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Komatsu S, Uemura M. Special Issue "State-of-the-Art Molecular Plant Sciences in Japan". Int J Mol Sci 2024; 25:2365. [PMID: 38397042 PMCID: PMC10888678 DOI: 10.3390/ijms25042365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Food shortages are one of the most serious problems caused by global warming and population growth in this century [...].
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Affiliation(s)
- Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-0028, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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2
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Takahashi H, Kono T, Sawada K, Kumano S, Tsuri Y, Maruyama M, Yoshimura M, Takahashi D, Kawamura Y, Uemura M, Nakabayashi S, Mori Y, Hosokawa Y, Yoshikawa HY. Spatiotemporal Control of Ice Crystallization in Supercooled Water via an Ultrashort Laser Impulse. J Phys Chem Lett 2023; 14:4394-4402. [PMID: 37154425 DOI: 10.1021/acs.jpclett.3c00414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Focused irradiation with ultrashort laser pulses realized the fine spatiotemporal control of ice crystallization in supercooled water. An effective multiphoton excitation at the laser focus generated shockwaves and bubbles, which acted as an impulse for inducing ice crystal nucleation. The impulse that was localized close to the laser focus and accompanied by a small temperature elevation allowed the precise position control of ice crystallization and its observation with spatiotemporal resolution of micrometers and microseconds using a microscope. To verify the versatility of this laser method, we also applied it using various aqueous systems (e.g., plant extracts). The systematic study of crystallization probability revealed that laser-induced cavitation bubbles play a crucial role in inducing ice crystal nucleation. This method can be used as a tool for studying ice crystallization dynamics in various natural and biological phenomena.
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Affiliation(s)
- Hozumi Takahashi
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Tatsuya Kono
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Kosuke Sawada
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Satoru Kumano
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yuka Tsuri
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Mihoko Maruyama
- Division of Electrical, Electronics and Infocommunications Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
- Graduate School of Life and Environmental Science, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Masashi Yoshimura
- Institute of Laser Engineering (ILE), Osaka University, 2-6 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
- Division of Life Science, Graduate School of Science & Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka 020-8550, Japan
| | - Seiichiro Nakabayashi
- Department of Chemistry, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama University, Shimo-okubo 255, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Yusuke Mori
- Division of Electrical, Electronics and Infocommunications Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Y Yoshikawa
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871, Japan
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Lonsdale A, Ceballos-Laita L, Takahashi D, Uemura M, Abadía J, Davis MJ, Bacic A, Doblin MS. LSPpred Suite: Tools for Leaderless Secretory Protein Prediction in Plants. Plants (Basel) 2023; 12:1428. [PMID: 37050054 PMCID: PMC10097205 DOI: 10.3390/plants12071428] [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: 12/18/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Plant proteins that are secreted without a classical signal peptide leader sequence are termed leaderless secretory proteins (LSPs) and are implicated in both plant development and (a)biotic stress responses. In plant proteomics experimental workflows, identification of LSPs is hindered by the possibility of contamination from other subcellar compartments upon purification of the secretome. Applying machine learning algorithms to predict LSPs in plants is also challenging due to the rarity of experimentally validated examples for training purposes. This work attempts to address this issue by establishing criteria for identifying potential plant LSPs based on experimental observations and training random forest classifiers on the putative datasets. The resultant plant protein database LSPDB and bioinformatic prediction tools LSPpred and SPLpred are available at lsppred.lspdb.org. The LSPpred and SPLpred modules are internally validated on the training dataset, with false positives controlled at 5%, and are also able to classify the limited number of established plant LSPs (SPLpred (3/4, LSPpred 4/4). Until such time as a larger set of bona fide (independently experimentally validated) LSPs is established using imaging technologies (light/fluorescence/electron microscopy) to confirm sub-cellular location, these tools represent a bridging method for predicting and identifying plant putative LSPs for subsequent experimental validation.
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Affiliation(s)
- Andrew Lonsdale
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Melissa J. Davis
- Bioinformatics, Walter and Eliza Hall Institute for Medical Research, Melbourne, VIC 3052, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Monika S. Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Watanabe E, Kondo M, Kamal MM, Uemura M, Takahashi D, Kawamura Y. Plasma membrane proteomic changes of Arabidopsis DRP1E during cold acclimation in association with the enhancement of freezing tolerance. Physiol Plant 2022; 174:e13820. [PMID: 36335535 DOI: 10.1111/ppl.13820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
The freezing tolerance of plants that live in cold regions increases after exposure to low temperature, a process termed cold acclimation (CA). During CA, restructuring of the plasma membrane (PM) is important to enhance freezing tolerance. We have previously shown that the function of DYNAMIN-RELATED PROTEIN 1 E (DRP1E), which regulates endocytosis by pinching vesicles from the PM, is associated with the enhancement of freezing tolerance during CA in Arabidopsis. DRP1E is predicted to play a role in reconstituting the PM composition during CA. In this study, to test the validity of this hypothesis, we studied the changes in PM proteome patterns induced by drp1e mutation. In a detailed physiological analysis, after 3 days of CA, only young leaves showed significantly less increase in freezing tolerance in the mutant than in the wild type (WT). Using nano-liquid chromatography-tandem mass spectrometry, 496 PM proteins were identified. Among these proteins, 81 or 71 proteins were specifically altered in the WT or the mutant, respectively, in response to CA. Principal component analysis showed that the proteomic pattern differed between the WT and the mutant upon cold acclimation (CA), suggesting that DRP1E contributes to reconstruction of the PM during CA. Cluster analysis revealed that proteins that were significantly increased in the mutant after CA were biased toward glycosylphosphatidylinositol-anchored proteins, such as fasciclin-like arabinogalactan proteins. Thus, a primary target of DRP1E-associated PM reconstruction during CA is considered to be glycosylphosphatidylinositol-anchored proteins, which may be removed from the PM by DRP1E in young leaves after 3 days of CA.
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Affiliation(s)
| | - Mariko Kondo
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Daisuke Takahashi
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Yukio Kawamura
- Faculty of Agriculture, Iwate University, Morioka, Japan
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
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Gutierrez M, Friedman C, Long G, Ascierto P, Melero I, Richards D, Bastos B, Moreno Garcia V, Uemura M, Conkling P, Corr B, Kim A, Zhu L, Hammell A, Perumal D, Chouzy A, Benavente F, Awosemo O, Hannah A, Le D. 740P Anti-cytotoxic T-lymphocyte antigen-4 (CTLA 4) probody BMS-986249 ± nivolumab (NIVO) in patients (pts) with advanced cancers: Updated phase I results. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.866] [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: 11/01/2022] Open
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6
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Boku S, Satake H, Ohta T, Mitani S, Kawakami K, Matsumoto T, Yamazaki E, Hasegawa H, Ikoma T, Uemura M, Yamaguchi T, Ishizuka Y, Kurokawa Y, Sakai D, Kawakami H, Shimokawa T, Tsujinaka T, Kato T, Satoh T, Kagawa Y. 440TiP TRESBIEN (OGSG 2101): Encorafenib, binimetinib and cetuximab for early relapse stage II/III BRAF V600E-mutated CRC. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.578] [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: 11/16/2022] Open
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7
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Inoue T, Taguchi S, Uemura M, Tsujimoto Y, Yamashita Y. P-185 The migration speed of nucleolar precursor bodies in pronuclei affects in vitro fertilization-derived human embryo ploidy status. Hum Reprod 2022. [DOI: 10.1093/humrep/deac107.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Study question
Does the migration speed of nucleolar precursor bodies (NPBs) in male and female pronuclei (mPN and fPN) affect in vitro fertilization (IVF)-derived embryo ploidy status?
Summary answer
The NPB migration speed in mPN impacts the IVF-derived human embryo ploidy status and this indicator could be an attractive marker for noninvasive embryo selection.
What is known already
NPBs are not considered as simple nucleolar components transmitted from an oocyte to an embryo, and they could participate in genome remodeling during embryo development. NPBs are essential only shortly after fertilization, suggesting that they may actively participate in centromeric chromatin establishment. A previous study demonstrated that NPBs migrated faster in intracytoplasmic sperm injection-derived zygotes having the potential to develop into a blastocyst and eventually into a baby (Inoue et al., 2021). However, the relationship between NPB migration speed and IVF-derived embryo ploidy status is unclear.
Study design, size, duration
The relationship between the NPB migration speed and embryo ploidy status was retrospectively analyzed in patients with recurrent assisted reproductive technology failure (euploid n =18; aneuploid n =19; and total = 219 NPBs). Archived time-lapse videos (images were recorded every 5 min; Geri+) from incubation after IVF were retrieved after the patients were identified for the study, and the NPB migration speed was analyzed. The retrospective analyses were performed with the patient’s identities masked.
Participants/materials, setting, methods
mPN and fPN were identified by appearance location in a zygote (fPN appearance is just below the polar bodies). The mPN, fPN, and 2–3 NPBs/PN central coordinates were measured by Kinovea (motion capture software). Their central coordinates were confirmed/revised every image and were decided. The migration distance of NPBs between two sequential images was calculated as the standard of the central PN coordinates. Thereafter, the migration speed of NPBs was calculated.
Main results and the role of chance
Both NPB speeds were significantly faster in the euploid than in the aneuploid groups (mPN: 4.08±0.61 vs. 3.54±0.54 µm/h, P =0.003, power [1-β]: 0.999, fPN: 4.03±0.89 vs. 3.26±0.45 µm/h, P <0.003, 1-β: 0.987). The NPB speed in mPN was correlated with that in fPN (rs =0.523, P =0.001). The ploidy status was related to the NPB speeds in mPN and fPN (P <0.05) in univariate logistic analysis including male/female ages, ICM/TE grades, and 29 morphokinetic parameters. The factors associated with ploidy status were the NPB speed in mPN (odds ratio [OR], 10.2; 95% confidence interval [CI], 1.90–54.90; P =0.007) and female age (OR, 0.8; 95%CI, 0.64–0.98; P =0.03) in multivariate logistic analysis. The cutoff value for the NPB speeds in mPN and fPN were 3.65 μm/h (specificity, 73.7%; sensitivity, 77.8%; AUC, 0.78; 95%CI, 0.62–0.93) and 3.77 μm/h (specificity, 89.5%; sensitivity, 66.7%; AUC, 0.78; 95%CI, 0.62–0.94). When the zygotes were categorized by their cutoff values, the euploid rate in zygotes with NPB speeds greater than the cutoff value was significantly higher than that in zygotes with the speeds less than the cutoff value (mPN = 73.7% vs. 22.2% [P =0.003]; fPN = 85.7% vs. 26.1% [P <0.001]).
Limitations, reasons for caution
The NPB migration in the z-axis direction could not be analyzed. NPB tracking could not be performed when NPBs were large in number or drastically moved. Our findings should help in elucidating the relationship, although they did not completely explain the relationship between NPB migration and embryo development.
Wider implications of the findings
The migration speed of NPBs impacts human embryo ploidy status. NPB migration speed may add clinical value for embryo selection, which may be associated with live birth, and consequently, the time of the live birth could be shorter. The indicator could be an attractive marker for noninvasive embryo selection.
Trial registration number
Not applicable
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Affiliation(s)
- T Inoue
- Umeda Fertility Clinic, Department of Gynecology , Osaka, Japan
- Hyogo College of Medicine, Department of Emergency- Disaster and Critical Care Medicine , Nishinomiya, Japan
| | - S Taguchi
- Umeda Fertility Clinic, Department of Gynecology , Osaka, Japan
| | - M Uemura
- Kansai University of Welfare Sciences, Department of Rehabilitation- Faculty of Health Science , Osaka, Japan
| | - Y Tsujimoto
- Umeda Fertility Clinic, Department of Gynecology , Osaka, Japan
| | - Y Yamashita
- Umeda Fertility Clinic, Department of Gynecology , Osaka, Japan
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Sugimoto N, Nakata K, Miyo M, Yoshioka S, Kagawa Y, Naito A, Tei M, Tamagawa H, Konishi K, Osawa H, Shingai T, Danno K, Nishida N, Sato G, Shimokawa T, Miyoshi N, Takahashi H, Uemura M, Yamamoto H, Murata K, Doki Y, Eguchi H. P-76 Phase II study of FOLFIRI plus ramucirumab with recurrent colorectal cancer refractory to adjuvant chemotherapy with oxaliplatin/fluoropyrimidine (RAINCLOUD). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.166] [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: 11/01/2022] Open
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9
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Fujise H, Uemura M, Hasegawa H, Ikeya D, Matsuda A, Morishita T, Madsen LB, Jensen F, Tolstikhin OI, Hishikawa A. Helicity-dependent dissociative tunneling ionization of CF 4 in multicycle circularly polarized intense laser fields. Phys Chem Chem Phys 2022; 24:8962-8969. [PMID: 35380001 DOI: 10.1039/d1cp05858d] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dissociative tunneling ionization of tetrafluoromethane (CF4) in circularly polarized ultrashort intense laser fields (35 fs, 0.8 × 1014 W cm-2, 1035 nm), CF4 → CF4+ + e- → CF3+ + F + e-, has been studied by three-dimensional electron-ion coincidence momentum imaging. The photoelectron angular distribution in the recoil frame revealed that the dissociative tunneling ionization occurs efficiently when the laser electric field points from F to C. The obtained results are qualitatively consistent with the theoretical predictions by the weak-field asymptotic theory (WFAT) for tunneling ionization from the highest and next-highest occupied molecular orbitals, HOMO (1t1), and HOMO-1 (4t2), respectively. On the other hand, the angular distribution shows clear dependences on the polarization helicity, indicating that the breaking of the C-F bonds is sensitive to the helicity of the multicycle circularly polarized laser fields.
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Affiliation(s)
- H Fujise
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan.
| | - M Uemura
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan.
| | - H Hasegawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan.
| | - D Ikeya
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan.
| | - A Matsuda
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan.
| | - T Morishita
- Institute for Advanced Science, The University of Electro-Communications, 1-5-1 Chofu-ga-oka, Chofu-shi, Tokyo 182-8585, Japan
| | - L B Madsen
- Department of Physics and Astronomy, Aarhus University, 8000 Aarhus C, Denmark
| | - F Jensen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - O I Tolstikhin
- Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - A Hishikawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan. .,Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
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Ceballos-Laita L, Takahashi D, Uemura M, Abadía J, López-Millán AF, Rodríguez-Celma J. Effects of Fe and Mn Deficiencies on the Root Protein Profiles of Tomato ( Solanum lycopersicum) Using Two-Dimensional Electrophoresis and Label-Free Shotgun Analyses. Int J Mol Sci 2022; 23:ijms23073719. [PMID: 35409079 PMCID: PMC8998858 DOI: 10.3390/ijms23073719] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 12/04/2022] Open
Abstract
Iron (Fe) and manganese (Mn) are two essential elements for plants that compete for the same uptake transporters and show conflicting interactions at the regulatory level. In order to understand the differential response to both metal deficiencies in plants, two proteomic techniques (two-dimensional gel electrophoresis and label-free shotgun) were used to study the proteome profiles of roots from tomato plants grown under Fe or Mn deficiency. A total of 119 proteins changing in relative abundance were confidently quantified and identified, including 35 and 91 in the cases of Fe deficiency and Mn deficiency, respectively, with 7 of them changing in both deficiencies. The identified proteins were categorized according to function, and GO-enrichment analysis was performed. Data showed that both deficiencies provoked a common and intense cell wall remodelling. However, the response observed for Fe and Mn deficiencies differed greatly in relation to oxidative stress, coumarin production, protein, nitrogen, and energy metabolism.
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Affiliation(s)
- Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, 50059 Zaragoza, Spain; (L.C.-L.); (J.A.); (A.F.L.-M.)
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (D.T.); (M.U.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (D.T.); (M.U.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, 50059 Zaragoza, Spain; (L.C.-L.); (J.A.); (A.F.L.-M.)
| | - Ana Flor López-Millán
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, 50059 Zaragoza, Spain; (L.C.-L.); (J.A.); (A.F.L.-M.)
| | - Jorge Rodríguez-Celma
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, 50059 Zaragoza, Spain; (L.C.-L.); (J.A.); (A.F.L.-M.)
- Correspondence:
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11
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Koide S, Nishizawa K, Saito N, Osuga R, Orikasa T, Uemura M. Study on Moisture Content Changes during Atmospheric Freeze Drying of Fresh-cut Japanese Radish and its Quality after Drying and Rehydration. J JPN SOC FOOD SCI 2021. [DOI: 10.3136/nskkk.68.464] [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: 11/03/2022]
Affiliation(s)
| | | | | | - Rei Osuga
- Faculty of Agriculture, Iwate University
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12
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Osuga R, Koide S, Abe Y, Orikasa T, Uemura M. Effect of Supercooled Storage on Maintaining the Quality of Fresh-cut Pear. J JPN SOC FOOD SCI 2021. [DOI: 10.3136/nskkk.68.455] [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: 11/03/2022]
Affiliation(s)
- Rei Osuga
- Faculty of Agriculture, Iwate University
| | | | - Yukino Abe
- Faculty of Agriculture, Iwate University
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13
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Juurakko CL, Bredow M, Nakayama T, Imai H, Kawamura Y, diCenzo GC, Uemura M, Walker VK. The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance. G3 (Bethesda) 2021; 11:6321953. [PMID: 34544140 PMCID: PMC8661430 DOI: 10.1093/g3journal/jkab198] [Citation(s) in RCA: 3] [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: 04/22/2021] [Accepted: 06/04/2021] [Indexed: 11/25/2022]
Abstract
In order to survive subzero temperatures, some plants undergo cold acclimation (CA) where low, nonfreezing temperatures, and/or shortened day lengths allow cold-hardening and survival during subsequent freeze events. Central to this response is the plasma membrane (PM), where low temperature is perceived and cellular homeostasis must be preserved by maintaining membrane integrity. Here, we present the first PM proteome of cold-acclimated Brachypodium distachyon, a model species for the study of monocot crops. A time-course experiment investigated CA-induced changes in the proteome following two-phase partitioning PM enrichment and label-free quantification by nano-liquid chromatography-mass spectrophotometry. Two days of CA were sufficient for membrane protection as well as an initial increase in sugar levels and coincided with a significant change in the abundance of 154 proteins. Prolonged CA resulted in further increases in soluble sugars and abundance changes in more than 680 proteins, suggesting both a necessary early response to low-temperature treatment, as well as a sustained CA response elicited over several days. A meta-analysis revealed that the identified PM proteins have known roles in low-temperature tolerance, metabolism, transport, and pathogen defense as well as drought, osmotic stress, and salt resistance suggesting crosstalk between stress responses, such that CA may prime plants for other abiotic and biotic stresses. The PM proteins identified here present keys to an understanding of cold tolerance in monocot crops and the hope of addressing economic losses associated with modern climate-mediated increases in frost events.
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Affiliation(s)
- Collin L Juurakko
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Melissa Bredow
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Takato Nakayama
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Yukio Kawamura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - George C diCenzo
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Matsuo Uemura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka, Iwate 020-8550, Japan.,United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Virginia K Walker
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.,Department of Biomedical and Molecular Sciences, School of Environmental Studies, Queen's University, Kingston, ON K7L 3N6, Canada
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14
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Nakata K, Sakai D, Hasegawa J, Kato T, Murata K, Ikenaga M, Kudo T, Uemura M, Satoh T, Mizushima T, Doki Y, Eguchi H. P-200 A phase II study of dose reductive XELOX plus bevacizumab in elderly or vulnerable patients with metastatic colorectal cancer: MCSGO-1202. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.05.255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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15
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Tominaga Y, Suzuki K, Uemura M, Kawamura Y. In Planta Monitoring of Cold-Responsive Promoter Activity Reveals a Distinctive Photoperiodic Response in Cold Acclimation. Plant Cell Physiol 2021; 62:43-52. [PMID: 33367798 DOI: 10.1093/pcp/pcaa138] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/18/2020] [Indexed: 06/12/2023]
Abstract
Plant cold acclimation involves complicated pathways that integrate signals from temperature changes and light conditions. To understand plant responses to environmental signals in detail, molecular events that are regulated by temperature and light must be investigated at the whole-plant level in a nondestructive way. Using the promoter of COR15A connected to the luciferase reporter gene as a cold-responsive indicator, we developed an in planta monitoring system for gene expression under controlled temperature and photoperiod conditions. COR15A promoter activity was intensified by day-night cycles at 2�C, while its induction was abruptly suppressed in the dark at 8�C or higher, indicating a difference in responsiveness to photocycle between these two acclimation conditions. Freeze-thawing tests of whole plants proved that lower acclimation temperature resulted in higher tolerance to freezing, consistent with the temperature-dependent induction of COR15A. Inhibition of photosynthetic electron transport by 3-(3,4-dichlorophenyl)-1,1-dimethylurea eliminated the responsiveness to the day-night cycles at 2�C, indicating a possibility that the photosynthetic redox and/or the accumulation of photosynthates modulate COR15A responsiveness to photoperiod during cold acclimation, in addition to the well-known regulation by CBF (C-repeat binding factor) genes. These findings indicate that the cold-responsive promoter is regulated by distinctive mechanisms dependent on temperature and simultaneously affected by photocycle and photosynthesis.
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Affiliation(s)
- Yoko Tominaga
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
| | - Kensaku Suzuki
- NARO Tohoku Agricultural Research Center, 4 Akahira, Shimo-Kuriyagawa, Morioka, 020-0198 Japan
| | - Matsuo Uemura
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
- Department of Plant-Biosciences, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
| | - Yukio Kawamura
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
- Department of Plant-Biosciences, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
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16
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Takahashi H, Miyoshi N, Uemura M, Mizushima T, Doki Y, Eguchi H. Indocyanine green near-infrared fluorescence imaging in laparoscopic resection of small bowel carcinoma for definitive central vascular ligation - a video vignette. Colorectal Dis 2020; 22:2347-2348. [PMID: 33245594 DOI: 10.1111/codi.15315] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 02/08/2023]
Affiliation(s)
- H Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - N Miyoshi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - M Uemura
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - T Mizushima
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Y Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - H Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
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17
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Ceballos-Laita L, Gutierrez-Carbonell E, Takahashi D, Lonsdale A, Abadía A, Doblin MS, Bacic A, Uemura M, Abadía J, López-Millán AF. Effects of Excess Manganese on the Xylem Sap Protein Profile of Tomato ( Solanum lycopersicum) as Revealed by Shotgun Proteomic Analysis. Int J Mol Sci 2020; 21:E8863. [PMID: 33238539 PMCID: PMC7700171 DOI: 10.3390/ijms21228863] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 01/12/2023] Open
Abstract
Metal toxicity is a common problem in crop species worldwide. Some metals are naturally toxic, whereas others such as manganese (Mn) are essential micro-nutrients for plant growth but can become toxic when in excess. Changes in the composition of the xylem sap, which is the main pathway for ion transport within the plant, is therefore vital to understanding the plant's response(s) to metal toxicity. In this study we have assessed the effects of exposure of tomato roots to excess Mn on the protein profile of the xylem sap, using a shotgun proteomics approach. Plants were grown in nutrient solution using 4.6 and 300 µM MnCl2 as control and excess Mn treatments, respectively. This approach yielded 668 proteins reliably identified and quantified. Excess Mn caused statistically significant (at p ≤ 0.05) and biologically relevant changes in relative abundance (≥2-fold increases or ≥50% decreases) in 322 proteins, with 82% of them predicted to be secretory using three different prediction tools, with more decreasing than increasing (181 and 82, respectively), suggesting that this metal stress causes an overall deactivation of metabolic pathways. Processes most affected by excess Mn were in the oxido-reductase, polysaccharide and protein metabolism classes. Excess Mn induced changes in hydrolases and peroxidases involved in cell wall degradation and lignin formation, respectively, consistent with the existence of alterations in the cell wall. Protein turnover was also affected, as indicated by the decrease in proteolytic enzymes and protein synthesis-related proteins. Excess Mn modified the redox environment of the xylem sap, with changes in the abundance of oxido-reductase and defense protein classes indicating a stress scenario. Finally, results indicate that excess Mn decreased the amounts of proteins associated with several signaling pathways, including fasciclin-like arabinogalactan-proteins and lipids, as well as proteases, which may be involved in the release of signaling peptides and protein maturation. The comparison of the proteins changing in abundance in xylem sap and roots indicate the existence of tissue-specific and systemic responses to excess Mn. Data are available via ProteomeXchange with identifier PXD021973.
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Affiliation(s)
- Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain; (L.C.-L.); (E.G.-C.); (A.A.); (A.F.L.-M.)
| | - Elain Gutierrez-Carbonell
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain; (L.C.-L.); (E.G.-C.); (A.A.); (A.F.L.-M.)
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (D.T.); (M.U.)
| | - Andrew Lonsdale
- School of Biosciences, The University of Melbourne, Parkville, VIC 3052, Australia;
| | - Anunciación Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain; (L.C.-L.); (E.G.-C.); (A.A.); (A.F.L.-M.)
| | - Monika S. Doblin
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant & Soil Sciences, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; (M.S.D.); (A.B.)
| | - Antony Bacic
- La Trobe Institute for Agriculture & Food, Department of Animal, Plant & Soil Sciences, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia; (M.S.D.); (A.B.)
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (D.T.); (M.U.)
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain; (L.C.-L.); (E.G.-C.); (A.A.); (A.F.L.-M.)
| | - Ana Flor López-Millán
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain; (L.C.-L.); (E.G.-C.); (A.A.); (A.F.L.-M.)
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18
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Kamal MM, Ishikawa S, Takahashi F, Suzuki K, Kamo M, Umezawa T, Shinozaki K, Kawamura Y, Uemura M. Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. Int J Mol Sci 2020; 21:E8631. [PMID: 33207747 PMCID: PMC7696906 DOI: 10.3390/ijms21228631] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/22/2022] Open
Abstract
Cold stress is one of the major factors limiting global crop production. For survival at low temperatures, plants need to sense temperature changes in the surrounding environment. How plants sense and respond to the earliest drop in temperature is still not clearly understood. The plasma membrane and its adjacent extracellular and cytoplasmic sites are the first checkpoints for sensing temperature changes and the subsequent events, such as signal generation and solute transport. To understand how plants respond to early cold exposure, we used a mass spectrometry-based phosphoproteomic method to study the temporal changes in protein phosphorylation events in Arabidopsis membranes during 5 to 60 min of cold exposure. The results revealed that brief cold exposures led to rapid phosphorylation changes in the proteins involved in cellular ion homeostasis, solute and protein transport, cytoskeleton organization, vesical trafficking, protein modification, and signal transduction processes. The phosphorylation motif and kinase-substrate network analysis also revealed that multiple protein kinases, including RLKs, MAPKs, CDPKs, and their substrates, could be involved in early cold signaling. Taken together, our results provide a first look at the cold-responsive phosphoproteome changes of Arabidopsis membrane proteins that can be a significant resource to understand how plants respond to an early temperature drop.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
| | - Shinnosuke Ishikawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Fuminori Takahashi
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Ko Suzuki
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Masaharu Kamo
- Department of Biochemistry, Iwate Medical University, Yahaba 028-3694, Japan; (K.S.); (M.K.)
| | - Taishi Umezawa
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei 184-8588, Japan; (S.I.); (T.U.)
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 3-1-1 Koyadai, Tsukuba 305-0074, Japan; (F.T.); (K.S.)
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; (M.M.K.); (Y.K.)
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
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19
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Kovács T, Ahres M, Pálmai T, Kovács L, Uemura M, Crosatti C, Galiba G. Decreased R:FR Ratio in Incident White Light Affects the Composition of Barley Leaf Lipidome and Freezing Tolerance in a Temperature-Dependent Manner. Int J Mol Sci 2020; 21:ijms21207557. [PMID: 33066276 PMCID: PMC7593930 DOI: 10.3390/ijms21207557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/29/2020] [Accepted: 10/08/2020] [Indexed: 02/06/2023] Open
Abstract
In cereals, C-repeat binding factor genes have been defined as key components of the light quality-dependent regulation of frost tolerance by integrating phytochrome-mediated light and temperature signals. This study elucidates the differences in the lipid composition of barley leaves illuminated with white light or white light supplemented with far-red light at 5 or 15 °C. According to LC-MS analysis, far-red light supplementation increased the amount of monogalactosyldiacylglycerol species 36:6, 36:5, and 36:4 after 1 day at 5 °C, and 10 days at 15 °C resulted in a perturbed content of 38:6 species. Changes were observed in the levels of phosphatidylethanolamine, and phosphatidylserine under white light supplemented with far-red light illumination at 15 °C, whereas robust changes were observed in the amount of several phosphatidylserine species at 5 °C. At 15 °C, the amount of some phosphatidylglycerol species increased as a result of white light supplemented with far-red light illumination after 1 day. The ceramide (42:2)-3 content increased regardless of the temperature. The double-bond index of phosphatidylglycerol, phosphatidylserine, phosphatidylcholine ceramide together with total double-bond index changed when the plant was grown at 15 °C as a function of white light supplemented with far-red light. white light supplemented with far-red light increased the monogalactosyldiacylglycerol/diacylglycerol ratio as well. The gene expression changes are well correlated with the alterations in the lipidome.
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Affiliation(s)
- Terézia Kovács
- Biological Research Centre, Institute of Plant Biology, H-6701 Szeged, Hungary;
- Department of Plant Biology, University of Szeged, 6720 Szeged, Hungary
- Correspondence:
| | - Mohamed Ahres
- Centre for Agricultural Research, Agricultural Institute, 2462 Martonvásár, Hungary; (M.A.); (T.P.); (G.G.)
- Festetics Doctoral School, Georgikon Campus, Szent István University, H-2100 Gödöllő, Hungary
| | - Tamás Pálmai
- Centre for Agricultural Research, Agricultural Institute, 2462 Martonvásár, Hungary; (M.A.); (T.P.); (G.G.)
| | - László Kovács
- Biological Research Centre, Institute of Plant Biology, H-6701 Szeged, Hungary;
| | - Matsuo Uemura
- Department of Plant-Bioscience, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan;
| | - Cristina Crosatti
- CREA Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, 29017 San Protaso, Italy;
| | - Gabor Galiba
- Centre for Agricultural Research, Agricultural Institute, 2462 Martonvásár, Hungary; (M.A.); (T.P.); (G.G.)
- Festetics Doctoral School, Georgikon Campus, Szent István University, H-2100 Gödöllő, Hungary
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20
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Adjei A, Beg M, Melear J, Thompson J, Tsai FC, Baranda J, Bastos B, Spira A, Lou Y, Seetharam M, Uemura M, Camidge D, Yamamoto N, Cowey C, Doi T, Anthony S, Janat-Amsbury M, Wade M, Bearss D, Sarantopoulos J. 536MO A phase I, first-in-human, safety, pharmacokinetic, and pharmacodynamic study of oral dubermatinib (TP-0903) in patients with advanced solid tumours. Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.08.650] [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] Open
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21
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Kamal MM, Erazo C, Tanino KK, Kawamura Y, Kasuga J, Laarveld B, Olkowski A, Uemura M. A single seed treatment mediated through reactive oxygen species increases germination, growth performance, and abiotic stress tolerance in Arabidopsis and rice. Biosci Biotechnol Biochem 2020; 84:2597-2608. [PMID: 32856556 DOI: 10.1080/09168451.2020.1808444] [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] [Indexed: 10/23/2022]
Abstract
Hydroxyl radical (•OH) is considered to be the most damaging among reactive oxygen species. Although afew studies have reported on its effects on growth and stress adaptation of plants, no detailed studies have been performed using •OH in germination and early seedling growth under abiotic stresses. Here we report a single seed treatment with •OH on germination and seedling growth of Arabidopsis and rice under non-stressed (ambient) and various abiotic-stressed conditions (chilling, high temperature, heat, and salinity). The treatment resulted in faster seed germination and early seedling growth under non-stressed conditions, and, interestingly, these effects were more prominent under abiotic stresses. In addition, Arabidopsis seedlings from treated seeds showed faster root growth and developed more lateral roots. These results show apositive and potential practical use for •OH in model and crop plants for direct seeding in the field, as well as improvement of tolerance against emerging stresses. Abbreviations: AUC: area under curve; MGT: mean germination time; t50: time to reach 50% germination; U7525: time for uniform germination from 25% to 75%; ROS: reactive oxygen species; GSI: germination speed index; SI: stress index; DI: dormancy index.
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Affiliation(s)
- Md Mostafa Kamal
- United Graduate School of Agricultural Sciences, Iwate University , Morioka, Japan
| | - Carlos Erazo
- College of Agriculture and Bioresources, University of Saskatchewan , Saskatoon, Canada
| | - Karen K Tanino
- College of Agriculture and Bioresources, University of Saskatchewan , Saskatoon, Canada
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University , Morioka, Japan.,Department of Plant-bioscience, Faculty of Agriculture, Iwate University , Morioka, Japan
| | - Jun Kasuga
- Research Center for Global Agromedicine, Obihiro University of Agriculture and Veterinary Medicine , Obihiro, Japan
| | - Bernard Laarveld
- College of Agriculture and Bioresources, University of Saskatchewan , Saskatoon, Canada
| | - Andrew Olkowski
- College of Agriculture and Bioresources, University of Saskatchewan , Saskatoon, Canada
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University , Morioka, Japan.,Department of Plant-bioscience, Faculty of Agriculture, Iwate University , Morioka, Japan
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22
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Choueiri TK, Motzer RJ, Rini BI, Haanen J, Campbell MT, Venugopal B, Kollmannsberger C, Gravis-Mescam G, Uemura M, Lee JL, Grimm MO, Gurney H, Schmidinger M, Larkin J, Atkins MB, Pal SK, Wang J, Mariani M, Krishnaswami S, Cislo P, Chudnovsky A, Fowst C, Huang B, di Pietro A, Albiges L. Updated efficacy results from the JAVELIN Renal 101 trial: first-line avelumab plus axitinib versus sunitinib in patients with advanced renal cell carcinoma. Ann Oncol 2020; 31:1030-1039. [PMID: 32339648 PMCID: PMC8436592 DOI: 10.1016/j.annonc.2020.04.010] [Citation(s) in RCA: 266] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/25/2020] [Accepted: 04/13/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND The phase 3 JAVELIN Renal 101 trial (NCT02684006) demonstrated significantly improved progression-free survival (PFS) with first-line avelumab plus axitinib versus sunitinib in advanced renal cell carcinoma (aRCC). We report updated efficacy data from the second interim analysis. PATIENTS AND METHODS Treatment-naive patients with aRCC were randomized (1 : 1) to receive avelumab (10 mg/kg) intravenously every 2 weeks plus axitinib (5 mg) orally twice daily or sunitinib (50 mg) orally once daily for 4 weeks (6-week cycle). The two independent primary end points were PFS and overall survival (OS) among patients with programmed death ligand 1-positive (PD-L1+) tumors. Key secondary end points were OS and PFS in the overall population. RESULTS Of 886 patients, 442 were randomized to the avelumab plus axitinib arm and 444 to the sunitinib arm; 270 and 290 had PD-L1+ tumors, respectively. After a minimum follow-up of 13 months (data cut-off 28 January 2019), PFS was significantly longer in the avelumab plus axitinib arm than in the sunitinib arm {PD-L1+ population: hazard ratio (HR) 0.62 [95% confidence interval (CI) 0.490-0.777]}; one-sided P < 0.0001; median 13.8 (95% CI 10.1-20.7) versus 7.0 months (95% CI 5.7-9.6); overall population: HR 0.69 (95% CI 0.574-0.825); one-sided P < 0.0001; median 13.3 (95% CI 11.1-15.3) versus 8.0 months (95% CI 6.7-9.8)]. OS data were immature [PD-L1+ population: HR 0.828 (95% CI 0.596-1.151); one-sided P = 0.1301; overall population: HR 0.796 (95% CI 0.616-1.027); one-sided P = 0.0392]. CONCLUSION Among patients with previously untreated aRCC, treatment with avelumab plus axitinib continued to result in a statistically significant improvement in PFS versus sunitinib; OS data were still immature. CLINICAL TRIAL NUMBER NCT02684006.
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Affiliation(s)
- T K Choueiri
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, USA.
| | - R J Motzer
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - B I Rini
- Cleveland Clinic, Cleveland, USA
| | - J Haanen
- Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M T Campbell
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Venugopal
- University of Glasgow, Beatson West of Scotland Cancer Centre, Glasgow, UK
| | | | - G Gravis-Mescam
- Institut Paoli-Calmettes, Department of Medical Oncology, Aix-Marseille Université, Inserm, CNRS, CRCM, Marseille, France
| | - M Uemura
- Osaka University Hospital, Osaka, Japan
| | - J L Lee
- University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea
| | - M-O Grimm
- Jena University Hospital, Department of Urology, Jena, Germany
| | - H Gurney
- Macquarie University, Sydney, Australia
| | - M Schmidinger
- Clinical Division of Oncology, Department of Medicine I Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - J Larkin
- Royal Marsden NHS Foundation Trust, London, UK
| | - M B Atkins
- Georgetown University Medical Center, Washington, DC
| | - S K Pal
- City of Hope National Medical Center, Duarte, USA
| | | | | | | | | | | | - C Fowst
- Pfizer Italia SRL, Milan, Italy
| | | | | | - L Albiges
- Institut Gustave Roussy, Villejuif, France
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23
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Yuki S, Bando H, Tsukada Y, Inamori K, Komatsu Y, Homma S, Uemura M, Kato T, Kotani D, Fukuoka S, Nakamura N, Fukui M, Wakabayashi M, Kojima M, Sato A, Togashi Y, Nishikawa H, Ito M, Yoshino T. SO-37 Short-term results of VOLTAGE-A: Nivolumab monotherapy and subsequent radical surgery following preoperative chemoradiotherapy in patients with microsatellite stability and microsatellite instability-high, locally advanced rectal cancer (EPOC 1504). Ann Oncol 2020. [DOI: 10.1016/j.annonc.2020.04.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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24
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Zhong Z, Kobayashi T, Zhu W, Imai H, Zhao R, Ohno T, Rehman SU, Uemura M, Tian J, Komatsu S. Plant-derived smoke enhances plant growth through ornithine-synthesis pathway and ubiquitin-proteasome pathway in soybean. J Proteomics 2020; 221:103781. [PMID: 32294531 DOI: 10.1016/j.jprot.2020.103781] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/31/2020] [Accepted: 04/11/2020] [Indexed: 11/20/2022]
Abstract
To investigate the mechanism of promotive effect of plant-derived smoke on the soybean growth, a gel-free/label-free proteomics was performed. Smoke solutions were irrigated on soybean or supplied simultaneously with flooding stress. Morphological and physiological analyses were performed for the confirmation of proteomic result. Metabolomic change was investigated to correlate proteomic change with metabolism regulation. Under normal condition, the length of root including hypocotyl increased in soybean treated with 2000 ppm plant-derived smoke within 4 days, as well as nitric oxide content. Proteins related to protein synthesis especially arginine metabolism were altered; metabolites related to amino acid, carboxylic acids, and sugars were mostly altered. Integrated analysis of omics data indicated that plant-derived smoke regulated nitrogen‑carbon transformation through ornithine synthesis pathway and promoted soybean normal growth. Under flooding, the number of lateral roots increased with root tip degradation in soybean treated with smoke solutions. Proteins related to ubiquitin-proteasome pathway were altered and led to sacrifice-for-survival-mechanism-driven degradation of root tip in soybean, which enabled accumulation of metabolites and guaranteed lateral root development during soybean recovery after flooding. These findings suggest that plant-derived smoke improves early stage of growth in soybean with regulation of ornithine-synthesis pathway and ubiquitin-proteasome pathway. BIOLOGICAL SIGNIFICANCE: Plant-derived smoke plays a key role in crop growth, however, the understanding of soybean in response to smoke treatment remains premature. Therefore, gel-free/label-free proteomic analysis was used for comprehensive study on the dual effect of smoke to soybean under normal and flooding conditions. Under normal condition, plant-derived smoke regulated nitrogen‑carbon transformation through ornithine synthesis pathway and resulted in the increase of the length of root including hypocotyl in soybean within 4 days. Under flooding condition, plant-derived smoke induced inhibition of ubiquitin-proteasome pathway and led to sacrifice-for-survival-mechanism-driven degradation of root tip in soybean, which enabled accumulation of metabolites and promoted lateral root development during soybean recovery after flooding.
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Affiliation(s)
- Zhuoheng Zhong
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan; College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Tomoki Kobayashi
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Wei Zhu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Rongyi Zhao
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Toshihisa Ohno
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Shafiq Ur Rehman
- Department of Botany, Kohat University of Science and Technology, Kohat 26000, Pakistan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
| | - Jingkui Tian
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China.
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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25
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Ninomiya I, Kanazawa M, Uemura M, Onodera O. Elevated serum pentraxin 3 levels might predict the diagnosis of branch atheromatous disease at a very early stage. Eur J Neurol 2020; 27:1279-1284. [PMID: 32250504 DOI: 10.1111/ene.14249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 01/28/2020] [Accepted: 03/29/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND AND PURPOSE Branch atheromatous disease (BAD) is one of the stroke subtypes caused by occlusion at the origin of a deep penetrating artery of the brain and is associated with a microatheroma or a junctional plaque. Patients with BAD often develop progressive worsening of neurologic deficits, although these patients often present minor stroke with clinical characteristics of lacunar syndrome at the onset. Pentraxin 3 (PTX3) is known to be a key molecule involved in the pathogenesis of atherosclerosis. Although a high level of serum PTX3 is observed in patients with acute coronary syndrome, there are no reports on PTX3 levels in patients with BAD. This study aimed to investigate whether serum PTX3 levels can distinguish BAD from other stroke subtypes. METHODS We investigated 93 patients with ischaemic stroke. Serum PTX3 levels on admission were measured using enzyme-linked immunosorbent assay in patients with BAD and those with other stroke subtypes (each n ≥ 20). RESULTS The median PTX3 levels in patients with BAD (4840 pg/mL) were higher than those with other subtypes of stroke (3397 pg/mL in lacunar stroke, 1298 pg/mL in large-artery atherosclerosis, 1470 pg/mL in cardioaortic embolism and 1006 pg/mL in control) (all P < 0.01). CONCLUSION Our results suggest that elevated serum PTX3 levels might predict the diagnosis of BAD at a very early stage.
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Affiliation(s)
- I Ninomiya
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - M Kanazawa
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - M Uemura
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
| | - O Onodera
- Department of Neurology, Brain Research Institute, Niigata University, Niigata, Japan
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26
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Rahman A, Kawamura Y, Maeshima M, Rahman A, Uemura M. Plasma Membrane Aquaporin Members PIPs Act in Concert to Regulate Cold Acclimation and Freezing Tolerance Responses in Arabidopsis thaliana. Plant Cell Physiol 2020; 61:787-802. [PMID: 31999343 DOI: 10.1093/pcp/pcaa005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/14/2020] [Indexed: 06/10/2023]
Abstract
Aquaporins play a major role in plant water uptake at both optimal and environmentally stressed conditions. However, the functional specificity of aquaporins under cold remains obscure. To get a better insight to the role of aquaporins in cold acclimation and freezing tolerance, we took an integrated approach of physiology, transcript profiling and cell biology in Arabidopsis thaliana. Cold acclimation resulted in specific upregulation of PIP1;4 and PIP2;5 aquaporin (plasma membrane intrinsic proteins) expression, and immunoblotting analysis confirmed the increase in amount of PIP2;5 protein and total amount of PIPs during cold acclimation, suggesting that PIP2;5 plays a major role in tackling the cold milieu. Although single mutants of pip1;4 and pip2;5 or their double mutant showed no phenotypic changes in freezing tolerance, they were more sensitive in root elongation and cell survival response under freezing stress conditions compared with the wild type. Consistently, a single mutation in either PIP1;4 or PIP2;5 altered the expression of a number of aquaporins both at the transcriptional and translational levels. Collectively, our results suggest that aquaporin members including PIP1;4 and PIP2;5 function in concert to regulate cold acclimation and freezing tolerance responses.
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Affiliation(s)
- Arifa Rahman
- The United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
| | - Yukio Kawamura
- The United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
- Department of Plant Bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
| | - Masayoshi Maeshima
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Abidur Rahman
- The United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
- Department of Plant Bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
- Agri-Innovation Center, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
| | - Matsuo Uemura
- The United Graduate School of Agricultural Sciences, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
- Department of Plant Bioscience, Faculty of Agriculture, Iwate University, Ueda 3-18-8, Morioka, 020-8550 Japan
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27
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Hiraki H, Watanabe M, Uemura M, Kawamura Y. Season specificity in the cold-induced calcium signal and the volatile chemicals in the atmosphere. Physiol Plant 2020; 168:803-818. [PMID: 31390065 DOI: 10.1111/ppl.13019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/12/2019] [Accepted: 08/02/2019] [Indexed: 06/10/2023]
Abstract
Cold-induced Ca2+ signals in plants are widely accepted to be involved in cold acclimation. Surprisingly, despite using Arabidopsis plants grown in a growth chamber, we observed a clear seasonal change in cold-induced Ca2+ signals only in roots. Ca2+ signals were captured using Arabidopsis expressing Yellow Cameleon 3.60. In winter, two Ca2+ signal peaks were observed during a cooling treatment from 20 to 0°C, but in summer only one small peak was observed under the same cooling condition. In the spring and autumn seasons, an intermediate type of Ca2+ signal, which had a delayed first peak and smaller second peaks compared with the those of the winter type, was observed. Volatile chemicals and/or particles in the air from the outside may affect plants in the growth chamber. This idea is supported by the fact that incubation of plants with activated carbon changed the intermediate-type Ca2+ signal to the summer-type. The seasonality was also observed in the freezing tolerance of plants cold-acclimated in a low-temperature chamber. The solar radiation intensity was weakly correlated, not only with the seasonal characteristics of the Ca2+ signal but also with freezing tolerance. It has been reported that the ethylene concentration in the atmosphere seasonally changes depending on the solar radiation intensity. Ethylene gas and 1-aminocyclopropane-1-carboxylic acid treatment affected the Ca2+ signals, the shape of which became a shape close to, but not the same as, the winter type from the other types, indicating that ethylene may be one of several factors influencing the cold-induced Ca2+ signal.
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Affiliation(s)
- Hayato Hiraki
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate, 020-8550, Japan
| | - Manabu Watanabe
- Field Science Center, Faculty of Agriculture, Iwate University, Iwate, 020-0611, Japan
| | - Matsuo Uemura
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate, 020-8550, Japan
- Department of Plant Bioscience, Iwate University, Iwate, 020-8550, Japan
| | - Yukio Kawamura
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate, 020-8550, Japan
- Department of Plant Bioscience, Iwate University, Iwate, 020-8550, Japan
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Koide S, Yoneyama A, Orikasa T, Uemura M. Assessing the supercooling of fresh-cut onions at −5°C using electrical impedance analysis. Food Quality and Safety 2020. [DOI: 10.1093/fqsafe/fyz044] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We supercooled fresh-cut onion at −5°C for 12 h. After supercooling, the electric impedance properties of the samples were evaluated by electrical impedance spectroscopy over the frequency range of 42 Hz − 5 MHz. The time-temperature profiles of samples indicated that the freezing point and supercooling point were −2.3°C ± 0.7°C and −6.9°C ± 1.0°C, respectively. The results indicated that 34 of the 36 supercooled samples exhibited a definite circular arc in the Cole-Cole plot, which suggested that the cell membrane remained intact during supercooling. In the other two samples which did not exhibit a definite circular arc, the cell membrane had sustained serious damage during supercooling. Furthermore, there was large difference in drip loss percentage between supercooled samples exhibited a definite circular arc in the Cole-Cole plot and samples not exhibiting a definite circular arc. Our results suggest that fresh-cut onions can be supercooled at −5°C.
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Affiliation(s)
- Shoji Koide
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Ami Yoneyama
- Faculty of Agriculture, Iwate University, Morioka, Japan
| | | | - Matsuo Uemura
- Faculty of Agriculture, Iwate University, Morioka, Japan
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29
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Kozuka T, Sawada Y, Imai H, Kanai M, Hirai MY, Mano S, Uemura M, Nishimura M, Kusaba M, Nagatani A. Regulation of Sugar and Storage Oil Metabolism by Phytochrome during De-etiolation. Plant Physiol 2020; 182:1114-1129. [PMID: 31748417 PMCID: PMC6997681 DOI: 10.1104/pp.19.00535] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/02/2019] [Indexed: 05/02/2023]
Abstract
Exposure of dark-grown (etiolated) seedlings to light induces the heterotrophic-to-photoautotrophic transition (de-etiolation) processes, including the formation of photosynthetic machinery in the chloroplast and cotyledon expansion. Phytochrome is a red (R)/far-red (FR) light photoreceptor that is involved in the various aspects of de-etiolation. However, how phytochrome regulates metabolic dynamics in response to light stimulus has remained largely unknown. In this study, to elucidate the involvement of phytochrome in the metabolic response during de-etiolation, we performed widely targeted metabolomics in Arabidopsis (Arabidopsis thaliana) wild-type and phytochrome A and B double mutant seedlings de-etiolated under R or FR light. The results revealed that phytochrome had strong impacts on the primary and secondary metabolism during the first 24 h of de-etiolation. Among those metabolites, sugar levels decreased during de-etiolation in a phytochrome-dependent manner. At the same time, phytochrome upregulated processes requiring sugars. Triacylglycerols are stored in the oil bodies as a source of sugars in Arabidopsis seedlings. Sugars are provided from triacylglycerols through fatty acid β-oxidation and the glyoxylate cycle in glyoxysomes. We examined if and how phytochrome regulates sugar production from oil bodies. Irradiation of the etiolated seedlings with R and FR light dramatically accelerated oil body mobilization in a phytochrome-dependent manner. Glyoxylate cycle-deficient mutants not only failed to mobilize oil bodies but also failed to develop thylakoid membranes and expand cotyledon cells upon exposure to light. Hence, phytochrome plays a key role in the regulation of metabolism during de-etiolation.
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Affiliation(s)
- Toshiaki Kozuka
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Hiroyuki Imai
- United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Masatake Kanai
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Mano
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Science, Iwate University, Morioka, Iwate 020-8550, Japan
| | - Mikio Nishimura
- Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Makoto Kusaba
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526 Japan
| | - Akira Nagatani
- Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Abstract
Shotgun proteomics allows for the comprehensive analysis of proteins extracted from plant cells, subcellular organelles, and membranes. Previously, two-dimensional gel electrophoresis-based proteomics was used for mass spectrometric analysis of plasma membrane proteins. However, this method is not fully applicable for highly hydrophobic proteins with multiple transmembrane domains. In order to solve this problem, we here describe a shotgun proteomics method using nano-LC-MS/MS for proteins in the plasma membrane and plasma membrane microdomain fractions. The results obtained are easily applicable to label-free protein semiquantification.
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Affiliation(s)
- Daisuke Takahashi
- Central Infrastructure Group: Genomics and Transcript Profiling, Max-Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Bin Li
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Takato Nakayama
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yukio Kawamura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan.
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka, Japan.
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31
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Miyoshi N, Fujino S, Saso K, Sasaki M, Ogino T, Takahashi H, Uemura M, Chu M, Mizushima T, Mori M, Doki Y. Patient-derived tumour model by new culture method leading to the precision medicine. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz421.021] [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: 11/13/2022] Open
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32
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Uemura M, Tomita Y, Miyake H, Hatakeyama S, Kanayama HO, Numakura K, Takagi T, Kato T, Eto M, Obara W, Uemura H, Motzer R, Fujii Y, Kamei Y, Oya M. Randomized phase III trial of avelumab + axitinib vs sunitinib as first-line treatment for advanced renal cell carcinoma: JAVELIN renal 101 Japanese subgroup analysis. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz249.052] [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: 11/13/2022] Open
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Affiliation(s)
| | - Rei Ohsuga
- Faculty of Agriculture, Iwate University
| | - Takahiro Orikasa
- Faculty of Agriculture, Iwate University
- Agri-Innovation Center, Iwate University
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Hiraki H, Uemura M, Kawamura Y. Calcium Signaling-Linked CBF/DREB1 Gene Expression was Induced Depending on the Temperature Fluctuation in the Field: Views from the Natural Condition of Cold Acclimation. Plant Cell Physiol 2019; 60:303-317. [PMID: 30380128 DOI: 10.1093/pcp/pcy210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/11/2018] [Accepted: 10/25/2018] [Indexed: 06/08/2023]
Abstract
Environmental adaptability is essential for plant survival. Though it is well known that a simple cooling or cold shock leads to Ca2+ signals, direct evidence has not been provided that plants use Ca2+ signals as a second messenger in the cold acclimation (CA) process in the field. By developing a technique to analyze Ca2+ signals using confocal cryomicroscopy, we investigated Ca2+ signals under several temperature conditions by combining the start temperature, cooling rate and cooling time duration. In both root and leaf cells, Ca2+ signals rapidly disappeared after cooling stopped, and thereafter under a constant low temperature no Ca2+ signal was observed. Interestingly, under the cooling regime from 2�C to -2�C, non-acclimated plants grown at 23�C hardly showed Ca2+ signals, but cold-acclimated plants at 2�C were able to form Ca2+ signals in root cells. These findings suggest that plants sense temperature decreases with Ca2+ signals while adjusting the temperature sensitivity to their own temperature environment. Furthermore, if the temperature is constant, no Ca2+ signal is induced even during CA. Then, we also focused on the CA under field conditions, rich in temperature fluctuations. In CA under field conditions, the expression patterns of CBF/DREB1 genes were distinctly different from those in artificial CA. Pharmacological studies with Ca2+ channel blockers showed that the Ca2+-induced expression of CBF/DREB1 genes was closely correlated with the amplitude of temperature fluctuation, suggesting that Ca2+ signals regulate CBF/DREB1 gene expression during CA under natural conditions.
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Affiliation(s)
- Hayato Hiraki
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
| | - Matsuo Uemura
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yukio Kawamura
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Japan
- Department of Plant-bioscience, Faculty of Agriculture, Iwate University, Morioka, Japan
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35
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Tanaka D, Niino T, Fujikawa S, Uemura M. Freeze-substitution transmission electron microscopy of gentian shoot tips cryopreserved at ultra low temperatures. Plant Biotechnol (Tokyo) 2018; 35:335-340. [PMID: 31892820 PMCID: PMC6905220 DOI: 10.5511/plantbiotechnology.18.0718a] [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] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/18/2018] [Indexed: 06/10/2023]
Abstract
Transmission electron microscopy (TEM) combined with freeze substitution was employed to examine the ultrastructure of cells of gentian shoot tips cooled to the ultra-low temperature of slush nitrogen and liquid nitrogen. When shoot tips were cooled in ultra-low temperature without plant vitrification solution 2 (PVS2) treatment, massive ice formation was observed throughout the cells, indicating that severe injury occurred during cooling. In contrast, when shoot tips were treated with PVS2 and subsequently cooled to ultra- low temperatures, no ice crystals were observed in the cells. In addition, the cells of PVS2-treated shoot tips exhibited considerable plasmolysis and formation of small vesicles in cytoplasm. These results clearly demonstrate that the PVS2 treatment is essential for preventing damage caused by ice formation and for successful cryopreservation of plant shoot tips.
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Affiliation(s)
- Daisuke Tanaka
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Takao Niino
- Gene Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | | | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan
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36
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Miki Y, Takahashi D, Kawamura Y, Uemura M. Temporal proteomics of Arabidopsis plasma membrane during cold- and de-acclimation. J Proteomics 2018; 197:71-81. [PMID: 30447334 DOI: 10.1016/j.jprot.2018.11.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 07/23/2018] [Revised: 10/27/2018] [Accepted: 11/09/2018] [Indexed: 01/19/2023]
Abstract
Freezing stress is one of the most important limiting factors of plant survival. Plants have developed a freezing adaptation mechanism upon sensing low temperatures (cold acclimation). Compositional changes in the plasma membrane, one of the initial sites of freezing injury, is prerequisite of achieving cold acclimation and have been investigated in several plant species. Conversely, the cold dehardening process at elevated temperatures (de-acclimation) has not yet been fully characterized and few studies have addressed the importance of the plasma membrane in the de-acclimation process. In the present study, we conducted shotgun proteomics with label-free semiquantification on plasma membrane fractions of Arabidopsis leaves during cold acclimation and de-acclimation. We consequently obtained a list of 873 proteins with significantly changed proteins in response to the two processes. Although the cold-acclimation-responsive proteins were globally returned to non-acclimated levels by de-acclimation, several representative cold-acclimation-responsive proteins tended to remain at higher abundance during de-acclimation process. Taken together, our results suggest plants deharden right after cold acclimation to restart growth and development but some cold-acclimation-induced changes of the plasma membrane may be maintained under de-acclimation to cope with the threat of sudden freezing during de-acclimation process. SIGNIFICANCE: Plant freezing tolerance can be enhanced by low temperature treatment (cold acclimation), while elevated temperatures right after cold acclimation can result in the dehardening of freezing tolerance (de-acclimation). However, the de-acclimation process, particularly its relevance to the plasma membrane as the primary site of freezing injury, has not been elucidated. In the present study, a comprehensive proteomic analysis of the plasma membrane during cold acclimation and de-acclimation was carried out as a first step to elucidating how plants respond to rising temperatures. Cold acclimation induced a number of proteomic changes as reported in previous studies, but most proteins, in general, immediately returned to NA levels during de-acclimation treatment for two days. However, the abundances of stress-related proteins (e.g. LTI29, COR78 and TIL) decreased slower than other functional proteins during de-acclimation. Therefore, plants harden during cold acclimation by aborting growth and development and accumulating stress-responsive proteins but seem to deharden quickly under subsequent elevated temperature to resume these processes while guarding against the threat of sudden temperature drops.
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Affiliation(s)
- Yushi Miki
- Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam D-14476, Germany
| | - Yukio Kawamura
- Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Matsuo Uemura
- Department of Plant-bioscience, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan; United Graduate School of Agricultural Sciences, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
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37
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Motzer R, Penkov K, Haanen J, Rini B, Albiges L, Campbell M, Kollmannsberger C, Negrier S, Uemura M, Lee J, Gurney H, Berger R, Schmidinger M, Larkin J, Atkins M, Wang J, Robbins P, Chudnovsky A, Di Pietro A, Choueiri T. JAVELIN renal 101: A randomized, phase III study of avelumab + axitinib vs sunitinib as first-line treatment of advanced renal cell carcinoma (aRCC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy424.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ceballos-Laita L, Gutierrez-Carbonell E, Imai H, Abadía A, Uemura M, Abadía J, López-Millán AF. Effects of manganese toxicity on the protein profile of tomato ( Solanum lycopersicum ) roots as revealed by two complementary proteomic approaches, two-dimensional electrophoresis and shotgun analysis. J Proteomics 2018; 185:51-63. [DOI: 10.1016/j.jprot.2018.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/11/2018] [Accepted: 06/19/2018] [Indexed: 12/31/2022]
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Bando H, Tsukada Y, Inamori K, Fukuoka S, Sasaki T, Nishizawa Y, Wakabayashi M, Kojima M, Togashi Y, Yuki S, Komatsu Y, Homma S, Hatanaka Y, Matsuno Y, Uemura M, Kato T, Sato A, Nishikawa H, Ito M, Yoshino T. VOLTAGE: Multicenter phase Ib/II study of nivolumab monotherapy and subsequent radical surgery following preoperative chemoradiotherapy (CRT) with capecitabine in patients with locally advanced rectal cancer (LARC). Ann Oncol 2018. [DOI: 10.1093/annonc/mdy151.227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Willick IR, Takahashi D, Fowler DB, Uemura M, Tanino KK. Tissue-specific changes in apoplastic proteins and cell wall structure during cold acclimation of winter wheat crowns. J Exp Bot 2018; 69:1221-1234. [PMID: 29373702 PMCID: PMC6019019 DOI: 10.1093/jxb/erx450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 05/22/2017] [Accepted: 11/29/2017] [Indexed: 05/04/2023]
Abstract
The wheat (Triticum aestivum L.) crown is the critical organ of low temperature stress survival over winter. In cold-acclimated crowns, ice formation in the apoplast causes severe tissue disruption as it grows at the expense of intracellular water. While previous crown studies have shown the vascular transition zone (VTZ) to have a higher freezing sensitivity than the shoot apical meristem (SAM), the mechanism behind the differential freezing response is not fully understood. Cooling cold-acclimated crowns to -10 °C resulted in an absence of VTZ tetrazolium chloride staining, whereas the temperatures at which 50% of the SAM stained positive and 50% of plants recovered (LT50) were similar after cold acclimation for 21 (-16 °C) and 42 d (-20 °C) at 4 °C. Proteomic analysis of the apoplastic fluids identified dehydrins, vernalization-responsive proteins, and cold shock proteins preferentially accumulated in the SAM. In contrast, modifications to the VTZ centered on increases in pathogenesis-related proteins, anti-freeze proteins, and sugar hydrolyzing enzymes. Fourier transform infrared spectroscopy focal plane array analysis identified the biochemical modification of the cell wall to enhance methyl-esterified cross-linking of glucuronoarabinoxylans in the VTZ. These findings indicate that the SAM and VTZ express two distinct tissue-specific apoplastic responses during cold acclimation.
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Affiliation(s)
- Ian R Willick
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Department of Plant-biosciences and Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - D Brian Fowler
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan
- Department of Plant-biosciences and Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Karen K Tanino
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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Soda T, Miyagawa Y, Ueda N, Takezawa K, Okuda H, Fukuhara S, Fujita K, Kiuchi H, Uemura M, Okamoto Y, Tsujimura A, Tanaka H, Nonomura N. Systematic characterization of human testis-specific actin capping protein β3 as a possible biomarker for male infertility. Hum Reprod 2018; 32:514-522. [PMID: 28104696 DOI: 10.1093/humrep/dew353] [Citation(s) in RCA: 6] [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: 08/27/2016] [Accepted: 12/16/2016] [Indexed: 11/13/2022] Open
Abstract
STUDY QUESTION Is actin capping protein (CP) β3 involved in human spermatogenesis and male infertility? SUMMARY ANSWER Human CPβ3 (hCPβ3) is expressed in testis, changes its localization dynamically during spermatogenesis, and has some association with male infertility. WHAT IS KNOWN ALREADY The testis-specific α subunit of CP (CPα3) was previously identified in human, and mutations in the cpα3 gene in mouse were shown to induce malformation of the sperm head and male infertility. However, CPβ3, which is considered to be a heterodimeric counterpart of CPα3, has been neither characterized in human nor reported in association with male infertility. STUDY DESIGN, SIZE, DURATION To confirm the existence of CPβ3 in human testis, fresh semen samples from proven fertile men were analyzed. To investigate protein expression during spermatogenesis, cryopreserved testis obtained from men with obstructive azoospermia were examined by immunofluorescent analysis. To assess the association of CP with male infertility, we compared protein expression of human CPα3 (hCPα3) and hCPβ3 using immunofluorescent analysis of cryopreserved sperm between men with normozoospermia (volunteers: Normo group, n = 20) and infertile men with oligozoospermia and/or asthenozoospermia (O + A group, n = 21). PARTICIPANTS/MATERIALS, SETTING, METHODS The tissue-specific expression of hCPβ3 was investigated by RT-PCR and Western blot analysis. To investigate whether hCPα3 and hCPβ3 form a heterodimer, a tandem expression vector containing hcpα3 tagged with monomeric red fluorescent protein 1 and hcpβ3 tagged with enhanced green fluorescent protein in a single plasmid was constructed and analyzed by co-immunoprecipitation (Co-IP) assay. The protein expression profiles of hCPα3 and hCPβ3 during spermatogenesis were examined by immunohistochemical analysis using human spermatogenic cells. The protein expressions of hCPα3 and hCPβ3 in sperm were compared between the Normo and O + A groups by immunohistochemical analysis. MAIN RESULTS AND THE ROLE OF CHANCE RT-PCR showed that mRNA of hcpβ3 was expressed exclusively in testis. Western blot analysis detected hCPβ3 with anti-bovine CPβ3 antibody. Co-IP assay with recombinant protein showed that hCPα3 and hCPβ3 form a protein complex. At each step during spermatogenesis, the cellular localization of hCPβ3 changed dynamically. In spermatogonia, hCPβ3 showed a slight signal in cytoplasm. hCPβ3 expression was conspicuous mainly from spermatocytes, and hCPβ3 localization dynamically migrated from cytoplasm to the acrosomal cap and acrosome. In mature spermatozoa, hCPβ3 accumulated in the postacrosomal region and less so at the midpiece of the tail. Double-staining analysis revealed that hCPα3 localization was identical to hCPβ3 at every step in the spermatogenic cells. Most spermatozoa from the Normo group were stained homogenously by both hCPα3 and hCPβ3. In contrast, significantly more spermatozoa in the O + A versus Normo group showed heterogeneous or lack of staining for either hCPα3 or hCPβ3 (abnormal staining) (P < 0.001). The percentage of abnormal staining was higher in the O + A group (52.4 ± 3.0%) than in the Normo group (31.2 ± 2.5%). Even by confining the observations to morphologically normal spermatozoa selected in accordance with David's criteria, the percentage of abnormal staining was still higher in the O + A group (39.9 ± 2.9%) versus the Normo group (22.5 ± 2.1%) (P < 0.001). hCPβ3 in conjunction with hCPα3 seemed to play an important role in spermatogenesis and may be associated with male infertility. LARGE SCALE DATA Not applicable. LIMITATIONS REASONS FOR CAUTION Owing to the difficulty of collecting fresh samples of human testis, we used cryopreserved samples from testicular sperm extraction. To examine the interaction of spermatogenic cells or localization in seminiferous tubules, fresh testis sample of healthy males are ideal. WIDER IMPLICATIONS OF THE FINDINGS The altered expression of hCPα3 and hCPβ3 may not only be a cause of male infertility but also a prognostic factor for the results of ART. They may be useful biomarkers to determine the fertilization ability of human sperm in ART. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by a Grant-in-Aid for Young Scientists (B) from the Japan Society for the Promotion of Science (JP16K20133). The authors declare no competing interests.
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Affiliation(s)
- T Soda
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Y Miyagawa
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - N Ueda
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - K Takezawa
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - H Okuda
- Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - S Fukuhara
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - K Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - H Kiuchi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - M Uemura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
| | - Y Okamoto
- Okamoto Clinic, Osaka 558-0004, Japan
| | - A Tsujimura
- Department of Urology, Juntendo University Urayasu Hospital, Urayasu 279-0021, Japan
| | - H Tanaka
- Molecular Biology laboratory, Faculty of Pharmaceutical Sciences, Nagasaki International University, Sasebo, Nagasaki 859-3298, Japan
| | - N Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Osaka 565-0871, Japan
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Ceballos-Laita L, Gutierrez-Carbonell E, Takahashi D, Abadía A, Uemura M, Abadía J, López-Millán AF. Data on xylem sap proteins from Mn- and Fe-deficient tomato plants obtained using shotgun proteomics. Data Brief 2018; 17:512-516. [PMID: 29876421 PMCID: PMC5988290 DOI: 10.1016/j.dib.2018.01.034] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/23/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023] Open
Abstract
This article contains consolidated proteomic data obtained from xylem sap collected from tomato plants grown in Fe- and Mn-sufficient control, as well as Fe-deficient and Mn-deficient conditions. Data presented here cover proteins identified and quantified by shotgun proteomics and Progenesis LC-MS analyses: proteins identified with at least two peptides and showing changes statistically significant (ANOVA; p ≤ 0.05) and above a biologically relevant selected threshold (fold ≥ 2) between treatments are listed. The comparison between Fe-deficient, Mn-deficient and control xylem sap samples using a multivariate statistical data analysis (Principal Component Analysis, PCA) is also included. Data included in this article are discussed in depth in the research article entitled “Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses” [1]. This dataset is made available to support the cited study as well to extend analyses at a later stage.
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Affiliation(s)
- Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Elain Gutierrez-Carbonell
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan.,Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Anunciación Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Matsuo Uemura
- Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Ana Flor López-Millán
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates St., Houston, TX 77030, USA
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Ibort P, Imai H, Uemura M, Aroca R. Proteomic analysis reveals that tomato interaction with plant growth promoting bacteria is highly determined by ethylene perception. J Plant Physiol 2018; 220:43-59. [PMID: 29145071 DOI: 10.1016/j.jplph.2017.10.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 09/12/2017] [Revised: 10/27/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
Feeding an increasing global population as well as reducing environmental impact of crops is the challenge for the sustainable intensification of agriculture. Plant-growth-promoting bacteria (PGPB) management could represent a suitable method but elucidation of their action mechanisms is essential for a proper and effective utilization. Furthermore, ethylene is involved in growth and response to environmental stimuli but little is known about the implication of ethylene perception in PGPB activity. The ethylene-insensitive tomato never ripe and its isogenic wild-type cv. Pearson lines inoculated with Bacillus megaterium or Enterobacter sp. C7 strains were grown until mature stage to analyze growth promotion, and bacterial inoculation effects on root proteomic profiles. Enterobacter C7 promoted growth in both plant genotypes, meanwhile Bacillus megaterium PGPB activity was only noticed in wt plants. Moreover, PGPB inoculation affected proteomic profile in a strain- and genotype-dependent manner modifying levels of stress-related and interaction proteins, and showing bacterial inoculation effects on antioxidant content and phosphorus acquisition capacity. Ethylene perception is essential for properly recognition of Bacillus megaterium and growth promotion mediated in part by increased levels of reduced glutathione. In contrast, Enterobacter C7 inoculation improves phosphorus nutrition keeping plants on growth independently of ethylene sensitivity.
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Affiliation(s)
- Pablo Ibort
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain.
| | - Hiroyuki Imai
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan.
| | - Ricardo Aroca
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín (EEZ-CSIC), Profesor Albareda 1, 18008 Granada, Spain.
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Abstract
Cryopreservation encompasses several interconnect disciplines including physiology and cryophysics. This chapter reviews the current techniques for cryopreservation of plant genetic resources (PGRs). Vitrification is an effective ice crystal avoidance mechanism for hydrated cells and tissues. With any cryopreservation method, whole or partial parts of specimens which are sufficiently dehydrated can be vitrified by rapid cooling in liquid nitrogen (LN). Techniques discussed are the vitrification protocol, encapsulation-vitrification protocol, droplet vitrification protocol (DV), vitrification protocol using cryo-plates (V cryo-plate), and air dehydration protocol using cryo-plates (D cryo-plate). In these DV, V, and D cryo-plate protocols, specimens to be cryopreserved are immersed directly into LN on aluminum foil strips or cryo-plates; removal from LN to rewarming solution results in a high level of plant regrowth with ultrarapid cooling and warming. The protocols were applied to a wide array of plant species including wild and multi-ploid species, although fine tuning of the protocols was required for successful application to specific plant species and lines. These three protocols efficiently complement each other and appear highly promising to facilitate large-scale cryobanking of PGRs in genebanks. Cryo-scanning electron microscopy makes it possible to examine the cellular and water behavior in plant tissues when immersed in LN. It has been verified that tissues cryopreserved by the process of vitrification and the cryo-plate protocols are cryopreservation methods for reliable long-term preservation of PGRs.
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Affiliation(s)
- Daisuke Tanaka
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Takao Niino
- Gene Research Center, University of Tsukuba, Tsukuba, Japan
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences and Department of Plant-biosciences, Faculty of Agriculture, Iwate University, Morioka, Japan
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Abstract
Freezing stress is accompanied by a state change from water to ice and has multiple facets causing dehydration; consequently, hyperosmotic and mechanical stresses coupled with unfavorable chilling stress act in a parallel way. Freezing tolerance varies widely among plant species, and, for example, most temperate plants can overcome deleterious effects caused by freezing temperatures in winter. Destabilization and dysfunction of the plasma membrane are tightly linked to freezing injury of plant cells. Plant freezing tolerance increases upon exposure to nonfreezing low temperatures (cold acclimation). Recent studies have unveiled pleiotropic responses of plasma membrane lipids and proteins to cold acclimation. In addition, advanced techniques have given new insights into plasma membrane structural non-homogeneity, namely, microdomains. This chapter describes physiological implications of plasma membrane responses enhancing freezing tolerance during cold acclimation, with a focus on microdomains.
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Affiliation(s)
- Daisuke Takahashi
- Central Infrastructure Group Genomics and Transcript Profiling, Max-Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences and Department of Plant-biosciences, Faculty of Agriculture, Iwate University, Morioka, Japan
| | - Yukio Kawamura
- Cryobiofrontier Research Center and Department of Plant-biosciences, and United Graduate School of Agricultural Sciences, Iwate University, Morioka, Iwate, Japan.
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Okuda S, Uemura N, Uemura M, Yamakado H, Takahashi R. A novel mice model for Parkinson’s disease: Fibril-inoculated mutant α-Synuclein BAC Transgenic Mice. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.2031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Uemura M, Ihara M, Maki T, Nakagomi T, Kaji S, Uemura K, Matsuyama T, Kinoshita A, Takahashi R. Pericyte-derived bone morphogenetic protein 4 underlies white matter damage after chronic hypoperfusion. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Diab A, Haymaker C, Uemura M, Murthy R, James M, Geib J, Cornfeld M, Swann S, Yee C, Wargo J, Amaria R, Patel S, Tawbi H, Glitza I, Woodman S, Hwu WJ, Davies M, Overwijk W, Bernatchez C, Hwu P. A Phase 1/2 trial of intratumoral (i.t.) IMO-2125 (IMO) in combination with checkpoint inhibitors (CPI) in PD-(L)1-refractory melanoma. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx376.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ceballos-Laita L, Gutierrez-Carbonell E, Takahashi D, Abadía A, Uemura M, Abadía J, López-Millán AF. Effects of Fe and Mn deficiencies on the protein profiles of tomato (Solanum lycopersicum) xylem sap as revealed by shotgun analyses. J Proteomics 2017; 170:117-129. [PMID: 28847647 DOI: 10.1016/j.jprot.2017.08.018] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/19/2017] [Accepted: 08/24/2017] [Indexed: 12/20/2022]
Abstract
The aim of this work was to study the effects of Fe and Mn deficiencies on the xylem sap proteome of tomato using a shotgun proteomic approach, with the final goal of elucidating plant response mechanisms to these stresses. This approach yielded 643 proteins reliably identified and quantified with 70% of them predicted as secretory. Iron and Mn deficiencies caused statistically significant and biologically relevant abundance changes in 119 and 118 xylem sap proteins, respectively. In both deficiencies, metabolic pathways most affected were protein metabolism, stress/oxidoreductases and cell wall modifications. First, results suggest that Fe deficiency elicited more stress responses than Mn deficiency, based on the changes in oxidative and proteolytic enzymes. Second, both nutrient deficiencies affect the secondary cell wall metabolism, with changes in Fe deficiency occurring via peroxidase activity, and in Mn deficiency involving peroxidase, Cu-oxidase and fasciclin-like arabinogalactan proteins. Third, the primary cell wall metabolism was affected by both nutrient deficiencies, with changes following opposite directions as judged from the abundances of several glycoside-hydrolases with endo-glycolytic activities and pectin esterases. Fourth, signaling pathways via xylem involving CLE and/or lipids as well as changes in phosphorylation and N-glycosylation also play a role in the responses to these stresses. Biological significance In spite of being essential for the delivery of nutrients to the shoots, our knowledge of xylem responses to nutrient deficiencies is very limited. The present work applies a shotgun proteomic approach to unravel the effects of Fe and Mn deficiencies on the xylem sap proteome. Overall, Fe deficiency seems to elicit more stress in the xylem sap proteome than Mn deficiency, based on the changes measured in proteolytic and oxido-reductase proteins, whereas both nutrients exert modifications in the composition of the primary and secondary cell wall. Cell wall modifications could affect the mechanical and permeability properties of the xylem sap vessels, and therefore ultimately affect solute transport and distribution to the leaves. Results also suggest that signaling cascades involving lipid and peptides might play a role in nutrient stress signaling and pinpoint interesting candidates for future studies. Finally, both nutrient deficiencies seem to affect phosphorylation and glycosylation processes, again following an opposite pattern.
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Affiliation(s)
- Laura Ceballos-Laita
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Elain Gutierrez-Carbonell
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Daisuke Takahashi
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Anunciación Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Matsuo Uemura
- United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan; Cryobiofrontier Research Center, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
| | - Javier Abadía
- Plant Stress Physiology Group, Plant Nutrition Department, Aula Dei Experimental Station, CSIC, P.O. Box 13034, 50080 Zaragoza, Spain
| | - Ana Flor López-Millán
- USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates St., Houston, TX 77030, USA.
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Fujita K, Nakai Y, Kawashima A, Ujike T, Nagahara A, Nakajima T, Inoue T, Lee CM, Uemura M, Miyagawa Y, Kaneda Y, Nonomura N. Phase I/II clinical trial to assess safety and efficacy of intratumoral and subcutaneous injection of HVJ-E in castration-resistant prostate cancer patients. Cancer Gene Ther 2017; 24:277-281. [PMID: 28497777 PMCID: PMC5562845 DOI: 10.1038/cgt.2017.15] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/04/2017] [Indexed: 12/27/2022]
Abstract
Inactivated Sendai virus particles (hemagglutinating virus of Japan envelope (HVJ-E)) have a novel antitumor effect: HVJ-E fused to prostate cancer cells via cell surface receptor causes apoptosis of prostate cancer cells in vitro and in vivo. HVJ-E also induces antitumor immunity by activating natural killer (NK) cells and cytotoxic T cells and suppressing regulatory T cells in vivo. We conducted an open-label, single-arm, phase I/II clinical trial in patients with castration-resistant prostate cancer (CRPC) to determine the safety and efficacy of intratumoral and subcutaneous injection of HVJ-E. Patients with CRPC who were docetaxel-resistant or could not receive docetaxel treatment were eligible. HVJ-E was injected directly into the prostate on day 1 and subcutaneously on days 5, 8 and 12 in two 28-day treatment cycles using a 3+3 dose-escalation design. The primary end points were to evaluate safety and tolerability of HVJ-E. The secondary end points were to analyze tumor immunity and antitumor effect. The study is registered at UMIN Clinical Trials Registry, number UMIN000006142. Seven patients were enrolled, and six patients received HVJ-E. Grade 2 or 3 adverse events (Common Terminology Criteria for Adverse Events Ver. 4.0) were urinary retention and lymphopenia from which the patients recovered spontaneously. No Grade 4 adverse events were observed. Radiographically, three patients had stable disease in the low-dose group, and one patient had stable disease and two had progressive disease in the high-dose group. The prostate-specific antigen (PSA) declined from 14 to 1.9 ng ml-1 in one patient in the low-dose group after two cycles of HVJ-E treatment, and the PSA response rate was 16.6%. NK cell activity was elevated from day 12 to day 28 after HVJ-E administration, whereas serum interleukin-6, interferon (IFN)-α, IFN-β and IFN-γ levels were not affected by HVJ-E treatment. Intratumoral and subcutaneous injections of HVJ-E are feasible and PSA response was observed in a subgroup of CRPC patients.
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Affiliation(s)
- K Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Nakai
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - A Kawashima
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - T Ujike
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - A Nagahara
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | | | - T Inoue
- Department of Medical Innovation, Osaka University Graduate School of Medicine, Suita, Japan
| | - C M Lee
- Department of Medical Innovation, Osaka University Graduate School of Medicine, Suita, Japan
| | - M Uemura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Miyagawa
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Kaneda
- Division of Gene Therapy Science, Osaka University Graduate School of Medicine, Suita, Japan
| | - N Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
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