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Lam DT, Kataoka T, Yamagishi H, Sun G, Udatsu T, Tanaka K, Ishikawa R. Origin of domesticated water chestnuts ( Trapa bispinosa Roxb.) and genetic variation in wild water chestnuts. Ecol Evol 2024; 14:e10925. [PMID: 38333092 PMCID: PMC10850921 DOI: 10.1002/ece3.10925] [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: 05/02/2023] [Revised: 10/09/2023] [Accepted: 01/24/2024] [Indexed: 02/10/2024] Open
Abstract
The water chestnut Trapa bispinosa Roxb. has been domesticated in China and has been reported as the only domesticated species of this genus. To understand the origin of T. bispinosa and its evolution pathway, we compared the genetic similarity and seed morphology of domesticated water chestnut T. bispinosa with three wild species T. natans, T. incisa, and T. japonica along with archeological seed samples from the Tianluoshan site (approximately 7000-6300 cal BP) in China. The largest seed size was observed only in the domesticated species, whereas other wild species showed smaller size including T. natans L. genetically close to the domesticated type, and T. incisa was the smallest in size. The volumes of the seed capsule and endosperm were measured using X ray CT scans, showing the ratios of total volumes between T. bispinosa and wild species ranged from 4.2 to 4.5. The ratios of endosperm volume ranged from 3.3 to 3.7. Both measurements showed domesticated species have larger seed volume. Genome size was indirectly estimated by flow cytometry. Domesticated species with larger seed size was estimated as diploid, as were the wild species except for tetraploid species T. japonica. Domesticated species clearly showed the largest edible organs, but it was not a result of ploidy level changes. Maternal lineages traced using complete whole chloroplast sequences, suggested that T. natans is the closest to T. bispinosa, both of which are close to T. japonica. The result was confirmed by PCR genotyping with chloroplast insertion/deletion (cpINDEL) markers developed in the study. T. incisa showed distinct plastid types within the species, and T. japonica showed a unique plastid genotype. Our study concludes the largest volumes for the edible endosperm have been accomplished through nearly 6000 years of artificial selection, but the domestication did not involve ploidy level changes.
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Affiliation(s)
- Dinh Thi Lam
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Taro Kataoka
- Faculty of Humanity and Social ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Hiroki Yamagishi
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Guoping Sun
- Zhejiang Provincial Research Institute of Cultural Relics and ArchaeologyHangzhouChina
| | | | - Katsunori Tanaka
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
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2
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Wang Y, Li X, Ishikawa R, Luo X. Editorial: Mining and utilization of favorable gene resources in rice. Front Plant Sci 2023; 14:1289069. [PMID: 37794934 PMCID: PMC10546390 DOI: 10.3389/fpls.2023.1289069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 10/06/2023]
Affiliation(s)
- Ying Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xueyong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori, Japan
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Fudan University, Shanghai, China
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3
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Yamada S, Itoh T, Ikegami T, Imai A, Mochizuki D, Nakanishi H, Ishikawa R, Kita J, Nakamura Y, Takizawa Y, Okamura J, Noda Y, Iwashita T, Hariyama T, Suzuki M, Misawa K, Kawasaki H. Association between human papillomavirus particle production and the severity of recurrent respiratory papillomatosis. Sci Rep 2023; 13:5514. [PMID: 37024540 PMCID: PMC10079853 DOI: 10.1038/s41598-023-32486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
Recurrent respiratory papillomatosis (RRP) has a wide range of severity. We investigate the relationship between human papillomavirus (HPV) particle production and severity of RRP. From September 2005 to June 2021, 68 RRP samples (from 29 patients) were included. HPV type was determined. HPV viral load, physical status, and demographic and clinical characteristics were assessed. Immunohistochemistry (IHC) was performed for p16, Ki-67, L1, and E4. We used NanoSuit-CLEM (correlative light and electron microscopy) and transmission electron microscopy (TEM) to examine the samples. The total number of surgeries in HPV-positive and HPV-negative cases were 3.78 (n = 55/68, range: 1-16) and 1.30 (n = 13/68, range: 1-3), respectively (p = 0.02). IHC showed that L1 and E4 were correlated and expressed on the tumour surface. NanoSuit-CLEM and TEM revealed HPV particles in L1-positive nuclei. L1 IHC-positive cases had a shorter surgical interval (p < 0.01) and more frequent surgeries (p = 0.04). P16 IHC, viral load, and physical status were not associated with disease severity. This study visualised HPV particle production in RRP for the first time. Persistent HPV particle infection was associated with severity. We suggest L1 IHC for evaluating RRP severity in addition to the Derkay score.
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Affiliation(s)
- Satoshi Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Toshiya Itoh
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
- Department of Obstetrics and Gynecology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Taro Ikegami
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Hiroshi Nakanishi
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Junya Kita
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yuki Nakamura
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yoshinori Takizawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Jun Okamura
- Department of Otorhinolaryngology, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
| | - Yoshihiro Noda
- Department of Otorhinolaryngology, Seirei Mikatahara General Hospital, Hamamatsu, Japan
| | - Toshihide Iwashita
- Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takahiko Hariyama
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Mikio Suzuki
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
| | - Hideya Kawasaki
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, 1-20-1 Handayama Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
- Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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Tanaka K, Sugiyama M, Shigita G, Murakami R, Duong TT, Aierken Y, Artemyeva AM, Mamypbelov Z, Ishikawa R, Nishida H, Kato K. Melon diversity on the Silk Road by molecular phylogenetic analysis in Kazakhstan melons. Breed Sci 2023; 73:219-229. [PMID: 37404344 PMCID: PMC10316308 DOI: 10.1270/jsbbs.22030] [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] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 01/16/2023] [Indexed: 07/06/2023]
Abstract
To uncover population structure, phylogenetic relationship, and diversity in melons along the famous Silk Road, a seed size measurement and a phylogenetic analysis using five chloroplast genome markers, 17 RAPD markers and 11 SSR markers were conducted for 87 Kazakh melon accessions with reference accessions. Kazakh melon accessions had large seed with exception of two accessions of weedy melon, Group Agrestis, and consisted of three cytoplasm types, of which Ib-1/-2 and Ib-3 were dominant in Kazakhstan and nearby areas such as northwestern China, Central Asia and Russia. Molecular phylogeny showed that two unique genetic groups, STIa-2 with Ib-1/-2 cytoplasm and STIa-1 with Ib-3 cytoplasm, and one admixed group, STIAD combined with STIa and STIb, were prevalent across all Kazakh melon groups. STIAD melons that phylogenetically overlapped with STIa-1 and STIa-2 melons were frequent in the eastern Silk Road region, including Kazakhstan. Evidently, a small population contributed to melon development and variation in the eastern Silk Road. Conscious preservation of fruit traits specific to Kazakh melon groups is thought to play a role in the conservation of Kazakh melon genetic variation during melon production, where hybrid progenies were generated through open pollination.
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Affiliation(s)
- Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama, Okayama 700-8530, Japan
| | - Ryoma Murakami
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Thanh-Thuy Duong
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue City, Vietnam
| | - Yasheng Aierken
- Center for Hami Melon, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Anna M Artemyeva
- All-Russian Institute of Plant Genetic Resources on the name of N.I.Vavilov (VIR), 42-44 Bolshaya Morskaya Street, Saint Petersburg 190000, Russian Federation
| | - Zharas Mamypbelov
- Kazakhstan Research Institute of Potato and Vegetable Growing LLC, 1 Nauryz Street, Karasay, Almaty 040917, Kazakhstan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama, Okayama 700-8530, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama, Okayama 700-8530, Japan
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Mawson T, Taplin DJ, Brown HG, Clark L, Ishikawa R, Seki T, Ikuhara Y, Shibata N, Paganin DM, Morgan MJ, Weyland M, Petersen TC, Findlay SD. Factors limiting quantitative phase retrieval in atomic-resolution differential phase contrast scanning transmission electron microscopy using a segmented detector. Ultramicroscopy 2022; 233:113457. [PMID: 35016130 DOI: 10.1016/j.ultramic.2021.113457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 08/17/2021] [Revised: 11/30/2021] [Accepted: 12/05/2021] [Indexed: 11/17/2022]
Abstract
Quantitative differential phase contrast imaging of materials in atomic-resolution scanning transmission electron microscopy using segmented detectors is limited by various factors, including coherent and incoherent aberrations, detector positioning and uniformity, and scan-distortion. By comparing experimental case studies of monolayer and few-layer graphene with image simulations, we explore which parameters require the most precise characterisation for reliable and quantitative interpretation of the reconstructed phases. Coherent and incoherent lens aberrations are found to have the most significant impact. For images over a large field of view, the impact of noise and non-periodic boundary conditions are appreciable, but in this case study have less of an impact than artefacts introduced by beam deflections coupling to beam scanning (imperfect tilt-shift purity).
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Affiliation(s)
- T Mawson
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - D J Taplin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - H G Brown
- Ian Holmes Imaging Center, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - L Clark
- School of Chemical and Process Engineering, University of Leeds, Leeds LS2 9JT, UK
| | - R Ishikawa
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - T Seki
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 3320012, Japan
| | - Y Ikuhara
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan
| | - N Shibata
- Institute of Engineering Innovation, University of Tokyo, Tokyo 113-8656, Japan
| | - D M Paganin
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - M J Morgan
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia
| | - M Weyland
- Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia; Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - T C Petersen
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia; Monash Centre for Electron Microscopy, Monash University, Clayton, Victoria 3800, Australia
| | - S D Findlay
- School of Physics and Astronomy, Monash University, Clayton, Victoria 3800, Australia.
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6
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Ichitani K, Toyomoto D, Uemura M, Monda K, Ichikawa M, Henry R, Sato T, Taura S, Ishikawa R. New Hybrid Spikelet Sterility Gene Found in Interspecific Cross between Oryza sativa and O. meridionalis. Plants 2022; 11:plants11030378. [PMID: 35161359 PMCID: PMC8839173 DOI: 10.3390/plants11030378] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/19/2022] [Accepted: 01/24/2022] [Indexed: 11/22/2022]
Abstract
Various kinds of reproductive barriers have been reported in intraspecific and interspecific crosses between the AA genome Oryza species, to which Asian rice (O. sativa) and African rice (O. glaberrima) belong. A hybrid seed sterility phenomenon was found in the progeny of the cross between O. sativa and O. meridionalis, which is found in Northern Australia and Indonesia and has diverged from the other AA genome species. This phenomenon could be explained by an egg-killer model. Linkage analysis using DNA markers showed that the causal gene was located on the distal end of chromosome 1. Because no known egg-killer gene was located in that chromosomal region, this gene was named HYBRID SPIKELET STERILITY 57 (abbreviated form, S57). In heterozygotes, the eggs carrying the sativa allele are killed, causing semi-sterility. This killer system works incompletely: some eggs carrying the sativa allele survive and can be fertilized. The distribution of alleles in wild populations of O. meridionalis was discussed from the perspective of genetic differentiation of populations.
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Affiliation(s)
- Katsuyuki Ichitani
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
- Correspondence: ; Tel.: +81-99-285-8547
| | - Daiki Toyomoto
- United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
| | - Masato Uemura
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
| | - Kentaro Monda
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
| | - Makoto Ichikawa
- Graduate School of Agriculture, Forestry and Fisheries, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia;
| | - Tadashi Sato
- Graduate School of Life Science, Tohoku University, Sendai 980-8577, Miyagi, Japan;
| | - Satoru Taura
- Institute of Gene Research, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Kagoshima, Japan;
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Aomori, Japan;
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Kobayashi J, Takeuchi R, Toyama Y, Gregorio ER, Kadriyan H, Estrada CAM, Motomura M, Wake N, Yamada K, Ishikawa R, Takakura M. Urgent need to strengthen school health in Asia and the Pacific islands. Pediatr Int 2021; 63:1419-1423. [PMID: 34258829 PMCID: PMC9298032 DOI: 10.1111/ped.14921] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022]
Abstract
In Asia and the Pacific island region, strengthening of school health activities and measures is urgently recommended to deal with the impact of the increasing risk of potential school closures due to continuation of the coronavirus disease 2019 (COVID-19) pandemic in 2021. As the incidence of COVID-19 in 2020 was relatively low in these regions, many of the countries were able to avoid prolonged school closures. However, even if vaccination is expanded in the future and the pandemic tends to come to an end, the risk of SARS-CoV-2 variants spreading among children will also increase, and the possibility of having to close schools again will also increase.
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Affiliation(s)
- Jun Kobayashi
- Department of Global Health, Graduate School of Health Sciences, University of the Ryukyus, Nakagami-gun, Okinawa, Japan.,Japanese Consortium for Global School Health and Research, Nakagami-gun, Okinawa, Japan.,College of Public Health, University of the Philippines Manila, Manila, Philippines
| | - Rie Takeuchi
- Department of Global Health, Graduate School of Health Sciences, University of the Ryukyus, Nakagami-gun, Okinawa, Japan.,Japanese Consortium for Global School Health and Research, Nakagami-gun, Okinawa, Japan.,JICA Okinawa, Urasoe City, Okinawa, Japan
| | - Yuko Toyama
- Faculty of Medicine, School of Health Sciences, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
| | - Ernesto R Gregorio
- College of Public Health, University of the Philippines Manila, Manila, Philippines
| | - Hamsu Kadriyan
- Faculty of Medicine, Mataram University, Kota Mataram, Indonesia
| | | | - Makoto Motomura
- Faculty of Humanities and Social Sciences, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
| | - Norie Wake
- Faculty of Medicine, School of Health Sciences, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
| | - Kyoko Yamada
- Global Education Institute, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
| | - Ryuji Ishikawa
- Faculty of Global and Regional Studies, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
| | - Minoru Takakura
- Department of Health Promotion & Development, Graduate School of Health Sciences, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
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8
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Ishizuka A, Ishizuka K, Ishikawa R, Shibata N, Ikuhara Y, Hashiguchi H, Sagawa R. Improving the depth resolution of STEM-ADF sectioning by 3D deconvolution. Microscopy (Oxf) 2021; 70:241-249. [PMID: 33048120 DOI: 10.1093/jmicro/dfaa056] [Citation(s) in RCA: 1] [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: 06/02/2020] [Revised: 09/01/2020] [Accepted: 10/08/2020] [Indexed: 11/12/2022] Open
Abstract
Although the possibility of locating single atom in three dimensions using the scanning transmission electron microscope (STEM) has been discussed with the advent of aberration correction technology, it is still a big challenge. In this report we have developed deconvolution routines based on maximum entropy method (MEM) and Richardson-Lucy algorithm (RLA), which are applicable to the STEM-annular dark-field (ADF) though-focus images to improve the depth resolution. The new three-dimensional (3D) deconvolution routines require a limited defocus-range of STEM-ADF images that covers a whole sample and some vacuum regions. Since the STEM-ADF probe is infinitely elongated along the optical axis, a 3D convolution is performed with a two-dimensional (2D) convolution over xy-plane using the 2D fast Fourier transform in reciprocal space, and a one-dimensional convolution along the z-direction in real space. Using our new deconvolution routines, we have processed simulated focal series of STEM-ADF images for single Ce dopants embedded in wurtzite-type AlN. Applying the MEM, the Ce peaks are clearly localized along the depth, and the peak width is reduced down to almost one half. We also applied the new deconvolution routines to experimental focal series of STEM-ADF images of a monolayer graphene. The RLA gives smooth and high-P/B ratio scattering distribution, and the graphene layer can be easily detected. Using our deconvolution algorithms, we can determine the depth locations of the heavy dopants and the graphene layer within the precision of 0.1 and 0.2 nm, respectively. Thus, the deconvolution must be extremely useful for the optical sectioning with 3D STEM-ADF images.
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Affiliation(s)
- A Ishizuka
- HREM Research Inc., 14-48 Matsukazedai, Higashimatsuyama, Saitama, Japan
| | - K Ishizuka
- HREM Research Inc., 14-48 Matsukazedai, Higashimatsuyama, Saitama, Japan
| | - R Ishikawa
- Institute of Engineering Innovation, University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama, Japan
| | - N Shibata
- Institute of Engineering Innovation, University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo, Japan.,Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya, Aichi, Japan
| | - Y Ikuhara
- Institute of Engineering Innovation, University of Tokyo, 2-11-16 Yayoi, Bunkyo, Tokyo, Japan.,Nanostructures Research Laboratory, Japan Fine Ceramics Center, Nagoya, Aichi, Japan
| | - H Hashiguchi
- JEOL Ltd, 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - R Sagawa
- JEOL Ltd, 3-1-2 Musashino, Akishima, Tokyo, Japan
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9
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Yamada S, Misawa K, Mima M, Imai A, Mochizuki D, Yamada T, Shinmura D, Kita J, Ishikawa R, Yamaguchi Y, Misawa Y, Kawasaki H, Mineta H. Telomere shortening in head and neck cancer: association between DNA demethylation and survival. J Cancer 2021; 12:2165-2172. [PMID: 33758594 PMCID: PMC7974875 DOI: 10.7150/jca.54760] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 10/20/2020] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
A growing body of evidence indicates that telomere dysfunction is a biological marker of progression in several types of cancer. However, the association between head and neck squamous cell carcinoma (HNSCC) and telomere length (TL) remains unknown. We measured the absolute TL levels in a well-characterised dataset of 211 tumoral vs normal tissues obtained from the same patients by quantitative polymerase chain reaction assay. Normalised TL levels were significantly lower in tumour samples than in normal tissue (P < 0.001) and there was a positive correlation between tumour tissue and normal mucosal tissue (R2 = 0.176, P < 0.001). We were able to distinguish two classes, one with a tumour/normal TL ratio ≤ 0.3 (38.4%), which showed clear telomere erosion, and the other with a tumour/normal TL ratio > 0.3 (61.6%), in which the TL was slightly shorter or longer than that in normal tissue. Notably, the tumour/normal TL ratio was correlated with the likelihood of disease recurrence (P = 0.002), the 5-hydroxymethylcytosine level (P = 0.043), and expression of the ten-eleven translocation (TET) gene (P = 0.043). Our findings show that TL shortening and subsequent low levels of 5-hydroxymethylcytosine and TET expression may contribute to development of HNSCC.
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Affiliation(s)
- Satoshi Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Taiki Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daichi Shinmura
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Junya Kita
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuki Yamaguchi
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideya Kawasaki
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
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10
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Misawa K, Yamada S, Mima M, Nakagawa T, Kurokawa T, Imai A, Mochizuki D, Shinmura D, Yamada T, Kita J, Ishikawa R, Yamaguchi Y, Misawa Y, Kanazawa T, Kawasaki H, Mineta H. Long interspersed nuclear element 1 hypomethylation has novel prognostic value and potential utility in liquid biopsy for oral cavity cancer. Biomark Res 2020; 8:53. [PMID: 33110605 PMCID: PMC7585304 DOI: 10.1186/s40364-020-00235-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 08/11/2020] [Accepted: 10/12/2020] [Indexed: 02/08/2023] Open
Abstract
Background New biomarkers are urgently needed to improve personalized treatment approaches for head and neck squamous cell carcinoma (HNSCC). Global DNA hypomethylation has wide-ranging functions in multistep carcinogenesis, and the hypomethylation of long interspersed nucleotide element-1 (LINE-1) is related to increased retrotransposon activity and induced genome instability. However, little information is available regarding LINE-1 hypomethylation and its prognostic implications in HNSCC. Methods In this study, we analyzed LINE-1 hypomethylation levels in a well-characterized dataset of 317 primary HNSCC tissues and 225 matched pairs of normal mucosa tissues, along with five oral cavity cancer (OCC) circulating tumor DNA (ctDNA) samples using quantitative real-time methylation and unmethylation PCR. The analysis was performed according to various clinical characteristics and prognostic implications. Results The results demonstrated that LINE-1 hypomethylation levels were significantly higher in the HNSCC tissues than in corresponding normal tissues from the same individuals (P < 0.001). Univariate analysis revealed that high levels of LINE-1 hypomethylation were correlated with poor disease-free survival (DFS; log-rank test, P = 0.038), whereas multivariate analysis demonstrated that they were significant independent prognostic factor for DFS (hazard ratio: 2.10, 95% confidence interval: 1.02–4.36; P = 0.045). Moreover, samples with high LINE-1 hypomethylation levels exhibited the greatest decrease in 5-hydroxymethylcytosine (5-hmC) levels and increase in tumor-suppressor gene methylation index (P = 0.006 and P < 0.001, respectively). Further, ctDNA studies also showed that LINE-1 hypomethylation had high predictive ability in OCC. Conclusions LINE-1 hypomethylation is associated with a higher risk of early OCC relapse, and is hence, a potential predictive biomarker for OCC. Furthermore, 5-hmC levels also exhibited predictive potential in OCC, based on their inverse correlation with LINE-1 hypomethylation levels. LINE-1 hypomethylation analysis, therefore, has applications in determining patient prognosis and real-time surveillance of disease recurrence, and could serve as an alternative method for OCC screening. Supplementary information Supplementary information accompanies this paper at 10.1186/s40364-020-00235-y.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Satoshi Yamada
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Masato Mima
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takuya Nakagawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoya Kurokawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Imai
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daiki Mochizuki
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daichi Shinmura
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Taiki Yamada
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Junya Kita
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Ryuji Ishikawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Yamaguchi
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Misawa
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takeharu Kanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi Japan
| | - Hideya Kawasaki
- Preeminent Medical Photonics Education and Research Center Institute for NanoSuit Research, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Mineta
- Department of Otorhinolaryngology /Head and Neck Surgery, 1-20-1 Handayama, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka 431-3192 Japan
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11
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Misawa K, Imai A, Kanazawa T, Mima M, Yamada S, Mochizuki D, Yamada T, Shinmura D, Ishikawa R, Kita J, Yamaguchi Y, Misawa Y, Mineta H. G Protein-Coupled Receptor Genes, PTGDR1, PTGDR2, and PTGIR, Are Candidate Epigenetic Biomarkers and Predictors for Treated Patients with HPV-Associated Oropharyngeal Cancer. Microorganisms 2020; 8:microorganisms8101504. [PMID: 33003642 PMCID: PMC7601742 DOI: 10.3390/microorganisms8101504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 08/27/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/26/2022] Open
Abstract
Differences in the biology of human papillomavirus (HPV)-associated oropharyngeal cancers (OPCs) and HPV-negative OPCs may have implications in patient management. Early detection is imperative to reduce HPV-associated OPC mortality. Circulating tumor DNA (ctDNA) can potentially serve as a biomarker for monitoring clinically relevant cancer-related genetic and epigenetic modifications. We analyzed the methylation status of 24 G protein-coupled receptor (GPCR) genes in verification (85 OPC primary samples) and validation (8 OPC ctDNA samples) studies using quantitative methylation-specific polymerase chain reaction (Q-MSP). The Q-MSP-based verification study with 85 OPC primary samples revealed the GPCR genes that were significantly associated with recurrence in high methylation groups (≥14 methylated genes) with OPC and HPV-associated OPC (p < 0.001). In the Kaplan–Meier estimate and multivariate Cox proportional hazard analyses, 13 GPCR genes were significantly related to increased recurrence in the methylation group. Furthermore, the validation study on ctDNA showed that three of these genes (Prostaglandin D2 receptor 1: PTGDR1, Prostaglandin D2 receptor 2: PTGDR2, and Prostaglandin I2 Receptor: PTGIR) had a prediction performance as emerging biomarkers. We characterized the relationship between the methylation status of GPCR genes and outcomes in HPV-associated OPC. Our results highlight the potential utility of ctDNA methylation-based detection for the clinical management of HPV-associated OPC.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
- Correspondence: ; Tel.: 81-53-435-2252; Fax: 81-53-435-2253
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Takeharu Kanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan;
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Satoshi Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Taiki Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Daichi Shinmura
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Jyunya Kita
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Yuki Yamaguchi
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan; (A.I.); (M.M.); (S.Y.); (D.M.); (T.Y.); (D.S.); (R.I.); (J.K.); (Y.Y.); (Y.M.); (H.M.)
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Tanaka K, Zhao C, Wang N, Kubota S, Kanehara M, Kamijo N, Ishikawa R, Tasaki H, Kanehara M, Liu B, Chen M, Nakamura SI, Udatsu T, Wang C. Classification of archaic rice grains excavated at the Mojiaoshan site within the Liangzhu site complex reveals an Indica and Japonica chloroplast complex. Food Prod Process and Nutr 2020. [DOI: 10.1186/s43014-020-00028-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
To understand rice types that were utilized during postdomestication and in the modern age and the potential of genetic research in aged rice materials, archaeogenetic analysis was conducted for two populations of archaic rice grains from the Mojiaoshan site during the Liangzhu Period in China (2940 to 2840 BC). Sequencing after the PCR amplification of three regions of the chloroplast genome and one region of the nuclear genome showed recovery rates that were comparable to those in previous studies except for one chloroplast genome region, suggesting that the materials used in this work were appropriate for recovering genetic information related to domestication traits by using advanced technology. Classification after sequencing in these regions proved the existence of Japonica and Indica chloroplasts in archaic grains from the west trench, which were subsequently classified into eight plastid groups (type I–VIII), and indicated that these rice grains derived from different maternal lineages were stored together in storage houses at the Mojiaohsan site. Among these plastid groups, type V exhibited the same sequences as two modern Indica accessions that are utilized in basic studies and rice breeding. It was inferred that part of the chloroplast genome of archaic rice has been preserved in modern genetic resources in these two modern Indica accessions, and the results indicated that rice related to their maternal ancestor was present at the Mojiaoshan site during the Liangzhu Period in China. The usefulness of archaeogenetic analysis can be demonstrated by our research data as well as previous studies, providing encouragement for the possibility that archaeogenetic analysis can be applied to older rice materials that were utilized in the rice-domesticated period.
Graphical abstract
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13
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Muto C, Tanaka K, Tabuchi H, Kurauchi N, Sato YI, Ishikawa R. Genetic diversity of preserved rice seed samples from the Mikawa area, Japan, stored in the Meiji era. Breed Sci 2020; 70:347-354. [PMID: 32714057 PMCID: PMC7372032 DOI: 10.1270/jsbbs.19143] [Citation(s) in RCA: 1] [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: 10/16/2019] [Accepted: 02/03/2020] [Indexed: 05/23/2023]
Abstract
Preserved rice (Oryza sativa L.) seeds stored for nearly a century as an emergency food stocks from the Mikawa area were investigated for their genetic diversity. Morphologically, the seeds appeared to be typical Japonica. One chloroplast INDEL petN-trnC, two nuclear INDELs Acp1 and Cat1, and three SNP markers in Starch synthase IIa were amplified to characterize the molecular profile. The efficiency of amplification varied among the markers. Most of preserved seeds were classified as Japonica, but some were identified as Indica. The heterozygous genotypes detected suggested a high frequency of outcrossing at that time. On the other hand, 21 SSR markers showed quite a high degree of amplification efficiency. Principal coordinate analysis and STRUCTURE analysis based on the SSR polymorphisms proved that the preserved seeds contained alleles that were not detected among current landraces and breeding varieties, and there were the expected three subpopulations among 96 preserved seeds. These results indicated that these preserved seeds from Mikawa area in Meiji era had high genetic diversity and consisted of some subpopulations including Indica landraces with typical Japonica seed shape. These lines were considered to have been lost from current genetic resources.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Hiroaki Tabuchi
- Miyakonojo Research Station, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Yokoichi-cho 6651-2, Miyakonojo, Miyazaki 885-0091, Japan
| | - Nobuyuki Kurauchi
- Department of International Development Studies, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Yo-Ichiro Sato
- Research Institute for Humanity and Nature (RIHN), 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047, Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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Taddesse L, Fukuta Y, Ishikawa R. Genetic study of diversity and blast resistance in Ethiopian rice cultivars adapted to different ecosystems. Breed Sci 2020; 70:303-312. [PMID: 32714052 PMCID: PMC7372019 DOI: 10.1270/jsbbs.18198] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 12/19/2019] [Indexed: 06/11/2023]
Abstract
Rice (Oryza sativa L.) has been considered one of the most important crops in Ethiopia. Landraces and improved accessions in Ethiopia were characterized on the basis of polymorphism data for SSR markers, and classified into two groups: I and II. Cluster I was further divided into two sub-clusters, Ia and Ib. Cluster Ia corresponded to Japonica-like type, Cluster Ib to Japonica type, and Cluster II to Indica type with some Indica-like type. Many landraces and improved varieties belonged to Cluster Ia. Superior landraces were included in Cluster Ib. Further categorization based on blast resistance demonstrated three groups: Clusters A, B1, and B2. Cluster A comprised accessions with relatively high resistance, whereas Clusters B1 and B2 included susceptible accessions. Most of the improved varieties were found in Cluster A. Superior landraces, X-Jigna classified into Ib or DNA type tended to be susceptible in Cluster B2 for blast resistance. These results demonstrated that traditional landraces preferred by farmers should be improved for disease resistance using blast-resistant varieties. In order to avoid hybrid sterility occurring in cross-hybridizing breeding between Indica and Japonica types, desirable parental accessions can be chosen within the same DNA cluster. The clustering information among accessions may be useful in breeding schemes for selection of counterparts in cross-breeding programs.
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Affiliation(s)
- Lakew Taddesse
- Fogera National Rice Research and Training Centre, Ethiopian Institute of Agricultural Research, 1937, Bahir Dar, Ethiopia
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Yoshimichi Fukuta
- Tropical Agriculture Research Front (TARF), Japan International Research Center for Agricultural Sciences (JIRCAS), Ishigaki, Okinawa 907-0002, Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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Hosokawa S, Mochizuki D, Takahashi G, Okamura J, Imai A, Ishikawa R, Takizawa Y, Yamatodani T, Misawa K, Mineta H. Authors' Reply: Relevance of Level IIb Neck Dissection in Patients with Head and Neck Squamous Cell Carcinomas. World J Surg 2020; 44:1693. [PMID: 32123979 DOI: 10.1007/s00268-020-05451-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seiji Hosokawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.
| | - Daiki Mochizuki
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Goro Takahashi
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Yamahoshi ENT Clinic, Hamamatsu, Japan
| | - Jun Okamura
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan.,Department of Otorhinolaryngology, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
| | - Atsushi Imai
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Ryuji Ishikawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Yoshinori Takizawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Takashi Yamatodani
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Kiyoshi Misawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
| | - Hiroyuki Mineta
- Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka, 431-3192, Japan
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Lam DT, Ichitani K, Henry RJ, Ishikawa R. Molecular and Morphological Divergence of Australian Wild Rice. Plants (Basel) 2020; 9:plants9020224. [PMID: 32050528 PMCID: PMC7076673 DOI: 10.3390/plants9020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/19/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022]
Abstract
Two types of perennial wild rice, Australian Oryza rufipogon and a new taxon Jpn2 have been observed in Australia in addition to the annual species Oryza meridionalis. Jpn2 is distinct owing to its larger spikelet size but shares O. meridionalis-like morphological features including a high density of bristle cells on the awn surface. All the morphological traits resemble O. meridionalis except for the larger spikelet size. Because Jpn2 has distinct cytoplasmic genomes, including the chloroplast (cp), cp insertion/deletion/simple sequence repeats were designed to establish marker systems to distinguish wild rice in Australia in different natural populations. It was shown that the new taxon is distinct from Asian O. rufipogon but instead resembles O. meridionalis. In addition, higher diversity was detected in north-eastern Australia. Reproductive barriers among species and Jpn2 tested by cross-hybridization suggested a unique biological relationship of Jpn2 with other species. Insertions of retrotransposable elements in the Jpn2 genome were extracted from raw reads generated using next-generation sequencing. Jpn2 tended to share insertions with other O. meridionalis accessions and with Australian O. rufipogon accessions in particular cases, but not Asian O. rufipogon except for two insertions. One insertion was restricted to Jpn2 in Australia and shared with some O. rufipogon in Thailand.
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Affiliation(s)
- Dinh Thi Lam
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan;
- Institute of Agricultural Science for Southern Vietnam, District 1, Ho Chi Minh City 121, Vietnam
| | - Katsuyuki Ichitani
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan;
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane QLD 4072, Australia;
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
- Correspondence: ; Tel.: +81-172-39-3778
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Misawa K, Mima M, Satoshi Y, Imai A, Mochizuki D, Ishikawa R, Kita J, Yamaguchi Y, Endo S, Misawa Y, Mineta H. Prostanoid receptor genes confer poor prognosis in head and neck squamous cell carcinoma via epigenetic inactivation. J Transl Med 2020; 18:31. [PMID: 31969157 PMCID: PMC6977280 DOI: 10.1186/s12967-020-02214-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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] [Received: 11/08/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background Chronic inflammation is a risk factor for head and neck squamous cell carcinoma (HNSCC) and other diseases. Prostanoid receptors are clearly involved in the development of many types of cancer. However, their role is not simple and is poorly understood in HNSCC. Methods Methylation profiles of prostanoid receptor family genes were generated for tumour samples obtained from 274 patients with HNSCC, including 69 hypopharynx, 51 larynx, 79 oral cavity, and 75 oropharynx tumour samples, by quantitative methylation-specific PCR. Promoter methylation was then evaluated with respect to various clinical characteristics and patient survival. Results The mean number of methylated genes per sample was 2.05 ± 2.59 (range 0 to 9). Promoters of PTGDR1, PTGDR2, PTGER1, PTGER2, PTGER3, PTGER4, PTGFR, PTGIR, and TBXA2R were methylated in 43.8%, 18.2%, 25.5%, 17.5%, 41.2%, 8.0%, 19.3%, 20.4%, and 11.3% of the samples, respectively. Methylation indices for prostanoid receptor family genes tended to be higher as the number of TET methylation events increased. Patients with 5–9 methylated genes had a significantly lower survival rate than that of patients with 0–4 methylated genes (log-rank test, P= 0.007). In multivariate analyses, PTGDR1 methylation was most highly correlated with recurrence in patients with hypopharyngeal cancer (P = 0.014). A similar correlation was observed for PTGER4 in patients with laryngeal cancer (P = 0.046). Methylation of the PTGIR and TBXA2R promoters was positively correlated with recurrence in oropharyngeal cancer (P = 0.028 and P = 0.006, respectively). Moreover, Patients with 5–9 methylated genes were extremely lower of 5hmC levels (P = 0.035) and was correlated with increasing expression of DNMT3A and DNMT3B (P < 0.05 and P < 0.05, respectively). Conclusion We characterised the relationship between the methylation status of prostanoid receptor genes and recurrence in HNSCC. These results provide new perspectives for the development of molecular targeted treatment approaches.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan.
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Yamada Satoshi
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Junya Kita
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Yuki Yamaguchi
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Shiori Endo
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
| | - Hiroyuki Mineta
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Shizuoka, 431-3192, Japan
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Misawa K, Yamada S, Mima M, Nakagawa T, Kurokawa T, Imai A, Mochizuki D, Morita K, Ishikawa R, Endo S, Misawa Y. 5-Hydroxymethylcytosine and ten-eleven translocation dioxygenases in head and neck carcinoma. J Cancer 2019; 10:5306-5314. [PMID: 31602281 PMCID: PMC6775623 DOI: 10.7150/jca.34806] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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] [Received: 03/12/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
Ten-eleven translocation (TET) enzymes are implicated in DNA demethylation through dioxygenase activity, which converts 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC). However, the specific roles of TET enzymes and 5-hmC levels in head and neck squamous cell carcinoma (HNSCC) have not yet been evaluated. In this study, we analyzed 5-hmC levels and TET mRNA expression in a well-characterized dataset of 117 matched pairs of HNSCC tissues and normal tissues. 5-hmC levels and TET mRNA expression were examined via enzyme-linked immunosorbent assay and quantitative real-time PCR, respectively. 5-hmC levels were evaluated according to various clinical characteristics and prognostic implications. Notably, we found that 5-hmC levels were significantly correlated with tumor stage (P = 0.032) and recurrence (P = 0.018). Univariate analysis revealed that low levels of 5-hmC were correlated with poor disease-free survival (DFS; log-rank test, P = 0.038). The expression of TET family genes was not associated with outcomes. In multivariate analysis, low levels of 5-hmC were evaluated as a significant independent prognostic factor of DFS (hazard ratio: 2.352, 95% confidence interval: 1.136-4.896; P = 0.021). Taken together, our findings showed that reduction of TET family gene expression and subsequent low levels of 5-hmC may affect the development of HNSCC.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Yamada
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takuya Nakagawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomoya Kurokawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kotaro Morita
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shiori Endo
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
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Hosokawa S, Takahashi G, Okamura J, Imai A, Mochizuki D, Ishikawa R, Takizawa Y, Yamatodani T, Misawa K, Mineta H. Management of elderly patients with head and neck carcinoma: analysis of outcomes for radical versus palliative treatment. Int J Clin Oncol 2019; 25:432-438. [DOI: 10.1007/s10147-019-01531-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/16/2019] [Indexed: 10/26/2022]
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20
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Muto C, Ebana K, Kawano K, Bounphanousay V, Bounphanousay C, Kanyavong K, Inthapanya P, Boualaphanh C, Sato T, Ishikawa R, Sato YI, Yanagihara S, Fukuta Y. Genetic variation in rice ( Oryza sativa L.) germplasm from northern Laos. Breed Sci 2019; 69:272-278. [PMID: 31481836 PMCID: PMC6711726 DOI: 10.1270/jsbbs.18086] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 01/28/2019] [Indexed: 06/10/2023]
Abstract
We assessed genetic variation in rice germplasm in northern Laos and Vientiane province from polymorphism data of SSR markers. We classified 314 accessions into three clusters; Ia (corresponding to the lowland Japonica Group), Ib (upland Japonica Group) and II (Indica Group). The accessions of cluster Ib grew mainly in mountainous fields, and those of cluster II grew commonly in basins and along rivers. The few accessions of cluster Ia grew in only three provinces: Houaphanh, Xiangkhouang and Vientiane. Lowland cultivars in cluster II were predominant in Vientiane. Variations in heading date under short-day conditions in 2014 and long-day conditions in 2015 indicate that many accessions were sensitive to the photoperiod on account of complex genetic mechanisms underlying both photoperiod sensitivity and basic vegetative growth. A total of 219 among whole accessions were classified into 6 groups: E1-3 and L1-3. E2 and E3 were dominant in clusters Ib and II; E1 and L1-3 were minor groups. These results demonstrate characteristic distributions of the Indica and Japonica Group's germplasms in northern Laos and their genetic variation in heading date.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Agriculture and Food Organization (NARO),
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
2638-809 Kirishima-Taguchi, Kirishima, Kagoshima 899-4201,
Japan
| | - Viengphone Bounphanousay
- Rice Research Centre, National Agriculture and Forestry Research Institute (NAFRI),
Nongviengkham, Vientiane,
Lao PDR
| | - Chay Bounphanousay
- Rice Research Centre, National Agriculture and Forestry Research Institute (NAFRI),
Nongviengkham, Vientiane,
Lao PDR
| | - Kongppanh Kanyavong
- Rice Research Centre, National Agriculture and Forestry Research Institute (NAFRI),
Nongviengkham, Vientiane,
Lao PDR
| | - Phoumi Inthapanya
- Rice Research Centre, National Agriculture and Forestry Research Institute (NAFRI),
Nongviengkham, Vientiane,
Lao PDR
| | - Chanthakone Boualaphanh
- Rice Research Centre, National Agriculture and Forestry Research Institute (NAFRI),
Nongviengkham, Vientiane,
Lao PDR
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University,
468-1 Aramaki Aza, Aoba-ku, Sendai, Miyagi 981-0845,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
3 Bunkyo-cho, Hirosaki, Aomori 036-8561,
Japan
| | - Yo-Ichiro Sato
- Research Institute for Humanity and Nature,
457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047,
Japan
| | - Seiji Yanagihara
- Japan International Research Center for Agricultural Sciences (JIRCAS),
1-1 Ohwashi, Tsukuba, Ibaraki 305-8686,
Japan
| | - Yoshimichi Fukuta
- Tropical Agriculture Research Front (TARF), JIRCAS,
1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa 907-0002,
Japan
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21
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Lam DT, Buu BC, Lang NT, Toriyama K, Nakamura I, Ishikawa R. Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta. Ecol Evol 2019; 9:2964-2977. [PMID: 30891229 PMCID: PMC6405534 DOI: 10.1002/ece3.4978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 10/11/2018] [Revised: 01/16/2019] [Accepted: 01/17/2019] [Indexed: 12/02/2022] Open
Abstract
Oryza rufipogon Griff. is a perennial species of wild rice widely distributed along the channels and rivers of the Mekong Delta, Vietnam. This study attempted to find centers of diversity among wild rice populations in this area and their inter-relationships. The highest genetic diversity was found in the Dong Thap population and the lowest in the Can Tho population. Maternal diversity evaluated using chloroplast INDELs detected ten plastid types, five of which were novel relative to other Asian countries. The mitochondrial genome suggested two unique deletions. One 699-bp deletion via short tandem repeats was accompanied by another deletion including orf153. All accessions carrying the mitochondrial type were found in a particular plastid type. This unique maternal lineage was confined to specific channels where it showed vigorous vegetative growth in comparison to upstream areas where various maternal lineages and maximum genetic diversity occurred. This area along the Mekong Delta is a center of not only nuclear but also maternal diversity.
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Affiliation(s)
- Dinh T. Lam
- United Graduate School of Agricultural ScienceIwate UniversityMoriokaJapan
- Institute of Agricultural Science for Southern VietnamHo Chi Minh CityVietnam
| | - Bui C. Buu
- Institute of Agricultural Science for Southern VietnamHo Chi Minh CityVietnam
| | - Nguyen T. Lang
- High Agricultural Technology Research Institute (HATRI)CanthoVietnam
| | - Kinya Toriyama
- Graduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Ikuo Nakamura
- Graduate School of HorticultureChiba UniversityMatsudoJapan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiJapan
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22
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Kaewcheenchai R, Promnart U, Soontrajarn K, Chotechuen S, Chitrakon S, Yuki H, Saito S, Sato YI, Ishikawa R. Diverse genetic variation in maternal lineages with high heterogeneity among in situ-conserved wild rice ( Oryza rufipogon Griff.) developed in Thailand. Breed Sci 2018; 68:614-621. [PMID: 30697123 PMCID: PMC6345232 DOI: 10.1270/jsbbs.16105] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
Wild rice, Oryza rufipogon, is a genetic resource that can be used to improve cultivated rice, but its populations are now decreasing in terms of both size and number. Extensive research on wild rice has been conducted in Thailand, where two in situ conservation sites have been preserved in natural areas where perennial wild rice predominates. The genetic structure of wild rice populations was investigated by examining both the chloroplast and nucleus genomes at sites of in situ conservation site in Thailand. One accession from an in situ-conserved site was re-sequenced against the chloroplast genome of O. sativa cv. 'Nipponbare' to develop chloroplast insertion/deletion (cpINDEL) markers. These cpINDEL markers revealed unique maternal lineages in the in situ-conserved populations upon comparison with other Asian wild rice accessions. Diverse genetic variation was also detected with SSR markers throughout the genome. Three populations differed from each other and also within single populations. The sub-populations within an in situ-conserved population showed a complex population structure due to their multiple maternal lineages and relatively higher number of haplotypes when they maintained a relatively large population size. Such a heterogeneous population would serve as a unique gene pool for rice breeding.
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Affiliation(s)
- Reunreudee Kaewcheenchai
- Suphan Buri Rice Research Center, Bureau of Rice Research and Development, Rice Department,
Suphan Buri 72000,
Thailand
| | - Udompan Promnart
- Prachin Buri Rice Research Center, Bureau of Rice Research and Development, Rice Department,
Prachin Buri 25150,
Thailand
| | - Kasem Soontrajarn
- Pathum Thani Rice Research Center, Bureau of Rice Research and Development, Rice Department,
Rangsit, Thanyaburi, Pathum Thani 12110,
Thailand
| | - Somsong Chotechuen
- Bureau of Rice Research and Development, Rice Department,
Ladyao Chatuchak, Bangkok 10900,
Thailand
| | - Songkran Chitrakon
- Bureau of Rice Research and Development, Rice Department,
Ladyao Chatuchak, Bangkok 10900,
Thailand
| | - Honami Yuki
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Seiya Saito
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | | | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
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23
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Misawa K, Mima M, Imai A, Mochizuki D, Misawa Y, Endo S, Ishikawa R, Kanazawa T, Mineta H. The neuropeptide genes SST, TAC1, HCRT, NPY, and GAL are powerful epigenetic biomarkers in head and neck cancer: a site-specific analysis. Clin Epigenetics 2018; 10:52. [PMID: 29682090 PMCID: PMC5896056 DOI: 10.1186/s13148-018-0485-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 12/29/2017] [Accepted: 03/28/2018] [Indexed: 02/07/2023] Open
Abstract
Background Staging and pathological grading systems are convenient but imperfect predictors of recurrence in head and neck squamous cell carcinoma (HNSCC). Identifying biomarkers for HNSCC that will progress and cause death is a critical research area, particularly if the biomarker can be linked to selection of patients. Therefore, to identify potential alternative prognostic markers, we investigated the methylation status of five neuropeptide gene promoters. The promoter methylation status was determined by quantitative methylation-specific PCR in 230 cases of HNSCC; 58 hypopharynx, 45 larynx, 56 oropharynx, and 71 oral cavity tumor samples were studied. Results The somatostatin (SST), tachykinin precursor 1 (TAC1), hypocretin neuropeptide precursor (HCRT), neuropeptide Y (NPY), and galanin (GAL) promoters were methylated in 84.3, 63.5, 32.6, 28.3, and 20.0%, respectively, of the samples. The mean number of methylated genes per sample was 2.29 (range, 0–5). Disease-free survival was lower in patients with 3–5 methylated genes than in those with 0–2 methylated genes (log-rank test, P = 0.007). In multivariate Cox proportional hazards analysis, TAC1 and GAL promoter methylation independently predicted recurrence (odds ratios 1.620, 95% confidence interval [CI] 1.018–2.578, P = 0.042, and odds ratios 1.692, 95% CI 1.063–2.694, P = 0.027, respectively). In patients with oral cancer, TAC1 methylation showed the best correlation with poor survival (odds ratio 4.427, 95% CI 1.634–12.00, P = 0.003). Similar findings were observed for HCRT and GAL in patients with laryngeal cancer and oropharyngeal cancer, respectively. Conclusion In this study, we demonstrated the methylation status of the neuropeptide-encoding genes SST, TAC1, HCRT, NPY, and GAL and its relationship with recurrence and survival in HNSCC. These methylation changes may serve as potential molecular markers for defining the risk and prognosis of HNSCC. Electronic supplementary material The online version of this article (10.1186/s13148-018-0485-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kiyoshi Misawa
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Masato Mima
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Atsushi Imai
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Daiki Mochizuki
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Yuki Misawa
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Shiori Endo
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Ryuji Ishikawa
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
| | - Takeharu Kanazawa
- 2Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Tochigi, Japan
| | - Hiroyuki Mineta
- 1Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Hamamatsu, Shizuoka 431-3192 Japan
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Misawa K, Misawa Y, Imai A, Mochizuki D, Endo S, Mima M, Ishikawa R, Kawasaki H, Yamatodani T, Kanazawa T. Epigenetic modification of SALL1 as a novel biomarker for the prognosis of early stage head and neck cancer. J Cancer 2018; 9:941-949. [PMID: 29581773 PMCID: PMC5868161 DOI: 10.7150/jca.23527] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 10/27/2017] [Accepted: 01/31/2018] [Indexed: 12/12/2022] Open
Abstract
This study examined Sal-like protein (SALL)1 methylation profiles in head and neck squamous-cell carcinoma (HNSCC) patients at diagnosis and follow-up, and evaluated their prognostic significance and value as a biomarker. SALL1 expression was examined in a panel of cell lines by quantitative reverse transcription PCR (qRT-PCR). Promoter methylation was determined by quantitative methylation-specific polymerase chain reaction (qMSP) and was compared to the clinical characteristics of 205 samples. SALL1 promoter methylation was associated with transcriptional inhibition and was correlated with disease recurrence in 31.7% of cases, with an odds ratio of 1.694 (95% confidence interval: 1.093-2.626; P = 0.018) by multivariate Cox proportional hazard regression analysis. SALL1 promoter hypermethylation showed highly discriminatory receiver operator characteristic curve profiles that clearly distinguished HNSCC from adjacent normal mucosal tissue, and was correlated with reduced disease-free survival in early stage T1 and T2 patients (log-rank test, P < 0.001). SALL1 methylation was significantly correlated with the methylation status of both SALL3 and CDH1. This study suggests that CpG hypermethylation is a likely mechanism of SALL1 gene inactivation, supporting the hypothesis that SALL1 might play a role in HNSCC tumorigenesis and could serve as an important biomarker.
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Affiliation(s)
- Kiyoshi Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Yuki Misawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Atsushi Imai
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Daiki Mochizuki
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Shiori Endo
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Masato Mima
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Ryuji Ishikawa
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hideya Kawasaki
- Department of Regenerative & Infectious Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takashi Yamatodani
- Department of Otolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Takeharu Kanazawa
- Department of Otolaryngology/Head and Neck Surgery, Jichi Medical University, Tochigi, Japan
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25
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Misawa Y, Misawa K, Kawasaki H, Imai A, Mochizuki D, Ishikawa R, Endo S, Mima M, Kanazawa T, Iwashita T, Mineta H. Evaluation of epigenetic inactivation of vascular endothelial growth factor receptors in head and neck squamous cell carcinoma. Tumour Biol 2017; 39:1010428317711657. [PMID: 28718364 DOI: 10.1177/1010428317711657] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The aim of this study was to determine the methylation status of the genes encoding the vascular endothelial growth factor receptors and to evaluate the usefulness of VEGFR methylation as a prognostic indicator in head and neck squamous cell carcinoma. VEGFR messenger RNA expression and promoter methylation were examined in a panel of cell lines via quantitative reverse transcription and methylation-specific polymerase chain reaction, respectively. Promoter methylation was compared with clinical characteristics in 128 head and neck squamous cell carcinoma samples. The normalized methylation values for the VEGFR1, VEGFR2 and VEGFR3 promoters tended to be higher in the tumour cell lines than in normal tonsil samples, whereas amounts of VEGFR1, VEGFR2 and VEGFR3 messenger RNA were significantly higher. Methylation of the VEGFR1 promoter (p = 0.003; 66/128 head and neck squamous cell carcinoma samples, 52%) and VEGFR3 promoter (p = 0.043; 53/128 head and neck squamous cell carcinoma samples, 41%) significantly correlated with recurrence, whereas methylation of the VEGFR2 promoter significantly correlated with lymph node metastasis (p = 0.046; 47/128 head and neck squamous cell carcinoma samples, 37%). Concurrent methylation of the VEGFR1 and VEGFR3 promoters significantly correlated with reduced disease-free survival (log-rank test, p = 0.009). In a multivariate logistic regression analysis, methylation of the VEGFR1, VEGFR3 and both the VEGFR1 and VEGFR3 promoters independently predicted recurrence (odds ratios and 95% confidence intervals: 3.19, 1.51-6.75 (p = 0.002); 2.24, 1.06-4.76 (p = 0.035); and 2.56, 1.09-6.05 (p = 0.032), respectively). Methylation of the VEGFR promoters predicts poor prognosis in head and neck squamous cell carcinoma patients.
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Affiliation(s)
- Yuki Misawa
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kiyoshi Misawa
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideya Kawasaki
- 2 Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Atsushi Imai
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Daiki Mochizuki
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ryuji Ishikawa
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shiori Endo
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Mima
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takeharu Kanazawa
- 3 Department of Otolaryngology - Head and Neck Surgery, Jichi Medical University, Shimotsuke, Japan
| | - Toshihide Iwashita
- 2 Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Mineta
- 1 Department of Otorhinolaryngology/Head and Neck Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
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Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnol J 2017; 15:765-774. [PMID: 27889940 PMCID: PMC5425390 DOI: 10.1111/pbi.12674] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/10/2016] [Accepted: 11/23/2016] [Indexed: 05/04/2023]
Abstract
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Dario Copetti
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityCairnsQLDAustralia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandToowoombaQLDAustralia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
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Kato H, Kato Y, Yoneyama R, Ishikawa R, Kojika M, Miyajima K, Takizawa N, Furukawa K. Review of PDT for lung cancer and future. Photodiagnosis Photodyn Ther 2017. [DOI: 10.1016/j.pdpdt.2017.01.067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Brown H, Ishikawa R, Sánchez-Santolino G, Lugg N, Ikuhara Y, Allen L, Shibata N. A new method to detect and correct sample tilt in scanning transmission electron microscopy bright-field imaging. Ultramicroscopy 2017; 173:76-83. [DOI: 10.1016/j.ultramic.2016.11.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/15/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022]
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29
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Muto C, Ishikawa R, Olsen KM, Kawano K, Bounphanousay C, Matoh T, Sato YI. Genetic diversity of the wx flanking region in rice landraces in northern Laos. Breed Sci 2016; 66:580-590. [PMID: 27795683 PMCID: PMC5010311 DOI: 10.1270/jsbbs.16032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 05/11/2016] [Indexed: 05/07/2023]
Abstract
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8602,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8560,
Japan
- Corresponding author (e-mail: )
| | - Kenneth M. Olsen
- Biology Department, Washington University,
St. Louis 63130-4899,
USA
| | - Kazuaki Kawano
- Institute of Southern Cultural Folklore,
Kirishima, Kagoshima 899-4201,
Japan
| | - Chay Bounphanousay
- Agricultural Research Centre, National Agriculture and Forestry Research Institute,
Nongviengkham, Vientiane 7170,
Lao P.D.R
| | - Toru Matoh
- Graduate School of Agriculture, Kyoto University,
Kyoto 606-8502,
Japan
| | - Yo-Ichiro Sato
- National Institutes for the Humanities,
Minato-ku, Tokyo 105-0001,
Japan
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30
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Ishikawa R, Badenoch N, Miyagi K, Medoruma K, Osada T, Onishi M. Multi-lineages of Shiikuwasha ( Citrus depressa Hayata) evaluated by using whole chloroplast genome sequences and its bio-diversity in Okinawa, Japan. Breed Sci 2016; 66:490-498. [PMID: 27795674 PMCID: PMC5010300 DOI: 10.1270/jsbbs.15151] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/19/2016] [Indexed: 06/02/2023]
Abstract
Shiikuwasha (Citrus depressa Hayata) is distributed from the South-west of the Japanese archipelago to Taiwan. In this study, re-sequencing against the orange (C. sinensis (L.) Osbeck) chloroplast genome was applied to one superior landrace of Shiikuwasha cultivated in Oku ward, Okinawa, Japan. The chloroplast genome of the landrace was estimated to comprise 160,118 bp, including 48 indels and 71 nucleotide substitutions against the reference genome. The presumptive chloroplast indels were confirmed by subsequent experiments, and these identified multiple maternal lineages among other landraces. Some of the orange SSR markers were available for genotyping of other superior landraces and were able to distinguish among them. These molecular markers were then applied for evaluation of genetic diversity among wild and cultivated Shiikuwasha accessions. Except for Oku ward, the cultivated populations were found to have lost their genetic diversity in comparison with wild populations. Groves in Oku ward maintained, or showed even higher genetic diversity than wild accessions in the surrounding areas by the force of villagers.
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Affiliation(s)
- Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Nathan Badenoch
- Center for Southeast Asian Studies, Kyoto University,
Kyoto, Kyoto 606-8501,
Japan
| | - Kunimasa Miyagi
- Association of Shishigaki Network,
Naha, Okinawa 902-0071,
Japan
| | - Kaname Medoruma
- Okinawa prefectural Chūbu Agricultural Development Center, Department of Agriculture, Forestry and Fisheries, Okinawa Prefecture,
Nago, Okinawa 904-2155,
Japan
| | - Toshiki Osada
- Research Institute of Humanity and Nature,
Kyoto, Kyoto 603-8047,
Japan
| | - Masayuki Onishi
- Research Center for Knowledge Science in Cultural Heritage, Doshisha University,
Kyoto, Kyoto 610-0394,
Japan
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31
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Yin H, Akimoto M, Kaewcheenchai R, Sotowa M, Ishii T, Ishikawa R. Inconsistent diversities between nuclear and plastid genomes of AA genome species in the genus Oryza. Genes Genet Syst 2015; 90:269-81. [PMID: 26687860 DOI: 10.1266/ggs.14-00063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
AA genome species in the genus Oryza are valuable resources for improvement of cultivated rice. Oryza rufipogon and O. barthii were progenitors of two domesticated rice species, O. sativa and O. glaberrima, respectively. We used chloroplast single-nucleotide repeats (RCt1-10) to evaluate genetic diversity among AA genome species. Higher diversity was detected in the American species O. glumaepatula and the Asian species O. rufipogon. Other chloroplast sequences indicated that O. glumaepatula shares high similarity with O. longistaminata. Insertions of retrotransposable elements, however, showed a close relation between O. barthii and O. glumaepatula. To clarify phylogenetic relationships among AA genomes, whole-genome sequences obtained from different species were used to develop chloroplast INDEL markers. The INDEL patterns clearly showed multiple maternal origins of O. glumaepatula. The complicated origins have resulted in high genetic diversity in this species. In contrast, the Australian endemic species O. meridionalis tended to show narrower diversity than the other species. High variation in O. rufipogon, reconfirmed using the chloroplast INDELs, covered the variation in O. meridionalis and part of the variation in O. glumaepatula. Maternal lineages including O. barthii, O. longistaminata and the remainder of O. glumaepatula were phylogenetically close to each other and carried low genetic diversity. They were separated from independent lineages, suggesting that they had diverged from a single ancestral maternal lineage, but diverged later to keep gene flow within respective species, as SSR compositions suggested. Genetic relationships among AA genome species indicate how these species have evolved and become distributed across four continents.
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Affiliation(s)
- Hao Yin
- United Graduate School of Agricultural Sciences, Iwate University
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32
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Harada M, Matsunaga A, Aoyama N, Abe Y, Yoneki K, Ishikawa R, Watanabe T, Shigeta K, Miyako Y, Kutsuna T, Matsuzawa R, Yoshida A. Decreased physical activity is associated with an increased incidence or progression of peripheral artery disease in hemodialysis patients. Physiotherapy 2015. [DOI: 10.1016/j.physio.2015.03.3331] [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: 10/23/2022]
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Watanabe T, Matsunaga A, Abe Y, Yoneki K, Harada M, Ishikawa R, Shigeta K, Kutsuna T, Matsuzawa R, Yoshida A. Relationship between physical function and plantar pressure distribution in hemodialysis patients with peripheral neuropathy. Physiotherapy 2015. [DOI: 10.1016/j.physio.2015.03.1626] [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: 10/23/2022]
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34
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Okada JT, Sit PHL, Watanabe Y, Barbiellini B, Ishikawa T, Wang YJ, Itou M, Sakurai Y, Bansil A, Ishikawa R, Hamaishi M, Paradis PF, Kimura K, Ishikawa T, Nanao S. Visualizing the mixed bonding properties of liquid boron with high-resolution x-ray Compton scattering. Phys Rev Lett 2015; 114:177401. [PMID: 25978262 DOI: 10.1103/physrevlett.114.177401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 06/04/2023]
Abstract
Bonding characteristics of liquid boron at 2500 K are studied by using high-resolution Compton scattering. An excellent agreement is found between the measurements and the corresponding Car-Parrinello molecular dynamics simulations. Covalent bond pairs are clearly shown to dominate in liquid boron along with the coexistence of diffuse pairs. Our study reveals the complex bonding pattern of liquid boron and gives insight into the unusual properties of this high-temperature liquid.
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Affiliation(s)
- J T Okada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Tsukuba, Ibaraki 305-8505, Japan
- PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 3-1-1, Yoshinodai, Chuo-ku, Sagamihara 252-5210, Japan
| | - P H-L Sit
- School of Energy and Environment, City University of Hong Kong Kowloon, Hong Kong S.A.R
| | - Y Watanabe
- Institute of Industrial Sciences, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - B Barbiellini
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - T Ishikawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Tsukuba, Ibaraki 305-8505, Japan
- The Graduate University for Advanced Studies (SOKENDAI), 3-1-1, Yoshinodai, Chuo-ku, Sagamihara 252-5210, Japan
| | - Y J Wang
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - M Itou
- Japan Synchrotron Radiation Research Institute, SPring-8 Sayo-cho, Hyogo 679-5198, Japan
| | - Y Sakurai
- Japan Synchrotron Radiation Research Institute, SPring-8 Sayo-cho, Hyogo 679-5198, Japan
| | - A Bansil
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, USA
| | - R Ishikawa
- Institute of Industrial Sciences, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - M Hamaishi
- Institute of Industrial Sciences, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
| | - P-F Paradis
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Tsukuba, Ibaraki 305-8505, Japan
| | - K Kimura
- Department of Advanced Materials Science, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan
| | - T Ishikawa
- RIKEN SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - S Nanao
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Tsukuba, Ibaraki 305-8505, Japan
- Institute of Industrial Sciences, The University of Tokyo, Meguro-ku, Tokyo, 153-8505, Japan
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Yoneki K, Matsunaga A, Kitagawa J, Abe Y, Harada M, Ishikawa R, Watanabe T, Matsuzawa R, Kutsuna T, Shigeta K, Yoshida A. Association of habitual physical activity with bone metabolism in hemodialysis patients. Physiotherapy 2015. [DOI: 10.1016/j.physio.2015.03.109] [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: 10/23/2022]
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Ootsuka K, Takahashi I, Tanaka K, Itani T, Tabuchi H, Yoshihashi T, Tonouchi A, Ishikawa R. Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan. Breed Sci 2014; 64:115-124. [PMID: 24987297 PMCID: PMC4065318 DOI: 10.1270/jsbbs.64.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 02/07/2014] [Indexed: 05/30/2023]
Abstract
Rice fragrance is an important characteristic for Southeast Asian consumers, and fragrant landraces from Japan were first recorded in the 17th century. Principal component analysis clearly showed that Japanese fragrant landraces were genetically different from non-Japanese fragrant landraces. Japanese fragrant landraces were composed of six clades, none of which carried the most common fragrance mutation, an 8-bp deletion in exon 7 of Badh2. Fragrant landraces comprised two major groups carrying different Badh2 mutations. One group carried a known SNP at exon13 and the other a SNP at the exon1-intron1 junction as splicing donor site. The latter was considered to be a potential splicing mutant group as a novel allele at Badh2. Heterozygosity (He) scores in the two fragrant groups were not significantly different from non-fragrant landraces and modern cultivars. However, lower He scores were found around the Badh2 locus in the two groups. The potential splicing mutant group showed a more extended haplotype than the E13 SNP group. A likely causal factor responsible for loss of function is a novel splicing mutation allele that may have been generated quite recently. The fragrance allele has dispersed as a result of out-crossing under local environmental conditions.
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Affiliation(s)
- Kenta Ootsuka
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Ikuya Takahashi
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Katsunori Tanaka
- Faculty of Humanity, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Tomio Itani
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima,
Shobara, Hiroshima 727-0023,
Japan
| | - Hiroaki Tabuchi
- Upland Farming Research Division, Miyakonojo Research Station, NARO Kyushu Okinawa Agricultural Research Center,
6651-2 Yokoichi, Miyakonojo, Miyazaki 885-0091,
Japan
| | - Tadashi Yoshihashi
- Post harvest Science and Technology Division, Japan International Research Center for Agricultural Sciences,
Tsukuba, Ibaraki 305-8686,
Japan
| | - Akio Tonouchi
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University,
Hirosaki, Aomori 036-8561,
Japan
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Brozynska M, Omar ES, Furtado A, Crayn D, Simon B, Ishikawa R, Henry RJ. Chloroplast Genome of Novel Rice Germplasm Identified in Northern Australia. Trop Plant Biol 2014; 7:111-120. [PMID: 25485030 PMCID: PMC4245483 DOI: 10.1007/s12042-014-9142-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/13/2014] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa L.) was probably domesticated from O. rufipogon in Asia in the last 10,000 years. Relatives of cultivated rice (A genome species of Oryza) are found in South America, Africa, Australia and Asia. These A genome species are the close relatives of cultivated rice and represent the effective gene pool for rice improvement. Members of this group in Northern Australia include, an annual species, O. meridionalis, and two recently distinguished perennial taxa, to one of which the name O. rufipogon has been applied and the other a perennial form of O. meridionalis. Comparison of whole chloroplast genome sequences of these taxa has now been used to determine the relationships between the wild taxa and cultivated rice. The chloroplast genomes of the perennials were both found to be distinguished from O. rufipogon from Asia by 124 or 125 variations and were distinguished from each other by 53 variations. These populations have remained isolated from the overwhelming genetic impact of the large domesticated rice populations in Asia and may be unique descendants of the gene pool from which domesticated rice arose. The conservation of this wild genetic resource may be critical for global food security.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Ernnie Syafika Omar
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Australia
| | - Bryan Simon
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori Japan
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
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Mutou C, Tanaka K, Ishikawa R. DNA extraction from rice endosperm (including a protocol for extraction of DNA from ancient seed samples). Methods Mol Biol 2014; 1099:7-15. [PMID: 24243191 DOI: 10.1007/978-1-62703-715-0_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Deoxyribonucleic acid (DNA) extracted from endosperm can be effectively used for rapid genotyping using seed tissue, to evaluate seed quality from packaged grains and to determine the purity of milled grains. Methods outlined here are optimal procedures to isolate DNA from endosperm tissue of modern rice grains and of aged rice remains preserved between 50 and 100 years. The extracted DNA can be used to amplify regions of chloroplast genomic DNA (ctDNA), mitochondrial genomic DNA (mtDNA), and nuclear genomic DNA using standard PCR protocols. In addition, we describe an optimal procedure to process archaeological grain specimens, aged for a couple of thousand years, to isolate DNA from these ancient samples, referred to here as ancient DNA (aDNA). The aDNA can be successfully amplified by PCR using appropriate primer pairs designed specifically for aDNA amplification.
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Affiliation(s)
- Chiaki Mutou
- National Institute of Aerobiological Sciences, Tsukuba, Ibaraki, Japan
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Sotowa M, Ootsuka K, Kobayashi Y, Hao Y, Tanaka K, Ichitani K, Flowers JM, Purugganan MD, Nakamura I, Sato YI, Sato T, Crayn D, Simon B, Waters DLE, Henry RJ, Ishikawa R. Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms. Rice (N Y) 2013; 6:26. [PMID: 24280095 PMCID: PMC3874672 DOI: 10.1186/1939-8433-6-26] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/09/2013] [Indexed: 05/02/2023]
Abstract
BACKGROUND The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice. RESULTS Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type). O. rufipogon accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like O. rufipogon) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian O. rufipogon in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian O. rufipogon. The meridionalis-type showed some similarities to O. meridionalis such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from O. meridionalis by the presence of a larger lemma and higher number of spikelets. CONCLUSION Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian O. rufipogon. One lineage is closely related to O. meridionalis and another to Asian O. rufipogon. The first was presumed to have evolved by divergence from O. meridionalis becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian O. rufipogon, possibly arrived in Australia later.
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Affiliation(s)
- Masahiro Sotowa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Kenta Ootsuka
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yuu Kobayashi
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Yin Hao
- Science of Cryobiosystem, The United Graduate School of Agriculture Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Katsunori Tanaka
- Faculty of Humanities, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Katsuyuki Ichitani
- Faculty of Agriculture, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Jonathan M Flowers
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Department of Biology and Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Ikuo Nakamura
- Graduate School of Horticulture, Chiba University, Matsudo 648, Matsudo, Chiba 0271-8510, Japan
| | - Yo-Ichiro Sato
- Research Institute for Humanity and Nature, Kyoto 603-8047, Japan
| | - Tadashi Sato
- Graduate School of Life Science, Tohoku University, Sendai, Miyagi 980-8577, Japan
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Queensland 6811, Australia
| | - Bryan Simon
- Queensland Herbarium, Brisbane Botanic Gardens Mt Coot-tha, Brisbane, Queensland 4066, Australia
| | - Daniel LE Waters
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
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Wang YP, Bounphanousay C, Kanyavong K, Nakamura I, Sato YI, Sato T, Zhang HS, Tang LH, Ishikawa R. Population structural analysis of an in-situ conservation site for wild rice in Laos. Genes Genet Syst 2013; 87:311-22. [PMID: 23412633 DOI: 10.1266/ggs.87.311] [Citation(s) in RCA: 6] [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] [Indexed: 11/23/2022] Open
Abstract
An in-situ conservation site in Laos for a mixture of annual and perennial wild rice, LV27, which is a single swamp with an observation pier has been developed. In order to develop a strategy for evaluation of natural resources, systematic leaf sampling has been conducted and their genetic characteristics measured with 16 SSR loci. In order to determine population structure, a small number of individuals localized together were regarded as sub-populations belonging to a single mother population. Annual individuals were clustered at particular peripheral areas of the pond. Perennial individuals were close by and growing within deeper pond water. Scores of observed heterozygosity (Ho) were not significantly different between annual and perennial sub-populations, but relatively lower in annual ones. Genetic distance among annual and perennial sub-populations in close juxtaposition at peripheral sites showed that annuals were clustered against perennials. In addition, comparison of perennial sub-populations peripheral areas and inside the swamp, found they clustered together and were some distance from annual ones. When the genetic components were compared in detail, private alleles were frequently found in annual plants, suggesting there might be restriction of gene flow between annual and perennial types. Partitions of deep water perennial sub-populations identified private alleles in particular areas, suggesting there were some areas with unique polymorphisms. Combining peripheral perennial sub-populations led to the disappearance of most private alleles which implied there is frequent gene flow among perennial sub-populations. This in-situ conservation site allowed us to observe the succession of populations and also to research detailed population structure of a typical wild population and this found wild rice genetic structure in this single swamp is complex. The data obtained will provide valuable insight about how to evaluate wild populations genetically and how to deal with such populations as field collections.
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Affiliation(s)
- Yan-Ping Wang
- College of Agriculture, University of Nanjing Agriculture, No. 1 Weigang, Nanjing 210095, China
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Waters DLE, Nock CJ, Ishikawa R, Rice N, Henry RJ. Chloroplast genome sequence confirms distinctness of Australian and Asian wild rice. Ecol Evol 2012; 2:211-7. [PMID: 22408737 PMCID: PMC3297189 DOI: 10.1002/ece3.66] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/30/2011] [Accepted: 10/03/2011] [Indexed: 12/16/2022] Open
Abstract
Cultivated rice (Oryza sativa) is an AA genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. The chloroplast genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the chloroplast genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The chloroplast genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon chloroplast genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.
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Higo H, Tahir M, Takashima K, Miura A, Watanabe K, Tagiri A, Ugaki M, Ishikawa R, Eiguchi M, Kurata N, Sasaki T, Richards E, Takano M, Kishimoto N, Kakutani T, Habu Y. DDM1 (decrease in DNA methylation) genes in rice (Oryza sativa). Mol Genet Genomics 2012; 287:785-92. [PMID: 22915302 DOI: 10.1007/s00438-012-0717-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Accepted: 08/03/2012] [Indexed: 11/28/2022]
Abstract
Regulation of cytosine methylation in the plant genome is of pivotal in determining the epigenetic states of chromosome regions. Relative tolerance of plant to deficiency in cytosine methylation provides unparalleled opportunities to study the mechanism for regulation of cytosine methylation. The Decrease in DNA Methylation 1 (DDM1) of Arabidopsis thaliana is one of the best characterized plant epigenetic regulators that are necessary for maintenance of cytosine methylation in genomic DNA. Although cytosine methylation could affect various aspects of plant growth and development including those related to agricultural importance, orthologs of DDM1 in plants other than Arabidopsis has not been studied in detail. In this study, we identified two rice genes with similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development and their amino acid sequences are 93 % identical to each other. Transgenic rice lines expressing the OsDDM1a cDNA in the antisense orientation exhibited genomic DNA hypomethylation. In those lines, repeated sequences were more severely affected than a single copy sequence as is the case in Arabidopsis ddm1 mutants. Transcripts derived from endogenous transposon-related loci were up-regulated in the antisense OsDDM1 lines, opening a possibility to identify and utilize potentially active transposons for rice functional genomics.
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Affiliation(s)
- Hiromi Higo
- CREST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
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Matsukawa H, Shinoda M, Fujii M, Takahashi O, Yamamoto D, Murakata A, Ishikawa R. Factors associated with lobar vs. non-lobar intracerebral hemorrhage. Acta Neurol Scand 2012; 126:116-21. [PMID: 22067041 DOI: 10.1111/j.1600-0404.2011.01615.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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: 12/17/2022]
Abstract
OBJECTIVES The relationship between body mass index (BMI) and stroke subtypes has received more research attention than that between BMI and location of intracerebral hemorrhage (ICH). Lobar hemorrhage (LH) differs from non-LH primarily in terms of etiology, i.e. cerebral amyloid angiopathy is the main cause of LH. This study aimed to determine the relationship between BMI and ICH. MATERIALS AND METHODS In this retrospective study involving 460 consecutive patients with ICH, BMI was significantly lower in LH than for other ICH locations. BMI categories were underweight (BMI < 18.5 kg/m(2)), normal weight (18.5-23.0 kg/m(2)), overweight (23.0-27.5 kg/m(2)), or obesity (≥27.5 kg/m(2)). Outcome at 1 year was evaluated by the modified Rankin Scale (mRS). We investigated the relationship of BMI and other clinical characteristics with LH and non-LH. RESULTS LH was associated with age (>70 years), underweight, unfavorable outcome (mRS ≥3), and daily alcohol consumption. Hypertension and intraventricular bleeding were significantly less common in patients with LH than those with non-LH. CONCLUSIONS Alongside risk factors conventionally thought to be related to LH, underweight may also be a LH-related factor, specifically in the elderly.
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Affiliation(s)
- H Matsukawa
- Department of Neurosurgery, St. Luke's International Hospital, Tokyo, Japan.
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Tanizawa Y, Okamoto Y, Tsuzuki K, Nagao Y, Yoshida N, Tero R, Iwasa S, Hiraishi A, Suda Y, Takikawa H, Numano R, Okada H, Ishikawa R, Sandhu A. Microorganism mediated synthesis of reduced graphene oxide films. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/352/1/012011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ishikawa R, Ko PJ, Kurokawa Y, Konagai M, Sandhu A. Electrophoretic deposition of high quality transparent conductive graphene films on insulating glass substrates. ACTA ACUST UNITED AC 2012. [DOI: 10.1088/1742-6596/352/1/012003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Okada JT, Sit PHL, Watanabe Y, Wang YJ, Barbiellini B, Ishikawa T, Itou M, Sakurai Y, Bansil A, Ishikawa R, Hamaishi M, Masaki T, Paradis PF, Kimura K, Ishikawa T, Nanao S. Persistence of covalent bonding in liquid silicon probed by inelastic x-ray scattering. Phys Rev Lett 2012; 108:067402. [PMID: 22401121 DOI: 10.1103/physrevlett.108.067402] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 06/28/2011] [Indexed: 05/31/2023]
Abstract
Metallic liquid silicon at 1787 K is investigated using x-ray Compton scattering. An excellent agreement is found between the measurements and the corresponding Car-Parrinello molecular dynamics simulations. Our results show persistence of covalent bonding in liquid silicon and provide support for the occurrence of theoretically predicted liquid-liquid phase transition in supercooled liquid states. The population of covalent bond pairs in liquid silicon is estimated to be 17% via a maximally localized Wannier function analysis. Compton scattering is shown to be a sensitive probe of bonding effects in the liquid state.
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Affiliation(s)
- J T Okada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Tsukuba, Ibaraki, Japan
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Washizaki T, Ishikawa R, Yoneda K, Kitagawa S, Kaizaki S, Fuyuhiro A, Kawata S. Reversible solid-state hydration and dehydration process involving anion transfer in a self-assembled Cu2 system. RSC Adv 2012. [DOI: 10.1039/c2ra21865h] [Citation(s) in RCA: 7] [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] [Indexed: 11/21/2022] Open
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Shimizu K, Kurosawa T, Ishikawa R, Sanjo T. Vasopressin secretion by hypertonic saline infusion during hemodialysis: effect of cardiopulmonary recirculation. Nephrol Dial Transplant 2011; 27:796-803. [DOI: 10.1093/ndt/gfr272] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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