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T. Ly V, Ehrlich D, Sevetson J, Hoffman RN, Salama SR, Kurniawan S, Teodorescu M. Gamifying cell culture training: The 'Seru-Otchi' experience for undergraduates. Heliyon 2024; 10:e30469. [PMID: 38737237 PMCID: PMC11088318 DOI: 10.1016/j.heliyon.2024.e30469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Working in a stem cell laboratory necessitates a thorough understanding of complex cell culture protocols, the operation of sensitive scientific equipment, adherence to safety standards, and general laboratory etiquette. For novice student researchers, acquiring the necessary specialized knowledge before their initial laboratory experience can be a formidable task. Similarly, for experienced laboratory personnel, efficiently and uniformly training new trainees to a rigorous standard presents a significant challenge. In response to these issues, we have developed an educational and interactive virtual cell culture environment. This interactive virtual lab aims to equip students with foundational knowledge in maintaining cortical brain organoids and to instill an understanding of pertinent safety procedures and laboratory etiquette. The gamification of this training process seeks to provide laboratory supervisors in highly specialized fields with an effective tool to integrate students into their work environments more rapidly and safely.
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Affiliation(s)
- Victoria T. Ly
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
| | - Drew Ehrlich
- Computational Media Department, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
| | - Jess Sevetson
- Department of Cellular, Molecular, and Developmental Biology, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
| | - Ryan N. Hoffman
- Department of Cellular, Molecular, and Developmental Biology, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
| | - Sofie R. Salama
- Department of Cellular, Molecular, and Developmental Biology, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
| | - Sri Kurniawan
- Computational Media Department, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
| | - Mircea Teodorescu
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA, 95060, USA
- University of California, Santa Cruz Genomics Institute, Santa Cruz, CA, 95060, USA
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2
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Elliott MAT, Schweiger HE, Robbins A, Vera-Choqqueccota S, Ehrlich D, Hernandez S, Voitiuk K, Geng J, Sevetson JL, Core C, Rosen YM, Teodorescu M, Wagner NO, Haussler D, Mostajo-Radji MA. Internet-Connected Cortical Organoids for Project-Based Stem Cell and Neuroscience Education. eNeuro 2023; 10:ENEURO.0308-23.2023. [PMID: 38016807 PMCID: PMC10755643 DOI: 10.1523/eneuro.0308-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/16/2023] [Accepted: 11/20/2023] [Indexed: 11/30/2023] Open
Abstract
The introduction of Internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell (PSC)-derived cortical organoids in two different settings: using microscopy to monitor organoid growth in an introductory tissue culture course and using high-density (HD) multielectrode arrays (MEAs) to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training.
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Affiliation(s)
- Matthew A T Elliott
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Hunter E Schweiger
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Ash Robbins
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Samira Vera-Choqqueccota
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Drew Ehrlich
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Computational Media, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Sebastian Hernandez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Kateryna Voitiuk
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Jinghui Geng
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Jess L Sevetson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Cordero Core
- Scientific Software Engineering Center, eScience Institute, University of Washington, Seattle, WA 98195
| | - Yohei M Rosen
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Mircea Teodorescu
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Nico O Wagner
- College of Arts and Sciences, University of San Francisco, San Francisco, CA 94117
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95060
| | - Mohammed A Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA 95060
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3
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Elliott MA, Schweiger HE, Robbins A, Vera-Choqqueccota S, Ehrlich D, Hernandez S, Voitiuk K, Geng J, Sevetson JL, Rosen YM, Teodorescu M, Wagner NO, Haussler D, Mostajo-Radji MA. Internet-connected cortical organoids for project-based stem cell and neuroscience education. bioRxiv 2023:2023.07.13.546418. [PMID: 37503236 PMCID: PMC10369936 DOI: 10.1101/2023.07.13.546418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The introduction of internet-connected technologies to the classroom has the potential to revolutionize STEM education by allowing students to perform experiments in complex models that are unattainable in traditional teaching laboratories. By connecting laboratory equipment to the cloud, we introduce students to experimentation in pluripotent stem cell-derived cortical organoids in two different settings: Using microscopy to monitor organoid growth in an introductory tissue culture course, and using high density multielectrode arrays to perform neuronal stimulation and recording in an advanced neuroscience mathematics course. We demonstrate that this approach develops interest in stem cell and neuroscience in the students of both courses. All together, we propose cloud technologies as an effective and scalable approach for complex project-based university training.
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Affiliation(s)
- Matthew A.T. Elliott
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Hunter E. Schweiger
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Ash Robbins
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Samira Vera-Choqqueccota
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Drew Ehrlich
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Computational Media, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sebastian Hernandez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Kateryna Voitiuk
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Jinghui Geng
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Jess L. Sevetson
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Yohei M. Rosen
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mircea Teodorescu
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Nico O. Wagner
- College of Arts and Sciences, University of San Francisco, San Francisco, CA, 94117, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mohammed A. Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
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4
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Seiler ST, Mantalas GL, Selberg J, Cordero S, Torres-Montoya S, Baudin PV, Ly VT, Amend F, Tran L, Hoffman RN, Rolandi M, Green RE, Haussler D, Salama SR, Teodorescu M. Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids. Sci Rep 2022; 12:20173. [PMID: 36418910 PMCID: PMC9684529 DOI: 10.1038/s41598-022-20096-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/08/2022] [Indexed: 11/27/2022] Open
Abstract
Organ-on-a-chip systems combine microfluidics, cell biology, and tissue engineering to culture 3D organ-specific in vitro models that recapitulate the biology and physiology of their in vivo counterparts. Here, we have developed a multiplex platform that automates the culture of individual organoids in isolated microenvironments at user-defined media flow rates. Programmable workflows allow the use of multiple reagent reservoirs that may be applied to direct differentiation, study temporal variables, and grow cultures long term. Novel techniques in polydimethylsiloxane (PDMS) chip fabrication are described here that enable features on the upper and lower planes of a single PDMS substrate. RNA sequencing (RNA-seq) analysis of automated cerebral cortex organoid cultures shows benefits in reducing glycolytic and endoplasmic reticulum stress compared to conventional in vitro cell cultures.
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Affiliation(s)
- Spencer T Seiler
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Gary L Mantalas
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - John Selberg
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sergio Cordero
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sebastian Torres-Montoya
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Pierre V Baudin
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Victoria T Ly
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Finn Amend
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Liam Tran
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Ryan N Hoffman
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Marco Rolandi
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Richard E Green
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sofie R Salama
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
| | - Mircea Teodorescu
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA.
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5
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Parks DF, Voitiuk K, Geng J, Elliott MAT, Keefe MG, Jung EA, Robbins A, Baudin PV, Ly VT, Hawthorne N, Yong D, Sanso SE, Rezaee N, Sevetson JL, Seiler ST, Currie R, Pollen AA, Hengen KB, Nowakowski TJ, Mostajo-Radji MA, Salama SR, Teodorescu M, Haussler D. IoT cloud laboratory: Internet of Things architecture for cellular biology. Internet Things (Amst) 2022; 20:100618. [PMID: 37383277 PMCID: PMC10305744 DOI: 10.1016/j.iot.2022.100618] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
The Internet of Things (IoT) provides a simple framework to control online devices easily. IoT is now a commonplace tool used by technology companies but is rarely used in biology experiments. IoT can benefit cloud biology research through alarm notifications, automation, and the real-time monitoring of experiments. We developed an IoT architecture to control biological devices and implemented it in lab experiments. Lab devices for electrophysiology, microscopy, and microfluidics were created from the ground up to be part of a unified IoT architecture. The system allows each device to be monitored and controlled from an online web tool. We present our IoT architecture so other labs can replicate it for their own experiments.
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Affiliation(s)
- David F Parks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kateryna Voitiuk
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jinghui Geng
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew A T Elliott
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew G Keefe
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Erik A Jung
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ash Robbins
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Pierre V Baudin
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Victoria T Ly
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nico Hawthorne
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Dylan Yong
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sebastian E Sanso
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Nick Rezaee
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jess L Sevetson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Spencer T Seiler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rob Currie
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Alex A Pollen
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Keith B Hengen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA 94143, USA
| | - Mohammed A Mostajo-Radji
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Sofie R Salama
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - David Haussler
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
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6
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Baudin PV, Sacksteder RE, Worthington AK, Voitiuk K, Ly VT, Hoffman RN, Elliott MA, Parks DF, Ward R, Torres-Montoya S, Amend F, Montellano Duran N, Vargas PA, Martinez G, Ramirez SM, Alvarado-Arnez LE, Ehrlich D, Rosen YM, Breevoort A, Schouten T, Kurniawan S, Haussler D, Teodorescu M, Mostajo-Radji MA. Cloud-controlled microscopy enables remote project-based biology education in underserved Latinx communities. Heliyon 2022; 8:e11596. [PMID: 36439758 PMCID: PMC9681640 DOI: 10.1016/j.heliyon.2022.e11596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/15/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Project-based learning (PBL) has long been recognized as an effective way to teach complex biology concepts. However, not all institutions have the resources to facilitate effective project-based coursework for students. We have developed a framework for facilitating PBL using remote-controlled internet-connected microscopes. Through this approach, one lab facility can host an experiment for many students around the world simultaneously. Experiments on this platform can be run on long timescales and with materials that are typically unavailable to high school classrooms. This allows students to perform novel research projects rather than just repeating standard classroom experiments. To investigate the impact of this program, we designed and ran six user studies with students worldwide. All experiments were hosted in Santa Cruz and San Francisco, California, with observations and decisions made remotely by the students using their personal computers and cellphones. In surveys gathered after the experiments, students reported increased excitement for science and a greater desire to pursue a career in STEM. This framework represents a novel, scalable, and effective PBL approach that has the potential to democratize biology and STEM education around the world.
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Affiliation(s)
- Pierre V. Baudin
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Raina E. Sacksteder
- Department of Microbiology and Environmental Toxicology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Atesh K. Worthington
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Institute for the Biology of Stem Cells, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Kateryna Voitiuk
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Victoria T. Ly
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Ryan N. Hoffman
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Matthew A.T. Elliott
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - David F. Parks
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | | | - Sebastian Torres-Montoya
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Finn Amend
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | | | - Paola A. Vargas
- Biotechnology, Universidad Catolica Boliviana San Pablo, Santa Cruz de la Sierra, Bolivia
| | - Guadalupe Martinez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Sandra M. Ramirez
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | | | - Drew Ehrlich
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Computational Media, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Yohei M. Rosen
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Arnar Breevoort
- Department of Neurology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Tallulah Schouten
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Sri Kurniawan
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Computational Media, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - David Haussler
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mircea Teodorescu
- Department of Electrical and Computer Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Mohammed A. Mostajo-Radji
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, 95060, USA
- Corresponding author at: Live Cell Biotechnology Discovery Lab, Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, 95060, USA.
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7
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Morris BI, Kittredge MJ, Casey B, Meng O, Chagas AM, Lamparter M, Thul T, Pask GM. PiSpy: An affordable, accessible, and flexible imaging platform for the automated observation of organismal biology and behavior. PLoS One 2022; 17:e0276652. [PMID: 36288371 PMCID: PMC9604989 DOI: 10.1371/journal.pone.0276652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
A great deal of understanding can be gleaned from direct observation of organismal growth, development, and behavior. However, direct observation can be time consuming and influence the organism through unintentional stimuli. Additionally, video capturing equipment can often be prohibitively expensive, difficult to modify to one's specific needs, and may come with unnecessary features. Here, we describe PiSpy, a low-cost, automated video acquisition platform that uses a Raspberry Pi computer and camera to record video or images at specified time intervals or when externally triggered. All settings and controls, such as programmable light cycling, are accessible to users with no programming experience through an easy-to-use graphical user interface. Importantly, the entire PiSpy system can be assembled for less than $100 using laser-cut and 3D-printed components. We demonstrate the broad applications and flexibility of PiSpy across a range of model and non-model organisms. Designs, instructions, and code can be accessed through an online repository, where a global community of PiSpy users can also contribute their own unique customizations and help grow the community of open-source research solutions.
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Affiliation(s)
- Benjamin I. Morris
- Program in Molecular Biology and Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- * E-mail: (BIM); (GMP)
| | - Marcy J. Kittredge
- Neuroscience Program, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Bea Casey
- Department of Electrical and Computer Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Owen Meng
- Department of Electrical and Computer Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - André Maia Chagas
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- TReND in Africa, Brighton, United Kingdom
- Gathering for Open Science Hardware
| | - Matt Lamparter
- Department of Electrical and Computer Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Thomas Thul
- Department of Biomedical Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Gregory M. Pask
- Program in Molecular Biology and Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- Department of Biology and Neuroscience Program, Middlebury College, Middlebury, Vermont, United States of America
- * E-mail: (BIM); (GMP)
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8
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Goss S, Barba Bazan C, Neuman K, Peng C, Begeja N, Suart CE, Truant R. Mod3D: A low-cost, flexible modular system of live-cell microscopy chambers and holders. PLoS One 2022; 17:e0269345. [PMID: 35657927 PMCID: PMC9165904 DOI: 10.1371/journal.pone.0269345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/18/2022] [Indexed: 11/23/2022] Open
Abstract
Live-cell microscopy imaging typically involves the use of high-quality glass-bottom chambers that allow cell culture, gaseous buffer exchange and optical properties suitable for microscopy applications. However, commercial sources of these chambers can add significant annual costs to cell biology laboratories. Consumer products in three-dimensional printing technology, for both Filament Deposition Modeling (FDM) and Masked Stereo Lithography (MSLA), have resulted in more biomedical research labs adopting the use of these devices for prototyping and manufacturing of lab plastic-based items, but rarely consumables. Here we describe a modular, live-cell chamber with multiple design options that can be mixed per experiment. Single reusable carriers and the use of biodegradable plastics, in a hybrid of FDM and MSLA manufacturing methods, reduce plastic waste. The system is easy to adapt to bespoke designs, with concept-to-prototype in a single day, offers significant cost savings to the users over commercial sources, and no loss in dimensional quality or reliability.
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Affiliation(s)
- Siobhan Goss
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Carlos Barba Bazan
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Kaitlyn Neuman
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Christina Peng
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Nola Begeja
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Celeste Elisabeth Suart
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Ray Truant
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Center for Advanced Light Microscopy (CALM), McMaster University, Hamilton, Ontario, Canada
- * E-mail:
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Mostajo-Radji MA. The emergence of neurodiplomacy. iScience 2022; 25:104370. [PMID: 35601914 PMCID: PMC9120262 DOI: 10.1016/j.isci.2022.104370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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