1
|
Hayashi M, Ohnuki S, Tsai Y, Kondo N, Zhou Y, Zhang H, Ishii NT, Ding T, Herbig M, Isozaki A, Ohya Y, Goda K. Is AI essential? Examining the need for deep learning in image-activated sorting of Saccharomyces cerevisiae. Lab Chip 2023; 23:4232-4244. [PMID: 37650583 DOI: 10.1039/d3lc00556a] [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] [Indexed: 09/01/2023]
Abstract
Artificial intelligence (AI) has become a focal point across a multitude of societal sectors, with science not being an exception. Particularly in the life sciences, imaging flow cytometry has increasingly integrated AI for automated management and categorization of extensive cell image data. However, the necessity of AI over traditional classification methods when extending imaging flow cytometry to include cell sorting remains uncertain, primarily due to the time constraints between image acquisition and sorting actuation. AI-enabled image-activated cell sorting (IACS) methods remain substantially limited, even as recent advancements in IACS have found success while largely relying on traditional feature gating strategies. Here we assess the necessity of AI for image classification in IACS by contrasting the performance of feature gating, classical machine learning (ML), and deep learning (DL) with convolutional neural networks (CNNs) in the differentiation of Saccharomyces cerevisiae mutant images. We show that classical ML could only yield a 2.8-fold enhancement in target enrichment capability, albeit at the cost of a 13.7-fold increase in processing time. Conversely, a CNN could offer an 11.0-fold improvement in enrichment capability at an 11.5-fold increase in processing time. We further executed IACS on mixed mutant populations and quantified target strain enrichment via downstream DNA sequencing to substantiate the applicability of DL for the proposed study. Our findings validate the feasibility and value of employing DL in IACS for morphology-based genetic screening of S. cerevisiae, encouraging its incorporation in future advancements of similar technologies.
Collapse
Affiliation(s)
- Mika Hayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Yating Tsai
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
| | - Yuqi Zhou
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Hongqian Zhang
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Natsumi Tiffany Ishii
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Tianben Ding
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Maik Herbig
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Mechanical Engineering, College of Science and Engineering, Ritsumeikan University, Shiga 525-8577, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan 430072, China
- CYBO, Tokyo 135-0064, Japan
| |
Collapse
|
2
|
Klinkaewboonwong N, Ohnuki S, Chadani T, Nishida I, Ushiyama Y, Tomiyama S, Isogai A, Goshima T, Ghanegolmohammadi F, Nishi T, Kitamoto K, Akao T, Hirata D, Ohya Y. Targeted Mutations Produce Divergent Characteristics in Pedigreed Sake Yeast Strains. Microorganisms 2023; 11:1274. [PMID: 37317248 DOI: 10.3390/microorganisms11051274] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 06/16/2023] Open
Abstract
Modification of the genetic background and, in some cases, the introduction of targeted mutations can play a critical role in producing trait characteristics during the breeding of crops, livestock, and microorganisms. However, the question of how similar trait characteristics emerge when the same target mutation is introduced into different genetic backgrounds is unclear. In a previous study, we performed genome editing of AWA1, CAR1, MDE1, and FAS2 on the standard sake yeast strain Kyokai No. 7 to breed a sake yeast with multiple excellent brewing characteristics. By introducing the same targeted mutations into other pedigreed sake yeast strains, such as Kyokai strains No. 6, No. 9, and No. 10, we were able to create sake yeasts with the same excellent brewing characteristics. However, we found that other components of sake made by the genome-edited yeast strains did not change in the exact same way. For example, amino acid and isobutanol contents differed among the strain backgrounds. We also showed that changes in yeast cell morphology induced by the targeted mutations also differed depending on the strain backgrounds. The number of commonly changed morphological parameters was limited. Thus, divergent characteristics were produced by the targeted mutations in pedigreed sake yeast strains, suggesting a breeding strategy to generate a variety of sake yeasts with excellent brewing characteristics.
Collapse
Affiliation(s)
- Norapat Klinkaewboonwong
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Tomoya Chadani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | - Ikuhisa Nishida
- Sakeology Center, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
| | - Yuto Ushiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
| | - Saki Tomiyama
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
| | - Atsuko Isogai
- National Research Institute of Brewing, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Tetsuya Goshima
- National Research Institute of Brewing, Higashi-Hiroshima, Hiroshima 739-0046, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Tomoyuki Nishi
- Sake Research Center, Asahi Sake Brewing Co., Ltd., Nagaoka, Niigata 949-5494, Japan
| | - Katsuhiko Kitamoto
- Department of Pharmaceutical and Medical Business Sciences, Nihon Pharmaceutical University, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Takeshi Akao
- National Research Institute of Brewing, Higashi-Hiroshima, Hiroshima 739-0046, Japan
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
| | - Dai Hirata
- Sakeology Center, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
- Sakeology Course, Graduate School of Science and Technology, Niigata University, 2-8050, Ikarashi, Niigata 950-2181, Japan
- Program of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8530, Japan
- Sake Research Center, Asahi Sake Brewing Co., Ltd., Nagaoka, Niigata 949-5494, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
3
|
Itto-Nakama K, Watanabe S, Ohnuki S, Kondo N, Kikuchi R, Nakamura T, Ogasawara W, Kasahara K, Ohya Y. Prediction of ethanol fermentation under stressed conditions using yeast morphological data. J Biosci Bioeng 2023; 135:210-216. [PMID: 36642617 DOI: 10.1016/j.jbiosc.2022.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/09/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023]
Abstract
A high sugar concentration is used as a starting condition in alcoholic fermentation by budding yeast, which shows changes in intracellular state and cell morphology under conditions of high-sugar stress. In this study, we developed artificial intelligence (AI) models to predict ethanol yields in yeast fermentation cultures under conditions of high-sugar stress using cell morphological data. Our method involves the extraction of high-dimensional morphological data from phase contrast images using image processing software, and predicting ethanol yields by supervised machine learning. The neural network algorithm produced the best performance, with a coefficient of determination (R2) of 0.95, and could predict ethanol yields well even 60 min in the future. Morphological data from cells cultured in low-glucose medium could not be used for accurate prediction under conditions of high-glucose stress. Cells cultured in high-concentration glucose medium were similar in terms of morphology to cells cultured under high osmotic pressure. Feeding experiments revealed that morphological changes differed depending on the fermentation phase. By monitoring the morphology of yeast under stress, it was possible to understand the intracellular physiological conditions, suggesting that analysis of cell morphology can aid the management and stable production of desired biocommodities.
Collapse
Affiliation(s)
- Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan
| | - Shun Watanabe
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan
| | - Ryota Kikuchi
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan; Circular Bioeconomy Development, Office of Society Academia Collaboration for Innovation, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Toru Nakamura
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan; Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Niigata 940-2188, Japan
| | - Ken Kasahara
- Chitose Laboratory Corp., Biotechnology Research Center, 2-13-3, Nogawahoncho, Miyamae-ku, Kawasaki, Kanagawa 216-0041, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba 277-8562, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
| |
Collapse
|
4
|
Zhao Y, Isozaki A, Herbig M, Hayashi M, Hiramatsu K, Yamazaki S, Kondo N, Ohnuki S, Ohya Y, Nitta N, Goda K. Intelligent sort-timing prediction for image-activated cell sorting. Cytometry A 2023; 103:88-97. [PMID: 35766305 DOI: 10.1002/cyto.a.24664] [Citation(s) in RCA: 1] [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: 03/25/2022] [Revised: 05/20/2022] [Accepted: 06/11/2022] [Indexed: 02/07/2023]
Abstract
Intelligent image-activated cell sorting (iIACS) has enabled high-throughput image-based sorting of single cells with artificial intelligence (AI) algorithms. This AI-on-a-chip technology combines fluorescence microscopy, AI-based image processing, sort-timing prediction, and cell sorting. Sort-timing prediction is particularly essential due to the latency on the order of milliseconds between image acquisition and sort actuation, during which image processing is performed. The long latency amplifies the effects of the fluctuations in the flow speed of cells, leading to fluctuation and uncertainty in the arrival time of cells at the sort point on the microfluidic chip. To compensate for this fluctuation, iIACS measures the flow speed of each cell upstream, predicts the arrival timing of the cell at the sort point, and activates the actuation of the cell sorter appropriately. Here, we propose and demonstrate a machine learning technique to increase the accuracy of the sort-timing prediction that would allow for the improvement of sort event rate, yield, and purity. Specifically, we trained an algorithm to predict the sort timing for morphologically heterogeneous budding yeast cells. The algorithm we developed used cell morphology, position, and flow speed as inputs for prediction and achieved 41.5% lower prediction error compared to the previously employed method based solely on flow speed. As a result, our technique would allow for an increase in the sort event rate of iIACS by a factor of ~2.
Collapse
Affiliation(s)
- Yaqi Zhao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Maik Herbig
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mika Hayashi
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Hiramatsu
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sota Yamazaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | | | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,CYBO, Tokyo, Japan.,Department of Bioengineering, University of California, California, Los Angeles, USA.,Institute of Technological Sciences, Wuhan University, Hubei, China
| |
Collapse
|
5
|
Ghanegolmohammadi F, Ohnuki S, Ohya Y. Assignment of unimodal probability distribution models for quantitative morphological phenotyping. BMC Biol 2022; 20:81. [PMID: 35361198 PMCID: PMC8969357 DOI: 10.1186/s12915-022-01283-6] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 03/17/2022] [Indexed: 01/02/2023] Open
Abstract
Background Cell morphology is a complex and integrative readout, and therefore, an attractive measurement for assessing the effects of genetic and chemical perturbations to cells. Microscopic images provide rich information on cell morphology; therefore, subjective morphological features are frequently extracted from digital images. However, measured datasets are fundamentally noisy; thus, estimation of the true values is an ultimate goal in quantitative morphological phenotyping. Ideal image analyses require precision, such as proper probability distribution analyses to detect subtle morphological changes, recall to minimize artifacts due to experimental error, and reproducibility to confirm the results. Results Here, we present UNIMO (UNImodal MOrphological data), a reliable pipeline for precise detection of subtle morphological changes by assigning unimodal probability distributions to morphological features of the budding yeast cells. By defining the data type, followed by validation using the model selection method, examination of 33 probability distributions revealed nine best-fitting probability distributions. The modality of the distribution was then clarified for each morphological feature using a probabilistic mixture model. Using a reliable and detailed set of experimental log data of wild-type morphological replicates, we considered the effects of confounding factors. As a result, most of the yeast morphological parameters exhibited unimodal distributions that can be used as basic tools for powerful downstream parametric analyses. The power of the proposed pipeline was confirmed by reanalyzing morphological changes in non-essential yeast mutants and detecting 1284 more mutants with morphological defects compared with a conventional approach (Box–Cox transformation). Furthermore, the combined use of canonical correlation analysis permitted global views on the cellular network as well as new insights into possible gene functions. Conclusions Based on statistical principles, we showed that UNIMO offers better predictions of the true values of morphological measurements. We also demonstrated how these concepts can provide biologically important information. This study draws attention to the necessity of employing a proper approach to do more with less. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01283-6.
Collapse
Affiliation(s)
- Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
6
|
Huang K, Matsumura H, Zhao Y, Herbig M, Yuan D, Mineharu Y, Harmon J, Findinier J, Yamagishi M, Ohnuki S, Nitta N, Grossman AR, Ohya Y, Mikami H, Isozaki A, Goda K. Deep imaging flow cytometry. Lab Chip 2022; 22:876-889. [PMID: 35142325 DOI: 10.1039/d1lc01043c] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Imaging flow cytometry (IFC) has become a powerful tool for diverse biomedical applications by virtue of its ability to image single cells in a high-throughput manner. However, there remains a challenge posed by the fundamental trade-off between throughput, sensitivity, and spatial resolution. Here we present deep-learning-enhanced imaging flow cytometry (dIFC) that circumvents this trade-off by implementing an image restoration algorithm on a virtual-freezing fluorescence imaging (VIFFI) flow cytometry platform, enabling higher throughput without sacrificing sensitivity and spatial resolution. A key component of dIFC is a high-resolution (HR) image generator that synthesizes "virtual" HR images from the corresponding low-resolution (LR) images acquired with a low-magnification lens (10×/0.4-NA). For IFC, a low-magnification lens is favorable because of reduced image blur of cells flowing at a higher speed, which allows higher throughput. We trained and developed the HR image generator with an architecture containing two generative adversarial networks (GANs). Furthermore, we developed dIFC as a method by combining the trained generator and IFC. We characterized dIFC using Chlamydomonas reinhardtii cell images, fluorescence in situ hybridization (FISH) images of Jurkat cells, and Saccharomyces cerevisiae (budding yeast) cell images, showing high similarities of dIFC images to images obtained with a high-magnification lens (40×/0.95-NA), at a high flow speed of 2 m s-1. We lastly employed dIFC to show enhancements in the accuracy of FISH-spot counting and neck-width measurement of budding yeast cells. These results pave the way for statistical analysis of cells with high-dimensional spatial information.
Collapse
Affiliation(s)
- Kangrui Huang
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Hiroki Matsumura
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Yaqi Zhao
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Maik Herbig
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Dan Yuan
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Yohei Mineharu
- Department of Neurosurgery, Kyoto University, Kyoto 606-8507, Japan
- Department of Artificial Intelligence in Healthcare and Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Jeffrey Harmon
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Justin Findinier
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, California 94305, USA
| | - Mai Yamagishi
- Department of Biological Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
| | | | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, California 94305, USA
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8654, Japan
| | - Hideharu Mikami
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
- Department of Bioengineering, University of California, Los Angeles, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Hubei 430072, China
| |
Collapse
|
7
|
Itto-Nakama K, Watanabe S, Kondo N, Ohnuki S, Kikuchi R, Nakamura T, Ogasawara W, Kasahara K, Ohya Y. AI-based forecasting of ethanol fermentation using yeast morphological data. Biosci Biotechnol Biochem 2021; 86:125-134. [PMID: 34751736 DOI: 10.1093/bbb/zbab188] [Citation(s) in RCA: 6] [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: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 11/12/2022]
Abstract
Several industries require getting information of products as soon as possible during fermentation. However, the trade-off between sensing speed and data quantity presents challenges for forecasting fermentation product yields. In this study, we tried to develop AI models to forecast ethanol yields in yeast fermentation cultures, using cell morphological data. Our platform involves the quick acquisition of yeast morphological images using a non-staining protocol, extraction of high-dimensional morphological data using image processing software, and forecasting of ethanol yields via supervised machine learning. We found that the neural network algorithm produced the best performance, which had a coefficient of determination of > 0.9 even at 30 and 60 min in the future. The model was validated using test data collected using the CalMorph-PC(10) system, which enables rapid image acquisition within 10 min. AI-based forecasting of product yields based on cell morphology will facilitate the management and stable production of desired biocommodities.
Collapse
Affiliation(s)
- Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan
| | - Shun Watanabe
- Chitose Laboratory Corp., Biotechnology Research Center, 907 Nogawa, Miyamae-ku, Kawasaki, Kanagawa, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan
| | - Ryota Kikuchi
- Chitose Laboratory Corp., Biotechnology Research Center, 907 Nogawa, Miyamae-ku, Kawasaki, Kanagawa, Japan.,Circular Bioeconomy Development, Office of Society Academia Collaboration for Innovation, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Kyoto, Japan
| | - Toru Nakamura
- NRI System Techno Ltd., 134 Godo-cho, Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, Japan
| | - Ken Kasahara
- Chitose Laboratory Corp., Biotechnology Research Center, 907 Nogawa, Miyamae-ku, Kawasaki, Kanagawa, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa, Chiba, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| |
Collapse
|
8
|
Yu H, Wang S, Zhang Y, Liu Q, Diao S, Liu P, Oono N, Ukai S, Wan F, Ohnuki S, Zhan Q. Response of nanoclusters to heavy-ion irradiation in an Fe-12Cr ODS steel. Fusion Engineering and Design 2021. [DOI: 10.1016/j.fusengdes.2021.112759] [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] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
9
|
Nakagawa Y, Ohnuki S, Kondo N, Itto-Nakama K, Ghanegolmohammadi F, Isozaki A, Ohya Y, Goda K. Are droplets really suitable for single-cell analysis? A case study on yeast in droplets. Lab Chip 2021; 21:3793-3803. [PMID: 34581379 DOI: 10.1039/d1lc00469g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases. In this work, we assessed the effect of culturing cells in droplets on the cellular function using yeast morphology as an indicator. Quantitative morphological analysis using CalMorph, an image-analysis program, demonstrated that cells cultured in flasks, large droplets, and small droplets significantly differed morphologically. From these differences, we identified that the cell cycle was delayed in droplets during the G1 phase and during the process of bud growth likely due to the checkpoint mechanism and impaired mitochondrial function, respectively. Furthermore, comparing small and large droplets, cells cultured in large droplets were morphologically more similar to those cultured in a flask, highlighting the advantage of increasing the droplet size. These results highlight a potential source of bias in cell analysis using droplets and reinforce the significance of assessing culture conditions of microfluidic cultivation methods for specific study cases.
Collapse
Affiliation(s)
- Yuta Nakagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
| |
Collapse
|
10
|
Ghanegolmohammadi F, Okada H, Liu Y, Itto-Nakama K, Ohnuki S, Savchenko A, Bi E, Yoshida S, Ohya Y. Defining Functions of Mannoproteins in Saccharomyces cerevisiae by High-Dimensional Morphological Phenotyping. J Fungi (Basel) 2021; 7:jof7090769. [PMID: 34575807 PMCID: PMC8466635 DOI: 10.3390/jof7090769] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Mannoproteins are non-filamentous glycoproteins localized to the outermost layer of the yeast cell wall. The physiological roles of these structural components have not been completely elucidated due to the limited availability of appropriate tools. As the perturbation of mannoproteins may affect cell morphology, we investigated mannoprotein mutants in Saccharomyces cerevisiae via high-dimensional morphological phenotyping. The mannoprotein mutants were morphologically classified into seven groups using clustering analysis with Gaussian mixture modeling. The pleiotropic phenotypes of cluster I mutant cells (ccw12Δ) indicated that CCW12 plays major roles in cell wall organization. Cluster II (ccw14Δ, flo11Δ, srl1Δ, and tir3Δ) mutants exhibited altered mother cell size and shape. Mutants of cluster III and IV exhibited no or very small morphological defects. Cluster V (dse2Δ, egt2Δ, and sun4Δ) consisted of endoglucanase mutants with cell separation defects due to incomplete septum digestion. The cluster VI mutant cells (ecm33Δ) exhibited perturbation of apical bud growth. Cluster VII mutant cells (sag1Δ) exhibited differences in cell size and actin organization. Biochemical assays further confirmed the observed morphological defects. Further investigations based on various omics data indicated that morphological phenotyping is a complementary tool that can help with gaining a deeper understanding of the functions of mannoproteins.
Collapse
Affiliation(s)
- Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroki Okada
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.O.); (E.B.)
| | - Yaxuan Liu
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
| | - Anna Savchenko
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
- Cardiovascular Research Institute Maastricht, Maastricht University Medical Center, ER 6229 Maastricht, The Netherlands
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (H.O.); (E.B.)
| | - Satoshi Yoshida
- School of International Liberal Studies, Nishi-Waseda Campus, Waseda University, Tokyo 169-8050, Japan;
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan or (F.G.); (Y.L.); (K.I.-N.); (S.O.); (A.S.)
- Correspondence:
| |
Collapse
|
11
|
García R, Itto-Nakama K, Rodríguez-Peña JM, Chen X, Sanz AB, de Lorenzo A, Pavón-Vergés M, Kubo K, Ohnuki S, Nombela C, Popolo L, Ohya Y, Arroyo J. Poacic acid, a β-1,3-glucan-binding antifungal agent, inhibits cell-wall remodeling and activates transcriptional responses regulated by the cell-wall integrity and high-osmolarity glycerol pathways in yeast. FASEB J 2021; 35:e21778. [PMID: 34383971 DOI: 10.1096/fj.202100278r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/26/2021] [Accepted: 06/21/2021] [Indexed: 01/10/2023]
Abstract
As a result of the relatively few available antifungals and the increasing frequency of resistance to them, the development of novel antifungals is increasingly important. The plant natural product poacic acid (PA) inhibits β-1,3-glucan synthesis in Saccharomyces cerevisiae and has antifungal activity against a wide range of plant pathogens. However, the mode of action of PA is unclear. Here, we reveal that PA specifically binds to β-1,3-glucan, its affinity for which is ~30-fold that for chitin. Besides its effect on β-1,3-glucan synthase activity, PA inhibited the yeast glucan-elongating activity of Gas1 and Gas2 and the chitin-glucan transglycosylase activity of Crh1. Regarding the cellular response to PA, transcriptional co-regulation was mediated by parallel activation of the cell-wall integrity (CWI) and high-osmolarity glycerol signaling pathways. Despite targeting β-1,3-glucan remodeling, the transcriptional profiles and regulatory circuits activated by caspofungin, zymolyase, and PA differed, indicating that their effects on CWI have different mechanisms. The effects of PA on the growth of yeast strains indicated that it has a mode of action distinct from that of echinocandins, suggesting it is a unique antifungal agent.
Collapse
Affiliation(s)
- Raúl García
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - José Manuel Rodríguez-Peña
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Xiaolin Chen
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Ana Belén Sanz
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Alba de Lorenzo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Mónica Pavón-Vergés
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Karen Kubo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
| | - César Nombela
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| | - Laura Popolo
- Department of Biosciences, University of Milan, Milan, Italy
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan.,Collaborative Research Institute for Innovative Microbiology (CRIIM), The University of Tokyo, Tokyo, Japan
| | - Javier Arroyo
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, IRYCIS, Madrid, Spain
| |
Collapse
|
12
|
Kintaka R, Makanae K, Namba S, Kato H, Kito K, Ohnuki S, Ohya Y, Andrews BJ, Boone C, Moriya H. Genetic profiling of protein burden and nuclear export overload. eLife 2020; 9:54080. [PMID: 33146608 PMCID: PMC7673788 DOI: 10.7554/elife.54080] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 11/01/2020] [Indexed: 12/11/2022] Open
Abstract
Overproduction (op) of proteins triggers cellular defects. One of the consequences of overproduction is the protein burden/cost, which is produced by an overloading of the protein synthesis process. However, the physiology of cells under a protein burden is not well characterized. We performed genetic profiling of protein burden by systematic analysis of genetic interactions between GFP-op, surveying both deletion and temperature-sensitive mutants in budding yeast. We also performed genetic profiling in cells with overproduction of triple-GFP (tGFP), and the nuclear export signal-containing tGFP (NES-tGFP). The mutants specifically interacted with GFP-op were suggestive of unexpected connections between actin-related processes like polarization and the protein burden, which was supported by morphological analysis. The tGFP-op interactions suggested that this protein probe overloads the proteasome, whereas those that interacted with NES-tGFP involved genes encoding components of the nuclear export process, providing a resource for further analysis of the protein burden and nuclear export overload.
Collapse
Affiliation(s)
- Reiko Kintaka
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Koji Makanae
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan
| | - Shotaro Namba
- Matching Program Course, Okayama University, Okayama, Japan
| | - Hisaaki Kato
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Keiji Kito
- Department of Life Sciences, School of Agriculture, Meiji University, Tokyo, Japan
| | - Shinsuke Ohnuki
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshikazu Ohya
- Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Brenda J Andrews
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada
| | - Charles Boone
- Donnelly Center for Cellular and Biomolecular Research, Department of Medical Genetics, University of Toronto, Toronto, Canada.,RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.,Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| |
Collapse
|
13
|
Isozaki A, Mikami H, Tezuka H, Matsumura H, Huang K, Akamine M, Hiramatsu K, Iino T, Ito T, Karakawa H, Kasai Y, Li Y, Nakagawa Y, Ohnuki S, Ota T, Qian Y, Sakuma S, Sekiya T, Shirasaki Y, Suzuki N, Tayyabi E, Wakamiya T, Xu M, Yamagishi M, Yan H, Yu Q, Yan S, Yuan D, Zhang W, Zhao Y, Arai F, Campbell RE, Danelon C, Di Carlo D, Hiraki K, Hoshino Y, Hosokawa Y, Inaba M, Nakagawa A, Ohya Y, Oikawa M, Uemura S, Ozeki Y, Sugimura T, Nitta N, Goda K. Intelligent image-activated cell sorting 2.0. Lab Chip 2020; 20:2263-2273. [PMID: 32459276 DOI: 10.1039/d0lc00080a] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The advent of intelligent image-activated cell sorting (iIACS) has enabled high-throughput intelligent image-based sorting of single live cells from heterogeneous populations. iIACS is an on-chip microfluidic technology that builds on a seamless integration of a high-throughput fluorescence microscope, cell focuser, cell sorter, and deep neural network on a hybrid software-hardware data management architecture, thereby providing the combined merits of optical microscopy, fluorescence-activated cell sorting (FACS), and deep learning. Here we report an iIACS machine that far surpasses the state-of-the-art iIACS machine in system performance in order to expand the range of applications and discoveries enabled by the technology. Specifically, it provides a high throughput of ∼2000 events per second and a high sensitivity of ∼50 molecules of equivalent soluble fluorophores (MESFs), both of which are 20 times superior to those achieved in previous reports. This is made possible by employing (i) an image-sensor-based optomechanical flow imaging method known as virtual-freezing fluorescence imaging and (ii) a real-time intelligent image processor on an 8-PC server equipped with 8 multi-core CPUs and GPUs for intelligent decision-making, in order to significantly boost the imaging performance and computational power of the iIACS machine. We characterize the iIACS machine with fluorescent particles and various cell types and show that the performance of the iIACS machine is close to its achievable design specification. Equipped with the improved capabilities, this new generation of the iIACS technology holds promise for diverse applications in immunology, microbiology, stem cell biology, cancer biology, pathology, and synthetic biology.
Collapse
Affiliation(s)
- Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Isozaki A, Nakagawa Y, Loo MH, Shibata Y, Tanaka N, Setyaningrum DL, Park JW, Shirasaki Y, Mikami H, Huang D, Tsoi H, Riche CT, Ota T, Miwa H, Kanda Y, Ito T, Yamada K, Iwata O, Suzuki K, Ohnuki S, Ohya Y, Kato Y, Hasunuma T, Matsusaka S, Yamagishi M, Yazawa M, Uemura S, Nagasawa K, Watarai H, Di Carlo D, Goda K. Sequentially addressable dielectrophoretic array for high-throughput sorting of large-volume biological compartments. Sci Adv 2020; 6:eaba6712. [PMID: 32524002 PMCID: PMC7259936 DOI: 10.1126/sciadv.aba6712] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/25/2020] [Indexed: 05/27/2023]
Abstract
Droplet microfluidics has become a powerful tool in precision medicine, green biotechnology, and cell therapy for single-cell analysis and selection by virtue of its ability to effectively confine cells. However, there remains a fundamental trade-off between droplet volume and sorting throughput, limiting the advantages of droplet microfluidics to small droplets (<10 pl) that are incompatible with long-term maintenance and growth of most cells. We present a sequentially addressable dielectrophoretic array (SADA) sorter to overcome this problem. The SADA sorter uses an on-chip array of electrodes activated and deactivated in a sequence synchronized to the speed and position of a passing target droplet to deliver an accumulated dielectrophoretic force and gently pull it in the direction of sorting in a high-speed flow. We use it to demonstrate large-droplet sorting with ~20-fold higher throughputs than conventional techniques and apply it to long-term single-cell analysis of Saccharomyces cerevisiae based on their growth rate.
Collapse
Affiliation(s)
- A. Isozaki
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Kanagawa Institute of Industrial Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki-shi, Kanagawa 213-0012, Japan
| | - Y. Nakagawa
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. H. Loo
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Y. Shibata
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - N. Tanaka
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - D. L. Setyaningrum
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - J.-W. Park
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Y. Shirasaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Faculty of Science Building 1 (East), Room 575, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - H. Mikami
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - D. Huang
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - H. Tsoi
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - C. T. Riche
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, 5121E Engineering V, Los Angeles, CA 90095, USA
| | - T. Ota
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - H. Miwa
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Y. Kanda
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - T. Ito
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - K. Yamada
- R&D Department, euglena Co., Ltd., 75-1, Ono-machi, Tsurumi-ku, Yokohama-shi 230-0046, Japan
| | - O. Iwata
- R&D Department, euglena Co., Ltd., 75-1, Ono-machi, Tsurumi-ku, Yokohama-shi 230-0046, Japan
| | - K. Suzuki
- R&D Department, euglena Co., Ltd., 75-1, Ono-machi, Tsurumi-ku, Yokohama-shi 230-0046, Japan
| | - S. Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Y. Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8589, Japan
| | - Y. Kato
- Graduate School of Science, Technology Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - T. Hasunuma
- Graduate School of Science, Technology Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - S. Matsusaka
- Clinical Research and Regional Innovation, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - M. Yamagishi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Faculty of Science Building 1 (East), Room 575, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - M. Yazawa
- Department of Rehabilitation and Regenerative Medicine, Pharmacology, Columbia University, 650 West 168th Street, BB1108, New York, NY 10032, USA
| | - S. Uemura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Faculty of Science Building 1 (East), Room 575, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - K. Nagasawa
- Division of Stem Cell Cellomics, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - H. Watarai
- Division of Stem Cell Cellomics, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
- Department of Immunology and Stem Cell Biology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - D. Di Carlo
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, 5121E Engineering V, Los Angeles, CA 90095, USA
| | - K. Goda
- Department of Chemistry, Graduate School of Science, University of Tokyo, East Chemistry Building, Room 213, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, 5121E Engineering V, Los Angeles, CA 90095, USA
- Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
- Institute of Technological Sciences, Wuhan University, Hubei 430072, China
| |
Collapse
|
15
|
Mikami H, Kawaguchi M, Huang CJ, Matsumura H, Sugimura T, Huang K, Lei C, Ueno S, Miura T, Ito T, Nagasawa K, Maeno T, Watarai H, Yamagishi M, Uemura S, Ohnuki S, Ohya Y, Kurokawa H, Matsusaka S, Sun CW, Ozeki Y, Goda K. Virtual-freezing fluorescence imaging flow cytometry. Nat Commun 2020; 11:1162. [PMID: 32139684 PMCID: PMC7058616 DOI: 10.1038/s41467-020-14929-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Abstract
By virtue of the combined merits of flow cytometry and fluorescence microscopy, imaging flow cytometry (IFC) has become an established tool for cell analysis in diverse biomedical fields such as cancer biology, microbiology, immunology, hematology, and stem cell biology. However, the performance and utility of IFC are severely limited by the fundamental trade-off between throughput, sensitivity, and spatial resolution. Here we present an optomechanical imaging method that overcomes the trade-off by virtually freezing the motion of flowing cells on the image sensor to effectively achieve 1000 times longer exposure time for microscopy-grade fluorescence image acquisition. Consequently, it enables high-throughput IFC of single cells at >10,000 cells s−1 without sacrificing sensitivity and spatial resolution. The availability of numerous information-rich fluorescence cell images allows high-dimensional statistical analysis and accurate classification with deep learning, as evidenced by our demonstration of unique applications in hematology and microbiology. High throughput imaging flow cytometry suffers from trade-offs between throughput, sensitivity and spatial resolution. Here the authors introduce a method to virtually freeze cells in the image acquisition window to enable 1000 times longer signal integration time and improve signal-to-noise ratio.
Collapse
Affiliation(s)
- Hideharu Mikami
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Makoto Kawaguchi
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chun-Jung Huang
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan.,Department of Photonics, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hiroki Matsumura
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takeaki Sugimura
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan.,Japan Science and Technology Agency, Saitama, 332-0012, Japan.,CYBO, Tokyo, 101-0022, Japan
| | - Kangrui Huang
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Cheng Lei
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shunnosuke Ueno
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Taichi Miura
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Takuro Ito
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan.,Japan Science and Technology Agency, Saitama, 332-0012, Japan
| | - Kazumichi Nagasawa
- Center for Stem Cell Biology and Regenerative Medicine, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Takanori Maeno
- Center for Stem Cell Biology and Regenerative Medicine, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Hiroshi Watarai
- Center for Stem Cell Biology and Regenerative Medicine, The University of Tokyo, Tokyo, 108-8639, Japan.,Department of Immunology and Stem Cell Biology, Faculty of Medicine, Kanazawa University, Ishikawa, 920-8640, Japan
| | - Mai Yamagishi
- Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Chiba, 277-8565, Japan
| | - Hiromi Kurokawa
- Department of Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8577, Japan
| | - Satoshi Matsusaka
- Department of Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, 305-8577, Japan.,Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, 135-8550, Japan
| | - Chia-Wei Sun
- Department of Photonics, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, 113-8656, Japan.
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, 113-0033, Japan. .,Japan Science and Technology Agency, Saitama, 332-0012, Japan. .,Institute of Technological Sciences, Wuhan University, Hubei, 430072, China. .,Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
16
|
Ohnuki S, Kashima M, Yamada T, Ghanegolmohammadi F, Zhou Y, Goshima T, Maruyama JI, Kitamoto K, Hirata D, Akao T, Ohya Y. Genome editing to generate nonfoam-forming sake yeast strains. Biosci Biotechnol Biochem 2019; 83:1583-1593. [PMID: 31189439 DOI: 10.1080/09168451.2019.1631146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mutations frequently occur during breeding of sake yeasts and result in unexpected phenotypes. Here, genome editing tools were applied to develop an ideal nonfoam-forming sake yeast strain, K7GE01, which had homozygous awa1∆/awa1∆ deletion alleles that were responsible for nonfoam formation and few off-target mutations. High-dimensional morphological phenotyping revealed no detectable morphological differences between the genome-edited strain and its parent, while the canonical nonfoam-forming strain, K701, showed obvious morphological changes. Small-scale fermentation tests also showed differences between components of sake produced by K7GE01 and K701. The K7GE01 strain produced sake with significant differences in the concentrations of ethyl acetate, malic acid, lactic acid, and acetic acid, while K701 produced sake with more differences. Our results indicated genuine phenotypes of awa1∆/awa1∆ in sake yeast isolates and showed the usefulness of genome editing tools for sake yeast breeding.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Mao Kashima
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Toshikazu Yamada
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Farzan Ghanegolmohammadi
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan
| | - Yan Zhou
- b National Research Institute of Brewing , Higashi-Hiroshima , Japan
| | - Tetsuya Goshima
- b National Research Institute of Brewing , Higashi-Hiroshima , Japan
| | - Jun-Ichi Maruyama
- c Department of Biotechnology , The University of Tokyo , Tokyo , Japan.,d Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Tokyo , Japan
| | - Katsuhiko Kitamoto
- e Department of Pharmaceutical and Medical Business Sciences , Nihon Pharmaceutical University , Bunkyo-ku , Japan
| | - Dai Hirata
- f Sake Research Center , Asahi Sake Brewing Co. Ltd ., Nagaoka , Japan.,g Department of Molecular Biotechnology , Graduate School of Advanced Sciences of Matter, Hiroshima University , Higashi-Hiroshima , Japan.,h Sakeology Center , Niigata University , Ikarashi , Japan
| | - Takeshi Akao
- b National Research Institute of Brewing , Higashi-Hiroshima , Japan
| | - Yoshikazu Ohya
- a Department of Integrated Biosciences, Graduate School of Frontier Sciences , The University of Tokyo , Kashiwa, Chiba , Japan.,d Collaborative Research Institute for Innovative Microbiology , The University of Tokyo , Tokyo , Japan.,i AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL) , National Institute of Advanced Industrial Science and Technology (AIST) , Kashiwa, Chiba , Japan
| |
Collapse
|
17
|
Kubo K, Okada H, Shimamoto T, Kimori Y, Mizunuma M, Bi E, Ohnuki S, Ohya Y. Implications of maintenance of mother-bud neck size in diverse vital processes of Saccharomyces cerevisiae. Curr Genet 2019; 65:253-267. [PMID: 30066140 DOI: 10.1007/s00294-018-0872-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/17/2018] [Accepted: 07/25/2018] [Indexed: 11/25/2022]
Abstract
The mother-bud neck is defined as the boundary between the mother cell and bud in budding microorganisms, wherein sequential morphological events occur throughout the cell cycle. This study was designed to quantitatively investigate the morphology of the mother-bud neck in budding yeast Saccharomyces cerevisiae. Observation of yeast cells with time-lapse microscopy revealed an increase of mother-bud neck size through the cell cycle. After screening of yeast non-essential gene-deletion mutants with the image processing software CalMorph, we comprehensively identified 274 mutants with broader necks during S/G2 phase. Among these yeasts, we extensively analyzed 19 representative deletion mutants with defects in genes annotated to six gene ontology terms (polarisome, actin reorganization, endosomal tethering complex, carboxy-terminal domain protein kinase complex, DNA replication, and maintenance of DNA trinucleotide repeats). The representative broad-necked mutants exhibited calcofluor white sensitivity, suggesting defects in their cell walls. Correlation analysis indicated that maintenance of mother-bud neck size is important for cellular processes such as cell growth, system robustness, and replicative lifespan. We conclude that neck-size maintenance in budding yeast is regulated by numerous genes and has several aspects that are physiologically significant.
Collapse
Affiliation(s)
- Karen Kubo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Hiroki Okada
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - Takuya Shimamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Department of Management and Information Sciences, Faculty of Environmental and Information Sciences, Fukui University of Technology, Gakuen, Fukui City, Fukui, 910-8505, Japan
| | - Masaki Mizunuma
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima, 739-8530, Japan
| | - Erfei Bi
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104-6058, USA
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, 277-8565, Japan.
| |
Collapse
|
18
|
Nemoto S, Ohnuki S, Abe F, Ohya Y. Simulated microgravity triggers characteristic morphology and stress response in Saccharomyces cerevisiae. Yeast 2018; 36:85-97. [PMID: 30350382 DOI: 10.1002/yea.3361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/20/2023] Open
Abstract
Reduction of gravity results in changes in gene expression and morphology in the budding yeast Saccharomyces cerevisiae. We studied the genes responsible for the morphological changes induced by simulated microgravity (SMG) using the yeast morphology data. We comprehensively captured the features of the morphological changes in yeast cells cultured in SMG with CalMorph, a high-throughput image-processing system. Statistical analysis revealed that 95 of 501 morphological traits were significantly affected, which included changes in bud direction, the ratio of daughter to mother cell size, the random daughter cell shape, the large mother cell size, bright nuclei in the M phase, and the decrease in angle between two nuclei. We identified downregulated genes that impacted the morphological changes in conditions of SMG by focusing on each of the morphological features individually. Gene Ontology (GO)-enrichment analysis indicated that morphological changes under conditions of SMG were caused by cooperative downregulation of 103 genes annotated to six GO terms, which included cytoplasmic ribonucleoprotein granule, RNA elongation, mitotic cell cycle phase transition, nucleocytoplasmic transport, protein-DNA complex subunit organization, and RNA localization. P-body formation was also promoted under conditions of SMG. These results suggest that cooperative downregulation of multiple genes occurs in conditions of SMG.
Collapse
Affiliation(s)
- Shota Nemoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fumiyoshi Abe
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Japan
| |
Collapse
|
19
|
Sing TL, Hung MP, Ohnuki S, Suzuki G, San Luis BJ, McClain M, Unruh JR, Yu Z, Ou J, Marshall-Sheppard J, Huh WK, Costanzo M, Boone C, Ohya Y, Jaspersen SL, Brown GW. The budding yeast RSC complex maintains ploidy by promoting spindle pole body insertion. J Cell Biol 2018; 217:2445-2462. [PMID: 29875260 PMCID: PMC6028538 DOI: 10.1083/jcb.201709009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/13/2018] [Accepted: 05/09/2018] [Indexed: 01/31/2023] Open
Abstract
Sing et al. characterize an unanticipated role for the Saccharomyces cerevisiae RSC complex in ploidy maintenance. They show that RSC promotes the distribution of Nbp1 and Ndc1 to the spindle pole body (SPB) to facilitate SPB maturation and accurate chromosome segregation. Ploidy is tightly regulated in eukaryotic cells and is critical for cell function and survival. Cells coordinate multiple pathways to ensure replicated DNA is segregated accurately to prevent abnormal changes in chromosome number. In this study, we characterize an unanticipated role for the Saccharomyces cerevisiae “remodels the structure of chromatin” (RSC) complex in ploidy maintenance. We show that deletion of any of six nonessential RSC genes causes a rapid transition from haploid to diploid DNA content because of nondisjunction events. Diploidization is accompanied by diagnostic changes in cell morphology and is stably maintained without further ploidy increases. We find that RSC promotes chromosome segregation by facilitating spindle pole body (SPB) duplication. More specifically, RSC plays a role in distributing two SPB insertion factors, Nbp1 and Ndc1, to the new SPB. Thus, we provide insight into a role for a SWI/SNF family complex in SPB duplication and ploidy maintenance.
Collapse
Affiliation(s)
- Tina L Sing
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Minnie P Hung
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Godai Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO
| | - Jiongwen Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jesse Marshall-Sheppard
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Won-Ki Huh
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO.,Department of Molecular and Integrative Physiology, University of Kansas Medical Centre, Kansas City, KS
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada .,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
20
|
Abstract
Haploinsufficiency, a dominant phenotype caused by a heterozygous loss-of-function mutation, has been rarely observed. However, high-dimensional single-cell phenotyping of yeast morphological characteristics revealed haploinsufficiency phenotypes for more than half of 1,112 essential genes under optimal growth conditions. Additionally, 40% of the essential genes with no obvious phenotype under optimal growth conditions displayed haploinsufficiency under severe growth conditions. Haploinsufficiency was detected more frequently in essential genes than in nonessential genes. Similar haploinsufficiency phenotypes were observed mostly in mutants with heterozygous deletion of functionally related genes, suggesting that haploinsufficiency phenotypes were caused by functional defects of the genes. A global view of the gene network was presented based on the similarities of the haploinsufficiency phenotypes. Our dataset contains rich information regarding essential gene functions, providing evidence that single-cell phenotyping is a powerful approach, even in the heterozygous condition, for analyzing complex biological systems. Diploid organisms harboring a wild-type gene and a loss-of-function mutation are called heterozygotes. They are expected to have weak or no individual phenotypes because the mutation is compensated for by the intact allele. The dominant inheritance of phenotypes in heterozygotes is an exceptional phenomenon called haploinsufficiency. Haploinsufficiency was thought to be a rare occurrence; however, a sensitive technique called high-dimensional single-cell phenotyping challenges this perspective. Investigations of single-cell phenotypes revealed that a large extent of the essential genes in yeast exhibit haploinsufficiency. Our analyses also provided crucial information on gene functional networks based on haploinsufficiency phenotypes. This work shows that high-dimensional single-cell phenotyping is a useful tool that can be used to better understand complex biological systems.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, Japan
- * E-mail:
| |
Collapse
|
21
|
Chen S, Wang Y, Hashimoto N, Ohnuki S. Post-irradiation annealing behavior of helium in irradiated Fe and ferritic-martensitic steels. Nuclear Materials and Energy 2018. [DOI: 10.1016/j.nme.2018.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
22
|
Suzuki G, Wang Y, Kubo K, Hirata E, Ohnuki S, Ohya Y. Global study of holistic morphological effectors in the budding yeast Saccharomyces cerevisiae. BMC Genomics 2018; 19:149. [PMID: 29458326 PMCID: PMC5819264 DOI: 10.1186/s12864-018-4526-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/05/2018] [Indexed: 11/16/2022] Open
Abstract
Background The size of the phenotypic effect of a gene has been thoroughly investigated in terms of fitness and specific morphological traits in the budding yeast Saccharomyces cerevisiae, but little is known about gross morphological abnormalities. Results We identified 1126 holistic morphological effectors that cause severe gross morphological abnormality when deleted, and 2241 specific morphological effectors with weak holistic effects but distinctive effects on yeast morphology. Holistic effectors fell into many gene function categories and acted as network hubs, affecting a large number of morphological traits, interacting with a large number of genes, and facilitating high protein expression. Holistic morphological abnormality was useful for estimating the importance of a gene to morphology. The contribution of gene importance to fitness and morphology could be used to efficiently classify genes into functional groups. Conclusion Holistic morphological abnormality can be used as a reproducible and reliable gene feature for high-dimensional morphological phenotyping. It can be used in many functional genomic applications. Electronic supplementary material The online version of this article (10.1186/s12864-018-4526-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Godai Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Yang Wang
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Karen Kubo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Eri Hirata
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan. .,AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Bldg. Kashiwa Research Complex 2, 5-1-5 Kahiwanoha, Kashiwa, Chiba Prefecture, 277-8565, Japan.
| |
Collapse
|
23
|
Abstract
When macroautophagy (autophagy) is induced by nutrient starvation or rapamycin treatment, Atg (autophagy-related) proteins are assembled at a restricted region close to the vacuole. Subsequently, the phagophore expands to form a closed autophagosome. In Saccharomyces cerevisiae cells overexpressing precursor Ape1 (prApe1), a specific autophagosome cargo protein, the phagophore can be visualized as a cup-shaped structure labeled with green fluorescent protein (GFP)-tagged Atg8. Previously, our group has shown that the maximum length of GFP-Atg8-labeled structures reflects the magnitude of bulk autophagy. In that study, the morphological parameters of the autophagy-related structures were extracted manually, requiring a great deal of time. Moreover, only well-expanded phagophores were subjected to further analysis. Here we report Qautas (Quantitative autophagy-related structure analysis system), a high-throughput and comprehensive system for morphological analysis of autophagy-related structures using a combination of image processing and machine learning. We describe both the manual method and Qautas in detail.
Collapse
Affiliation(s)
- Tatsuya Kawaoka
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| | - Shinsuke Ohnuki
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| | - Yoshikazu Ohya
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| | - Kuninori Suzuki
- a Department of Integrated Biosciences , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan.,b Bioimaging Center , Graduate School of Frontier Sciences , University of Tokyo , Kashiwa , Chiba , Japan
| |
Collapse
|
24
|
Ghanegolmohammadi F, Yoshida M, Ohnuki S, Sukegawa Y, Okada H, Obara K, Kihara A, Suzuki K, Kojima T, Yachie N, Hirata D, Ohya Y. Systematic analysis of Ca 2+ homeostasis in Saccharomyces cerevisiae based on chemical-genetic interaction profiles. Mol Biol Cell 2017; 28:3415-3427. [PMID: 28566553 PMCID: PMC5687040 DOI: 10.1091/mbc.e17-04-0216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/23/2017] [Accepted: 05/24/2017] [Indexed: 12/20/2022] Open
Abstract
We investigated the global landscape of Ca2+ homeostasis in budding yeast based on high-dimensional chemical-genetic interaction profiles. The morphological responses of 62 Ca2+-sensitive (cls) mutants were quantitatively analyzed with the image processing program CalMorph after exposure to a high concentration of Ca2+ After a generalized linear model was applied, an analysis of covariance model was used to detect significant Ca2+-cls interactions. We found that high-dimensional, morphological Ca2+-cls interactions were mixed with positive (86%) and negative (14%) chemical-genetic interactions, whereas one-dimensional fitness Ca2+-cls interactions were all negative in principle. Clustering analysis with the interaction profiles revealed nine distinct gene groups, six of which were functionally associated. In addition, characterization of Ca2+-cls interactions revealed that morphology-based negative interactions are unique signatures of sensitized cellular processes and pathways. Principal component analysis was used to discriminate between suppression and enhancement of the Ca2+-sensitive phenotypes triggered by inactivation of calcineurin, a Ca2+-dependent phosphatase. Finally, similarity of the interaction profiles was used to reveal a connected network among the Ca2+ homeostasis units acting in different cellular compartments. Our analyses of high-dimensional chemical-genetic interaction profiles provide novel insights into the intracellular network of yeast Ca2+ homeostasis.
Collapse
Affiliation(s)
| | - Mitsunori Yoshida
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yuko Sukegawa
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- AIST-UTokyo Advanced Operand-Measurement Technology Open Innovation Laboratory, Kashiwa 277-0882, Japan
| | - Hiroki Okada
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058
| | - Keisuke Obara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Akio Kihara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Kuninori Suzuki
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
- Bioimaging Center, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Tetsuya Kojima
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904, Japan
- PRESTO, Japan Science and Technology Agency, Tokyo 102-0076, Japan
| | - Dai Hirata
- Research and Development Department, Asahi Sake Brewing Co., Nagaoka 949-5494, Japan
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima 739-8530, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, University of Tokyo, Kashiwa 277-8562, Japan
| |
Collapse
|
25
|
Watanabe D, Kaneko A, Sugimoto Y, Ohnuki S, Takagi H, Ohya Y. Promoter engineering of the Saccharomyces cerevisiae RIM15 gene for improvement of alcoholic fermentation rates under stress conditions. J Biosci Bioeng 2017; 123:183-189. [DOI: 10.1016/j.jbiosc.2016.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 07/14/2016] [Accepted: 08/12/2016] [Indexed: 01/05/2023]
|
26
|
Abstract
The demand for phenomics, a high-dimensional and high-throughput phenotyping method, has been increasing in many fields of biology. The budding yeast Saccharomyces cerevisiae, a unicellular model organism, provides an invaluable system for dissecting complex cellular processes using high-resolution phenotyping. Moreover, the addition of spatial and temporal attributes to subcellular structures based on microscopic images has rendered this cell phenotyping system more reliable and amenable to analysis. A well-designed experiment followed by appropriate multivariate analysis can yield a wealth of biological knowledge. Here we review recent advances in cell imaging and illustrate their broad applicability to eukaryotic cells by showing how these techniques have advanced our understanding of budding yeast.
Collapse
Affiliation(s)
- Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Yoshitaka Kimori
- Department of Imaging Science, Center for Novel Science Initiatives, National Institutes of Natural Sciences, Okazaki 444-8787, Japan
| | - Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, Japan
| |
Collapse
|
27
|
Nagakura H, Wakasugi T, Ohkubo K, Tanioka T, Endo T, Isobe S, Wang Y, Hashimoto N, Ohnuki S. B12-O-21Development of High Pressure Gas Environmental Cell and its Application to Hydrogen Reaction. Microscopy (Oxf) 2015. [DOI: 10.1093/jmicro/dfv108] [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
|
28
|
Kurishiba R, Endo T, Miyazaki N, Wang Y, Oka H, Sato Y, Sawa A, Hashimoto N, Ohnuki S. B23-P-16Multi-layer Method combined with Nano-indentation, FIB and XTEM for Nano-hardness Measurement. Microscopy (Oxf) 2015. [DOI: 10.1093/jmicro/dfv290] [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: 11/12/2022] Open
|
29
|
Gebre AA, Okada H, Kim C, Kubo K, Ohnuki S, Ohya Y. Profiling of the effects of antifungal agents on yeast cells based on morphometric analysis. FEMS Yeast Res 2015; 15:fov040. [DOI: 10.1093/femsyr/fov040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
|
30
|
Liu P, Zhu Y, Zhao M, Jiang S, Liu C, Wang Y, Wan F, Ohnuki S, Zhan Q. The effect of isotope on the dynamic behavior of 〈100〉 vacancy-type dislocation loop in deuterium-implanted Fe. Fusion Engineering and Design 2015. [DOI: 10.1016/j.fusengdes.2015.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
31
|
Okada H, Ohnuki S, Ohya Y. Quantification of cell, actin, and nuclear DNA morphology with high-throughput microscopy and CalMorph. Cold Spring Harb Protoc 2015; 2015:408-12. [PMID: 25834262 DOI: 10.1101/pdb.prot078667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Automated image acquisition and processing systems have been developed to quantitatively describe yeast cell morphology. These systems are superior to the preceding qualitative methods in terms of reproducibility, as they completely avoid subjective recognition of images. Because high-throughput microscopy has enabled rapid production of numerous cellular images, reinforcement of high-performance and high-throughput automated image-processing techniques has been in increasing demand in the field of biology. This protocol describes how to use a high-throughput microscope in conjunction with the image-processing software CalMorph, which outputs more than 500 morphological parameters, for quantification of cell, actin, and nuclear DNA morphology.
Collapse
Affiliation(s)
- Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture 277-8562, Japan
| |
Collapse
|
32
|
Abstract
Discovering the intracellular target of drugs is a fundamental challenge in biomedical research. We developed an image-based technique with which we were able to identify intracellular target of the compounds in the yeast Saccharomyces cerevisiae. Here, we describe the rationale of the technique, staining of yeast cells, image acquisition, data processing, and statistical analysis required for prediction of drug targets.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba Prefecture, 277-8562, Japan
| | | | | |
Collapse
|
33
|
Zhao M, Liu P, Bai J, Zhu Y, Wan F, Ohnuki S, Zhan Q. In-situ observation of the effect of the precipitate/matrix interface on the evolution of dislocation structures in CLAM steel during irradiation. Fusion Engineering and Design 2014. [DOI: 10.1016/j.fusengdes.2014.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
34
|
Endo T, Sugino Y, Ohono N, Ukai S, Miyazaki N, Wang Y, Ohnuki S. Three-dimensional characterization of ODS ferritic steel using by FIB-SEM serial sectioning method. Microscopy (Oxf) 2014; 63 Suppl 1:i23. [DOI: 10.1093/jmicro/dfu052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
35
|
Nogami S, Ohnuki S, Ohya Y. Hyperspectral imaging techniques for the characterization of Haematococcus pluvialis (Chlorophyceae). J Phycol 2014; 50:939-947. [PMID: 26988647 DOI: 10.1111/jpy.12226] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/25/2014] [Indexed: 06/05/2023]
Abstract
A hyperspectral imaging camera was combined with a bright-field microscope to investigate the intracellular distribution of pigments in cells of the green microalga Haematococcus pluvialis, a synonym for H. lacustris (Chlorophyceae). We applied multivariate curve resolution to the hyperspectral image data to estimate the pigment contents in culture and revealed that the predicted values were consistent with actual measurements obtained from extracted pigments. Because it was possible to estimate pigment contents in every pixel, the intracellular distribution of the pigments was investigated during various life-cycle stages. Astaxanthin was localized specifically at the eyespot of zoospores in early culture stages. Then, it became widely distributed in cells, but subsequently localized differently than the chl. Integrated with our recently developed image-processing program "HaematoCalMorph," the hyperspectral imaging system was useful for monitoring intracellular distributions of pigments during culture as well as for studying cellular responses under various conditions.
Collapse
Affiliation(s)
- Satoru Nogami
- Laboratory of Signal Transduction, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB101, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- JST-CREST, Kashiwa, 277-8562, Japan
| | - Shinsuke Ohnuki
- Laboratory of Signal Transduction, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB101, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- JST-CREST, Kashiwa, 277-8562, Japan
| | - Yoshikazu Ohya
- Laboratory of Signal Transduction, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, FSB101, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8562, Japan
- JST-CREST, Kashiwa, 277-8562, Japan
| |
Collapse
|
36
|
Okada H, Ohnuki S, Roncero C, Konopka JB, Ohya Y. Distinct roles of cell wall biogenesis in yeast morphogenesis as revealed by multivariate analysis of high-dimensional morphometric data. Mol Biol Cell 2013; 25:222-33. [PMID: 24258022 PMCID: PMC3890343 DOI: 10.1091/mbc.e13-07-0396] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
To better define how cell wall structure affects morphogenesis, the morphology of yeast cells was analyzed quantitatively after treatment with the three drugs that inhibit different aspects of cell wall synthesis. These drugs induced both similar effects, including broader necks and increased morphological variation, and distinct effects. The cell wall of budding yeast is a rigid structure composed of multiple components. To thoroughly understand its involvement in morphogenesis, we used the image analysis software CalMorph to quantitatively analyze cell morphology after treatment with drugs that inhibit different processes during cell wall synthesis. Cells treated with cell wall–affecting drugs exhibited broader necks and increased morphological variation. Tunicamycin, which inhibits the initial step of N-glycosylation of cell wall mannoproteins, induced morphologies similar to those of strains defective in α-mannosylation. The chitin synthase inhibitor nikkomycin Z induced morphological changes similar to those of mutants defective in chitin transglycosylase, possibly due to the critical role of chitin in anchoring the β-glucan network. To define the mode of action of echinocandin B, a 1,3-β-glucan synthase inhibitor, we compared the morphology it induced with mutants of Fks1 that contains the catalytic domain for 1,3-β-glucan synthesis. Echinocandin B exerted morphological effects similar to those observed in some fks1 mutants, with defects in cell polarity and reduced glucan synthesis activity, suggesting that echinocandin B affects not only 1,3-β-glucan synthesis, but also another functional domain. Thus our multivariate analyses reveal discrete functions of cell wall components and increase our understanding of the pharmacology of antifungal drugs.
Collapse
Affiliation(s)
- Hiroki Okada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8561, Japan Instituto de Biología Funcional y Genómica and Departamento de Microbiología y Genética, CSIC/Universidad de Salamanca, 37007 Salamanca, Spain Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794
| | | | | | | | | |
Collapse
|
37
|
Ohnuki S, Nogami S, Ota S, Watanabe K, Kawano S, Ohya Y. Image-Based Monitoring System for Green Algal Haematococcus pluvialis (Chlorophyceae) Cells during Culture. ACTA ACUST UNITED AC 2013; 54:1917-29. [DOI: 10.1093/pcp/pct126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
38
|
Ohnuki S, Enomoto K, Yoshimoto H, Ohya Y. Dynamic changes in brewing yeast cells in culture revealed by statistical analyses of yeast morphological data. J Biosci Bioeng 2013; 117:278-84. [PMID: 24012106 DOI: 10.1016/j.jbiosc.2013.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 08/08/2013] [Accepted: 08/13/2013] [Indexed: 10/26/2022]
Abstract
The vitality of brewing yeasts has been used to monitor their physiological state during fermentation. To investigate the fermentation process, we used the image processing software, CalMorph, which generates morphological data on yeast mother cells and bud shape, nuclear shape and location, and actin distribution. We found that 248 parameters changed significantly during fermentation. Successive use of principal component analysis (PCA) revealed several important features of yeast, providing insight into the dynamic changes in the yeast population. First, PCA indicated that much of the observed variability in the experiment was summarized in just two components: a change with a peak and a change over time. Second, PCA indicated the independent and important morphological features responsible for dynamic changes: budding ratio, nucleus position, neck position, and actin organization. Thus, the large amount of data provided by imaging analysis can be used to monitor the fermentation processes involved in beer and bioethanol production.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Bioscience, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kenichi Enomoto
- Research Laboratories for Brewing, Kirin Brewery Company, Limited, 17-1 Namamugi 1-chome, Tsurumi-ku, Yokohama, Kanagawa 230-8628, Japan
| | - Hiroyuki Yoshimoto
- Research Laboratories for Brewing, Kirin Brewery Company, Limited, 17-1 Namamugi 1-chome, Tsurumi-ku, Yokohama, Kanagawa 230-8628, Japan
| | - Yoshikazu Ohya
- Department of Integrated Bioscience, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| |
Collapse
|
39
|
Yvert G, Ohnuki S, Nogami S, Imanaga Y, Fehrmann S, Schacherer J, Ohya Y. Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast. BMC Syst Biol 2013; 7:54. [PMID: 23822767 PMCID: PMC3711934 DOI: 10.1186/1752-0509-7-54] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 06/21/2013] [Indexed: 01/31/2023]
Abstract
Background Most quantitative measures of phenotypic traits represent macroscopic contributions of large numbers of cells. Yet, cells of a tissue do not behave similarly, and molecular studies on several organisms have shown that regulations can be highly stochastic, sometimes generating diversified cellular phenotypes within tissues. Phenotypic noise, defined here as trait variability among isogenic cells of the same type and sharing a common environment, has therefore received a lot of attention. Given the potential fitness advantage provided by phenotypic noise in fluctuating environments, the possibility that it is directly subjected to evolutionary selection is being considered. For selection to act, phenotypic noise must differ between contemporary genotypes. Whether this is the case or not remains, however, unclear because phenotypic noise has very rarely been quantified in natural populations. Results Using automated image analysis, we describe here the phenotypic diversity of S. cerevisiae morphology at single-cell resolution. We profiled hundreds of quantitative traits in more than 1,000 cells of 37 natural strains, which represent various geographical and ecological origins of the species. We observed abundant trait variation between strains, with no correlation with their ecological origin or population history. Phenotypic noise strongly depended on the strain background. Noise variation was largely trait-specific (specific strains showing elevated noise for subset of traits) but also global (a few strains displaying elevated noise for many unrelated traits). Conclusions Our results demonstrate that phenotypic noise does differ quantitatively between natural populations. This supports the possibility that, if noise is adaptive, microevolution may tune it in the wild. This tuning may happen on specific traits or by varying the degree of global phenotypic buffering.
Collapse
Affiliation(s)
- Gaël Yvert
- Laboratoire de Biologie Moléculaire de la Cellule, Ecole Normale Supérieure de Lyon; CNRS, Université Lyon 1, 46 Allée d'Italie, Lyon F-69007, France.
| | | | | | | | | | | | | |
Collapse
|
40
|
Yoshida M, Ohnuki S, Yashiroda Y, Ohya Y. Profilin is required for Ca2+ homeostasis and Ca2+-modulated bud formation in yeast. Mol Genet Genomics 2013; 288:317-28. [PMID: 23708467 DOI: 10.1007/s00438-013-0752-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 05/10/2013] [Indexed: 12/11/2022]
Abstract
A cls5-1 mutant of Saccharomyces cerevisiae is specifically sensitive to high concentrations of Ca2+, with elevated intracellular calcium content and altered cell morphology in the presence of 100 mM Ca2+. To reveal the mechanisms of the Ca2+-sensitive phenotype, we investigated the gene responsible and its interacting network. We demonstrated that CLS5 is identical to PFY1, encoding profilin. Involvement of profilin in the maintenance of intracellular Ca2+ homeostasis was supported by the fact that both exchangeable and non-exchangeable intracellular Ca2+ pools in the cls5-1 mutant are higher than those of the wild-type strain. Several mutations of the genes whose proteins physically interact with profilin resulted in the Ca2+-sensitive phenotype. Examination of the intracellular Ca2+ pools indicated that Bni1p, Bem1p, Rho1p, and Cla4p are also required for the maintenance of Ca2+ homeostasis. Quantitative morphological analysis revealed that the Ca2+-induced morphological changes in cls5-1 cells are similar to bem1 and cls4-1 cells. Common Ca2+-induced morphological changes were an increase in cell size and a decrease of the ratio of budded cells in the population. Since a mutation allele of cls4-1 is located in the CDC24 gene, we suggest that profilin, Bem1p, and Cdc24p are required for Ca2+-modulated bud formation. Thus, profilin is involved in Ca2+ regulation in two ways: the first is Ca2+ homeostasis by coordination with Bni1p, Bem1p, Rho1p, and Cla4p, and the second is the requirement of Ca2+ for bud formation by coordination with Bem1p and Cdc24p.
Collapse
Affiliation(s)
- Mitsunori Yoshida
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Building FBS-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | | | | | | |
Collapse
|
41
|
Iwaki A, Ohnuki S, Suga Y, Izawa S, Ohya Y. Vanillin inhibits translation and induces messenger ribonucleoprotein (mRNP) granule formation in saccharomyces cerevisiae: application and validation of high-content, image-based profiling. PLoS One 2013; 8:e61748. [PMID: 23637899 PMCID: PMC3634847 DOI: 10.1371/journal.pone.0061748] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/13/2013] [Indexed: 11/18/2022] Open
Abstract
Vanillin, generated by acid hydrolysis of lignocellulose, acts as a potent inhibitor of the growth of the yeast Saccharomyces cerevisiae. Here, we investigated the cellular processes affected by vanillin using high-content, image-based profiling. Among 4,718 non-essential yeast deletion mutants, the morphology of those defective in the large ribosomal subunit showed significant similarity to that of vanillin-treated cells. The defects in these mutants were clustered in three domains of the ribosome: the mRNA tunnel entrance, exit and backbone required for small subunit attachment. To confirm that vanillin inhibited ribosomal function, we assessed polysome and messenger ribonucleoprotein granule formation after treatment with vanillin. Analysis of polysome profiles showed disassembly of the polysomes in the presence of vanillin. Processing bodies and stress granules, which are composed of non-translating mRNAs and various proteins, were formed after treatment with vanillin. These results suggest that vanillin represses translation in yeast cells.
Collapse
Affiliation(s)
- Aya Iwaki
- The Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
| | - Shinsuke Ohnuki
- The Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Yohei Suga
- The Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Shingo Izawa
- The Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Matsugasaki, Kyoto, Japan
| | - Yoshikazu Ohya
- The Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
| |
Collapse
|
42
|
Ohnuki S, Kobayashi T, Ogawa H, Kozone I, Ueda JY, Takagi M, Shin-Ya K, Hirata D, Nogami S, Ohya Y. Analysis of the biological activity of a novel 24-membered macrolide JBIR-19 in Saccharomyces cerevisiae by the morphological imaging program CalMorph. FEMS Yeast Res 2012; 12:293-304. [PMID: 22129199 DOI: 10.1111/j.1567-1364.2011.00770.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/23/2011] [Accepted: 11/24/2011] [Indexed: 11/29/2022] Open
Abstract
To investigate the biological activity of a novel 24-membered macrolide compound, JBIR-19, isolated from the culture broth of the entomopathogenic fungus Metarhizium sp. fE61, morphological changes in yeast cells were examined using the automated image-processing program CalMorph. Principal components analysis was used to elucidate dynamic changes in the phenotypes, revealing two independent effects of JBIR-19 in yeast cells: bud elongation and increased size of the actin region. Using a fitness assay, we identified the genes required for robust growth in the presence of JBIR-19. Among these were CCW12, YLR111W, and DHH1, which are also involved in abnormal bud morphology. Based on these results and others, we predict intracellular targets of JBIR-19 and its functional interactions.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Uchidi Y, Ohnuki S, Hashimoto N, Suda T, Nagai T, Shibayama T, Hamada K, Akasaka N, Yamashita S, Ohstuka S, Yoshitake T. Effect of Minor Alloying Element on Dispersing Nano-particles in ODS Steel. ACTA ACUST UNITED AC 2011. [DOI: 10.1557/proc-981-0981-jj07-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractFrom the irradiation resistance and high-temperature strength, oxide dispersion strengthened (ODS) ferritic steels are candidate materials for advanced and fusion reactors. For the development of advanced steels the key issue is to homogenize nano-particles into matrix. Recent studies have indicated that Ti addition can homogenize Y-Ti complex particles into ferrite matrix, but the reason of the effect of additional elements has not been clarified. In this model study, we focus on the effect of additional elements, such as IV and V families and other oxide formers, which can control potentially the distribution of the oxide particles. The materials used in this study were based on Fe-9Cr-Y2O3 alloys which were mechanical alloyed (MA) from the powder of Fe, Cr and Y2O3, which was added systematically with the element of Ti, Zr, Ta, V, Nb, Hf, Al, Si and others. Usually ODS fabrication process is required for hot extrusion, but we annealed up to 1150 C for simplify the microstructure. To evaluate the distribution of ODS particles; we used TEM equipped with EDS after electro-polishing or FIB techniques. (1) In the case of Si or Al addition, oxides were disappeared after MA process, which means Y2O3 and other elements should be in solution at non-equilibrium condition. Two types of oxides of Y2O3 and Al2O3 or SiO2 developed after the annealing at 850 C, but only complex oxides were developed after the annealing at 1150 C. This result suggests that the oxide formation is independent process for Y and Si or Al. (2) In the case of Ti addition, oxides also were disappeared after MA process, but developed after annealing at 1150 C. This means that Ti can stabilize complex oxides of Y and Ti, and enhance the fine distribution of the oxides comparing with simple Fe-9Cr-Y2O3 alloy.
Collapse
|
44
|
Abstract
Background Drug discovery and development are predicated on elucidation of the potential mechanisms of action and cellular targets of candidate chemical compounds. Recent advances in high-content imaging techniques allow simultaneous analysis of a range of cellular events. In this study, we propose a novel strategy to identify drug targets by combining genetic screening and high-content imaging in yeast. Methodology In this approach, we infer the cellular functions affected by candidate drugs by comparing morphologic changes induced by the compounds with the phenotypes of yeast mutants. Conclusions Using this method and four well-characterized reagents, we successfully identified previously known target genes of the compounds as well as other genes involved with functionally related cellular pathways. This is the first demonstration of a genetic high-content assay that can be used to identify drug targets based on morphologic phenotypes of a reference mutant panel.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Satomi Oka
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Satoru Nogami
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- * E-mail:
| |
Collapse
|
45
|
Yamagishi H, Ohnuki S, Nogami S, Ogata T, Ohya Y. Role of bottom-fermenting brewer's yeast KEX2 in high temperature resistance and poor proliferation at low temperatures. J GEN APPL MICROBIOL 2010; 56:297-312. [DOI: 10.2323/jgam.56.297] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
46
|
Ohnuki S, Nogami S, Ohya Y. A microfluidic device to acquire high-magnification microphotographs of yeast cells. Cell Div 2009; 4:5. [PMID: 19317904 PMCID: PMC2669073 DOI: 10.1186/1747-1028-4-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2008] [Accepted: 03/24/2009] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Yeast cell morphology was investigated to reveal the molecular mechanisms of cell morphogenesis and to identify key factors of other processes such as cell cycle progression. We recently developed a semi-automatic image processing program called CalMorph, which allows us to quantitatively analyze yeast cell morphology with the 501 parameters as biological traits and uncover statistical relationships between cell morphological phenotypes and genotypes. However, the current semi-automatic method is not suitable for morphological analysis of large-scale yeast mutants for the reliable prediction of gene functions because of its low-throughput especially at the manual image-acquiring process. RESULTS In this study, we developed a microfluidic chip designed to acquire successive microscopic images of yeast cells suitable for CalMorph image analysis. With the microfluidic chip, the morphology of living cells and morphological changes that occur during the cell cycle were successfully characterized. CONCLUSION The microfluidic chip enabled us to acquire the images faster than the conventional method. We speculate that the use of microfluidic chip is effective in acquiring images of large-scale for automated analysis of yeast strains.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg, FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
| | | | | |
Collapse
|
47
|
Ohnuki S, Nogami S, Kanai H, Hirata D, Nakatani Y, Morishita S, Ohya Y. Diversity of Ca2+-induced morphology revealed by morphological phenotyping of Ca2+-sensitive mutants of Saccharomyces cerevisiae. Eukaryot Cell 2007; 6:817-30. [PMID: 17351076 PMCID: PMC1899241 DOI: 10.1128/ec.00012-07] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Yeast cell morphology can be treated as a quantitative trait using the image processing software CalMorph. In the present study, we investigated Ca(2+)-induced morphological changes in Ca(2+)-sensitive (cls) mutants of Saccharomyces cerevisiae, based on the discovery that the characteristic Ca(2+)-induced morphological changes in the Ca(2+)-sensitive mutant zds1 reflect changes in the Ca(2+) signaling-mediated cell cycle control pathway. By applying hierarchical cluster analysis to the quantitative morphological data of 58 cls mutants, 31 of these mutants were classified into seven classes based on morphological similarities. The patterns of morphological change induced by Ca(2+) in one class differed from those of another class. Based on the results obtained using versatile methods for phenotypic analysis, we conclude that a high concentration of Ca(2+) exerts a wide variety of effects on yeast and that there are multiple Ca(2+)-regulatory pathways that are distinct from the Zds1p-related pathway.
Collapse
Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bldg. FSB-101, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | | | | | | | | | | | | |
Collapse
|
48
|
Wakai E, Ohtsuka H, Matsukawa S, Furuya K, Tanigawa H, Oka K, Ohnuki S, Yamamoto T, Takada F, Jitsukawa S. Mechanical properties of small size specimens of F82H steel. Fusion Engineering and Design 2006. [DOI: 10.1016/j.fusengdes.2005.08.072] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
49
|
Takahashi H, Hidaka Y, Ohnuki S. Observation of point defect production and clustering by high voltage electron microscopy: Interaction of point defect with solutes. Micron 1996. [DOI: 10.1016/0968-4328(96)00012-1] [Citation(s) in RCA: 9] [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: 11/28/2022]
|
50
|
Takeyama T, Ohnuki S, Takahashi H. Direct observation of radiation induced segregation near grain boundary and void in copper alloys. ACTA ACUST UNITED AC 1980. [DOI: 10.1016/0036-9748(80)90214-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|