published food values have considered cooking effect, allowing for cooking loss in the assessment of vitamin intake in Japan has been difficult.Subjects/Methods:Seven-day dietary records and a fasting blood sample were collected from 102 men and 113 women in August of 1994 or 1995. Vitamin intake were estimated using two food databases, one composed of raw food only and the second of cooked food. Estimates were compared with blood levels.Results:Water-soluble vitamin intake using a food database including cooked food was lower than intakes estimated using a database composed of raw food only, except for pantothenic acid and vitamin B 12 intake. In particular, vitamin B 1 intake was 18.9% lower in men and 16.8% lower in women. However, when subjects were classified into the same and adjacent categories by joint classification by quintiles, appreciable change in ranking of a subject was not observed. Furthermore, the relationship between vitamin intake and biomarker did not improve when intake was calculated using a food database including cooked food.Conclusion:Although the effect of cooking loss on absolute values is not negligible, this might not significantly impact the ranking of subject intake estimations of vitamin intake in epidemiological studies. © 2011 Macmillan Publishers Limited. All rights reserved.


Wakamori K.,Japan Manned Space Systems Corporation | Ichikawa D.,Japan Manned Space Systems Corporation | Suzuki M.,Tokyo University of Agriculture
International Geoscience and Remote Sensing Symposium (IGARSS) | Year: 2014

An operational processing and analysis system for rice growth monitoring has been developed at Japan Manned Space Systems Corporation and Tokyo University of Agriculture. The system processes DMC images having capability to multi-temporal observation during the growing season and generates image maps for rice growing status through satellite-derived NDVI-SPAD value. The monitoring was conducted in paddy fields of northern part of Japan. Mapping algorithm was established by correlation NDVI derived from DMC images and ground collected SPAD value. The relation of NDVI and SPAD value can be grouped greatly between varieties in the growing process of rice. © 2014 IEEE.


Wigglesworth K.,The Jackson Laboratory | Lee K.-B.,Chonnam National University | Emori C.,Tokyo University of Agriculture | Sugiura K.,Tokyo University of Agriculture | Eppig J.J.,The Jackson Laboratory
Biology of Reproduction | Year: 2015

Cumulus cells and mural granulosa cells (MGCs) have functionally distinct roles in antral follicles, and comparison of their transcriptomes at a global and systems level can propel future studies on mechanisms underlying their functional diversity. These cells were isolated from small and large antral follicles before and after stimulation of immature mice with gonadotropins, respectively. Both cell types underwent dramatic transcriptomic changes, and differences between them increased with follicular growth. Although cumulus cells of both stages of follicular development are competent to undergo expansion in vitro, they were otherwise remarkably dissimilar with transcriptomic changes quantitatively equivalent to those of MGCs. Gene ontology analysis revealed that cumulus cells of small follicles were enriched in transcripts generally associated with catalytic components of metabolic processes, while those from large follicles were involved in regulation of metabolism, cell differentiation, and adhesion. Contrast of cumulus cells versus MGCs revealed that cumulus cells were enriched in transcripts associated with metabolism and cell proliferation while MGCs were enriched for transcripts involved in cell signaling and differentiation. In vitro and in vivo models were used to test the hypothesis that higher levels of transcripts in cumulus cells versus MGCs is the result of stimulation by oocyte-derived paracrine factors (ODPFs). Surprisingly ~48% of transcripts higher in cumulus cells than MGCs were not stimulated by ODPFs. Those stimulated by ODPFs were mainly associated with cell division, mRNA processing, or the catalytic pathways of metabolism, while those not stimulated by ODPFs were associated with regulatory processes such as signaling, transcription, phosphorylation, or the regulation of metabolism. © 2015 by the Society for the Study of Reproduction, Inc.


Pellicer J.,University of Barcelona | Garnatje T.,Institute Botanic Of Barcelona Csic Icub | Hidalgo O.,Ohio University | Tagashira N.,Hiroshima Jogakuin University | And 2 more authors.
Plant Biosystems | Year: 2010

Fluorescent in situ hybridisation (FISH) of 5S and 18S-5.8S-26S ribosomal DNA was carried out in two species of the genus Artemisia, belonging to the subgenera Artemisia (A. medioxima) and Absinthium (A. lagocephala), each one showing both low and high ploidy levels (2x, 4x and 16x, and 2x and 6x, respectively). Both species have a base chromosome number of x=9. Linkage of both rDNA genes has been observed confirming previous results. Diploid A. lagocephala (2n=18) shows three rDNA loci, and the hexaploid six. Also in A. medioxima, the number of rDNA loci does not increase in the proportion given by the ploidy level, and a relative loss is found. In this species, the diploid population shows two rDNA loci, the tetraploid four, and the hexaidecaploid has around 20. The results evidence a relative loss of rDNA loci and heterochromatin, a phenomenon that is more pronounced at higher ploidy levels. Nevertheless, the DAPI banding pattern of A. lagocephala does not follow this trend, as it shows a spectacular increase of heterochromatic bands at the hexaploid level. These results are discussed in the light of possible chromosome restructuring and gene silencing mechanisms that take place during polyploidy, and more especially allopolyploid formation. © 2010 Società Botanica Italiana.


Kim O.-K.,Tokyo University of Agriculture | Mizutani T.,Tokyo University of Agriculture | Natsuaki K.T.,Tokyo University of Agriculture | Lee K.-W.,Kyungpook National University | Soe K.,Ministry of Agriculture and Irrigation
Journal of Phytopathology | Year: 2010

Bottle gourd [Lagenaria siceraria (Mol.) Standl.] plants showing leaf mosaic and mottle were observed in Myanmar in 2007 and shown by RT-PCR and ELISA to be infected with Cucumber green mottle mosaic virus (CGMMV). This is the first report of the virus occurring in Myanmar. Despite considerable differences in geographical origins, natural host species and year of sampling of 22 CGMMV isolates, we found low genetic variation of the CP gene except for isolates GR3 and GR5, which showed similarity higher than 97%; based on the MP gene, and 16 CGMMV isolates showed similarity higher than 94% in nucleotide identities by pairwise comparison. Using MluI restriction endonuclease for CP genes, the CGMMV isolates fell into three types: Type I and Type II were included in the SH group and Type III in the W group. The two CGMMV isolates from Myanmar were found to belong to Type I and Type III, respectively. © 2009 Blackwell Verlag GmbH.


Matsuyama S.,Japan National Agriculture and Food Research Organization | Sakaguchi Y.,Tokyo University of Agriculture | Kimura K.,Japan National Agriculture and Food Research Organization
Journal of Reproduction and Development | Year: 2012

Elevated concentrations of circulating progesterone (P4) in the immediate post-ovulation period are associated with advancement of conceptus elongation in cattle. Superovulated (SOV) cattle have not only elevated plasma P4 concentrations but also multiple embryos in the uterus because of the formation of multiple corpora lutea. We examined the relationship between plasma P4 concentration and uterine glucose level in the immediate post-ovulation period and the presence and growth of multiple conceptuses in SOV cattle. SOV cattle were artificially inseminated with frozen-thawed semen at standing estrus (day 0), and the conceptuses were recovered by nonsurgical flushing of the uterus on day 13. In the SOV cattle, there were quadratic relationships between plasma P4 concentration on days 4, 5 and 7 and conceptus length and between number of conceptuses in the uterus and conceptus length. These results suggest that conceptus growth in SOV cattle is regulated by both systemic P4 level and number of conceptuses and that there are ranges of plasma P4 concentrations and numbers of conceptuses in the uterus that are suitable for conceptus growth and development. Plasma P4 concentrations on days 5 and 7, but not the numbers of conceptuses, were quadratically correlated with uterine glucose levels on day 13 in SOV cattle. In addition, conceptus length was positively correlated with uterine glucose level in SOV cattle. Accordingly, regardless of the number of conceptuses in the uterus, the plasma P4 concentration was well correlated with the regulation of conceptus growth via changes in uterine glucose levels in SOV cattle. © 2012 by the Society for Reproduction and Development.


Sakurai T.,Tokyo University of Agriculture | Kashimura O.,Tokyo University of Agriculture | Kano Y.,University of Electro - Communications | Ohno H.,Kyorin University | And 3 more authors.
Journal of Physiological Sciences | Year: 2013

We examined the role of nitric oxide (NO) in muscle repair and regeneration following repetitive eccentric contractions (ECC). A standardized exercise protocol was used to create eccentric contraction-induced injury to the left tibialis anterior muscle of 48 male Wistar rats (body wt 250-350 g), using a customized isokinetic test device and a bout of 40 ECCs under electrical stimulation. A nitric oxide synthase inhibitor, N(G)-nitro-l-arginine-methyl ester (l-NAME; 35 mg kg-1 day-1), was included in the diet for half the animals (n = 24) beginning 3 days prior to the ECC and continuing throughout the experiment, whereas the other half (n = 24) received a control diet. ECC/+l-NAME and ECC/-l-NAME were killed after the ECC protocol at 0, 1, 3 and 7 days (n = 6 on each day). An unexercised contralateral limb with and without l-NAME infusion served as a respective control muscle at each time point. Muscle NO content, skeletal muscle damage, leukocyte infiltration, calpain activity, and MyoD and myogenin expression were assessed. NO has both pro-inflammatory and anti-inflammatory properties, and several possible roles for NO in skeletal muscle damage have been postulated. NO content was greater in the ECC/-l-NAME group at all time points (p < 0.05) compared to ECC/+l-NAME. Additionally, significant differences in NO content were observed on day 0 (p < 0.05), and day 3 (p < 0.05), ECC/+l-NAME versus ECC/-l-NAME. One day following the bout of ECC, and NO levels were increased in the ECC/-l-NAME group. Three days following ECC, there was greater myofiber damage (measured by β-glucuronidase activity) and leukocyte invasion in the ECC/-l-NAME group as compared to the ECC/+l-NAME group. One day after ECC, calpain activity was significantly increased in ECC/-l-NAME compared with control muscles (p < 0.05). On days 3 and 7, Myo-D and myogenin gene expression was increased in both groups; however, the degree of regeneration was less in the ECC/+l-NAME-treated animals. These data suggest that NO dynamics have important implications in the regulation of various factors during skeletal muscle regeneration following damaging eccentric muscle contractions. © 2013 The Physiological Society of Japan and Springer Japan.


Basti L.,Japan National Research Institute of Fisheries Science | Endo M.,Tokyo University of Marine Science and Technology | Segawa S.,Tokyo University of Agriculture | Shumway S.E.,University of Connecticut | And 2 more authors.
Aquatic Toxicology | Year: 2015

circualrisquama. The harmful dinoflagellate, Heterocapsa circularisquama, has been causing mass mortalities of bivalve molluscs in Japan, at relatively low cell densities. Although several studies have been conducted to determine the toxicity mechanisms, the specific cause of death is still unclear. In a previous study, in our laboratory, it was shown that H. circularisquama (103cellsml-1) caused extensive cytotoxicity in the gills of short-neck clams, Ruditapes philippinarum. In the present study, Mediterranean mussels, Mytilus galloprovincialis, were exposed to H. circularisquama at four cell densities (5, 50, 500, 103cellsml-1), three temperatures (15, 20, and 25°C), and three exposure durations (3, 24, and 48h), and the pathologies in nine organs (gills, labial palps, mantle, hepatopancreas, stomach, intestines, exhalant siphon, adductor muscles, and foot) were assessed. Foot, adductor muscles, and exhalent siphons of mussels were not affected; however, 16 inflammatory (hemocytic infiltration and aggregation, diapedesis, hyperplasia, hypertrophy, edema, melanization, and firbrosis) and degenerative (thrombus, thrombosed edema, cilia matting and exfoliation, epithelial desquamation, atrophy, and necrosis) pathologies were identified in the gills, labial palps, mantle, hepatopancreas, stomach, and intestines. The total prevalence and total intensity of pathology in each individual mussel, and the prevalence and intensity of pathology in each organ increased significantly with increased cell density, exposure duration, and temperature. The prevalence of pathology was the highest in gills, followed by the prevalence in labial palps, mantle, stomach, and intestines. Pathology was least prevalent in the hepatopancreas. The intensity of pathology was the highest in the gills, followed by the labial palps and mantle, the stomach and intestines, and the hepatopancreas. This detailed quantitative histopathological study demonstrates that exposure to H. circularisquama induces a broad cytotoxic effect in six vital organs, even at low density (5cellsml-1) and low temperature (15°C), but not in muscular organs. Combining cell density, time, and duration of exposure, the organ most affected by the harmful alga was the gill, followed by the labial palps and mantle, the stomach and intestines, and the hepatopancreas. The results of this pathological analysis show that exposure to H. ciruclarisquama severely affects the gills, the labial palps, and mantle thereby interfering with particle clearance and sorting, cleansing, and respiration, but also affects the stomach, intestines, and hepatopancreas, altering the digestive processes and possibly detoxification pathways, if mussels are able to detoxify the toxins of H. circularisquama. In the most severe cases, bivalves would most likely have died as a result of combined severe alterations of the vital functions, failure of tissue repair, and moderate to heavy hemorrhaging in both the external organs and the digestive organs concomitantly with light to moderate alterations in the detoxifying processes. © 2015.


Mori S.,Japan National Agriculture and Food Research Organization | Suzuki K.,Tokyo University of Agriculture | Oda R.,Tokyo University of Agriculture | Higuchi K.,Tokyo University of Agriculture | And 4 more authors.
Soil Science and Plant Nutrition | Year: 2011

Suaeda salsa can grow well in saline soils with high sodium (Na)-low potassium (K) concentrations. While high Na accumulation in plant tissues plays an important role in osmoregulation and maintenance of water absorption for normal growth of Suaeda salsa, characteristics of Na and K absorption in S. salsa grown in such saline soils have not been elucidated. We thus examined Na and K absorption characteristics of S. salsa grown in nutrient solutions of graded sodium chloride (NaCl) with 1 mmol L -1 K or of graded potassium chloride (KCl) with 1 mmol L -1 Na. The K accumulation capacity in S. salsa plant tissues was greater than the Na accumulation capacity. Although Na showed no competitive effects on K absorption, K application suppressed Na absorption drastically. Selectivity for K over Na in the absorption system became higher than that for Na over K concomitantly with increased Na or K concentration in the medium, indicating that Suaeda salsa is able to absorb K effectively with absorption of a large amount of Na. Sodium absorption was significantly decreased by tetraethylammonium (typical K channel inhibitor). Calcium (Ca) application increased not Na absorption but K absorption, resulting in enhancement of selectivity for K over Na. We speculate Na absorption pathways in S. salsa are partly mediated by AKT1 (Arabidopsis K transporter 1) type K channel and LCT (a low-affinity cation transporter) and NSCCs (non-selective cation channels) are not the major Na absorption pathway. These results may provide an explanation for the fact that S. salsa can grow well under saline soils with high Na-low K concentrations. © 2011 Japanese Society of Soil Science and Plant Nutrition.


Takeda K.,Japan National Agriculture and Food Research Organization | Tasai M.,Japan National Agriculture and Food Research Organization | Akagi S.,Japan National Agriculture and Food Research Organization | Matsukawa K.,Japan National Agriculture and Food Research Organization | And 8 more authors.
Mitochondrion | Year: 2010

Microinjection of isolated mitochondria into oocytes is an effective method to introduce exogenous mitochondrial DNA. In nuclear transfer procedures in which donor cell mitochondria are transferred with nuclei into recipient oocytes; development and survival rates of reconstructed embryos may be also directly influenced by mitochondrial viability. Mitochondrial viability is dramatically affected by cell culture conditions, such as serum starvation prior to nuclear transfer. This study was conducted to examine the influence of exogenous mitochondria using bovine and mouse parthenogenetic models. Mitochondria were isolated from primary cells at confluency and after serum starvation. The bovine oocytes injected with serum-starved mitochondria showed lower rates of morula and blastocyst formation when compared to uninjected controls (P < 0.05). However, the developmental rates between non-starved mitochondria injection and controls were not different (P > 0.05). The murine oocytes injected with serum-starved mitochondria showed lower rates of development when compared with non-starved mitochondria and controls (P < 0.01). In contrast to mitochondria transfer, ooplasm transfer did not affect murine or bovine parthenogenetic development (P > 0.05). The overall results showed that injection of serum-starved mitochondria influenced parthenogenetic development of both bovine and murine oocytes. Our results illustrate that the somatic mitochondria introduction accompanying nuclei has the capacity to affect reconstructed embryo development; particularly when using serum-starved cells as donor cells. © 2009 Mitochondria Research Society.


Wang H.,King's College | Morishita Y.,Tokyo University of Agriculture | Miura D.,Tokyo University of Agriculture | Naranjo J.R.,CSIC - National Center for Biotechnology | And 3 more authors.
Molecular Brain | Year: 2012

Background: Fragile X syndrome is caused by lack of fragile X mental retardation protein (FMRP) due to silencing of the FMR1 gene. The metabotropic glutamate receptors (mGluRs) in the central nervous system contribute to higher brain functions including learning/memory, mental disorders and persistent pain. The transcription factor cyclic AMP-responsive element binding protein (CREB) is involved in important neuronal functions, such as synaptic plasticity and neuronal survival. Our recent study has shown that stimulation of Group I mGluRs upregulated FMRP and activated CREB in anterior cingulate cortex (ACC), a key region for brain cognitive and executive functions, suggesting that activation of Group I mGluRs may upregulate FMRP through CREB signaling pathway. Results: In this study, we demonstrate that CREB contributes to the regulation of FMRP by Group I mGluRs. In ACC neurons of adult mice overexpressing dominant active CREB mutant, the upregulation of FMRP by stimulating Group I mGluR is enhanced compared to wild-type mice. However, the regulation of FMRP by Group I mGluRs is not altered by overexpression of Ca2+-insensitive mutant form of downstream regulatory element antagonist modulator (DREAM), a transcriptional repressor involved in synaptic transmission and plasticity. Conclusion: Our study has provided further evidence for CREB involvement in regulation of FMRP by Group I mGluRs in ACC neurons, and may help to elucidate the pathogenesis of fragile X syndrome. © 2012 Wang et al.; licensee BioMed Central Ltd.


Calumpang S.M.F.,University of the Philippines at Los Baños | Ohsawa K.,Tokyo University of Agriculture
Journal of the International Society for Southeast Asian Agricultural Sciences | Year: 2015

Insecticide use in eggplant is frequent due to the eggplant fruit and shoot borer (EFSB), Leucinodes orbonalis Guenee (Lepidoptera: Crambidae). Food safety, environmental and human health issues for applicators have been raised. There is a need to explore ecological approaches to reduce pesticide use. We tested the hypothesis that volatile organic chemicals from marigold flowers, Tagetes erecta L. (Asteraceae) disrupt host-finding behavior of EFSB. The methods include host- finding behavioral assays in cages and Y-tube olfactometric bioassays to identify volatile chemicals in marigold flowers that repel EFSB. Behavioral bioassays were conducted at the National Crop Protection Center, College of Agriculture, University of the Philippines Los Baños from 2010 to 2011. Olfactometric bioassays using volatile organic chemicals of marigold flowers were conducted in 2013-2014. Fewer female adult landings were observed on the host plant, eggplant when marigold was present than eggplant alone, in laboratory cage bioassays over a 24 period. The percentage of damaged eggplants with marigold was significantly lower than sole eggplant. The average percent of shoot damage per eggplant with marigold was likewise significantly lower than sole eggplant. The repellency of volatile organic chemicals emitted by marigold flowers was likewise demonstrated with citral and 1-dodecene showing 64-68% repellency to female EFSB. A 10- flower equivalent displayed 72% repellency. Field trials need to be conducted to evaluate the appropriate cropping system that can effectively reduce EFSB populations. © 2015 International Society for Southeast Asian Agricultural Sciences. All rights reserved.


Takachi R.,Tohoku University | Takachi R.,Research Center for Cancer Prevention and Screening | Inoue M.,Research Center for Cancer Prevention and Screening | Sawada N.,Research Center for Cancer Prevention and Screening | And 6 more authors.
Nutrition and Cancer | Year: 2010

Although dietary risk factors may differ between localized and advanced prostate cancer, data on associations between the consumption of fruits and vegetables and risk of localized and advanced cancers are limited. We examined associations between fruit and vegetable consumption and risk of prostate cancer in a Japanese population. During 1995-1998, a validated food frequency questionnaire was administered to 43,475 men aged 45-74 yr. During 321,061 person-years of follow-up until the end of 2004, 339 cases of prostate cancer were identified. Consumption of fruits or total vegetables was not associated with a decreased risk of total prostate cancer, with corresponding multivariate hazard ratios of the highest vs. lowest quartiles of 1.09 (95% CI = 0.77-1.53; trend P = 0.39) for fruits and 1.33 (95% CI = 0.93-1.91; trend P = 0.52) for total vegetables. Also, no association was observed for intake of either fruits or vegetables (total or any subtype) with localized or advanced prostate cancer. This prospective cohort study suggests that consumption of fruits or vegetables may not be associated with the risk of either localized or advanced prostate cancer in Japanese men. However, the possibility of confounding by detection bias on the risk of localized cancer could not be totally ruled out. Copyright © 2010, Taylor & Francis Group, LLC.


Taira N.,Okayama University | Iwata H.,Aichi Cancer Center Hospital | Hasegawa Y.,Hirosaki Municipal Hospital | Sakai T.,Cancer Institute Hospital | And 6 more authors.
Breast Cancer Research and Treatment | Year: 2014

Trials of adjuvant endocrine therapy for breast cancer have shown that aromatase inhibitors have little impact on global health-related quality of life (HRQoL), but have significant effects on patient-reported endocrine symptoms (ESs). There are few studies of HRQoL and psychological distress during preoperative endocrine therapy performed to determine endocrine responsiveness. The NEOS trial is a multicenter, phase 3 randomized controlled trial in postmenopausal women with hormone receptor-positive breast cancer. The primary aim of the trial was to evaluate the need for adjuvant chemotherapy in patients with clinical T1c-T2N0M0, hormone receptor-positive tumors who responded to neoadjuvant letrozole (LET) administered for 24-28 weeks before surgery. The primary endpoint was disease-free survival and the secondary endpoints included adverse events, HRQoL, and cost-effectiveness. In a HRQoL sub-study, subjects were assessed at baseline and 4 and 16 weeks after starting neoadjuvant LET, using the functional assessment of cancer therapy-breast and its ES subscale, and the hospital anxiety and depression scale. HRQoL and psychosocial distress were analyzed in the uncontrolled phase during 24-28 weeks of neoadjuvant LET therapy in the NEOS trial. From May 16, 2008, to December 14, 2011, 503 patients were recruited into the HRQoL sub-study. The full analysis set included 497 patients with a mean age of 63-years old. The questionnaire response rates at enrollment and 4 and 16 weeks were 94.4, 90.7, and 89.1 %, respectively. There were no significant changes in the FACT-G or B-trial outcome index over time, but the social and family well-being score and the ES subscale deteriorated significantly, and the number of patients with clinically significant hot flush increased significantly. Anxiety, depression, and emotional well-being improved significantly after neoadjuvant LET. Neoadjuvant endocrine therapy with LET had no impact on global HRQoL, but did influence endocrine-related symptoms such as hot flush. This study is registered as UMIN000001090. © 2014 Springer Science+Business Media New York.


Ogawa T.,Tokyo University of Agriculture | Kameyama Y.,Tokyo University of Agriculture | Kanazawa Y.,Nishi Nippon Junior College | Suzuki K.,Tokyo University of Agriculture | Somego M.,Tokyo University of Agriculture
Scientia Horticulturae | Year: 2012

Flowering cherry trees (Prunus subgenus Cerasus) are characterized by beautiful flowers along with the existence of hundreds of flower ornamental cultivars. The long history of cultivation of flowering cherries, however, has caused significant confusion over names and origins. We conducted experimental crosses and AFLP analysis to reveal the origins or parentages of early-flowering cherry cultivars, Prunus×kanzakura cv. Atami-zakura and Prunus×kanzakura cv. Kawazu-zakura. Multivariate analysis based on pairwise genetic similarity (principal coordinate analysis; PCoA), and Bayesian statistical methods to find genetic group (STRUCTURE analysis) and to classify samples into different hybrid classes (NewHybrids) clearly demonstrated that (1) Prunus×kanzakura cv. Atami-zakura is the F 1 hybrid between P. jamasakura and P. campanulata, and (2) Prunus×kanzakura cv. Kawazu-zakura is the F 1 hybrid between P. lannesiana var. speciosa and P. campanulata. The experimental crosses revealed the significant difficulty of generating these hybrids. In addition, 18 of 20 and six of six samples of Prunus×kanzakura cv. Atami-zakura and Prunus×kanzakura cv. Kawazu-zakura, respectively, are classified into a single AFLP genotype. It is apparent that the original trees or genets of these taxa have long been propagated by grafting over several tens to one hundred years. © 2012 Elsevier B.V.


Dizon T.O.,University of the Philippines at Los Baños | Damasco O.P.,University of the Philippines at Los Baños | Lobina I.T.,University of the Philippines at Los Baños | Pinili M.S.,Tokyo University of Agriculture | And 2 more authors.
Journal of the International Society for Southeast Asian Agricultural Sciences | Year: 2012

Gamma rays using Cobalt 60 (60Co) irradiation method was conducted to determine the sensitivity doses and response of in vitro propagated abaca to Banana bunchy top (BBT) and Banana bract mosaic (BBrM) diseases. Abaca cultivars (cvs) Tinawagan Pula (TP) and Tangongon (TG) were studied. Both cvs. had similar biological/physiological reactions to gamma rays resulting to high mortality and low shoot proliferation at higher dosage. The LD30 for shoot proliferation was established at 10 to 15 Gy. Cultivar response (shoot growth per sub-culture cycle) on post-irradiation showed that cv. TG had higher tolerance to gamma ray than cv. TP. A total of 3,210 and 3,765 irradiated abaca including the non-irradiated control were aphid- and mechanically-inoculated with Banana bunchy top virus (BBTV) and Banana bract mosaic virus (BBrMV), respectively. Three months after inoculation, the initial PCR-based diagnosis on putative resistant (PR) materials showed 43 TP (0.6%) and 9 TG (0.9%) selected abaca lines were consistently found negative to BBTV and 36 TP (1.6%) and 15 TG (0.9%) were initially uninfected with BBrMV. Although field trial of these lines and yield components are necessary for final selection, this study showed the bench mark and possibility of mutation breeding to produce virus resistant abaca. As gamma irradiation dose (LD30) coupled with in vitro propagation was established in abaca, screening and generating PR lines against viruses infecting abaca can be easily achieved over the conventional breeding works.


Ikegaya K.,Mitsubishi Group | Nokihara K.,Shimadzu Scientific Research Inc. | Yasuhara T.,Tokyo University of Agriculture
Bioscience, Biotechnology and Biochemistry | Year: 2010

Since human serum albumin has one sulfhydryl group and 17 disulfides, reactive sulfhydryl groups give rise to heterogeneity. The present paper presents a comparison of sulfhydryl heterogeneity in human serum albumin and recombinant human serum albumin for clinical use. Low molecular weight sulfhydryl compounds were identified from both sources. The recombinant albumin had a much higher sulfhydryl content than plasma serum albumin.


Hara A.,Research Center for Cancer Prevention and Screening | Sasazuki S.,Research Center for Cancer Prevention and Screening | Inoue M.,Research Center for Cancer Prevention and Screening | Shimazu T.,Research Center for Cancer Prevention and Screening | And 6 more authors.
BMC Public Health | Year: 2011

Background: Despite the popular use of vitamin supplements and several prospective cohort studies investigating their effect on cancer incidence and cardiovascular disease (CVD), scientific data supporting their benefits remain controversial. Inconsistent results may be partly explained by the fact that use of supplements is an inconsistent behavior in individuals. We examined whether vitamin supplement use patterns affect cancer and CVD risk in a population-based cohort study in Japan. Methods. A total of 28,903 men and 33,726 women in the Japan Public Health Center-based Prospective Study cohort, who answered questions about vitamin supplement use in the first survey from 1990-1994 and the second survey from 1995-1998, were categorized into four groups (never use, past use, recent use, and consistent use) and followed to the end of 2006 for cancer and 2005 for CVD. Sex-specific hazard ratios (HRs) and 95% confidence intervals (95% CIs) were used to describe the relative risks of cancer and CVD associated with vitamin supplement use. Results: During follow-up, 4501 cancer and 1858 CVD cases were identified. Multivariate adjusted analysis revealed no association of any pattern of vitamin supplement use with the risk of cancer and CVD in men. In women, consistent use was associated with lower risk of CVD (HR 0.60, 95% CI 0.41-0.89), whereas past (HR 1.17, 95% CI 1.02-1.33) and recent use (HR 1.24, 95% CI 1.01-1.52) were associated with higher risk of cancer. Conclusions: To our knowledge, this is the first prospective cohort study to examine simultaneously the associations between vitamin supplement use patterns and risk of cancer and CVD. This prospective cohort study demonstrated that vitamin supplement use has little effect on the risk of cancer or CVD in men. In women, however, consistent vitamin supplement use might reduce the risk of CVD. Elevated risk of cancer associated with past and recent use of vitamin supplements in women may be partly explained by preexisting diseases or unhealthy background, but we could not totally control for this in our study. © 2011 Hara et al; licensee BioMed Central Ltd.


Norikoshi R.,Japan National Agriculture and Food Research Organization | Norikoshi R.,Tokyo University of Agriculture | Shibata T.,Tokyo University of Agriculture | Niki T.,Japan National Agriculture and Food Research Organization | Ichimura K.,Japan National Agriculture and Food Research Organization
Postharvest Biology and Technology | Year: 2016

Treatment with sucrose promoted petal growth associated with flower opening in cut roses. We investigated the effect of sucrose treatment on cell size and subcellular concentration of soluble carbohydrates in petals of cut rose cv. Sonia flowers. Petals of sucrose-treated flowers, but not control flowers, markedly curved outward, resulting in complete reflection. Petal fresh weight (FW), petal area, and adaxial epidermal cell size in the control flowers increased with time, and treatment with sucrose accelerated this increase, indicating that sucrose promotes petal cell expansion. Glucose, fructose, sucrose, methyl glucoside, and xylose were detected in the petals. In the petals of control flowers, concentration of these carbohydrates, except fructose, decreased. Sucrose treatment markedly increased glucose and fructose concentrations in petals. Estimation of subcellular volumes based on transmission electron micrographs showed that volume of cell walls and vacuoles in the petals of control flowers increased in response to sucrose treatment. Sucrose treatment increased glucose and fructose concentrations in the vacuole and glucose, fructose, and xylose concentrations in the apoplast. We concluded that sucrose treatment increases glucose and fructose concentrations in the vacuole, which may reduce the osmotic potential of the symplast and increase water uptake leading to cell expansion during flower opening. © 2016 Elsevier B.V.


Tadaishi M.,Japan National Institute of Health Sciences | Tadaishi M.,Tokyo University of Agriculture | Miura S.,Japan National Institute of Health Sciences | Kai Y.,Japan National Institute of Health Sciences | And 3 more authors.
PLoS ONE | Year: 2011

Background: Maximal oxygen uptake (VO 2max) predicts mortality and is associated with endurance performance. Trained subjects have a high VO 2max due to a high cardiac output and high metabolic capacity of skeletal muscles. Peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a nuclear receptor coactivator, promotes mitochondrial biogenesis, a fiber-type switch to oxidative fibers, and angiogenesis in skeletal muscle. Because exercise training increases PGC-1α in skeletal muscle, PGC-1α-mediated changes may contribute to the improvement of exercise capacity and VO 2max. There are three isoforms of PGC-1α mRNA. PGC-1α-b protein, whose amino terminus is different from PGC-1α-a protein, is a predominant PGC-1α isoform in response to exercise. We investigated whether alterations of skeletal muscle metabolism by overexpression of PGC-1α-b in skeletal muscle, but not heart, would increase VO 2max and exercise capacity. Methodology/Principal Findings: Transgenic mice showed overexpression of PGC-1α-b protein in skeletal muscle but not in heart. Overexpression of PGC-1α-b promoted mitochondrial biogenesis 4-fold, increased the expression of fatty acid transporters, enhanced angiogenesis in skeletal muscle 1.4 to 2.7-fold, and promoted exercise capacity (expressed by maximum speed) by 35% and peak oxygen uptake by 20%. Across a broad range of either the absolute exercise intensity, or the same relative exercise intensities, lipid oxidation was always higher in the transgenic mice than wild-type littermates, suggesting that lipid is the predominant fuel source for exercise in the transgenic mice. However, muscle glycogen usage during exercise was absent in the transgenic mice. Conclusions/Significance: Increased mitochondrial biogenesis, capillaries, and fatty acid transporters in skeletal muscles may contribute to improved exercise capacity via an increase in fatty acid utilization. Increases in PGC-1α-b protein or function might be a useful strategy for sedentary subjects to perform exercise efficiently, which would lead to prevention of life-style related diseases and increased lifespan. © 2011 Tadaishi et al.


Shiotsu F.,Ibaraki UniversityIbaraki | Abe J.,Tokai University | Gau M.,Japan National Agriculture and Food Research Organization | Uwatoko N.,Japan National Agriculture and Food Research Organization | Morita S.,Tokyo University of Agriculture
Plant Production Science | Year: 2016

The production of cellulosic bioethanol from non-edible plants is a potential countermeasure against global warming. Erianthus species provide cellulosic raw material for bioethanol because they have high biomass productivity and high tolerance to environmental stress, associated with their large, deep root systems. However, it is difficult to select Erianthus species for breeding by direct observation of their root systems because the roots are widely dispersed in the soil. Instead, we examined shoot morphological traits that could be closely related to root morphology to find effective reference indices for selection. The potential to evaluate root structure and function in Erianthus according to bleeding rate was also examined. An analysis of root–shoot relationships in seedlings indicated that root number and mean length were closely related to stem number and diameter, respectively. These results suggest that root–shoot relationships may provide useful criteria for selective breeding of root systems in Erianthus. © 2016 The Author(s).


Watanabe S.,Tokyo University of Agriculture | Hanaoka M.,Chiba University | Ohba Y.,Tokyo University of Agriculture | Ono T.,Tokyo University of Agriculture | And 6 more authors.
Plant and Cell Physiology | Year: 2013

Ferrochelatase (FECH) is an essential enzyme for the final step of heme biosynthesis. In green plants, its activity has been reported in both plastids and mitochondria. However, the precise subcellular localization of FECH remains uncertain. In this study, we analyzed the localization of FECH in the unicellular red alga, Cyanidioschyzon merolae. Immunoblot and enzyme activity analyses of subcellular fractions localized little FECH in the plastid. In addition, immunofluorescence microscopy identified that both intrinsic and hemagglutinin (HA)-tagged FECH are localized in the mitochondrion. We therefore conclude that FECH is localized in the mitochondrion in C. merolae. © 2013 The Author.


Akanuma G.,Chuo University | Kobayashi A.,Chuo University | Suzuki S.,Rikkyo University | Suzuki S.,University of Tokyo | And 7 more authors.
Journal of Bacteriology | Year: 2014

To elucidate the biological functions of the ribosomal protein L34, which is encoded by the rpmH gene, the rpmH deletion mutant of Bacillus subtilis and two suppressor mutants were characterized. Although the ΔrpmH mutant exhibited a severe slowgrowth phenotype, additional mutations in the yhdP or mgtE gene restored the growth rate of the ΔrpmH strain. Either the disruption of yhdP, which is thought to be involved in the efflux of Mg2+, or overexpression of mgtE, which plays a major role in the import of Mg2+, could suppress defects in both the formation of the 70S ribosome and growth caused by the absence of L34. Interestingly, the Mg2+ content was lower in the ΔrpmH cells than in the wild type, and the Mg2+ content in the ΔrpmH cells was restored by either the disruption of yhdP or overexpression of mgtE. In vitro experiments on subunit association demonstrated that 50S subunits that lacked L34 could form 70S ribosomes only at a high concentration of Mg2+. These results showed that L34 is required for efficient 70S ribosome formation and that L34 function can be restored partially by Mg2+. In addition, the Mg2+ content was consistently lower in mutants that contained significantly reduced amounts of the 70S ribosome, such as the ΔrplA (L1) and ΔrplW (L23) strains and mutant strains with a reduced number of copies of the rrn operon. Thus, the results indicated that the cellular Mg2+ content is influenced by the amount of 70S ribosomes. © 2014, American Society for Microbiology.


Nonaka M.,University of Tokyo | Nonaka M.,Chiyoda Corporation | Nonaka M.,University of Edinburgh | Kim R.,University of Tokyo | And 20 more authors.
Neuron | Year: 2014

CREB is a pivotal mediator of activity-regulated gene transcription that underlies memory formation and allocation. The contribution of a key CREB cofactor, CREB-regulated transcription coactivator 1 (CRTC1), has, however, remained elusive. Here we show that several constitutive kinase pathways and an activity-regulated phosphatase, calcineurin, converge to determine the nucleocytoplasmic shuttling of CRTC1. This, in turn, triggered an activity-dependent association of CRTC1 with CREB-dependent regulatory elements found on IEG promoters. Forced expression of nuclear CRTC1 in hippocampal neurons activated CREB-dependent transcription, and was sufficient to enhance contextual fear memory. Surprisingly, during contextual fear conditioning, we found evidence of nuclear recruitment of endogenous CRTC1 only in the basolateral amygdala, and not in the hippocampus. Consistently, CRTC1 knockdown in the amygdala, but not in the hippocampus, significantly attenuated fear memory. Thus, CRTC1 has a wide impact on CREB-dependent memory processes, but fine-tunes CREB output in a region-specific manner. © 2014 Elsevier Inc.


Sakai H.,Japan National Institute of Agrobiological Science | Lee S.S.,Japan National Institute of Agrobiological Science | Tanaka T.,Japan National Institute of Agrobiological Science | Numa H.,Japan National Institute of Agrobiological Science | And 16 more authors.
Plant and Cell Physiology | Year: 2013

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/ ) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics. © 2013 The Author 2013. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.


Hirao Y.,Japan National Agriculture and Food Research Organization | Naruse K.,Japan National Agriculture and Food Research Organization | Kaneda M.,Tokyo University of Agriculture and Technology | Kaneda M.,Japan National Agriculture and Food Research Organization | And 8 more authors.
Biology of Reproduction | Year: 2013

Because of recent advancements in reproductive technology, oocytes have attained an increasingly enriched value as a unique cell population in the production of offspring. The growing oocytes in the ovary are an immediate potential source that serve this need; however, complete oocyte growth before use is crucial. Our research objective was to create in vitro-grown (IVG) oocytes that would have the ability to perform specialized activities, including nuclear reprogramming, as an alternative to in vivo-grown oocytes. Bovine oocyte-granulosa cell complexes with a mean oocyte diameter of approximately 100 lm were cultured on Millicell membrane inserts, with culture medium supplemented with 4% polyvinylpyrrolidone (molecular weight, 360 000), 20 ng/ml androstenedione, 2 mM hypoxanthine, and 5 ng/ml bone morphogenetic protein 7. Oocyte viability after the 14-day culture period was 95%, and there was a 71% increase in oocyte volume. Upon induction of oocyte maturation, 61% of the IVG oocytes extruded a polar body. Eighty-four percent of the reconstructed IVG oocytes that used cumulus cells as donor cells underwent cleavage, and half of them became blastocysts. DNA methylation analyses of the satellite I and II regions of the blastocysts revealed a similar highly methylated status in the cloned embryos derived from in vivo-grown and IVG oocytes. Finally, one of the nine embryos reconstructed from the IVG oocytes developed into a living calf following embryo transfer. Fertility of the offspring was confirmed. In conclusion, the potential of a proportion of the IVG oocytes was comparable to that of in vivo-grown oocytes. © 2013 by the Society for the Study of Reproduction, Inc.


Fujiwara T.,Rikkyo University | Kuroiwa H.,Rikkyo University | Yagisawa F.,Rikkyo University | Ohnuma M.,Rikkyo University | And 7 more authors.
Plant Cell | Year: 2010

Vacuoles/lysosomes function in endocytosis and in storage and digestion of metabolites. These organelles are inherited by the daughter cells in eukaryotes. However, the mechanisms of this inheritance are poorly understood because the cells contain multiple vacuoles that behave randomly. The primitive red alga Cyanidioschyzon merolae has a minimum set of organelles. Here, we show that C. merolae contains about four vacuoles that are distributed equally between the daughter cells by binding to dividing mitochondria. Binding is mediated by VIG1, a 30-kD coiled-coil protein identified by microarray analyses and immunological assays. VIG1 appears on the surface of free vacuoles in the cytosol and then tethers the vacuoles to the mitochondria. The vacuoles are released from the mitochondrion in the daughter cells following VIG1 digestion. Suppression of VIG1 by antisense RNA disrupted the migration of vacuoles. Thus, VIG1 is essential for tethering vacuoles to mitochondria during vacuole inheritance in C. merolae. © 2010 American Society of Plant Biologists.


Ogino Y.,Graduate University for Advanced Studies | Kuraku S.,RIKEN | Ishibashi H.,Ehime University | Miyakawa H.,Graduate University for Advanced Studies | And 7 more authors.
Molecular Biology and Evolution | Year: 2016

Steroid hormone receptor family provides an example of evolution of diverse transcription factors through wholegenome duplication (WGD). However, little is known about how their functions have been evolved after the duplication. Teleosts present a good model to investigate an accurate evolutionary history of protein function after WGD, because a teleost-specific WGD (TSGD) resulted in a variety of duplicated genes in modern fishes. This study focused on the evolution of androgen receptor (AR) gene, as two distinct paralogs, ARa and ARb, have evolved in teleost lineage after TSGD. ARa showed a unique intracellular localization with a higher transactivation response than that of ARb. Using site-directed mutagenesis and computational prediction of protein-ligand interactions, we identified two key substitutions generating a new functionality of euteleost ARa. The substitution in the hinge region contributes to the unique intracellular localization of ARa. The substitution on helices 10/11 in the ligand-binding domain possibly modulates hydrogen bonds that stabilize the receptor-ligand complex leading to the higher transactivation response of ARa. These substitutions were conserved in Acanthomorpha (spiny-rayed fish) ARas, but not in an earlier branching lineage among teleosts, Japanese eel. Insertion of these substitutions into ARs from Japanese eel recapitulates the evolutionary novelty of euteleost ARa. These findings together indicate that the substitutions generating a new functionality of teleost ARa were fixed in teleost genome after the divergence of the Elopomorpha lineage. Our findings provide a molecular explanation for an adaptation process leading to generation of the hyperactive AR subtype after TSGD. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.


Soma A.,Rikkyo University | Soma A.,Chiba University | Sugahara J.,Keio University | Onodera A.,Rikkyo University | And 10 more authors.
Scientific Reports | Year: 2013

The limited locations of tRNA introns are crucial for eukaryal tRNA-splicing endonuclease recognition. However, our analysis of the nuclear genome of an early-diverged red alga, Cyanidioschyzon merolae, demonstrated the first evidence of nuclear-encoded tRNA genes that contain ectopic and/or multiple introns. Some genes exhibited both intronic and permuted structures in which the 39-half of the tRNA coding sequence lies upstream of the 59-half, and an intron is inserted into either half. These highly disrupted tRNA genes, which account for 63% of all nuclear tRNA genes, are expressed via the orderly and sequential processing of bulge-helix-bulge (BHB) motifs at intron-exon junctions and termini of permuted tRNA precursors, probably by a C. merolae tRNA-splicing endonuclease with an unidentified subunit architecture. The results revealed a considerable diversity in eukaryal tRNA intron properties and endonuclease architectures, which will help to elucidate the acquisition mechanism of the BHB-mediated disrupted tRNA genes.


Hiura H.,Tohoku University | Sugawara A.,Tohoku University | Ogawa H.,Tokyo University of Agriculture | John R.M.,University of Cardiff | And 13 more authors.
Nucleic Acids Research | Year: 2010

The parent-of-origin specific expression of imprinted genes relies on DNA methylation of CpGdinucleotides at differentially methylated regions (DMRs) during gametogenesis. To date, four paternally methylated DMRs have been identified in screens based on conventional approaches. These DMRs are linked to the imprinted genes H19, Gtl2 (IG-DMR), Rasgrf1 and, most recently, Zdbf2 which encodes zinc finger, DBF-type containing 2. In this study, we applied a novel methylated-DNA immunoprecipitation-on-chip (meDIP-on-chip) method to genomic DNA from mouse parthenogenetic-and androgenetic-derived stem cells and sperm and identified 458 putative DMRs. This included the majority of known DMRs. We further characterized the paternally methylated Zdbf2/ ZDBF2 DMR. In mice, this extensive germ line DMR spanned 16 kb and possessed an unusual tripartite structure. Methylation was dependent on DNA methyltransferase 3a (Dnmt3a), similar to H19 DMR and IG-DMR. In both humans and mice, the adjacent gene, Gpr1/GPR1, which encodes a G-proteincoupled receptor 1 protein with transmembrane domain, was also imprinted and paternally expressed. The Gpr1-Zdbf2 domain was most similar to the Rasgrf1 domain as both DNA methylation and the actively expressed allele were in cis on the paternal chromosome. This work demonstrates the effectiveness of meDIP-on-chip as a technique for identifying DMRs. © The Author(s) 2010. Published by Oxford University Press.


Iwata Y.,Japan National Agriculture and Food Research Organization | Yazaki T.,Japan National Agriculture and Food Research Organization | Suzuki S.,Tokyo University of Agriculture | Hirota T.,Japan National Agriculture and Food Research Organization
Annals of Glaciology | Year: 2013

To evaluate water and anion movement in an agricultural field in different frost conditions, a paired-plot field experiment was conducted at an agricultural site in northern Japan where a significant decrease in the frost depth has occurred during the past 20 years. Snow cover was removed to enhance soil freezing in one plot (treated plot), whereas natural conditions were maintained in a control plot. The maximum frost depth was 0.43m in the treated plot and 0.11m in the control plot, which induced substantial differences in water movement throughout the winter. A substantial amount of water moved upward before the onset of snowmelt. However, nitrate did not move markedly before the snowmelt period in either plot. The amount of snowmelt infiltration in the control plot was larger than in the treated plot. Correspondingly, the peak of nitrate content in the control plot was deeper than that in the treated plot after the snowmelt period. Soil freezing, snow accumulation and snowmelt processes were simulated reasonably well using a one-dimensional numerical model: Simultaneous Heat and Water (SHAW). Nevertheless, the model performed poorly for simulating soil thawing and soil water movement, suggesting a need for improvement.


Patent
Tokyo University of Agriculture and Yokogawa Electric Corporation | Date: 2012-08-01

There is provided a nucleic acid extraction method applicable to microbes in a relatively wide range, and capable of rapidly extracting nucleic acid. The nucleic acid extraction method comprises the steps of introducing a cell suspension into a vessel, sealing the vessel, and preheating a heater up to a set temperature not lower than 100C. Further, the method comprises the step of bringing the vessel into contact with the heater heated up to the set temperature, thereby heating the cell suspension housed in the vessel up to a prescribed highest temperature at not lower than 100C with the vessel held in a sealed state.


PubMed | Tokyo University of Agriculture, University of Salford, Jikei University School of Medicine, University of Tokyo and King's College London
Type: Journal Article | Journal: Nanomedicine : nanotechnology, biology, and medicine | Year: 2016

The magnetic technique for sentinel node biopsy provides a radioisotope-free alternative for staging breast cancer. It requires refinement to reduce residual iron content at injection sites by maximising lymphatic uptake to prevent void artefacts on magnetic resonance imaging (MRI), which could adversely affect clinical use. The site and timing of injection of magnetic tracer was evaluated in a murine tumour model (right hind limb) in 24 wild type mice. Right-sided intratumoural and left sided subcutaneous injection of magnetic tracer and assessment of nodal iron uptake on MRI, surgical excision and histopathological grading at time frames up to 24 hours were performed. Rapid iron uptake on MRI, smaller void artefacts(P<0.001) and a significant increase in iron content with time were identified in the subcutaneous injection group (r=0.937; P<0.001).Subcutaneous injection and increasing delay between tracer injection and surgery is beneficial for lymphatic iron uptake.Sentinel lymph node biopsy (SLNB) has been the standard of care in breast cancer management for some time. Recent development has seen the introduction of magnetic tracer for SLNB. In this article, the authors investigated the refined use of magnetic tracer in determining the optimal timing of administration and the location of injection. The findings should provide more data on the future use of this new technique.


PubMed | Tokyo University of Agriculture, Chitose Laboratory Corporation and Keio University
Type: Journal Article | Journal: Genes to cells : devoted to molecular & cellular mechanisms | Year: 2016

Single-nucleotide polymorphisms (SNPs) are one of the main causes of evolution. The distribution of human SNPs, which were examined in detail genomewide, was analyzed. Three discrete databases of human SNPs were used for this analysis, and similar results were obtained from these databases. It was found that the distribution of the distance between SNPs was approximated by the power law, and the shape of the regions including SNPs had the so-called fractal structure. Although the reason why the distribution of SNPs obeys such a certain law of physics is unclear, a speculation was attempted in connection with the three-dimensional structure of human chromatin which has a fractal structure.


PubMed | University of Miyazaki, Tokyo Institute of Technology, Japan National Institute of Polar Research, Tokyo University of Information Sciences and 13 more.
Type: | Journal: Current biology : CB | Year: 2016

The Palaeognathae comprise the flightless ratites and the volant tinamous, and together with the Neognathae constitute the extant members of class Aves. It is commonly believed that Palaeognathae originated in Gondwana since most of the living species are found in the Southern Hemisphere [1-3]. However, this hypothesis has been questioned because the fossil paleognaths are mostly from the Northern Hemisphere in their earliest time (Paleocene) and possessed many putative ancestral characters [4]. Uncertainties regarding the origin and evolution of Palaeognathae stem from the difficulty in estimating their divergence times [1, 2] and their remarkable morphological convergence. Here, we recovered nuclear genome fragments from extinct elephant birds, which enabled us to reconstruct a reliable phylogenomic time tree for the Palaeognathae. Based on the tree, we identified homoplasies in morphological traits of paleognaths and reconstructed their morphology-based phylogeny including fossil species without molecular data. In contrast to the prevailing theories, the fossil paleognaths from the Northern Hemisphere were placed as the basal lineages. Combined with our stable divergence time estimates that enabled a valid argument regarding the correlation with geological events, we propose a new evolutionary scenario thatcontradicts the traditional view. The ancestral Palaeognathae were volant, as estimated from their molecular evolutionary rates, and originated during the Late Cretaceous in the Northern Hemisphere. They migrated to the Southern Hemisphere and speciated explosively around the Cretaceous-Paleogene boundary. They then extended their distribution to the Gondwana-derived landmasses, such as New Zealand and Madagascar, by overseas dispersal. Gigantism subsequently occurred independently on each landmass.


PubMed | Tokyo University of Agriculture, University of California, Ehime University, Wakayama Medical University and 2 more.
Type: Journal Article | Journal: Molecular biology and evolution | Year: 2015

Steroid hormone receptor family provides an example of evolution of diverse transcription factors through whole-genome duplication (WGD). However, little is known about how their functions have been evolved after the duplication. Teleosts present a good model to investigate an accurate evolutionary history of protein function after WGD, because a teleost-specific WGD (TSGD) resulted in a variety of duplicated genes in modern fishes. This study focused on the evolution of androgen receptor (AR) gene, as two distinct paralogs, AR and AR, have evolved in teleost lineage after TSGD. AR showed a unique intracellular localization with a higher transactivation response than that of AR. Using site-directed mutagenesis and computational prediction of protein-ligand interactions, we identified two key substitutions generating a new functionality of euteleost AR. The substitution in the hinge region contributes to the unique intracellular localization of AR. The substitution on helices 10/11 in the ligand-binding domain possibly modulates hydrogen bonds that stabilize the receptor-ligand complex leading to the higher transactivation response of AR. These substitutions were conserved in Acanthomorpha (spiny-rayed fish) ARs, but not in an earlier branching lineage among teleosts, Japanese eel. Insertion of these substitutions into ARs from Japanese eel recapitulates the evolutionary novelty of euteleost AR. These findings together indicate that the substitutions generating a new functionality of teleost AR were fixed in teleost genome after the divergence of the Elopomorpha lineage. Our findings provide a molecular explanation for an adaptation process leading to generation of the hyperactive AR subtype after TSGD.


PubMed | Tokyo University of Agriculture, Chuo University and Rikkyo University
Type: Journal Article | Journal: Journal of bacteriology | Year: 2014

To elucidate the biological functions of the ribosomal protein L34, which is encoded by the rpmH gene, the rpmH deletion mutant of Bacillus subtilis and two suppressor mutants were characterized. Although the rpmH mutant exhibited a severe slow-growth phenotype, additional mutations in the yhdP or mgtE gene restored the growth rate of the rpmH strain. Either the disruption of yhdP, which is thought to be involved in the efflux of Mg(2+), or overexpression of mgtE, which plays a major role in the import of Mg(2+), could suppress defects in both the formation of the 70S ribosome and growth caused by the absence of L34. Interestingly, the Mg(2+) content was lower in the rpmH cells than in the wild type, and the Mg(2+) content in the rpmH cells was restored by either the disruption of yhdP or overexpression of mgtE. In vitro experiments on subunit association demonstrated that 50S subunits that lacked L34 could form 70S ribosomes only at a high concentration of Mg(2+). These results showed that L34 is required for efficient 70S ribosome formation and that L34 function can be restored partially by Mg(2+). In addition, the Mg(2+) content was consistently lower in mutants that contained significantly reduced amounts of the 70S ribosome, such as the rplA (L1) and rplW (L23) strains and mutant strains with a reduced number of copies of the rrn operon. Thus, the results indicated that the cellular Mg(2+) content is influenced by the amount of 70S ribosomes.


PubMed | Tokyo University of Agriculture, Graduate University for Advanced Studies, Rikkyo University and Japan National Food Research Institute
Type: Journal Article | Journal: Microbiology (Reading, England) | Year: 2016

The genome of Bacillus subtilis strain 168 encodes ten rRNA (rrn) operons. We previously reported that strains with only a single rrn operon had a decreased growth and sporulation frequency. We report here the isolation and characterization of suppressor mutants from seven strains that each have a single rrn operon (rrnO, A, J, I, E, D or B). The suppressor mutants for strain RIK656 with a single rrnO operon had a higher frequency of larger colonies. These suppressor mutants had not only increased growth rates, but also increased sporulation frequencies and ribosome levels compared to the parental mutant strain RIK656. Quantitative PCR analyses showed that all these suppressor mutants had an increased number of copies of the rrnO operon. Suppressor mutants were also isolated from the six other strains with single rrn operons (rrnA, J, I, E, D or B). Next generation and capillary sequencing showed that all of the suppressor mutants had tandem repeats of the chromosomal locus containing the remaining rrn operon (amplicon). These amplicons varied in size from approximately 9 to 179kb. The amplifications were likely to be initiated by illegitimate recombination between non- or micro-homologous sequences, followed by unequal crossing-over during DNA replication. These results are consistent with our previous report that rrn operon copy number has a major role in cellular processes such as cell growth and sporulation.


PubMed | Tokyo University of Agriculture and Nagoya Research Institute
Type: Journal Article | Journal: Food chemistry | Year: 2015

Collagen was prepared from common minke whale unesu and characterised. The yield of collagen was high, about 28.4% on a wet weight basis. By SDS-PAGE and CM-Toyopearl 650M column chromatography, the collagen was classified as type I collagen. The denaturation temperature of the collagen was 31.5C, about 6-7C lower than that of porcine collagen. Attenuated total reflectance-FTIR analysis indicated that acid-soluble collagen from common minke whale unesu held its triple helical structure well, but the structures of porcine skin collagen and pepsin-solubilized collagen from common minke whale unesu were changed slightly, due to the loss of N- and C-terminus domains.


PubMed | Tokyo University of Agriculture, King Abdulaziz University, University of Tokyo and Gregor Mendel Institute of Molecular Plant Biology
Type: Journal Article | Journal: PloS one | Year: 2015

Phosphate is an essential macronutrient in plant growth and development; however, the concentration of inorganic phosphate (Pi) in soil is often suboptimal for crop performance. Accordingly, plants have developed physiological strategies to adapt to low Pi availability. Here, we report that typical Pi starvation responses in Arabidopsis are partially dependent on the strigolactone (SL) signaling pathway. SL treatment induced root hair elongation, anthocyanin accumulation, activation of acid phosphatase, and reduced plant weight, which are characteristic responses to phosphate starvation. Furthermore, the expression profile of SL-response genes correlated with the expression of genes induced by Pi starvation. These results suggest a potential overlap between SL signaling and Pi starvation signaling pathways in plants.


PubMed | Tokyo University of Agriculture and Japan National Agriculture and Food Research Organization
Type: Journal Article | Journal: Journal of bioscience and bioengineering | Year: 2014

We truncated the short arm of chromosome 3 to delete the aflatoxin biosynthesis gene homolog cluster using telomeric repeats in Aspergillus oryzae. The predicted deletion was confirmed by Southern blot analyses. This telomere-mediated chromosomal truncation method enables the development of an artificial chromosome in A.oryzae.


PubMed | Tokyo University of Agriculture, Chiyoda Corporation, Japan National Cardiovascular Center Research Institute, Saitama University and University of Tokyo
Type: Journal Article | Journal: Neuron | Year: 2014

CREB is a pivotal mediator of activity-regulated gene transcription that underlies memory formation and allocation. The contribution of a key CREB cofactor, CREB-regulated transcription coactivator 1 (CRTC1), has, however, remained elusive. Here we show that several constitutive kinase pathways and an activity-regulated phosphatase, calcineurin, converge to determine the nucleocytoplasmic shuttling of CRTC1. This, in turn, triggered an activity-dependent association of CRTC1 with CREB-dependent regulatory elements found on IEG promoters. Forced expression of nuclear CRTC1 in hippocampal neurons activated CREB-dependent transcription, and was sufficient to enhance contextual fear memory. Surprisingly, during contextual fear conditioning, we found evidence of nuclear recruitment of endogenous CRTC1 only in the basolateral amygdala, and not in the hippocampus. Consistently, CRTC1 knockdown in the amygdala, but not in the hippocampus, significantly attenuated fear memory. Thus, CRTC1 has a wide impact on CREB-dependent memory processes, but fine-tunes CREB output in a region-specific manner.


PubMed | Fukuoka University, Shinshu University, Tohoku University, Osaka National Research Institute and 19 more.
Type: | Journal: Acta neuropathologica | Year: 2017

Intracranial germ cell tumors (iGCTs) are the second most common brain tumors among children under 14 in Japan. The World Health Organization classification recognizes several subtypes of iGCTs, which are conventionally subclassified into pure germinoma or non-germinomatous GCTs. Recent exhaustive genomic studies showed that mutations of the genes involved in the MAPK and/or PI3K pathways are common in iGCTs; however, the mechanisms of how different subtypes develop, often as a mixed-GCT, are unknown. To elucidate the pathogenesis of iGCTs, we investigated 61 GCTs of various subtypes by genome-wide DNA methylation profiling. We showed that pure germinomas are characterized by global low DNA methylation, a unique epigenetic feature making them distinct from all other iGCTs subtypes. The patterns of methylation strongly resemble that of primordial germ cells (PGC) at the migration phase, possibly indicating the cell of origin for these tumors. Unlike PGC, however, hypomethylation extends to long interspersed nuclear element retrotransposons. Histologically and epigenetically distinct microdissected components of mixed-GCTs shared identical somatic mutations in the MAPK or PI3K pathways, indicating that they developed from a common ancestral cell.


PubMed | Tokyo University of Agriculture and Japan National Agriculture and Food Research Organization
Type: Journal Article | Journal: Breeding science | Year: 2016

A quantitative trait locus (QTL) controlling wheat grain protein content (GPC) and flour protein content (FPC) was identified using doubled haploid (DH) lines developed from a cross between the hard red winter wheat variety Yumechikara with a high protein content used for bread making, and the soft red winter wheat Kitahonami with a low protein content used for Japanese white salted noodles. A single major QTL,


PubMed | Tokyo University of Agriculture, National Institute of Genetics Mishima, Graduate University for Advanced Studies and Japan Science and Technology Agency
Type: | Journal: Frontiers in plant science | Year: 2015

The unicellular red alga Cyanidioschyzon merolae is a model organism for studying the basic biology of photosynthetic organisms. The C. merolae cell is composed of an extremely simple set of organelles. The genome is completely sequenced. Gene targeting and a heat-shock inducible gene expression system has been recently established. However, a conditional gene knockdown system has not been established, which is required for the examination of function of genes that are essential to cell viability and primary mutant defects. In the current study, we first evaluated the expression of a transgene from two chromosomal neutral loci located in the intergenic region between CMD184C and CMD185C, and a region upstream of the URA5.3 gene. There was no significant difference in expression between them and this result suggests that both may be used as neutral loci. We then designed an inducible and repressible gene expression by using promoters of nitrate-assimilation genes. The expression of nitrate-assimilation genes such as NR (nitrate reductase), NIR (nitrite reductase), and NRT (the nitrate/nitrite transporter) are reversibly regulated by their dependence on nitrogen sources. We constructed stable strains in which a cassette containing the NR, NIR, or NRT promoter and sfGFP gene was inserted in a region upstream of URA5.3 and examined the efficacy of the promoters. The NR, NIR, and NRT promoters were constitutively activated in the nitrate medium, whereas their activities were extremely low in presence of ammonium. The activation of each promoter was immediately inhibited within a period of 1 h by the addition of ammonium. Thus, a conditional knockdown system in C. merolae was successfully established. The activity varies among the promoters, and each is selectable according to the expression level of a target gene estimated by RNA-sequencing. This method is applicable to defects in genes of interest in photosynthetic organism.


PubMed | Tokyo University of Agriculture, Fukushima Medical University and Rikkyo University
Type: Journal Article | Journal: Microbiology (Reading, England) | Year: 2016

Ribosome dimers are a translationally inactive form of ribosomes found in Escherichia coli and many other bacterial cells. In this study, we found that the 70S ribosomes of Bacillus subtilis dimerized during the early stationary phase and these dimers remained in the cytoplasm until regrowth was initiated. Ribosome dimerization during the stationary phase required the hpf gene, which encodes a homologue of the E. coli hibernation-promoting factor (Hpf). The expression of hpf was induced at an early stationary phase and its expression was observed throughout the rest of the experimental period, including the entire 6 h of the stationary phase. Ribosome dimerization followed the induction of hpf in WT cells, but the dimerization was impaired in cells harbouring a deletion in the hpf gene. Although the absence of ribosome dimerization in these Hpf-deficient cells did not affect their viability in the stationary phase, their ability to regrow from the stationary phase decreased. Thus, following the transfer of stationary-phase cells to fresh LB medium, hpf mutant cells grew slower than WT cells. This observed lag in growth of hpf cells was probably due to a delay in restoring their translational activity. During regrowth, the abundance of ribosome dimers in WT cells decreased with a concomitant increase in the abundance of 70S ribosomes and growth rate. These results suggest that the ribosome dimers, by providing 70S ribosomes to the cells, play an important role in facilitating rapid and efficient regrowth of cells under nutrient-rich conditions.


PubMed | Tokyo University of Agriculture, Chonnam National University and The Jackson Laboratory
Type: Journal Article | Journal: Biology of reproduction | Year: 2015

Cumulus cells and mural granulosa cells (MGCs) have functionally distinct roles in antral follicles, and comparison of their transcriptomes at a global and systems level can propel future studies on mechanisms underlying their functional diversity. These cells were isolated from small and large antral follicles before and after stimulation of immature mice with gonadotropins, respectively. Both cell types underwent dramatic transcriptomic changes, and differences between them increased with follicular growth. Although cumulus cells of both stages of follicular development are competent to undergo expansion in vitro, they were otherwise remarkably dissimilar with transcriptomic changes quantitatively equivalent to those of MGCs. Gene ontology analysis revealed that cumulus cells of small follicles were enriched in transcripts generally associated with catalytic components of metabolic processes, while those from large follicles were involved in regulation of metabolism, cell differentiation, and adhesion. Contrast of cumulus cells versus MGCs revealed that cumulus cells were enriched in transcripts associated with metabolism and cell proliferation while MGCs were enriched for transcripts involved in cell signaling and differentiation. In vitro and in vivo models were used to test the hypothesis that higher levels of transcripts in cumulus cells versus MGCs is the result of stimulation by oocyte-derived paracrine factors (ODPFs). Surprisingly 48% of transcripts higher in cumulus cells than MGCs were not stimulated by ODPFs. Those stimulated by ODPFs were mainly associated with cell division, mRNA processing, or the catalytic pathways of metabolism, while those not stimulated by ODPFs were associated with regulatory processes such as signaling, transcription, phosphorylation, or the regulation of metabolism.


PubMed | Mitsubishi Group, Tokyo University of Agriculture, Sakata Seed Corporation and Japan National Institute of Agrobiological Science
Type: | Journal: Scientific reports | Year: 2015

Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.


PubMed | Indian National Institute for Interdisciplinary Science and Technology, Leibniz Institute DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH and Tokyo University of Agriculture
Type: Journal Article | Journal: Systematic and applied microbiology | Year: 2016

Three strains, namely L3B39(T), L3D16, and L1E9, were obtained while studying the cultivable rhizosphere bacteria of saline tolerant pokkali rice, at Kerala, India. The novel strains were negative for many plant growth promoting plate assays such as phytohormone and siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase and growth in nitrogen free agar medium but found to utilize malic acid, citrate, D-glucose, L-arabinose, and D-maltose, important components of the plant root exudates, indicating that they are normal plant rhizosphere residents without yet known benefits to the plant. The 16S rRNA gene analysis placed these strains in the genus Vogesella, forming a separate branch independent of the previously described type strains of this genus in all tree making algorithms applied. Vogesella perlucida DS-28(T) was the type strain with highest 16S rRNA sequence similarity (97.59%). DNA-DNA hybridization values among these novel strains were above 85% andthat with Vogesella perlucida LMG 24214(T) was below 50%. Phenotypically, the novel strains can be differentiated from Vogesella perlucida LMG 24214(T) by many characters such as NaCl tolerance, growth temperature, and utilization of L-arabinose, D-maltose, and citrate. These novel strains contain C16:16c/C16:17c and C16:0 as major fatty acids, ubiquinone Q-8 as the major respiratory quinone, and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Based on the results obtained from the polyphasic taxonomic approach we conclude that the strains belong to a novel Vogesella species for which the name Vogesella oryzae sp.nov. is proposed. The type strain is L3B39(T) (= LMG 28272(T)=DSM 28780(T)).


PubMed | University of Connecticut, Tokyo University of Agriculture, Japan National Research Institute of Fisheries Science and Tokyo University of Marine Science and Technology
Type: | Journal: Aquatic toxicology (Amsterdam, Netherlands) | Year: 2015

The harmful dinoflagellate, Heterocapsa circularisquama, has been causing mass mortalities of bivalve molluscs in Japan, at relatively low cell densities. Although several studies have been conducted to determine the toxicity mechanisms, the specific cause of death is still unclear. In a previous study, in our laboratory, it was shown that H. circularisquama (10(3) cells ml(-1)) caused extensive cytotoxicity in the gills of short-neck clams, Ruditapes philippinarum. In the present study, Mediterranean mussels, Mytilus galloprovincialis, were exposed to H. circularisquama at four cell densities (5, 50, 500, 10(3) cells ml(-1)), three temperatures (15, 20, and 25C), and three exposure durations (3, 24, and 48 h), and the pathologies in nine organs (gills, labial palps, mantle, hepatopancreas, stomach, intestines, exhalant siphon, adductor muscles, and foot) were assessed. Foot, adductor muscles, and exhalent siphons of mussels were not affected; however, 16 inflammatory (hemocytic infiltration and aggregation, diapedesis, hyperplasia, hypertrophy, edema, melanization, and firbrosis) and degenerative (thrombus, thrombosed edema, cilia matting and exfoliation, epithelial desquamation, atrophy, and necrosis) pathologies were identified in the gills, labial palps, mantle, hepatopancreas, stomach, and intestines. The total prevalence and total intensity of pathology in each individual mussel, and the prevalence and intensity of pathology in each organ increased significantly with increased cell density, exposure duration, and temperature. The prevalence of pathology was the highest in gills, followed by the prevalence in labial palps, mantle, stomach, and intestines. Pathology was least prevalent in the hepatopancreas. The intensity of pathology was the highest in the gills, followed by the labial palps and mantle, the stomach and intestines, and the hepatopancreas. This detailed quantitative histopathological study demonstrates that exposure to H. circularisquama induces a broad cytotoxic effect in six vital organs, even at low density (5 cells ml(-1)) and low temperature (15C), but not in muscular organs. Combining cell density, time, and duration of exposure, the organ most affected by the harmful alga was the gill, followed by the labial palps and mantle, the stomach and intestines, and the hepatopancreas. The results of this pathological analysis show that exposure to H. ciruclarisquama severely affects the gills, the labial palps, and mantle thereby interfering with particle clearance and sorting, cleansing, and respiration, but also affects the stomach, intestines, and hepatopancreas, altering the digestive processes and possibly detoxification pathways, if mussels are able to detoxify the toxins of H. circularisquama. In the most severe cases, bivalves would most likely have died as a result of combined severe alterations of the vital functions, failure of tissue repair, and moderate to heavy hemorrhaging in both the external organs and the digestive organs concomitantly with light to moderate alterations in the detoxifying processes.


PubMed | Tokyo University of Agriculture, Yamagata University and National Defense Medical College Research Institute
Type: Journal Article | Journal: Journal of biomedical optics | Year: 2015

Diffuse reflectance spectroscopy using a fiber optic probe is a promising technique for evaluating the optical properties of biological tissue. We herein present a method for determining the reduced scattering coefficient, s, the absorption coefficient, a, and the tissue oxygen saturation, StO2, of in vivo brain tissue using a single-reflectance fiber probe with two source-collector geometries. We performed in vivo recordings of diffuse reflectance spectra and of the electrophysiological signals for exposed rat brain during the cortical spreading depression evoked by the topical application of KCl. The time courses of a at 500, 570, and 584 nm indicated the hemodynamic change in the cerebral cortex as well as StO2. At 570 nm, the time course of s was well correlated with that of a, which also reflects the scattering by RBCs. On the other hand, increases in s at 500 and 584 nm and a decrease in s at 800 nm were observed before the profound increase in a, and these occurrences were synchronized with the negative dc shift of the local field potential. The resultant change in the slope of s is indicative of the morphological changes in the cellular and subcellular structures induced by the depolarization due to the temporal depression of the neuronal bioelectrical activity. The results of the present study indicate the potential application of the proposed method in evaluating the pathophysiological conditions of in vivo brain.


PubMed | Japan National Institute of Advanced Industrial Science and Technology, Tokyo University of Agriculture, Graduate University for Advanced Studies and Kitasato University
Type: Journal Article | Journal: Proceedings of the National Academy of Sciences of the United States of America | Year: 2015

Dragonflies are colorful and large-eyed animals strongly dependent on color vision. Here we report an extraordinary large number of opsin genes in dragonflies and their characteristic spatiotemporal expression patterns. Exhaustive transcriptomic and genomic surveys of three dragonflies of the family Libellulidae consistently identified 20 opsin genes, consisting of 4 nonvisual opsin genes and 16 visual opsin genes of 1 UV, 5 short-wavelength (SW), and 10 long-wavelength (LW) type. Comprehensive transcriptomic survey of the other dragonflies representing an additional 10 families also identified as many as 15-33 opsin genes. Molecular phylogenetic analysis revealed dynamic multiplications and losses of the opsin genes in the course of evolution. In contrast to many SW and LW genes expressed in adults, only one SW gene and several LW genes were expressed in larvae, reflecting less visual dependence and LW-skewed light conditions for their lifestyle under water. In this context, notably, the sand-burrowing or pit-dwelling species tended to lack SW gene expression in larvae. In adult visual organs: (i) many SW genes and a few LW genes were expressed in the dorsal region of compound eyes, presumably for processing SW-skewed light from the sky; (ii) a few SW genes and many LW genes were expressed in the ventral region of compound eyes, probably for perceiving terrestrial objects; and (iii) expression of a specific LW gene was associated with ocelli. Our findings suggest that the stage- and region-specific expressions of the diverse opsin genes underlie the behavior, ecology, and adaptation of dragonflies.


PubMed | Tokyo University of Agriculture, Japan National Agriculture and Food Research Organization, Kyoto University and Kyushu University
Type: Journal Article | Journal: Nature | Year: 2016

The female germ line undergoes a unique sequence of differentiation processes that confers totipotency to the egg. The reconstitution of these events in vitro using pluripotent stem cells is a key achievement in reproductive biology and regenerative medicine. Here we report successful reconstitution in vitro of the entire process of oogenesis from mouse pluripotent stem cells. Fully potent mature oocytes were generated in culture from embryonic stem cells and from induced pluripotent stem cells derived from both embryonic fibroblasts and adult tail tip fibroblasts. Moreover, pluripotent stem cell lines were re-derived from the eggs that were generated in vitro, thereby reconstituting the full female germline cycle in a dish. This culture system will provide a platform for elucidating the molecular mechanisms underlying totipotency and the production of oocytes of other mammalian species in culture.


Kaku T.,Kyoto University | Kaida R.,Tokyo University of Agriculture | Baba K.,Kyoto University | Hartati S.,Indonesian Institute of Sciences | And 2 more authors.
Journal of Wood Science | Year: 2011

Recalcitrance to saccharifi cation is a major limiting factor of the conversion of lignocellulosic biomass to ethanol. Levels of wood saccharification and subsequent ethanol production were higher in transgenic mangium (Acacia mangium) trees overexpressing xyloglucanase than in wild-type plants, even after delignification of the wood. We propose that a decrease in the quantity of xyloglucan that is intercalated into cellulose microfibrils could facilitate the process of saccharification. © 2011 The Japan Wood Research Society.


Yamasaki M.,Tokyo University of Agriculture | Terao T.,NEWJEC Inc.
Civil-Comp Proceedings | Year: 2013

This paper describes a mechanism for creating 3D highway shapes and producing drawings with the data input and creation function in OHPASS. The functions developed include a method for creating 3D terrain and control points that are input using Civil 3D, and a function for incorporating the calculated results back into Civil 3D. In addition the system is linked with UC-win/Road Ver.9.0 (produced by FORUM8 Co., Ltd.), 3D VR (Virtual reality) system designed especially for creating a variety of 3D models and running many types of realistic simulations within the 3D VR environment built by the software itself. UC-win/Road is capable of providing various real-time presentations with CG after generating a three-dimensional VR space, and is being utilized extensively in landscape examination, design consultation, and for presentations at project briefings. The authors have developed a function that loads the results of the road alignment examination obtained in OHPASS, and displays them as horizontal and vertical drawings within the UC-win/Road 3D VR environment. As a feature of OHPASS, it is possible to examine two or more alignments by changing design conditions. Now a function for selecting and loading each and every alignment has been added so that the multiple results of the road alignment examination can be loaded. In the study, described in this paper, the authors have attempted to link OHPASS, an optimal road alignment search program, with three-dimensional CAD. In addition, by enabling the optimal design calculation results to be loaded into 3D CAD, graphical representations of the design the results can be linked with a 3D VR system. As the design results can be linked with a 3D VR system, they can used to create an integrated 3D VR system. The 3D VR system enables the realistic surrounding landscape of the designed project to be viewed. Within the 3D VR system, dynamic 3D space can be controlled in real time, for example, it is possible to "drive" on the designed road in virtual space as if we are actually driving .These driving experiences and the visualization in the 3D VR system allows us to examine and evaluate the designed project effectively. © Civil-Comp Press, 2013.


Sagane Y.,Tokyo University of Agriculture | Miyashita S.-I.,Tokyo University of Agriculture | Miyata K.,Tokyo University of Agriculture | Miyata K.,Japan Society for the Promotion of Science | And 10 more authors.
Biochemical and Biophysical Research Communications | Year: 2012

In cell culture supernatants, the botulinum neurotoxin (BoNT) exists as part of a toxin complex (TC) in which nontoxic nonhemagglutinin (NTNHA) and/or hemagglutinins (HAs) are assembled onto the BoNT. A series of investigations indicated that formation of the TC is vital for delivery of the toxin to nerve cells through the digestive tract. In the assembly process, BoNT binds to NTNHA yielding M-TC, and it then matures into L-TC by further association with the HAs via NTNHA in the M-TC. Here, we report a crystal structure of the NTNHA from Clostridium botulinum serotype D strain 4947. Additionally, we performed small-angle X-ray scattering (SAXS) analysis of the NTNHA and the M-TC to elucidate the solution structure. The crystal structure of D-4947 NTNHA revealed that BoNT and NTNHA share a closely related structure consisting of three domains. The SAXS image indicated that, even though the N-terminal two-thirds of the NTNHA molecule had an apparently similar conformation in both the crystal and solution structures, the C-terminal third of the molecule showed a more extended structure in the SAXS image than that seen in the crystallographic image. The discrepancy between the crystal and solution structures implies a high flexibility of the C-terminal third domain of NTNHA, which is involved in binding to BoNT. Structural dynamics of the NTNHA molecule revealed by SAXS may explain its binding to BoNT to form the BoNT/NTNHA complex. © 2012 Elsevier Inc.


Shiwa Y.,Tokyo University of Agriculture | Shiwa Y.,Iwate Medical University | Yoshikawa H.,Tokyo University of Agriculture | Tanaka T.,Tokai University | Ogura M.,Tokai University
Journal of Biochemistry | Year: 2015

The DegS-DegU two-component regulatory system regulates many cellular events in Bacillus subtilis. Genes for DegSU constitutes an operon directed by the P1 promoter and downstream degU is autoregulated via the P3 promoter activated by phosphorylated DegU. In the Gram-positive bacteria, Spx plays a major role in the protection system against oxidative stresses as a transcriptional regulator. Spx is a substrate of the ATP-dependent ClpXP protease. It regulates diamide-stress regulon in addition to many genes with unknown functions. We have found that null mutations for clpX and clpP, which encode the subunits for the protease ClpXP, enhanced the DegU level through activation of the P1 promoter. We isolated four suppressors for the clpP-enhancing effect. Whole-genome sequencing of the suppressors revealed that two have a point mutation in spx and the rest have a deletion of spx. The clpP-enhancing effect on degS-lacZ expression was abolished in the spx disruptant. These results show that the degSU operon is a new target of Spx-mediated positive regulation. Furthermore, we found that the P1 promoter was induced by glucose and that this induction was greatly reduced in the spx mutant. These results suggested that Spx-mediated glucose induction at the P1 promoter. © 2014 The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.


Yokoyama E.,Chiba Prefectural Institute of Public Health | Murakami K.,Fukuoka Institute of Health Environmental | Shiwa Y.,Tokyo University of Agriculture | Ishige T.,Tokyo University of Agriculture | And 3 more authors.
Infection, Genetics and Evolution | Year: 2014

Salmonella enterica subsp. enterica serovar Infantis has been reported to be carried asymptomatically in chickens and isolated from some human patients with diarrhea. The aim of this study was to investigate the phylogeny of S. Infantis strains isolated in Japan from chicken meat, chicken egg shells, environmental samples from a grading and packing center for chicken eggs (GP center), diarrhea patients, and asymptomatic carriers based on whole genome sequence data. The S. Infantis strains were in five clusters in a phylogenetic tree reconstructed by the maximum likelihood method. The five clusters were confirmed by neighbor-net and Bayesian cluster analyses. Two of the five clusters formed a group containing all of the strains isolated from chicken meat and some of the strains isolated from diarrhea patients and asymptomatic carriers. The median-joining network reconstructed in this study showed that strains in one of these two clusters diverged from one node with similar relatively short branches, suggesting clonal dissemination of these strains. The other three clusters formed a group containing all of the strains isolated from chicken egg shells and the GP center, and the remaining strains from diarrhea patients and asymptomatic carriers. Interestingly, strains isolated from patients did not cluster in only one group, indicating that none of the S. Infantis strains in this study had significantly higher human pathogenicity. The population genetic analyses in this study showed the separation of the five clusters into two groups was concordant with the sources where the strains in the clusters were isolated. These results suggested that evolutionary groups with higher hierarchy than the clusters identified in this study may be present, although such groups could not be determined by phylogenetic, neighbor-net, and Bayesian analyses in this study. Determination of higher level S. Infantis evolutionary groups should be investigated using other types of genetic markers. © 2014 Elsevier B.V.


Schuergers N.,Albert Ludwigs University of Freiburg | Ruppert U.,Justus Liebig University | Watanabe S.,Tokyo University of Agriculture | Nurnberg D.J.,Queen Mary, University of London | And 4 more authors.
Molecular Microbiology | Year: 2014

The bacterial RNA-binding protein Hfq functions in post-transcriptional regulation of gene expression. There is evidence in a range of bacteria for specific subcellular localization of Hfq; however, the mechanism and role of Hfq localization remain unclear. Cyanobacteria harbour a subfamily of Hfq that is structurally conserved but exhibits divergent RNA binding sites. Mutational analysis in the cyanobacterium Synechocystis sp. PCC 6803 revealed that several conserved amino acids on the proximal side of the Hfq hexamer are crucial not only for Hfq-dependent RNA accumulation but also for phototaxis, the latter of which depends on type IV pili. Co-immunoprecipitation and yeast two-hybrid analysis show that the secretion ATPase PilB1 (a component of the type IV pilus base) is an interaction partner of Hfq. Fluorescence microscopy revealed that Hfq is localized to the cytoplasmic membrane in a PilB1-dependent manner. Concomitantly, Hfq-dependent RNA accumulation is abrogated in a ΔpilB1 mutant, indicating that localization to the pilus base via interaction with PilB1 is essential for Hfq function in cyanobacteria. © 2014 John Wiley & Sons Ltd.


Yuh S.,Tokyo University of Agriculture | Yuh S.,Iwate Medical University | Hiroaki Y.,Tokyo University of Agriculture | Yuu H.,Toyohashi University of Technology | And 9 more authors.
DNA Research | Year: 2014

Enterococcus mundtii QU 25, a non-dairy bacterial strain of ovine faecal origin, can ferment both cellobiose and xylose to produce L-lactic acid. The use of this strain is highly desirable for economical L-lactate production from renewable biomass substrates. Genome sequence determination is necessary for the genetic improvement of this strain. We report the complete genome sequence of strain QU 25, primarily determined using Pacific Biosciences sequencing technology. The E. mundtii QU 25 genome comprises a 3 022 186-bp single circular chromosome (GC content, 38.6%) and five circular plasmids: pQY182, pQY082, pQY039, pQY024, and pQY003. In all, 2900 protein-coding sequences, 63 tRNA genes, and 6 rRNA operonswere predicted in theQU25chromosome. Plasmid pQY024 harbours genes for mundticin production. We found that strain QU 25 produces a bacteriocin, suggesting that mundticin-encoded genes on plasmid pQY024 were functional. For lactic acid fermentation, two gene clusters were identified - one involved in the initial metabolism of xylose and uptake of pentose and the second containing genes for the pentose phosphate pathway and uptake of related sugars. This is the first complete genome sequence of an E. mundtii strain. The data provide insights into lactate production in this bacterium and its evolution among enterococci. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.


Koyabu D.,University of Zürich | Koyabu D.,University of Tokyo | Endo H.,University of Tokyo | Mitgutsch C.,University of Zürich | And 7 more authors.
EvoDevo | Year: 2011

Background: Here we provide the most comprehensive study to date on the cranial ossification sequence in Lipotyphla, the group which includes shrews, moles and hedgehogs. This unique group, which encapsulates diverse ecological modes, such as terrestrial, subterranean, and aquatic lifestyles, is used to examine the evolutionary lability of cranial osteogenesis and to investigate the modularity of development.Results: An acceleration of developmental timing of the vomeronasal complex has occurred in the common ancestor of moles. However, ossification of the nasal bone has shifted late in the more terrestrial shrew mole. Among the lipotyphlans, sequence heterochrony shows no significant association with modules derived from developmental origins (that is, neural crest cells vs. mesoderm derived parts) or with those derived from ossification modes (that is, dermal vs. endochondral ossification).Conclusions: The drastic acceleration of vomeronasal development in moles is most likely coupled with the increased importance of the rostrum for digging and its use as a specialized tactile surface, both fossorial adaptations. The late development of the nasal in shrew moles, a condition also displayed by hedgehogs and shrews, is suggested to be the result of an ecological reversal to terrestrial lifestyle and reduced functional importance of the rostrum. As an overall pattern in lipotyphlans, our results reject the hypothesis that ossification sequence heterochrony occurs in modular fashion when considering the developmental patterns of the skull. We suggest that shifts in the cranial ossification sequence are not evolutionarily constrained by developmental origins or mode of ossification. © 2011 Koyabu et al; licensee BioMed Central Ltd.


Masuda H.,University of Tokyo | Masuda H.,Ishikawa Prefectural University | Ishimaru Y.,University of Tokyo | Ishimaru Y.,Tohoku University | And 9 more authors.
Scientific Reports | Year: 2012

To address the problem of iron-deficiency anemia, one of the most prevalent human micronutrient deficiencies globally, iron-biofortified rice was produced using three transgenic approaches: by enhancing iron storage in grains via expression of the iron storage protein ferritin using endosperm-specific promoters, enhancing iron translocation through overproduction of the natural metal chelator nicotianamine, and enhancing iron flux into the endosperm by means of iron(II)-nicotianamine transporter OsYSL2 expression under the control of an endosperm-specific promoter and sucrose transporter promoter. Our results indicate that the iron concentration in greenhouse-grown T 2 polished seeds was sixfold higher and that in paddy field-grown T 3 polished seeds was 4.4-fold higher than that in non-transgenic seeds, with no defect in yield. Moreover, the transgenic seeds accumulated zinc up to 1.6-times in the field. Our results demonstrate that introduction of multiple iron homeostasis genes is more effective for iron biofortification than the single introduction of individual genes.


Sato K.,Kyoto University | Takeuchi J.S.,Kyoto University | Misawa N.,Kyoto University | Izumi T.,U.S. National Cancer Institute | And 13 more authors.
PLoS Pathogens | Year: 2014

Several APOBEC3 proteins, particularly APOBEC3D, APOBEC3F, and APOBEC3G, induce G-to-A hypermutations in HIV-1 genome, and abrogate viral replication in experimental systems, but their relative contributions to controlling viral replication and viral genetic variation in vivo have not been elucidated. On the other hand, an HIV-1-encoded protein, Vif, can degrade these APOBEC3 proteins via a ubiquitin/proteasome pathway. Although APOBEC3 proteins have been widely considered as potent restriction factors against HIV-1, it remains unclear which endogenous APOBEC3 protein(s) affect HIV-1 propagation in vivo. Here we use a humanized mouse model and HIV-1 with mutations in Vif motifs that are responsible for specific APOBEC3 interactions, DRMR/AAAA (4A) or YRHHY/AAAAA (5A), and demonstrate that endogenous APOBEC3D/F and APOBEC3G exert strong anti-HIV-1 activity in vivo. We also show that the growth kinetics of 4A HIV-1 negatively correlated with the expression level of APOBEC3F. Moreover, single genome sequencing analyses of viral RNA in plasma of infected mice reveal that 4A HIV-1 is specifically and significantly diversified. Furthermore, a mutated virus that is capable of using both CCR5 and CXCR4 as entry coreceptor is specifically detected in 4A HIV-1-infected mice. Taken together, our results demonstrate that APOBEC3D/F and APOBEC3G fundamentally work as restriction factors against HIV-1 in vivo, but at the same time, that APOBEC3D and APOBEC3F are capable of promoting viral diversification and evolution in vivo. © 2014.


Grzeskowiak L.,University of Turku | Endo A.,Tokyo University of Agriculture | Beasley S.,Vetcare Ltd. | Salminen S.,University of Turku
Anaerobe | Year: 2015

Dogs and cats have been cohabiting with us for thousands of years. They are the major human companions. Today, dogs and cats live in urban areas. Cats and most dogs are on high carbohydrate diets and face similar life-style challenges as the human beings. The health and well-being of companion animals, just as their owners, depends on the gut microbes. Providing a proper care and nutritionally balanced diet to companion animals is recognised as a part of our responsibility to maintain the health and well being of our pet. However, as microbiota differences may facilitate exposure to pathogens and harmful environmental influences, it is prudent to search for novel tools to protect dogs and cats and at the same time the human owners from pathogens. Specific probiotic strains and/or their defined combinations may be useful in the canine and feline nutrition, therapy, and care. Probiotic supplementations have been successful in the prevention and treatment of acute gastroenteritis, treatment of IBD, and prevention of allergy in companion animals. New challenges for probiotic applications include maintenance of obesity and overweight, urogenital tract infections, Helicobacter gastritis and parasitic infections. The probiotics of human origin appear to be among the new promising tools for the maintenance of pets' health. However, the host-derived microorganisms might be the most appropriate probiotic source. Therefore, more controlled trials are needed to characterise new and safe probiotic preparations with an impact on general health and well being as well as health maintenance in dogs and cats. © 2015 Elsevier Ltd.


Sakaguchi Y.,University of Miyazaki | Suzuki T.,Tokyo University of Agriculture | Yamamoto Y.,Okayama University | Nishikawa A.,Tokyo University of Agriculture and Technology | And 2 more authors.
Research in Microbiology | Year: 2015

In Clostridium botulinum, the characteristics of type C and D strains are quite different from other types, and they are classified as group III. They produce C2 binary toxin and C3 exoenzyme in addition to type C and D neurotoxins. Two different phages and many plasmids are identified in the organisms. The genes of neurotoxin and C3 exoenzyme are converted from toxigenic strains to non-toxigenic strains by the specific bacteriophages (phages), whereas, the C2 toxin gene is carried by large or small plasmids. Classification of type C and D strains has been in confusion because 1) antigenicity of type C and D neurotoxins is complex, 2) the cells produce two types of toxins, neurotoxin and C2 toxin, and 3) some non-toxigenic strains can be converted to produce C or D neurotoxin by the infection with phages. Until now, entire nucleotide sequences of cell chromosomes, phages, and plasmids have been determined. Since both genetic and protein-chemical analyses have been clarifying the above confusions, these data are reviewed historically. © 2014 Institut Pasteur.


Zuo Y.,CAS Institute of Botany | Zuo Y.,University of Chinese Academy of Sciences | Chen Z.,Wenshan Institute of Sanqi Research | Kondo K.,Tokyo University of Agriculture | And 3 more authors.
Planta Medica | Year: 2011

Ginsengs (Panax, Araliaceae) are among the plants best known for their medicinal properties. Many ginseng species are endangered due to over-exploitation of natural resources - a situation difficult to remedy while there are no reliable, practical methods for species identification. We screened eleven candidate DNA barcoding loci to establish an accurate and effective Panax species identification system, both for commercial and conservation purposes. We used 95 ginseng samples, representing all the species in the genus. We found considerable differences in the performance of the potential barcoding regions. The sequencing of atpF-atpH was unsuccessful due to poly-N structures. The rbcL, rpoB, and rpoC1 regions were found to be mostly invariable, with only four to eight variable sites. Using matK, psbKI, psbM-trnD, rps16 and nad1, we could identify four to six out of eight considerably divergent species but only one to five out of nineteen clusters within the P. bipinnatifidus species group. psbA-trnH and ITS were the most variable loci, working very well both in species and cluster identifications. We demonstrated that the combination of psbA-trnH and ITS is sufficient for identifying all the species and clusters in the genus. © Georg Thieme Verlag KG Stuttgart New York.


Hakuno F.,University of Tokyo | Yamauchi Y.,Nagoya University | Yamauchi Y.,Hair Clinic Reve 21 Corporation | Kaneko G.,University of Tokyo | And 7 more authors.
PLoS ONE | Year: 2011

Insulin-like growth factors (IGFs) are well known to play essential roles in enhancement of myogenic differentiation. In this report we showed that initial IGF-I signal activation but long-term IGF-1 signal termination are required for myogenic differentiation. L6 myoblast stably transfected with myc-epitope tagged insulin receptor substrate-1, myc-IRS-1 (L6-mIRS1) was unable to differentiate into myotubes, indicating that IRS-1 constitutive expression inhibited myogenesis. To elucidate the molecular mechanisms underlying myogenic inhibition, IGF-I signaling was examined. IGF-I treatment of control L6 cells for 18 h resulted in a marked suppression of IGF-I stimulated IRS-1 association with the p85 PI 3-kinase and suppression of activation of Akt that correlated with a down regulation of IRS-1 protein. L6-mIRS1 cells, in contrast, had sustained high levels of IRS-1 protein following 18 h of IGF-I treatment with persistent p85 PI 3-kinase association with IRS-1, Akt phosphorylation and phosphorylation of the downstream Akt substrate, Foxo1. Consistent with Foxo1 phosphorylation, Foxo1 protein was excluded from the nuclei in L6-mIRS1 cells, whereas Foxo1 was localized in the nuclei in control L6 cells during induction of differentiation. In addition, L6 cells stably expressing a dominant-interfering form of Foxo1, Δ256Foxo1 (L6-Δ256Foxo1) were unable to differentiate into myotubes. Together, these data demonstrate that IGF-I regulation of Foxo1 nuclear localization is essential for the myogenic program in L6 cells but that persistent activation of IGF-1 signaling pathways results in a negative feedback to prevent myogenesis. © 2011 Hakuno et al.


Nagatomo H.,Hokkaido University | Kagawa S.,Hokkaido University | Kishi Y.,Tokyo University of Agriculture | Takuma T.,Saga Prefectural Livestock Experiment Station | And 7 more authors.
Biology of Reproduction | Year: 2013

Mice and cattle use distinct pathways for the first cell segregation into inner cell mass (ICM) and trophectoderm (TE) lineages at the blastocyst stage. However, limited knowledge is available regarding the reliable transcriptional networks that orchestrate the complex developmental processes at this stage in nonrodent species. In order to elucidate the site-dominant transcriptomic properties of bovine blastocysts, we separated cell samples into the ICM and TE using both mechanical and chemical methods and performed in silico prescreening for candidate genes that were site-dominantly expressed in bovine blastocysts. We further performed quantitative real-time PCR and in situ hybridization using the site-specific cell samples. As a result, we identified seven ICM-dominant genes and five TEdominant genes not found in earlier studies. Our findings provide novel insights into the mechanism of cell-fate specification in the pre-implantation bovine embryo. © 2013 by the Society for the Study of Reproduction, Inc.


Tashiro K.,Tokyo Institute of Technology | Teissier A.,University Paris Diderot | Kobayashi N.,Tokyo Institute of Technology | Nakanishi A.,Tokyo Institute of Technology | And 12 more authors.
PLoS ONE | Year: 2011

Short interspersed repetitive elements (SINEs) are highly repeated sequences that account for a significant proportion of many eukaryotic genomes and are usually considered "junk DNA". However, we previously discovered that many AmnSINE1 loci are evolutionarily conserved across mammalian genomes, suggesting that they may have acquired significant functions involved in controlling mammalian-specific traits. Notably, we identified the AS021 SINE locus, located 390 kbp upstream of Satb2. Using transgenic mice, we showed that this SINE displays specific enhancer activity in the developing cerebral cortex. The transcription factor Satb2 is expressed by cortical neurons extending axons through the corpus callosum and is a determinant of callosal versus subcortical projection. Mouse mutants reveal a crucial function for Sabt2 in corpus callosum formation. In this study, we compared the enhancer activity of the AS021 locus with Satb2 expression during telencephalic development in the mouse. First, we showed that the AS021 enhancer is specifically activated in early-born Satb2 + neurons. Second, we demonstrated that the activity of the AS021 enhancer recapitulates the expression of Satb2 at later embryonic and postnatal stages in deep-layer but not superficial-layer neurons, suggesting the possibility that the expression of Satb2 in these two subpopulations of cortical neurons is under genetically distinct transcriptional control. Third, we showed that the AS021 enhancer is activated in neurons projecting through the corpus callosum, as described for Satb2 + neurons. Notably, AS021 drives specific expression in axons crossing through the ventral (TAG1 -/NPY +) portion of the corpus callosum, confirming that it is active in a subpopulation of callosal neurons. These data suggest that exaptation of the AS021 SINE locus might be involved in enhancement of Satb2 expression, leading to the establishment of interhemispheric communication via the corpus callosum, a eutherian-specific brain structure. © 2011 Tashiro et al.


Nakahigashi K.,Keio University | Takai Y.,Keio University | Shiwa Y.,Tokyo University of Agriculture | Shiwa Y.,Iwate Medical University | And 7 more authors.
BMC Genomics | Year: 2014

Background: There is a significant difference between synonymous codon usage in many organisms, and it is known that codons used more frequently generally showed efficient decoding rate. At the gene level, however, there are conflicting reports on the existence of a correlation between codon adaptation and translation efficiency, even in the same organism. Results: To resolve this issue, we cultured Escherichia coli under conditions designed to maintain constant levels of mRNA and protein and subjected the cells to ribosome profiling (RP) and mRNA-seq analyses. We showed that the RP results correlated more closely with protein levels generated under similar culture conditions than with the mRNA abundance from the mRNA-seq. Our result indicated that RP/mRNA ratio could be used as a measure of translation efficiency at gene level. On the other hand, the RP data showed that codon-specific ribosome density at the decoding site negatively correlated with codon usage, consistent with the hypothesis that preferred codons display lower ribosome densities due to their faster decoding rate. However, highly codon-adapted genes showed higher ribosome densities at the gene level, indicating that the efficiency of translation initiation, rather than higher elongation efficiency of preferred codons, exerted a greater effect on ribosome density and thus translation efficiency. Conclusions: These findings indicate that evolutionary pressure on highly expressed genes influenced both codon bias and translation initiation efficiency and therefore explains contradictory findings that codon usage bias correlates with translation efficiency of native genes, but not with the artificially created gene pool, which was not subjected to evolution pressure. © Nakahigashi et al.; licensee BioMed Central.


Endo A.,University of Turku | Endo A.,Tokyo University of Agriculture | Prtty A.,University of Turku | Kalliomki M.,University of Turku | And 2 more authors.
Anaerobe | Year: 2014

Microbial contact begins prior to birth and continues rapidly thereafter. Few long term follow-up studies have been reported and we therefore characterized the development of intestinal microbiota of ten subjects from the 2nd week of life to 13 years of age. PCR-denaturing gradient gel electrophoresis combined with several bacterial group-specific primer sets demonstrated the colonization steps of defined bacterial groups in the microbiota. Bifidobacterium species were seen throughout the test period in all subjects. Bacteroides fragilis group and Blautia coccoides-Eubacterium rectale group species were not detected in several subjects during the first 6 months of life but were commonly seen after 12 months of life. Streptococcus group appeared during early life but was not seen in several subjects at the age of 13 years. Although a few species were linked with the increasing age, major bacterial species in the groups did not change dramatically. Rather considerable changes were found in the relative abundances of each bacterial species. Clustering analysis of total bacterial flora indicated that the microbiota changed considerably between 6 months and 12 months of life, and, at the age of 12 months, the intestinal microbiota was already converted toward a profile characteristic of an adult microbiota. Probiotic supplementation in the beginning of life did not have major impacts on later microbiota development. © 2014 Elsevier Ltd.


Ito H.,Tokyo University of Agriculture | Sagane Y.,Sars International Center for Marine Molecular Biology | Miyata K.,Tokyo University of Agriculture | Inui K.,Tokyo University of Agriculture | And 10 more authors.
FEMS Immunology and Medical Microbiology | Year: 2011

A large size botulinum toxin complex (L-TC) is composed of a single neurotoxin (BoNT), a single nontoxic nonhaemagglutinin (NTNHA) and a haemagglutinin (HA) complex. The HA complex is comprised of three HA-70 molecules and three arm structures of HA-33/HA-17 that consist of two HA-33 and a single HA-17. In addition to the mature L-TC, smaller TCs are present in cultures: M-TC (BoNT/NTNHA), M-TC/HA-70 and immature L-TCs with fewer HA-33/HA-17 arms than mature L-TC. Because L-TC displays higher oral toxicity than pure BoNT, it was presumed that nontoxic proteins are critical for food poisoning. In this study, the absorption of TCs across intestinal epithelial cells was assessed by examining the cell binding and monolayer transport of serotype D toxins in the rat intestinal epithelial cell line IEC-6. All TCs, including pure BoNT, displayed binding and transport, with mature L-TC showing the greatest potency. Inhibition experiments using antibodies revealed that BoNT, HA-70 and HA-33 could be responsible for the binding and transport. The findings here indicate that all TCs can transport across the cell layer via a sialic acid-dependent process. Nonetheless, binding and transport markedly increased with number of HA-33/HA-17 arms in the TC. We therefore conclude that the HA-33/HA-17 arm is not necessarily required for, but facilitates, transport of botulinum toxin complexes. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd.


Yoshizaki T.,Tokyo University of Agriculture | Yoshizaki T.,Japan Society for the Promotion of Science | Kawano Y.,Tokyo University of Agriculture | Tada Y.,Tokyo University of Agriculture | And 6 more authors.
Journal of Biological Rhythms | Year: 2013

Circadian variation in cardiac autonomic nervous system activity and behavior during the day shifts of shift workers has not hitherto been clarified. This study examined diurnal 24-h variation in heart rate variability (HRV), sleep-wake cycle, physical activity, and food intake during the day shift in rotating shift workers. The subjects were female nurses and caregivers working at a health care facility (14 day workers and 13 rotating shift workers). Each subject was asked to undergo 24-h electrocardiograph and step count recordings. Coarse graining spectral analysis was used for approximately 10-min segments of HRV (600 beats) to derive the total power (TOT: >0.04 Hz), integrated power in the low-frequency (LF: 0.04-0.15 Hz) and high-frequency (HF: >0.15 Hz) ranges, the ratio of HF power to TOT (HF nu), and the ratio of LF power to HF power (LF/HF). Double cosinor analysis was used to obtain 24-h and 12-h period variations in variables of HRV and physical activity. While no difference was found in the acrophases of either period for step counts or in the 12-h period of HRV variables between the groups, the acrophases of the 24-h period for HRV variables were delayed by 1.3 to 5.5 h in rotating shift workers, and their differences in HF power, HF nu, and LF/HF reached a significant level (p < 0.05). On the days of the experiment, retiring time, waking up time, total time in bed, sleep efficiency, and mealtimes and energy intake for each diet did not differ between the groups. These results suggest that there is a possibility of an abnormal phase angle between circadian variation in cardiac autonomic nervous system activity and the sleep-wake cycle during the day shift in shift workers. © 2013 The Author(s).


Shida S.,Tokyo University of Agriculture | Hiziroglu S.,Oklahoma State University
Forest Products Journal | Year: 2010

The objective of this study was to evaluate shear strength characteristics of four commonly used Japanese species, namely, Japanese cedar-sugi (Cryptomeria japonica D. Don), Japanese cypress-hinoki (Chamaecyparis obusta Endl.), false arborvitae-hiba (Thuobsis dolabrate Sieb, et Zuce), and Japanese larch-karamatsu (Larix leptlepis Gordon), as function of their surface quality. Samples with radial and tangential grain orientations from each species were prepared using a planer and sanded with one of the sandpapers with 80-, 120-, and 240-grit size. A stylus type of equipment was employed to determine surface roughness of each sample before they were bonded in radial and tangential pairs using polyvinyl acetate (PVAc) adhesive at a spread rate of 260 g/m2. None of the samples showed any superiority from each other in terms of their surface quality based on three parameters: average roughness (Ra), mean peak-to-valley height (R2), and maximum roughness (Zrmax). Average roughness value of both tangential and radial surfaces of the samples sanded with 80-grit sandpaper resulted in significant differences from those of the control samples. The highest shear strength value was 96.1 kg/cm2 for the radial karamatsu samples sanded with 80-grit sandpaper followed by tangential hinoki samples with the value of 79.6 kg/cm2. In general, the samples finished with 80-grit sandpaper resulted in higher shear strength values than the others tested in this work. It appears that stylus-type equipment can be used to evaluate surface quality of such solid wood samples. Based on the results of this study, sanding of the samples with 80-grit sandpaper improved overall shear strength of the specimens by developing a better glue line between two pieces. © Forest Products Society 2010.

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