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Yoon S, Kilicarslan You D, Jeong U, Lee M, Kim E, Jeon TJ, Kim SM. Microfluidics in High-Throughput Drug Screening: Organ-on-a-Chip and C. elegans-Based Innovations. BIOSENSORS 2024; 14:55. [PMID: 38275308 PMCID: PMC10813408 DOI: 10.3390/bios14010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The development of therapeutic interventions for diseases necessitates a crucial step known as drug screening, wherein potential substances with medicinal properties are rigorously evaluated. This process has undergone a transformative evolution, driven by the imperative need for more efficient, rapid, and high-throughput screening platforms. Among these, microfluidic systems have emerged as the epitome of efficiency, enabling the screening of drug candidates with unprecedented speed and minimal sample consumption. This review paper explores the cutting-edge landscape of microfluidic-based drug screening platforms, with a specific emphasis on two pioneering approaches: organ-on-a-chip and C. elegans-based chips. Organ-on-a-chip technology harnesses human-derived cells to recreate the physiological functions of human organs, offering an invaluable tool for assessing drug efficacy and toxicity. In parallel, C. elegans-based chips, boasting up to 60% genetic homology with humans and a remarkable affinity for microfluidic systems, have proven to be robust models for drug screening. Our comprehensive review endeavors to provide readers with a profound understanding of the fundamental principles, advantages, and challenges associated with these innovative drug screening platforms. We delve into the latest breakthroughs and practical applications in this burgeoning field, illuminating the pivotal role these platforms play in expediting drug discovery and development. Furthermore, we engage in a forward-looking discussion to delineate the future directions and untapped potential inherent in these transformative technologies. Through this review, we aim to contribute to the collective knowledge base in the realm of drug screening, providing valuable insights to researchers, clinicians, and stakeholders alike. We invite readers to embark on a journey into the realm of microfluidic-based drug screening platforms, fostering a deeper appreciation for their significance and promising avenues yet to be explored.
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Affiliation(s)
- Sunhee Yoon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Dilara Kilicarslan You
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Uiechan Jeong
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Mina Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Eunhye Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
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Li B, Nelson MS, Chacko JV, Cudworth N, Eliceiri KW. Hardware-software co-design of an open-source automatic multimodal whole slide histopathology imaging system. JOURNAL OF BIOMEDICAL OPTICS 2023; 28:026501. [PMID: 36761254 PMCID: PMC9905038 DOI: 10.1117/1.jbo.28.2.026501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Significance Advanced digital control of microscopes and programmable data acquisition workflows have become increasingly important for improving the throughput and reproducibility of optical imaging experiments. Combinations of imaging modalities have enabled a more comprehensive understanding of tissue biology and tumor microenvironments in histopathological studies. However, insufficient imaging throughput and complicated workflows still limit the scalability of multimodal histopathology imaging. Aim We present a hardware-software co-design of a whole slide scanning system for high-throughput multimodal tissue imaging, including brightfield (BF) and laser scanning microscopy. Approach The system can automatically detect regions of interest using deep neural networks in a low-magnification rapid BF scan of the tissue slide and then conduct high-resolution BF scanning and laser scanning imaging on targeted regions with deep learning-based run-time denoising and resolution enhancement. The acquisition workflow is built using Pycro-Manager, a Python package that bridges hardware control libraries of the Java-based open-source microscopy software Micro-Manager in a Python environment. Results The system can achieve optimized imaging settings for both modalities with minimized human intervention and speed up the laser scanning by an order of magnitude with run-time image processing. Conclusions The system integrates the acquisition pipeline and data analysis pipeline into a single workflow that improves the throughput and reproducibility of multimodal histopathological imaging.
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Affiliation(s)
- Bin Li
- University of Wisconsin–Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
- University of Wisconsin–Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
| | - Michael S. Nelson
- University of Wisconsin–Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
- University of Wisconsin–Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Jenu V. Chacko
- University of Wisconsin–Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
| | - Nathan Cudworth
- University of Wisconsin–Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
- University of Wisconsin–Madison, Department of Medical Physics, Madison, Wisconsin, United States
| | - Kevin W. Eliceiri
- University of Wisconsin–Madison, Center for Quantitative Cell Imaging, Madison, Wisconsin, United States
- University of Wisconsin–Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
- Morgridge Institute for Research, Madison, Wisconsin, United States
- University of Wisconsin–Madison, Department of Medical Physics, Madison, Wisconsin, United States
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Saberi-Bosari S, Flores KB, San-Miguel A. Deep learning-enabled analysis reveals distinct neuronal phenotypes induced by aging and cold-shock. BMC Biol 2020; 18:130. [PMID: 32967665 PMCID: PMC7510121 DOI: 10.1186/s12915-020-00861-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/01/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Access to quantitative information is crucial to obtain a deeper understanding of biological systems. In addition to being low-throughput, traditional image-based analysis is mostly limited to error-prone qualitative or semi-quantitative assessment of phenotypes, particularly for complex subcellular morphologies. The PVD neuron in Caenorhabditis elegans, which is responsible for harsh touch and thermosensation, undergoes structural degeneration as nematodes age characterized by the appearance of dendritic protrusions. Analysis of these neurodegenerative patterns is labor-intensive and limited to qualitative assessment. RESULTS In this work, we apply deep learning to perform quantitative image-based analysis of complex neurodegeneration patterns exhibited by the PVD neuron in C. elegans. We apply a convolutional neural network algorithm (Mask R-CNN) to identify neurodegenerative subcellular protrusions that appear after cold-shock or as a result of aging. A multiparametric phenotypic profile captures the unique morphological changes induced by each perturbation. We identify that acute cold-shock-induced neurodegeneration is reversible and depends on rearing temperature and, importantly, that aging and cold-shock induce distinct neuronal beading patterns. CONCLUSION The results of this work indicate that implementing deep learning for challenging image segmentation of PVD neurodegeneration enables quantitatively tracking subtle morphological changes in an unbiased manner. This analysis revealed that distinct patterns of morphological alteration are induced by aging and cold-shock, suggesting different mechanisms at play. This approach can be used to identify the molecular components involved in orchestrating neurodegeneration and to characterize the effect of other stressors on PVD degeneration.
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Affiliation(s)
- Sahand Saberi-Bosari
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Kevin B Flores
- Department of Mathematics, North Carolina State University, Raleigh, NC, 27695, USA
| | - Adriana San-Miguel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA.
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Fageot J, Aziznejad S, Unser M, Uhlmann V. Support and approximation properties of Hermite splines. JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS 2020; 368:112503. [PMID: 32255895 PMCID: PMC6919321 DOI: 10.1016/j.cam.2019.112503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 07/25/2019] [Indexed: 06/11/2023]
Abstract
In this paper, we formally investigate two mathematical aspects of Hermite splines that are relevant to practical applications. We first demonstrate that Hermite splines are maximally localized, in the sense that the size of their support is minimal among pairs of functions with identical reproduction properties. Then, we precisely quantify the approximation power of Hermite splines for the reconstruction of functions and their derivatives. It is known that the Hermite and B-spline approximation schemes have the same approximation order. More precisely, their approximation error vanishes as O ( T 4 ) when the step size T goes to zero. In this work, we show that they actually have the same asymptotic approximation error constants, too. Therefore, they have identical asymptotic approximation properties. Hermite splines combine optimal localization and excellent approximation power, while retaining interpolation properties and closed-form expression, in contrast to existing similar functions. These findings shed a new light on the convenience of Hermite splines in the context of computer graphics and geometrical design.
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Affiliation(s)
- Julien Fageot
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, 1015 Lausanne, Switzerland
| | - Shayan Aziznejad
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, 1015 Lausanne, Switzerland
| | - Michael Unser
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, 1015 Lausanne, Switzerland
| | - Virginie Uhlmann
- Biomedical Imaging Group, École polytechnique fédérale de Lausanne (EPFL), Station 17, 1015 Lausanne, Switzerland
- European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
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Midkiff D, San-Miguel A. Microfluidic Technologies for High Throughput Screening Through Sorting and On-Chip Culture of C. elegans. Molecules 2019; 24:molecules24234292. [PMID: 31775328 PMCID: PMC6930626 DOI: 10.3390/molecules24234292] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 02/07/2023] Open
Abstract
The nematode Caenorhabditis elegans is a powerful model organism that has been widely used to study molecular biology, cell development, neurobiology, and aging. Despite their use for the past several decades, the conventional techniques for growth, imaging, and behavioral analysis of C. elegans can be cumbersome, and acquiring large data sets in a high-throughput manner can be challenging. Developments in microfluidic “lab-on-a-chip” technologies have improved studies of C. elegans by increasing experimental control and throughput. Microfluidic features such as on-chip control layers, immobilization channels, and chamber arrays have been incorporated to develop increasingly complex platforms that make experimental techniques more powerful. Genetic and chemical screens are performed on C. elegans to determine gene function and phenotypic outcomes of perturbations, to test the effect that chemicals have on health and behavior, and to find drug candidates. In this review, we will discuss microfluidic technologies that have been used to increase the throughput of genetic and chemical screens in C. elegans. We will discuss screens for neurobiology, aging, development, behavior, and many other biological processes. We will also discuss robotic technologies that assist in microfluidic screens, as well as alternate platforms that perform functions similar to microfluidics.
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Apiou-Sbirlea G, Choe R, Kleemann M, Tromberg BJ. Special Section Guest Editorial: Translational Biophotonics. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-2. [PMID: 30770679 PMCID: PMC6988178 DOI: 10.1117/1.jbo.24.2.021200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This guest editorial introduces the special section on Translational Biophotonics.
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Affiliation(s)
- Gabriela Apiou-Sbirlea
- Massachusetts General Hospital Research Institute, Wellman Center for Photomedicine and Harvard Medi
| | - Regine Choe
- University of Rochester, Department of Biomedical Engineering, 204 Robert B. Goergen Hall, Rochester
| | - Markus Kleemann
- University Vascular Center Lübeck, University of Lübeck, Department of Surgery, University Medical C
| | - Bruce J Tromberg
- Beckman Laser Institute and Medical Clinic, 1002 Health Sciences Road East, University of California
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