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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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2
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Maurya R, Gohil N, Bhattacharjee G, Alzahrani KJ, Ramakrishna S, Singh V. Microfluidics for single cell analysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:203-215. [PMID: 35033285 DOI: 10.1016/bs.pmbts.2021.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Cells have several internal molecules that are present in low amounts and any fluctuation in its number drives a change in cell behavior. These molecules present inside the cells are continuously fluctuating, thus producing noises in the intrinsic environment and thereby directly affecting the cellular behavior. Single-cell analysis using microfluidics is an important tool for monitoring cell behavior by analyzing internal molecules. Several gene circuits have been designed for this purpose that are labeled with fluorescence encoding genes for monitoring cell dynamics and behavior. We discuss herewith designed and fabricated microfluidics devices that are used for trapping and tracking cells under controlled environmental conditions. This chapter highlights microfluidics chip for monitoring cells to promote their basic understanding.
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Affiliation(s)
- Rupesh Maurya
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Nisarg Gohil
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Gargi Bhattacharjee
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, South Korea; College of Medicine, Hanyang University, Seoul, South Korea
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana, Gujarat, India.
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3
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Gradient Tracking by Yeast GPCRs in a Microfluidics Chamber. Methods Mol Biol 2021. [PMID: 34085275 DOI: 10.1007/978-1-0716-1221-7_18] [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
Cells typically exist in a highly dynamic environment, which cannot easily be recreated in culture dishes or microwell plates. Microfluidic devices can provide precise control of the time, dose, and orientation of a stimulus, while simultaneously capturing quantitative single-cell data. The approach is particularly powerful when combined with the genetically tractable yeast model organism. The GPCR pathway in yeast is structurally conserved and functionally interchangeable with those in humans. We describe the implementation of a microfluidic device to investigate morphological and transcriptional responses of yeast to a gradient or pulse administration of a GPCR ligand, the peptide mating pheromone α-factor.
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4
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Lawson M, Elf J. Imaging-based screens of pool-synthesized cell libraries. Nat Methods 2021; 18:358-365. [PMID: 33589838 DOI: 10.1038/s41592-020-01053-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 12/21/2020] [Indexed: 01/30/2023]
Abstract
Mapping a genetic perturbation to a change in phenotype is at the core of biological research. Advances in microscopy have transformed these studies, but they have largely been confined to examining a few strains or cell lines at a time. In parallel, there has been a revolution in creating synthetic libraries of genetically altered cells with relative ease. Here we describe methods that combine these powerful tools to perform live-cell imaging of pool-generated strain libraries for improved biological discovery.
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Affiliation(s)
- Michael Lawson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Johan Elf
- Department of Cell and Molecular Biology Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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5
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O'Laughlin R, Jin M, Li Y, Pillus L, Tsimring LS, Hasty J, Hao N. Advances in quantitative biology methods for studying replicative aging in Saccharomyces cerevisiae. TRANSLATIONAL MEDICINE OF AGING 2019; 4:151-160. [PMID: 33880425 PMCID: PMC8054985 DOI: 10.1016/j.tma.2019.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Aging is a complex, yet pervasive phenomenon in biology. As human cells steadily succumb to the deteriorating effects of aging, so too comes a host of age-related ailments such as neurodegenerative disorders, cardiovascular disease and cancer. Therefore, elucidation of the molecular networks that drive aging is of paramount importance to human health. Progress toward this goal has been aided by studies from simple model organisms such as Saccharomyces cerevisiae. While work in budding yeast has already revealed much about the basic biology of aging as well as a number of evolutionarily conserved pathways involved in this process, recent technological advances are poised to greatly expand our knowledge of aging in this simple eukaryote. Here, we review the latest developments in microfluidics, single-cell analysis and high-throughput technologies for studying single-cell replicative aging in S. cerevisiae. We detail the challenges each of these methods addresses as well as the unique insights into aging that each has provided. We conclude with a discussion of potential future applications of these techniques as well as the importance of single-cell dynamics and quantitative biology approaches for understanding cell aging.
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Affiliation(s)
- Richard O'Laughlin
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Meng Jin
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Yang Li
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lorraine Pillus
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.,UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA, 92093, USA
| | - Lev S Tsimring
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jeff Hasty
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.,BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Nan Hao
- BioCircuits Institute, University of California San Diego, La Jolla, CA, 92093, USA.,Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
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6
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Marinkovic ZS, Vulin C, Acman M, Song X, Di Meglio JM, Lindner AB, Hersen P. A microfluidic device for inferring metabolic landscapes in yeast monolayer colonies. eLife 2019; 8:e47951. [PMID: 31259688 PMCID: PMC6624017 DOI: 10.7554/elife.47951] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 06/30/2019] [Indexed: 01/15/2023] Open
Abstract
Microbial colonies are fascinating structures in which growth and internal organization reflect complex morphogenetic processes. Here, we generated a microfluidics device with arrays of long monolayer yeast colonies to further global understanding of how intercellular metabolic interactions affect the internal structure of colonies within defined boundary conditions. We observed the emergence of stable glucose gradients using fluorescently labeled hexose transporters and quantified the spatial correlations with intra-colony growth rates and expression of other genes regulated by glucose availability. These landscapes depended on the external glucose concentration as well as secondary gradients, for example amino acid availability. This work demonstrates the regulatory genetic networks governing cellular physiological adaptation are the key to internal structuration of cellular assemblies. This approach could be used in the future to decipher the interplay between long-range metabolic interactions, cellular development and morphogenesis in more complex systems.
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Affiliation(s)
- Zoran S Marinkovic
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- U1001 INSERMParisFrance
- CRIUniversité de ParisParisFrance
| | - Clément Vulin
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- Institute of Biogeochemistry and Pollutant DynamicsETH ZürichZürichSwitzerland
- Department of Environmental MicrobiologyEawagDübendorfSwitzerland
| | - Mislav Acman
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
- CRIUniversité de ParisParisFrance
| | | | - Jean-Marc Di Meglio
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
| | | | - Pascal Hersen
- Laboratoire Matière et Systèmes ComplexesUMR 7057 CNRS and Université de ParisParisFrance
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7
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Bashor CJ, Patel N, Choubey S, Beyzavi A, Kondev J, Collins JJ, Khalil AS. Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies. Science 2019; 364:593-597. [PMID: 31000590 DOI: 10.1126/science.aau8287] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 04/03/2019] [Indexed: 12/21/2022]
Abstract
Eukaryotic genes are regulated by multivalent transcription factor complexes. Through cooperative self-assembly, these complexes perform nonlinear regulatory operations involved in cellular decision-making and signal processing. In this study, we apply this design principle to synthetic networks, testing whether engineered cooperative assemblies can program nonlinear gene circuit behavior in yeast. Using a model-guided approach, we show that specifying the strength and number of assembly subunits enables predictive tuning between linear and nonlinear regulatory responses for single- and multi-input circuits. We demonstrate that assemblies can be adjusted to control circuit dynamics. We harness this capability to engineer circuits that perform dynamic filtering, enabling frequency-dependent decoding in cell populations. Programmable cooperative assembly provides a versatile way to tune the nonlinearity of network connections, markedly expanding the engineerable behaviors available to synthetic circuits.
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Affiliation(s)
- Caleb J Bashor
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Nikit Patel
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sandeep Choubey
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - Ali Beyzavi
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
| | - Jané Kondev
- Department of Physics, Brandeis University, Waltham, MA 02453, USA
| | - James J Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA. .,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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8
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Belova AM, Basmanov DV, Prusakov KA, Lazarev VN, Klinov DV. A Microfluidic Platform for the Development of a Biosensor Based on Genetically Modified Helicobacter pylori Single Cells. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350918050020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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9
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Controllable stress patterns over multi-generation timescale in microfluidic devices. Methods Cell Biol 2018. [PMID: 30165960 DOI: 10.1016/bs.mcb.2018.07.003] [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
The generation of complex temporal stress patterns may be instrumental to investigate the adaptive properties of individual cells submitted to environmental stress on physiological timescale. However, it is difficult to accurately control stress concentration over time in bulk experiments. Here, we describe a microfluidics-based protocol to induce tightly controllable H2O2 stress in budding yeast while constantly monitoring cell growth with single cell resolution over multi-generation timescale. Moreover, we describe a simple methodology to produce ramping H2O2 stress to investigate the homeostatic properties of the H2O2 scavenging system.
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10
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Garmendia-Torres C, Tassy O, Matifas A, Molina N, Charvin G. Multiple inputs ensure yeast cell size homeostasis during cell cycle progression. eLife 2018; 7:34025. [PMID: 29972352 PMCID: PMC6085122 DOI: 10.7554/elife.34025] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 07/01/2018] [Indexed: 12/27/2022] Open
Abstract
Coordination of cell growth with division is essential for proper cell function. In budding yeast, although some molecular mechanisms responsible for cell size control during G1 have been elucidated, the mechanism by which cell size homeostasis is established remains to be discovered. Here, we developed a new technique based on quantification of histone levels to monitor cell cycle progression in individual cells with unprecedented accuracy. Our analysis establishes the existence of a mechanism controlling bud size in G2/M that prevents premature onset of anaphase, and controls the overall size variability. While most G1 mutants do not display impaired size homeostasis, mutants in which cyclin B-Cdk regulation is altered display large size variability. Our study thus demonstrates that size homeostasis is not controlled by a G1-specific mechanism alone but is likely to be an emergent property resulting from the integration of several mechanisms that coordinate cell and bud growth with division.
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Affiliation(s)
- Cecilia Garmendia-Torres
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Olivier Tassy
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Audrey Matifas
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Nacho Molina
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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11
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Potvin-Trottier L, Luro S, Paulsson J. Microfluidics and single-cell microscopy to study stochastic processes in bacteria. Curr Opin Microbiol 2018; 43:186-192. [PMID: 29494845 PMCID: PMC6044433 DOI: 10.1016/j.mib.2017.12.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/13/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023]
Abstract
Bacteria have molecules present in low and fluctuating numbers that randomize cell behaviors. Understanding these stochastic processes and their impact on cells has, until recently, been limited by the lack of single-cell measurement methods. Here, we review recent developments in microfluidics that enable following individual cells over long periods of time under precisely controlled conditions, and counting individual fluorescent molecules in many cells. We showcase discoveries that were made possible using these devices in various aspects of microbiology, such as antibiotic tolerance/persistence, cell-size control, cell-fate determination, DNA damage response, and synthetic biology.
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Affiliation(s)
- Laurent Potvin-Trottier
- Biophysics PhD Program, Harvard University, Cambridge, MA 02138, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Scott Luro
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Johan Paulsson
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
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12
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Kim M, Bae J, Kim T. Long-Term and Programmable Bacterial Subculture in Completely Automated Microchemostats. Anal Chem 2017; 89:9676-9684. [DOI: 10.1021/acs.analchem.7b01076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Minseok Kim
- Department
of Mechanical Engineering, and ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Juyeol Bae
- Department
of Mechanical Engineering, and ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Taesung Kim
- Department
of Mechanical Engineering, and ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Ulsan 44919, Republic of Korea
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13
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Dunham MJ, Kerr EO, Miller AW, Payen C. Chemostat Culture for Yeast Physiology and Experimental Evolution. Cold Spring Harb Protoc 2017; 2017:pdb.top077610. [PMID: 28679718 DOI: 10.1101/pdb.top077610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Continuous culture provides many benefits over the classical batch style of growing yeast cells. Steady-state cultures allow for precise control of growth rate and environment. Cultures can be propagated for weeks or months in these controlled environments, which is important for the study of experimental evolution. Despite these advantages, chemostats have not become a highly used system, in large part because of their historical impracticalities, including low throughput, large footprint, systematic complexity, commercial unavailability, high cost, and insufficient protocol availability. However, we have developed methods for building a relatively simple, low-cost, small footprint array of chemostats that can be run in multiples of 32. This "ministat array" can be applied to problems in yeast physiology and experimental evolution.
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Affiliation(s)
- Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Emily O Kerr
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Aaron W Miller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Celia Payen
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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14
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Sheats J, Sclavi B, Cosentino Lagomarsino M, Cicuta P, Dorfman KD. Role of growth rate on the orientational alignment of Escherichia coli in a slit. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170463. [PMID: 28680690 PMCID: PMC5493932 DOI: 10.1098/rsos.170463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 05/08/2023]
Abstract
We present experimental data on the nematic alignment of Escherichia coli bacteria confined in a slit, with an emphasis on the effect of growth rate and corresponding changes in cell aspect ratio. Global alignment with the channel walls arises from the combination of local nematic ordering of nearby cells, induced by cell division and the elongated shape of the cells, and the preferential orientation of cells proximate to the side walls of the slit. Decreasing the growth rate leads to a decrease in alignment with the walls, which is attributed primarily to effects of changing cell aspect ratio rather than changes in the variance in cell area. Decreasing confinement also reduces the degree of alignment by a similar amount as a decrease in the growth rate, but the distribution of the degree of alignment differs. The onset of alignment with the channel walls is coincident with the slits reaching their steady-state occupancy and connected to the re-orientation of locally aligned regions with respect to the walls during density fluctuations.
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Affiliation(s)
- Julian Sheats
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Bianca Sclavi
- LBPA, UMR 8113 du CNRS, École Normale Supérieure de Cachan, Cachan, France
| | - Marco Cosentino Lagomarsino
- Sorbonne Universités, Université Pierre et Marie Curie, 4 Place Jussieu, Paris, France
- CNRS, UMR7238 Computational and Quantitative Biology, Paris, France
- IFOM Institute for Molecular Oncology, Milan, Italy
| | - Pietro Cicuta
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota—Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455, USA
- Author for correspondence: Kevin D. Dorfman e-mail:
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15
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Jo MC, Qin L. Microfluidic Platforms for Yeast-Based Aging Studies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5787-5801. [PMID: 27717149 PMCID: PMC5554731 DOI: 10.1002/smll.201602006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 08/30/2016] [Indexed: 06/06/2023]
Abstract
The budding yeast Saccharomyces cerevisiae has been a powerful model for the study of aging and has enabled significant contributions to our understanding of basic mechanisms of aging in eukaryotic cells. However, the laborious low-throughput nature of conventional methods of performing aging assays limits the pace of discoveries in this field. Some of the technical challenges of conventional aging assay methods can be overcome by use of microfluidic systems coupled to time-lapse microscopy. One of the major advantages is the ability of a microfluidic system to perform long-term cell culture under well-defined environmental conditions while tracking individual yeast. Here, recent advancements in microfluidic platforms for various yeast-based studies including replicative lifespan assay, long-term culture and imaging, gene expression, and cell signaling are discussed. In addition, emerging problems and limitations of current microfluidic approaches are examined and perspectives on the future development of this dynamic field are presented.
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Affiliation(s)
- Myeong Chan Jo
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, 77030, USA
- Department of Cell and Developmental Biology, Weill Medical College of Cornell University, New York, NY, 10065, USA
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16
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17
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Buffi N, Beggah S, Truffer F, Geiser M, van Lintel H, Renaud P, van der Meer JR. An automated microreactor for semi-continuous biosensor measurements. LAB ON A CHIP 2016; 16:1383-1392. [PMID: 27001545 DOI: 10.1039/c6lc00119j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Living bacteria or yeast cells are frequently used as bioreporters for the detection of specific chemical analytes or conditions of sample toxicity. In particular, bacteria or yeast equipped with synthetic gene circuitry that allows the production of a reliable non-cognate signal (e.g., fluorescent protein or bioluminescence) in response to a defined target make robust and flexible analytical platforms. We report here how bacterial cells expressing a fluorescence reporter ("bactosensors"), which are mostly used for batch sample analysis, can be deployed for automated semi-continuous target analysis in a single concise biochip. Escherichia coli-based bactosensor cells were continuously grown in a 13 or 50 nanoliter-volume reactor on a two-layered polydimethylsiloxane-on-glass microfluidic chip. Physiologically active cells were directed from the nl-reactor to a dedicated sample exposure area, where they were concentrated and reacted in 40 minutes with the target chemical by localized emission of the fluorescent reporter signal. We demonstrate the functioning of the bactosensor-chip by the automated detection of 50 μgarsenite-As l(-1) in water on consecutive days and after a one-week constant operation. Best induction of the bactosensors of 6-9-fold to 50 μg l(-1) was found at an apparent dilution rate of 0.12 h(-1) in the 50 nl microreactor. The bactosensor chip principle could be widely applicable to construct automated monitoring devices for a variety of targets in different environments.
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Affiliation(s)
- Nina Buffi
- Laboratory for Microsystems Engineering, Ecole Polytechnique de Lausanne, Station 17, CH-1015 Lausanne, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
| | - Frederic Truffer
- Institute of Systems Engineering, University of Applied Sciences and Arts of Western Switzerland, 1950 Sion, Switzerland
| | - Martial Geiser
- Institute of Systems Engineering, University of Applied Sciences and Arts of Western Switzerland, 1950 Sion, Switzerland
| | - Harald van Lintel
- Laboratory for Microsystems Engineering, Ecole Polytechnique de Lausanne, Station 17, CH-1015 Lausanne, Switzerland
| | - Philippe Renaud
- Laboratory for Microsystems Engineering, Ecole Polytechnique de Lausanne, Station 17, CH-1015 Lausanne, Switzerland
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18
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Jin SH, Jang SC, Lee B, Jeong HH, Jeong SG, Lee SS, Kim KP, Lee CS. Monitoring of chromosome dynamics of single yeast cells in a microfluidic platform with aperture cell traps. LAB ON A CHIP 2016; 16:1358-1365. [PMID: 26980179 DOI: 10.1039/c5lc01422k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chromosome movement plays important roles in DNA replication, repair, genetic recombination, and epigenetic phenomena during mitosis and meiosis. In particular, chromosome movement in the nuclear space is essential for the reorganization of the nucleus. However, conventional methods for analyzing the chromosome movements in vivo have been limited by technical constraints of cell trapping, cell cultivation, oxygenation, and in situ imaging. Here, we present a simple microfluidic platform with aperture-based cell trapping arrays to monitor the chromosome dynamics in single living cells for a desired period of time. Under the optimized conditions, our microfluidic platform shows a single-cell trapping efficiency of 57%. This microfluidic approach enables in situ imaging of intracellular dynamics in living cells responding to variable input stimuli under the well-controlled microenvironment. As a validation of this microfluidic platform, we investigate the fundamental features of the dynamic cellular response of the individual cells treated with different stimuli and drug. We prove the basis for dynamic chromosome movement in single yeast cells to be the telomere and nuclear envelope ensembles that attach to and move in concert with nuclear actin cables. Therefore, these results illustrate the monitoring of cellular functions and obtaining of dynamic information at a high spatiotemporal resolution through the integration of a simple microfluidic platform.
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Affiliation(s)
- Si Hyung Jin
- Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
| | - Sung-Chan Jang
- Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
| | - Byungjin Lee
- Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
| | - Heon-Ho Jeong
- Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
| | - Seong-Geun Jeong
- Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
| | - Sung Sik Lee
- Institute of Biochemistry, ETH Zürich, Zürich, CH 8093, Switzerland. leesu@ ethz.ch and Scientific Center for Optical and Electron Microscopy (ScopeM), ETH Zürich, Zürich, CH-8093, Switzerland
| | - Keun Pil Kim
- Department of Life Science, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering, Chungnam National University, 99 Daehak-ro, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
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19
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Veliz-Cuba A, Hirning AJ, Atanas AA, Hussain F, Vancia F, Josić K, Bennett MR. Sources of Variability in a Synthetic Gene Oscillator. PLoS Comput Biol 2015; 11:e1004674. [PMID: 26693906 PMCID: PMC4692282 DOI: 10.1371/journal.pcbi.1004674] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/25/2015] [Indexed: 11/19/2022] Open
Abstract
Synthetic gene oscillators are small, engineered genetic circuits that produce periodic variations in target protein expression. Like other gene circuits, synthetic gene oscillators are noisy and exhibit fluctuations in amplitude and period. Understanding the origins of such variability is key to building predictive models that can guide the rational design of synthetic circuits. Here, we developed a method for determining the impact of different sources of noise in genetic oscillators by measuring the variability in oscillation amplitude and correlations between sister cells. We first used a combination of microfluidic devices and time-lapse fluorescence microscopy to track oscillations in cell lineages across many generations. We found that oscillation amplitude exhibited high cell-to-cell variability, while sister cells remained strongly correlated for many minutes after cell division. To understand how such variability arises, we constructed a computational model that identified the impact of various noise sources across the lineage of an initial cell. When each source of noise was appropriately tuned the model reproduced the experimentally observed amplitude variability and correlations, and accurately predicted outcomes under novel experimental conditions. Our combination of computational modeling and time-lapse data analysis provides a general way to examine the sources of variability in dynamic gene circuits.
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Affiliation(s)
- Alan Veliz-Cuba
- Department of Biosciences, Rice University, Houston, Texas, United States of America
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Andrew J. Hirning
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Adam A. Atanas
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Faiza Hussain
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Flavia Vancia
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
| | - Krešimir Josić
- Department of Mathematics, University of Houston, Houston, Texas, United States of America
- Department of Biology & Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Matthew R. Bennett
- Department of Biosciences, Rice University, Houston, Texas, United States of America
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
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20
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Abstract
Bacteria are known to consume some sugars over others, although recent work reported by Koirala and colleagues in this issue of the Journal of Bacteriology (S. Koirala, X. Wang, and C. V. Rao, J Bacteriol 198:386-393, 2016, http://dx.doi.org/10.1128/JB.00709-15) revealed that individual cells do not necessarily follow this hierarchy. By studying the preferential consumption of l-arabinose over d-xylose in Escherichia coli, those authors found that subpopulations consume one, the other, or both sugars through cross-repression between utilization pathways. Their findings challenge classic assertions about established hierarchies and can guide efforts to engineer the simultaneous utilization of multiple sugars.
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21
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Jo MC, Liu W, Gu L, Dang W, Qin L. High-throughput analysis of yeast replicative aging using a microfluidic system. Proc Natl Acad Sci U S A 2015; 112:9364-9. [PMID: 26170317 PMCID: PMC4522780 DOI: 10.1073/pnas.1510328112] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Saccharomyces cerevisiae has been an important model for studying the molecular mechanisms of aging in eukaryotic cells. However, the laborious and low-throughput methods of current yeast replicative lifespan assays limit their usefulness as a broad genetic screening platform for research on aging. We address this limitation by developing an efficient, high-throughput microfluidic single-cell analysis chip in combination with high-resolution time-lapse microscopy. This innovative design enables, to our knowledge for the first time, the determination of the yeast replicative lifespan in a high-throughput manner. Morphological and phenotypical changes during aging can also be monitored automatically with a much higher throughput than previous microfluidic designs. We demonstrate highly efficient trapping and retention of mother cells, determination of the replicative lifespan, and tracking of yeast cells throughout their entire lifespan. Using the high-resolution and large-scale data generated from the high-throughput yeast aging analysis (HYAA) chips, we investigated particular longevity-related changes in cell morphology and characteristics, including critical cell size, terminal morphology, and protein subcellular localization. In addition, because of the significantly improved retention rate of yeast mother cell, the HYAA-Chip was capable of demonstrating replicative lifespan extension by calorie restriction.
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Affiliation(s)
- Myeong Chan Jo
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065
| | - Wei Liu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Liang Gu
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030
| | - Weiwei Dang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030; Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065;
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23
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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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24
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Vasdekis AE, Stephanopoulos G. Review of methods to probe single cell metabolism and bioenergetics. Metab Eng 2015; 27:115-135. [PMID: 25448400 PMCID: PMC4399830 DOI: 10.1016/j.ymben.2014.09.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/26/2022]
Abstract
Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed.
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Affiliation(s)
- Andreas E Vasdekis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99354, USA.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139, USA.
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25
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Park JW, Na SC, Nguyen TQ, Paik SM, Kang M, Hong D, Choi IS, Lee JH, Jeon NL. Live cell imaging compatible immobilization of Chlamydomonas reinhardtii in microfluidic platform for biodiesel research. Biotechnol Bioeng 2014; 112:494-501. [PMID: 25220860 DOI: 10.1002/bit.25453] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/19/2014] [Accepted: 09/05/2014] [Indexed: 11/06/2022]
Abstract
This paper describes a novel surface immobilization method for live-cell imaging of Chlamydomonas reinhardtii for continuous monitoring of lipid droplet accumulation. Microfluidics allows high-throughput manipulation and analysis of single cells in precisely controlled microenvironment. Fluorescence imaging based quantitative measurement of lipid droplet accumulation in microalgae had been difficult due to their intrinsic motile behavior. We present a simple surface immobilization method using gelatin coating as the "biological glue." We take advantage of hydroxyproline (Hyp)-based non-covalent interaction between gelatin and the outer cell wall of microalgae to anchor the cells inside the microfluidic device. We have continuously monitored single microalgal cells for up to 6 days. The immobilized microalgae remain viable (viability was comparable to bulk suspension cultured controls). When exposed to wall shear stress, most of the cells remain attached up to 0.1 dyne/cm(2) . Surface immobilization allowed high-resolution, live-cell imaging of mitotic process in real time-which followed previously reported stages in mitosis of suspension cultured cells. Use of gelatin coated microfluidics devices can result in better methods for microalgae strain screening and culture condition optimization that will help microalgal biodiesel become more economically viable.
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Affiliation(s)
- Jae Woo Park
- Division of WCU (World Class University) Multiscale Mechanical Design, School of Mechanical and Aerospace Engineering, Seoul National University, Seoul, Korea
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26
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Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods 2014; 11:443-8. [PMID: 24608180 PMCID: PMC4016179 DOI: 10.1038/nmeth.2879] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 01/16/2014] [Indexed: 01/06/2023]
Abstract
Cells adjust to changes in environmental conditions using complex regulatory programs. These cellular programs are the result of an intricate interplay between gene expression, cellular growth and protein degradation. Technologies that enable simultaneous and time-resolved measurements of these variables are necessary to dissect cellular homeostatic strategies. Here we report the development of an automated flow cytometry robotic setup that enables real-time measurement of precise and simultaneous relative growth and protein synthesis rates of multiplexed microbial populations across many conditions. These measurements generate quantitative profiles of dynamically evolving protein synthesis and degradation rates. We demonstrate this setup in the context of gene regulation of the unfolded protein response (UPR) of Saccharomyces cerevisiae and uncover a dynamic and complex landscape of gene expression, growth dynamics and proteolysis following perturbations.
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Affiliation(s)
- Ignacio A Zuleta
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| | - Andrés Aranda-Díaz
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| | - Hao Li
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
| | - Hana El-Samad
- 1] Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA. [2] The California Institute for Quantitative Biosciences, San Francisco, California, USA
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27
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28
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Park J, Wu J, Polymenis M, Han A. Microchemostat array with small-volume fraction replenishment for steady-state microbial culture. LAB ON A CHIP 2013; 13:4217-4224. [PMID: 23986263 DOI: 10.1039/c3lc50665g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A chemostat is a bioreactor in which microorganisms can be cultured at steady-state by controlling the rate of culture medium inflow and waste outflow, thus maintaining media composition over time. Even though many microbial studies could greatly benefit from studying microbes in steady-state conditions, high instrument cost, complexity, and large reagent consumption hamper the routine use of chemostats. Microfluidic-based chemostats (i.e. microchemostats) can operate with significantly smaller reagent consumption while providing accurate chemostatic conditions at orders of magnitude lower cost compared to conventional chemostats. Also, microchemostats have the potential to significantly increase the throughput by integrating arrays of microchemostats. We present a microchemostat array with a unique two-depth culture chamber design that enables small-volume fraction replenishment of culture medium as low as 1% per replenishment cycle in a 250 nl volume. A system having an array of 8 microchemostats on a 40 × 60 mm(2) footprint could be automatically operated in parallel by a single controller unit as a demonstration for potential high throughput microbial studies. The model organism, Saccharomyces cerevisiae, successfully reached a stable steady-state of different cell densities as a demonstration of the chemostatic functionality by programming the dilution rates. Chemostatic functionality of the system was further confirmed by quantifying the budding index as a function of dilution rate, a strong indicator of growth-dependent cell division. In addition, the small-volume fraction replenishment feature minimized the cell density fluctuation during the culture. The developed system provides a robust, low-cost, and higher throughput solution to furthering studies in microbial physiology.
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Affiliation(s)
- Jaewon Park
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
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29
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Zopf CJ, Maheshri N. Acquiring fluorescence time-lapse movies of budding yeast and analyzing single-cell dynamics using GRAFTS. J Vis Exp 2013:e50456. [PMID: 23892428 DOI: 10.3791/50456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challenges to obtaining and analyzing fluorescence movies of single cells. We describe here a simple protocol using a commercially available microfluidic culture device to generate such data, and a MATLAB-based, graphical user interface (GUI) -based software package to quantify the fluorescence images. The software segments and tracks cells, enables the user to visually curate errors in the data, and automatically assigns lineage and division times. The GUI further analyzes the time series to produce whole cell traces as well as their first and second time derivatives. While the software was designed for S. cerevisiae, its modularity and versatility should allow it to serve as a platform for studying other cell types with few modifications.
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Affiliation(s)
- Christopher J Zopf
- Department of Chemical Engineering, Massachusetts Institute of Technology, USA
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30
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Construction and use of a microfluidic dissection platform for long-term imaging of cellular processes in budding yeast. Nat Protoc 2013; 8:1019-27. [DOI: 10.1038/nprot.2013.060] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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31
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Moolman MC, Huang Z, Krishnan ST, Kerssemakers JWJ, Dekker NH. Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria. J Nanobiotechnology 2013; 11:12. [PMID: 23575419 PMCID: PMC3658940 DOI: 10.1186/1477-3155-11-12] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 04/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Controlled restriction of cellular movement using microfluidics allows one to study individual cells to gain insight into aspects of their physiology and behaviour. For example, the use of micron-sized growth channels that confine individual Escherichia coli has yielded novel insights into cell growth and death. To extend this approach to other species of bacteria, many of whom have dimensions in the sub-micron range, or to a larger range of growth conditions, a readily-fabricated device containing sub-micron features is required. RESULTS Here we detail the fabrication of a versatile device with growth channels whose widths range from 0.3 μm to 0.8 μm. The device is fabricated using electron beam lithography, which provides excellent control over the shape and size of different growth channels and facilitates the rapid-prototyping of new designs. Features are successfully transferred first into silicon, and subsequently into the polydimethylsiloxane that forms the basis of the working microfluidic device. We demonstrate that the growth of sub-micron scale bacteria such as Lactococcus lactis or Escherichia coli cultured in minimal medium can be followed in such a device over several generations. CONCLUSIONS We have presented a detailed protocol based on electron beam fabrication together with specific dry etching procedures for the fabrication of a microfluidic device suited to study submicron-sized bacteria. We have demonstrated that both Gram-positive and Gram-negative bacteria can be successfully loaded and imaged over a number of generations in this device. Similar devices could potentially be used to study other submicron-sized organisms under conditions in which the height and shape of the growth channels are crucial to the experimental design.
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Affiliation(s)
- M Charl Moolman
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Zhuangxiong Huang
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Sriram Tiruvadi Krishnan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Jacob WJ Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
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32
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Microfabricated devices in microbial bioenergy sciences. Trends Biotechnol 2013; 31:225-32. [DOI: 10.1016/j.tibtech.2012.12.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/01/2012] [Accepted: 12/11/2012] [Indexed: 01/18/2023]
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33
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Prindle A, Selimkhanov J, Danino T, Samayoa P, Goldberg A, Bhatia SN, Hasty J. Genetic Circuits in Salmonella typhimurium. ACS Synth Biol 2012; 1:458-464. [PMID: 23097749 PMCID: PMC3477097 DOI: 10.1021/sb300060e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Indexed: 01/31/2023]
Abstract
Synthetic biology has rapidly progressed over the past decade and is now positioned to impact important problems in health and energy. In the clinical arena, the field has thus far focused primarily on the use of bacteria and bacteriophages to overexpress therapeutic gene products. The next generation of multigene circuits will control the triggering, amplitude, and duration of therapeutic activity in vivo. This will require a host organism that is easy to genetically modify, leverages existing successful circuit designs, and has the potential for use in humans. Here, we show that gene circuits that were originally constructed and tested in Escherichia coli translate to Salmonella typhimurium, a therapeutically relevant microbe with attenuated strains that have exhibited safety in several human clinical trials. These strains are essentially nonvirulent, easy to genetically program, and specifically grow in tumor environments. Developing gene circuits on this platform could enhance our ability to bring sophisticated genetic programming to cancer therapy, setting the stage for a new generation of synthetic biology in clinically relevant microbes.
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Affiliation(s)
- Arthur Prindle
- Department of Bioengineering, University of California, San Diego, San Diego, California,
United States
| | - Jangir Selimkhanov
- Department of Bioengineering, University of California, San Diego, San Diego, California,
United States
| | - Tal Danino
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Phillip Samayoa
- Bioinformatics
Program, University of California, San Diego, La Jolla, California,
United States
| | - Anna Goldberg
- Department of Bioengineering, University of California, San Diego, San Diego, California,
United States
| | - Sangeeta N. Bhatia
- Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts
02139, United States
| | - Jeff Hasty
- Department of Bioengineering, University of California, San Diego, San Diego, California,
United States
- Bioinformatics
Program, University of California, San Diego, La Jolla, California,
United States
- BioCircuits
Institute, University of California, San Diego, San Diego, California,
United States
- Molecular
Biology Section, Division
of Biological Science, University of California, San Diego, La Jolla, California 92093, United States
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34
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Whole lifespan microscopic observation of budding yeast aging through a microfluidic dissection platform. Proc Natl Acad Sci U S A 2012; 109:4916-20. [PMID: 22421136 DOI: 10.1073/pnas.1113505109] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Important insights into aging have been generated with the genetically tractable and short-lived budding yeast. However, it is still impossible today to continuously track cells by high-resolution microscopic imaging (e.g., fluorescent imaging) throughout their entire lifespan. Instead, the field still needs to rely on a 50-y-old laborious and time-consuming method to assess the lifespan of yeast cells and to isolate differentially aged cells for microscopic snapshots via manual dissection of daughter cells from the larger mother cell. Here, we are unique in achieving continuous and high-resolution microscopic imaging of the entire replicative lifespan of single yeast cells. Our microfluidic dissection platform features an optically prealigned single focal plane and an integrated array of soft elastomer-based micropads, used together to allow for trapping of mother cells, removal of daughter cells, monitoring gradual changes in aging, and unprecedented microscopic imaging of the whole aging process. Using the platform, we found remarkable age-associated changes in phenotypes (e.g., that cells can show strikingly differential cell and vacuole morphologies at the moment of their deaths), indicating substantial heterogeneity in cell aging and death. We envision the microfluidic dissection platform to become a major tool in aging research.
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35
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Walker J, Storch G, Quach-Wong B, Sonnenfeld J, Aaron G. Propagation of epileptiform events across the corpus callosum in a cingulate cortical slice preparation. PLoS One 2012; 7:e31415. [PMID: 22363643 PMCID: PMC3283628 DOI: 10.1371/journal.pone.0031415] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 01/10/2012] [Indexed: 11/19/2022] Open
Abstract
We report on a novel mouse in vitro brain slice preparation that contains intact callosal axons connecting anterior cingulate cortices (ACC). Callosal connections are demonstrated by the ability to regularly record epileptiform events between hemispheres (bilateral events). That the correlation of these events depends on the callosum is demonstrated by the bisection of the callosum in vitro. Epileptiform events are evoked with four different methods: (1) bath application of bicuculline (a GABA-A antagonist); (2) bicuculline+MK801 (an NMDA receptor antagonist), (3) a zero magnesium extracellular solution (0Mg); (4) focal application of bicuculline to a single cortical hemisphere. Significant increases in the number of epileptiform events, as well as increases in the ratio of bilateral events to unilateral events, are observed during bath applications of bicuculline, but not during applications of bicuculline+MK-801. Long ictal-like events (defined as events >20 seconds) are only observed in 0Mg. Whole cell patch clamp recordings of single neurons reveal strong feedforward inhibition during focal epileptiform events in the contralateral hemisphere. Within the ACC, we find differences between the rostral areas of ACC vs. caudal ACC in terms of connectivity between hemispheres, with the caudal regions demonstrating shorter interhemispheric latencies. The morphologies of many patch clamped neurons show callosally-spanning axons, again demonstrating intact callosal circuits in this in vitro preparation.
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Affiliation(s)
- Jeffrey Walker
- Department of Biology, Program in Neuroscience and Behavior, Wesleyan University, Middletown, Connecticut, United States of America
| | - Gregory Storch
- Department of Biology, Program in Neuroscience and Behavior, Wesleyan University, Middletown, Connecticut, United States of America
| | - Bonnie Quach-Wong
- Department of Biology, Program in Neuroscience and Behavior, Wesleyan University, Middletown, Connecticut, United States of America
| | - Julian Sonnenfeld
- Department of Biology, Program in Neuroscience and Behavior, Wesleyan University, Middletown, Connecticut, United States of America
| | - Gloster Aaron
- Department of Biology, Program in Neuroscience and Behavior, Wesleyan University, Middletown, Connecticut, United States of America
- * E-mail:
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36
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Ooms MD, Sieben VJ, Pierobon SC, Jung EE, Kalontarov M, Erickson D, Sinton D. Evanescent photosynthesis: exciting cyanobacteria in a surface-confined light field. Phys Chem Chem Phys 2012; 14:4817-23. [DOI: 10.1039/c2cp40271h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Wang L, Liu J, Li X, Shi J, Hu J, Cui R, Zhang ZL, Pang DW, Chen Y. Growth propagation of yeast in linear arrays of microfluidic chambers over many generations. BIOMICROFLUIDICS 2011; 5:44118-441189. [PMID: 22662064 PMCID: PMC3364811 DOI: 10.1063/1.3668243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 11/17/2011] [Indexed: 05/04/2023]
Abstract
The growth of microorganisms is often confined in restricting geometries. In this work, we designed a device to study the growth propagation of budding yeast along linear arrays of microfluidic chambers. Vacuum assisted cell loading was used to seed cells of limited numbers in the up-most chambers of each linear array. Once loaded, cells grow until confluent and then overgrow, pushing some of the newborns into the neighboring downstream chamber through connection channels. Such a scenario repeats sequentially along the whole linear chamber arrays. We observed that the propagation speed of yeast population along the linear arrays was strongly channel geometry dependent. When the connection channel is narrow and long, the amount of cells delivered into the downstream chamber is small so that cells grow over several generations in the same chamber before passing into the next chamber. Consequently, a population growth of more than 50 generations could be observed along a single linear array. We also provided a mathematical model to quantitatively interpret the observed growth dynamics.
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38
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Rinott R, Jaimovich A, Friedman N. Exploring transcription regulation through cell-to-cell variability. Proc Natl Acad Sci U S A 2011; 108:6329-34. [PMID: 21444810 PMCID: PMC3076844 DOI: 10.1073/pnas.1013148108] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The regulation of cellular protein levels is a complex process involving many regulatory mechanisms, each introducing stochastic events, leading to variability of protein levels between isogenic cells. Previous studies have shown that perturbing genes involved in transcription regulation affects the amount of cell-to-cell variability in protein levels, but to date there has been no systematic characterization of variability in expression as a phenotype. In this research, we use single-cell expression levels of two fluorescent reporters driven by two different promoters under a wide range of genetic perturbations in Saccharomyces cerevisiae, to identify proteins that affect variability in the expression of these reporters. We introduce computational methodology to determine the variability caused by each perturbation and distinguish between global variability, which affects both reporters in a coordinated manner (e.g., due to cell size variability), and local variability, which affects the individual reporters independently (e.g., due to stochastic events in transcription initiation). Classifying genes by their variability phenotype (the effect of their deletion on reporter variability) identifies functionally coherent groups, which broadly correlate with the different stages of transcriptional regulation. Specifically, we find that most processes whose perturbation affects global variability are related to protein synthesis, protein transport, and cell morphology, whereas most processes whose perturbations affect local variability are related to DNA maintenance, chromatin regulation, and RNA synthesis. Moreover, we demonstrate that the variability phenotypes of different protein complexes provide insights into their cellular functions. Our results establish the utility of variability phenotype for dissecting the regulatory mechanisms involved in gene expression.
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Affiliation(s)
- Ruty Rinott
- School of Computer Science and Engineering and
- Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel; and
| | - Ariel Jaimovich
- School of Computer Science and Engineering and
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Nir Friedman
- School of Computer Science and Engineering and
- Institute of Life Sciences, Hebrew University, Jerusalem 91904, Israel; and
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39
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Vyawahare S, Griffiths AD, Merten CA. Miniaturization and parallelization of biological and chemical assays in microfluidic devices. ACTA ACUST UNITED AC 2011; 17:1052-65. [PMID: 21035727 DOI: 10.1016/j.chembiol.2010.09.007] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 08/31/2010] [Accepted: 09/07/2010] [Indexed: 12/29/2022]
Abstract
Microfluidic systems are an attractive solution for the miniaturization of biological and chemical assays. The typical sample volume can be reduced up to 1 million-fold, and a superb level of spatiotemporal control is possible, facilitating highly parallelized assays with drastically increased throughput and reduced cost. In this review, we focus on systems in which multiple reactions are spatially separated by immobilization of reagents on two-dimensional arrays, or by compartmentalization in microfabricated reaction chambers or droplets. These systems have manifold applications, and some, such as next-generation sequencing are already starting to transform biology. This is likely the first step in a biotechnological transformation comparable to that already brought about by the microprocessor in electronics. We discuss both current applications and likely future impacts in areas such as the study of single cells/single organisms and high-throughput screening.
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Affiliation(s)
- Saurabh Vyawahare
- Microfluidics Laboratory, Physical Sciences-Oncology Center, Physics Department, Princeton University, Princeton, NJ 08544, USA
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40
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Ferry MS, Razinkov IA, Hasty J. Microfluidics for synthetic biology: from design to execution. Methods Enzymol 2011; 497:295-372. [PMID: 21601093 DOI: 10.1016/b978-0-12-385075-1.00014-7] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
With the expanding interest in cellular responses to dynamic environments, microfluidic devices have become important experimental platforms for biological research. Microfluidic "microchemostat" devices enable precise environmental control while capturing high quality, single-cell gene expression data. For studies of population heterogeneity and gene expression noise, these abilities are crucial. Here, we describe the necessary steps for experimental microfluidics using devices created in our lab as examples. First, we discuss the rational design of microchemostats and the tools available to predict their performance. We carefully analyze the critical parts of an example device, focusing on the most important part of any microchemostat: the cell trap. Next, we present a method for generating on-chip dynamic environments using an integrated fluidic junction coupled to linear actuators. Our system relies on the simple modulation of hydrostatic pressure to alter the mixing ratio between two source reservoirs and we detail the software and hardware behind it. To expand the throughput of microchemostat experiments, we describe how to build larger, parallel versions of simpler devices. To analyze the large amounts of data, we discuss methods for automated cell tracking, focusing on the special problems presented by Saccharomyces cerevisiae cells. The manufacturing of microchemostats is described in complete detail: from the photolithographic processing of the wafer to the final bonding of the PDMS chip to glass coverslip. Finally, the procedures for conducting Escherichia coli and S. cerevisiae microchemostat experiments are addressed.
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Affiliation(s)
- M S Ferry
- Department of Bioengineering, University of California, San Diego, California, USA
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41
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Wong I, Atsumi S, Huang WC, Wu TY, Hanai T, Lam ML, Tang P, Yang J, Liao JC, Ho CM. An agar gel membrane-PDMS hybrid microfluidic device for long term single cell dynamic study. LAB ON A CHIP 2010; 10:2710-2719. [PMID: 20664845 DOI: 10.1039/c004719h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Significance of single cell measurements stems from the substantial temporal fluctuations and cell-cell variability possessed by individual cells. A major difficulty in monitoring surface non-adherent cells such as bacteria and yeast is that these cells tend to aggregate into clumps during growth, obstructing the tracking or identification of single-cells over long time periods. Here, we developed a microfluidic platform for long term single-cell tracking and cultivation with continuous media refreshing and dynamic chemical perturbation capability. The design highlights a simple device-assembly process between PDMS microchannel and agar membrane through conformal contact, and can be easily adapted by microbiologists for their routine laboratory use. The device confines cell growth in monolayer between an agar membrane and a glass surface. Efficient nutrient diffusion through the membrane and reliable temperature maintenance provide optimal growth condition for the cells, which exhibited fast exponential growth and constant distribution of cell sizes. More than 24 h of single-cell tracking was demonstrated on a transcription-metabolism integrated synthetic biological model, the gene-metabolic oscillator. Single cell morphology study under alcohol toxicity allowed us to discover and characterize cell filamentation exhibited by different E. coli isobutanol tolerant strains. We believe this novel device will bring new capabilities to quantitative microbiology, providing a versatile platform for single cell dynamic studies.
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Affiliation(s)
- Ieong Wong
- Department of Mechanical and Aerospace Engineering, University of California, Los Angeles, CA 90095, USA
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High-throughput microfluidic system for long-term bacterial colony monitoring and antibiotic testing in zero-flow environments. Biosens Bioelectron 2010; 26:1993-9. [PMID: 20880691 DOI: 10.1016/j.bios.2010.08.062] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 07/29/2010] [Accepted: 08/22/2010] [Indexed: 12/28/2022]
Abstract
In this study, a high-throughput microfluidic system is presented. The system is comprised of seven parallel channels. Each channel contains 32 square-shaped microchambers. After simulation studies on samples loaded into the microchambers, and the solute exchange between the microchambers and channels, the long-term culture of Escherichia coli (E. coli) HB101 in the microchambers is realized. Using the principle that L-arabinose (L-Ara) can induce recombinant E. coli HB101 pGLO to synthesize green fluorescent protein (GFP), the real-time analysis of GFP expression in different initial bacterial densities is performed. The results demonstrate that higher initial loading densities of the bacterial colony cause bacterial cell to enter log-phase proliferation sooner. High or low initial loading densities of the bacterial cell suspension induce the same maximum growth rates during the log-phase. Quantitative on-chip analysis of tetracycline and erythromycin inhibition on bacterial cell growth is also conducted. Bacterial morphology changes during antibiotic treatment are observed. The results show that tetracycline and erythromycin exhibit different inhibition activities in E. coli cells. Concentrations of 3 μg/mL tetracycline can facilitate the formation of long filamentous bacteria with the average length of more than 50 μm. This study provides an on-chip framework for bacteriological research in a high-throughput manner and the development of recombinant bacteria-based biosensors for the detection of specific substances.
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Dechant R, Binda M, Lee SS, Pelet S, Winderickx J, Peter M. Cytosolic pH is a second messenger for glucose and regulates the PKA pathway through V-ATPase. EMBO J 2010; 29:2515-26. [PMID: 20581803 DOI: 10.1038/emboj.2010.138] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 05/28/2010] [Indexed: 01/04/2023] Open
Abstract
Glucose is the preferred carbon source for most cell types and a major determinant of cell growth. In yeast and certain mammalian cells, glucose activates the cAMP-dependent protein kinase A (PKA), but the mechanisms of PKA activation remain unknown. Here, we identify cytosolic pH as a second messenger for glucose that mediates activation of the PKA pathway in yeast. We find that cytosolic pH is rapidly and reversibly regulated by glucose metabolism and identify the vacuolar ATPase (V-ATPase), a proton pump required for the acidification of vacuoles, as a sensor of cytosolic pH. V-ATPase assembly is regulated by cytosolic pH and is required for full activation of the PKA pathway in response to glucose, suggesting that it mediates, at least in part, the pH signal to PKA. Finally, V-ATPase is also regulated by glucose in the Min6 beta-cell line and contributes to PKA activation and insulin secretion. Thus, these data suggest a novel and potentially conserved glucose-sensing pathway and identify a mechanism how cytosolic pH can act as a signal to promote cell growth.
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Simpson ML, Cox CD, Allen MS, McCollum JM, Dar RD, Karig DK, Cooke JF. Noise in biological circuits. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2010; 1:214-25. [PMID: 20049792 DOI: 10.1002/wnan.22] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Noise biology focuses on the sources, processing, and biological consequences of the inherent stochastic fluctuations in molecular transitions or interactions that control cellular behavior. These fluctuations are especially pronounced in small systems where the magnitudes of the fluctuations approach or exceed the mean value of the molecular population. Noise biology is an essential component of nanomedicine where the communication of information is across a boundary that separates small synthetic and biological systems that are bound by their size to reside in environments of large fluctuations. Here we review the fundamentals of the computational, analytical, and experimental approaches to noise biology. We review results that show that the competition between the benefits of low noise and those of low population has resulted in the evolution of genetic system architectures that produce an uneven distribution of stochasticity across the molecular components of cells and, in some cases, use noise to drive biological function. We review the exact and approximate approaches to gene circuit noise analysis and simulation, and review many of the key experimental results obtained using flow cytometry and time-lapse fluorescent microscopy. In addition, we consider the probative value of noise with a discussion of using measured noise properties to elucidate the structure and function of the underlying gene circuit. We conclude with a discussion of the frontiers of and significant future challenges for noise biology.
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Abstract
The engineering of genetic circuits with predictive functionality in living cells represents a defining focus of the expanding field of synthetic biology. This focus was elegantly set in motion a decade ago with the design and construction of a genetic toggle switch and an oscillator, with subsequent highlights that have included circuits capable of pattern generation, noise shaping, edge detection and event counting. Here we describe an engineered gene network with global intercellular coupling that is capable of generating synchronized oscillations in a growing population of cells. Using microfluidic devices tailored for cellular populations at differing length scales, we investigate the collective synchronization properties along with spatiotemporal waves occurring at millimetre scales. We use computational modelling to describe quantitatively the observed dependence of the period and amplitude of the bulk oscillations on the flow rate. The synchronized genetic clock sets the stage for the use of microbes in the creation of a macroscopic biosensor with an oscillatory output. Furthermore, it provides a specific model system for the generation of a mechanistic description of emergent coordinated behaviour at the colony level.
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46
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The pedestrian watchmaker: genetic clocks from engineered oscillators. FEBS Lett 2010; 583:3931-7. [PMID: 19903483 DOI: 10.1016/j.febslet.2009.10.089] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 10/26/2009] [Indexed: 01/29/2023]
Abstract
The crucial role of time-keeping has required organisms to develop sophisticated regulatory networks to ensure the reliable propagation of periodic behavior. These biological clocks have long been a focus of research; however, a clear understanding of how they maintain oscillations in the face of unpredictable environments and the inherent noise of biological systems remains elusive. Here, we review the current understanding of circadian oscillations using Drosophila melanogaster as a typical example and discuss the utility of an alternative synthetic biology approach to studying these highly intricate systems.
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Abstract
During the past 10 years, major developments in live-cell imaging methods have accompanied growing interest in the application of microfluidic techniques to biological imaging. The broad design possibilities of microfabrication and its relative ease of implementation have led to the development of a number of powerful imaging assays. Specifically, there has been great interest in the development of devices in which single cells can be followed in real-time over the course of several generations while the growth environment is changed. With standard perfusion chambers, the duration of a typical experiment is limited to one cell generation time. Using microfluidics, however, long-term imaging setups have been developed which can measure the effects of temporally controlled gene expression or pathway activation while tracking individual cells over the course of many generations. In this paper, we describe the details of fabricating such a microfluidic device for the purpose of long-term imaging of proliferating cells, the assembly of its individual components into a complete device, and then we give an example of how to use such a device to monitor real-time changes in gene expression in budding yeast. Our goal is to make this technique accessible to cell biology researchers without prior experience with microfluidic systems.
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Affiliation(s)
- Gilles Charvin
- Laboratoire Joliot-Curie & Laboratoire de Physique, Ecole Normale Supérieure, Lyon, France
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48
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Cookson NA, Cookson SW, Tsimring LS, Hasty J. Cell cycle-dependent variations in protein concentration. Nucleic Acids Res 2009; 38:2676-81. [PMID: 20019065 PMCID: PMC2860113 DOI: 10.1093/nar/gkp1069] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Computational modeling of biological systems has become an effective tool for analyzing cellular behavior and for elucidating key properties of the intricate networks that underlie experimental observations. While most modeling techniques rely heavily on the concentrations of intracellular molecules, little attention has been paid to tracking and simulating the significant volume fluctuations that occur over each cell division cycle. Here, we use fluorescence microscopy to acquire single cell volume trajectories for a large population of Saccharomyces cerevisiae cells. Using this data, we generate a comprehensive set of statistics that govern the growth and division of these cells over many generations, and we discover several interesting trends in their size, growth and protein production characteristics. We use these statistics to develop an accurate model of cell cycle volume dynamics, starting at cell birth. Finally, we demonstrate the importance of tracking volume fluctuations by combining cell division dynamics with a minimal gene expression model for a constitutively expressed fluorescent protein. The significant oscillations in the cellular concentration of a stable, highly expressed protein mimic the observed experimental trajectories and demonstrate the fundamental impact that the cell cycle has on cellular functions.
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Affiliation(s)
- Natalie A Cookson
- Department of Bioengineering, BioCircuits Institute, Molecular Biology Section, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
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Tracking lineages of single cells in lines using a microfluidic device. Proc Natl Acad Sci U S A 2009; 106:18149-54. [PMID: 19826080 DOI: 10.1073/pnas.0903163106] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Cells within a genetically identical population exhibit phenotypic variation that in some cases can persist across multiple generations. However, information about the temporal variation and familial dependence of protein levels remains hidden when studying the population as an ensemble. To correlate phenotypes with the age and genealogy of single cells over time, we developed a microfluidic device that enables us to track multiple lineages in parallel by trapping single cells and constraining them to grow in lines for as many as 8 divisions. To illustrate the utility of this method, we investigate lineages of cells expressing one of 3 naturally regulated proteins, each with a different representative expression behavior. Within lineages deriving from single cells, we observe genealogically related clusters of cells with similar phenotype; cluster sizes vary markedly among the 3 proteins, suggesting that the time scale of phenotypic persistence is protein-specific. Growing lines of cells also allows us to dynamically track temporal fluctuations in protein levels at the same time as pedigree relationships among the cells as they divide in the chambers. We observe bursts in expression levels of the heat shock protein Hsp12-GFP that occur simultaneously in mother and daughter cells. In contrast, the ribosomal protein Rps8b-GFP shows relatively constant levels of expression over time. This method is an essential step toward understanding the time scales of phenotypic variation and correlations in phenotype among single cells within a population.
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Ducret A, Maisonneuve E, Notareschi P, Grossi A, Mignot T, Dukan S. A microscope automated fluidic system to study bacterial processes in real time. PLoS One 2009; 4:e7282. [PMID: 19789641 PMCID: PMC2748647 DOI: 10.1371/journal.pone.0007282] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 09/08/2009] [Indexed: 11/19/2022] Open
Abstract
Most time lapse microscopy experiments studying bacterial processes ie growth, progression through the cell cycle and motility have been performed on thin nutrient agar pads. An important limitation of this approach is that dynamic perturbations of the experimental conditions cannot be easily performed. In eukaryotic cell biology, fluidic approaches have been largely used to study the impact of rapid environmental perturbations on live cells and in real time. However, all these approaches are not easily applicable to bacterial cells because the substrata are in all cases specific and also because microfluidics nanotechnology requires a complex lithography for the study of micrometer sized bacterial cells. In fact, in many cases agar is the experimental solid substratum on which bacteria can move or even grow. For these reasons, we designed a novel hybrid micro fluidic device that combines a thin agar pad and a custom flow chamber. By studying several examples, we show that this system allows real time analysis of a broad array of biological processes such as growth, development and motility. Thus, the flow chamber system will be an essential tool to study any process that take place on an agar surface at the single cell level.
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Affiliation(s)
- Adrien Ducret
- Aix Marseille Université - Laboratoire de Chimie Bactérienne (UPR 9043) - Institut de Microbiologie de la Méditerranée (IFR 88) - CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Etienne Maisonneuve
- Aix Marseille Université - Laboratoire de Chimie Bactérienne (UPR 9043) - Institut de Microbiologie de la Méditerranée (IFR 88) - CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Philippe Notareschi
- Aix Marseille Université - Laboratoire de Chimie Bactérienne (UPR 9043) - Institut de Microbiologie de la Méditerranée (IFR 88) - CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Alain Grossi
- Aix Marseille Université - Laboratoire de Chimie Bactérienne (UPR 9043) - Institut de Microbiologie de la Méditerranée (IFR 88) - CNRS, 31, Chemin Joseph Aiguier, Marseille, France
| | - Tâm Mignot
- Aix Marseille Université - Laboratoire de Chimie Bactérienne (UPR 9043) - Institut de Microbiologie de la Méditerranée (IFR 88) - CNRS, 31, Chemin Joseph Aiguier, Marseille, France
- * E-mail: (TM); (SD)
| | - Sam Dukan
- Aix Marseille Université - Laboratoire de Chimie Bactérienne (UPR 9043) - Institut de Microbiologie de la Méditerranée (IFR 88) - CNRS, 31, Chemin Joseph Aiguier, Marseille, France
- * E-mail: (TM); (SD)
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