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Liu Y, Niu J, Ye F, Solberg T, Lu B, Wang C, Nowacki M, Gao S. Dynamic DNA N 6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus. Genome Res 2024; 34:256-271. [PMID: 38471739 PMCID: PMC10984389 DOI: 10.1101/gr.278796.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
The formation of resting cysts commonly found in unicellular eukaryotes is a complex and highly regulated survival strategy against environmental stress that involves drastic physiological and biochemical changes. Although most studies have focused on the morphology and structure of cysts, little is known about the molecular mechanisms that control this process. Recent studies indicate that DNA N 6-adenine methylation (6mA) could be dynamically changing in response to external stimuli; however, its potential role in the regulation of cyst formation remains unknown. We used the ciliate Pseudocohnilembus persalinus, which can be easily induced to form cysts to investigate the dynamic pattern of 6mA in trophonts and cysts. Single-molecule real-time (SMRT) sequencing reveals high levels of 6mA in trophonts that decrease in cysts, along with a conversion of symmetric 6mA to asymmetric 6mA. Further analysis shows that 6mA, a mark of active transcription, is involved in altering the expression of encystment-related genes through changes in 6mA levels and 6mA symmetric-to-asymmetric conversion. Most importantly, we show that reducing 6mA levels by knocking down the DNA 6mA methyltransferase PpAMT1 accelerates cyst formation. Taken together, we characterize the genome-wide 6mA landscape in P. persalinus and provide insights into the role of 6mA in gene regulation under environmental stress in eukaryotes. We propose that 6mA acts as a mark of active transcription to regulate the encystment process along with symmetric-to-asymmetric conversion, providing important information for understanding the molecular response to environmental cues from the perspective of 6mA modification.
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Affiliation(s)
- Yongqiang Liu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Junhua Niu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Fei Ye
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Therese Solberg
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
- Department of Molecular Biology, Keio University School of Medicine, 160-8582 Tokyo, Japan
- Human Biology Microbiome Quantum Research Center (WPI-Bio2Q), Keio University, 108-8345 Tokyo, Japan
| | - Borong Lu
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Chundi Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai 264209, China
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
| | - Shan Gao
- MOE Key Laboratory of Evolution and Marine Biodiversity and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Shimada Y, Hasegawa Y, Harada Y, Nakamura R, Matsuoka T, Arikawa M. Signaling in temperature-induced resting cyst formation in the ciliated protozoan Colpoda cucullus. Eur J Protistol 2021; 79:125800. [PMID: 34049128 DOI: 10.1016/j.ejop.2021.125800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022]
Abstract
The terrestrial ciliated protozoan Colpoda cucullus inhabits soil. When the habitat conditions become unfavorable, the vegetative cells of C. cucullus quickly transform into resting cysts. C. cucullus culture is established in our laboratory, and encystment is routinely induced by the addition of Ca2+ to overpopulated vegetative cells. However, an increase in Ca2+ concentration and overpopulation of vegetative cells do not always occur in natural. We investigated the effect of temperature and found that cyst formation was induced by a rapid increase of 5 °C within 2 min but not by a decrease. Moreover, an increase in intracellular Ca2+ concentrations is essential, but Ca2+ inflow does not necessarily occur during encystment. Ca2+ image analysis showed that Ca2+ is stored in vesicular structures and released into the cytoplasm within 60 s after temperature stimulation. Multiple signaling pathways are activated after the release of Ca2+ from vesicles, and cAMP is a candidate second messenger with a crucial role in the process of temperature-induced encystment. Further studies are needed to clarify the mechanism underlying the sensing of temperature and release of Ca2+ from vesicles.
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Affiliation(s)
- Yuto Shimada
- Graduate School of Integrated Arts and Sciences, Applied Science Program, Kochi University, Kochi, Japan
| | - Yuya Hasegawa
- Graduate School of Integrated Arts and Sciences, Applied Science Program, Kochi University, Kochi, Japan
| | - Yuya Harada
- Graduate School of Integrated Arts and Sciences, Applied Science Program, Kochi University, Kochi, Japan
| | - Rikiya Nakamura
- Graduate School of Integrated Arts and Sciences, Applied Science Program, Kochi University, Kochi, Japan
| | - Tatsuomi Matsuoka
- Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi, Japan
| | - Mikihiko Arikawa
- Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi, Japan.
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Matsuoka T. Early signaling pathways mediating dormant cyst formation in terrestrial unicellular eukaryote Colpoda. FEMS Microbiol Lett 2021; 368:6156630. [PMID: 33677557 DOI: 10.1093/femsle/fnab019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 02/24/2021] [Indexed: 12/23/2022] Open
Abstract
Dormant (resting) cyst formation (encystment) in unicellular eukaryotes is the process of a large-scale digestion of vegetative cell structures and reconstruction into the dormant form, which is performed by cell signaling pathways accompanied by up- or down-regulation of protein expression, and by posttranslational modification such as phosphorylation. In this review, the author describes the morphogenetic events during encystment of Colpoda and the early molecular events in the Ca2+/calmodulin-triggered signaling pathways for encystment, based mainly on our research results of the past 10 years; especially, the author discusses the role of c-AMP dependently phosphorylated proteins (ribosomal P0 protein, ribosomal S5 protein, Rieske iron-sulfur protein, actin and histone H4) and encystment-dependently upregulated (EF-1α-HSP60, actin-related protein) and downregulated proteins (ATP synthase β-chain). In addition, the roles of AMPK, a key molecule in the signaling pathways leading to Colpoda encystment, and differentially expressed genes and proteins during encystment of other ciliates are discussed.
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Affiliation(s)
- Tatsuomi Matsuoka
- Department of Biological Science, Faculty of Science and Technology, Kochi University, Akebono-cho 2-5-1, Kochi, Japan
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Sogame Y, Kojima K, Takeshita T, Kikuchi S, Shimada Y, Nakamura R, Arikawa M, Miyata S, Kinoshita E, Suizu F, Matsuoka T. Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics. ACTA PROTOZOOL 2021. [DOI: 10.4467/16890027ap.20.009.13264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Assays of protein contained in water-soluble fraction of encysting cells Colpoda cucullus Nag-1 by two-dimensional electrophoresis (2-D PAGE) and mass spectrometry (MS) revealed that the amount of β-tubulin abruptly increased in 2.5–10 h after encystment induction. Judging from the results that total α-tubulin content did not decrease much until 12 h after encystment induction, the result indicates that disassembly of microtubules may occur soon after encystment is induced. Therefore, we tried to visualize dynamics of microtubules. Immunofluorescence microscopy using anti-α-tubulin antibody indicated that disassembly of axonemal microtubules of cilia became within 1.5 h after encystment induction, and resorbed in 3 days. Although the cytoplasmic microtubules failed to be visualized clearly, encystmentdependent globulation of cells was promoted by taxol, an inhibitor of disassembly of microtubules. It is possible that a temporary formation of cytoplasmic microtubules may be involved in cell globulation.
The phosphorylation level of actin (43 kDa) became slightly elevated just after encystment induction. Lepidosomes, the sticky small globes surrounding encysting cells, were vividly stained with Acti-stain 555 phalloidin, suggesting that 43-kDa actin or its homologues may be contained in lepidosomes.
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Affiliation(s)
- Yoichiro Sogame
- National Institute of Technology Fukushima College, Iwaki, Fukushima Japan
| | - Katsuhiko Kojima
- Department of Microbiology and Immunology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Toshikazu Takeshita
- Department of Microbiology and Immunology, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano 390-8621, Japan
| | - Shiho Kikuchi
- Department of Biological Science, Faculty of Science, Kochi University, Kochi, Japan
| | - Yuto Shimada
- Department of Biological Science, Faculty of Science, Kochi University, Kochi, Japan
| | - Rikiya Nakamura
- Department of Biological Science, Faculty of Science, Kochi University, Kochi, Japan
| | - Mikihiko Arikawa
- Department of Biological Science, Faculty of Science, Kochi University, Kochi, Japan
| | - Seiji Miyata
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science, Graduate School of Biomedical Sciences, Hiroshima University, Kasumi 1-2-3, Hiroshima 734-8553, Japan
| | - Futoshi Suizu
- Division of Cancer Biology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tatsuomi Matsuoka
- Department of Biological Science, Faculty of Science, Kochi University, Kochi, Japan
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Novel insights into molecular mechanisms of Pseudourostyla cristata encystment using comparative transcriptomics. Sci Rep 2019; 9:19109. [PMID: 31836801 PMCID: PMC6911008 DOI: 10.1038/s41598-019-55608-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/20/2019] [Indexed: 12/17/2022] Open
Abstract
The encystment of many ciliates is an advanced survival strategy against adversity and the most important reason for ciliates existence worldwide. However, the molecular mechanism for the encystment of free-living ciliates is poorly understood. Here, we performed comparative transcriptomic analysis of dormant cysts and trophonts from Pseudourostyla cristata using transcriptomics, qRT-PCR and bioinformatic techniques. We identified 2565 differentially expressed unigenes between the dormant cysts and the trophonts. The total number of differentially expressed genes in GO database was 1752. The differential unigenes noted to the GO terms were 1993. These differential categories were mainly related to polyamine transport, pectin decomposition, cytoplasmic translation, ribosome, respiratory chain, ribosome structure, ion channel activity, and RNA ligation. A total of 224 different pathways were mapped. Among them, 184 pathways were upregulated, while 162 were downregulated. Further investigation showed that the calcium and AMPK signaling pathway had important induction effects on the encystment. In addition, FOXO and ubiquitin-mediated proteolysis signaling pathway jointly regulated the encystment. Based on these findings, we propose a hypothetical signaling network that regulates Pseudourostyla cristata encystment. Overall, these results provide deeper insights into the molecular mechanisms of ciliates encystment and adaptation to adverse environments.
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Large-scale identification of encystment-related proteins and genes in Pseudourostyla cristata. Sci Rep 2015; 5:11360. [PMID: 26079518 PMCID: PMC4650649 DOI: 10.1038/srep11360] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/22/2015] [Indexed: 11/08/2022] Open
Abstract
The transformation of a ciliate into cyst is an advance strategy against an adverse situation. However, the molecular mechanism for the encystation of free-living ciliates is poorly understood. A large-scale identification of the encystment-related proteins and genes in ciliate would provide us with deeper insights into the molecular mechanisms for the encystations of ciliate. We identified the encystment-related proteins and genes in Pseudourostyla cristata with shotgun LC-MS/MS and scale qRT-PCR, respectively, in this report. A total of 668 proteins were detected in the resting cysts, 102 of these proteins were high credible proteins, whereas 88 high credible proteins of the 724 total proteins were found in the vegetative cells. Compared with the vegetative cell, 6 specific proteins were found in the resting cyst. However, the majority of high credible proteins in the resting cyst and the vegetative cell were co-expressed. We compared 47 genes of the co-expressed proteins with known functions in both the cyst and the vegetative cell using scale qRT-PCR. Twenty-seven of 47 genes were differentially expressed in the cyst compared with the vegetative cell. In our identifications, many uncharacterized proteins were also found. These results will help reveal the molecular mechanism for the formation of cyst in ciliates.
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Sogame Y, Kojima K, Takeshita T, Kinoshita E, Matsuoka T. Identification of Differentially Expressed Water-insoluble Proteins in the Encystment Process of Colpoda cucullus
by Two-dimensional Electrophoresis and LC-MS/MS Analysis. J Eukaryot Microbiol 2013; 61:51-60. [DOI: 10.1111/jeu.12086] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/01/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Affiliation(s)
- Yoichiro Sogame
- Department of Biological Science; Faculty of Science; Kochi University; Kochi 780-8520 Japan
| | - Katsuhiko Kojima
- Department of Microbiology and Immunology; Shinshu University School of Medicine; 3-1-1 Asahi Matsumoto Nagano 390-8621 Japan
| | - Toshikazu Takeshita
- Department of Microbiology and Immunology; Shinshu University School of Medicine; 3-1-1 Asahi Matsumoto Nagano 390-8621 Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science; Graduate School of Biomedical Sciences; Hiroshima University; Kasumi 1-2-3 Hiroshima 734-8553 Japan
| | - Tatsuomi Matsuoka
- Department of Biological Science; Faculty of Science; Kochi University; Kochi 780-8520 Japan
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Sogame Y, Kojima K, Takeshita T, Kinoshita E, Matsuoka T. EF-1α and Mitochondrial ATP Synthase β Chain: Alteration of their Expression in Encystment-Induced Colpoda cucullus. J Eukaryot Microbiol 2012; 59:401-6. [DOI: 10.1111/j.1550-7408.2012.00628.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/26/2012] [Indexed: 11/29/2022]
Affiliation(s)
- Yoichiro Sogame
- Department of Biological Science; Faculty of Science; Kochi University; Kochi; 780-8520; Japan
| | - Katsuhiko Kojima
- Department of Microbiology and Immunology; Shinshu University School of Medicine; 3-1-1 Asahi; Matsumoto; Nagano; 390-8621; Japan
| | - Toshikazu Takeshita
- Department of Microbiology and Immunology; Shinshu University School of Medicine; 3-1-1 Asahi; Matsumoto; Nagano; 390-8621; Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science; Graduate School of Biomedical Sciences; Hiroshima University; Kasumi 1-2-3; Hiroshima; 734-8553; Japan
| | - Tatsuomi Matsuoka
- Department of Biological Science; Faculty of Science; Kochi University; Kochi; 780-8520; Japan
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Culture Age, Intracellular Ca(2+) Concentration, and Protein Phosphorylation in Encystment-Induced Colpoda cucullus. Indian J Microbiol 2012; 52:666-9. [PMID: 24293728 DOI: 10.1007/s12088-012-0274-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 05/03/2012] [Indexed: 10/28/2022] Open
Abstract
In Colpoda cucullus, intracellular Ca(2+) mediates the encystment induction and protein phosphorylation that occur just prior to morphogenetic transformation into the resting form. When rapidly growing cells were stimulated to encyst, encystment was not readily induced, and the protein phosphorylation level was lower. On the other hand, in post-growing cells stimulated to encyst, the encystment rate and protein phosphorylation level were elevated. These results suggest that protein phosphorylation is closely linked to encystment induction. Why, then, are the protein phosphorylation level and encystment rate difficult to elevate in the rapidly growing cells? Fura 2 ratiometry showed that the intracellular Ca(2+) concentration (F340/F380 ratio) was raised in rapidly growing cells as well as in post-growing cells when the cells were stimulated to encyst. It is presumed that the Ca(2+)-mediated signal transduction pathways for protein phosphorylation and encystment may be triggered in rapidly growing cells, but downstream certain steps may be suppressed by certain intracellular components.
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Sogame Y, Kojima K, Takeshita T, Fujiwara S, Miyata S, Kinoshita E, Matsuoka T. Protein phosphorylation in encystment-induced Colpoda cucullus: localization and identification of phosphoproteins. FEMS Microbiol Lett 2012; 331:128-35. [DOI: 10.1111/j.1574-6968.2012.02560.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Revised: 03/23/2012] [Accepted: 03/23/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Yoichiro Sogame
- Institute of Biological Science; Faculty of Science; Kochi University; Kochi; Japan
| | - Katsuhiko Kojima
- Department of Microbiology and Immunology; Shinshu University School of Medicine; Nagano; Japan
| | - Toshikazu Takeshita
- Department of Microbiology and Immunology; Shinshu University School of Medicine; Nagano; Japan
| | - Shigeki Fujiwara
- Department of Applied Science; Faculty of Science; Kochi University; Kochi; Japan
| | - Seiji Miyata
- Department of Applied Biology; Kyoto Institute of Technology; Kyoto; Japan
| | - Eiji Kinoshita
- Department of Functional Molecular Science; Graduate School of Biomedical Sciences; Hiroshima University; Hiroshima; Japan
| | - Tatsuomi Matsuoka
- Institute of Biological Science; Faculty of Science; Kochi University; Kochi; Japan
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Plattner H, Sehring IM, Mohamed IK, Miranda K, De Souza W, Billington R, Genazzani A, Ladenburger EM. Calcium signaling in closely related protozoan groups (Alveolata): non-parasitic ciliates (Paramecium, Tetrahymena) vs. parasitic Apicomplexa (Plasmodium, Toxoplasma). Cell Calcium 2012; 51:351-82. [PMID: 22387010 DOI: 10.1016/j.ceca.2012.01.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 01/10/2012] [Accepted: 01/12/2012] [Indexed: 12/20/2022]
Abstract
The importance of Ca2+-signaling for many subcellular processes is well established in higher eukaryotes, whereas information about protozoa is restricted. Recent genome analyses have stimulated such work also with Alveolates, such as ciliates (Paramecium, Tetrahymena) and their pathogenic close relatives, the Apicomplexa (Plasmodium, Toxoplasma). Here we compare Ca2+ signaling in the two closely related groups. Acidic Ca2+ stores have been characterized in detail in Apicomplexa, but hardly in ciliates. Two-pore channels engaged in Ca2+-release from acidic stores in higher eukaryotes have not been stingently characterized in either group. Both groups are endowed with plasma membrane- and endoplasmic reticulum-type Ca2+-ATPases (PMCA, SERCA), respectively. Only recently was it possible to identify in Paramecium a number of homologs of ryanodine and inositol 1,3,4-trisphosphate receptors (RyR, IP3R) and to localize them to widely different organelles participating in vesicle trafficking. For Apicomplexa, physiological experiments suggest the presence of related channels although their identity remains elusive. In Paramecium, IP3Rs are constitutively active in the contractile vacuole complex; RyR-related channels in alveolar sacs are activated during exocytosis stimulation, whereas in the parasites the homologous structure (inner membrane complex) may no longer function as a Ca2+ store. Scrutinized comparison of the two closely related protozoan phyla may stimulate further work and elucidate adaptation to parasitic life. See also "Conclusions" section.
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Affiliation(s)
- H Plattner
- Department of Biology, University of Konstanz, P.O. Box 5560, 78457 Konstanz, Germany.
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