1
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Algorri JF, Roldán-Varona P, Fernández-Manteca MG, López-Higuera JM, Rodriguez-Cobo L, Cobo-García A. Photonic Microfluidic Technologies for Phytoplankton Research. BIOSENSORS 2022; 12:1024. [PMID: 36421145 PMCID: PMC9688872 DOI: 10.3390/bios12111024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 06/16/2023]
Abstract
Phytoplankton is a crucial component for the correct functioning of different ecosystems, climate regulation and carbon reduction. Being at least a quarter of the biomass of the world's vegetation, they produce approximately 50% of atmospheric O2 and remove nearly a third of the anthropogenic carbon released into the atmosphere through photosynthesis. In addition, they support directly or indirectly all the animals of the ocean and freshwater ecosystems, being the base of the food web. The importance of their measurement and identification has increased in the last years, becoming an essential consideration for marine management. The gold standard process used to identify and quantify phytoplankton is manual sample collection and microscopy-based identification, which is a tedious and time-consuming task and requires highly trained professionals. Microfluidic Lab-on-a-Chip technology represents a potential technical solution for environmental monitoring, for example, in situ quantifying toxic phytoplankton. Its main advantages are miniaturisation, portability, reduced reagent/sample consumption and cost reduction. In particular, photonic microfluidic chips that rely on optical sensing have emerged as powerful tools that can be used to identify and analyse phytoplankton with high specificity, sensitivity and throughput. In this review, we focus on recent advances in photonic microfluidic technologies for phytoplankton research. Different optical properties of phytoplankton, fabrication and sensing technologies will be reviewed. To conclude, current challenges and possible future directions will be discussed.
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Affiliation(s)
- José Francisco Algorri
- Photonics Engineering Group, Universidad de Cantabria, 39005 Santander, Spain
- CIBER de Bioingeniera, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Pablo Roldán-Varona
- Photonics Engineering Group, Universidad de Cantabria, 39005 Santander, Spain
- CIBER de Bioingeniera, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | | | - José Miguel López-Higuera
- Photonics Engineering Group, Universidad de Cantabria, 39005 Santander, Spain
- CIBER de Bioingeniera, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Luis Rodriguez-Cobo
- Photonics Engineering Group, Universidad de Cantabria, 39005 Santander, Spain
- CIBER de Bioingeniera, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Adolfo Cobo-García
- Photonics Engineering Group, Universidad de Cantabria, 39005 Santander, Spain
- CIBER de Bioingeniera, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria Valdecilla (IDIVAL), 39011 Santander, Spain
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2
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Zhang Y, Guo X, Yang H, Shi S. The Studies in Constructing Yeast Cell Factories for the Production of Fatty Acid Alkyl Esters. Front Bioeng Biotechnol 2022; 9:799032. [PMID: 35087801 PMCID: PMC8787340 DOI: 10.3389/fbioe.2021.799032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/19/2021] [Indexed: 12/25/2022] Open
Abstract
Fatty acid alkyl esters have broad applications in biofuels, lubricant formulas, paints, coatings, and cosmetics. Traditionally, these esters are mostly produced through unsustainable and energy-intensive processes. In contrast, microbial production of esters from renewable and sustainable feedstocks may provide a promising alternative and has attracted widespread attention in recent years. At present, yeasts are used as ideal hosts for producing such esters, due to their availability for high-density fermentation, resistance to phage infection, and tolerance against toxic inhibitors. Here, we summarize recent development on the biosynthesis of alkyl esters, including fatty acid ethyl esters (FAEEs), fatty acid short-branched chain alkyl esters (FASBEs), and wax esters (WEs) by various yeast cell factories. We focus mainly on the enzyme engineering strategies of critical wax ester synthases, and the pathway engineering strategies employed for the biosynthesis of various ester products. The bottlenecks that limit productivity and their potential solutions are also discussed in this review.
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Affiliation(s)
- Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xiao Guo
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huaiyi Yang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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3
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Light sheet based volume flow cytometry (VFC) for rapid volume reconstruction and parameter estimation on the go. Sci Rep 2022; 12:78. [PMID: 34997009 PMCID: PMC8741756 DOI: 10.1038/s41598-021-03902-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/06/2021] [Indexed: 11/08/2022] Open
Abstract
Optical imaging is paramount for disease diagnosis and to access its progression over time. The proposed optical flow imaging (VFC/iLIFE) is a powerful technique that adds new capabilities (3D volume visualization, organelle-level resolution, and multi-organelle screening) to the existing system. Unlike state-of-the-art point-illumination-based biomedical imaging techniques, the sheet-based VFC technique is capable of single-shot sectional visualization, high throughput interrogation, real-time parameter estimation, and instant volume reconstruction with organelle-level resolution of live specimens. The specimen flow system was realized on a multichannel (Y-type) microfluidic chip that enables visualization of organelle distribution in several cells in-parallel at a relatively high flow-rate (2000 nl/min). The calibration of VFC system requires the study of point emitters (fluorescent beads) at physiologically relevant flow-rates (500-2000 nl/min) for determining flow-induced optical aberration in the system point spread function (PSF). Subsequently, the recorded raw images and volumes were computationally deconvolved with flow-variant PSF to reconstruct the cell volume. High throughput investigation of the mitochondrial network in HeLa cancer cell was carried out at sub-cellular resolution in real-time and critical parameters (mitochondria count and size distribution, morphology, entropy, and cell strain statistics) were determined on-the-go. These parameters determine the physiological state of cells, and the changes over-time, revealing the metastatic progression of diseases. Overall, the developed VFC system enables real-time monitoring of sub-cellular organelle organization at a high-throughput with high-content capacity.
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4
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Zheng X, Duan X, Tu X, Jiang S, Song C. The Fusion of Microfluidics and Optics for On-Chip Detection and Characterization of Microalgae. MICROMACHINES 2021; 12:1137. [PMID: 34683188 PMCID: PMC8540680 DOI: 10.3390/mi12101137] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 01/21/2023]
Abstract
It has been demonstrated that microalgae play an important role in the food, agriculture and medicine industries. Additionally, the identification and counting of the microalgae are also a critical step in evaluating water quality, and some lipid-rich microalgae species even have the potential to be an alternative to fossil fuels. However, current technologies for the detection and analysis of microalgae are costly, labor-intensive, time-consuming and throughput limited. In the past few years, microfluidic chips integrating optical components have emerged as powerful tools that can be used for the analysis of microalgae with high specificity, sensitivity and throughput. In this paper, we review recent optofluidic lab-on-chip systems and techniques used for microalgal detection and characterization. We introduce three optofluidic technologies that are based on fluorescence, Raman spectroscopy and imaging-based flow cytometry, each of which can achieve the determination of cell viability, lipid content, metabolic heterogeneity and counting. We analyze and summarize the merits and drawbacks of these micro-systems and conclude the direction of the future development of the optofluidic platforms applied in microalgal research.
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Affiliation(s)
| | | | | | | | - Chaolong Song
- School of Mechanical Engineering and Electronic Information, China University of Geosciences, Wuhan 430074, China; (X.Z.); (X.D.); (X.T.); (S.J.)
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5
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How does the Internet of Things (IoT) help in microalgae biorefinery? Biotechnol Adv 2021; 54:107819. [PMID: 34454007 DOI: 10.1016/j.biotechadv.2021.107819] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/27/2021] [Accepted: 08/22/2021] [Indexed: 12/14/2022]
Abstract
Microalgae biorefinery is a platform for the conversion of microalgal biomass into a variety of value-added products, such as biofuels, bio-based chemicals, biomaterials, and bioactive substances. Commercialization and industrialization of microalgae biorefinery heavily rely on the capability and efficiency of large-scale cultivation of microalgae. Thus, there is an urgent need for novel technologies that can be used to monitor, automatically control, and precisely predict microalgae production. In light of this, innovative applications of the Internet of things (IoT) technologies in microalgae biorefinery have attracted tremendous research efforts. IoT has potential applications in a microalgae biorefinery for the automatic control of microalgae cultivation, monitoring and manipulation of microalgal cultivation parameters, optimization of microalgae productivity, identification of toxic algae species, screening of target microalgae species, classification of microalgae species, and viability detection of microalgal cells. In this critical review, cutting-edge IoT technologies that could be adopted to microalgae biorefinery in the upstream and downstream processing are described comprehensively. The current advances of the integration of IoT with microalgae biorefinery are presented. What this review discussed includes automation, sensors, lab-on-chip, and machine learning, which are the main constituent elements and advanced technologies of IoT. Specifically, future research directions are discussed with special emphasis on the development of sensors, the application of microfluidic technology, robotized microalgae, high-throughput platforms, deep learning, and other innovative techniques. This review could contribute greatly to the novelty and relevance in the field of IoT-based microalgae biorefinery to develop smarter, safer, cleaner, greener, and economically efficient techniques for exhaustive energy recovery during the biorefinery process.
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6
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Abstract
As a high-throughput data analysis technique, photon time stretching (PTS) is widely used in the monitoring of rare events such as cancer cells, rough waves, and the study of electronic and optical transient dynamics. The PTS technology relies on high-speed data collection, and the large amount of data generated poses a challenge to data storage and real-time processing. Therefore, how to use compatible optical methods to filter and process data in advance is particularly important. The time-lens proposed, based on the duality of time and space as an important data processing method derived from PTS, achieves imaging of time signals by controlling the phase information of the timing signals. In this paper, an optical neural network based on the time-lens (TL-ONN) is proposed, which applies the time-lens to the layer algorithm of the neural network to realize the forward transmission of one-dimensional data. The recognition function of this optical neural network for speech information is verified by simulation, and the test recognition accuracy reaches 95.35%. This architecture can be applied to feature extraction and classification, and is expected to be a breakthrough in detecting rare events such as cancer cell identification and screening.
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7
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Khatiwada B, Sunna A, Nevalainen H. Molecular tools and applications of Euglena gracilis: From biorefineries to bioremediation. Biotechnol Bioeng 2020; 117:3952-3967. [PMID: 32710635 DOI: 10.1002/bit.27516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/17/2020] [Accepted: 07/23/2020] [Indexed: 12/19/2022]
Abstract
Euglena gracilis is a promising source of commercially important metabolites such as vitamins, wax esters, paramylon, and amino acids. However, the molecular tools available to create improved Euglena strains are limited compared to other microorganisms that are currently exploited in the biotechnology industry. The complex poly-endosymbiotic nature of the Euglena genome is a major bottleneck for obtaining a complete genome sequence and thus represents a notable shortcoming in gaining molecular information of this organism. Therefore, the studies and applications have been more focused on using the wild-type strain or its variants and optimizing the nutrient composition and cultivation conditions to enhance the production of biomass and valuable metabolites. In addition to producing metabolites, the E. gracilis biorefinery concept also provides means for the production of biofuels and biogas as well as residual biomass for the remediation of industrial and municipal wastewater. Using Euglena for bioremediation of environments contaminated with heavy metals is of special interest due to the strong ability of the organism to accumulate and sequester these compounds. The published draft genome and transcriptome will serve as a basis for further molecular studies of Euglena and provide a guide for the engineering of metabolic pathways of relevance for the already established as well as novel applications.
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Affiliation(s)
- Bishal Khatiwada
- Department Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Anwar Sunna
- Department Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
| | - Helena Nevalainen
- Department Molecular Sciences, Macquarie University, Sydney, Australia.,Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, Australia
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8
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Spontaneous mutation rate as a source of diversity for improving desirable traits in cultured microalgae. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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9
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Girault M, Beneyton T, Del Amo Y, Baret JC. Microfluidic technology for plankton research. Curr Opin Biotechnol 2018; 55:134-150. [PMID: 30326407 PMCID: PMC6378650 DOI: 10.1016/j.copbio.2018.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 02/06/2023]
Abstract
Plankton produces numerous chemical compounds used in cosmetics and functional foods. They also play a key role in the carbon budget on the Earth. In a context of global change, it becomes important to understand the physiological response of these microorganisms to changing environmental conditions. Their adaptations and the response to specific environmental conditions are often restricted to a few active cells or individuals in large populations. Using analytical capabilities at the subnanoliter scale, microfluidic technology has also demonstrated a high potential in biological assays. Here, we review recent advances in microfluidic technologies to overcome the current challenges in high content analysis both at population and the single cell level.
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Affiliation(s)
- Mathias Girault
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Thomas Beneyton
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France
| | - Yolanda Del Amo
- Université de Bordeaux - OASU, UMR CNRS 5805 EPOC (Environnements et Paléoenvironnements Océaniques et Continentaux), Station Marine d'Arcachon, 33120 Arcachon, France
| | - Jean-Christophe Baret
- Centre de Recherche Paul Pascal, Unité Mixte de Recherche 5031, Université de Bordeaux, Centre National de la Recherche Scientifique, 33600 Pessac, France.
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10
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Ota S, Horisaki R, Kawamura Y, Ugawa M, Sato I, Hashimoto K, Kamesawa R, Setoyama K, Yamaguchi S, Fujiu K, Waki K, Noji H. Ghost cytometry. Science 2018; 360:1246-1251. [PMID: 29903975 DOI: 10.1126/science.aan0096] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/10/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Ghost imaging is a technique used to produce an object's image without using a spatially resolving detector. Here we develop a technique we term "ghost cytometry," an image-free ultrafast fluorescence "imaging" cytometry based on a single-pixel detector. Spatial information obtained from the motion of cells relative to a static randomly patterned optical structure is compressively converted into signals that arrive sequentially at a single-pixel detector. Combinatorial use of the temporal waveform with the intensity distribution of the random pattern allows us to computationally reconstruct cell morphology. More importantly, we show that applying machine-learning methods directly on the compressed waveforms without image reconstruction enables efficient image-free morphology-based cytometry. Despite a compact and inexpensive instrumentation, image-free ghost cytometry achieves accurate and high-throughput cell classification and selective sorting on the basis of cell morphology without a specific biomarker, both of which have been challenging to accomplish using conventional flow cytometers.
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Affiliation(s)
- Sadao Ota
- Thinkcyte Inc., 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan. .,University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Ryoichi Horisaki
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,Department of Information and Physical Sciences, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoko Kawamura
- Thinkcyte Inc., 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Masashi Ugawa
- Thinkcyte Inc., 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Issei Sato
- Thinkcyte Inc., 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi-shi, Saitama 332-0012, Japan.,RIKEN AIP, Nihonbashi 1-chome Mitsui Building, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Kazuki Hashimoto
- University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Japan Aerospace Exploration Agency, 6-13-1 Osawa, Mitaka-shi, Tokyo 181-0015, Japan
| | - Ryosuke Kamesawa
- Thinkcyte Inc., 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kotaro Setoyama
- Thinkcyte Inc., 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Satoko Yamaguchi
- University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Katsuhito Fujiu
- University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Kayo Waki
- University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroyuki Noji
- University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,ImPACT Program, Cabinet Office, Government of Japan, Chiyoda-ku Tokyo 100-8914, Japan
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11
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12
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Muñoz HE, Li M, Riche CT, Nitta N, Diebold E, Lin J, Owsley K, Bahr M, Goda K, Di Carlo D. Single-Cell Analysis of Morphological and Metabolic Heterogeneity in Euglena gracilis by Fluorescence-Imaging Flow Cytometry. Anal Chem 2018; 90:11280-11289. [DOI: 10.1021/acs.analchem.8b01794] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Hector E. Muñoz
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Ming Li
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
- Department of Electrical Engineering, University of California, Los Angeles, California 90095, United States
- School of Engineering, Macquarie University, Sydney 2109, Australia
| | - Carson T. Riche
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
| | - Nao Nitta
- Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Eric Diebold
- Omega Biosystems Incorporated, San Jose, California 95131, United States
| | - Jonathan Lin
- Omega Biosystems Incorporated, San Jose, California 95131, United States
| | - Keegan Owsley
- Omega Biosystems Incorporated, San Jose, California 95131, United States
| | - Matthew Bahr
- Omega Biosystems Incorporated, San Jose, California 95131, United States
| | - Keisuke Goda
- Department of Electrical Engineering, University of California, Los Angeles, California 90095, United States
- Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, California 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, California 90095, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California 90095, United States
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13
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Lei C, Kobayashi H, Wu Y, Li M, Isozaki A, Yasumoto A, Mikami H, Ito T, Nitta N, Sugimura T, Yamada M, Yatomi Y, Di Carlo D, Ozeki Y, Goda K. High-throughput imaging flow cytometry by optofluidic time-stretch microscopy. Nat Protoc 2018; 13:1603-1631. [DOI: 10.1038/s41596-018-0008-7] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Miura T, Mikami H, Isozaki A, Ito T, Ozeki Y, Goda K. On-chip light-sheet fluorescence imaging flow cytometry at a high flow speed of 1 m/s. BIOMEDICAL OPTICS EXPRESS 2018; 9:3424-3433. [PMID: 29984107 PMCID: PMC6033546 DOI: 10.1364/boe.9.003424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 06/03/2018] [Accepted: 06/13/2018] [Indexed: 05/02/2023]
Abstract
We present on-chip fluorescence imaging flow cytometry by light-sheet excitation on a mirror-embedded microfluidic chip. The method allows us to obtain microscopy-grade fluorescence images of cells flowing at a high speed of 1 m/s, which is comparable to the flow speed of conventional non-imaging flow cytometers. To implement the light-sheet excitation of flowing cells in a microchannel, we designed and fabricated a mirror-embedded PDMS-based microfluidic chip. To show its broad utility, we used the method to classify large populations of microalgal cells (Euglena gracilis) and human cancer cells (human adenocarcinoma cells). Our method holds promise for large-scale single-cell analysis.
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Affiliation(s)
- Taichi Miura
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Hideharu Mikami
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Isozaki
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Takuro Ito
- Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, University of Tokyo, Tokyo 113-8656, Japan
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
- Japan Science and Technology Agency, Saitama 332-0012, Japan
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15
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Zhao W, Wang C, Chen H, Chen M, Yang S. High-speed cell recognition algorithm for ultrafast flow cytometer imaging system. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-8. [PMID: 29623704 DOI: 10.1117/1.jbo.23.4.046001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/16/2018] [Indexed: 06/08/2023]
Abstract
An optical time-stretch flow imaging system enables high-throughput examination of cells/particles with unprecedented high speed and resolution. A significant amount of raw image data is produced. A high-speed cell recognition algorithm is, therefore, highly demanded to analyze large amounts of data efficiently. A high-speed cell recognition algorithm consisting of two-stage cascaded detection and Gaussian mixture model (GMM) classification is proposed. The first stage of detection extracts cell regions. The second stage integrates distance transform and the watershed algorithm to separate clustered cells. Finally, the cells detected are classified by GMM. We compared the performance of our algorithm with support vector machine. Results show that our algorithm increases the running speed by over 150% without sacrificing the recognition accuracy. This algorithm provides a promising solution for high-throughput and automated cell imaging and classification in the ultrafast flow cytometer imaging platform.
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Affiliation(s)
- Wanyue Zhao
- Tsinghua University, National Laboratory for Information Science and Technology, Department of Elect, China
| | - Chao Wang
- University of Kent, School of Engineering and Digital Arts, Canterbury, United Kingdom
| | - Hongwei Chen
- Tsinghua University, National Laboratory for Information Science and Technology, Department of Elect, China
| | - Minghua Chen
- Tsinghua University, National Laboratory for Information Science and Technology, Department of Elect, China
| | - Sigang Yang
- Tsinghua University, National Laboratory for Information Science and Technology, Department of Elect, China
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16
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Guo B, Lei C, Wu Y, Kobayashi H, Ito T, Yalikun Y, Lee S, Isozaki A, Li M, Jiang Y, Yasumoto A, Di Carlo D, Tanaka Y, Yatomi Y, Ozeki Y, Goda K. Optofluidic time-stretch quantitative phase microscopy. Methods 2017; 136:116-125. [PMID: 29031836 DOI: 10.1016/j.ymeth.2017.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 11/18/2022] Open
Abstract
Innovations in optical microscopy have opened new windows onto scientific research, industrial quality control, and medical practice over the last few decades. One of such innovations is optofluidic time-stretch quantitative phase microscopy - an emerging method for high-throughput quantitative phase imaging that builds on the interference between temporally stretched signal and reference pulses by using dispersive properties of light in both spatial and temporal domains in an interferometric configuration on a microfluidic platform. It achieves the continuous acquisition of both intensity and phase images with a high throughput of more than 10,000 particles or cells per second by overcoming speed limitations that exist in conventional quantitative phase imaging methods. Applications enabled by such capabilities are versatile and include characterization of cancer cells and microalgal cultures. In this paper, we review the principles and applications of optofluidic time-stretch quantitative phase microscopy and discuss its future perspective.
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Affiliation(s)
- Baoshan Guo
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Cheng Lei
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan.
| | - Yi Wu
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | | | - Takuro Ito
- Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Yaxiaer Yalikun
- Laboratory for Integrated Biodevices, Quantitative Biology Center, RIKEN, Osaka 565-0871, Japan
| | - Sangwook Lee
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Akihiro Isozaki
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Ming Li
- Department of Bioengineering, Mechanical Engineering, and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Yiyue Jiang
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan
| | - Atsushi Yasumoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, 113-8655, Japan
| | - Dino Di Carlo
- Department of Bioengineering, Mechanical Engineering, and California NanoSystems Institute, University of California, Los Angeles, CA 90095, USA
| | - Yo Tanaka
- Laboratory for Integrated Biodevices, Quantitative Biology Center, RIKEN, Osaka 565-0871, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, 113-8655, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, University of Tokyo, Tokyo 113-8656, Japan
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo 113-0033, Japan; Japan Science and Technology Agency, Kawaguchi 332-0012, Japan; Department of Electrical Engineering, University of California, Los Angeles, CA 90095, USA.
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17
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Guo B, Lei C, Kobayashi H, Ito T, Yalikun Y, Jiang Y, Tanaka Y, Ozeki Y, Goda K. High-throughput, label-free, single-cell, microalgal lipid screening by machine-learning-equipped optofluidic time-stretch quantitative phase microscopy. Cytometry A 2017; 91:494-502. [PMID: 28399328 DOI: 10.1002/cyto.a.23084] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/19/2017] [Accepted: 01/23/2017] [Indexed: 12/16/2022]
Abstract
The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO2 via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner. Here high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy was demonstrated. In particular, Euglena gracilis, an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement), within lipid droplets was investigated. The optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch quantitative phase microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase maps of every single cell at a high throughput of 10,000 cells/s, enabling accurate cell classification without the need for fluorescent staining. Specifically, the dataset was used to characterize heterogeneous populations of E. gracilis cells under two different culture conditions (nitrogen-sufficient and nitrogen-deficient) and achieve the cell classification with an error rate of only 2.15%. The method holds promise as an effective analytical tool for microalgae-based biofuel production. © 2017 International Society for Advancement of Cytometry.
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Affiliation(s)
- Baoshan Guo
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan
| | - Cheng Lei
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.,Department of Electronic Engineering, Tsinghua University, Beijing, 100084, China
| | | | - Takuro Ito
- Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan
| | - Yaxiaer Yalikun
- Laboratory for Integrated Biodevices, Quantitative Biology Center, RIKEN, Osaka, 565-0871, Japan
| | - Yiyue Jiang
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevices, Quantitative Biology Center, RIKEN, Osaka, 565-0871, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, University of Tokyo, Tokyo, 113-8656, Japan
| | - Keisuke Goda
- Department of Chemistry, University of Tokyo, Tokyo, 113-0033, Japan.,Japan Science and Technology Agency, Kawaguchi, 332-0012, Japan.,Department of Electrical Engineering, University of California, Los Angeles, California, 90095
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