1
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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2
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Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. Single mutation makes Escherichia coli an insect mutualist. Nat Microbiol 2022; 7:1141-1150. [PMID: 35927448 PMCID: PMC9352592 DOI: 10.1038/s41564-022-01179-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023]
Abstract
Microorganisms often live in symbiosis with their hosts, and some are considered mutualists, where all species involved benefit from the interaction. How free-living microorganisms have evolved to become mutualists is unclear. Here we report an experimental system in which non-symbiotic Escherichia coli evolves into an insect mutualist. The stinkbug Plautia stali is typically associated with its essential gut symbiont, Pantoea sp., which colonizes a specialized symbiotic organ. When sterilized newborn nymphs were infected with E. coli rather than Pantoea sp., only a few insects survived, in which E. coli exhibited specific localization to the symbiotic organ and vertical transmission to the offspring. Through transgenerational maintenance with P. stali, several hypermutating E. coli lines independently evolved to support the host's high adult emergence and improved body colour; these were called 'mutualistic' E. coli. These mutants exhibited slower bacterial growth, smaller size, loss of flagellar motility and lack of an extracellular matrix. Transcriptomic and genomic analyses of 'mutualistic' E. coli lines revealed independent mutations that disrupted the carbon catabolite repression global transcriptional regulator system. Each mutation reproduced the mutualistic phenotypes when introduced into wild-type E. coli, confirming that single carbon catabolite repression mutations can make E. coli an insect mutualist. These findings provide an experimental system for future work on host-microbe symbioses and may explain why microbial mutualisms are omnipresent in nature.
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Affiliation(s)
- Ryuichi Koga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.
| | - Minoru Moriyama
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Naoko Onodera-Tanifuji
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshiko Ishii
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiroki Takai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Masaki Mizutani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Kohei Oguchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Reiko Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shingo Suzuki
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahide Seki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yutaka Suzuki
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yudai Nishide
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,National Agriculture and Food Research Organization, Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Takahiro Hosokawa
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Chikara Furusawa
- Center for Biosystem Dynamics Research, RIKEN, Osaka, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
| | - Takema Fukatsu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan. .,Department of Biological Sciences, The University of Tokyo, Tokyo, Japan. .,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
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3
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Yamauchi S, Nozoe T, Okura R, Kussell E, Wakamoto Y. A unified framework for measuring selection on cellular lineages and traits. eLife 2022; 11:72299. [PMID: 36472074 PMCID: PMC9725751 DOI: 10.7554/elife.72299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/28/2022] [Indexed: 12/12/2022] Open
Abstract
Intracellular states probed by gene expression profiles and metabolic activities are intrinsically noisy, causing phenotypic variations among cellular lineages. Understanding the adaptive and evolutionary roles of such variations requires clarifying their linkage to population growth rates. Extending a cell lineage statistics framework, here we show that a population's growth rate can be expanded by the cumulants of a fitness landscape that characterize how fitness distributes in a population. The expansion enables quantifying the contribution of each cumulant, such as variance and skewness, to population growth. We introduce a function that contains all the essential information of cell lineage statistics, including mean lineage fitness and selection strength. We reveal a relation between fitness heterogeneity and population growth rate response to perturbation. We apply the framework to experimental cell lineage data from bacteria to mammalian cells, revealing distinct levels of growth rate gain from fitness heterogeneity across environments and organisms. Furthermore, third or higher order cumulants' contributions are negligible under constant growth conditions but could be significant in regrowing processes from growth-arrested conditions. We identify cellular populations in which selection leads to an increase of fitness variance among lineages in retrospective statistics compared to chronological statistics. The framework assumes no particular growth models or environmental conditions, and is thus applicable to various biological phenomena for which phenotypic heterogeneity and cellular proliferation are important.
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Affiliation(s)
- Shunpei Yamauchi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of TokyoTokyoJapan
| | - Takashi Nozoe
- Department of Basic Science, Graduate School of Arts and Sciences, The University of TokyoTokyoJapan
| | - Reiko Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of TokyoTokyoJapan
| | - Edo Kussell
- Department of Biology, New York UniversityNew YorkUnited States,Department of Physics, New York UniversityNew YorkUnited States
| | - Yuichi Wakamoto
- Department of Basic Science, Graduate School of Arts and Sciences, The University of TokyoTokyoJapan,Research Center for Complex Systems Biology, The University of TokyoTokyoJapan,Universal Biology Institute, The University of TokyoTokyoJapan
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4
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Wu Y, Zhao L, Chang Y, Zhao L, Guo G, Wang X. Ultra-thin temperature controllable microwell array chip for continuous real-time high-resolution imaging of living single cells. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.05.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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5
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Du H, Xu W, Zhang Z, Han X. Bacterial Behavior in Confined Spaces. Front Cell Dev Biol 2021; 9:629820. [PMID: 33816474 PMCID: PMC8012557 DOI: 10.3389/fcell.2021.629820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/19/2021] [Indexed: 11/30/2022] Open
Abstract
In confined spaces, bacteria exhibit unexpected cellular behaviors that are related to the biogeochemical cycle and human health. Types of confined spaces include lipid vesicles, polymer vesicles, emulsion droplets, microfluidic chips, and various laboratory-made chambers. This mini-review summarizes the behaviors of living bacteria in these confined spaces, including (a) growth and proliferation, (b) cell communication, and (c) motion. Future trends and challenges are also discussed in this paper.
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Affiliation(s)
- Hang Du
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China.,Center for Marine Antifouling Engineering Technology of Shandong Province, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Weili Xu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Zhizhou Zhang
- Center for Marine Antifouling Engineering Technology of Shandong Province, School of Marine Science and Technology, Harbin Institute of Technology, Weihai, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
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6
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On-Chip Micro Mixer Driven by Elastic Wall with Virtual Actuator. MICROMACHINES 2021; 12:mi12020217. [PMID: 33670037 PMCID: PMC7926952 DOI: 10.3390/mi12020217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 11/17/2022]
Abstract
In this paper, we propose an on-chip micromixer driven by an elastic wall with a virtual actuator. The on-chip micro mixer is composed of a circular chamber surrounded by a ring-shaped channel under isolation with an elastic wall. When vibrational pressure is put on the driving channel by an actuator, the volume of the circular chamber changes through the deformation of the elastic wall, as if there exists a virtual actuator near the wall. As a result, the liquid in the circular chamber is pushed out and pulled through the neck channel. This action creates a swirling flow in the circular chamber while maintaining isolation from the driving channel. Through experiments, we confirmed the swirling flow under an isolated environment using an air-based valve. The advantage of this approach is that the micromixer can be designed with a single layer having a simple mechanism.
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Manzoor AA, Romita L, Hwang DK. A review on microwell and microfluidic geometric array fabrication techniques and its potential applications in cellular studies. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23875] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ahmad Ali Manzoor
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| | - Lauren Romita
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| | - Dae Kun Hwang
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
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8
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Kimoto T, Suzuki K, Fukuda T, Emoto A. An on-demand bench-top fabrication process for fluidic chips based on cross-diffusion through photopolymerization. BIOMICROFLUIDICS 2020; 14:044104. [PMID: 32699564 PMCID: PMC7354092 DOI: 10.1063/5.0014956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
In this paper, we propose a novel approach to fabricate fluidic chips. The method utilizes molecular cross-diffusion, induced by photopolymerization under ultraviolet (UV) irradiation in a channel pattern, to form the channel structures. During channel structure formation, the photopolymer layer still contains many uncured molecules. Subsequently, a top substrate is attached to the channel structure under adequate pressure, and the entire chip is homogenously irradiated by UV light. Immediately thereafter, a sufficiently sealed fluidic chip is formed. Using this fabrication process, the channel pattern of a chip can be designed quickly by a computer as binary images, and practical chips can be produced on demand at a benchtop, instead of awaiting production in specialized factories.
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Affiliation(s)
- Takumi Kimoto
- Graduate School of Science and Engineering, Doshisha University, 1-3 Tatara-Miyakodani, Kyotanabe, Kyoto 610-0321, Japan
| | - Kou Suzuki
- Graduate School of Science and Engineering, Doshisha University, 1-3 Tatara-Miyakodani, Kyotanabe, Kyoto 610-0321, Japan
| | - Takashi Fukuda
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Akira Emoto
- Institute of Post-LED Photonics (pLED), Tokushima University, 2-1 Minami-Josanjima, Tokushima, Tokushima 770-8506, Japan
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9
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Takano M, Yura K, Uyeda T, Yasuda K. Biophysics at Waseda University. Biophys Rev 2020; 12:225-232. [PMID: 32157615 PMCID: PMC7242523 DOI: 10.1007/s12551-020-00638-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 02/05/2020] [Indexed: 12/20/2022] Open
Abstract
Biophysics in Waseda University was started in 1965 as one of the three key research areas that constitute the Physics Department. In the biophysics group, one theoretical lab and two experimental labs are now working on the cutting-edge themes on biophysics, disseminating the ideas and knowledge of biophysics to undergraduate and graduate students from the viewpoint of physics.
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Affiliation(s)
- Mitsunori Takano
- Department of Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Kei Yura
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Taro Uyeda
- Department of Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Kenji Yasuda
- Department of Physics, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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10
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Long-term observation of Magnetospirillum gryphiswaldense in a microfluidic channel. Arch Microbiol 2019; 201:1427-1433. [PMID: 31414157 PMCID: PMC6817740 DOI: 10.1007/s00203-019-01713-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/22/2019] [Accepted: 08/02/2019] [Indexed: 11/02/2022]
Abstract
We controlled and observed individual magneto-tactic bacteria (Magnetospirillum gryphiswaldense) inside a \documentclass[12pt]{minimal}
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\begin{document}$$5\, \upmu \hbox {m}$$\end{document}5μm-high microfluidic channel for over 4 h. After a period of constant velocity, the duration of which varied between bacteria, all observed bacteria showed a gradual decrease in their velocity of about \documentclass[12pt]{minimal}
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\begin{document}$$25\, \hbox {nm}/\hbox {s}^2$$\end{document}25nm/s2. After coming to a full stop, different behaviour was observed, ranging from rotation around the centre of mass synchronous with the direction of the external magnetic field, to being completely immobile. Our results suggest that the influence of the high-intensity illumination and the presence of the channel walls are important parameters to consider when performing observations of such long duration.
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11
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Agarose-based microwell array chip for high-throughput screening of functional microorganisms. Talanta 2019; 191:342-349. [DOI: 10.1016/j.talanta.2018.08.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 11/23/2022]
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12
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Morita M, Katoh K, Noda N. Direct Observation of Bacterial Growth in Giant Unilamellar Vesicles: A Novel Tool for Bacterial Cultures. ChemistryOpen 2018; 7:845-849. [PMID: 30402373 PMCID: PMC6208190 DOI: 10.1002/open.201800126] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Indexed: 12/28/2022] Open
Abstract
Bacterial cultivation techniques are classic, basic, and common processes used to characterize the physiological activity of bacteria in their environment. Owing to recent advances in bacterial cultivation techniques, the physiological activity of bacteria can be elucidated at the single-cell culture level. Here, we report a novel method to monitor the real-time activity of bacterial growth at the single-cell level inside giant unilamellar vesicles (GUVs). This method consists of two steps: 1) encapsulation of single bacteria in 1-33 pL scale GUVs and 2) immobilization of the GUVs on a planar lipid bilayer membrane on a glass surface. We directly observed single E. coli cells actively growing to a great number of cells inside GUVs. GUVs also protected the bacteria from external antibiotic compounds during prolonged cultivation for more than 24 h. This approach can be applied widely in the fields of biochemistry, biotechnology, microbiology, and synthetic biology.
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Affiliation(s)
- Masamune Morita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Center 6 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
| | - Kaoru Katoh
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Center 6 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
| | - Naohiro Noda
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST), Center 6 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
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13
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Takayama T, Miyashiro H, Tsai CHD, Ito H, Kaneko M. On-chip density mixer enhanced by air chamber. BIOMICROFLUIDICS 2018; 12:044108. [PMID: 30057654 PMCID: PMC6041114 DOI: 10.1063/1.5033482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/26/2018] [Indexed: 06/08/2023]
Abstract
This paper proposes an on-chip density mixer that can achieve even density in a target chamber with a swirling flow enhanced by an air chamber. The system is composed of a main channel, a target chamber where two liquids with different densities are included, an isolated air chamber, and an external vibration pump driven by a piezo actuator at the entrance of the main channel. The air chamber is expected to amplify the vibration owing to structure softening. The amplification would be more pronounced at the resonance frequencies of the structure. We developed the system and conducted experiments. We showed that the swirling motion in the target chamber with an air chamber is stronger than that without an air chamber. We also confirmed that the time resulting in even density is shorter when the pump is driven at a resonance frequency. An air-based virtual valve is introduced for maintaining a constant density in the target chamber.
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Affiliation(s)
- Toshio Takayama
- Department of Mechanical Engineering, Osaka University, Suita 565-0871, Japan
| | - Hiroki Miyashiro
- Department of Mechanical Engineering, Osaka University, Suita 565-0871, Japan
| | - Chia-Hung Dylan Tsai
- Department of Mechanical Engineering, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Hiroaki Ito
- Department of Mechanical Engineering, Osaka University, Suita 565-0871, Japan
| | - Makoto Kaneko
- Department of Mechanical Engineering, Osaka University, Suita 565-0871, Japan
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14
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Nai C, Meyer V. From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology. Trends Microbiol 2018; 26:538-554. [DOI: 10.1016/j.tim.2017.11.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/25/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023]
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15
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Wang C, Liu W, Wei Q, Ren L, Tan M, Yu Y. A novel dual-well array chip for efficiently trapping single-cell in large isolated micro-well without complicated accessory equipment. BIOMICROFLUIDICS 2018; 12:034103. [PMID: 29774084 PMCID: PMC5938174 DOI: 10.1063/1.5030203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Conventional cell-sized well arrays have advantages of high occupancy, simple operation, and low cost for capturing single-cells. However, they have insufficient space for including reagents required for cell treatment or analysis, which restricts the wide application of cell-sized well arrays as a single-cell research tool alone. Here, we present a novel dual-well array chip, which integrates capture-wells (20 μm in diameter) with reaction-wells (100 μm in diameter) and describe a flow method for convenient single-cell analysis requiring neither complicated infra-structure nor high expenditure, while enabling highly efficient single cell trapping (75.8%) with only 11.3% multi-cells. Briefly, the cells are first loaded into the dual-wells by gravity and then multi-cells in the reaction-wells are washed out by phosphate buffer saline. Next, biochemical reagents are loaded into reaction-wells using the scraping method and the chip is packed as a sandwich structure. We thereby successfully measured intracellular β-galactosidase activity of K562 cells at the single-cell level. We also used computational simulations to illustrate the working principle of dual-well structure and found out a relationship between the wall shear stress distribution and the aspect ratio of the dual-well array chip which provides theoretical guidance for designing multi-wells chip for convenient single-cell analysis. Our work produced the first dual-well chip that can simultaneously provide a high occupancy rate for single cells and sufficient space for reagents, as well as being low in cost and simple to operate. We believe that the feasibility and convenience of our method will enhance its use as a practical single-cell research tool.
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Affiliation(s)
| | | | | | | | | | - Yude Yu
- Author to whom correspondence should be addressed: . Tel.: 86-10-82304979
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16
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Heins AL, Weuster-Botz D. Population heterogeneity in microbial bioprocesses: origin, analysis, mechanisms, and future perspectives. Bioprocess Biosyst Eng 2018. [PMID: 29541890 DOI: 10.1007/s00449-018-1922-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Population heterogeneity is omnipresent in all bioprocesses even in homogenous environments. Its origin, however, is only so well understood that potential strategies like bet-hedging, noise in gene expression and division of labour that lead to population heterogeneity can be derived from experimental studies simulating the dynamics in industrial scale bioprocesses. This review aims at summarizing the current state of the different parts of single cell studies in bioprocesses. This includes setups to visualize different phenotypes of single cells, computational approaches connecting single cell physiology with environmental influence and special cultivation setups like scale-down reactors that have been proven to be useful to simulate large-scale conditions. A step in between investigation of populations and single cells is studying subpopulations with distinct properties that differ from the rest of the population with sub-omics methods which are also presented here. Moreover, the current knowledge about population heterogeneity in bioprocesses is summarized for relevant industrial production hosts and mixed cultures, as they provide the unique opportunity to distribute metabolic burden and optimize production processes in a way that is impossible in traditional monocultures. In the end, approaches to explain the underlying mechanism of population heterogeneity and the evidences found to support each hypothesis are presented. For instance, population heterogeneity serving as a bet-hedging strategy that is used as coordinated action against bioprocess-related stresses while at the same time spreading the risk between individual cells as it ensures the survival of least a part of the population in any environment the cells encounter.
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Affiliation(s)
- Anna-Lena Heins
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany.
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstr. 15, 85748, Garching, Germany
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17
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Zhang P, Xiao Y, Li Z, Guo J, Lu L. Microalgae in Microwell Arrays Exhibit Differences with Those in Flasks: Evidence from Growth Rate, Cellular Carotenoid, and Oxygen Production. FRONTIERS IN PLANT SCIENCE 2018; 8:2251. [PMID: 29379513 PMCID: PMC5770892 DOI: 10.3389/fpls.2017.02251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
Microalgae are cultivated in macro-scale reactors traditionally and the relevant knowledge is based on bulk analysis. Whether the knowledge and laws are true for cells under micro-cultivation is still unknown. To better understand microalgal physiology, micro-cultivation of microalgae, and unicellular tracking and analysis of its response in vivo is necessary. In the study, cellular responses of Chlorella vulgaris to micro-cultivation is studied, with cells in flasks as a control. Five different microwell depths ranging from 10 to 200 μm with a fixed diameter of 100 μm, and four diameter levels from 30 to 200 μm with a fixed depth 60 μm were investigated. Unicellular dynamics showed that cell number differences among various types of microwells with different initial cell numbers decreased as cultivation processed. Besides, the specific growth rate of C. vulgaris on microwell arrays was much higher than that in flasks and so cells on microwell arrsys can be much sensitive to pollutants. Thus, the interesting characteristics may be used in cell sensor applications to enhance sensitivity. The specific growth rate of C. vulgaris on microwell arrays decreased gradually as the microwell diameter increased from 30 to 200 μm while presented a unimodal trend as depth decreased from 200 to 10 μm. Furthermore, we used Raman Spectroscopy and Non-invasive Micro-test Technique to analyze cellular responses in microwells for the first time to track the changes in vivo. Results indicated that unicellular carotenoid content increased as microwells became larger and shallower. The flow rate of oxygen rose gradually as the depth increased from 10 to 100 μm, but then decreased rapidly as the depth deepened to 200 μm. In fact, it is a combined result of cell physiology and density. In summary, cells in microwells with the diameter/depth ratio ~1 owned the highest specific growth rates and oxygen flow rates. Simulations also suggested that better mass transfer occurred in microwells with higher diameter-to-depth ratios.
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Affiliation(s)
- Ping Zhang
- Department of Environmental Science and Engineering, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
- CAS Key Lab of Reservoir Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Yan Xiao
- CAS Key Lab of Reservoir Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Zhe Li
- Department of Environmental Science and Engineering, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
- CAS Key Lab of Reservoir Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
| | - Jinsong Guo
- Department of Environmental Science and Engineering, College of Urban Construction and Environmental Engineering, Chongqing University, Chongqing, China
| | - Lunhui Lu
- CAS Key Lab of Reservoir Environment, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, China
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18
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Cohen L, Walt DR. Single-Molecule Arrays for Protein and Nucleic Acid Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:345-363. [PMID: 28301748 DOI: 10.1146/annurev-anchem-061516-045340] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The last few years have seen breakthroughs that will transform our ability to measure important analytes. Miniaturization of reaction volumes and confinement of analytes of interest into ultrasmall containers have greatly enhanced the sensitivity and throughput of many detection methods. Fabrication of microwell arrays and implementation of bead-based assays have been instrumental in the development of methods for measuring relevant biomolecules, with applications to both diagnostics and fundamental biological studies. In this review, we describe how microwell arrays are fabricated and utilized for measuring analytes of interest. We then discuss the fundamental concepts of digital enzyme-linked immunosorbent assay (ELISA) using single-molecule arrays and applications of microwell arrays to ultrasensitive protein measurements. We also explore the utility of microwell arrays for nucleic acid detection and applications for single-cell studies.
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Affiliation(s)
- Limor Cohen
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155;
| | - David R Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155;
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19
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Mansoorifar A, Koklu A, Sabuncu AC, Beskok A. Dielectrophoresis assisted loading and unloading of microwells for impedance spectroscopy. Electrophoresis 2017; 38:1466-1474. [PMID: 28256738 PMCID: PMC5547746 DOI: 10.1002/elps.201700020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 12/19/2022]
Abstract
Dielectric spectroscopy (DS) is a noninvasive, label-free, fast, and promising technique for measuring dielectric properties of biological cells in real time. We demonstrate a microchip that consists of electro-activated microwell arrays for positive dielectrophoresis assisted cell capture, DS measurements, and negative dielectrophoresis driven cell unloading; thus, providing a high-throughput cell analysis platform. To the best of our knowledge, this is the first microfluidic chip that combines electro-activated microwells and DS to analyze biological cells. Device performance is tested using Saccharomyces cerevisiae (yeast) cells. DEP response of yeast cells is determined by measuring their Clausius-Mossotti factor using biophysical models in parallel plate microelectrode geometry. This information is used to determine the excitation frequency to load and unload wells. Effect of yeast cells on the measured impedance spectrum was examined both experimentally and numerically. Good match between the numerical and experimental results establishes the potential use of the microchip device for extracting subcellular properties of biological cells in a rapid and nonexpensive manner.
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Affiliation(s)
- Amin Mansoorifar
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75205, USA
| | - Anil Koklu
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75205, USA
| | - Ahmet Can Sabuncu
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75205, USA
| | - Ali Beskok
- Department of Mechanical Engineering, Southern Methodist University, Dallas, TX 75205, USA
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20
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Abstract
Cellular populations in both nature and the laboratory are composed of phenotypically heterogeneous individuals that compete with each other resulting in complex population dynamics. Predicting population growth characteristics based on knowledge of heterogeneous single-cell dynamics remains challenging. By observing groups of cells for hundreds of generations at single-cell resolution, we reveal that growth noise causes clonal populations of Escherichia coli to double faster than the mean doubling time of their constituent single cells across a broad set of balanced-growth conditions. We show that the population-level growth rate gain as well as age structures of populations and of cell lineages in competition are predictable. Furthermore, we theoretically reveal that the growth rate gain can be linked with the relative entropy of lineage generation time distributions. Unexpectedly, we find an empirical linear relation between the means and the variances of generation times across conditions, which provides a general constraint on maximal growth rates. Together, these results demonstrate a fundamental benefit of noise for population growth, and identify a growth law that sets a "speed limit" for proliferation.
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21
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Nawaz AA, Chen Y, Nama N, Nissly RH, Ren L, Ozcelik A, Wang L, McCoy JP, Levine SJ, Huang TJ. Acoustofluidic Fluorescence Activated Cell Sorter. Anal Chem 2015; 87:12051-8. [PMID: 26331909 PMCID: PMC4888785 DOI: 10.1021/acs.analchem.5b02398] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Selective isolation of cell subpopulations with defined biological characteristics is crucial for many biological studies and clinical applications. In this work, we present the development of an acoustofluidic fluorescence activated cell sorting (FACS) device that simultaneously performs on-demand, high-throughput, high-resolution cell detection and sorting, integrated onto a single chip. Our acoustofluidic FACS device uses the "microfluidic drifting" technique to precisely focus cells/particles three dimensionally and achieves a flow of single-file particles/cells as they pass through a laser interrogation region. We then utilize short bursts (150 μs) of standing surface acoustic waves (SSAW) triggered by an electronic feedback system to sort fluorescently labeled particles/cells with desired biological properties. We have demonstrated continuous isolation of fluorescently labeled HeLa cells from unlabeled cells at a throughput of ∼1200 events/s with a purity reaching 92.3 ± 3.39%. Furthermore, 99.18% postsort cell viability indicates that our acoustofluidic sorting technique maintains a high integrity of cells. Therefore, our integrated acoustofluidic FACS device is demonstrated to achieve two-way cell sorting with high purity, biocompatibility, and biosafety. We believe that our device has significant potential for use as a low-cost, high-performance, portable, and user-friendly FACS instrument.
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Affiliation(s)
- Ahmad Ahsan Nawaz
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad H-12, Pakistan
| | - Yuchao Chen
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Nitesh Nama
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ruth Helmus Nissly
- Microscopy and Cytometry Facility, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Liqiang Ren
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Adem Ozcelik
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Lin Wang
- Ascent Bio-Nano Technologies Inc., State College, Pennsylvania 16801, United States
| | - J. Philip McCoy
- National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, United States
| | - Stewart J. Levine
- National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, United States
| | - Tony Jun Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Conejero-Muriel M, Rodríguez-Ruiz I, Martínez-Rodríguez S, Llobera A, Gavira JA. McCLEC, a robust and stable enzymatic based microreactor platform. LAB ON A CHIP 2015; 15:4083-9. [PMID: 26334474 DOI: 10.1039/c5lc00776c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A microfluidic chip for cross-linked enzyme crystals (McCLEC) is presented and demonstrated to be a stable, reusable and robust biocatalyst-based device with very promising biotechnological applications. The cost-effective microfluidic platform allows in situ crystallization, cross-linking and enzymatic reaction assays on a single device. A large number of enzymatic reuses of the McCLEC platform were achieved and a comparative analysis is shown illustrating the efficiency of the process and its storage stability for more than one year.
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Affiliation(s)
- Mayte Conejero-Muriel
- Laboratorio de Estudios Cristalográficos, Laboratorio de Estudios Cristalográficos, IACT (CSIC-UGR), Avda de las Palmeras, 4, 18100 Armilla, Granada, Spain.
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23
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Wang C, Yu C. Analytical characterization using surface-enhanced Raman scattering (SERS) and microfluidic sampling. NANOTECHNOLOGY 2015; 26:092001. [PMID: 25676092 DOI: 10.1088/0957-4484/26/9/092001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
With the rapid development of analytical techniques, it has become much easier to detect chemical and biological analytes, even at very low detection limits. In recent years, techniques based on vibrational spectroscopy, such as surface enhanced Raman spectroscopy (SERS), have been developed for non-destructive detection of pathogenic microorganisms. SERS is a highly sensitive analytical tool that can be used to characterize chemical and biological analytes interacting with SERS-active substrates. However, it has always been a challenge to obtain consistent and reproducible SERS spectroscopic results at complicated experimental conditions. Microfluidics, a tool for highly precise manipulation of small volume liquid samples, can be used to overcome the major drawbacks of SERS-based techniques. High reproducibility of SERS measurement could be obtained in continuous flow generated inside microfluidic devices. This article provides a thorough review of the principles, concepts and methods of SERS-microfluidic platforms, and the applications of such platforms in trace analysis of chemical and biological analytes.
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24
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Focaroli S, Mazzitelli S, Falconi M, Luca G, Nastruzzi C. Preparation and validation of low cost microfluidic chips using a shrinking approach. LAB ON A CHIP 2014; 14:4007-16. [PMID: 25144915 DOI: 10.1039/c4lc00679h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The present paper describes the production of microfluidic chips using an approach based on shrinkable biocompatible polymers (i.e. agarose) for the production of size controlled microfluidic channels. In addition, all steps of chip production were carried out using an inexpensive approach that uses low cost chemicals and equipment. The produced chips were then validated by producing monodisperse polymeric microparticles for drug delivery and hydrogel microfibers for cell embedding.
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Affiliation(s)
- S Focaroli
- DIBINEM-Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
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25
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Zheng GX, Li YJ, Qi LL, Liu XM, Wang H, Yu SP, Wang YH. Marine phytoplankton motility sensor integrated into a microfluidic chip for high-throughput pollutant toxicity assessment. MARINE POLLUTION BULLETIN 2014; 84:147-154. [PMID: 24882443 DOI: 10.1016/j.marpolbul.2014.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 06/03/2023]
Abstract
A microfluidic chip was designed to assess the toxicity of pollutants in a high-throughput way by using marine phytoplankton motility as a sensor signal. In this chip, multiple gradient generators (CGGs) with diffusible chambers enable large scale of dose-response bioassays to be performed in a simple way. Two mobile marine phytoplankton cells were confined on-chip and stimulated by 8 concentrations (generated by CGG) of Hg, Pb, Cu and phenol singly, as well as Cu and phenol jointly. CASA system was used to characterize motility by motile percentage (%MOT), curvilinear velocity (VCL), average path velocity (VAP) and straight line velocity (VSL). In all cases, dose-dependent inhibitions of motility were observed. In the present system, only 2h was needed to predict EC50. Thus, the developed microfluidic chip device was proved to be useful as a rapid/simple and high-throughput test method in marine pollution toxicity assessment.
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Affiliation(s)
- Guo-xia Zheng
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China.
| | - Ya-jie Li
- Medical School, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China
| | - Lin-lin Qi
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Medical School, Dalian University, Dalian, China
| | - Xian-ming Liu
- Microfluidic Research Institute, Dalian University, Dalian, China; Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Hu Wang
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China
| | - Shu-ping Yu
- Chemical and Environmental Engineering Institute, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China
| | - Yun-hua Wang
- Medical School, Dalian University, Dalian, China; Microfluidic Research Institute, Dalian University, Dalian, China.
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26
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Yue T, Nakajima M, Takeuchi M, Fukuda T. Improved Laser Manipulation for On-chip Fabricated Microstructures Based on Solution Replacement and Its Application in Single Cell Analysis. INT J ADV ROBOT SYST 2014. [DOI: 10.5772/57518] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In this paper, we present the fabrication and assembly of microstructures inside a microfluidic device based on a photocrosslinkable resin and optical tweezers. We also report a method of solution replacement inside the microfluidic channel in order to improve the manipulation performance and apply the assembled microstructures for single cell cultivation. By the illumination of patterned ultraviolet (UV) through a microscope, microstructures of arbitrary shape were fabricated by the photocrosslinkable resin inside a microfluidic channel. Based on the microfluidic channel with both glass and polydimethylsiloxane (PDMS) surfaces, immovable and movable microstructures were fabricated and manipulated. The microstructures were fabricated at the desired places and manipulated by the optical tweezers. A rotational microstructure including a microgear and a rotation axis was assembled and rotated in demonstrating this technique. The improved laser manipulation of microstructures was achieved based on the on-chip solution replacement method. The manipulation speed of the microstructures increased when the viscosity of the solvent decreased. The movement efficiency of the fabricated microstructures inside the lower viscosity solvent was evaluated and compared with those microstructures inside the former high viscosity solvent. A novel cell cage was fabricated and the cultivation of a single yeast cell ( w303) was demonstrated in the cell cage, inside the microfluidic device.
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Affiliation(s)
- Tao Yue
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
| | - Masahiro Nakajima
- Center for Micro-Nano Mechatronics of Nagoya University, Nagoya, Japan
| | - Masaru Takeuchi
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
| | - Toshio Fukuda
- Department of Micro-Nano Systems Engineering, Nagoya University, Nagoya, Japan
- School of Mechatronic Engineering, Beijing Institute of Technology, Beijing, China
- Faculty of Science and Engineering, Meijo University, Nagoya, Japan
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27
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Xu Z, Oleschuk RD. A fluorous porous polymer monolith photo-patterned chromatographic column for the separation of a flourous/fluorescently labeled peptide within a microchip. Electrophoresis 2013; 35:441-9. [DOI: 10.1002/elps.201300365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/15/2013] [Accepted: 10/15/2013] [Indexed: 11/12/2022]
Affiliation(s)
- Zhenpo Xu
- Department of Chemistry; Queen's University; Kingston Ontario Canada
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28
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Yasuda K. On-chip cellomics: Single-cell-based constructive cell-network assay for quasi-in vivo screening of cardiotoxicity. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2013; 2013:2825-8. [PMID: 24110315 DOI: 10.1109/embc.2013.6610128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have developed methods and systems of analyzing epigenetic information in cells, as well as that of genetic information, to expand our understanding of how living systems are determined. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an 'algebraic' system (emphasis on temporal aspects) and as a 'geometric' system (emphasis on spatial aspects). As an example of the 'geometric' system, we have developed an quasi-in vivo hiPS cardiomyocyte network assay and confirmed that it can predict the risk of lethal arrythmia correctly in 22 compounds. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.
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29
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Shirokawa Y, Shimada M. Sex allocation pattern of the diatom Cyclotella meneghiniana. Proc Biol Sci 2013; 280:20130503. [PMID: 23760641 DOI: 10.1098/rspb.2013.0503] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Sex allocation is one of the most successful applications of evolutionary game theory. This theory has usually been applied to multicellular organisms; however, conditional sex allocation in unicellular organisms remains an unexplored field of research. Observations at the cellular level are indispensable for an understanding of the phenotypic sex allocation strategy among individuals within clonal unicellular organisms. The diatom Cyclotella meneghiniana, in which the sexes are generated from vegetative cells, is suitable for investigating effects of phenotypic plasticity factors on sex allocation while excluding genetic differences. We designed a microfluidic system that allowed us to trace the fate of individual cells. Sex allocation by individual mother cells was affected by cell lineage, cell size and cell density. Sibling cell pairs tended to differentiate into the same fates (split sex ratio). We found a significant negative correlation between the cell area of the mother cell and sex ratio of the two sibling cells. The male-biased sex ratio declined with higher local cell population density, supporting the fertility insurance hypothesis. Our results characterize multiple non-genetic factors that affect the phenotypic single cell-level sex allocation. Sex allocation in diatoms may provide a model system for testing evolutionary game theory in unicellular organisms.
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Affiliation(s)
- Y Shirokawa
- Department of Systems Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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30
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Semi-circular microgrooves to observe active movements of individual Navicula pavillardii cells. J Microbiol Methods 2013; 92:349-54. [DOI: 10.1016/j.mimet.2013.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/10/2013] [Accepted: 01/10/2013] [Indexed: 11/20/2022]
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31
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On-chip cellomics assay enabling algebraic and geometric understanding of epigenetic information in cellular networks of living systems. 1. Temporal aspects of epigenetic information in bacteria. SENSORS 2012; 12:7169-206. [PMID: 22969343 PMCID: PMC3435972 DOI: 10.3390/s120607169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 05/24/2012] [Accepted: 05/24/2012] [Indexed: 11/16/2022]
Abstract
A series of studies aimed at developing methods and systems of analyzing epigenetic information in cells and in cell networks, as well as that of genetic information, was examined to expand our understanding of how living systems are determined. Because cells are minimum units reflecting epigenetic information, which is considered to map the history of a parallel-processing recurrent network of biochemical reactions, their behaviors cannot be explained by considering only conventional DNA information-processing events. The role of epigenetic information on cells, which complements their genetic information, was inferred by comparing predictions from genetic information with cell behaviour observed under conditions chosen to reveal adaptation processes, population effects and community effects. A system of analyzing epigenetic information was developed starting from the twin complementary viewpoints of cell regulation as an “algebraic” system (emphasis on temporal aspects) and as a “geometric” system (emphasis on spatial aspects). Exploiting the combination of latest microfabrication technology and measurement technologies, which we call on-chip cellomics assay, we can control and re-construct the environments and interaction of cells from “algebraic” and “geometric” viewpoints. In this review, temporal viewpoint of epigenetic information, a part of the series of single-cell-based “algebraic” and “geometric” studies of celluler systems in our research groups, are summerized and reported. The knowlege acquired from this study may lead to the use of cells that fully control practical applications like cell-based drug screening and the regeneration of organs.
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32
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Lei H, Zhang Y, Li B. Particle separation in fluidic flow by optical fiber. OPTICS EXPRESS 2012; 20:1292-1300. [PMID: 22274474 DOI: 10.1364/oe.20.001292] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We report a separation of two different size particles in fluidic flow by an optical fiber. With a light of 1.55 μm launched into the fiber, particles in stationary water were massively trapped and assembled around the fiber by a negative photophoretic force. By introducing a fluidic flow, the assembled particles were separated into two different downstream positions according to their sizes by the negative photophoretic force and the dragging force acted on the particles. The intensity distribution of light leaked from the fiber and the asymmetry factor of energy distribution have been analysed as crucial factors in this separation. Poly(methyl methacrylate) particles (5-/10-μm diameter), SiO(2) particles (2.08-/5.65-μm diameter), and SiO(2) particles (2.08-μm diameter) mixed with yeast cells were used to demonstrate the effectiveness of the separation. The separation mechanism has also been numerical simulated and theoretical interpreted.
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Affiliation(s)
- Hongxiang Lei
- State Key Laboratory of Optoelectronic Materials and Technologies, School of Physics and Engineering, Sun Yat-Sen University, Guangzhou, China
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33
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Kim SH, Fourmy D, Fujii T. Expanding the horizons for single-cell applications on lab-on-a-chip devices. Methods Mol Biol 2012; 853:199-210. [PMID: 22323149 DOI: 10.1007/978-1-61779-567-1_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Stochastic events in gene expression, protein synthesis, and metabolite synthesis or degradation lead to cellular heterogeneity essential to life. In a tissue as we see in organs, there is strong heterogeneity among the constituting cells critical to its function. Thus, there exists a strong demand to develop new micro/nanosystems that would enable us to conduct single-cell analysis. This field is rapidly growing, as exemplified below with recent emerging technologies that now reveal sensitive single-cell "omics" analysis. We describe in the review some of the most promising technologies that will certainly transform our view of biology in the near future.
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Affiliation(s)
- Soo Hyeon Kim
- JST-CREST, Institute of Industrial Science, University of Tokyo, Tokyo, Japan
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34
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Murase A, Kubota Y, Hirayama S, Kumashiro Y, Okano T, Mayama S, Umemura K. Two-dimensional trajectory analysis of the diatom Navicula sp. using a micro chamber. J Microbiol Methods 2011; 87:316-9. [PMID: 21963449 DOI: 10.1016/j.mimet.2011.09.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 09/14/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
We describe a trajectory analysis of diatom cell locomotion by combining a micro chamber and two-dimensional position coordinate analysis. By shutting cells in a micro chamber, continuous microscopic observation of Navicula sp. cells was possible. The trajectory of each cell was visualized once every second by using position coordinate analysis although time resolution of previous papers were range of minutes. Our data revealed frequent change of movement direction. Furthermore, the correlation between the distances moved, the velocity, and the acceleration of the cells was discussed in detail.
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Affiliation(s)
- Ayumu Murase
- Faculty of Science, Tokyo University of Science, Tokyo, Japan
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35
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Abstract
We present a formulation of branching and aging processes that allows age distributions along lineages to be studied within populations, and provides a new interpretation of classical results in the theory of aging. We establish a variational principle for the stable age distribution along lineages. Using this optimal lineage principle, we show that the response of a population's growth rate to age-specific changes in mortality and fecundity--a key quantity that was first calculated by Hamilton--is given directly by the age distribution along lineages. We apply our method also to the Bellman-Harris process, in which both mother and progeny are rejuvenated at each reproduction event, and show that this process can be mapped to the classic aging process such that age statistics in the population and along lineages are identical. Our approach provides both a theoretical framework for understanding the statistics of aging in a population, and a new method of analytical calculations for populations with age structure. We discuss generalizations for populations with multiple phenotypes, and more complex aging processes. We also provide a first experimental test of our theory applied to bacterial populations growing in a microfluidics device.
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Affiliation(s)
- Yuichi Wakamoto
- Research Center for Complex Systems Biology, University of Tokyo, 3-8-1 Komaba Meguro-ku Tokyo 153-8902, Japan
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36
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Buffi N, Merulla D, Beutier J, Barbaud F, Beggah S, van Lintel H, Renaud P, van der Meer JR. Development of a microfluidics biosensor for agarose-bead immobilized Escherichia coli bioreporter cells for arsenite detection in aqueous samples. LAB ON A CHIP 2011; 11:2369-77. [PMID: 21614381 DOI: 10.1039/c1lc20274j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Contamination with arsenic is a recurring problem in both industrialized and developing countries. Drinking water supplies for large populations can have concentrations much higher than the permissible levels (for most European countries and the United States, 10 μg As per L; elsewhere, 50 μg As per L). Arsenic analysis requires high-end instruments, which are largely unavailable in developing countries. Bioassays based on genetically engineered bacteria have been proposed as suitable alternatives but such tests would profit from better standardization and direct incorporation into sensing devices. The goal of this work was to develop and test microfluidic devices in which bacterial bioreporters could be embedded, exposed and reporter signals detected, as a further step towards a complete miniaturized bacterial biosensor. The signal element in the biosensor is a nonpathogenic laboratory strain of Escherichia coli, which produces a variant of the green fluorescent protein after contact to arsenite and arsenate. E. coli bioreporter cells were encapsulated in agarose beads and incorporated into a microfluidic device where they were captured in 500 × 500 μm(2) cages and exposed to aqueous samples containing arsenic. Cell-beads frozen at -20 °C in the microfluidic chip retained inducibility for up to a month and arsenic samples with 10 or 50 μg L(-1) could be reproducibly discriminated from the blank. In the 0-50 μg L(-1) range and with an exposure time of 200 minutes, the rate of signal increase was linearly proportional to the arsenic concentration. The time needed to reliably and reproducibly detect a concentration of 50 μg L(-1) was 75-120 minutes, and 120-180 minutes for a concentration of 10 μg L(-1).
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Affiliation(s)
- Nina Buffi
- Laboratory of Microsystems Engineering, Ecole Polytechnique Fédérale Lausanne, EPFL-STI-LMIS, Lausanne, Switzerland.
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Abstract
The coming of age of whole‐cell biosensors, combined with the continuing advances in array technologies, has prepared the ground for the next step in the evolution of both disciplines – the whole‐cell array. In the present review, we highlight the state‐of‐the‐art in the different disciplines essential for a functional bacterial array. These include the genetic engineering of the biological components, their immobilization in different polymers, technologies for live cell deposition and patterning on different types of solid surfaces, and cellular viability maintenance. Also reviewed are the types of signals emitted by the reporter cell arrays, some of the transduction methodologies for reading these signals and the mathematical approaches proposed for their analysis. Finally, we review some of the potential applications for bacterial cell arrays, and list the future needs for their maturation: a richer arsenal of high‐performance reporter strains, better methodologies for their incorporation into hardware platforms, design of appropriate detection circuits, the continuing development of dedicated algorithms for multiplex signal analysis and – most importantly – enhanced long‐term maintenance of viability and activity on the fabricated biochips.
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Affiliation(s)
- Tal Elad
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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38
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Park J, Kerner A, Burns MA, Lin XN. Microdroplet-enabled highly parallel co-cultivation of microbial communities. PLoS One 2011; 6:e17019. [PMID: 21364881 PMCID: PMC3045426 DOI: 10.1371/journal.pone.0017019] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 01/18/2011] [Indexed: 12/19/2022] Open
Abstract
Microbial interactions in natural microbiota are, in many cases, crucial for the sustenance of the communities, but the precise nature of these interactions remain largely unknown because of the inherent complexity and difficulties in laboratory cultivation. Conventional pure culture-oriented cultivation does not account for these interactions mediated by small molecules, which severely limits its utility in cultivating and studying "unculturable" microorganisms from synergistic communities. In this study, we developed a simple microfluidic device for highly parallel co-cultivation of symbiotic microbial communities and demonstrated its effectiveness in discovering synergistic interactions among microbes. Using aqueous micro-droplets dispersed in a continuous oil phase, the device could readily encapsulate and co-cultivate subsets of a community. A large number of droplets, up to ∼1,400 in a 10 mm × 5 mm chamber, were generated with a frequency of 500 droplets/sec. A synthetic model system consisting of cross-feeding E. coli mutants was used to mimic compositions of symbionts and other microbes in natural microbial communities. Our device was able to detect a pair-wise symbiotic relationship when one partner accounted for as low as 1% of the total population or each symbiont was about 3% of the artificial community.
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Affiliation(s)
- Jihyang Park
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alissa Kerner
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mark A. Burns
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Xiaoxia Nina Lin
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
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39
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Okano K, Yu D, Matsui A, Maezawa Y, Hosokawa Y, Kira A, Matsubara M, Liau I, Tsubokawa H, Masuhara H. Induction of cell-cell connections by using in situ laser lithography on a perfluoroalkyl-coated cultivation platform. Chembiochem 2011; 12:795-801. [PMID: 21341350 DOI: 10.1002/cbic.201000497] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Indexed: 11/11/2022]
Abstract
This article describes a novel laser-directed microfabrication method carried out in aqueous solution for the organization of cell networks on a platform. A femtosecond (fs) laser was applied to a platform culturing PC12, HeLa, or normal human astrocyte (NHA) cells to manipulate them and to facilitate mutual connections. By applying an fs-laser-induced impulsive force, cells were detached from their original location on the plate, and translocated onto microfabricated cell-adhesive domains that were surrounded with a cell-repellent perfluoroalkyl (R(f)) polymer. Then the fs-laser pulse-train was applied to the R(f) polymer surface to modify the cell-repellent surface, and to make cell-adhesive channels of several μm in width between each cell-adhesive domain. PC12 cells elongated along the channels and made contact with others cells. HeLa and NHA cells also migrated along the channels and connected to the other cells. Surface analysis by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM) confirmed that the R(f) polymer was partially decomposed. The method presented here could contribute not only to the study of developing networks of neuronal, glial, and capillary cells, but also to the quantitative analysis of nerve function.
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Affiliation(s)
- Kazunori Okano
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
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40
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Xu CX, Yin XF. Continuous cell introduction and rapid dynamic lysis for high-throughput single-cell analysis on microfludic chips with hydrodynamic focusing. J Chromatogr A 2011; 1218:726-32. [DOI: 10.1016/j.chroma.2010.11.049] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 10/18/2022]
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41
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Zhao S, Chen A, Revzin A, Pan T. Stereomask lithography (SML): a universal multi-object micro-patterning technique for biological applications. LAB ON A CHIP 2011; 11:224-30. [PMID: 21113523 DOI: 10.1039/c0lc00275e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The advent of biological micro-patterning techniques has given new impetus to many areas of biological research, including quantitative biochemical analysis, tissue engineering, biosensing, and regenerative medicine. Derived from photolithography or soft lithography, current bio-patterning approaches have yet to completely address the needs of out-of-cleanroom, universal applicability, high feature resolution, as well as multi-object placement, though many have shown great promise to precisely pattern one specific biomaterial. In this paper, we present a novel versatile biological lithography technique to achieve integrated multi-object patterning with high feature resolution and high adaptability to various biomaterials, referred to as stereomask lithography (SML). Successive patterning of multiple objects is enabled by using unique three-dimensional masks (i.e., the stereomasks), which lay out current micropatterns while protecting pre-existing biological features on the substrate. Furthermore, high-precision reversible alignment among multiple bio-objects is achieved by adopting a peg-in-hole design between the substrate and stereomasks. We demonstrate that the SML technique is capable of constructing a complex biological microenvironment with various bio-functional components at the single-cell resolution, which to the best of our knowledge has not been realized before.
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Affiliation(s)
- Siwei Zhao
- Micro-Nano Innovations (MiNI) Laboratory, Department of Biomedical Engineering, University of California, Davis, CA, USA
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42
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Kinnunen P, Sinn I, McNaughton BH, Newton DW, Burns MA, Kopelman R. Monitoring the growth and drug susceptibility of individual bacteria using asynchronous magnetic bead rotation sensors. Biosens Bioelectron 2011; 26:2751-5. [PMID: 21095112 PMCID: PMC3059723 DOI: 10.1016/j.bios.2010.10.010] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 10/05/2010] [Accepted: 10/06/2010] [Indexed: 12/16/2022]
Abstract
Continuous growth of individual bacteria has been previously studied by direct observation using optical imaging. However, optical microscopy studies are inherently diffraction limited and limited in the number of individual cells that can be continuously monitored. Here we report on the use of the asynchronous magnetic bead rotation (AMBR) sensor, which is not diffraction limited. The AMBR sensor allows for the measurement of nanoscale growth dynamics of individual bacterial cells, over multiple generations. This torque-based magnetic bead sensor monitors variations in drag caused by the attachment and growth of a single bacterial cell. In this manner, we observed the growth and division of individual Escherichia coli, with 80-nm sensitivity to the cell length. Over the life cycle of a cell, we observed up to a 300% increase in the rotational period of the biosensor due to increased cell volume. In addition, we observed single bacterial cell growth response to antibiotics. This work demonstrates the non-microscopy limited AMBR biosensor for monitoring individual cell growth dynamics, including cell elongation, generation time, lag time, and division, as well as their sensitivity to antibiotics.
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Affiliation(s)
- Paivo Kinnunen
- University of Michigan, Applied Physics Program, 2477 Randall Laboratory, Ann Arbor, MI 48109-1120, USA
- University of Michigan, Department of Chemistry, 930 N. University, Ann Arbor, MI 48109-1055, USA
| | - Irene Sinn
- University of Michigan, Department of Chemistry, 930 N. University, Ann Arbor, MI 48109-1055, USA
- University of Michigan, Department of Biomedical Engineering, 2200 Bonisteel, Ann Arbor, MI 48109-2099, USA
- University of Michigan, Department of Chemical Engineering, 2300 Hayward St., 3074 Dow, Ann Arbor, MI 48109-2136, USA
| | - Brandon H. McNaughton
- University of Michigan, Applied Physics Program, 2477 Randall Laboratory, Ann Arbor, MI 48109-1120, USA
- University of Michigan, Department of Chemistry, 930 N. University, Ann Arbor, MI 48109-1055, USA
- University of Michigan, Department of Biomedical Engineering, 2200 Bonisteel, Ann Arbor, MI 48109-2099, USA
| | - Duane W. Newton
- University of Michigan Health System, Clinical Microbiology and Virology Laboratories, 2F461 University Hospital, Box 5054; The University of Michigan Medical School, Department of Pathology, 1301 Catherine Ann Arbor, MI 48109-0054, USA
| | - Mark A. Burns
- University of Michigan, Department of Chemical Engineering, 2300 Hayward St., 3074 Dow, Ann Arbor, MI 48109-2136, USA
| | - Raoul Kopelman
- University of Michigan, Applied Physics Program, 2477 Randall Laboratory, Ann Arbor, MI 48109-1120, USA
- University of Michigan, Department of Chemistry, 930 N. University, Ann Arbor, MI 48109-1055, USA
- University of Michigan, Department of Biomedical Engineering, 2200 Bonisteel, Ann Arbor, MI 48109-2099, USA
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Wu J, Zhang M, Chen L, Yu V, Tin-Yum Wong J, Zhang X, Qin J, Wen W. Patterning cell using Si-stencil for high-throughput assay. RSC Adv 2011. [DOI: 10.1039/c1ra00520k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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44
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Huang M, Fan S, Xing W, Liu C. Microfluidic cell culture system studies and computational fluid dynamics. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.mcm.2010.01.024] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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45
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Teramoto J, Yamanishi Y, Magdy ESH, Hasegawa A, Kori A, Nakajima M, Arai F, Fukuda T, Ishihama A. Single live-bacterial cell assay of promoter activity and regulation. Genes Cells 2010; 15:1111-22. [DOI: 10.1111/j.1365-2443.2010.01449.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Maruyama H, Fukuda T, Arai F. Optical Adhesion Control of Hydrogel Microtools for On-Demand Immobilization and Measurement of Cells on a Microfluidic Chip. JOURNAL OF ROBOTICS AND MECHATRONICS 2010. [DOI: 10.20965/jrm.2010.p0631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optical adhesion control of hydrogel microtools, made of hydrophilic photo-crosslinkable resin, was developed for on-demand immobilization and measurement of cells on a microfluidic chip. The hydrogel microtool was manipulated by optical tweezers and modified by spiropyran chromospheres, which was a photochromic polymer. We developed on-demand control of uni/bidirectional adhesiveness of the microtool by control of electrolyte concentration in a solution. Photo illumination controls the adhesiveness of the microtools. In case of unidirectional control of adhesiveness, the microtools adhere to glass, other microtools and cells by illumination of ultraviolet (UV) light. Spiropyran chromospheres were used for bidirectional control of adhesiveness to cell. In case of bidirectional control of adhesiveness, the microtools adhere to cells by UV illumination. On the other hand, the microtool detaches from the adhered cells by visible (VIS) light illumination. Electrolyte concentration in the solution controlled these adhesiveness controls. Adherence of the microtool was enough to keep its position on a microfluidic chip. We applied these immobilization methods to measure the local conditions around cells by modifying the microtool with a pH indicator, bromothymol blue (BTB). Local measurements of the ambient pH value of yeast cells were performed by immobilizing the cell on the surface of the pH sensing microtool. Moreover, culture monitoring of a single yeast cell was demonstrated by immobilization to the microtool.
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47
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Matsumura K, Yagi T, Hattori A, Soloviev M, Yasuda K. Using single cell cultivation system for on-chip monitoring of the interdivision timer in Chlamydomonas reinhardtii cell cycle. J Nanobiotechnology 2010; 8:23. [PMID: 20868509 PMCID: PMC2955706 DOI: 10.1186/1477-3155-8-23] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 09/25/2010] [Indexed: 01/09/2023] Open
Abstract
Regulation of cell cycle progression in changing environments is vital for cell survival and maintenance, and different regulation mechanisms based on cell size and cell cycle time have been proposed. To determine the mechanism of cell cycle regulation in the unicellular green algae Chlamydomonas reinhardtii, we developed an on-chip single-cell cultivation system that allows for the strict control of the extracellular environment. We divided the Chlamydomonas cell cycle into interdivision and division phases on the basis of changes in cell size and found that, regardless of the amount of photosynthetically active radiation (PAR) and the extent of illumination, the length of the interdivision phase was inversely proportional to the rate of increase of cell volume. Their product remains constant indicating the existence of an 'interdivision timer'. The length of the division phase, in contrast, remained nearly constant. Cells cultivated under light-dark-light conditions did not divide unless they had grown to twice their initial volume during the first light period. This indicates the existence of a 'commitment sizer'. The ratio of the cell volume at the beginning of the division phase to the initial cell volume determined the number of daughter cells, indicating the existence of a 'mitotic sizer'.
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Affiliation(s)
- Kazunori Matsumura
- Kanagawa Academy of Science and Technology, KSP East 310, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa 213-0012, Japan.
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HUO DQ, LIU Z, Hou CJ, YANG J, LUO XG, FA HB, DONG JL, ZHANG YC, ZHANG GP, LI JJ. Recent Advances on Optical Detection Methods and Techniques for Cell-based Microfluidic Systems. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60067-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Kawai-Noma S, Pack CG, Kojidani T, Asakawa H, Hiraoka Y, Kinjo M, Haraguchi T, Taguchi H, Hirata A. In vivo evidence for the fibrillar structures of Sup35 prions in yeast cells. ACTA ACUST UNITED AC 2010; 190:223-31. [PMID: 20643880 PMCID: PMC2930275 DOI: 10.1083/jcb.201002149] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Correlative light and electron microscopy provides support for the linear amalgamation of yeast prion proteins. Yeast prion [PSI+] is caused by aggregated structures of the Sup35 protein. Although Sup35 forms typical amyloid fibrils in vitro, there is no direct evidence for the fibrillar structures of Sup35 in vivo. We analyzed [PSI+] cells in which Sup35 fused with green fluorescent protein (GFP) formed aggregates visible by fluorescence microscopy using thin-section electron microscopy (EM). Rapid-freeze EM combined with an immunogold-labeling technique as well as correlative light EM, which allows high-resolution imaging by EM of the same structure observed by light (fluorescence) microscopy, shows that the aggregates contain bundled fibrillar structures of Sup35-GFP. Additional biochemical and fluorescent correlation spectroscopy results suggest that the Sup35 oligomers diffused in the [PSI+] lysates adopt fibril-like shapes. Our findings demonstrate that [PSI+] cells contain Sup35 fibrillar structures closely related to those formed in vitro and provide insight into the molecular mechanism by which Sup35 aggregates are assembled and remodeled in [PSI+] cells.
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Affiliation(s)
- Shigeko Kawai-Noma
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
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50
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Where microbiology meets microengineering: design and applications of reporter bacteria. Nat Rev Microbiol 2010; 8:511-22. [DOI: 10.1038/nrmicro2392] [Citation(s) in RCA: 404] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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