1
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Naigles B, Narla AV, Soroczynski J, Tsimring LS, Hao N. Quantifying dynamic pro-inflammatory gene expression and heterogeneity in single macrophage cells. J Biol Chem 2023; 299:105230. [PMID: 37689116 PMCID: PMC10579967 DOI: 10.1016/j.jbc.2023.105230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 09/11/2023] Open
Abstract
Macrophages must respond appropriately to pathogens and other pro-inflammatory stimuli in order to perform their roles in fighting infection. One way in which inflammatory stimuli can vary is in their dynamics-that is, the amplitude and duration of stimulus experienced by the cell. In this study, we performed long-term live cell imaging in a microfluidic device to investigate how the pro-inflammatory genes IRF1, CXCL10, and CXCL9 respond to dynamic interferon-gamma (IFNγ) stimulation. We found that IRF1 responds to low concentration or short duration IFNγ stimulation, whereas CXCL10 and CXCL9 require longer or higherconcentration stimulation to be expressed. We also investigated the heterogeneity in the expression of each gene and found that CXCL10 and CXCL9 have substantial cell-to-cell variability. In particular, the expression of CXCL10 appears to be largely stochastic with a subpopulation of nonresponding cells across all the stimulation conditions tested. We developed both deterministic and stochastic models for the expression of each gene. Our modeling analysis revealed that the heterogeneity in CXCL10 can be attributed to a slow chromatin-opening step that is on a similar timescale to that of adaptation of the upstream signal. In this way, CXCL10 expression in individual cells can remain stochastic in response to each pulse of repeated stimulation, which we also validated by experiments. Together, we conclude that pro-inflammatory genes in the same signaling pathway can respond to dynamic IFNγ stimulus with very different response features and that upstream signal adaptation can contribute to shaping heterogeneous gene expression.
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Affiliation(s)
- Beverly Naigles
- Department of Molecular Biology, University of California San Diego, La Jolla, California, USA
| | - Avaneesh V Narla
- Department of Physics, University of California San Diego, La Jolla, California, USA
| | - Jan Soroczynski
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, New York, USA
| | - Lev S Tsimring
- Synthetic Biology Institute, University of California San Diego, La Jolla, California, USA
| | - Nan Hao
- Department of Molecular Biology, University of California San Diego, La Jolla, California, USA; Synthetic Biology Institute, University of California San Diego, La Jolla, California, USA; Department of Bioengineering, University of California San Diego, La Jolla, California, USA.
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2
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Reliable cell retention of mammalian suspension cells in microfluidic cultivation chambers. Sci Rep 2023; 13:3857. [PMID: 36890160 PMCID: PMC9995442 DOI: 10.1038/s41598-023-30297-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/21/2023] [Indexed: 03/10/2023] Open
Abstract
Microfluidic cultivation, with its high level of environmental control and spatio-temporal resolution of cellular behavior, is a well-established tool in today's microfluidics. Yet, reliable retention of (randomly) motile cells inside designated cultivation compartments still represents a limitation, which prohibits systematic single-cell growth studies. To overcome this obstacle, current approaches rely on complex multilayer chips or on-chip valves, which makes their application for a broad community of users infeasible. Here, we present an easy-to-implement cell retention concept to withhold cells inside microfluidic cultivation chambers. By introducing a blocking structure into a cultivation chamber's entrance and nearly closing it, cells can be manually pushed into the chamber during loading procedures but are unable to leave it autonomously in subsequent long-term cultivation. CFD simulations as well as trace substance experiments confirm sufficient nutrient supply within the chamber. Through preventing recurring cell loss, growth data obtained from Chinese hamster ovary cultivation on colony level perfectly match data determined from single-cell data, which eventually allows reliable high throughput studies of single-cell growth. Due to its transferability to other chamber-based approaches, we strongly believe that our concept is also applicable for a broad range of cellular taxis studies or analyses of directed migration in basic or biomedical research.
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3
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Okeyo KO, Hiyaji R, Oana H. A single-cell surgery microfluidic device for transplanting tumor cytoplasm into dendritic cells without nuclei mixing. Biotechnol J 2023; 18:e2200135. [PMID: 36412930 DOI: 10.1002/biot.202200135] [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: 06/18/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
Abstract
This study aimed to demonstrate the feasibility of generating tumor cell vaccine models by single-cell surgery in a microfluidic device that integrates one-to-one electrofusion, shear flow reseparation, and on-device culture. The device was microfabricated from polydimethylsiloxane (PDMS) and consisted of microorifices (aperture size: ∼3 μm) for one-to-one fusion, and microcages for on-device culture. Using the device, we could achieve one-to-one electrofusion of leukemic plasmacytoid dendritic cells (DC-like cells) and Jurkat cells with a fusion efficiency of ∼ 80%. Fusion via the narrow microorifices allowed DC-like cells to acquire cytoplasmic contents of the Jurkat cells while preventing nuclei mixing. After fusion, the DC-like cells were selectively reseparated from the Jurkat cells by shear flow application to generate tumor nuclei-free antigen-recipient DC-like (tarDC-like) cells. When cultured as single cells on the device, these cells could survive under gentle medium perfusion with a median survival time of 11.5 h, although a few cells could survive longer than 36 h. Overall, this study demonstrates single-cell surgery in a microfluidic device for potential generation of dendritic cell vaccines which are uncontaminated with tumor nucleic materials. We believe that this study will inspire the generation of safer tumor cell vaccines for cancer immunotherapy.
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Affiliation(s)
- Kennedy Omondi Okeyo
- Institute for Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Ryuta Hiyaji
- Department of Mechanical Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hidehiro Oana
- Department of Mechanical Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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4
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Kenneweg P, Stallmann D, Hammer B. Novel transfer learning schemes based on Siamese networks and synthetic data. Neural Comput Appl 2022; 35:8423-8436. [PMID: 36568475 PMCID: PMC9757634 DOI: 10.1007/s00521-022-08115-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022]
Abstract
Transfer learning schemes based on deep networks which have been trained on huge image corpora offer state-of-the-art technologies in computer vision. Here, supervised and semi-supervised approaches constitute efficient technologies which work well with comparably small data sets. Yet, such applications are currently restricted to application domains where suitable deep network models are readily available. In this contribution, we address an important application area in the domain of biotechnology, the automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation, where data characteristics are very dissimilar to existing domains and trained deep networks cannot easily be adapted by classical transfer learning. We propose a novel transfer learning scheme which expands a recently introduced Twin-VAE architecture, which is trained on realistic and synthetic data, and we modify its specialized training procedure to the transfer learning domain. In the specific domain, often only few to no labels exist and annotations are costly. We investigate a novel transfer learning strategy, which incorporates a simultaneous retraining on natural and synthetic data using an invariant shared representation as well as suitable target variables, while it learns to handle unseen data from a different microscopy technology. We show the superiority of the variation of our Twin-VAE architecture over the state-of-the-art transfer learning methodology in image processing as well as classical image processing technologies, which persists, even with strongly shortened training times and leads to satisfactory results in this domain. The source code is available at https://github.com/dstallmann/transfer_learning_twinvae, works cross-platform, is open-source and free (MIT licensed) software. We make the data sets available at https://pub.uni-bielefeld.de/record/2960030.
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Affiliation(s)
- Philip Kenneweg
- grid.7491.b0000 0001 0944 9128Machine Learning Group, Bielefeld University, Bielefeld, Germany
| | - Dominik Stallmann
- grid.7491.b0000 0001 0944 9128Machine Learning Group, Bielefeld University, Bielefeld, Germany
| | - Barbara Hammer
- grid.7491.b0000 0001 0944 9128Machine Learning Group, Bielefeld University, Bielefeld, Germany
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5
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Guo L, Shan J, Ran P, Yin S, Liu C, Li J. Permeation-Enhanced Degassing Method Based on Xylem Embolism Repair and Gas Permeable Materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12373-12381. [PMID: 36171077 DOI: 10.1021/acs.langmuir.2c02145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Microfluidic devices have developed a wide range of applications in the fields of biomedicine, chemistry, and analytical science. But it is easy to form and accumulate bubbles in microfluidic devices. These bubbles could decrease the detection sensitivity, cause inaccurate analysis results, and even damage the functional region of the device. Inspired by the embolism repair mechanism of angiosperms and the permeability of gas permeable materials, this work proposes a bioinspired permeation-enhanced degassing method. Bionic redundant pits are used in this method to keep bubbles from spreading between microchannels and maintain the continuity of the flow. A hydrophobic gas permeable material is used to enhance the bubble capture capability and accelerate the degassing process. This method can eliminate bubbles automatically and continuously in real time without auxiliary equipment. Compared to the bubble removal only depending on solution in water, the degassing effect of the permeation-enhanced degassing method shows about 1.6 times improvement in the same conditions, and the capability of trapping bubbles is improved by 1.33 times. In this paper, this method was integrated into a concentration gradient generator and a cell culture device. The results show that the concentration gradient generator with degassing structures can dissolve bubbles in a rapid way and reach the stability of the concentration gradient within 5-15 min. The degassing method can run for a long time and improve the cell density and cell viability of HeLa cells up to 2.64 and 1.12 times, respectively. The method has a broad application prospect in microfluidic fields including biomedical fluid processing, virus detection, and microscale reactor operation.
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Affiliation(s)
- Lihua Guo
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian 116024, China
| | - Jie Shan
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian 116024, China
| | - Penghui Ran
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian 116024, China
| | - Shuqing Yin
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian 116024, China
| | - Chong Liu
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian 116024, China
- Key Laboratory for Precision and Non-traditional Machining Technology of Ministry of Education, Dalian University of Technology, Dalian 116024, China
| | - Jingmin Li
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian 116024, China
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6
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The VersaLive platform enables microfluidic mammalian cell culture for versatile applications. Commun Biol 2022; 5:1034. [PMID: 36175545 PMCID: PMC9522807 DOI: 10.1038/s42003-022-03976-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 09/12/2022] [Indexed: 01/09/2023] Open
Abstract
Microfluidic-based cell culture allows for precise spatio-temporal regulation of microenvironment, live cell imaging and better recapitulation of physiological conditions, while minimizing reagents’ consumption. Despite their usefulness, most microfluidic systems are designed with one specific application in mind and usually require specialized equipment and expertise for their operation. All these requirements prevent microfluidic-based cell culture to be widely adopted. Here, we designed and implemented a versatile and easy-to-use perfusion cell culture microfluidic platform for multiple applications (VersaLive) requiring only standard pipettes. Here, we showcase the multiple uses of VersaLive (e.g., time-lapse live cell imaging, immunostaining, cell recovery, cell lysis, plasmid transfection) in mammalian cell lines and primary cells. VersaLive could replace standard cell culture formats in several applications, thus decreasing costs and increasing reproducibility across laboratories. The layout, documentation and protocols are open-source and available online at https://versalive.tigem.it/. VersaLive is a versatile microfluidic platform with flexible input modes and low-volume media reservoirs that can be used for time-lapse live cell imaging, immunostaining, cell recovery, cell lysis and plasmid transfection.
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7
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Yang M, Sun N, Luo Y, Lai X, Li P, Zhang Z. Emergence of debubblers in microfluidics: A critical review. BIOMICROFLUIDICS 2022; 16:031503. [PMID: 35757146 PMCID: PMC9217167 DOI: 10.1063/5.0088551] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/31/2022] [Indexed: 05/10/2023]
Abstract
Bubbles in microfluidics-even those that appear to be negligibly small-are pervasive and responsible for the failure of many biological and chemical experiments. For instance, they block current conduction, damage cell membranes, and interfere with detection results. To overcome this unavoidable and intractable problem, researchers have developed various methods for capturing and removing bubbles from microfluidics. Such methods are multifarious and their working principles are very different from each other. In this review, bubble-removing methods are divided into two broad categories: active debubblers (that require external auxiliary equipment) and passive debubblers (driven by natural processes). In each category, three main types of methods are discussed along with their advantages and disadvantages. Among the active debubblers, those assisted by lasers, acoustic generators, and negative pressure pumps are discussed. Among the passive debubblers, those driven by buoyancy, the characteristics of gas-liquid interfaces, and the hydrophilic and hydrophobic properties of materials are discussed. Finally, the challenges and prospects of the bubble-removal technologies are reviewed to refer researchers to microfluidics and inspire further investigations in this field.
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Affiliation(s)
| | - Nan Sun
- School of Automation, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | | | | | - Peiru Li
- School of Automation, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zhenyu Zhang
- School of Automation, Nanjing University of Information Science and Technology, Nanjing 210044, China
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8
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Guo L, Liu Y, Ran P, Wang G, Shan J, Li X, Liu C, Li J. A bioinspired bubble removal method in microchannels based on angiosperm xylem embolism repair. MICROSYSTEMS & NANOENGINEERING 2022; 8:34. [PMID: 35402001 PMCID: PMC8940964 DOI: 10.1038/s41378-022-00367-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/23/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
It is difficult to remove and eliminate bubbles in microchannels in many devices used in various biomedical fields, such as those needed for microfluidic immunoassays, point-of-care testing, and cell biology evaluations. Accumulated bubbles are associated with a number of negative outcomes, including a decrease in device sensitivity, inaccuracy of analysis results, and even functional failure. Xylem conduits of angiosperm have the ability to remove bubbles in obstructed conduits. Inspired by such an embolism repair mechanism, this paper proposes a bioinspired bubble removal method, which exhibits a prominent ability to dissolve bubbles continuously within a large range of flow rates (2 µL/min-850 µL/min) while retaining the stability and continuity of the flow without auxiliary equipment. Such a method also shows significant bubble removal stability in dealing with Newtonian liquids and non-Newtonian fluids, especially with high viscosity (6.76 Pa s) and low velocity (152 nL/min). Such advantages associated with the proposed bioinspired method reveal promising application prospects in macro/microfluidic fields ranging from 3D printing, implantable devices, virus detection, and biomedical fluid processing to microscale reactor operation and beyond.
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Affiliation(s)
- Lihua Guo
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
| | - Yuanchang Liu
- Department of Mechanical Engineering, University College London, Torrington Place, London, WC1E 7JE UK
| | - Penghui Ran
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
| | - Gang Wang
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
| | - Jie Shan
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
| | - Xudong Li
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
| | - Chong Liu
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
| | - Jingmin Li
- Key Laboratory for Micro/Nano Technology and System of Liaoning Province, Dalian University of Technology, Dalian, China
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9
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Novel Microfluidics Device for Rapid Antibiotics Susceptibility Screening. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12042198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In recent years, excessive utilization of antibiotics has led to the emergence of antibiotic microbial resistance on a planetary scale. This recent phenomenon represents a serious threat to public health, as well as an enormous burden for healthcare systems’ budgets worldwide. Novel, rapid and cheap methods for antibiotic susceptibility screening are urgently needed for this obstacle to be overcome. In this paper, we present a microfluidic device for on-chip antibiotic resistance testing, which allows for antibiotic microbial resistance detection within 6 hours. The design, fabrication and experimental utilization of the device are thoroughly described and analyzed, as well as possibilities for future automation of the whole process. The accessibility of such a device for all people, regardless of economic status, was of utmost importance for us during the development of the project.
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10
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Russo M, Cejas CM, Pitingolo G. Advances in microfluidic 3D cell culture for preclinical drug development. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 187:163-204. [PMID: 35094774 DOI: 10.1016/bs.pmbts.2021.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Drug development is often a very long, costly, and risky process due to the lack of reliability in the preclinical studies. Traditional current preclinical models, mostly based on 2D cell culture and animal testing, are not full representatives of the complex in vivo microenvironments and often fail. In order to reduce the enormous costs, both financial and general well-being, a more predictive preclinical model is needed. In this chapter, we review recent advances in microfluidic 3D cell culture showing how its development has allowed the introduction of in vitro microphysiological systems, laying the foundation for organ-on-a-chip technology. These findings provide the basis for numerous preclinical drug discovery assays, which raise the possibility of using micro-engineered systems as emerging alternatives to traditional models, based on 2D cell culture and animals.
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Affiliation(s)
- Maria Russo
- Microfluidics, MEMS, Nanostructures (MMN), CNRS UMR 8231, Institut Pierre Gilles de Gennes (IPGG) ESPCI Paris, PSL Research University, Paris France.
| | - Cesare M Cejas
- Microfluidics, MEMS, Nanostructures (MMN), CNRS UMR 8231, Institut Pierre Gilles de Gennes (IPGG) ESPCI Paris, PSL Research University, Paris France
| | - Gabriele Pitingolo
- Bioassays, Microsystems and Optical Engineering Unit, BIOASTER, Paris France
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11
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Täuber S, Schmitz J, Blöbaum L, Fante N, Steinhoff H, Grünberger A. How to Perform a Microfluidic Cultivation Experiment—A Guideline to Success. BIOSENSORS 2021; 11:bios11120485. [PMID: 34940242 PMCID: PMC8699335 DOI: 10.3390/bios11120485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 12/19/2022]
Abstract
As a result of the steadily ongoing development of microfluidic cultivation (MC) devices, a plethora of setups is used in biological laboratories for the cultivation and analysis of different organisms. Because of their biocompatibility and ease of fabrication, polydimethylsiloxane (PDMS)-glass-based devices are most prominent. Especially the successful and reproducible cultivation of cells in microfluidic systems, ranging from bacteria over algae and fungi to mammalians, is a fundamental step for further quantitative biological analysis. In combination with live-cell imaging, MC devices allow the cultivation of small cell clusters (or even single cells) under defined environmental conditions and with high spatio-temporal resolution. Yet, most setups in use are custom made and only few standardised setups are available, making trouble-free application and inter-laboratory transfer tricky. Therefore, we provide a guideline to overcome the most frequently occurring challenges during a MC experiment to allow untrained users to learn the application of continuous-flow-based MC devices. By giving a concise overview of the respective workflow, we give the reader a general understanding of the whole procedure and its most common pitfalls. Additionally, we complement the listing of challenges with solutions to overcome these hurdles. On selected case studies, covering successful and reproducible growth of cells in MC devices, we demonstrate detailed solutions to solve occurring challenges as a blueprint for further troubleshooting. Since developer and end-user of MC devices are often different persons, we believe that our guideline will help to enhance a broader applicability of MC in the field of life science and eventually promote the ongoing advancement of MC.
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Affiliation(s)
- Sarah Täuber
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Luisa Blöbaum
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Niklas Fante
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
| | - Heiko Steinhoff
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany; (S.T.); (J.S.); (L.B.); (N.F.); (H.S.)
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
- Correspondence:
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12
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Schmitz J, Hertel O, Yermakov B, Noll T, Grünberger A. Growth and eGFP Production of CHO-K1 Suspension Cells Cultivated From Single Cell to Laboratory Scale. Front Bioeng Biotechnol 2021; 9:716343. [PMID: 34722476 PMCID: PMC8554123 DOI: 10.3389/fbioe.2021.716343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/13/2021] [Indexed: 11/23/2022] Open
Abstract
Scaling down bioproduction processes has become a major driving force for more accelerated and efficient process development over the last decades. Especially expensive and time-consuming processes like the production of biopharmaceuticals with mammalian cell lines benefit clearly from miniaturization, due to higher parallelization and increased insights while at the same time decreasing experimental time and costs. Lately, novel microfluidic methods have been developed, especially microfluidic single-cell cultivation (MSCC) devices have been proved to be valuable to miniaturize the cultivation of mammalian cells. So far, growth characteristics of microfluidic cultivated cell lines were not systematically compared to larger cultivation scales; however, validation of a miniaturization tool against initial cultivation scales is mandatory to prove its applicability for bioprocess development. Here, we systematically investigate growth, morphology, and eGFP production of CHO-K1 cells in different cultivation scales ranging from a microfluidic chip (230 nl) to a shake flask (125 ml) and laboratory-scale stirred tank bioreactor (2.0 L). Our study shows a high comparability regarding specific growth rates, cellular diameters, and eGFP production, which proves the feasibility of MSCC as a miniaturized cultivation tool for mammalian cell culture. In addition, we demonstrate that MSCC provides insights into cellular heterogeneity and single-cell dynamics concerning growth and production behavior which, when occurring in bioproduction processes, might severely affect process robustness.
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Affiliation(s)
- Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Oliver Hertel
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.,Cell Culture Technology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Boris Yermakov
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Thomas Noll
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.,Cell Culture Technology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany.,Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
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13
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Pedone E, de Cesare I, Zamora-Chimal CG, Haener D, Postiglione L, La Regina A, Shannon B, Savery NJ, Grierson CS, di Bernardo M, Gorochowski TE, Marucci L. Cheetah: A Computational Toolkit for Cybergenetic Control. ACS Synth Biol 2021; 10:979-989. [PMID: 33904719 DOI: 10.1021/acssynbio.0c00463] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Advances in microscopy, microfluidics, and optogenetics enable single-cell monitoring and environmental regulation and offer the means to control cellular phenotypes. The development of such systems is challenging and often results in bespoke setups that hinder reproducibility. To address this, we introduce Cheetah, a flexible computational toolkit that simplifies the integration of real-time microscopy analysis with algorithms for cellular control. Central to the platform is an image segmentation system based on the versatile U-Net convolutional neural network. This is supplemented with functionality to robustly count, characterize, and control cells over time. We demonstrate Cheetah's core capabilities by analyzing long-term bacterial and mammalian cell growth and by dynamically controlling protein expression in mammalian cells. In all cases, Cheetah's segmentation accuracy exceeds that of a commonly used thresholding-based method, allowing for more accurate control signals to be generated. Availability of this easy-to-use platform will make control engineering techniques more accessible and offer new ways to probe and manipulate living cells.
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Affiliation(s)
- Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Irene de Cesare
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
| | - Criseida G. Zamora-Chimal
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
| | - David Haener
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
| | - Lorena Postiglione
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
| | - Antonella La Regina
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Barbara Shannon
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Nigel J. Savery
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
| | - Claire S. Grierson
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
| | - Mario di Bernardo
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- Department of EE and ICT, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
| | - Thomas E. Gorochowski
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
- School of Biological Sciences, University of Bristol, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Ada Lovelace Building, University Walk, BS8 1TW Bristol, United Kingdom
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, BS8 1TD Bristol, United Kingdom
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ Bristol, United Kingdom
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14
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Stallmann D, Göpfert JP, Schmitz J, Grünberger A, Hammer B. Towards an automatic analysis of CHO-K1 suspension growth in microfluidic single-cell cultivation. Bioinformatics 2021; 37:3632-3639. [PMID: 34019074 DOI: 10.1093/bioinformatics/btab386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/04/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Innovative microfluidic systems carry the promise to greatly facilitate spatio-temporal analysis of single cells under well-defined environmental conditions, allowing novel insights into population heterogeneity and opening new opportunities for fundamental and applied biotechnology. Microfluidics experiments, however, are accompanied by vast amounts of data, such as time series of microscopic images, for which manual evaluation is infeasible due to the sheer number of samples. While classical image processing technologies do not lead to satisfactory results in this domain, modern deep learning technologies such as convolutional networks can be sufficiently versatile for diverse tasks, including automatic cell counting as well as the extraction of critical parameters, such as growth rate. However, for successful training, current supervised deep learning requires label information, such as the number or positions of cells for each image in a series; obtaining these annotations is very costly in this setting. RESULTS We propose a novel machine learning architecture together with a specialized training procedure, which allows us to infuse a deep neural network with human-powered abstraction on the level of data, leading to a high-performing regression model that requires only a very small amount of labeled data. Specifically, we train a generative model simultaneously on natural and synthetic data, so that it learns a shared representation, from which a target variable, such as the cell count, can be reliably estimated. AVAILABILITY The project is cross-platform, open-source and free (MIT licensed) software. We make the source code available at https://github.com/dstallmann/cell_cultivation_analysis; the data set is available at https://pub.uni-bielefeld.de/record/2945513.
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Affiliation(s)
| | - Jan P Göpfert
- Machine Learning Group, Bielefeld University, Germany
| | - Julian Schmitz
- Multiscale Bioengineering, Bielefeld University, Germany
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15
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Park S, Cho H, Kim J, Han KH. Lateral Degassing Method for Disposable Film-Chip Microfluidic Devices. MEMBRANES 2021; 11:membranes11050316. [PMID: 33925874 PMCID: PMC8146472 DOI: 10.3390/membranes11050316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/21/2022]
Abstract
It is critical to develop a fast and simple method to remove air bubbles inside microchannels for automated, reliable, and reproducible microfluidic devices. As an active degassing method, this study introduces a lateral degassing method that can be easily implemented in disposable film-chip microfluidic devices. This method uses a disposable film-chip microchannel superstrate and a reusable substrate, which can be assembled and disassembled simply by vacuum pressure. The disposable microchannel superstrate is readily fabricated by bonding a microstructured polydimethylsiloxane replica and a silicone-coated release polymeric thin film. The reusable substrate can be a plate that has no function or is equipped with the ability to actively manipulate and sense substances in the microchannel by an elaborately patterned energy field. The degassing rate of the lateral degassing method and the maximum available pressure in the microchannel equipped with lateral degassing were evaluated. The usefulness of this method was demonstrated using complex structured microfluidic devices, such as a meandering microchannel, a microvortex, a gradient micromixer, and a herringbone micromixer, which often suffer from bubble formation. In conclusion, as an easy-to-implement and easy-to-use technique, the lateral degassing method will be a key technique to address the bubble formation problem of microfluidic devices.
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16
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Pelletier JF, Sun L, Wise KS, Assad-Garcia N, Karas BJ, Deerinck TJ, Ellisman MH, Mershin A, Gershenfeld N, Chuang RY, Glass JI, Strychalski EA. Genetic requirements for cell division in a genomically minimal cell. Cell 2021; 184:2430-2440.e16. [PMID: 33784496 DOI: 10.1016/j.cell.2021.03.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 01/27/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. Although this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics that result in irregular morphologies. A genome with 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents morphology similar to that of JCVI-syn1.0. We further identified seven of these 19 genes, including two known cell division genes, ftsZ and sepF, a hydrolase of unknown substrate, and four genes that encode membrane-associated proteins of unknown function, which are required together to restore a phenotype similar to that of JCVI-syn1.0. This result emphasizes the polygenic nature of cell division and morphology in a genomically minimal cell.
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Affiliation(s)
- James F Pelletier
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Lijie Sun
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Kim S Wise
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, University of California-San Diego, La Jolla, CA 92037, USA
| | - Andreas Mershin
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil Gershenfeld
- Center for Bits and Atoms, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA.
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17
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de Cesare I, Zamora-Chimal CG, Postiglione L, Khazim M, Pedone E, Shannon B, Fiore G, Perrino G, Napolitano S, di Bernardo D, Savery NJ, Grierson C, di Bernardo M, Marucci L. ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices. ACS OMEGA 2021; 6:2473-2476. [PMID: 33553865 PMCID: PMC7859942 DOI: 10.1021/acsomega.0c03906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/20/2020] [Indexed: 05/14/2023]
Abstract
Extracting quantitative measurements from time-lapse images is necessary in external feedback control applications, where segmentation results are used to inform control algorithms. We describe ChipSeg, a computational tool that segments bacterial and mammalian cells cultured in microfluidic devices and imaged by time-lapse microscopy, which can be used also in the context of external feedback control. The method is based on thresholding and uses the same core functions for both cell types. It allows us to segment individual cells in high cell density microfluidic devices, to quantify fluorescent protein expression over a time-lapse experiment, and to track individual mammalian cells. ChipSeg enables robust segmentation in external feedback control experiments and can be easily customized for other experimental settings and research aims.
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Affiliation(s)
- Irene de Cesare
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
| | - Criseida G. Zamora-Chimal
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| | - Lorena Postiglione
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
| | - Mahmoud Khazim
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- School
of Cellular and Molecular Medicine, University
of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Elisa Pedone
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- School
of Cellular and Molecular Medicine, University
of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Barbara Shannon
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Gianfranco Fiore
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| | - Giansimone Perrino
- Telethon
Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Sara Napolitano
- Telethon
Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Diego di Bernardo
- Telethon
Institute of Genetic and Medicine Via Campi Flegrei 34, 80078 Pozzuoli, Italy
- Department
of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, 80125 Naples, Italy
| | - Nigel J. Savery
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Biochemistry, University of Bristol, University Walk, Bristol BS8 1TD, U.K.
| | - Claire Grierson
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
| | - Mario di Bernardo
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- Department
of EE and ICT, University of Naples Federico
II, Via Claudio 21, 80125 Naples, Italy
| | - Lucia Marucci
- Department
of Engineering Mathematics, University of
Bristol, Woodland Road, Bristol BS8 1UB, U.K.
- BrisSynBio,
Life Sciences Building, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, U.K.
- School
of Cellular and Molecular Medicine, University
of Bristol, University Walk, Bristol BS8 1TD, U.K.
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18
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Student S, Milewska M, Ostrowski Z, Gut K, Wandzik I. Microchamber microfluidics combined with thermogellable glycomicrogels – Platform for single cells study in an artificial cellular microenvironment. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 119:111647. [DOI: 10.1016/j.msec.2020.111647] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/07/2020] [Accepted: 10/14/2020] [Indexed: 12/20/2022]
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19
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Khazim M, Pedone E, Postiglione L, di Bernardo D, Marucci L. A Microfluidic/Microscopy-Based Platform for on-Chip Controlled Gene Expression in Mammalian Cells. Methods Mol Biol 2021; 2229:205-219. [PMID: 33405224 DOI: 10.1007/978-1-0716-1032-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Applications of control engineering to mammalian cell biology have been recently implemented for precise regulation of gene expression. In this chapter, we report the main experimental and computational methodologies to implement automatic feedback control of gene expression in mammalian cells using a microfluidics/microscopy platform.
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Affiliation(s)
- Mahmoud Khazim
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- BrisSynBio, Bristol, UK
| | - Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- BrisSynBio, Bristol, UK
| | - Lorena Postiglione
- Department of Engineering Mathematics, University of Bristol, Bristol, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- BrisSynBio, Bristol, UK
| | | | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, UK.
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
- BrisSynBio, Bristol, UK.
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20
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Schmitz J, Täuber S, Westerwalbesloh C, von Lieres E, Noll T, Grünberger A. Development and application of a cultivation platform for mammalian suspension cell lines with single-cell resolution. Biotechnol Bioeng 2020; 118:992-1005. [PMID: 33200818 DOI: 10.1002/bit.27627] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/28/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022]
Abstract
In bioproduction processes, cellular heterogeneity can cause unpredictable process outcomes or even provoke process failure. Still, cellular heterogeneity is not examined systematically in bioprocess research and development. One reason for this shortcoming is the applied average bulk analyses, which are not able to detect cell-to-cell differences. In this study, we present a microfluidic tool for mammalian single-cell cultivation (MaSC) of suspension cells. The design of our platform allows cultivation in highly controllable environments. As a model system, Chinese hamster ovary cells (CHO-K1) were cultivated over 150 h. Growth behavior was analyzed on a single-cell level and resulted in growth rates between 0.85 and 1.16 day-1 . At the same time, heterogeneous growth and division behavior, for example, unequal division time, as well as rare cellular events like polynucleation or reversed mitosis were observed, which would have remained undetected in a standard population analysis based on average measurements. Therefore, MaSC will open the door for systematic single-cell analysis of mammalian suspension cells. Possible fields of application represent basic research topics like cell-to-cell heterogeneity, clonal stability, pharmaceutical drug screening, and stem cell research, as well as bioprocess related topics such as media development and novel scale-down approaches.
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Affiliation(s)
- Julian Schmitz
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Sarah Täuber
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Christoph Westerwalbesloh
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Eric von Lieres
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thomas Noll
- Cell Culture Technology, Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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21
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Mudla A, Jiang Y, Arimoto KI, Xu B, Rajesh A, Ryan AP, Wang W, Daugherty MD, Zhang DE, Hao N. Cell-cycle-gated feedback control mediates desensitization to interferon stimulation. eLife 2020; 9:58825. [PMID: 32945770 PMCID: PMC7500952 DOI: 10.7554/elife.58825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
Cells use molecular circuits to interpret and respond to extracellular cues, such as hormones and cytokines, which are often released in a temporally varying fashion. In this study, we combine microfluidics, time-lapse microscopy, and computational modeling to investigate how the type I interferon (IFN)-responsive regulatory network operates in single human cells to process repetitive IFN stimulation. We found that IFN-α pretreatments lead to opposite effects, priming versus desensitization, depending on input durations. These effects are governed by a regulatory network composed of a fast-acting positive feedback loop and a delayed negative feedback loop, mediated by upregulation of ubiquitin-specific peptidase 18 (USP18). We further revealed that USP18 upregulation can only be initiated at the G1/early S phases of cell cycle upon the treatment onset, resulting in heterogeneous and delayed induction kinetics in single cells. This cell cycle gating provides a temporal compartmentalization of feedback loops, enabling duration-dependent desensitization to repetitive stimulations.
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Affiliation(s)
- Anusorn Mudla
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Yanfei Jiang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Kei-Ichiro Arimoto
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Bingxian Xu
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Adarsh Rajesh
- Department of Bioengineering, University of California, San Diego, La Jolla, United States
| | - Andy P Ryan
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Wei Wang
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, United States
| | - Matthew D Daugherty
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
| | - Dong-Er Zhang
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States.,Department of Pathology, Moores UCSD Cancer Center, University of California, San Diego, La Jolla, United States
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, United States
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22
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Dame K, Ribeiro AJ. Microengineered systems with iPSC-derived cardiac and hepatic cells to evaluate drug adverse effects. Exp Biol Med (Maywood) 2020; 246:317-331. [PMID: 32938227 PMCID: PMC7859673 DOI: 10.1177/1535370220959598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hepatic and cardiac drug adverse effects are among the leading causes of attrition in drug development programs, in part due to predictive failures of current animal or in vitro models. Hepatocytes and cardiomyocytes differentiated from human induced pluripotent stem cells (iPSCs) hold promise for predicting clinical drug effects, given their human-specific properties and their ability to harbor genetically determined characteristics that underlie inter-individual variations in drug response. Currently, the fetal-like properties and heterogeneity of hepatocytes and cardiomyocytes differentiated from iPSCs make them physiologically different from their counterparts isolated from primary tissues and limit their use for predicting clinical drug effects. To address this hurdle, there have been ongoing advances in differentiation and maturation protocols to improve the quality and use of iPSC-differentiated lineages. Among these are in vitro hepatic and cardiac cellular microsystems that can further enhance the physiology of cultured cells, can be used to better predict drug adverse effects, and investigate drug metabolism, pharmacokinetics, and pharmacodynamics to facilitate successful drug development. In this article, we discuss how cellular microsystems can establish microenvironments for these applications and propose how they could be used for potentially controlling the differentiation of hepatocytes or cardiomyocytes. The physiological relevance of cells is enhanced in cellular microsystems by simulating properties of tissue microenvironments, such as structural dimensionality, media flow, microfluidic control of media composition, and co-cultures with interacting cell types. Recent studies demonstrated that these properties also affect iPSC differentiations and we further elaborate on how they could control differentiation efficiency in microengineered devices. In summary, we describe recent advances in the field of cellular microsystems that can control the differentiation and maturation of hepatocytes and cardiomyocytes for drug evaluation. We also propose how future research with iPSCs within engineered microenvironments could enable their differentiation for scalable evaluations of drug effects.
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Affiliation(s)
- Keri Dame
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translation Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Alexandre Js Ribeiro
- Division of Applied Regulatory Science, Office of Clinical Pharmacology, Office of Translation Sciences, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
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23
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Bae J, Ju J, Kim D, Kim T. Double-Sided Microwells with a Stepped Through-Hole Membrane for High-Throughput Microbial Assays. Anal Chem 2020; 92:9501-9510. [PMID: 32571023 DOI: 10.1021/acs.analchem.0c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To improve the throughput of microwell arrays for identifying immense cellular diversities even at a single-bacteria level, further miniaturization or densification of the microwells has been an obvious breakthrough. However, controlling millions of nanoliter samples or more at the microscale remains technologically difficult and has been spatially restricted to a single open side of the microwells. Here we employed a stepped through-hole membrane to utilize the bottom as well as top side of a high-density nanoliter microwell array, thus improving spatial efficiency. The stepped structure shows additional effectiveness for handling several millions of nanoliter bacterial samples in the overall perspectives of controllability, throughput, simplicity, versatility, and automation by using novel methods for three representative procedures in bacterial assays: partitioning cells, manipulating the chemical environment, and extracting selected cells. As a potential application, we show proof-of-concept isolation of rare cells in a mixed ratio of 1 to around 106 using a single chip. Our device can be further applied to various biological studies pertaining to synthetic biology, drug screening, mutagenesis, and single-cell heterogeneity.
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Affiliation(s)
- Juyeol Bae
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Janghyun Ju
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Dahyun Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Taesung Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
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24
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Chen P, Li S, Guo Y, Zeng X, Liu BF. A review on microfluidics manipulation of the extracellular chemical microenvironment and its emerging application to cell analysis. Anal Chim Acta 2020; 1125:94-113. [PMID: 32674786 DOI: 10.1016/j.aca.2020.05.065] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Spatiotemporal manipulation of extracellular chemical environments with simultaneous monitoring of cellular responses plays an essential role in exploring fundamental biological processes and expands our understanding of underlying mechanisms. Despite the rapid progress and promising successes in manipulation strategies, many challenges remain due to the small size of cells and the rapid diffusion of chemical molecules. Fortunately, emerging microfluidic technology has become a powerful approach for precisely controlling the extracellular chemical microenvironment, which benefits from its integration capacity, automation, and high-throughput capability, as well as its high resolution down to submicron. Here, we summarize recent advances in microfluidics manipulation of the extracellular chemical microenvironment, including the following aspects: i) Spatial manipulation of chemical microenvironments realized by convection flow-, diffusion-, and droplet-based microfluidics, and surface chemical modification; ii) Temporal manipulation of chemical microenvironments enabled by flow switching/shifting, moving/flowing cells across laminar flows, integrated microvalves/pumps, and droplet manipulation; iii) Spatiotemporal manipulation of chemical microenvironments implemented by a coupling strategy and open-space microfluidics; and iv) High-throughput manipulation of chemical microenvironments. Finally, we briefly present typical applications of the above-mentioned technical advances in cell-based analyses including cell migration, cell signaling, cell differentiation, multicellular analysis, and drug screening. We further discuss the future improvement of microfluidics manipulation of extracellular chemical microenvironments to fulfill the needs of biological and biomedical research and applications.
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Affiliation(s)
- Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yiran Guo
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xuemei Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China.
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25
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Scott HL, Buckner N, Fernandez-Albert F, Pedone E, Postiglione L, Shi G, Allen N, Wong LF, Magini L, Marucci L, O'Sullivan GA, Cole S, Powell J, Maycox P, Uney JB. A dual druggable genome-wide siRNA and compound library screening approach identifies modulators of parkin recruitment to mitochondria. J Biol Chem 2020; 295:3285-3300. [PMID: 31911436 PMCID: PMC7062187 DOI: 10.1074/jbc.ra119.009699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/20/2019] [Indexed: 01/07/2023] Open
Abstract
Genetic and biochemical evidence points to an association between mitochondrial dysfunction and Parkinson's disease (PD). PD-associated mutations in several genes have been identified and include those encoding PTEN-induced putative kinase 1 (PINK1) and parkin. To identify genes, pathways, and pharmacological targets that modulate the clearance of damaged or old mitochondria (mitophagy), here we developed a high-content imaging-based assay of parkin recruitment to mitochondria and screened both a druggable genome-wide siRNA library and a small neuroactive compound library. We used a multiparameter principal component analysis and an unbiased parameter-agnostic machine-learning approach to analyze the siRNA-based screening data. The hits identified in this analysis included specific genes of the ubiquitin proteasome system, and inhibition of ubiquitin-conjugating enzyme 2 N (UBE2N) with a specific antagonist, Bay 11-7082, indicated that UBE2N modulates parkin recruitment and downstream events in the mitophagy pathway. Screening of the compound library identified kenpaullone, an inhibitor of cyclin-dependent kinases and glycogen synthase kinase 3, as a modulator of parkin recruitment. Validation studies revealed that kenpaullone augments the mitochondrial network and protects against the complex I inhibitor MPP+. Finally, we used a microfluidics platform to assess the timing of parkin recruitment to depolarized mitochondria and its modulation by kenpaullone in real time and with single-cell resolution. We demonstrate that the high-content imaging-based assay presented here is suitable for both genetic and pharmacological screening approaches, and we also provide evidence that pharmacological compounds modulate PINK1-dependent parkin recruitment.
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Affiliation(s)
- Helen L Scott
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nicola Buckner
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | | | - Elisa Pedone
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lorena Postiglione
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Gongyu Shi
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Nicholas Allen
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom
| | - Liang-Fong Wong
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lorenzo Magini
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom
| | - Lucia Marucci
- Department of Engineering and Mathematics, University of Bristol, Bristol BS8 1TD, United Kingdom; BrisSynBio, Bristol BS8 1QU, United Kingdom
| | - Gregory A O'Sullivan
- Takeda Cambridge Ltd., Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Sarah Cole
- Takeda Ventures, Inc., 61 Aldwych, London WC2B 4A, United Kingdom
| | - Justin Powell
- Takeda Cambridge Ltd., Cambridge Science Park, Cambridge CB4 0PZ, United Kingdom
| | - Peter Maycox
- Takeda Ventures, Inc., 61 Aldwych, London WC2B 4A, United Kingdom
| | - James B Uney
- Bristol Medical School, University of Bristol, Bristol BS8 1TD, United Kingdom.
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26
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Levitsky Y, Pegouske DJ, Hammer SS, Frantz NL, Fisher KP, Muchnik AB, Saripalli AR, Kirschner P, Bazil JN, Busik JV, Proshlyakov DA. Micro-respirometry of whole cells and isolated mitochondria. RSC Adv 2019; 9:33257-33267. [PMID: 32123561 PMCID: PMC7051014 DOI: 10.1039/c9ra05289e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Oxygen consumption is a key metric of metabolism in aerobic organisms. Current respirometric methods led to seminal discoveries despite limitations such as high sample demand, exchange with atmospheric O2, and cumulative titration protocols leading to limited choice of useable tissue, complex data interpretation, and restricted experimental design. We developed a sensitive and customizable method of measuring O2 consumption rates by a variety of biological samples in microliter volumes without interference from the aerobic environment. We demonstrate that O2 permeability of the photopolymer, VeroClear, is comparable to that of polyetheretherketone (0.125 vs. 0.143 barrer, respectively) providing an efficient barrier to oxygen ingress. Optical transparency of VeroClear, combined with high resolution 3D printing, allows for optode-based oxygen detection in enclosed samples. These properties yield a microrespirometer with over 100× dynamic range for O2 consumption rates. Importantly, the enclosed respirometer configuration and very low oxygen permeability of materials makes it suitable, with resin pre-conditioning, for quantitative assessment of O2 consumption rates at any desired [O2], including hyperbaric, physiological or hypoxic conditions as necessary for each cell type. We characterized two configurations to study soluble enzymes, isolated mitochondria, cells in suspension, and adherent cells cultured on-chip. Improved sensitivity allows for routine quantitative detection of respiration by as few as several hundred cells. Specific activity of cell suspensions in the microrespirometer was in close agreement with that obtained by high-resolution polarographic respirometry. Adherent cell protocols allowed for physiologically relevant assessment of respiration in retinal pigment epithelial cells, ARPE-19, which displayed lower metabolic rates compared with those in suspension. By exchanging medium composition, we demonstrate that cells can be transiently inhibited by cyanide and that 99.6% of basal O2 uptake is recovered upon its removal. This approach is amenable to new experimental designs and precision measurements on limited sample quantities across basic research and applied fields. 3D printed microfluidic respirometer allows for quantitative investigation of biological energy transduction in adherent and suspension samples.![]()
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Affiliation(s)
- Yan Levitsky
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.,Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - David J Pegouske
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Sandra S Hammer
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Nathan L Frantz
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Kiera P Fisher
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Artem B Muchnik
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | | | - Philip Kirschner
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Jason N Bazil
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Julia V Busik
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Denis A Proshlyakov
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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27
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Heterogeneity Studies of Mammalian Cells for Bioproduction: From Tools to Application. Trends Biotechnol 2019; 37:645-660. [DOI: 10.1016/j.tibtech.2018.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022]
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28
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Eilenberger C, Spitz S, Bachmann BEM, Ehmoser EK, Ertl P, Rothbauer M. The Usual Suspects 2019: of Chips, Droplets, Synthesis, and Artificial Cells. MICROMACHINES 2019; 10:E285. [PMID: 31035574 PMCID: PMC6562886 DOI: 10.3390/mi10050285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/03/2022]
Abstract
Synthetic biology aims to understand fundamental biological processes in more detail than possible for actual living cells. Synthetic biology can combat decomposition and build-up of artificial experimental models under precisely controlled and defined environmental and biochemical conditions. Microfluidic systems can provide the tools to improve and refine existing synthetic systems because they allow control and manipulation of liquids on a micro- and nanoscale. In addition, chip-based approaches are predisposed for synthetic biology applications since they present an opportune technological toolkit capable of fully automated high throughput and content screening under low reagent consumption. This review critically highlights the latest updates in microfluidic cell-free and cell-based protein synthesis as well as the progress on chip-based artificial cells. Even though progress is slow for microfluidic synthetic biology, microfluidic systems are valuable tools for synthetic biology and may one day help to give answers to long asked questions of fundamental cell biology and life itself.
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Affiliation(s)
- Christoph Eilenberger
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Sarah Spitz
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Barbara Eva Maria Bachmann
- Austrian Cluster for Tissue Regeneration, Vienna, Austria; Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Allgemeine Unfallversicherungsanstalt (AUVA) Research Centre, A-1200 Vienna, Austria.
| | - Eva Kathrin Ehmoser
- Institute of Synthetic Bioarchitectures, Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, A-1190 Vienna, Austria.
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry, Institute of Chemical Technologies and Analytics, Faculty of Technical Chemistry, Vienna University of Technology, A-1060 Vienna, Austria.
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29
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Bhattacharya A, Brea RJ, Niederholtmeyer H, Devaraj NK. A minimal biochemical route towards de novo formation of synthetic phospholipid membranes. Nat Commun 2019; 10:300. [PMID: 30655537 PMCID: PMC6336818 DOI: 10.1038/s41467-018-08174-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/14/2018] [Indexed: 11/30/2022] Open
Abstract
All living cells consist of membrane compartments, which are mainly composed of phospholipids. Phospholipid synthesis is catalyzed by membrane-bound enzymes, which themselves require pre-existing membranes for function. Thus, the principle of membrane continuity creates a paradox when considering how the first biochemical membrane-synthesis machinery arose and has hampered efforts to develop simplified pathways for membrane generation in synthetic cells. Here, we develop a high-yielding strategy for de novo formation and growth of phospholipid membranes by repurposing a soluble enzyme FadD10 to form fatty acyl adenylates that react with amine-functionalized lysolipids to form phospholipids. Continuous supply of fresh precursors needed for lipid synthesis enables the growth of vesicles encapsulating FadD10. Using a minimal transcription/translation system, phospholipid vesicles are generated de novo in the presence of DNA encoding FadD10. Our findings suggest that alternate chemistries can produce and maintain synthetic phospholipid membranes and provides a strategy for generating membrane-based materials. The origin of phospholipids, the primary constituents of cell membranes, is uncertain. Here, the authors develop an in vitro system to synthesize phospholipid molecules from water-soluble single-chain amphiphilic precursors via a reaction catalysed by the mycobacterial ligase FadD10.
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Affiliation(s)
- Ahanjit Bhattacharya
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, Natural Sciences Building 3328, San Diego, CA, 92093, USA
| | - Roberto J Brea
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, Natural Sciences Building 3328, San Diego, CA, 92093, USA
| | - Henrike Niederholtmeyer
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, Natural Sciences Building 3328, San Diego, CA, 92093, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, Natural Sciences Building 3328, San Diego, CA, 92093, USA.
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30
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Khazim M, Postiglione L, Pedone E, Rocca DL, Zahra C, Marucci L. Towards automated control of embryonic stem cell pluripotency. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.ifacol.2019.12.240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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Chagnon-Lessard S, Godin M, Pelling AE. Time dependence of cellular responses to dynamic and complex strain fields. Integr Biol (Camb) 2019; 11:4-15. [PMID: 30778578 DOI: 10.1093/intbio/zyy002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/08/2018] [Indexed: 11/13/2022]
Abstract
Exposing cells to an unconventional sequence of physical cues can reveal subtleties of cellular sensing and response mechanisms. We investigated the mechanoresponse of cyclically stretched fibroblasts under a spatially non-uniform strain field which was subjected to repeated changes in stretching directions over 55 h. A polydimethylsiloxane microfluidic stretcher array optimized for complex staining procedures and imaging was developed to generate biologically relevant strain and strain gradient amplitudes. We demonstrated that cells can successfully reorient themselves repeatedly, as the main cyclical stretching direction is consecutively switched between two perpendicular directions every 11 h. Importantly, from one reorientation to the next, the extent to which cells reorient themselves perpendicularly to the local strain direction progressively decreases, while their tendency to align perpendicularly to the strain gradient direction increases. We demonstrate that these results are consistent with our finding that cellular responses to strains and strain gradients occur on two distinct time scales, the latter being slower. Overall, our results reveal the absence of major irreversible cellular changes that compromise the ability to sense and reorient to changing strain directions under the conditions of this experiment. On the other hand, we show how the history of strain field dynamics can influence the cellular realignment behavior, due to the interplay of complex time-dependent responses.
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Affiliation(s)
| | - Michel Godin
- Department of Physics, STEM Building 150 Louis Pasteur, Ottawa, Canada.,Department of Mechanical Engineering, Site Building, 800 King Edward Avenue, University of Ottawa, ON, Canada.,Ottawa-Carleton Institute for Biomedical Engineering, Ottawa, ON, Canada
| | - Andrew E Pelling
- Department of Physics, STEM Building 150 Louis Pasteur, Ottawa, Canada.,Department of Biology, Gendron Hall, 30 Marie Curie, University of Ottawa, Ottawa, ON, Canada.,Institute for Science Society and Policy, Simard Hall, 60 University, University of Ottawa, Ottawa, ON, Canada.,SymbioticA, School of Anatomy, Physiology and Human Biology, University of Western Australia, Perth, WA, Australia
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32
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Postiglione L, Napolitano S, Pedone E, Rocca DL, Aulicino F, Santorelli M, Tumaini B, Marucci L, di Bernardo D. Regulation of Gene Expression and Signaling Pathway Activity in Mammalian Cells by Automated Microfluidics Feedback Control. ACS Synth Biol 2018; 7:2558-2565. [PMID: 30346742 DOI: 10.1021/acssynbio.8b00235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene networks and signaling pathways display complex topologies and, as a result, complex nonlinear behaviors. Accumulating evidence shows that both static (concentration) and dynamical (rate-of-change) features of transcription factors, ligands and environmental stimuli control downstream processes and ultimately cellular functions. Currently, however, methods to generate stimuli with the desired features to probe cell response are still lacking. Here, combining tools from Control Engineering and Synthetic Biology (cybergenetics), we propose a simple and cost-effective microfluidics-based platform to precisely regulate gene expression and signaling pathway activity in mammalian cells by means of real-time feedback control. We show that this platform allows (i) to automatically regulate gene expression from inducible promoters in different cell types, including mouse embryonic stem cells; (ii) to precisely regulate the activity of the mTOR signaling pathway in single cells; (iii) to build a biohybrid oscillator in single embryonic stem cells by interfacing biological parts with virtual in silico counterparts. Ultimately, this platform can be used to probe gene networks and signaling pathways to understand how they process static and dynamic features of specific stimuli, as well as for the rapid prototyping of synthetic circuits for biotechnology and biomedical purposes.
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Affiliation(s)
- Lorena Postiglione
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Sara Napolitano
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Elisa Pedone
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
| | - Daniel L. Rocca
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
- BrisSynBio, Bristol BS8 1TQ, U.K
| | - Francesco Aulicino
- BrisSynBio, Bristol BS8 1TQ, U.K
- Department of Biochemistry, University of Bristol, Bristol BS8 1UB, U.K
| | - Marco Santorelli
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Barbara Tumaini
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1UB, U.K
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1UB, U.K
- BrisSynBio, Bristol BS8 1TQ, U.K
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
- Department of Chemical, Materials and Industrial Engineering, University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy
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Abstract
Microfluidics has played a vital role in developing novel methods to investigate biological phenomena at the molecular and cellular level during the last two decades. Microscale engineering of cellular systems is nevertheless a nascent field marked inherently by frequent disruptive advancements in technology such as PDMS-based soft lithography. Viable culture and manipulation of cells in microfluidic devices requires knowledge across multiple disciplines including molecular and cellular biology, chemistry, physics, and engineering. There has been numerous excellent reviews in the past 15 years on applications of microfluidics for molecular and cellular biology including microfluidic cell culture (Berthier et al., 2012; El-Ali, Sorger, & Jensen, 2006; Halldorsson et al., 2015; Kim et al., 2007; Mehling & Tay, 2014; Sackmann et al., 2014; Whitesides, 2006; Young & Beebe, 2010), cell culture models (Gupta et al., 2016; Inamdar & Borenstein, 2011; Meyvantsson & Beebe, 2008), cell secretion (Schrell et al., 2016), chemotaxis (Kim & Wu, 2012; Wu et al., 2013), neuron culture (Millet & Gillette, 2012a, 2012b), drug screening (Dittrich & Manz, 2006; Eribol, Uguz, & Ulgen, 2016; Wu, Huang, & Lee, 2010), cell sorting (Autebert et al., 2012; Bhagat et al., 2010; Gossett et al., 2010; Wyatt Shields Iv, Reyes, & López, 2015), single cell studies (Lecault et al., 2012; Reece et al., 2016; Yin & Marshall, 2012), stem cell biology (Burdick & Vunjak-Novakovic, 2009; Wu et al., 2011; Zhang & Austin, 2012), cell differentiation (Zhang et al., 2017a), systems biology (Breslauer, Lee, & Lee, 2006), 3D cell culture (Huh et al., 2011; Li et al., 2012; van Duinen et al., 2015), spheroids and organoids (Lee et al., 2016; Montanez-Sauri, Beebe, & Sung, 2015; Morimoto & Takeuchi, 2013; Skardal et al., 2016; Young, 2013), organ-on-chip (Bhatia & Ingber, 2014; Esch, Bahinski, & Huh, 2015; Huh et al., 2011; van der Meer & van den Berg, 2012), and tissue engineering (Andersson & Van Den Berg, 2004; Choi et al., 2007; Hasan et al., 2014). In this chapter, we provide an overview of PDMS-based microdevices for microfluidic cell culture. We discuss the advantages and challenges of using PDMS-based soft lithography for microfluidic cell culture and highlight recent progress and future directions in this area.
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Affiliation(s)
- Melikhan Tanyeri
- Biomedical Engineering Program, Duquesne University, Pittsburgh, PA, United States
| | - Savaş Tay
- Institute of Molecular Engineering, University of Chicago, Chicago, IL, United States; Institute of Genomics and Systems Biology, University of Chicago, Chicago, IL, United States.
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34
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Varma S, Voldman J. Caring for cells in microsystems: principles and practices of cell-safe device design and operation. LAB ON A CHIP 2018; 18:3333-3352. [PMID: 30324208 PMCID: PMC6254237 DOI: 10.1039/c8lc00746b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Microfluidic device designers and users continually question whether cells are 'happy' in a given microsystem or whether they are perturbed by micro-scale technologies. This issue is normally brought up by engineers building platforms, or by external reviewers (academic or commercial) comparing multiple technological approaches to a problem. Microsystems can apply combinations of biophysical and biochemical stimuli that, although essential to device operation, may damage cells in complex ways. However, assays to assess the impact of microsystems upon cells have been challenging to conduct and have led to subjective interpretation and evaluation of cell stressors, hampering development and adoption of microsystems. To this end, we introduce a framework that defines cell health, describes how device stimuli may stress cells, and contrasts approaches to measure cell stress. Importantly, we provide practical guidelines regarding device design and operation to minimize cell stress, and recommend a minimal set of quantitative assays that will enable standardization in the assessment of cell health in diverse devices. We anticipate that as microsystem designers, reviewers, and end-users enforce such guidelines, we as a community can create a set of essential principles that will further the adoption of such technologies in clinical, translational and commercial applications.
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Affiliation(s)
- Sarvesh Varma
- Department of Electrical Engineering and Computer Science
, Massachusetts Institute of Technology
,
77 Massachusetts Avenue, Room 36-824
, Cambridge
, USA
.
; Fax: +617 258 5846
; Tel: +617 253 1583
| | - Joel Voldman
- Department of Electrical Engineering and Computer Science
, Massachusetts Institute of Technology
,
77 Massachusetts Avenue, Room 36-824
, Cambridge
, USA
.
; Fax: +617 258 5846
; Tel: +617 253 1583
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35
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Microfluidic Transfection for High-Throughput Mammalian Protein Expression. Methods Mol Biol 2018. [PMID: 30242688 DOI: 10.1007/978-1-4939-8730-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Mammalian synthetic biology and cell biology would greatly benefit from improved methods for highly parallel transfection, culturing, and interrogation of mammalian cells. Transfection is routinely performed on high-throughput microarrays, but this setup requires manual cell culturing and precludes precise control over the cell environment. As an alternative, microfluidic transfection devices streamline cell loading and culturing. Up to 280 transfections can be implemented on the chip at high efficiency. The culturing environment is tightly regulated and chambers physically separate the transfection reactions, preventing cross-contamination. Unlike typical biological assays that rely on end-point measurements, the microfluidic chip can be integrated with high-content imaging, enabling the evaluation of cellular behavior and protein expression dynamics over time.
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36
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Dettinger P, Frank T, Etzrodt M, Ahmed N, Reimann A, Trenzinger C, Loeffler D, Kokkaliaris KD, Schroeder T, Tay S. Automated Microfluidic System for Dynamic Stimulation and Tracking of Single Cells. Anal Chem 2018; 90:10695-10700. [PMID: 30059208 DOI: 10.1021/acs.analchem.8b00312] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic environments determine cell fate decisions and function. Understanding the relationship between extrinsic signals on cellular responses and cell fate requires the ability to dynamically change environmental inputs in vitro, while continuously observing individual cells over extended periods of time. This is challenging for nonadherent cells, such as hematopoietic stem and progenitor cells, because media flow displaces and disturbs such cells, preventing culture and tracking of single cells. Here, we present a programmable microfluidic system designed for the long-term culture and time-lapse imaging of nonadherent cells in dynamically changing cell culture conditions without losing track of individual cells. The dynamic, valve-controlled design permits targeted seeding of cells in up to 48 independently controlled culture chambers, each providing sufficient space for long-term cell colony expansion. Diffusion-based media exchange occurs rapidly and minimizes displacement of cells and eliminates shear stress. The chip was successfully tested with long-term culture and tracking of primary hematopoietic stem and progenitor cells, and murine embryonic stem cells. This system will have important applications to analyze dynamic signaling inputs controlling fate choices.
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Affiliation(s)
- Philip Dettinger
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Tino Frank
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Martin Etzrodt
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Nouraiz Ahmed
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Andreas Reimann
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Christoph Trenzinger
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Konstantinos D Kokkaliaris
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland
| | - Savaş Tay
- Department of Biosystems Science and Engineering , ETH Zurich, Mattenstrasse 26 4058 Basel , Switzerland.,Institute for Molecular Engineering , The University of Chicago , 5640 S. Ellis Ave , Chicago , Illinois 60637 , United States
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37
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Wu W. A pressure-driven gas-diffusion/permeation micropump for self-activated sample transport in an extreme micro-environment. Analyst 2018; 143:4819-4835. [DOI: 10.1039/c8an01120f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The pressure-driven gas-diffusion/permeation micropump is highlighted for stable microdroplet/liquid delivery under extreme conditions,e.g.high temperature, and a three-dimensional, long-distance and complex-topology microchannel.
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Affiliation(s)
- Wenming Wu
- State Key Laboratory of Applied Optics
- Changchun Institute of Optics
- Fine Mechanics and Physics
- Chinese Academy of Sciences
- Changchun
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38
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Yang Y, Le Gac S, Terstappen LWMM, Rho HS. Parallel probing of drug uptake of single cancer cells on a microfluidic device. Electrophoresis 2017; 39:548-556. [DOI: 10.1002/elps.201700351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/07/2017] [Accepted: 11/20/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Yoonsun Yang
- Medical Cell BioPhysics Group; MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente; The Netherlands
| | - Séverine Le Gac
- Applied Microfluidics for BioEngineering Research Group; MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Engineering and Technical Medicine; University of Twente; The Netherlands
| | - Leon WMM Terstappen
- Medical Cell BioPhysics Group; MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente; The Netherlands
| | - Hoon Suk Rho
- Applied Microfluidics for BioEngineering Research Group; MESA+ Institute for Nanotechnology, MIRA Institute for Biomedical Engineering and Technical Medicine; University of Twente; The Netherlands
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Woodruff K, Maerkl SJ. Microfluidic Module for Real-Time Generation of Complex Multimolecule Temporal Concentration Profiles. Anal Chem 2017; 90:696-701. [PMID: 29183126 DOI: 10.1021/acs.analchem.7b04099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We designed a microfluidic module that generates complex and dynamic concentration profiles of multiple molecules over a large concentration range using pulse-width modulation (PWM). Our PWM module can combine up to six different inputs and select among three downstream mixing channels, as required by the application. The module can produce concentrations with a dynamic range of three decades. We created complex, temporal concentration profiles of two molecules, with each concentration independently controllable, and show that the PWM module can execute rapid concentration changes as well as long-time scale pharmacokinetic profiles. Concentration profiles were generated for molecules with molecular weights ranging from 560 Da to 150 kDa. Our PWM module produces robust and precise concentration profiles under a variety of operating conditions, making it ideal for integration with existing microfluidic devices for advanced cell and pharmacokinetic studies.
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Affiliation(s)
- Kristina Woodruff
- Institute of Bioengineering, School of Engineering and School of Life Science, École Polytechnique Fédérale de Lausanne , Lausanne, Switzerland
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering and School of Life Science, École Polytechnique Fédérale de Lausanne , Lausanne, Switzerland
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Lin Y, Gordon O, Khan MR, Vasquez N, Genzer J, Dickey MD. Vacuum filling of complex microchannels with liquid metal. LAB ON A CHIP 2017; 17:3043-3050. [PMID: 28805880 DOI: 10.1039/c7lc00426e] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
This paper describes the utilization of vacuum to fill complex microchannels with liquid metal. Microchannels filled with liquid metal are useful as conductors for soft and stretchable electronics, as well as for microfluidic components such as electrodes, antennas, pumps, or heaters. Liquid metals are often injected manually into the inlet of a microchannel using a syringe. Injection can only occur if displaced air in the channels has a pathway to escape, which is usually accomplished using outlets. The positive pressure (relative to atmosphere) needed to inject fluids can also cause leaks or delamination of the channels during injection. Here we show a simple and hands-free method to fill microchannels with liquid metal that addresses these issues. The process begins by covering a single inlet with liquid metal. Placing the entire structure in a vacuum chamber removes the air from the channels and the surrounding elastomer. Restoring atmospheric pressure in the chamber creates a positive pressure differential that pushes the metal into the channels. Experiments and a simple model of the filling process both suggest that the elastomeric channel walls absorb residual air displaced by the metal as it fills the channels. Thus, the metal can fill dead-ends with features as small as several microns and branched structures within seconds without the need for any outlets. The method can also fill completely serpentine microchannels up to a few meters in length. The ability to fill dense and complex geometries with liquid metal in this manner may enable broader application of liquid metals in electronic and microfluidic applications.
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Affiliation(s)
- Yiliang Lin
- Department of Chemical & Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695-7905, USA.
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Yu ZTF, Cheung MK, Liu SX, Fu J. Accelerated Biofluid Filling in Complex Microfluidic Networks by Vacuum-Pressure Accelerated Movement (V-PAM). SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:4521-30. [PMID: 27409528 PMCID: PMC6215695 DOI: 10.1002/smll.201601231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 06/11/2016] [Indexed: 05/27/2023]
Abstract
Rapid fluid transport and exchange are critical operations involved in many microfluidic applications. However, conventional mechanisms used for driving fluid transport in microfluidics, such as micropumping and high pressure, can be inaccurate and difficult for implementation for integrated microfluidics containing control components and closed compartments. Here, a technology has been developed termed Vacuum-Pressure Accelerated Movement (V-PAM) capable of significantly enhancing biofluid transport in complex microfluidic environments containing dead-end channels and closed chambers. Operation of the V-PAM entails a pressurized fluid loading into microfluidic channels where gas confined inside can rapidly be dissipated through permeation through a thin, gas-permeable membrane sandwiched between microfluidic channels and a network of vacuum channels. Effects of different structural and operational parameters of the V-PAM for promoting fluid filling in microfluidic environments have been studied systematically. This work further demonstrates the applicability of V-PAM for rapid filling of temperature-sensitive hydrogels and unprocessed whole blood into complex irregular microfluidic networks such as microfluidic leaf venation patterns and blood circulatory systems. Together, the V-PAM technology provides a promising generic microfluidic tool for advanced fluid control and transport in integrated microfluidics for different microfluidic diagnosis, organs-on-chips, and biomimetic studies.
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Affiliation(s)
- Zeta Tak For Yu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mei Ki Cheung
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Shirley Xiaosu Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Michigan Center for Integrative Research in Critical Care, University of Michigan, Ann Arbor, MI 48109, USA
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Borek B, Hasty J, Tsimring L. Turing Patterning Using Gene Circuits with Gas-Induced Degradation of Quorum Sensing Molecules. PLoS One 2016; 11:e0153679. [PMID: 27148743 PMCID: PMC4858293 DOI: 10.1371/journal.pone.0153679] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 04/01/2016] [Indexed: 01/30/2023] Open
Abstract
The Turing instability was proposed more than six decades ago as a mechanism leading to spatial patterning, but it has yet to be exploited in a synthetic biology setting. Here we characterize the Turing instability in a specific gene circuit that can be implemented in vitro or in populations of clonal cells producing short-range activator N-Acyl homoserine lactone (AHL) and long-range inhibitor hydrogen peroxide (H2O2) gas. Slowing the production rate of the AHL-degrading enzyme, AiiA, generates stable fixed states, limit cycle oscillations and Turing patterns. Further tuning of signaling parameters determines local robustness and controls the range of unstable wavenumbers in the patterning regime. These findings provide a roadmap for optimizing spatial patterns of gene expression based on familiar quorum and gas sensitive E. coli promoters. The circuit design and predictions may be useful for (re)programming spatial dynamics in synthetic and natural gene expression systems.
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Affiliation(s)
- Bartłomiej Borek
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
| | - Jeff Hasty
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
- Department of Bioengineering, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0412, United States of America
- Molecular Biology Section, Division of Biological Sciences, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0116, United States of America
| | - Lev Tsimring
- BioCircuits Institute, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0328, United States of America
- San Diego Center for Systems Biology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA, 92037-0375, United States of America
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Fracassi C, Postiglione L, Fiore G, di Bernardo D. Automatic Control of Gene Expression in Mammalian Cells. ACS Synth Biol 2016; 5:296-302. [PMID: 26414746 DOI: 10.1021/acssynbio.5b00141] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Automatic control of gene expression in living cells is paramount importance to characterize both endogenous gene regulatory networks and synthetic circuits. In addition, such a technology can be used to maintain the expression of synthetic circuit components in an optimal range in order to ensure reliable performance. Here we present a microfluidics-based method to automatically control gene expression from the tetracycline-inducible promoter in mammalian cells in real time. Our approach is based on the negative-feedback control engineering paradigm. We validated our method in a monoclonal population of cells constitutively expressing a fluorescent reporter protein (d2EYFP) downstream of a minimal CMV promoter with seven tet-responsive operator motifs (CMV-TET). These cells also constitutively express the tetracycline transactivator protein (tTA). In cells grown in standard growth medium, tTA is able to bind the CMV-TET promoter, causing d2EYFP to be maximally expressed. Upon addition of tetracycline to the culture medium, tTA detaches from the CMV-TET promoter, thus preventing d2EYFP expression. We tested two different model-independent control algorithms (relay and proportional-integral (PI)) to force a monoclonal population of cells to express an intermediate level of d2EYFP equal to 50% of its maximum expression level for up to 3500 min. The control input is either tetracycline-rich or standard growth medium. We demonstrated that both the relay and PI controllers can regulate gene expression at the desired level, despite oscillations (dampened in the case of the PI controller) around the chosen set point.
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Affiliation(s)
- Chiara Fracassi
- TeleThon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Lorena Postiglione
- TeleThon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
- Department
of Electrical Engineering and Information Technology, University of Naples Federico II, 80125 Naples, Italy
| | - Gianfranco Fiore
- TeleThon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Diego di Bernardo
- TeleThon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
- Department
of Electrical Engineering and Information Technology, University of Naples Federico II, 80125 Naples, Italy
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A High-Throughput Microfluidic Platform for Mammalian Cell Transfection and Culturing. Sci Rep 2016; 6:23937. [PMID: 27030663 PMCID: PMC4814922 DOI: 10.1038/srep23937] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/16/2016] [Indexed: 11/28/2022] Open
Abstract
Mammalian synthetic biology could be augmented through the development of high-throughput microfluidic systems that integrate cellular transfection, culturing, and imaging. We created a microfluidic chip that cultures cells and implements 280 independent transfections at up to 99% efficiency. The chip can perform co-transfections, in which the number of cells expressing each protein and the average protein expression level can be precisely tuned as a function of input DNA concentration and synthetic gene circuits can be optimized on chip. We co-transfected four plasmids to test a histidine kinase signaling pathway and mapped the dose dependence of this network on the level of one of its constituents. The chip is readily integrated with high-content imaging, enabling the evaluation of cellular behavior and protein expression dynamics over time. These features make the transfection chip applicable to high-throughput mammalian protein and synthetic biology studies.
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Postiglione L, Santorelli M, Tumaini B, di Bernardo D. From a discrete to continuous actuation for improved real-time control of gene expression in mammalian cells. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.ifacol.2016.12.096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Xu L, Lee H, Jetta D, Oh KW. Vacuum-driven power-free microfluidics utilizing the gas solubility or permeability of polydimethylsiloxane (PDMS). LAB ON A CHIP 2015; 15:3962-79. [PMID: 26329518 DOI: 10.1039/c5lc00716j] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Suitable pumping methods for flow control remain a major technical hurdle in the path of biomedical microfluidic systems for point-of-care (POC) diagnostics. A vacuum-driven power-free micropumping method provides a promising solution to such a challenge. In this review, we focus on vacuum-driven power-free microfluidics based on the gas solubility or permeability of polydimethylsiloxane (PDMS); degassed PDMS can restore air inside itself due to its high gas solubility or gas permeable nature. PDMS allows the transfer of air into a vacuum through it due to its high gas permeability. Therefore, it is possible to store or transfer air into or through the gas soluble or permeable PDMS in order to withdraw liquids into the embedded dead-end microfluidic channels. This article provides a comprehensive look at the physics of the gas solubility and permeability of PDMS, a systematic review of different types of vacuum-driven power-free microfluidics, and guidelines for designing solubility-based or permeability-based PDMS devices, alongside existing applications. Advanced topics and the outlook in using micropumping that utilizes the gas solubility or permeability of PDMS will be also discussed. We strongly recommend that microfluidics and lab-on-chip (LOC) communities harness vacuum energy to develop smart vacuum-driven microfluidic systems.
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Affiliation(s)
- Linfeng Xu
- SMALL (Sensors and MicroActuators Learning Laboratory), Department of Electrical Engineering, State University of New York at Buffalo, Buffalo, NY 14260, USA.
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Liu J, Fu H, Yang T, Li S. Automatic sequential fluid handling with multilayer microfluidic sample isolated pumping. BIOMICROFLUIDICS 2015; 9:054118. [PMID: 26487904 PMCID: PMC4592428 DOI: 10.1063/1.4932303] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/21/2015] [Indexed: 06/05/2023]
Abstract
To sequentially handle fluids is of great significance in quantitative biology, analytical chemistry, and bioassays. However, the technological options are limited when building such microfluidic sequential processing systems, and one of the encountered challenges is the need for reliable, efficient, and mass-production available microfluidic pumping methods. Herein, we present a bubble-free and pumping-control unified liquid handling method that is compatible with large-scale manufacture, termed multilayer microfluidic sample isolated pumping (mμSIP). The core part of the mμSIP is the selective permeable membrane that isolates the fluidic layer from the pneumatic layer. The air diffusion from the fluidic channel network into the degassing pneumatic channel network leads to fluidic channel pressure variation, which further results in consistent bubble-free liquid pumping into the channels and the dead-end chambers. We characterize the mμSIP by comparing the fluidic actuation processes with different parameters and a flow rate range of 0.013 μl/s to 0.097 μl/s is observed in the experiments. As the proof of concept, we demonstrate an automatic sequential fluid handling system aiming at digital assays and immunoassays, which further proves the unified pumping-control and suggests that the mμSIP is suitable for functional microfluidic assays with minimal operations. We believe that the mμSIP technology and demonstrated automatic sequential fluid handling system would enrich the microfluidic toolbox and benefit further inventions.
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Affiliation(s)
- Jixiao Liu
- Department of Fluid Control and Automation, Harbin Institute of Technology , Harbin 150001, China
| | - Hai Fu
- Department of Fluid Control and Automation, Harbin Institute of Technology , Harbin 150001, China
| | - Tianhang Yang
- Department of Fluid Control and Automation, Harbin Institute of Technology , Harbin 150001, China
| | - Songjing Li
- Department of Fluid Control and Automation, Harbin Institute of Technology , Harbin 150001, China
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Graham PJ, Riordon J, Sinton D. Microalgae on display: a microfluidic pixel-based irradiance assay for photosynthetic growth. LAB ON A CHIP 2015; 15:3116-24. [PMID: 26085371 DOI: 10.1039/c5lc00527b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Microalgal biofuel is an emerging sustainable energy resource. Photosynthetic growth is heavily dependent on irradiance, therefore photobioreactor design optimization requires comprehensive screening of irradiance variables, such as intensity, time variance and spectral composition. Here we present a microfluidic irradiance assay which leverages liquid crystal display technology to provide multiplexed screening of irradiance conditions on growth. An array of 238 microreactors are operated in parallel with identical chemical environments. The approach is demonstrated by performing three irradiance assays. The first assay evaluates the effect of intensity on growth, quantifying saturating intensity. The second assay quantifies the influence of time-varied intensity and the threshold frequency for growth. Lastly, the coupled influence of red-blue spectral composition and intensity is assessed. Each multiplexed assay is completed within three days. In contrast, completing the same number of experiments using conventional incubation flasks would require several years. Not only does our approach enable more rapid screening, but the short optical path avoids self-shading issues inherent to flask based systems.
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Affiliation(s)
- Percival J Graham
- Department of Mechanical and Industrial Engineering and Institute for Sustainable Energy, University of Toronto, 5 King's College Road, Toronto, ON M5S 3G8, Canada.
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Frey O, Rudolf F, Schmidt GW, Hierlemann A. Versatile, simple-to-use microfluidic cell-culturing chip for long-term, high-resolution, time-lapse imaging. Anal Chem 2015; 87:4144-51. [PMID: 25837982 PMCID: PMC7610638 DOI: 10.1021/ac504611t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Optical long-term observation of individual cells, combined with modern data analysis tools, allows for a detailed study of cell-to-cell variability, heredity, and differentiation. We developed a microfluidic device featuring facile cell loading, simple and robust operation, and which is amenable to high-resolution life-cell imaging. Different cell strains can be grown in parallel in the device under constant or changing media perfusion without cross-talk between the cell ensembles. The culturing chamber has been optimized for use with nonadherent cells, such as Saccharomyces cerevisiae, and enables controlled colony growth over multiple generations under aerobic or anaerobic conditions. Small changes in the layout will make the device also useable with bacteria or mammalian cells. The platform can be readily set up in every laboratory with minimal additional requirements and can be operated without technology training.
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Affiliation(s)
- Olivier Frey
- ETH Zürich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Fabian Rudolf
- ETH Zürich, Department of Biosystems Science and Engineering, Computational Systems Biology Group, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Gregor W. Schmidt
- ETH Zürich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Andreas Hierlemann
- ETH Zürich, Department of Biosystems Science and Engineering, Bio Engineering Laboratory, Mattenstrasse 26, 4058 Basel, Switzerland
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