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Ohga H, Shibata K, Sakanoue R, Ogawa T, Kitano H, Kai S, Ohta K, Nagano N, Nagasako T, Uchida S, Sakuma T, Yamamoto T, Kim S, Tashiro K, Kuhara S, Gen K, Fujiwara A, Kazeto Y, Kobayashi T, Matsuyama M. Development of a chub mackerel with less-aggressive fry stage by genome editing of arginine vasotocin receptor V1a2. Sci Rep 2023; 13:3190. [PMID: 36823281 PMCID: PMC9950132 DOI: 10.1038/s41598-023-30259-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Genome editing is a technology that can remarkably accelerate crop and animal breeding via artificial induction of desired traits with high accuracy. This study aimed to develop a chub mackerel variety with reduced aggression using an experimental system that enables efficient egg collection and genome editing. Sexual maturation and control of spawning season and time were technologically facilitated by controlling the photoperiod and water temperature of the rearing tank. In addition, appropriate low-temperature treatment conditions for delaying cleavage, shape of the glass capillary, and injection site were examined in detail in order to develop an efficient and robust microinjection system for the study. An arginine vasotocin receptor V1a2 (V1a2) knockout (KO) strain of chub mackerel was developed in order to reduce the frequency of cannibalistic behavior at the fry stage. Video data analysis using bioimage informatics quantified the frequency of aggressive behavior, indicating a significant 46% reduction (P = 0.0229) in the frequency of cannibalistic behavior than in wild type. Furthermore, in the V1a2 KO strain, the frequency of collisions with the wall and oxygen consumption also decreased. Overall, the manageable and calm phenotype reported here can potentially contribute to the development of a stable and sustainable marine product.
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Affiliation(s)
- Hirofumi Ohga
- grid.177174.30000 0001 2242 4849Aqua-Bioresource Innovation Center (ABRIC) Karatsu Satellite, Faculty of Agriculture, Kyushu University, Saga, 847-0132 Japan
| | - Koki Shibata
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Ryo Sakanoue
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Takuma Ogawa
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Hajime Kitano
- grid.410851.90000 0004 1764 1824Fishery Third Group, Marine Fisheries Research and Development Center, Japan Fisheries Research and Education Agency (FRA), Kanagawa, 221-8529 Japan
| | - Satoshi Kai
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Kohei Ohta
- grid.177174.30000 0001 2242 4849Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395 Japan
| | - Naoki Nagano
- grid.410849.00000 0001 0657 3887Laboratory of Aquaculture, Faculty of Agriculture, University of Miyazaki, Miyazaki, 889-2192 Japan
| | - Tomoya Nagasako
- grid.177174.30000 0001 2242 4849Human Interface Laboratory, Factory of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395 Japan
| | - Seiichi Uchida
- grid.177174.30000 0001 2242 4849Human Interface Laboratory, Factory of Information Science and Electrical Engineering, Kyushu University, Fukuoka, 819-0395 Japan
| | - Tetsushi Sakuma
- grid.257022.00000 0000 8711 3200Molecular Genetics Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8526 Japan
| | - Takashi Yamamoto
- grid.257022.00000 0000 8711 3200Molecular Genetics Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, 739-8526 Japan
| | - Sangwan Kim
- grid.177174.30000 0001 2242 4849Laboratory of Molecular Gene Technics, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Kosuke Tashiro
- grid.177174.30000 0001 2242 4849Laboratory of Molecular Gene Technics, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Satoru Kuhara
- grid.177174.30000 0001 2242 4849Laboratory of Molecular Gene Technics, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Koichiro Gen
- Planning and Coordination Department, Fisheries Technology Institute, FRA, Nagasaki, 851-2213 Japan
| | - Atushi Fujiwara
- grid.410851.90000 0004 1764 1824Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, FRA, Mie, 516-0193 Japan
| | - Yukinori Kazeto
- Fisheries Technology Institute, Minamiizu Field Station, FRA, Shizuoka, 415-0156 Japan
| | - Takanori Kobayashi
- grid.410851.90000 0004 1764 1824Aquatic Breeding Division, Aquaculture Research Department, Fisheries Technology Institute, FRA, Kanagawa, 236-8648 Japan
| | - Michiya Matsuyama
- ABRIC, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan.
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Pham KD, Hakozaki Y, Takamizawa T, Yamazaki A, Yamazaki H, Mori K, Aburatani S, Tashiro K, Kuhara S, Takaku H, Shida Y, Ogasawara W. Analysis of the light regulatory mechanism in carotenoid production in Rhodosporidium toruloides NBRC 10032. Biosci Biotechnol Biochem 2021; 85:1899-1909. [PMID: 34124766 DOI: 10.1093/bbb/zbab109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/06/2021] [Indexed: 11/14/2022]
Abstract
Light stimulates carotenoid production in an oleaginous yeast Rhodosporidium toruloides NBRC 10032 by promoting carotenoid biosynthesis genes. These genes undergo two-step transcriptional activation. The potential light regulator, Cryptochrome DASH (CRY1), has been suggested to contribute to this mechanism. In this study, based on KU70 (a component of nonhomologous end joining (NHEJ)) disrupting background, CRY1 disruptant was constructed to clarify CRY1 function. From analysis of CRY1 disruptant, it was suggested that CRY1 has the activation role of the carotenogenic gene expression. To obtain further insights into the light response, mutants varying carotenoid production were generated. Through analysis of mutants, the existence of the control two-step gene activation was proposed. In addition, our data analysis showed the strong possibility that R. toruloides NBRC 10032 is a homo-diploid strain.
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Affiliation(s)
- Khanh Dung Pham
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | - Yuuki Hakozaki
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | - Takeru Takamizawa
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | - Atsushi Yamazaki
- Biological Resource Center, National Institute of Technology and Evaluation (NITE), Chiba, Japan
| | - Harutake Yamazaki
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | | | - Sachiyo Aburatani
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Kosuke Tashiro
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Satoru Kuhara
- Graduate School of Genetic Resource Technology, Kyushu University, Fukuoka, Japan
| | - Hiroaki Takaku
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Niigata, Japan
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Pham KD, Shida Y, Miyata A, Takamizawa T, Suzuki Y, Ara S, Yamazaki H, Masaki K, Mori K, Aburatani S, Hirakawa H, Tashiro K, Kuhara S, Takaku H, Ogasawara W. Effect of light on carotenoid and lipid production in the oleaginous yeast Rhodosporidium toruloides. Biosci Biotechnol Biochem 2020; 84:1501-1512. [PMID: 32189572 DOI: 10.1080/09168451.2020.1740581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The oleaginous yeast Rhodosporodium toruloides is receiving widespread attention as an alternative energy source for biofuels due to its unicellular nature, high growth rate and because it can be fermented on a large-scale. In this study, R. toruloides was cultured under both light and dark conditions in order to understand the light response involved in lipid and carotenoid biosynthesis. Our results from phenotype and gene expression analysis showed that R. toruloides responded to light by producing darker pigmentation with an associated increase in carotenoid production. Whilst there was no observable difference in lipid production, slight changes in the fatty acid composition were recorded. Furthermore, a two-step response was found in three genes (GGPSI, CAR1, and CAR2) under light conditions and the expression of the gene encoding the photoreceptor CRY1 was similarly affected.
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Affiliation(s)
- Khanh Dung Pham
- Department of Bioengineering, Nagaoka University of Technology , Niigata, Japan
| | - Yosuke Shida
- Department of Bioengineering, Nagaoka University of Technology , Niigata, Japan
| | - Atsushi Miyata
- Department of Bioengineering, Nagaoka University of Technology , Niigata, Japan
| | - Takeru Takamizawa
- Department of Bioengineering, Nagaoka University of Technology , Niigata, Japan
| | - Yoshiyuki Suzuki
- Advanced Course, National Institute of Technology, Nagaoka College , Niigata, Japan
| | - Satoshi Ara
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences , Niigata, Japan
| | - Harutake Yamazaki
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences , Niigata, Japan
| | - Kazuo Masaki
- Brewing Technology Division, National Research Institute of Brewing (NRIB) , Hiroshima, Japan
| | - Kazuki Mori
- Advance Course, National Institute of Technology, Kagoshima College , Kagoshima, Japan
| | - Sachiyo Aburatani
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo, Japan
| | - Hideki Hirakawa
- Facility for Genome Informatics, Kazusa DNA Research Institute , Ibaraki, Japan
| | - Kosuke Tashiro
- Faculty of Agriculture, Kyushu University , Fukuoka, Japan
| | - Satoru Kuhara
- Graduate School of Genetic Resource Technology, Kyushu University , Fukuoka, Japan
| | - Hiroaki Takaku
- Faculty of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences , Niigata, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology , Niigata, Japan
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Hata J, Ohara T, Katakura Y, Shimizu K, Yamashita S, Yoshida D, Honda T, Hirakawa Y, Shibata M, Sakata S, Kitazono T, Kuhara S, Ninomiya T. Association Between Serum β-Alanine and Risk of Dementia. Am J Epidemiol 2019; 188:1637-1645. [PMID: 31127276 DOI: 10.1093/aje/kwz116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 11/12/2022] Open
Abstract
We examined the association between serum concentrations of β-alanine, a metabolite of carnosine and anserine, and the risk of dementia in a general population of elderly Japanese persons. In 2007, 1,475 residents of Hisayama, Japan, aged 60-79 years and without dementia were divided into 4 groups according to quartiles of serum β-alanine concentrations (quartile 1, lowest; quartile 4, highest) and followed for a median of 5.3 years. During follow-up, 117 subjects developed all-cause dementia (Alzheimer in 77 cases and vascular dementia in 31). The risk of all-cause dementia decreased with increasing serum β-alanine levels after adjustment for potential confounding factors (quartile 2, hazard ratio (HR) = 0.73 (95% confidence interval (CI): 0.45, 1.18); quartile 3, HR = 0.50 (95% CI: 0.28, 0.89); quartile 4, HR = 0.50 (95% CI: 0.27, 0.92); P = 0.01 for trend). A similar inverse association was observed for Alzheimer disease (quartile 2, HR = 0.78 (95% CI: 0.44, 1.38); quartile 3, HR = 0.53 (95% CI: 0.26, 1.06); quartile 4, HR = 0.53 (95% CI: 0.25, 1.10); P = 0.04 for trend) but not for vascular dementia. We found that higher serum β-alanine levels were significantly associated with lower risks of all-cause dementia and Alzheimer disease. Because serum β-alanine levels reflect intakes of carnosine/anserine, higher intakes of carnosine/anserine might be beneficial for the prevention of dementia.
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Affiliation(s)
- Jun Hata
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tomoyuki Ohara
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshinori Katakura
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Kuniyoshi Shimizu
- Department of Agro-Environmental Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Shuntaro Yamashita
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Daigo Yoshida
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takanori Honda
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoichiro Hirakawa
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mao Shibata
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoko Sakata
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takanari Kitazono
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoru Kuhara
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Toshiharu Ninomiya
- Department of Epidemiology and Public Health, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Center for Cohort Studies, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Hirasawa H, Shioya K, Mori K, Tashiro K, Aburatani S, Shida Y, Kuhara S, Ogasawara W. Cellulase productivity of Trichoderma reesei mutants developed in Japan varies with varying pH conditions. J Biosci Bioeng 2019; 128:264-273. [DOI: 10.1016/j.jbiosc.2019.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/07/2019] [Accepted: 03/09/2019] [Indexed: 01/08/2023]
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Hori K, Hashimoto T, Kuhara S. Basic study of random sampling for compressed sensing using MRI simulator. Hell J Nucl Med 2019; 22 Suppl 2:141. [PMID: 31802054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/11/2019] [Indexed: 06/10/2023]
Abstract
INTRODUCTION Magnetic resonance imaging (MRI) is a tomography technology that enables the depiction of anatomical structures with information about various features. Compressed sensing (CS) technology has recently been used for magnetic resonance image reconstruction from sparse information. Random sampling methods based on the various probability density function (PDF) are being developed to allow the efficient application of CS technology. Accurate numerical simulation is obviously important for the evaluation of the sampling method that are developed. In this study, the simulation method with MRI simulator and actual MRI scanner was carried out. Moreover, the difference between the result acquired from our simulation and basic one was revealed. METHODS We first examined a basic method using a 2D Shepp-Logan phantom. This method was only conducted with k-space data obtained from the 2D Fourier transform of the original image. Our method of numerical simulation was applied with the MRI simulator (Bloch Solver, MRI simulations Inc.), an actual MRI system (Vantage Titan 3T, Canon Medical Systems) and a phantom (CAGN-3.0T phantom, Kato Medience). The real and imaginary part of the k-space were acquired with the MRI simulator using a phase map that was imaged by the actual MRI scanner. Random sampling was performed with two types of PDF and image reconstruction was processed by projection onto convex sets (POCS). Hermitian symmetry is a point-symmetry respect to origin and each point located on the opposite side maintains a relation of complex conjugate. Thus, there is no need to acquire data that formed in point-symmetry with the data that had already been acquired. We used the gaussian random sampling method (GA) and a method that considered Hermitian symmetry (GH). The image quality was evaluated using the normalized root mean squared error (NRMSE). RESULTS AND DISCUSSION In the basic simulation, the average and standard deviation of NRMSE from GH was better than that from GA because consideration of the Hermitian symmetry enables the efficient acquisition of data. However, in our method of numerical simulation, the average and standard deviation of the NRMSE from GH was worse than that from GA. In this simulation method, the phase error was included in the real and imaginary part of the k-space; thus, the Hermitian symmetry cannot hold and the calculation error of reconstruction images from GH stood out. CONCLUSION The method of numerical simulation with the MRI simulator using a phase map was close to the actual conditions and was considered to be useful for the validation of new sampling methods. The random sampling method using GH is expected to be useful for the highly efficient acquisition of data under ideal conditions; however, more accurate phase correction is necessary to apply the actual measurement data.
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Affiliation(s)
- K Hori
- Kyorin University Graduate School of Health Sciences, Tokyo, Japan.
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Nakashima Y, Kounoura M, Malasuk C, Nakakubo K, Watanabe N, Iwata S, Morita K, Oki Y, Kuhara S, Tashiro K, Nakanishi Y. Continuous cell culture monitoring using a compact microplate reader with a silicone optical technology-based spatial filter. Rev Sci Instrum 2019; 90:035106. [PMID: 30927768 DOI: 10.1063/1.5054824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/23/2019] [Indexed: 06/09/2023]
Abstract
Continuous cell monitoring is very important for the maintenance and control of cell multiplication and differentiation. This paper presents a compact microplate reader that is able to continuously measure a 24-well microplate (6 × 4 wells) using the optical absorption measurement method. The 24-channel plate reader consisted of a spatial filter, light emitting diode light source, and color sensors and was similarly sized with the cell culture microwell plates. A spatial filter was previously fabricated by our group using silicone optical technology (SOT). This SOT-based spatial filter has an excellent noise reduction effect. Light reflection at the optical path interface can be absorbed and only forward light can be transmitted; accordingly, a larger S/N ratio than that of conventional optical systems is expected. The fabricated 24-channel plate reader permits real-time cell monitoring during cultivation on the clean bench and in cell culture conditions by incorporating the SOT spatial filter. Using the device, it was possible to continuously evaluate the concentration and pH of reagents in the 24 wells in real time. Moreover, cell activity and protein production were detectable using the device. These results suggest that the newly fabricated device is a promising tool for the evaluation of cell behaviors for cell management.
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Affiliation(s)
- Y Nakashima
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 096-8555, Japan
| | - M Kounoura
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 096-8555, Japan
| | - C Malasuk
- Department of I&E Visionaries, Kyusyu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - K Nakakubo
- Department of I&E Visionaries, Kyusyu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - N Watanabe
- Graduate School of Bioresource and Bioenvironmental Science, Kyusyu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - S Iwata
- Graduate School of Bioresource and Bioenvironmental Science, Kyusyu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - K Morita
- Department of I&E Visionaries, Kyusyu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Y Oki
- Department of I&E Visionaries, Kyusyu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - S Kuhara
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 812-8581, Japan
| | - K Tashiro
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 812-8581, Japan
| | - Y Nakanishi
- Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 096-8555, Japan
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Kadooka K, Sato M, Matsumoto T, Kuhara S, Katakura Y, Fujimura T. Pig testis extract augments adiponectin expression and secretion through the peroxisome proliferator-activated receptor signaling pathway in 3T3-L1 adipocytes. Cytotechnology 2018; 70:983-992. [PMID: 29582200 DOI: 10.1007/s10616-018-0213-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/05/2018] [Indexed: 01/14/2023] Open
Abstract
Adiponectin is a key molecule whose upregulation may ameliorate symptoms of type 2 diabetes mellitus and disorders of lipid metabolism. Several plant-derived components have been shown to enhance adiponectin secretion; however, there have been no reports on the effects of animal-derived products. Therefore, in the current study, we investigated whether hot-water extracts of specific livestock by-products induce the expression of adiponectin in mouse 3T3-L1 adipocytes. Out of the 11 extracts tested, pig testis extract (PTE) was found to enhance adiponectin expression and secretion by 3T3-L1 cells. Furthermore, simultaneous treatment with PTE and daidzein, a soy phytoestrogen, synergistically enhanced adiponectin secretion. Moreover, pretreatment with an estrogen receptor β antagonist (PHTPP) diminished adiponectin secretion from daidzein-treated cells but not from PTE-treated cells. Transcriptome analyses revealed that both daidzein and PTE regulate the peroxisome proliferator-activated receptor signaling pathway, although differences in the regulation of gene expression were observed between PTE- and daidzein-treated cells. These results suggest that PTE ameliorates lipid metabolic dysfunction by promoting adipocyte differentiation and enhancing adiponectin secretion via a mechanism different from that of daidzein.
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Affiliation(s)
- Keishi Kadooka
- R&D Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, Japan
| | - Mikako Sato
- R&D Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, Japan.
| | - Takashi Matsumoto
- R&D Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, Japan
| | - Satoru Kuhara
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Yoshinori Katakura
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, Japan
| | - Tatsuya Fujimura
- R&D Center, NH Foods Ltd., 3-3 Midorigahara, Tsukuba, Ibaraki, Japan
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Ezura K, Ji-Seong K, Mori K, Suzuki Y, Kuhara S, Ariizumi T, Ezura H. Genome-wide identification of pistil-specific genes expressed during fruit set initiation in tomato (Solanum lycopersicum). PLoS One 2017; 12:e0180003. [PMID: 28683065 PMCID: PMC5500324 DOI: 10.1371/journal.pone.0180003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
Fruit set involves the developmental transition of an unfertilized quiescent ovary in the pistil into a fruit. While fruit set is known to involve the activation of signals (including various plant hormones) in the ovary, many biological aspects of this process remain elusive. To further expand our understanding of this process, we identified genes that are specifically expressed in tomato (Solanum lycopersicum L.) pistils during fruit set through comprehensive RNA-seq-based transcriptome analysis using 17 different tissues including pistils at six different developmental stages. First, we identified 532 candidate genes that are preferentially expressed in the pistil based on their tissue-specific expression profiles. Next, we compared our RNA-seq data with publically available transcriptome data, further refining the candidate genes that are specifically expressed within the pistil. As a result, 108 pistil-specific genes were identified, including several transcription factor genes that function in reproductive development. We also identified genes encoding hormone-like peptides with a secretion signal and cysteine-rich residues that are conserved among some Solanaceae species, suggesting that peptide hormones may function as signaling molecules during fruit set initiation. This study provides important information about pistil-specific genes, which may play specific roles in regulating pistil development in relation to fruit set.
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Affiliation(s)
- Kentaro Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kim Ji-Seong
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kazuki Mori
- Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Satoru Kuhara
- Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Mori K, Shirasawa K, Nogata H, Hirata C, Tashiro K, Habu T, Kim S, Himeno S, Kuhara S, Ikegami H. Corrigendum: Identification of RAN1 orthologue associated with sex determination through whole genome sequencing analysis in fig (Ficus carica L.). Sci Rep 2017; 7:46784. [PMID: 28488674 PMCID: PMC5424537 DOI: 10.1038/srep46784] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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11
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Wong PS, Tashiro K, Kuhara S, Aburatani S. Elucidation of the sequential transcriptional activity in Escherichia coli using time-series RNA-seq data. Bioinformation 2017; 13:25-30. [PMID: 28479747 PMCID: PMC5405090 DOI: 10.6026/97320630013025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 01/25/2017] [Indexed: 11/23/2022] Open
Abstract
Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. Here, we present a new method to augment regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity. We apply our method on a time-series RNA-Seq data set of Escherichia coli as it transitions from growth to stationary phase over five hours and investigate the various activity in gene regulation process by taking advantage of the correlation between regulatory gene pairs to examine their activity on a dynamic network. We analyse the changes in metabolic activity of the pagP gene and associated transcription factors during phase transition, and visualize the sequential transcriptional activity to describe the change in metabolic pathway activity originating from the pagP transcription factor, phoP. We observe a shift from amino acid and nucleic acid metabolism, to energy metabolism during the transition to stationary phase in E. coli.
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Affiliation(s)
- Pui Shan Wong
- Biotechnology Research Institute for Drug Discovery, National Institute of AIST, Tokyo, Japan
| | - Kosuke Tashiro
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Satoru Kuhara
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Sachiyo Aburatani
- Biotechnology Research Institute for Drug Discovery, National Institute of AIST, Tokyo, Japan.,Com. Bio Big Data Open Innovation Lab. (CBBD-OIL), National Institute of AIST, Tokyo, Japan
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12
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Sakata M, Seno M, Matsusaka H, Takahashi K, Nakamura Y, Yamagata Y, Angeles ER, Mochizuki T, Kumamaru T, Sato M, Enomoto A, Tashiro K, Kuhara S, Satoh H, Yoshimura A. Development and evaluation of rice giant embryo mutants for high oil content originated from a high-yielding cultivar 'Mizuhochikara'. Breed Sci 2016; 66:425-33. [PMID: 27436953 PMCID: PMC4902460 DOI: 10.1270/jsbbs.15135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/15/2016] [Indexed: 05/03/2023]
Abstract
Rice bran oil is a byproduct of the milling of rice (Oryza sativa L.). It offers various health benefits and has a beneficial fatty acid composition. To increase the amount of rice bran as a sink for triacylglycerol (TAG), we developed and characterized new breeding materials with giant embryos. To induce mutants, we treated fertilized egg cells of the high-yielding cultivar 'Mizuhochikara' with N-methyl-N-nitrosourea (MNU). By screening M2 seeds, we isolated four giant embryo mutant lines. Genetic analysis revealed that the causative loci in lines MGE12 and MGE13 were allelic to giant embryo (ge) on chromosome 7, and had base changes in the causal gene Os07g0603700. On the other hand, the causative loci in lines MGE8 and MGE14 were not allelic to ge, and both were newly mapped on chromosome 3. The TAG contents of all four mutant lines increased relative to their wild type, 'Mizuhochikara'. MGE13 was agronomically similar to 'Mizuhochikara' and would be useful for breeding for improved oil content.
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Affiliation(s)
- Mitsukazu Sakata
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Mari Seno
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Kiyomi Takahashi
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Yuki Nakamura
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Enrique R. Angeles
- Institute of Tropical Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Toshihiro Mochizuki
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Masao Sato
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Akiko Enomoto
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Kosuke Tashiro
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Satoru Kuhara
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Hikaru Satoh
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
| | - Atsushi Yoshimura
- Faculty of Agriculture, Kyushu University,
6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581,
Japan
- Corresponding author (e-mail: )
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13
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Monda K, Araki H, Kuhara S, Ishigaki G, Akashi R, Negi J, Kojima M, Sakakibara H, Takahashi S, Hashimoto-Sugimoto M, Goto N, Iba K. Enhanced Stomatal Conductance by a Spontaneous Arabidopsis Tetraploid, Me-0, Results from Increased Stomatal Size and Greater Stomatal Aperture. Plant Physiol 2016; 170:1435-44. [PMID: 26754665 PMCID: PMC4775119 DOI: 10.1104/pp.15.01450] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/08/2016] [Indexed: 05/03/2023]
Abstract
The rate of gas exchange in plants is regulated mainly by stomatal size and density. Generally, higher densities of smaller stomata are advantageous for gas exchange; however, it is unclear what the effect of an extraordinary change in stomatal size might have on a plant's gas-exchange capacity. We investigated the stomatal responses to CO2 concentration changes among 374 Arabidopsis (Arabidopsis thaliana) ecotypes and discovered that Mechtshausen (Me-0), a natural tetraploid ecotype, has significantly larger stomata and can achieve a high stomatal conductance. We surmised that the cause of the increased stomatal conductance is tetraploidization; however, the stomatal conductance of another tetraploid accession, tetraploid Columbia (Col), was not as high as that in Me-0. One difference between these two accessions was the size of their stomatal apertures. Analyses of abscisic acid sensitivity, ion balance, and gene expression profiles suggested that physiological or genetic factors restrict the stomatal opening in tetraploid Col but not in Me-0. Our results show that Me-0 overcomes the handicap of stomatal opening that is typical for tetraploids and achieves higher stomatal conductance compared with the closely related tetraploid Col on account of larger stomatal apertures. This study provides evidence for whether larger stomatal size in tetraploids of higher plants can improve stomatal conductance.
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Affiliation(s)
- Keina Monda
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Hiromitsu Araki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Satoru Kuhara
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Genki Ishigaki
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Ryo Akashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Juntaro Negi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Mikiko Kojima
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Hitoshi Sakakibara
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Sho Takahashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Mimi Hashimoto-Sugimoto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Nobuharu Goto
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
| | - Koh Iba
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka 819-0395, Japan (K.M., J.N., S.T., M.H.-S., K.I.);Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan (H.A., S.K);Department of Animal and Grassland Sciences, Faculty of Agriculture, University of Miyazaki, Miyazaki 889-2192, Japan (G.I., R.A.);RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan (M.K., H.S.); andRIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki 305-0074, Japan (N.G.)
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14
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Shibata M, Mekuchi M, Mori K, Muta S, Chowdhury VS, Nakamura Y, Ojima N, Saitoh K, Kobayashi T, Wada T, Inouye K, Kuhara S, Tashiro K. Transcriptomic features associated with energy production in the muscles of Pacific bluefin tuna and Pacific cod. Biosci Biotechnol Biochem 2016; 80:1114-24. [PMID: 26924100 DOI: 10.1080/09168451.2016.1151341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bluefin tuna are high-performance swimmers and top predators in the open ocean. Their swimming is grounded by unique features including an exceptional glycolytic potential in white muscle, which is supported by high enzymatic activities. Here we performed high-throughput RNA sequencing (RNA-Seq) in muscles of the Pacific bluefin tuna (Thunnus orientalis) and Pacific cod (Gadus macrocephalus) and conducted a comparative transcriptomic analysis of genes related to energy production. We found that the total expression of glycolytic genes was much higher in the white muscle of tuna than in the other muscles, and that the expression of only six genes for glycolytic enzymes accounted for 83.4% of the total. These expression patterns were in good agreement with the patterns of enzyme activity previously reported. The findings suggest that the mRNA expression of glycolytic genes may contribute directly to the enzymatic activities in the muscles of tuna.
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Affiliation(s)
- Mami Shibata
- a Graduate School of Bioresource and Bioenvironmental Sciences , Kyushu University , Fukuoka , Japan
| | - Miyuki Mekuchi
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | - Kazuki Mori
- c Biotechnology Research Institute for Drug Discovery , National Institute of Advanced Industrial Science and Technology (AIST) , Tokyo , Japan
| | - Shigeru Muta
- d Laboratory of Molecular Gene Techniques, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture , Kyushu University , Fukuoka , Japan
| | - Vishwajit Sur Chowdhury
- e Division for Experimental Natural Science, Faculty of Arts and Science , Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University , Fukuoka , Japan
| | - Yoji Nakamura
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | - Nobuhiko Ojima
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | - Kenji Saitoh
- b Research Center for Aquatic Genomics, National Research Institute of Fisheries Science , Fisheries Research Agency , Yokohama , Japan
| | | | - Tokio Wada
- f Fisheries Research Agency , Yokohama , Japan
| | - Kiyoshi Inouye
- g Japan Fisheries Science and Technology Association , Tokyo , Japan
| | - Satoru Kuhara
- d Laboratory of Molecular Gene Techniques, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture , Kyushu University , Fukuoka , Japan
| | - Kosuke Tashiro
- d Laboratory of Molecular Gene Techniques, Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture , Kyushu University , Fukuoka , Japan
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15
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Nagayoshi Y, Kumagae K, Mori K, Tashiro K, Nakamura A, Fujino Y, Hiromasa Y, Iwamoto T, Kuhara S, Ohshima T, Doi K. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8. Front Microbiol 2016; 7:50. [PMID: 26941711 PMCID: PMC4763002 DOI: 10.3389/fmicb.2016.00050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/12/2016] [Indexed: 12/11/2022] Open
Abstract
A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell.
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Affiliation(s)
- Yuko Nagayoshi
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Kenta Kumagae
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Kazuki Mori
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Ayano Nakamura
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
| | - Yasuhiro Fujino
- Faculty of Arts and Science, Kyushu University Fukuoka, Japan
| | - Yasuaki Hiromasa
- Faculty of Agriculture, Attached Promotive Center for International Education and Research of Agriculture, Kyushu University Fukuoka, Japan
| | - Takeo Iwamoto
- Core Research Facilities, Research Center for Medical Sciences, Jikei University School of Medicine Tokyo, Japan
| | - Satoru Kuhara
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University Fukuoka, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology Osaka, Japan
| | - Katsumi Doi
- Faculty of Agriculture, Institute of Genetic Resources, Kyushu University Fukuoka, Japan
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16
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Hayashi N, Ono R, Nakano R, Shiratani M, Tashiro K, Kuhara S, Yasuda K, Hagiwara H. DNA Microarray Analysis of Plant Seeds Irradiated by Active Oxygen Species in Oxygen Plasma. Plasma Med 2016. [DOI: 10.1615/plasmamed.2016018933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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17
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Shida Y, Yamaguchi K, Nitta M, Nakamura A, Takahashi M, Kidokoro SI, Mori K, Tashiro K, Kuhara S, Matsuzawa T, Yaoi K, Sakamoto Y, Tanaka N, Morikawa Y, Ogasawara W. The impact of a single-nucleotide mutation of bgl2 on cellulase induction in a Trichoderma reesei mutant. Biotechnol Biofuels 2015; 8:230. [PMID: 26719764 PMCID: PMC4696228 DOI: 10.1186/s13068-015-0420-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/15/2015] [Indexed: 05/10/2023]
Abstract
BACKGROUND The filamentous fungus Trichoderma reesei (anamorph of Hypocrea jecorina) produces increased cellulase expression when grown on cellulose or its derivatives as a sole carbon source. It has been believed that β-glucosidases of T. reesei not only metabolize cellobiose but also contribute in the production of inducers of cellulase gene expression by their transglycosylation activity. The cellulase hyper-producing mutant PC-3-7 developed in Japan has enhanced cellulase production ability when cellobiose is used as the inducer. The comparative genomics analysis of PC-3-7 and its parent revealed a single-nucleotide mutation within the bgl2 gene encoding intracellular β-glucosidase II (BGLII/Cel1a), giving rise to an amino acid substitution in PC-3-7, which could potentially account for the enhanced cellulase expression when these strains are cultivated on cellulose and cellobiose. RESULTS To analyze the effects of the BGLII mutation in cellulase induction, we constructed both a bgl2 revertant and a disruptant. Enzymatic analysis of the transformant lysates showed that the strain expressing mutant BGLII exhibited weakened cellobiose hydrolytic activity, but produced some transglycosylation products, suggesting that the SNP in bgl2 strongly diminished cellobiase activity, but did not result in complete loss of function of BGLII. The analysis of the recombinant BGLII revealed that transglycosylation products might be oligosaccharides, composed probably of glucose linked β-1,4, β-1,3, or a mixture of both. PC-3-7 revertants of bgl2 exhibited reduced expression and inducibility of cellulase during growth on cellulose and cellobiose substrates. Furthermore, the effect of this bgl2 mutation was reproduced in the common strain QM9414 in which the transformants showed cellulase production comparable to that of PC-3-7. CONCLUSION We conclude that BGLII plays an important role in cellulase induction in T. reesei and that the bgl2 mutation in PC-3-7 brought about enhanced cellulase expression on cellobiose. The results of the investigation using PC-3-7 suggested that other mutation(s) in PC-3-7 could also contribute to cellulase induction. Further investigation is essential to unravel the mechanism responsible for cellulase induction in T. reesei.
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Affiliation(s)
- Yosuke Shida
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kaori Yamaguchi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Mikiko Nitta
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
- />Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 Japan
| | - Ayana Nakamura
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Machiko Takahashi
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Shun-ichi Kidokoro
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Kazuki Mori
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Kosuke Tashiro
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Satoru Kuhara
- />Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka, 812-8581 Japan
| | - Tomohiko Matsuzawa
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Katsuro Yaoi
- />Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566 Japan
| | - Yasumitsu Sakamoto
- />School of Pharmacy, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Iwate 028-3694 Japan
| | - Nobutada Tanaka
- />School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555 Japan
| | - Yasushi Morikawa
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
| | - Wataru Ogasawara
- />Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 Japan
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Arakawa F, Kimura Y, Yoshida N, Miyoshi H, Doi A, Yasuda K, Nakajima K, Kiyasu J, Niino D, Sugita Y, Tashiro K, Kuhara S, Seto M, Ohshima K. Identification of miR-15b as a transformation-related factor in mantle cell lymphoma. Int J Oncol 2015; 48:485-92. [PMID: 26676972 PMCID: PMC4725451 DOI: 10.3892/ijo.2015.3295] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/24/2015] [Indexed: 12/12/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive B cell lymphoma with a poor prognosis. It is characterized by the t(11;14)(q13;q32) translocation, resulting in overexpression of CCND1. Morphologically, MCL is categorised into two types: classical MCL (cMCL) and aggressive MCL (aMCL), with a proportion of cMCL progressing to develop into aMCL. miRNAs are currently considered to be important regulators for cell behavior and are deregulated in many malignancies. Although several genetic alterations have been implicated in the transformation of cMCL to aMCL, the involvement of miRNAs in transformation is not known. In an effort to identify the miRNAs related to the transformation of MCL, miRNA microarray analyses were used for cMCL and aMCL cases. These analyses demonstrated significant differences in the expression of seven microRNAs based on a t-test (p-value <0.05); miR-15b was greatly upregulated in aMCL. Locked nucleic acid in situ hybridization showed increased staining of miR-15b in formalin-fixed paraffin-embedded sections of aMCL. These results correlated well with the microRNA microarray analysis. Although the molecular functions of miR-15b are largely unknown, it has been found to be associated with the cell cycle and apoptosis. However, the physiological significance of increased miR-15b in MCL is still unknown. Our present findings suggest that the upregulated expression of miR-15b is likely to play an important role in the transformation of cMCL to aMCL.
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Affiliation(s)
- Fumiko Arakawa
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Yoshizo Kimura
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Noriaki Yoshida
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Hiroaki Miyoshi
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Atushi Doi
- Cell Innovator Inc., Venture Business Laboratory of Kyushu University, Fukuoka, Japan
| | - Kaori Yasuda
- Cell Innovator Inc., Venture Business Laboratory of Kyushu University, Fukuoka, Japan
| | - Kazutaka Nakajima
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Junichi Kiyasu
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Daisuke Niino
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Yasuo Sugita
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology and Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Satoru Kuhara
- Laboratory of Molecular Gene Technology and Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Masao Seto
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
| | - Koichi Ohshima
- Department of Pathology, School of Medicine, Kurume University, Kurume, Japan
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19
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Araki H, Pang X, Komatsu N, Soejima M, Miyata N, Takaki M, Muta S, Sasada T, Noguchi M, Koda Y, Itoh K, Kuhara S, Tashiro K. Haptoglobin promoter polymorphism rs5472 as a prognostic biomarker for peptide vaccine efficacy in castration-resistant prostate cancer patients. Cancer Immunol Immunother 2015; 64:1565-73. [PMID: 26428930 PMCID: PMC11028849 DOI: 10.1007/s00262-015-1756-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 09/07/2015] [Indexed: 01/16/2023]
Abstract
Personalized peptide vaccination (PPV) is an attractive approach to cancer immunotherapy with strong immune-boosting effects conferring significant clinical benefit. However, as with most therapeutic agents, there is a difference in clinical efficacy among patients receiving PPV. Therefore, a useful biomarker is urgently needed for prognosticating clinical outcomes to preselect patients who would benefit the most from PPV. In this retrospective study, to detect a molecular prognosticator of clinical outcomes for PPV, we analyzed whole-genome gene expression profiles of peripheral blood mononuclear cells (PBMCs) in castration-resistant prostate cancer (CRPC) patients before administration of PPV. Cox regression analysis revealed that mRNA expression of myeloperoxidase, haptoglobin, and neutrophil elastase was significantly associated with overall survival (OS) among vaccinated CRPC patients (adjusted P < 0.01). By promoter sequence analysis of these three genes, we found that rs5472 of haptoglobin (HP), an acute-phase plasma glycoprotein, was strongly correlated to OS of vaccinated CRPC patients (P = 0.0047, hazard ratio 0.47; 95 % confidence interval 0.28-0.80). Furthermore, both HP mRNA expression in PBMCs and protein level in plasma of CRPC patients before administration of PPV exhibited rs5472 dependence (P < 0.001 for mRNA expression and P < 0.05 for protein level). Our findings suggest that rs5472 may play an important role in the immune response to PPV via regulation of HP. Thus, we concluded that rs5472 is a potential prognostic biomarker for PPV.
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Affiliation(s)
- Hiromitsu Araki
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan
| | - Xiaoliang Pang
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan
| | - Nobukazu Komatsu
- Department of Immunology and Immunotherapy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Mikiko Soejima
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan
| | - Nawoe Miyata
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan
| | - Mari Takaki
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan
| | - Shigeru Muta
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan
| | - Tetsuro Sasada
- Department of Immunology and Immunotherapy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Masanori Noguchi
- Clinical Research Division of Research Center for Innovative Cancer Therapy, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan
| | - Yoshiro Koda
- Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Japan
| | - Kyogo Itoh
- Cancer Vaccine Center, Kurume University, Kurume, Japan
| | - Satoru Kuhara
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-Ku, Fukuoka, 812-8581, Japan.
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20
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Kadooka K, Fujii K, Matsumoto T, Sato M, Morimatsu F, Tashiro K, Kuhara S, Katakura Y. Mechanisms and consequences of carnosine-induced activation of intestinal epithelial cells. J Funct Foods 2015. [DOI: 10.1016/j.jff.2014.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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21
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Eguchi R, Yoshigai E, Koga T, Kuhara S, Tashiro K. Spatiotemporal expression of Prdm genes during Xenopus development. Cytotechnology 2015; 67:711-9. [PMID: 25690332 DOI: 10.1007/s10616-015-9846-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/16/2015] [Indexed: 11/25/2022] Open
Abstract
Epigenetic regulation is known to be important in embryonic development, cell differentiation and regulation of cancer cells. Molecular mechanisms of epigenetic modification have DNA methylation and histone tail modification such as acetylation, phosphorylation and ubiquitination. Until now, many kinds of enzymes that modify histone tail with various functional groups have been reported and regulate the epigenetic state of genes. Among them, Prdm genes were identified as histone methyltransferase. Prdm genes are characterized by an N-terminal PR/SET domain and C-terminal some zinc finger domains and therefore they are considered to have both DNA-binding ability and methylation activity. Among vertebrate, fifteen members are estimated to belong to Prdm genes family. Even though Prdm genes are thought to play important roles for cell fate determination and cell differentiation, there is an incomplete understanding of their expression and functions in early development. Here, we report that Prdm genes exhibit dynamic expression pattern in Xenopus embryogenesis. By whole mount in situ hybridization analysis, we show that Prdm genes are expressed in spatially localized manners in embryo and all of Prdm genes are expressed in neural cells in developing central nervous systems. Our study suggests that Prdm genes may be new candidates to function in neural cell differentiation.
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Affiliation(s)
- Rieko Eguchi
- Graduate School of Systems Life Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka-shi, Fukuoka, 8128581, Japan,
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22
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Nagayoshi K, Ueki T, Tashiro K, Mizuuchi Y, Manabe T, Araki H, Oda Y, Kuhara S, Tanaka M. Galanin plays an important role in cancer invasiveness and is associated with poor prognosis in stage II colorectal cancer. Oncol Rep 2014; 33:539-46. [PMID: 25504183 PMCID: PMC4306273 DOI: 10.3892/or.2014.3660] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/20/2014] [Indexed: 12/13/2022] Open
Abstract
Reliable predictors of tumor recurrence for patients with stage II colorectal cancer (CRC) are needed to select patients who should receive adjuvant chemotherapy. Although galanin (GAL) is expressed in several malignant tumors and is associated with cell proliferation and tumor growth, the prognostic value of GAL expression in CRC is poorly understood. We compared GAL expression between 56 patients with stage II and III CRC who developed tumor recurrences and 56 patients who did not. The clinical and prognostic significance of GAL expression was examined using our data and independent public datasets. We also analyzed the influence of GAL expression on the proliferation and invasive activity of CRC cells. Higher expression of GAL was associated with tumor recurrence among the CRC patients (P<0.001). Stage II CRC patients who presented with high expression levels of GAL had significantly poorer prognosis than those with low expression levels of GAL [5-year overall survival: hazard ratio (HR), 7.31; 95% confidence interval (CI), 2.38–24.04; P<0.001; 5-year recurrence-free survival: HR, 3.99; 95% CI, 1.61–9.44; P=0.004], but there was no association between GAL expression and survival in stage III CRC patients. These findings were supported by analysis of two public datasets. Functionally, siRNA-mediated silencing of GAL resulted in a significant decrease in the proliferative and invasive activities of CRC cells. In conclusion, high expression of GAL is associated with poor prognosis of stage II CRC patients and GAL expression may be related to the aggressive behavior of CRC.
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Affiliation(s)
- Kinuko Nagayoshi
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Higashi‑ku, Fukuoka 812-8582, Japan
| | - Takashi Ueki
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Higashi‑ku, Fukuoka 812-8582, Japan
| | - Kosuke Tashiro
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yusuke Mizuuchi
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Tatsuya Manabe
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Higashi‑ku, Fukuoka 812-8582, Japan
| | - Hiromitsu Araki
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoru Kuhara
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan
| | - Masao Tanaka
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Higashi‑ku, Fukuoka 812-8582, Japan
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23
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Hayashida S, Kuroda K, Ohta K, Kuhara S, Fukuda K, Sakaki Y. Molecular Cloning of the Glucoamylase I Gene ofAspergillus awamorivar.kawachifor Localization of the Raw-starch-affinity Site. ACTA ACUST UNITED AC 2014. [DOI: 10.1080/00021369.1989.10869434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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24
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Oba T, Kusumoto K, Kichise Y, Izumoto E, Nakayama S, Tashiro K, Kuhara S, Kitagaki H. Variations in mitochondrial membrane potential correlate with malic acid production by natural isolates ofSaccharomyces cerevisiaesake strains. FEMS Yeast Res 2014; 14:789-96. [DOI: 10.1111/1567-1364.12170] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 05/01/2014] [Accepted: 05/21/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Takahiro Oba
- Biotechnology and Food Research Institute; Fukuoka Industrial Technology Center; Kurume Fukuoka Japan
| | - Kenichi Kusumoto
- Biotechnology and Food Research Institute; Fukuoka Industrial Technology Center; Kurume Fukuoka Japan
| | - Yuki Kichise
- Department of Biochemistry and Applied Chemistry; Kurume National College of Technology; Kurume Fukuoka Japan
| | - Eiji Izumoto
- Department of Biochemistry and Applied Chemistry; Kurume National College of Technology; Kurume Fukuoka Japan
| | - Shunichi Nakayama
- Department of Fermentation Science and Technology; Faculty of Applied Bio-science; Tokyo University of Agriculture; Setagaya-ku Tokyo Japan
| | - Kosuke Tashiro
- Graduate School of Genetic Resources Technology; Kyushu University; Higashi-ku Fukuoka Japan
| | - Satoru Kuhara
- Graduate School of Genetic Resources Technology; Kyushu University; Higashi-ku Fukuoka Japan
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25
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Hashikawa K, Yasumoto S, Nakashima K, Arakawa F, Kiyasu J, Kimura Y, Saruta H, Nakama T, Yasuda K, Tashiro K, Kuhara S, Hashimoto T, Ohshima K. Microarray analysis of gene expression by microdissected epidermis and dermis in mycosis fungoides and adult T-cell leukemia/lymphoma. Int J Oncol 2014; 45:1200-8. [PMID: 24970722 DOI: 10.3892/ijo.2014.2524] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 05/14/2014] [Indexed: 11/05/2022] Open
Abstract
The characteristic histopathological feature of mycosis fungoides (MF) and adult T-cell leukemia/lymphoma (ATLL) is epidermotropism. To identify the mechanism for epidermotropism of lymphoma cells, total RNAs were obtained from skin biopsies of epidermis and dermis of MF and ATLL patients by means of laser capture microdissection, and used for subsequent complementary DNA (cDNA) microarray experiments. This procedure has made it possible for us to observe and evaluate the regional environment of MF and ATLL. Hierarchical cluster analysis revealed that the cDNAs could be clearly differentiated into MF and ATLL. CCL27 was expressed in the dermis generated from keratinocytes, CCR4/CCR6/CCR7/CCR10/cutaneous lymphocyte-associated antigen (CLA) lymphoma cells in the dermis, and CCL21 in the extracellular matrix (stroma). Lymphotoxin (LT) β and CCL21 expression was significantly higher and that of CCR10 relatively for MF, while CCR4 and CLA expression was relatively higher for ATLL. In the epithelium, keratinocytes expressed CCL20/CCL27, and lymphoma cells CCR4/CCR6/CCR10, while CCR4, CCR6, CCL20 and CCL27 expression was relatively higher for ATLL than MF. The dermis of MF, but not that of ATLL, showed correlation between CCR7 and CCL21. These findings support the suggestion that chemokines and chemokine receptors are involved in the pathogenesis of MF and ATLL, indicate that cutaneous homing seems to be different for MF and ATLL, and point to the possibility that cutaneous T-cell lymphomas originate in regulatory T cells, especially in the case of ATLL.
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Affiliation(s)
- Keiko Hashikawa
- Department of Dermatology, Kurume University School of Medicine, Japan
| | | | | | - Fumiko Arakawa
- Department of Pathology, Kurume University School of Medicine, Japan
| | - Junichi Kiyasu
- Department of Pathology, Kurume University School of Medicine, Japan
| | - Yoshizo Kimura
- Department of Pathology, Kurume University School of Medicine, Japan
| | - Hiroshi Saruta
- Department of Dermatology, Kurume University School of Medicine, Japan
| | - Takekuni Nakama
- Department of Dermatology, Kurume University School of Medicine, Japan
| | - Kaori Yasuda
- Cell Innovator, Inc., Venture Business Laboratory of Kyushu University, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technics, Department of Genetic Resources Technology, Graduate School of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Japan
| | - Satoru Kuhara
- Laboratory of Molecular Gene Technics, Department of Genetic Resources Technology, Graduate School of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Japan
| | - Takashi Hashimoto
- Department of Dermatology, Kurume University School of Medicine, Japan
| | - Koichi Ohshima
- Department of Pathology, Kurume University School of Medicine, Japan
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26
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Ono T, Kuhara S. A novel method for gathering and prioritizing disease candidate genes based on construction of a set of disease-related MeSH® terms. BMC Bioinformatics 2014; 15:179. [PMID: 24917541 PMCID: PMC4068192 DOI: 10.1186/1471-2105-15-179] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 06/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the molecular mechanisms involved in disease is critical for the development of more effective and individualized strategies for prevention and treatment. The amount of disease-related literature, including new genetic information on the molecular mechanisms of disease, is rapidly increasing. Extracting beneficial information from literature can be facilitated by computational methods such as the knowledge-discovery approach. Several methods for mining gene-disease relationships using computational methods have been developed, however, there has been a lack of research evaluating specific disease candidate genes. RESULTS We present a novel method for gathering and prioritizing specific disease candidate genes. Our approach involved the construction of a set of Medical Subject Headings (MeSH) terms for the effective retrieval of publications related to a disease candidate gene. Information regarding the relationships between genes and publications was obtained from the gene2pubmed database. The set of genes was prioritized using a "weighted literature score" based on the number of publications and weighted by the number of genes occurring in a publication. Using our method for the disease states of pain and Alzheimer's disease, a total of 1101 pain candidate genes and 2810 Alzheimer's disease candidate genes were gathered and prioritized. The precision was 0.30 and the recall was 0.89 in the case study of pain. The precision was 0.04 and the recall was 0.6 in the case study of Alzheimer's disease. The precision-recall curve indicated that the performance of our method was superior to that of other publicly available tools. CONCLUSIONS Our method, which involved the use of a set of MeSH terms related to disease candidate genes and a novel weighted literature score, improved the accuracy of gathering and prioritizing candidate genes by focusing on a specific disease.
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Affiliation(s)
| | - Satoru Kuhara
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki Higashi-ku, Fukuoka 812-8581, Japan.
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27
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Tuncel A, Kawaguchi J, Ihara Y, Matsusaka H, Nishi A, Nakamura T, Kuhara S, Hirakawa H, Nakamura Y, Cakir B, Nagamine A, Okita TW, Hwang SK, Satoh H. The rice endosperm ADP-glucose pyrophosphorylase large subunit is essential for optimal catalysis and allosteric regulation of the heterotetrameric enzyme. Plant Cell Physiol 2014; 55:1169-83. [PMID: 24747952 DOI: 10.1093/pcp/pcu057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Although an alternative pathway has been suggested, the prevailing view is that starch synthesis in cereal endosperm is controlled by the activity of the cytosolic isoform of ADPglucose pyrophosphorylase (AGPase). In rice, the cytosolic AGPase isoform is encoded by the OsAGPS2b and OsAGPL2 genes, which code for the small (S2b) and large (L2) subunits of the heterotetrameric enzyme, respectively. In this study, we isolated several allelic missense and nonsense OsAGPL2 mutants by N-methyl-N-nitrosourea (MNU) treatment of fertilized egg cells and by TILLING (Targeting Induced Local Lesions in Genomes). Interestingly, seeds from three of the missense mutants (two containing T139I and A171V) were severely shriveled and had seed weight and starch content comparable with the shriveled seeds from OsAGPL2 null mutants. Results from kinetic analysis of the purified recombinant enzymes revealed that the catalytic and allosteric regulatory properties of these mutant enzymes were significantly impaired. The missense heterotetramer enzymes and the S2b homotetramer had lower specific (catalytic) activities and affinities for the activator 3-phosphoglycerate (3-PGA). The missense heterotetramer enzymes showed more sensitivity to inhibition by the inhibitor inorganic phosphate (Pi) than the wild-type AGPase, while the S2b homotetramer was profoundly tolerant to Pi inhibition. Thus, our results provide definitive evidence that starch biosynthesis during rice endosperm development is controlled predominantly by the catalytic activity of the cytoplasmic AGPase and its allosteric regulation by the effectors. Moreover, our results show that the L2 subunit is essential for both catalysis and allosteric regulatory properties of the heterotetramer enzyme.
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Affiliation(s)
- Aytug Tuncel
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USAThese authors contributed equally to this work
| | - Joe Kawaguchi
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 JapanThese authors contributed equally to this work
| | - Yasuharu Ihara
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | | | - Aiko Nishi
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | | | - Satoru Kuhara
- Department of Genetic Resources Technology, Kyushu University, Fukuoka, 812-8581 Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Department of Plant Genome Research, Kisarazu, Japan
| | - Yasunori Nakamura
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita City, 010-0195 Japan
| | - Bilal Cakir
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Ai Nagamine
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USAFaculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
| | - Hikaru Satoh
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
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Oba T, Nomiyama S, Hirakawa H, Tashiro K, Kuhara S. Asp578 in LEU4p Is One of the Key Residues for Leucine Feedback Inhibition Release in Sake Yeast. Biosci Biotechnol Biochem 2014; 69:1270-3. [PMID: 16041129 DOI: 10.1271/bbb.69.1270] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We identified a new mutation, Asp578Tyr, in alpha-isopropylmalate synthase (a LEU4 gene product) that releases leucine feedback inhibition and causes hyperproduction of isoamyl alcohol (i-AmOH) in sake yeast. Spontaneous sake yeast mutants that express resistance to 5,5,5-trifluoro-DL-leucine (TFL) were isolated, and a mutant strain, TFL20, was characterized at the genetic and biochemical levels. An enzyme assay for alpha-isopropylmalate synthase showed that strain TFL20 was released from feedback inhibition by L-leucine. Furthermore, DNA sequencing of the LEU4 gene for a haploid of the mutant TFL20 revealed that aspartic acid in position 578 changes to tyrosine. A comparison of the three-dimensional structures of wild-type LEU4p and mutant LEU4D578Yp by the homology modeling method showed that Asp578 is important for leucine feedback inhibition. We conclude that the mutation from Asp to Tyr in 578 is a novel change causing release from leucine feedback inhibition.
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Affiliation(s)
- Takahiro Oba
- Biotechnology and Food Research Institute, Fukuoka Industrial Technology Center, Aikawa-machi 1465-5, Kurume, Fukuoka 839-0861.
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29
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Taniguchi Y, Yamada Y, Maruyama O, Kuhara S, Ikeda D. The purity measure for genomic regions leads to horizontally transferred genes. J Bioinform Comput Biol 2013; 11:1343002. [PMID: 24372031 DOI: 10.1142/s0219720013430026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Sequence analysis is important to understand a genome, and a number of approaches such as sequence alignments and hidden Markov models have been employed. In the field of text mining, the purity measure is developed to detect unusual regions of a string without any domain knowledge. It is reported in that work that only RNAs and transposons are shown to have high purity values. In this work, the purity values of regions of various bacterial genome sequences are computed, and those regions are analyzed extensively. It is found that mobile elements and phages as well as RNAs and transposons have high purity values. It is interesting that they are all classified into a group of horizontally transferred genes. This means that the purity measure is useful to predict horizontally transferred genes.
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Affiliation(s)
- Yuta Taniguchi
- Department of Informatics, Kyushu University, Fukuoka, Japan
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Hirakawa H, Shirasawa K, Kosugi S, Tashiro K, Nakayama S, Yamada M, Kohara M, Watanabe A, Kishida Y, Fujishiro T, Tsuruoka H, Minami C, Sasamoto S, Kato M, Nanri K, Komaki A, Yanagi T, Guoxin Q, Maeda F, Ishikawa M, Kuhara S, Sato S, Tabata S, Isobe SN. Dissection of the octoploid strawberry genome by deep sequencing of the genomes of Fragaria species. DNA Res 2013; 21:169-81. [PMID: 24282021 PMCID: PMC3989489 DOI: 10.1093/dnares/dst049] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species.
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Affiliation(s)
- Hideki Hirakawa
- 1 Kazusa DNA Research Institute, Kazusa-Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan
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Komatsu N, Pang X, Araki H, Koda Y, Soejima K, Sasada T, Tashiro K, Kuhara S, Itoh K. Association of haptoglobin genetic polymorphism with overall survival in advanced castration-resistant prostate cancer patients with personalized peptide vaccination. J Immunother Cancer 2013. [PMCID: PMC3991181 DOI: 10.1186/2051-1426-1-s1-p56] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Kimura Y, Arakawa F, Kiyasu J, Miyoshi H, Yoshida M, Ichikawa A, Niino D, Sugita Y, Okamura T, Doi A, Yasuda K, Tashiro K, Kuhara S, Ohshima K. The Wnt signaling pathway and mitotic regulators in the initiation and evolution of mantle cell lymphoma: Gene expression analysis. Int J Oncol 2013; 43:457-68. [PMID: 23760751 DOI: 10.3892/ijo.2013.1982] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 05/20/2013] [Indexed: 11/06/2022] Open
Abstract
For an accurate understanding of mantle cell lymphoma (MCL), molecular behavior could be staged into two major events: lymphomagenesis with the t(11;14) translocation (initiation), and evolution into a more aggressive form (transformation). Unfortunately, it is still unknown which genes contribute to each event. In this study, we performed cDNA microarray experiments designed based on the concept that morphologically heterogeneous MCL samples would provide insights into the role of aberrant gene expression for both events. A total of 15 MCLs were collected from the files, which include a total of 237 MCL patients confirmed by histology as CCND1-positive. We posited four stepwise morphological grades for MCL: MCL in situ, MCL with classical form (cMCL), MCL with aggressive form (aMCL), and MCL with intermediate morphology between classical and aggressive forms at the same site (iMCL). To identify genes involved in initiation, we compared the tumor cells of MCL in situ (n=4) with normal mantle zone B lymphocytes (n=4), which were selected by laser microdissection (LMD). To identify genes contributing to transformation, we selected the overlapping genes differentially expressed between both cMCL (n=4) vs. aMCL (n=5) and classical vs. aggressive areas in iMCL (n=2) obtained by LMD. A significant number of genes (n=23, p=0.016) belonging to the Wnt signaling pathway were differentially expressed in initiation. This specific activation was confirmed by immuno-histochemistry, as MCL in situ had nuclear localization of phosphorylated-β-catenin with high levels of cytoplasmic Wnt3 staining. For transformation, identified 60 overlapping genes included a number of members of the p53 interaction network (CDC2, BIRC5 and FOXM1), which is known to mediate cell cycle progression during the G2/M transition. Thus, we observe that the Wnt signaling pathway may play an important role in initial lymphomagenesis in addition to t(11;14) translocations, and that specific mitotic regulators facilitate transformation into more aggressive forms.
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Affiliation(s)
- Yoshizo Kimura
- Department of Pathology, School of Medicine, Kurume University, Kurume, Fukuoka, Japan.
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Nakamura Y, Sasaki N, Kobayashi M, Ojima N, Yasuike M, Shigenobu Y, Satomi M, Fukuma Y, Shiwaku K, Tsujimoto A, Kobayashi T, Nakayama I, Ito F, Nakajima K, Sano M, Wada T, Kuhara S, Inouye K, Gojobori T, Ikeo K. The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PLoS One 2013; 8:e57122. [PMID: 23536760 PMCID: PMC3594237 DOI: 10.1371/journal.pone.0057122] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/09/2013] [Indexed: 11/18/2022] Open
Abstract
Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.
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Affiliation(s)
- Yoji Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
- * E-mail: (YN); (TG)
| | - Naobumi Sasaki
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masahiro Kobayashi
- Seikai National Fisheries Research Institute, Fisheries Research Agency, Nagasaki-shi, Nagasaki, Japan
| | - Nobuhiko Ojima
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Motoshige Yasuike
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Yuya Shigenobu
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Masataka Satomi
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | | | - Koji Shiwaku
- Hitachi Solutions, Ltd., Shinagawa-ku, Tokyo, Japan
| | | | | | - Ichiro Nakayama
- Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | - Fuminari Ito
- National Research Institute of Aquaculture, Fisheries Research Agency, Minami-ise, Mie, Japan
| | - Kazuhiro Nakajima
- Japan Sea National Fisheries Research Institute, Fisheries Research Agency, Chuou-ku, Niigata, Japan
| | - Motohiko Sano
- National Research Institute of Fisheries Science, Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Tokio Wada
- Fisheries Research Agency, Yokohama, Kanagawa, Japan
| | - Satoru Kuhara
- Division of Molecular Biosciences, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Higashi-ku, Fukuoka, Japan
| | | | - Takashi Gojobori
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
- * E-mail: (YN); (TG)
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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Affara M, Sanders D, Araki H, Tamada Y, Dunmore BJ, Humphreys S, Imoto S, Savoie C, Miyano S, Kuhara S, Jeffries D, Print C, Charnock-Jones DS. Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis. BMC Genomics 2013; 14:23. [PMID: 23324451 PMCID: PMC3570387 DOI: 10.1186/1471-2164-14-23] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 12/07/2012] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Apoptosis is a critical process in endothelial cell (EC) biology and pathology, which has been extensively studied at protein level. Numerous gene expression studies of EC apoptosis have also been performed, however few attempts have been made to use gene expression data to identify the molecular relationships and master regulators that underlie EC apoptosis. Therefore, we sought to understand these relationships by generating a Bayesian gene regulatory network (GRN) model. RESULTS ECs were induced to undergo apoptosis using serum withdrawal and followed over a time course in triplicate, using microarrays. When generating the GRN, this EC time course data was supplemented by a library of microarray data from EC treated with siRNAs targeting over 350 signalling molecules.The GRN model proposed Vasohibin-1 (VASH1) as one of the candidate master-regulators of EC apoptosis with numerous downstream mRNAs. To evaluate the role played by VASH1 in EC, we used siRNA to reduce the expression of VASH1. Of 10 mRNAs downstream of VASH1 in the GRN that were examined, 7 were significantly up- or down-regulated in the direction predicted by the GRN.Further supporting an important biological role of VASH1 in EC, targeted reduction of VASH1 mRNA abundance conferred resistance to serum withdrawal-induced EC death. CONCLUSION We have utilised Bayesian GRN modelling to identify a novel candidate master regulator of EC apoptosis. This study demonstrates how GRN technology can complement traditional methods to hypothesise the regulatory relationships that underlie important biological processes.
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Affiliation(s)
- Muna Affara
- Department of Obstetrics and Gynaecology, University of Cambridge, The Rosie Hospital, Robinson Way, Cambridge CB2 0SW, UK
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Jairin J, Kobayashi T, Yamagata Y, Sanada-Morimura S, Mori K, Tashiro K, Kuhara S, Kuwazaki S, Urio M, Suetsugu Y, Yamamoto K, Matsumura M, Yasui H. A simple sequence repeat- and single-nucleotide polymorphism-based genetic linkage map of the brown planthopper, Nilaparvata lugens. DNA Res 2012. [PMID: 23204257 PMCID: PMC3576655 DOI: 10.1093/dnares/dss030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we developed the first genetic linkage map for the major rice insect pest, the brown planthopper (BPH, Nilaparvata lugens). The linkage map was constructed by integrating linkage data from two backcross populations derived from three inbred BPH strains. The consensus map consists of 474 simple sequence repeats, 43 single-nucleotide polymorphisms, and 1 sequence-tagged site, for a total of 518 markers at 472 unique positions in 17 linkage groups. The linkage groups cover 1093.9 cM, with an average distance of 2.3 cM between loci. The average number of marker loci per linkage group was 27.8. The sex-linkage group was identified by exploiting X-linked and Y-specific markers. Our linkage map and the newly developed markers used to create it constitute an essential resource and a useful framework for future genetic analyses in BPH.
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Affiliation(s)
- Jirapong Jairin
- Ubon Ratchathani Rice Research Center, PO Box 65, Muang, Ubon Ratchathani 34000, Thailand
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Nitta M, Furukawa T, Shida Y, Mori K, Kuhara S, Morikawa Y, Ogasawara W. A new Zn(II)2Cys6-type transcription factor BglR regulates β-glucosidase expression in Trichoderma reesei. Fungal Genet Biol 2012; 49:388-97. [DOI: 10.1016/j.fgb.2012.02.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/07/2012] [Accepted: 02/25/2012] [Indexed: 11/25/2022]
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Yoshida S, Arakawa F, Higuchi F, Ishibashi Y, Goto M, Sugita Y, Nomura Y, Niino D, Shimizu K, Aoki R, Hashikawa K, Kimura Y, Yasuda K, Tashiro K, Kuhara S, Nagata K, Ohshima K. Gene expression analysis of rheumatoid arthritis synovial lining regions by cDNA microarray combined with laser microdissection: up-regulation of inflammation-associated STAT1, IRF1, CXCL9, CXCL10, and CCL5. Scand J Rheumatol 2012; 41:170-9. [PMID: 22401175 PMCID: PMC3400100 DOI: 10.3109/03009742.2011.623137] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Objectives The main histological change in rheumatoid arthritis (RA) is the villous proliferation of synovial lining cells, an important source of cytokines and chemokines, which are associated with inflammation. The aim of this study was to evaluate gene expression in the microdissected synovial lining cells of RA patients, using those of osteoarthritis (OA) patients as the control. Methods Samples were obtained during total joint replacement from 11 RA and five OA patients. Total RNA from the synovial lining cells was derived from selected specimens by laser microdissection (LMD) for subsequent cDNA microarray analysis. In addition, the expression of significant genes was confirmed immunohistochemically. Results The 14 519 genes detected by cDNA microarray were used to compare gene expression levels in synovial lining cells from RA with those from OA patients. Cluster analysis indicated that RA cells, including low- and high-expression subgroups, and OA cells were stored in two main clusters. The molecular activity of RA was statistically consistent with its clinical and histological activity. Expression levels of signal transducer and activator of transcription 1 (STAT1), interferon regulatory factor 1 (IRF1), and the chemokines CXCL9, CXCL10, and CCL5 were statistically significantly higher in the synovium of RA than in that of OA. Immunohistochemically, the lining synovium of RA, but not that of OA, clearly expressed STAT1, IRF1, and chemokines, as was seen in microarray analysis combined with LMD. Conclusions Our findings indicate an important role for lining synovial cells in the inflammatory and proliferative processes of RA. Further understanding of the local signalling in structural components is important in rheumatology.
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Affiliation(s)
- S Yoshida
- Department of Pathology, School of Medicine, Kurume University, Japan
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Imoto S, Savoie CJ, Aburatani S, Kim S, Tashiro K, Kuhara S, Miyano S. Use of Gene Networks for Identifying and Validating Drug Targets. J Bioinform Comput Biol 2012; 1:459-74. [PMID: 15290765 DOI: 10.1142/s0219720003000290] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2002] [Revised: 05/21/2003] [Accepted: 05/22/2003] [Indexed: 11/18/2022]
Abstract
We propose a new method for identifying and validating drug targets by using gene networks, which are estimated from cDNA microarray gene expression profile data. We created novel gene disruption and drug response microarray gene expression profile data libraries for the purpose of drug target elucidation. We use two types of microarray gene expression profile data for estimating gene networks and then identifying drug targets. The estimated gene networks play an essential role in understanding drug response data and this information is unattainable from clustering methods, which are the standard for gene expression analysis. In the construction of gene networks, we use the Bayesian network model. We use an actual example from analysis of the Saccharomyces cerevisiae gene expression profile data to express a concrete strategy for the application of gene network information to drug discovery.
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Affiliation(s)
- Seiya Imoto
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639 Japan.
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Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG. Gene network inference and visualization tools for biologists: application to new human transcriptome datasets. Nucleic Acids Res 2011; 40:2377-98. [PMID: 22121215 PMCID: PMC3315333 DOI: 10.1093/nar/gkr902] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.
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Affiliation(s)
- Daniel Hurley
- Auckland Bioengineering Institute, Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Maki Y, Takahashi Y, Arikawa Y, Watanabe S, Aoshima K, Eguchi Y, Ueda T, Aburatani S, Kuhara S, Okamoto M. AN INTEGRATED COMPREHENSIVE WORKBENCH FOR INFERRING GENETIC NETWORKS: VOYAGENE. J Bioinform Comput Biol 2011; 2:533-50. [PMID: 15359425 DOI: 10.1142/s0219720004000727] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Revised: 03/04/2004] [Accepted: 03/22/2004] [Indexed: 11/18/2022]
Abstract
We propose an integrated, comprehensive network-inferring system for genetic interactions, named VoyaGene, which can analyze experimentally observed expression profiles by using and combining the following five independent inferring models: Clustering, Threshold-Test, Bayesian, multi-level digraph and S-system models. Since VoyaGene also has effective tools for visualizing the inferred results, researchers may evaluate the combination of appropriate inferring models, and can construct a genetic network to an accuracy that is beyond the reach of a single inferring model. Through the use of VoyaGene, the present study demonstrates the effectiveness of combining different inferring models.
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Affiliation(s)
- Yukihiro Maki
- Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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Komatsu N, Matsueda S, Tashiro K, Ioji T, Shichijo S, Noguchi M, Yamada A, Doi A, Suekane S, Moriya F, Matsuoka K, Kuhara S, Itoh K, Sasada T. Gene expression profiles in peripheral blood as a biomarker in cancer patients receiving peptide vaccination. Cancer 2011; 118:3208-21. [PMID: 22071976 DOI: 10.1002/cncr.26636] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 08/26/2011] [Accepted: 09/16/2011] [Indexed: 12/12/2022]
Abstract
BACKGROUND Because only a subset of patients show clinical responses to peptide-based cancer vaccination, it is critical to identify biomarkers for selecting patients who would most likely benefit from this treatment. METHODS The authors characterized the gene expression profiles in peripheral blood of vaccinated patients to identify biomarkers to predict patient prognosis. Peripheral blood was obtained from advanced castration-resistant prostate cancer patients, who survived for >900 days (long-term survivors, n = 20) or died within 300 days (short-term survivors, n = 20) after treatment with personalized peptide vaccination. Gene expression profiles in prevaccination and postvaccination peripheral blood mononuclear cells (PBMCs) were assessed by DNA microarray. RESULTS There were no statistically significant differences in the clinical or pathological features between the 2 groups. Microarray analysis of prevaccination PBMCs identified 19 genes that were differentially expressed between the short-term and long-term survivors. Among the 15 up-regulated genes in the short-term survivors, 13 genes, which were also differentially expressed in postvaccination PBMCs, were associated with gene signatures of granulocytes. When a set of 4 differentially expressed genes were selected as the best combination to determine patient survival, prognosis was correctly predicted in 12 of 13 patients in a validation set (accuracy, 92%). CONCLUSIONS These results suggested that abnormal granulocytes present in the PBMC faction may contribute to poor prognosis in advanced prostate cancer patients receiving personalized peptide vaccination. Gene expression profiling in peripheral blood might thus be informative for devising better therapeutic strategies by predicting patient prognosis after cancer vaccines.
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Affiliation(s)
- Nobukazu Komatsu
- Department of Immunology and Immunotherapy, Kurume University School of Medicine, Kurume, Fukuoka, Japan
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Okada T, Kanao S, Kuhara S, Ninomiya A, Fujimoto K, Kido A, Togashi K. Whole-heart coronary MR angiography under a single breath-hold: a comparative study with respiratory-gated acquisition using a multi-element phased-array coil. Clin Radiol 2011; 66:1060-3. [PMID: 21925298 DOI: 10.1016/j.crad.2011.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2011] [Revised: 05/31/2011] [Accepted: 06/06/2011] [Indexed: 11/26/2022]
Abstract
AIM To compare visualization using whole-heart coronary magnetic resonance angiography (CMRA) acquired during a single breath-hold (BH) with that using conventional respiratory-gated (RG) CMRA. MATERIALS AND METHODS The CMRAs of 14 healthy subjects under either BH or RG conditions were studied using a 1.5 T system equipped with a whole-body phased-array coil and 16-channel receivers. The BH examination was accelerated using parallel imaging (PI) by factors of 2.5 and 2 in the phase and section directions, respectively. For the RG examination, a PI factor of 2 was used only in the phase direction. The visualization quality of 15 coronary segments using each condition was evaluated with a five-point scale (0-4). Differences between two conditions were compared at segments with an average score greater than 2 in RG-CMRA. RESULTS The average examination time for BH and RG acquisition scans was 34 s and 11 min 31 s, respectively. Ten segments (segments 1-3, 5-9, 11, and 13) had average scores higher than 2 in RG-CMRA. Of these, BH-CMRA had significantly lower scores than RG-CMRA at six segments (segments 1, 5-8, and 11) after correction for multiple comparisons (p<0.005). However, in BH-CMRA, proximal segments (segments 1-2, 5-7, and 11) showed average scores over 2, indicating marginally acceptable image quality. CONCLUSION Compared with the relatively limited degree of image degradation with RG-CMRA, the present data suggest that BH-CMRA would be useful for screening and as an adjunct to RG-CMRA that is occasionally incomplete.
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Affiliation(s)
- T Okada
- Diagnostic Imaging and Nuclear Medicine, Kyoto University Graduate School of Medicine, Sakyoku, Kyoto, Japan.
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Akao T, Yashiro I, Hosoyama A, Kitagaki H, Horikawa H, Watanabe D, Akada R, Ando Y, Harashima S, Inoue T, Inoue Y, Kajiwara S, Kitamoto K, Kitamoto N, Kobayashi O, Kuhara S, Masubuchi T, Mizoguchi H, Nakao Y, Nakazato A, Namise M, Oba T, Ogata T, Ohta A, Sato M, Shibasaki S, Takatsume Y, Tanimoto S, Tsuboi H, Nishimura A, Yoda K, Ishikawa T, Iwashita K, Fujita N, Shimoi H. Whole-genome sequencing of sake yeast Saccharomyces cerevisiae Kyokai no. 7. DNA Res 2011; 18:423-34. [PMID: 21900213 PMCID: PMC3223075 DOI: 10.1093/dnares/dsr029] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The term ‘sake yeast’ is generally used to indicate the Saccharomyces cerevisiae strains that possess characteristics distinct from others including the laboratory strain S288C and are well suited for sake brewery. Here, we report the draft whole-genome shotgun sequence of a commonly used diploid sake yeast strain, Kyokai no. 7 (K7). The assembled sequence of K7 was nearly identical to that of the S288C, except for several subtelomeric polymorphisms and two large inversions in K7. A survey of heterozygous bases between the homologous chromosomes revealed the presence of mosaic-like uneven distribution of heterozygosity in K7. The distribution patterns appeared to have resulted from repeated losses of heterozygosity in the ancestral lineage of K7. Analysis of genes revealed the presence of both K7-acquired and K7-lost genes, in addition to numerous others with segmentations and terminal discrepancies in comparison with those of S288C. The distribution of Ty element also largely differed in the two strains. Interestingly, two regions in chromosomes I and VII of S288C have apparently been replaced by Ty elements in K7. Sequence comparisons suggest that these gene conversions were caused by cDNA-mediated recombination of Ty elements. The present study advances our understanding of the functional and evolutionary genomics of the sake yeast.
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Affiliation(s)
- Takeshi Akao
- National Research Institute of Brewing, Higashi-hiroshima, Japan
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Miyake M, Takemasa I, Matoba R, Tanino M, Niijima S, Ikeda M, Yamamoto H, Sekimoto M, Kuhara S, Okayama T, Monden M, Matsubara K, Mori M. Heterogeneity of colorectal cancers and extraction of discriminator gene signatures for personalized prediction of prognosis. Int J Oncol 2011; 39:781-9. [PMID: 21701771 DOI: 10.3892/ijo.2011.1092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 04/12/2011] [Indexed: 11/05/2022] Open
Abstract
Dissected specimens of colorectal cancer (CRC) have been intensively studied using molecular sketches (gene signatures) to obtain a set of discriminator gene signatures for accurate prognosis prediction in individual patients. The discriminators obtained so far are not universally applicable, as the gene sets reflect the method and site of the study. In this study, we show that dissected stage II and III CRC samples are significantly heterogeneous in molecular sketches, and are not appropriate sources for discriminator extraction unless handled individually. To search for an accurate discriminator gene set for prediction of metastases, we need to start with less heterogeneous stage II CRC. We examined 198 (92 stage II and 106 stage III) CRC dissected samples for the predictability of discriminator gene signatures by analyzing stage II CRC alone, stage III alone, or in combination. The best predictive power of discriminator genes was obtained only when these genes were extracted and validated with stage II CRC samples. An accurate discriminator gene set for the prediction of CRC metastases can be obtained by focusing on stage II CRC samples.
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Affiliation(s)
- M Miyake
- Department of Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
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Hishigaki H, Kuhara S. hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds. Database (Oxford) 2011; 2011:bar017. [PMID: 21586548 PMCID: PMC3096323 DOI: 10.1093/database/bar017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Drug-induced QT interval prolongation is one of the most common reasons for the withdrawal of drugs from the market. In the past decade, at least nine drugs, i.e. terfenadine, astemizole, grepafloxacin, terodiline, droperidol, lidoflazine, sertindole, levomethadyl and cisapride, have been removed from the market or their use has been severely restricted because of drug-induced QT interval prolongation. Therefore, this irregularity is a major safety concern in the case of drugs submitted for regulatory approval. The most common mechanism of drug-induced QT interval prolongation may be drug-related inhibition of the human ether-á-go-go-related gene (hERG) channel, which subsequently results in prolongation of the cardiac action potential duration (APD). hERGAPDbase is a database of electrophysiological experimental data documenting potential hERG channel inhibitory actions and the APD-prolongation activities of chemical compounds. All data entries are manually collected from scientific papers and curated by a person. With hERGAPDbase, we aim to provide useful information for chemical and pharmacological scientists and enable easy access to electrophysiological experimental data on chemical compounds. Database URL: http://www.grt.kyushu-u.ac.jp/hergapdbase/
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Affiliation(s)
- Haretsugu Hishigaki
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Matsueda S, Sasada T, Komatsu N, Ioji T, Shichijo S, Noguchi M, Tashiro K, Kuhara S, Itoh K. Abstract 760: Gene expression profiling in cancer vaccine: A new tool for cancer vaccine development. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
(Introduction) Recently, cancer vaccines have emerged as one of the promising therapeutic options. However, it is still difficult to predict clinical responses in vaccinated patients prior to vaccination. For further development of this field, it would be of critical importance to identify biomarkers for selecting patients adequate for cancer vaccination. To identify reliable biomarkers, we characterized gene expression profiles by the DNA microarray technology (Illumina) in PBMC from prostate cancer patients that showed better or worse responses to the personalized peptide vaccination (survival time > 900 or < 300 days, respectively; n = 20 each).
(Method) Total RNA was prepared from frozen-PBMCs prior to vaccination and hybridized. Detailed statistical analysis was performed to select genes that help predict patient clinical responses. In addition, to validate the result, 10 additional PBMC samples were analyzed in discriminant analysis.
(Result) A combination of genes was selected as a predictive biomarker. In discriminant analysis, the identified genes clearly discriminated long-term survivors from short-term survivors to the peptide vaccination.
(Conclusion) The identified gene set in PBMC may be useful as a biomarker in selecting patients adequate for personalized peptide vaccines. The detailed characterization of individual genes identified is currently underway.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 760. doi:10.1158/1538-7445.AM2011-760
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Affiliation(s)
| | | | | | - Tetsuya Ioji
- 1Kurume University School of Medicine, Kurume, Japan
| | | | | | | | | | - Kyogo Itoh
- 1Kurume University School of Medicine, Kurume, Japan
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Asada M, Hirakawa H, Kuhara S. Classification of Bacteria Based on the Biases of Terminal Amino Acid Residues. Protein J 2011; 30:290-7. [DOI: 10.1007/s10930-011-9332-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nakamura A, Ueno T, Yagi Y, Okuda K, Ogata T, Nakamura T, Torimura T, Iwamoto H, Ramadoss S, Sata M, Tsutsumi V, Yasuda K, Tomiyasu Y, Obayashi K, Tashiro K, Kuhara S. Human primary cultured hepatic stellate cells can be cryopreserved. Med Mol Morphol 2010; 43:107-15. [PMID: 20683699 DOI: 10.1007/s00795-009-0484-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 11/04/2009] [Indexed: 12/28/2022]
Abstract
We compared the morphological and functional characteristics of cultured unfrozen hepatic stellate cells (HSCs) and cryopreserved HSCs obtained from human livers. We used liver tissues obtained by surgical resection from patients with metastatic liver cancer or with hepatocellular carcinoma. HSCs were isolated and allowed to spread in culture. Comparison of morphological and functional features between the unfrozen HSCs and cryopreserved HSCs was performed at each passage using the following techniques: light microscopy, immunohistochemistry, cell growth curve, metallothionein (MTT) assay, and PI staining, Western blot, real-time polymerase chain reaction (PCR), and gene expression analysis using microarrays. The purity of HSCs was more than 90% in all passages. alpha-Smooth muscle actin (SMA-)positive HSCs gradually increased in successive passages, and the positive cell rate and rate of increase in cell number were similar in both groups. Expression of platelet-derived growth factor (PDGF) receptor, transforming growth factor (TGF)-beta receptor, and alpha-SMA mRNAs and protein was similar during each passage in the two groups. Gene expression was nearly identical at each passage in unfrozen and frozen/thawed samples obtained from the same patient. In conclusion, an adequate protocol for the cryopreservation of human primary cultured HSCs could be established.
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Affiliation(s)
- Anna Nakamura
- Research Center for Innovative Cancer Therapy, Kurume University, 67 Asahi-machi, Kurume, 830-0011, Japan
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Abstract
Computational models known as neural networks discriminate among different types of nonlinear data, enabling the design of flexible calculation through machine-learning algorithms. Thanks to the simplicity of calculation, the nearest neighbor algorithm is a well-studied classification method. If the nearest neighbor algorithm inference is shown by a network model consisting of a neuron model representing data, it may become deterministic with adjustable parameters. We propose a new neuron model using the generalized mean and have designed a practical neural network framework based on the nearest neighbor algorithm. Because our proposed parallel distributed processing model is not simply a distance comparison between two points, it uses information from a whole body of data. This makes our classification superior to the nearest neighbor algorithm for algorithmic principles.
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Hirasaki M, Nakamura F, Yamagishi K, Numamoto M, Shimada Y, Uehashi K, Muta S, Sugiyama M, Kaneko Y, Kuhara S, Harashima S. Deciphering cellular functions of protein phosphatases by comparison of gene expression profiles in Saccharomyces cerevisiae. J Biosci Bioeng 2009; 109:433-41. [PMID: 20347764 DOI: 10.1016/j.jbiosc.2009.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 10/24/2009] [Accepted: 10/26/2009] [Indexed: 10/20/2022]
Abstract
Expression profiles of protein phosphatase (PPase) disruptants were analyzed by use of Pearson's correlation coefficient to find profiles that correlated with those of 316 Reference Gene (RG) disruptants harboring deletions in genes with known functions. Twenty-six Deltappase disruptants exhibited either a positive or negative correlation with 94 RG disruptants when the p value for Pearson's correlation coefficient was >0.2. Some of the predictions that arose from this analysis were tested experimentally and several new Delta ppase phenotypes were found. Notably, Delta sit4 and Delta siw14 disruptants exhibited hygromycin B sensitivity, Delta sit4 and Delta ptc1 disruptants grew slowly on glycerol medium, the Delta ptc1 disruptant was found to be sensitive to calcofluor white and congo red, while the Delta ppg1 disruptant was found to be sensitive to congo red. Because on-going analysis of expression profiles of Saccharomyces cerevisiae disruptants is rapidly generating new data, we suggest that the approach used in the present study to explore PPase function is also applicable to other genes.
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Affiliation(s)
- Masataka Hirasaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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