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Frey N, Sönmez UM, Minden J, LeDuc P. Microfluidics for understanding model organisms. Nat Commun 2022; 13:3195. [PMID: 35680898 PMCID: PMC9184607 DOI: 10.1038/s41467-022-30814-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
New microfluidic systems for whole organism analysis and experimentation are catalyzing biological breakthroughs across many fields, from human health to fundamental biology principles. This perspective discusses recent microfluidic tools to study intact model organisms to demonstrate the tremendous potential for these integrated approaches now and into the future. We describe these microsystems' technical features and highlight the unique advantages for precise manipulation in areas including immobilization, automated alignment, sorting, sensory, mechanical and chemical stimulation, and genetic and thermal perturbation. Our aim is to familiarize technologically focused researchers with microfluidics applications in biology research, while providing biologists an entrée to advanced microengineering techniques for model organisms. Building small-scale tools for biology research eliminates the need for time-consuming methods and enables novel experimental paradigms. Here, the authors discuss microfluidics' potential for manipulating or stimulating model organisms and identify barriers to making these tools accessible.
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Affiliation(s)
- Nolan Frey
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Utku M Sönmez
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Jonathan Minden
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Philip LeDuc
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Computation Biology, Carnegie Mellon University, Pittsburgh, PA, USA. .,Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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Wan J, Lu H. Enabling high-throughput single-animal gene-expression studies with molecular and micro-scale technologies. LAB ON A CHIP 2020; 20:4528-4538. [PMID: 33237042 PMCID: PMC7769683 DOI: 10.1039/d0lc00881h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gene expression and regulation play diverse and important roles across all living systems. By quantifying the expression, whether in a sample of single cells, a specific tissue, or in a whole animal, one can gain insights into the underlying biology. Many biological questions now require single-animal and tissue-specific resolution, such as why individuals, even within an isogenic population, have variations in development and aging across different tissues and organs. The popular techniques that quantify the transcriptome (e.g. RNA-sequencing) process populations of animals and cells together and thus, have limitations in both individual and spatial resolution. There are single-animal assays available (e.g. fluorescent reporters); however, they suffer other technical bottlenecks, such as a lack of robust sample-handling methods. Microfluidic technologies have demonstrated various improvements throughout the years, and it is likely they can enhance the impact of these single-animal gene-expression assays. In this perspective, we aim to highlight how the engineering/method-development field have unique opportunities to create new tools that can enable us to robustly answer the next set of important questions in biology that require high-density, high-quality gene expression data.
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Affiliation(s)
- Jason Wan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA.
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Zabihihesari A, Hilliker AJ, Rezai P. Localized microinjection of intact Drosophila melanogaster larva to investigate the effect of serotonin on heart rate. LAB ON A CHIP 2020; 20:343-355. [PMID: 31828261 DOI: 10.1039/c9lc00963a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In this paper, we present a novel hybrid microfluidic device for localized microinjection and heart monitoring of intact Drosophila melanogaster larvae at different developmental stages. Drosophila heart at the larval stage has been used as a model for cardiac disorder studies. However, previous pharmacological and toxicological cardiac studies are limited to dissected (semi-intact) Drosophila larvae which cannot be used for post-treatment studies. Challenges associated with microinjection of intact larvae include delicate handling of individual larvae, proper orientation for microneedle penetration, localized microinjection with controlled amount of chemicals into the hemolymph and reversible immobilization for post-injection phenotypic studies, all addressed by our microfluidic device. Larva loading and orientation were achieved by glass capillaries integrated into the PDMS microfluidic device. Side suction channels were used for immobilization prior to heart activity recording. Localized microinjection was achieved with a one degree-of-freedom microneedle and a custom-made pressure driven reagent delivery system, without any adverse effect on heart rate and animal viability. Precision in localized injection into the body cavity close to the heart chamber or the fat body was demonstrated with our microfluidic device. A MATLAB-based heartbeat quantification technique was used to investigate the dose-dependent effect of serotonin (5-hydroxytryptamine), a neurotransmitter, on the heart rate of intact Drosophila larvae, for the first time. Injection of 40 nL serotonin with ≥0.01 mM concentration significantly increased the heart rate of 3rd instar larvae by 21 ± 7% (SEM). Injection of 5 nL serotonin with a concentration of 0.01 mM significantly increased the heart rate of 2nd instar larvae by 12 ± 3% (SEM). The proposed microfluidic injection and heartbeat monitoring technique can be used for dye angiography and hemolymph circulation studies as well as screening intravenous drugs in vivo using the whole-animal Drosophila melanogaster.
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Affiliation(s)
- Alireza Zabihihesari
- Department of Mechanical Engineering, York University, BRG 433B, 4700 Keele St, Toronto, ON M3J 1P3, Canada.
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, BRG 433B, 4700 Keele St, Toronto, ON M3J 1P3, Canada.
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Zabihihesari A, Hilliker AJ, Rezai P. Fly-on-a-Chip: Microfluidics for Drosophila melanogaster Studies. Integr Biol (Camb) 2020; 11:425-443. [DOI: 10.1093/intbio/zyz037] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 12/16/2022]
Abstract
Abstract
The fruit fly or Drosophila melanogaster has been used as a promising model organism in genetics, developmental and behavioral studies as well as in the fields of neuroscience, pharmacology, and toxicology. Not only all the developmental stages of Drosophila, including embryonic, larval, and adulthood stages, have been used in experimental in vivo biology, but also the organs, tissues, and cells extracted from this model have found applications in in vitro assays. However, the manual manipulation, cellular investigation and behavioral phenotyping techniques utilized in conventional Drosophila-based in vivo and in vitro assays are mostly time-consuming, labor-intensive, and low in throughput. Moreover, stimulation of the organism with external biological, chemical, or physical signals requires precision in signal delivery, while quantification of neural and behavioral phenotypes necessitates optical and physical accessibility to Drosophila. Recently, microfluidic and lab-on-a-chip devices have emerged as powerful tools to overcome these challenges. This review paper demonstrates the role of microfluidic technology in Drosophila studies with a focus on both in vivo and in vitro investigations. The reviewed microfluidic devices are categorized based on their applications to various stages of Drosophila development. We have emphasized technologies that were utilized for tissue- and behavior-based investigations. Furthermore, the challenges and future directions in Drosophila-on-a-chip research, and its integration with other advanced technologies, will be discussed.
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Affiliation(s)
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
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Wu Q, Kumar N, Velagala V, Zartman JJ. Tools to reverse-engineer multicellular systems: case studies using the fruit fly. J Biol Eng 2019; 13:33. [PMID: 31049075 PMCID: PMC6480878 DOI: 10.1186/s13036-019-0161-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/07/2019] [Indexed: 01/08/2023] Open
Abstract
Reverse-engineering how complex multicellular systems develop and function is a grand challenge for systems bioengineers. This challenge has motivated the creation of a suite of bioengineering tools to develop increasingly quantitative descriptions of multicellular systems. Here, we survey a selection of these tools including microfluidic devices, imaging and computer vision techniques. We provide a selected overview of the emerging cross-talk between engineering methods and quantitative investigations within developmental biology. In particular, the review highlights selected recent examples from the Drosophila system, an excellent platform for understanding the interplay between genetics and biophysics. In sum, the integrative approaches that combine multiple advances in these fields are increasingly necessary to enable a deeper understanding of how to analyze both natural and synthetic multicellular systems.
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Affiliation(s)
- Qinfeng Wu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Nilay Kumar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Vijay Velagala
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Jeremiah J. Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
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Peimani AR, Zoidl G, Rezai P. A microfluidic device to study electrotaxis and dopaminergic system of zebrafish larvae. BIOMICROFLUIDICS 2018; 12:014113. [PMID: 29464011 PMCID: PMC5803004 DOI: 10.1063/1.5016381] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/25/2018] [Indexed: 06/08/2023]
Abstract
The zebrafish is a lower vertebrate model organism offering multiple applications for both fundamental and biomedical research into the nervous system from genes to behaviour. Investigation of zebrafish larvae's movement in response to various stimuli, which involves the dopaminergic system, is of interest in the field of sensory-motor integration. Nevertheless, the conventional methods of movement screening in Petri dishes and multi-well plates are mostly qualitative, uncontrollable, and inaccurate in terms of stimulus delivery and response analysis. We recently presented a microfluidic device built as a versatile platform for fluid flow stimulation and high speed time-lapse imaging of rheotaxis behaviour of zebrafish larvae. Here, we describe for the first time that this microfluidic device can also be used to test zebrafish larvae's sense of the electric field and electrotaxis in a systemic manner. We further show that electrotaxis is correlated with the dopamine signalling pathway in a time of day dependent manner and by selectively involving the D2-like dopamine receptors. The primary outcomes of this research opens avenues to study the molecular and physiological basis of electrotaxis, the effects of known agonist and antagonist compounds on the dopaminergic system, and the screen of novel pharmacological tools in the context of neurodegenerative disorders. We propose that this microfluidic device has broad application potential, including the investigation of complex stimuli, biological pathways, behaviors, and brain disorders.
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Affiliation(s)
- Amir Reza Peimani
- Department of Mechanical Engineering, York University, Toronto, Ontario M3J 1P3, Canada
| | - Georg Zoidl
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, Ontario M3J 1P3, Canada
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Miniaturized Sensors and Actuators for Biological Studies on Small Model Organisms of Disease. ENERGY, ENVIRONMENT, AND SUSTAINABILITY 2018. [DOI: 10.1007/978-981-10-7751-7_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Nady A, Peimani AR, Zoidl G, Rezai P. A microfluidic device for partial immobilization, chemical exposure and behavioural screening of zebrafish larvae. LAB ON A CHIP 2017; 17:4048-4058. [PMID: 29068019 DOI: 10.1039/c7lc00786h] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The zebrafish larva is an important vertebrate model for sensory-motor integration studies, genetic screening, and drug discovery because of its excellent characteristics such as optical transparency, genetic manipulability, and genetic similarity to humans. Operations such as precise manipulation of zebrafish larvae, controlled exposure to chemicals, and behavioural monitoring are of utmost importance to the abovementioned studies. In this work, a novel microfluidic device is presented to easily stabilize an individual larva's head using a microfluidic trap while leaving the majority of the body and the tail unhindered to move freely in a downstream chamber. The device is equipped with a microvalve to prevent the larva's escape from the trap and a microchannel beside the larva's head to expose it to chemicals at desired concentrations and times, while investigating multiple behaviours such as the tail, eye, and mouth movement frequencies. An in situ air bubble removal module was also incorporated to increase the yield of experiments. The functionality of our device in comparison to a conventional droplet-based technique was tested using l-arginine exposure and viability assays. We found that the larvae in the device and the droplet exhibit similar tail and eye response trends to nM-mM concentrations of l-arginine, and that the survival of the larvae is not affected by the device. However, the tail responses in the device were numerically higher than the droplet-tested larvae at nM-mM l-arginine concentrations. In the future, our device has the potential to be used for conducting simultaneous whole-brain functional imaging, upon optimized immobilization of the brain, and behavioural analysis to uncover differences between diseased and healthy states in zebrafish.
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Affiliation(s)
- Asal Nady
- Department of Biology, York University, Toronto, ON, Canada
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Ghaemi R, Rezai P, Nejad FR, Selvaganapathy PR. Characterization of microfluidic clamps for immobilizing and imaging of Drosophila melanogaster larva's central nervous system. BIOMICROFLUIDICS 2017; 11:034113. [PMID: 28580046 PMCID: PMC5446281 DOI: 10.1063/1.4984767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/18/2017] [Indexed: 05/16/2023]
Abstract
Drosophila melanogaster is a well-established model organism to understand biological processes and study human diseases at the molecular-genetic level. The central nervous system (CNS) of Drosophila larvae is widely used as a model to study neuron development and network formation. This has been achieved by using various genetic manipulation tools such as microinjection to knock down certain genes or over-express proteins for visualizing the cellular activities. However, visualization of an intact-live neuronal response in larva's Central Nervous System (CNS) is challenging due to robust digging/burrowing behaviour that impedes neuroimaging. To address this problem, dissection is used to isolate and immobilize the CNS from the rest of the body. In order to obtain a true physiological response from the Drosophila CNS, it is important to avoid dissection, while the larva should be kept immobilized. In this paper, a series of microfluidic clamps were investigated for intact immobilization of the larva. As a result, an optimized structure for rapid mechanical immobilization of Drosophila larvae for CNS imaging was determined. The clamping and immobilization processes were characterized by imaging and movement measurement of the CNS through the expression of genetically encoded Calcium sensor GCaMP5 in all sensory and cholinergic interneurons. The optimal structure that included two 3D constrictions inside a narrowed channel considerably reduced the internal CNS capsule movements. It restricts the CNS movement to 10% of the motion from a glued larva and allows motion of only 10 ± 30 μm over 350 s immobilization which was sufficient for CNS imaging. These larva-on-a-chip platforms can be useful for studying CNS responses to sensory cues such as sound, light, chemosensory, tactile, and electric/magnetic fields.
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Affiliation(s)
- Reza Ghaemi
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Pouya Rezai
- Department of Mechanical Engineering, York University, Toronto, Ontario M3J 1P3, Canada
| | - Fatemeh Rafiei Nejad
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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