1
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Cong L, Guo X, Wang J, Meng F, Zhao J, Xu W, Shi W, Liang C, Shi Z, Xu S. In-droplet multiplex immunoassays for hypoxia-induced single-cell cytokines. Talanta 2024; 278:126548. [PMID: 39008932 DOI: 10.1016/j.talanta.2024.126548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/21/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Abstract
Cytokine expression is an important biomarker in understanding hypoxia microenvironments in tumor growth and metastasis. In-droplet-based immunoassays performed above the target cell membrane were employed to track the cytokines of single cells with the aid of three types of immuno-nanoprobes (one capture nanoprobe and two reporter nanoprobes). Single cells and nanoprobes were co-packaged in water-in-oil microdroplets (about 100 μm in diameter) using a cross-shaped microfluidic chip. In each droplet, capture nanoprobes would be first fixed to the cell surface by linking to membrane proteins that have been streptavidinized. Then, the capture nanoprobes can collect cell-secreted cytokines (VEGF and IL-8) by the antibodies, followed by two reporter nanoprobes that emit distinguishable fluorescence. Fluorescence imaging was utilized to record the signal outputs of two reporter probes, which reflect cytokine expressions secreted by a single tumor cell. The cytokine levels at different degrees of hypoxia induction were assessed. Multiple chemometric methods were adopted to distinguish differences in the secretion of two cytokines and the results demonstrated a positive correlation. This study developed an in-droplet, dual-target, simultaneous biosensing strategy for a single cell, which is helpful for understanding the impacts of hypoxia microenvironments on cell cytokines that are vital for assessing early cancer diagnosis and prognosis.
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Affiliation(s)
- Lili Cong
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Xiaolei Guo
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Jiaqi Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Fanxiang Meng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Junyi Zhao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Weiqing Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China; Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Wei Shi
- Key Lab for Molecular Enzymology & Engineering of Ministry of Education, Jilin University, Changchun, 130012, PR China
| | - Chongyang Liang
- Institute of Frontier Medical Science, Jilin University, Changchun, 130021, PR China
| | - Zhan Shi
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Shuping Xu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China; Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130012, PR China; Center for Supramolecular Chemical Biology, College of Chemistry, Jilin University, Changchun, 130012, PR China.
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2
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Su Y, Zhou L. Review of single-molecule immunoassays: Non-chip and on-chip Assays. Anal Chim Acta 2024; 1322:342885. [PMID: 39182983 DOI: 10.1016/j.aca.2024.342885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 06/17/2024] [Accepted: 06/17/2024] [Indexed: 08/27/2024]
Abstract
Enhancing the sensitivity of immunoassays is an important requirement in the field of immunology, especially in light of rapid developments in genetic testing, making the detection of low-abundance protein biomarkers crucial. Therefore, innovations in highly sensitive immunoassays are imperative. This demand has led to the emergence of single-molecule immunoassays (SMIs), driving advancements in early diagnostic techniques, and ushering in a new era of immunoassays. This review begins by tracing the development of immunoassays and offers a detailed discussion of SMI technology across two distinct pathways: non-chip (SMI without microfluidic chips) and on-chip (SMI with microfluidic chips). Furthermore, we evaluated and compared these methods using two pathways. In addition, this review discusses the significance of SMI techniques in the diagnosis of various diseases and their current applications in laboratory and clinical settings. The progress of SMI in commercial applications and suggestions for innovative directions are also summarized. Despite the considerable potential of SMI, these technologies face challenges in practical application, particularly in developing countries and economically disadvantaged regions. The final section of this review addresses the challenges and prospects of these technologies.
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Affiliation(s)
- Yan Su
- State Key Laboratory of Biochemical Engineering, PLA Key Laboratory of Biopharmaceutical Production & Formulation Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China
| | - Lei Zhou
- State Key Laboratory of Biochemical Engineering, PLA Key Laboratory of Biopharmaceutical Production & Formulation Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China; Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Innovation Academy for Green Manufacture Institute, Chinese Academy of Sciences, Beijing, 100190, China; Biosafety Research Center Yangtze River Delta in Zhangjiagang, Suzhou, 215611, China.
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3
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Malik L, Nandy S, Satpathi NS, Ghosh D, Laurell T, Sen AK. Ultrasound reforms droplets. LAB ON A CHIP 2024. [PMID: 39225030 DOI: 10.1039/d4lc00507d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Size-controlled monodisperse droplets are indispensable in food, cosmetics, and healthcare industries. Although emulsion formation from bulk phases is well-explored, a robust in situ method to continuously reform existing emulsions is unavailable. Remarkably, we introduce a continuous flow acousto-microfluidics technique which enables simultaneous trapping-coalescence-splitting of droplets to reform an existing polydisperse emulsion into size-controlled droplets with improved monodispersity. In contrast to conventional approaches, our platform enables controlling droplet characteristics in situ by regulating acoustic power without altering hydrodynamical parameters thereby improving response time and facilitates continuous nozzle-less clogging-free droplet generation from a liquid plug in a chamber instead of from a liquid stream at a narrow junction. The technique can process polydisperse droplets produced not only due to fluid-source fluctuations or unstable jetting regime but also externally by non-microfluidic or inexpensive setups. Our theoretical scaling suggests that the sum of capillary (Ca) and acousto-capillary (Caa) numbers ∼ (1), and predicts the generated droplet size, both agreeing well with the experimental findings. We identify acousto-visco-capillary number, Caav = (Ca Caa)1/2, which governs the generated droplet size. We also explore and characterize acoustic streaming- and coalescence-based mixing of samples inside the trapped plug. Distinctively, our platform is amenable to continuous mixing of inhomogeneous droplets, offering monodisperse mixed-sample droplets, and holds the potential to match current throughput standards through suitable design modifications.
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Affiliation(s)
- Lokesh Malik
- Micro Nano Bio Fluidics Unit, Department of Mechanical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India.
| | - Subhas Nandy
- Micro Nano Bio Fluidics Unit, Department of Mechanical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India.
| | - Niladri Sekhar Satpathi
- Micro Nano Bio Fluidics Unit, Department of Mechanical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India.
| | - Debasish Ghosh
- Micro Nano Bio Fluidics Unit, Department of Mechanical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India.
| | - Thomas Laurell
- Division of Nanobiotechnology, Department of Biomedical Engineering, Lund University, Lund, Sweden
| | - Ashis Kumar Sen
- Micro Nano Bio Fluidics Unit, Department of Mechanical Engineering, Indian Institute of Technology (IIT) Madras, Chennai, Tamil Nadu, India.
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4
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Wu S, Morotti ALM, Yang J, Wang E, Tatsis EC. Single-cell RNA sequencing facilitates the elucidation of the complete biosynthesis of the antidepressant hyperforin in St. John's wort. MOLECULAR PLANT 2024; 17:1439-1457. [PMID: 39135343 DOI: 10.1016/j.molp.2024.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 08/27/2024]
Abstract
Hyperforin is the compound responsible for the effectiveness of St. John's wort (Hypericum perforatum) as an antidepressant, but its complete biosynthetic pathway remains unknown. Gene discovery based on co-expression analysis of bulk RNA-sequencing data or genome mining failed to discover the missing steps in hyperforin biosynthesis. In this study, we sequenced the 1.54-Gb tetraploid H. perforatum genome assembled into 32 chromosomes with the scaffold N50 value of 42.44 Mb. By single-cell RNA sequencing, we identified a type of cell, "Hyper cells", wherein hyperforin biosynthesis de novo takes place in both the leaves and flowers. Through pathway reconstitution in yeast and tobacco, we identified and characterized four transmembrane prenyltransferases (HpPT1-4) that are localized at the plastid envelope and complete the hyperforin biosynthetic pathway. The hyperforin polycyclic scaffold is created by a reaction cascade involving an irregular isoprenoid coupling and a tandem cyclization. Our findings reveal how and where hyperforin is biosynthesized, enabling synthetic-biology reconstitution of the complete pathway. Thus, this study not only deepens our comprehension of specialized metabolism at the cellular level but also provides strategic guidance for elucidation of the biosynthetic pathways of other specializied metabolites in plants.
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Affiliation(s)
- Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jun Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Evangelos C Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Science, Shanghai 200032, China.
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5
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Dortaj H, Amani AM, Tayebi L, Azarpira N, Ghasemi Toudeshkchouei M, Hassanpour-Dehnavi A, Karami N, Abbasi M, Najafian-Najafabadi A, Zarei Behjani Z, Vaez A. Droplet-based microfluidics: an efficient high-throughput portable system for cell encapsulation. J Microencapsul 2024; 41:479-501. [PMID: 39077800 DOI: 10.1080/02652048.2024.2382744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 07/17/2024] [Indexed: 07/31/2024]
Abstract
One of the goals of tissue engineering and regenerative medicine is restoring primary living tissue function by manufacturing a 3D microenvironment. One of the main challenges is protecting implanted non-autologous cells or tissues from the host immune system. Cell encapsulation has emerged as a promising technique for this purpose. It involves entrapping cells in biocompatible and semi-permeable microcarriers made from natural or synthetic polymers that regulate the release of cellular secretions. In recent years, droplet-based microfluidic systems have emerged as powerful tools for cell encapsulation in tissue engineering and regenerative medicine. These systems offer precise control over droplet size, composition, and functionality, allowing for creating of microenvironments that closely mimic native tissue. Droplet-based microfluidic systems have extensive applications in biotechnology, medical diagnosis, and drug discovery. This review summarises the recent developments in droplet-based microfluidic systems and cell encapsulation techniques, as well as their applications, advantages, and challenges in biology and medicine. The integration of these technologies has the potential to revolutionise tissue engineering and regenerative medicine by providing a precise and controlled microenvironment for cell growth and differentiation. By overcoming the immune system's challenges and enabling the release of cellular secretions, these technologies hold great promise for the future of regenerative medicine.
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Affiliation(s)
- Hengameh Dortaj
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, USA
| | - Negar Azarpira
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Ashraf Hassanpour-Dehnavi
- Tissue Engineering Lab, Department of Anatomical Sciences, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Karami
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Atefeh Najafian-Najafabadi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Zarei Behjani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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6
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Tian Z, Wang X, Chen J. On-chip dielectrophoretic single-cell manipulation. MICROSYSTEMS & NANOENGINEERING 2024; 10:117. [PMID: 39187499 PMCID: PMC11347631 DOI: 10.1038/s41378-024-00750-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/07/2024] [Accepted: 07/07/2024] [Indexed: 08/28/2024]
Abstract
Bioanalysis at a single-cell level has yielded unparalleled insight into the heterogeneity of complex biological samples. Combined with Lab-on-a-Chip concepts, various simultaneous and high-frequency techniques and microfluidic platforms have led to the development of high-throughput platforms for single-cell analysis. Dielectrophoresis (DEP), an electrical approach based on the dielectric property of target cells, makes it possible to efficiently manipulate individual cells without labeling. This review focusses on the engineering designs of recent advanced microfluidic designs that utilize DEP techniques for multiple single-cell analyses. On-chip DEP is primarily effectuated by the induced dipole of dielectric particles, (i.e., cells) in a non-uniform electric field. In addition to simply capturing and releasing particles, DEP can also aid in more complex manipulations, such as rotation and moving along arbitrary predefined routes for numerous applications. Correspondingly, DEP electrodes can be designed with different patterns to achieve different geometric boundaries of the electric fields. Since many single-cell analyses require isolation and compartmentalization of individual cells, specific microstructures can also be incorporated into DEP devices. This article discusses common electrical and physical designs of single-cell DEP microfluidic devices as well as different categories of electrodes and microstructures. In addition, an up-to-date summary of achievements and challenges in current designs, together with prospects for future design direction, is provided.
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Affiliation(s)
- Zuyuan Tian
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada
| | - Xihua Wang
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada
| | - Jie Chen
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, AB, T6G 1H9, Canada.
- Academy for Engineering & Technology, Fudan University, Shanghai, 200433, China.
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7
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Han J, Zhang H, Li Y, Huang C, Guzman AR, Han A. High-Efficiency Interdigitated Electrode-Based Droplet Merger for Enabling Error-Free Droplet Microfluidic Systems. Anal Chem 2024; 96. [PMID: 39146475 PMCID: PMC11359384 DOI: 10.1021/acs.analchem.4c02376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/07/2024] [Accepted: 08/08/2024] [Indexed: 08/17/2024]
Abstract
Merging two droplets into a droplet to add and mix two contents is one of the common droplet microfluidic functions with droplet generation and sorting, performing broad ranges of biological and chemical assays in droplets. However, traditional droplet-merging techniques often encounter unsynchronized droplets, causing overmerging or mis-merging, and unwanted merging outside of the desired zone. This is more severe when the incoming droplets to be merged are polydisperse in their sizes, often observed in assays that require long-term incubation, elevated-temperature, and/or multiple droplet processing steps. Here, we developed an interdigitated electrode (IDE)-based droplet merger consisting of a droplet autosynchronizing channel and a merging channel. The autosynchronizing channel provides >95% merging efficiency even when 20% polydispersity in the droplet size exists. The highly localized and enhanced dielectrophoretic force generated by the IDEs on the channel bottom allows droplet merging at an extremely low voltage (4.5 V) and only locally at the IDE region. A systematic evaluation of how various design and operation parameters of the IDE merger, such as IDE finger dimensions, dielectric coating layer thickness, droplet size, and droplet flow speed impact the performance was conducted. The optimized device showed consistent performance even when operating for up to 100 h consecutively at high throughput (100 droplets/s). The presented technology has been integrated into a droplet microfluidics workflow to test the lytic activities of bacteriophage on bacterial host cells with 100% merging efficiency. We expect this function to be integrated into droplet microfluidic systems performing broad ranges of high-throughput chemical and biological assays.
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Affiliation(s)
- Jeong
Jae Han
- Department
of Multidisciplinary Engineering, Texas
A&M University, College Station, Texas 77843, United States
| | - Han Zhang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Yuwen Li
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Can Huang
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Adrian R. Guzman
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
| | - Arum Han
- Department
of Electrical and Computer Engineering, Texas A&M University, College
Station, Texas 77843, United States
- Department
of Biomedical Engineering, Texas A&M
University, College Station, Texas 77843, United States
- Department
of Chemical Engineering, Texas A&M University, College Station, Texas 77843, United States
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8
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Yu MC, Sun YS. A Droplet-Based Microfluidic Platform for High-Throughput Culturing of Yeast Cells in Various Conditions. MICROMACHINES 2024; 15:1034. [PMID: 39203685 PMCID: PMC11356446 DOI: 10.3390/mi15081034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024]
Abstract
Yeast plays a significant role in a variety of fields. In particular, it is extensively used as a model organism in genetics and cellular biology studies, and is employed in the production of vaccines, pharmaceuticals, and biofuels. Traditional "bulk"-based studies on yeast growth often overlook cellular variability, emphasizing the need for single-cell analysis. Micro-droplets, tiny liquid droplets with high surface-area-to-volume ratios, offer a promising platform for investigating single or a small number of cells, allowing precise control and monitoring of individual cell behaviors. Microfluidic devices, which facilitate the generation of micro-droplets, are advantageous due to their reduced volume requirements and ability to mimic in vivo micro-environments. This study introduces a custom-designed microfluidic device to encapsulate yeasts in micro-droplets under various conditions in a parallel manner. The results reveal that optimal glucose concentrations promoted yeast growth while cycloheximide and Cu2+ ions inhibited it. This platform enhances yeast cultivation strategies and holds potential for high-throughput single-cell investigations in more complex organisms.
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Affiliation(s)
| | - Yung-Shin Sun
- Department of Physics, Fu-Jen Catholic University, New Taipei City 24205, Taiwan;
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9
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Fischer K, Lulla A, So TY, Pereyra-Gerber P, Raybould MIJ, Kohler TN, Yam-Puc JC, Kaminski TS, Hughes R, Pyeatt GL, Leiss-Maier F, Brear P, Matheson NJ, Deane CM, Hyvönen M, Thaventhiran JED, Hollfelder F. Rapid discovery of monoclonal antibodies by microfluidics-enabled FACS of single pathogen-specific antibody-secreting cells. Nat Biotechnol 2024:10.1038/s41587-024-02346-5. [PMID: 39143416 DOI: 10.1038/s41587-024-02346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/27/2024] [Indexed: 08/16/2024]
Abstract
Monoclonal antibodies are increasingly used to prevent and treat viral infections and are pivotal in pandemic response efforts. Antibody-secreting cells (ASCs; plasma cells and plasmablasts) are an excellent source of high-affinity antibodies with therapeutic potential. Current methods to study antigen-specific ASCs either have low throughput, require expensive and labor-intensive screening or are technically demanding and therefore not widely accessible. Here we present a straightforward technology for the rapid discovery of monoclonal antibodies from ASCs. Our approach combines microfluidic encapsulation of single cells into an antibody capture hydrogel with antigen bait sorting by conventional flow cytometry. With our technology, we screened millions of mouse and human ASCs and obtained monoclonal antibodies against severe acute respiratory syndrome coronavirus 2 with high affinity (<1 pM) and neutralizing capacity (<100 ng ml-1) in 2 weeks with a high hit rate (>85% of characterized antibodies bound the target). By facilitating access to the underexplored ASC compartment, the approach enables efficient antibody discovery and immunological studies into the generation of protective antibodies.
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Affiliation(s)
- Katrin Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tsz Y So
- MRC Toxicology Unit, Gleeson Building, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Robert Hughes
- MRC Toxicology Unit, Gleeson Building, Cambridge, UK
| | | | | | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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10
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Hulme JP. Emerging Diagnostics in Clostridioides difficile Infection. Int J Mol Sci 2024; 25:8672. [PMID: 39201359 PMCID: PMC11354687 DOI: 10.3390/ijms25168672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 09/02/2024] Open
Abstract
Clostridioides difficile detection in community settings is time-intensive, resulting in delays in diagnosing and quarantining infected individuals. However, with the advent of semi-automated devices and improved algorithms in recent decades, the ability to discern CDI infection from asymptomatic carriage has significantly improved. This, in turn, has led to efficiently regulated monitoring systems, further reducing endemic risk, with recent concerns regarding a possible surge in hospital-acquired Clostridioides difficile infections post-COVID failing to materialize. This review highlights established and emerging technologies used to detect community-acquired Clostridioides difficile in research and clinical settings.
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Affiliation(s)
- John P Hulme
- Department of Bio-Nano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
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11
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Welch LG, Estranero J, Tourlomousis P, Wootton RCR, Radu V, González-Fernández C, Puchtler TJ, Murzeau CM, Dieckmann NMG, Shibahara A, Longbottom BW, Bryant CE, Talbot EL. A programmable and automated optical electrowetting-on-dielectric (oEWOD) driven platform for massively parallel and sequential processing of single cell assay operations. LAB ON A CHIP 2024; 24:3763-3774. [PMID: 39037291 DOI: 10.1039/d4lc00245h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Recently, there has been an increasing emphasis on single cell profiling for high-throughput screening workflows in drug discovery and life sciences research. However, the biology underpinning these screens is often complex and is insufficiently addressed by singleplex assay screens. Traditional single cell screening technologies have created powerful sets of 'omic data that allow users to bioinformatically infer biological function, but have as of yet not empowered direct functional analysis at the level of each individual cell. Consequently, screening campaigns often require multiple secondary screens leading to laborious, time-consuming and expensive workflows in which attrition points may not be queried until late in the process. We describe a platform that harnesses droplet microfluidics and optical electrowetting-on-dielectric (oEWOD) to perform highly-controlled sequential and multiplexed single cell assays in massively parallelised workflows to enable complex cell profiling during screening. Soluble reagents or objects, such as cells or assay beads, are encapsulated into droplets of media in fluorous oil and are actively filtered based on size and optical features ensuring only desirable droplets (e.g. single cell droplets) are retained for analysis, thereby overcoming the Poisson probability distribution. Droplets are stored in an array on a temperature-controlled chip and the history of individual droplets is logged from the point of filter until completion of the workflow. On chip, droplets are subject to an automated and flexible suite of operations including the merging of sample droplets and the fluorescent acquisition of assay readouts to enable complex sequential assay workflows. To demonstrate the broad utility of the platform, we present examples of single-cell functional workflows for various applications such as antibody discovery, infectious disease, and cell and gene therapy.
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Affiliation(s)
- Lawrence G Welch
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Jasper Estranero
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | | | - Robert C R Wootton
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Valentin Radu
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | | | - Tim J Puchtler
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Claire M Murzeau
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Nele M G Dieckmann
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Aya Shibahara
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Brooke W Longbottom
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
| | - Clare E Bryant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Emma L Talbot
- Lightcast Discovery Ltd, Broers Building, 21 JJ Thomson Avenue, Cambridge, CB3 0FA, UK.
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12
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Cheng YC, Zhang Y, Tripathi S, Harshavardhan BV, Jolly MK, Schiebinger G, Levine H, McDonald TO, Michor F. Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition. Proc Natl Acad Sci U S A 2024; 121:e2406842121. [PMID: 39093947 PMCID: PMC11317558 DOI: 10.1073/pnas.2406842121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
Exploring the complexity of the epithelial-to-mesenchymal transition (EMT) unveils a diversity of potential cell fates; however, the exact timing and mechanisms by which early cell states diverge into distinct EMT trajectories remain unclear. Studying these EMT trajectories through single-cell RNA sequencing is challenging due to the necessity of sacrificing cells for each measurement. In this study, we employed optimal-transport analysis to reconstruct the past trajectories of different cell fates during TGF-beta-induced EMT in the MCF10A cell line. Our analysis revealed three distinct trajectories leading to low EMT, partial EMT, and high EMT states. Cells along the partial EMT trajectory showed substantial variations in the EMT signature and exhibited pronounced stemness. Throughout this EMT trajectory, we observed a consistent downregulation of the EED and EZH2 genes. This finding was validated by recent inhibitor screens of EMT regulators and CRISPR screen studies. Moreover, we applied our analysis of early-phase differential gene expression to gene sets associated with stemness and proliferation, pinpointing ITGB4, LAMA3, and LAMB3 as genes differentially expressed in the initial stages of the partial versus high EMT trajectories. We also found that CENPF, CKS1B, and MKI67 showed significant upregulation in the high EMT trajectory. While the first group of genes aligns with findings from previous studies, our work uniquely pinpoints the precise timing of these upregulations. Finally, the identification of the latter group of genes sheds light on potential cell cycle targets for modulating EMT trajectories.
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Affiliation(s)
- Yu-Chen Cheng
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Yun Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100021, China
| | - Shubham Tripathi
- Yale Center for Systems and Engineering Immunology and Department of Immunobiology, Yale School of Medicine, New Haven, CT06510
| | - B. V. Harshavardhan
- Interdisciplinary Mathematics Initiative, Indian Institute of Science, Bangalore560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore560012, India
| | - Geoffrey Schiebinger
- Department of Mathematics, University of British Columbia, Vancouver, BCV6T 1Z2, Canada
| | - Herbert Levine
- Center for Theoretical Biological Physics, Northeastern University, Boston, MA02115
- Department of Physics, Northeastern University, Boston, MA02115
| | - Thomas O. McDonald
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
| | - Franziska Michor
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA02215
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA02138
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA02138
- The Ludwig Center at Harvard, Boston, MA02115
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13
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Cowell TW, Jing W, Noh H, Han HS. Drop-by-Drop Addition of Reagents to a Double Emulsion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404121. [PMID: 39101620 DOI: 10.1002/smll.202404121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/08/2024] [Indexed: 08/06/2024]
Abstract
Developments in droplet microfluidics have facilitated an era of high-throughput, sensitive single-cell, or single-molecule measurements capable of tackling the heterogeneity present in biological systems. Relying on single emulsion (SE) compartments, droplet assays achieve absolute quantification of nucleic acids, massively parallel single-cell profiling, and more. Double emulsions (DEs) have seen recent interest for their potential to build upon SE techniques. DEs are compatible with flow cytometry enabling high-throughput multi-parameter drop screening and eliminate content mixing due to coalescence during lengthy workflows. Despite these strengths, DEs lack important technical functions that exist in SEs such as methods for adding reagents to droplets on demand. Consequently, DEs cannot be used for multistep workflows which has limited their adoption in assay development. Here, strategies to enable reagent addition and other active manipulations on DEs are reported by converting DE inputs to SEs on chip. After conversion, drops are manipulated using existing SE techniques, including reagent addition, before reforming a DE at the outlet. Device designs and operation conditions achieving drop-by-drop reagent addition to DEs are identified and used as part of a multi-step aptamer screening assay performed entirely in DE drops. This work enables the further development of multistep DE droplet assays.
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Affiliation(s)
- Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Matthews Ave, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, 61801, USA
| | - Wenyang Jing
- Department of Biophysics, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
| | - Heewon Noh
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Matthews Ave, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Matthews Ave, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, IL, 61801, USA
- Department of Biophysics, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Matthews Ave, Urbana, IL, 61801, USA
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14
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Xu J, Liu S, Ai Y, Zhang Y, Li S, Li Y. Establishment and transcriptome analysis of single blastomere-derived cell lines from zebrafish. J Genet Genomics 2024:S1673-8527(24)00196-6. [PMID: 39097227 DOI: 10.1016/j.jgg.2024.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/29/2024] [Accepted: 07/29/2024] [Indexed: 08/05/2024]
Abstract
Maintaining chromosome euploidy in zebrafish embryonic cells is challenging because of the degradation of genomic integrity during cell passaging. In this study, we report the derivation of zebrafish cell lines from single blastomeres. These cell lines have a stable chromosome status attributed to BMP4 and exhibit continuous proliferation in vitro. Twenty zebrafish cell lines are successfully established from single blastomeres. Single-cell transcriptome sequencing analysis confirms the fidelity of gene expression profiles throughout long-term culturing of at least 45 passages. The long-term cultured cells are specialized into epithelial cells, exhibiting similar expression patterns validated by integrative transcriptomic analysis. Overall, this work provides a protocol for establishing zebrafish cell lines from single blastomeres, which can serve as valuable tools for in vitro investigations of epithelial cell dynamics in terms of life-death balance and cell fate determination during normal homeostasis.
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Affiliation(s)
- Jia Xu
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Siqi Liu
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yirui Ai
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunbin Zhang
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shifeng Li
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yiping Li
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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15
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Cremaschini S, Torriero N, Maceri C, Poles M, Cleve S, Crestani B, Meggiolaro A, Pierno M, Mistura G, Brun P, Ferraro D. Magnetic Stirring Device for Limiting the Sedimentation of Cells inside Microfluidic Devices. SENSORS (BASEL, SWITZERLAND) 2024; 24:5014. [PMID: 39124061 PMCID: PMC11314744 DOI: 10.3390/s24155014] [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: 06/28/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
In experiments considering cell handling in microchannels, cell sedimentation in the storage container is a key problem because it affects the reproducibility of the experiments. Here, a simple and low-cost cell mixing device (CMD) is presented; the device is designed to prevent the sedimentation of cells in a syringe during their injection into a microfluidic channel. The CMD is based on a slider crank device made of 3D-printed parts that, combined with a permanent magnet, actuate a stir bar placed into the syringe containing the cells. By using A549 cell lines, the device is characterized in terms of cell viability (higher than 95%) in different mixing conditions, by varying the oscillation frequency and the overall mixing time. Then, a dedicated microfluidic experiment is designed to evaluate the injection frequency of the cells within a microfluidic chip. In the presence of the CMD, a higher number of cells are injected into the microfluidic chip with respect to the static conditions (2.5 times), proving that it contrasts cell sedimentation and allows accurate cell handling. For these reasons, the CMD can be useful in microfluidic experiments involving single-cell analysis.
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Affiliation(s)
| | - Noemi Torriero
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Chiara Maceri
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Maria Poles
- Department of Medicine, University of Verona, 37124 Verona, Italy
| | - Sarah Cleve
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Beatrice Crestani
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Alessio Meggiolaro
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Matteo Pierno
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Giampaolo Mistura
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, 35121 Padua, Italy
| | - Davide Ferraro
- Department of Physics and Astronomy, University of Padua, 35131 Padua, Italy
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16
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Xu B, Liu LH, Lai S, Chen J, Wu S, Lei W, Lin H, Zhang Y, Hu Y, He J, Chen X, He Q, Yang M, Wang H, Zhao X, Wang M, Luo H, Ge Q, Gao H, Xia J, Cao Z, Zhang B, Jiang A, Wu YR. Directed Evolution of Escherichia coli Nissle 1917 to Utilize Allulose as Sole Carbon Source. SMALL METHODS 2024; 8:e2301385. [PMID: 38415955 DOI: 10.1002/smtd.202301385] [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: 10/11/2023] [Revised: 02/19/2024] [Indexed: 02/29/2024]
Abstract
Sugar substitutes are popular due to their akin taste and low calories. However, excessive use of aspartame and erythritol can have varying effects. While D-allulose is presently deemed a secure alternative to sugar, its excessive consumption is not devoid of cellular stress implications. In this study, the evolution of Escherichia coli Nissle 1917 (EcN) is directed to utilize allulose as sole carbon source through a combination of adaptive laboratory evolution (ALE) and fluorescence-activated droplet sorting (FADS) techniques. Employing whole genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats interference (CRISPRi) in conjunction with compensatory expression displayed those genetic mutations in sugar and amino acid metabolic pathways, including glnP, glpF, gmpA, nagE, pgmB, ybaN, etc., increased allulose assimilation. Enzyme-substrate dynamics simulations and deep learning predict enhanced substrate specificity and catalytic efficiency in nagE A247E and pgmB G12R mutants. The findings evince that these mutations hold considerable promise in enhancing allulose uptake and facilitating its conversion into glycolysis, thus signifying the emergence of a novel metabolic pathway for allulose utilization. These revelations bear immense potential for the sustainable utilization of D-allulose in promoting health and well-being.
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Affiliation(s)
- Bo Xu
- School of Basic Medical Sciences, Hubei University of Science and Technology, Xianning, 437100, P. R. China
| | - Li-Hua Liu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, P. R. China
| | - Shijing Lai
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Jingjing Chen
- Yeasen Biotechnology (Shanghai) Co., Ltd, Shanghai, 200000, P. R. China
| | - Song Wu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Wei Lei
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Houliang Lin
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Yu Zhang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Yucheng Hu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Jingtao He
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Xipeng Chen
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Qian He
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Min Yang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Haimei Wang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Xuemei Zhao
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Man Wang
- Yeasen Biotechnology (Shanghai) Co., Ltd, Shanghai, 200000, P. R. China
| | - Haodong Luo
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
- Biology Department and Institute of Marine Sciences, College of Science, Shantou University, Shantou, 515063, P. R. China
| | - Qijun Ge
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Huamei Gao
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Jiaqi Xia
- School of Basic Medicine, Jiamusi University, Jiamusi, 154000, P. R. China
| | - Zhen Cao
- Yeasen Biotechnology (Shanghai) Co., Ltd, Shanghai, 200000, P. R. China
| | - Baoxun Zhang
- College of Chemistry and Chemical Engineering, Southwest University, Chongqing, 400715, P. R. China
| | - Ao Jiang
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
| | - Yi-Rui Wu
- Tidetron Bioworks Technology (Guangzhou) Co., Ltd., Guangzhou Qianxiang Bioworks Co., Ltd, Guangzhou, Guangdong, 510000, P. R. China
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17
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Wippold JA, Chu M, Renberg R, Li Y, Adams B, Han A. XPORT ENTRAP: A droplet microfluidic platform for enhanced DNA transfer between microbial species. N Biotechnol 2024; 81:10-19. [PMID: 38408724 DOI: 10.1016/j.nbt.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/20/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
A significant hurdle for the widespread implementation and use of synthetic biology is the challenge of highly efficient introduction of DNA into microorganisms. This is especially a barrier for the utilization of non-model organisms and/or novel chassis species for a variety of applications, ranging from molecular biology to biotechnology and biomanufacturing applications. Common approaches to episomal and chromosomal gene editing, which employ techniques such as chemical competence and electroporation, are typically only amenable to a small subset of microbial species while leaving the vast majority of microorganisms in nature genetically inaccessible. To address this challenge, we have employed the previously described B. subtilis broad-host conjugation strain, XPORT, which was modularly designed for loading DNA cargo and conjugating such DNA into recalcitrant microbes. In this current work, we have leveraged and adapted the XPORT strain for use in a droplet microfluidic platform to enable increased efficiency of conjugation-based DNA transfer. The system named DNA ENTRAP (DNA ENhanced TRAnsfer Platform) utilizes cell-encapsulated water-in-oil emulsion droplets as pico-liter-volume bioreactors that allows controlled contacts between the donor and receiver cells within the emulsion bioreactor. This allowed enhanced XPORT-mediated genetic transfer over the current benchtop XPORT process, demonstrated using two different Bacillus subtilis strains (donor and receiver), as well as increased throughput (e.g., number of successfully conjugated cells) due to the automated assay steps inherent to microfluidic lab-on-a-chip systems. DNA ENTRAP paves the way for a streamlined automation of culturing and XPORT-mediated genetic transfer processes as well as future high-throughput cell engineering and screening applications.
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Affiliation(s)
- Jose A Wippold
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA
| | - Monica Chu
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA
| | - Rebecca Renberg
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA
| | - Yuwen Li
- Department of Electrical and Computer Engineering, USA
| | - Bryn Adams
- United States Combat Capabilities Development Command Army Research Laboratory - DEVCOM ARL, Adelphi, MD, USA.
| | - Arum Han
- Department of Electrical and Computer Engineering, USA; Department of Biomedical Engineering, USA; Department of Chemical Engineering, Texas A&M University, College Station, TX, USA.
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18
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Chen HC, Ma Y, Cheng J, Chen YC. Advances in Single-Cell Techniques for Linking Phenotypes to Genotypes. CANCER HETEROGENEITY AND PLASTICITY 2024; 1:0004. [PMID: 39156821 PMCID: PMC11328949 DOI: 10.47248/chp2401010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Single-cell analysis has become an essential tool in modern biological research, providing unprecedented insights into cellular behavior and heterogeneity. By examining individual cells, this approach surpasses conventional population-based methods, revealing critical variations in cellular states, responses to environmental cues, and molecular signatures. In the context of cancer, with its diverse cell populations, single-cell analysis is critical for investigating tumor evolution, metastasis, and therapy resistance. Understanding the phenotype-genotype relationship at the single-cell level is crucial for deciphering the molecular mechanisms driving tumor development and progression. This review highlights innovative strategies for selective cell isolation based on desired phenotypes, including robotic aspiration, laser detachment, microraft arrays, optical traps, and droplet-based microfluidic systems. These advanced tools facilitate high-throughput single-cell phenotypic analysis and sorting, enabling the identification and characterization of specific cell subsets, thereby advancing therapeutic innovations in cancer and other diseases.
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Affiliation(s)
- Hsiao-Chun Chen
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
| | - Yushu Ma
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
| | - Jinxiong Cheng
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, USA
| | - Yu-Chih Chen
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, USA
- CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
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19
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Li Z, Wang Q, Niu Y, Wang R, Zhao W, Zhang C, Wang G, Wang K. Dynamic behavior of DNA molecules in microchannels: exploring deflective, elliptical, and spin motions induced by Saffman and Magnus forces. LAB ON A CHIP 2024; 24:3704-3717. [PMID: 38953215 DOI: 10.1039/d4lc00140k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Precise manipulation of individual DNA molecules entering and leaving the channel ports, as well as their smooth passage across the channel, is essential for the detection and screening of DNA molecules using nano-/micro-fluidic technologies. In this paper, by combining single-molecule fluorescence imaging and numerical simulations, the motion states of DNA molecules translocating through a microfluidic channel under the action of the applied electric field are monitored and analyzed in detail. It is found that, under certain conditions of the applied electric field DNA molecules exhibit various motion states, including translation crossing, deflection outflow, reverse outflow, reciprocal movement, and elliptical movement. Simulations indicate that, under the action of Saffman force, DNA molecules can only undergo deflective motion when they experience a velocity gradient in the microchannel flow field; and they can only undergo elliptical motion when their deflective motion is accompanied by a spin motion. In this case, the Magnus force also plays an important role. The detailed study and elucidation of the movement states, dynamic characteristics and mechanisms of DNA molecules such as the deflective and elliptical motions under the actions of Saffman and Magnus forces have helpful implications for the development of related DNA/gene nano-/microfluidic chips, and for the separation, screening and detection of DNA molecules.
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Affiliation(s)
- Zhiwei Li
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
| | - Qiong Wang
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
| | - Yong Niu
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
| | - Ruiyu Wang
- College of Electronic Science & Engineering, Jilin University, China
| | - Wei Zhao
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
| | - Chen Zhang
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
| | - Guiren Wang
- Mechanical Engineering Department & Biomedical Engineering Department, University of South Carolina, Columbia, SC 29208, USA
| | - Kaige Wang
- Key Laboratory of Photoelectric Technology of Shaanxi Province, National Center for International Research of Photoelectric Technology & Nano-Functional Materials and Application, Institute of Photonics and Photon-Technology, Northwest University, Xi'an 710069, China.
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20
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Shin SW, Mudvari P, Thaploo S, Wheeler MA, Douek DC, Quintana FJ, Boritz EA, Abate AR, Clark IC. FIND-seq: high-throughput nucleic acid cytometry for rare single-cell transcriptomics. Nat Protoc 2024:10.1038/s41596-024-01021-y. [PMID: 39039320 DOI: 10.1038/s41596-024-01021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 05/09/2024] [Indexed: 07/24/2024]
Abstract
Rare cells have an important role in development and disease, and methods for isolating and studying cell subsets are therefore an essential part of biology research. Such methods traditionally rely on labeled antibodies targeted to cell surface proteins, but large public databases and sophisticated computational approaches increasingly define cell subsets on the basis of genomic, epigenomic and transcriptomic sequencing data. Methods for isolating cells on the basis of nucleic acid sequences powerfully complement these approaches by providing experimental access to cell subsets discovered in cell atlases, as well as those that cannot be otherwise isolated, including cells infected with pathogens, with specific DNA mutations or with unique transcriptional or splicing signatures. We recently developed a nucleic acid cytometry platform called 'focused interrogation of cells by nucleic acid detection and sequencing' (FIND-seq), capable of isolating rare cells on the basis of RNA or DNA markers, followed by bulk or single-cell transcriptomic analysis. This platform has previously been used to characterize the splicing-dependent activation of the transcription factor XBP1 in astrocytes and HIV persistence in memory CD4 T cells from people on long-term antiretroviral therapy. Here, we outline the molecular and microfluidic steps involved in performing FIND-seq, including protocol updates that allow detection and whole transcriptome sequencing of rare HIV-infected cells that harbor genetically intact virus genomes. FIND-seq requires knowledge of microfluidics, optics and molecular biology. We expect that FIND-seq, and this comprehensive protocol, will enable mechanistic studies of rare HIV+ cells, as well as other cell subsets that were previously difficult to recover and sequence.
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Affiliation(s)
- Seung Won Shin
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
| | - Iain C Clark
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences (QB3), University of California Berkeley, Berkeley, CA, USA.
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21
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Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. Nat Commun 2024; 15:5888. [PMID: 39003254 PMCID: PMC11246512 DOI: 10.1038/s41467-024-50046-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 06/27/2024] [Indexed: 07/15/2024] Open
Abstract
Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.
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Affiliation(s)
- Yang Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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22
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Saleski TE, Peng H, Lengger B, Wang J, Jensen MK, Jensen ED. High-throughput G protein-coupled receptor-based autocrine screening for secondary metabolite production in yeast. Biotechnol Bioeng 2024. [PMID: 38973176 DOI: 10.1002/bit.28797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/09/2024]
Abstract
Biosensors are valuable tools in accelerating the test phase of the design-build-test-learn cycle of cell factory development, as well as in bioprocess monitoring and control. G protein-coupled receptor (GPCR)-based biosensors enable cells to sense a wide array of molecules and environmental conditions in a specific manner. Due to the extracellular nature of their sensing, GPCR-based biosensors require compartmentalization of distinct genotypes when screening production levels of a strain library to ensure that detected levels originate exclusively from the strain under assessment. Here, we explore the integration of production and sensing modalities into a single Saccharomyces cerevisiae strain and compartmentalization using three different methods: (1) cultivation in microtiter plates, (2) spatial separation on agar plates, and (3) encapsulation in water-in-oil-in-water double emulsion droplets, combined with analysis and sorting via a fluorescence-activated cell sorting machine. Employing tryptamine and serotonin as proof-of-concept target molecules, we optimize biosensing conditions and demonstrate the ability of the autocrine screening method to enrich for high producers, showing the enrichment of a serotonin-producing strain over a nonproducing strain. These findings illustrate a workflow that can be adapted to screening for a wide range of complex chemistry at high throughput using commercially available microfluidic systems.
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Affiliation(s)
- Tatyana E Saleski
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Huadong Peng
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Bettina Lengger
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jinglin Wang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Michael Krogh Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Emil D Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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23
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Rupp BT, Cook CD, Purcell EA, Pop M, Radomski AE, Mesyngier N, Bailey RC, Nagrath S. CellMag-CARWash: A High Throughput Droplet Microfluidic Device for Live Cell Isolation and Single Cell Applications. Adv Biol (Weinh) 2024; 8:e2400066. [PMID: 38741244 DOI: 10.1002/adbi.202400066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Indexed: 05/16/2024]
Abstract
The recent push toward understanding an individual cell's behavior and identifying cellular heterogeneity has created an unmet need for technologies that can probe live cells at the single-cell level. Cells within a population are known to exhibit heterogeneous responses to environmental cues. These differences can lead to varied cellular states, behavior, and responses to therapeutics. Techniques are needed that are not only capable of processing and analyzing cellular populations at the single cell level, but also have the ability to isolate specific cell populations from a complex sample at high throughputs. The new CellMag-Coalesce-Attract-Resegment Wash (CellMag-CARWash) system combines positive magnetic selection with droplet microfluidic devices to isolate cells of interest from a mixture with >93% purity and incorporate treatments within individual droplets to observe single cell biological responses. This workflow is shown to be capable of probing the single cell extracellular vesicle (EV) secretion of MCF7 GFP cells. This article reports the first measurement of β-Estradiol's effect on EV secretion from MCF7 cells at the single cell level. Single cell processing revealed that MCF7 GFP cells possess a heterogeneous response to β-Estradiol stimulation with a 1.8-fold increase relative to the control.
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Affiliation(s)
- Brittany T Rupp
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Claire D Cook
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Emma A Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matei Pop
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Abigail E Radomski
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Mesyngier
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ryan C Bailey
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
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24
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Zhou G, Li T, Du J, Wu M, Lin D, Pu W, Zhang J, Gu Z. Harnessing HetHydrogel: A Universal Platform to Dropletize Single-Cell Multiomics. SMALL METHODS 2024; 8:e2301631. [PMID: 38419597 DOI: 10.1002/smtd.202301631] [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: 11/25/2023] [Revised: 01/12/2024] [Indexed: 03/02/2024]
Abstract
A universal platform is developed for dropletizing single cell plate-based multiomic assays, consisting of three main pillars: a miniaturized open Heterogeneous Hydrogel reactor (abbreviated HetHydrogel) for multi-step biochemistry, its tunable permeability that allows Tn5 tagmentation, and single cell droplet barcoding. Through optimizing the HetHydrogel manufacturing procedure, the chemical composition, and cell permeation conditions, simultaneous high-throughput mitochondrial DNA genotyping and chromatin profiling at the single-cell level are demonstrated using a mixed-species experiment. This platform offers a powerful way to investigate the genotype-phenotype relationships of various mtDNA mutations in biological processes. The HetHydrogel platform is believed to have the potential to democratize droplet technologies, upgrading a whole range of plate-based single cell assays to high throughput format.
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Affiliation(s)
- Guoqiang Zhou
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Ting Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Jingjing Du
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Mengying Wu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Deng Lin
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Weilin Pu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
- Zhejiang Lab, Hangzhou, 310000, China
| | - Zhenglong Gu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
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25
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Zath GK, Thomas MM, Loveday EK, Bikos DA, Sanche S, Ke R, Brooke CB, Chang CB. Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR). PLoS Pathog 2024; 20:e1012257. [PMID: 38950082 PMCID: PMC11244780 DOI: 10.1371/journal.ppat.1012257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 07/12/2024] [Accepted: 05/13/2024] [Indexed: 07/03/2024] Open
Abstract
An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 101 to 104 viruses per cell, and H1N1 ranging from 101 to 103 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.
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Affiliation(s)
- Geoffrey K. Zath
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Mallory M. Thomas
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, United States of America
| | - Emma K. Loveday
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Dimitri A. Bikos
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, United States of America
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, United States of America
| | - Steven Sanche
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Ruian Ke
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Christopher B. Brooke
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, United States of America
| | - Connie B. Chang
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, United States of America
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26
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Wulandari DA, Tsuru K, Minamihata K, Wakabayashi R, Egami G, Kawabe Y, Kamihira M, Goto M, Kamiya N. Design and validation of functionalized redox-responsive hydrogel beads for high-throughput screening of antibody-secreting mammalian cells. J Biosci Bioeng 2024; 138:89-95. [PMID: 38644063 DOI: 10.1016/j.jbiosc.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
Antibody drugs play a vital role in diagnostics and therapy. However, producing antibodies from mammalian cells is challenging owing to cellular heterogeneity, which can be addressed by applying droplet-based microfluidic platforms for high-throughput screening (HTS). Here, we designed an integrated system based on disulfide-bonded redox-responsive hydrogel beads (redox-HBs), which were prepared through enzymatic hydrogelation, to compartmentalize, screen, select, retrieve, and recover selected Chinese hamster ovary (CHO) cells secreting high levels of antibodies. Moreover, redox-HBs were functionalized with protein G as an antibody-binding module to capture antibodies secreted from encapsulated cells. As proof-of-concept, cells co-producing immunoglobulin G (IgG) as the antibody and green fluorescent protein (GFP) as the reporter molecule, denoted as CHO(IgG/GFP), were encapsulated into functionalized redox-HBs. Additionally, antibody-secreting cells were labeled with protein L-conjugated horseradish peroxidase using a tyramide amplification system, enabling fluorescence staining of the antibody captured inside the beads. Redox-HBs were then applied to fluorescence-activated droplet sorting, and selected redox-HBs were degraded by reducing the disulfide bonds to recover the target cells. The results indicated the potential of the developed HTS platform for selecting a single cell viable for biopharmaceutical production.
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Affiliation(s)
- Diah Anggraini Wulandari
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kyosuke Tsuru
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Go Egami
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshinori Kawabe
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masamichi Kamihira
- Department of Chemical Engineering, Faculty of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; Division of Biotechnology, Center for Future Chemistry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan.
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27
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Sharkey C, White R, Finocchiaro M, Thomas J, Estevam J, Konry T. Advancing Point-of-Care Applications with Droplet Microfluidics: From Single-Cell to Multicellular Analysis. Annu Rev Biomed Eng 2024; 26:119-139. [PMID: 38316063 DOI: 10.1146/annurev-bioeng-110222-102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Recent advances in single-cell and multicellular microfluidics technology have provided powerful tools for studying cancer biology and immunology. The ability to create controlled microenvironments, perform high-throughput screenings, and monitor cellular interactions at the single-cell level has significantly advanced our understanding of tumor biology and immune responses. We discuss cutting-edge multicellular and single-cell microfluidic technologies and methodologies utilized to investigate cancer-immune cell interactions and assess the effectiveness of immunotherapies. We explore the advantages and limitations of the wide range of 3D spheroid and single-cell microfluidic models recently developed, highlighting the various approaches in device generation and applications in immunotherapy screening for potential opportunities for point-of-care approaches.
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Affiliation(s)
- Christina Sharkey
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
- Department of Surgery, Division of Urology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel White
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Michael Finocchiaro
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Judene Thomas
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Jose Estevam
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
| | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA;
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28
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Yang Y, Vagin SI, Rieger B, Destgeer G. Fabrication of Crescent Shaped Microparticles for Particle Templated Droplet Formation. Macromol Rapid Commun 2024; 45:e2300721. [PMID: 38615246 DOI: 10.1002/marc.202300721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Crescent-shaped hydrogel microparticles are shown to template uniform volume aqueous droplets upon simple mixing with aqueous and oil media for various bioassays. This emerging "lab on a particle" technique requires hydrogel particles with tunable material properties and dimensions. The crescent shape of the particles is attained by aqueous two-phase separation of polymers followed by photopolymerization of the curable precursor. In this work, the phase separation of poly(ethylene glycol) diacrylate (PEGDA, Mw 700) and dextran (Mw 40 000) for tunable manufacturing of crescent-shaped particles is investigated. The particles' morphology is precisely tuned by following a phase diagram, varying the UV intensity, and adjusting the flow rates of various streams. The fabricated particles with variable dimensions encapsulate uniform aqueous droplets upon mixing with an oil phase. The particles are fluorescently labeled with red and blue emitting dyes at variable concentrations to produce six color-coded particles. The blue fluorescent dye shows a moderate response to the pH change. The fluorescently labeled particles are able to tolerate an extremely acidic solution (pH 1) but disintegrate within an extremely basic solution (pH 14). The particle-templated droplets are able to effectively retain the disintegrating particle and the fluorescent signal at pH 14.
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Affiliation(s)
- Yimin Yang
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
| | - Sergei I Vagin
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Bernhard Rieger
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Ghulam Destgeer
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
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29
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Mao Y, Yang Y, Lin F, Chu H, Zhou L, Han J, Zhou J, Su X. Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing. Microorganisms 2024; 12:1168. [PMID: 38930550 PMCID: PMC11206075 DOI: 10.3390/microorganisms12061168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The genome of the B. cereus SCL10 strain was sequenced and assembled, revealing a size of 4,979,182 bp and 5167 coding genes. The genes involved in biological functions were annotated by using the GO, COG, KEGG, NR, and Swiss-Prot databases. The results showed that genes related to alkyl hydroperoxide reductase (ahpC, ahpF), DNA-binding proteins from starved cells (dps), spore and biofilm formation (spoVG, spo0A, gerP), cold shock-like protein (cspC, cspE), ATP-dependent chaperone (clpB), and photolyase, small, acid-soluble spore protein (SASP) and DNA repair protein (recA, radD) could explain the stress resistance. These findings suggest that antioxidant activity, sporulation, biofilm formation, and DNA protection may be considered as the main resistance mechanisms under exposure to radiation in the B. cereus SCL10 strain.
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Affiliation(s)
- Yanzhen Mao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Ye Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Fu Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Hanyu Chu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Lijie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo 315832, China; (Y.M.); (Y.Y.); (F.L.); (H.C.); (L.Z.); (J.H.); (X.S.)
- School of Marine Science, Ningbo University, Ningbo 315832, China
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30
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Moses E, Atlan T, Sun X, Franěk R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. NATURE AGING 2024; 4:791-813. [PMID: 38750187 DOI: 10.1038/s43587-024-00632-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/10/2024] [Indexed: 05/22/2024]
Abstract
Classical evolutionary theories propose tradeoffs among reproduction, damage repair and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. In this study, we used the turquoise killifish (Nothobranchius furzeri) to genetically arrest germline development at discrete stages and examine how different modes of infertility impact life history. We first constructed a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. We show here that germline depletion-but not arresting germline differentiation-enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted Caenorhabditis elegans. Our results, therefore, demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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Affiliation(s)
- Eitan Moses
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Tehila Atlan
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Xue Sun
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Roman Franěk
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Atif Siddiqui
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | | | - Sagiv Shifman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - David M Zucker
- Department of Statistics and Data Science, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Oron-Gottesman
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University School of Medicine, Jerusalem, Israel
| | - Oren Ram
- Department of Biochemistry, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Itamar Harel
- Department of Genetics, Silberman Institute, Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel.
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Ahmadi F, Tran H, Letourneau N, Little SR, Fortin A, Moraitis AN, Shih SCC. An Automated Single-Cell Droplet-Digital Microfluidic Platform for Monoclonal Antibody Discovery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308950. [PMID: 38441226 DOI: 10.1002/smll.202308950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/30/2024] [Indexed: 06/27/2024]
Abstract
Monoclonal antibody (mAb) discovery plays a prominent role in diagnostic and therapeutic applications. Droplet microfluidics has become a standard technology for high-throughput screening of antibody-producing cells due to high droplet single-cell confinement frequency and rapid analysis and sorting of the cells of interest with their secreted mAbs. In this work, a new method is described for on-demand co-encapsulation of cells that eliminates the difficulties associated with washing in between consecutive steps inside the droplets and enables the washing and addition of fresh media. The new platform identifies hybridoma cells that are expressing antibodies of interest using antibody-characterization assays to find the best-performing or rare-cell antibody candidates.
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Affiliation(s)
- Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Hao Tran
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
| | - Natasha Letourneau
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Samuel R Little
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Annie Fortin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Anna N Moraitis
- Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
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32
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Omidfar K, Kashanian S. A mini review on recent progress of microfluidic systems for antibody development. J Diabetes Metab Disord 2024; 23:323-331. [PMID: 38932846 PMCID: PMC11196548 DOI: 10.1007/s40200-024-01386-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/06/2024] [Indexed: 06/28/2024]
Abstract
Objectives Antibody is specific reagent that be utilized in various field of biomedical research. Monoclonal antibodies are mostly produced using two common techniques namely hybridoma and antibody engineering, which suffer from some limitations such as boring screening procedures, long production time, low efficacy and a degree of automation. To address these limitations, various microfluidics techniques have been developed for the antibody isolation and screening. Methods This study specifically investigates nearly recent reports published in peer-reviewed journals indexed in various databases including Web of Science, Scopus, PubMed, Google Scholar, and Science Direct. Results In this study, we identified a total of seventy papers from a pool of 130 articles. These papers focus on the application of three major groups of microfluidic platforms, namely valves, microwells, and droplets, in the development of antibodies using hybridoma method and phage display technology. We provide a summary of these applications and also discuss the key findings in this field. Additionally, we illustrate our discussion with several examples to enhance understanding. Conclusions Microfluidics has the potential to serve as a valuable tool in streamlining complex laboratory procedures involved in antibody discovery. However, it is important to note that microfluidics is limited to laboratory settings. Further enhancements are needed to address existing challenges and to make microfluidics a reliable, accurate, and cost-effective tool for antibody discovery.
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Affiliation(s)
- Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular–Cellular Sciences Institute, Tehran University of Medical Sciences, P.O. Box 14395/1179, Tehran, IR Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sohiela Kashanian
- Faculty of Chemistry, Razi University, Kermanshah, 6714414971 Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah, 6714414971 Iran
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33
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Jain A, Stavrakis S, deMello A. Droplet-based microfluidics and enzyme evolution. Curr Opin Biotechnol 2024; 87:103097. [PMID: 38430713 DOI: 10.1016/j.copbio.2024.103097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Enzymes are widely used as catalysts in the chemical and pharmaceutical industries. While successful in many situations, they must usually be adapted to operate efficiently under nonnatural conditions. Enzyme engineering allows the creation of novel enzymes that are stable at elevated temperatures or have higher activities and selectivities. Current enzyme engineering techniques require the production and testing of enzyme variant libraries to identify members with desired attributes. Unfortunately, traditional screening methods cannot screen such large mutagenesis libraries in a robust and timely manner. Droplet-based microfluidic systems can produce, process, and sort picoliter droplets at kilohertz rates and have emerged as powerful tools for library screening and thus enzyme engineering. We describe how droplet-based microfluidics has been used to advance directed evolution.
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Affiliation(s)
- Ankit Jain
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8093 Zürich, Switzerland.
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34
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Sullivan MR, Finocchiaro M, Yang Y, Thomas J, Ali A, Kaplan I, Abdulhamid Y, Bobilev E, Sheffer M, Romee R, Konry T. An innovative single-cell approach for phenotyping and functional genotyping of CAR NK cells. J Immunother Cancer 2024; 12:e008912. [PMID: 38821719 PMCID: PMC11149162 DOI: 10.1136/jitc-2024-008912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND To accelerate the translation of novel immunotherapeutic treatment approaches, the development of analytic methods to assess their efficacy at early in vitro stages is necessary. Using a droplet-based microfluidic platform, we have established a method for multiparameter quantifiable phenotypic and genomic observations of immunotherapies. Chimeric antigen receptor (CAR) natural killer (NK) cells are of increased interest in the current immunotherapy landscape and thus provide an optimal model for evaluating our novel methodology. METHODS For this approach, NK cells transduced with a CD19 CAR were compared with non-transduced NK cells in their ability to kill a lymphoma cell line. Using our microfluidic platform, we were able to quantify the increase in cytotoxicity and synaptic contact formation of CAR NK cells over non-transduced NK cells. We then optimized our droplet sorter and successfully used it to separate NK cells based on target cell killing to perform transcriptomic analyses. RESULTS Our data revealed expected improvement in cytotoxicity with the CD19 CAR but more importantly, provided unique insights into the factors involved in the cytotoxic mechanisms of CAR NK cells. This demonstrates a novel, improved system for accelerating the pre-clinical screening of future immunotherapy treatments. CONCLUSIONS This study provides a new potential approach for enhanced early screening of immunotherapies to improve their development, with a highly relevant cell model to demonstrate. Additionally, our validation studies provided some potential insights into transcriptomic determinants influencing CAR NK cytotoxicity.
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Affiliation(s)
- Matthew Ryan Sullivan
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Michael Finocchiaro
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Yichao Yang
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Judene Thomas
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Alaa Ali
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Isabel Kaplan
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yasmin Abdulhamid
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Eden Bobilev
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Michal Sheffer
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Rizwan Romee
- Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts, USA
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35
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Tutoni GG, McDonald SM, Zhong R, Lu A, Huang TJ, Becker ML. Microfluidic Assembly of Degradable, Stereocomplexed Hydrogel Microparticles. J Am Chem Soc 2024; 146:14705-14714. [PMID: 38749060 DOI: 10.1021/jacs.4c02317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Hydrogel microparticles (HMPs) have been investigated widely for their use in tissue engineering and drug delivery applications. However, translation of these highly tunable systems has been hindered by covalent cross-linking methods within microparticles. Stereocomplexation, a stereospecific form of physical cross-linking, provides a robust yet degradable alternative for creating translationally relevant HMPs. Herein, 4-arm polyethylene glycol (PEG) stars were used as macromolecular initiators from which oligomeric poly(l-lactic acid) (PLLA) was polymerized with a degree of polymerization (DPn) of 20 on each arm. Similarly, complementary propargyl-containing ABA cross-linkers with enantiomeric poly(d-lactic acid) (PDLA) segments (DPn = 20) on each arm. Droplets of these gel precursors were formed via a microfluidic organic-in-oil-in-water system where microparticles self-assembled via stereocomplexation and were stabilized after precipitation in deionized water. By varying the flow rate of the dispersed phase, well-defined microparticles with diameters of 33.7 ± 0.5, 62.4 ± 0.6, and 105.7 ± 0.8 μm were fabricated. Gelation due to stereocomplexation was confirmed via wide-angle X-ray scattering in which HMPs exhibited the signature diffraction pattern of stereocomplexed PLA at 2θ = 12.2, 21.2, 24.2°. Differential scanning calorimetry also confirmed stereocomplexation by the appearance of a crystallization exotherm (Tc = 37 °C) and a high-temperature endotherm (Tm = 159 °C) that does not appear in the homocrystallization of PLLA or the hydrogel precursors. Additionally, the propargyl handle present on the cross-linker allows for pre- or post-assembly thiol-yne "click" functionalization as demonstrated by the addition of thiol-containing fluorophores to the HMPs.
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Affiliation(s)
- Gianna G Tutoni
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Samantha M McDonald
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Ruoyu Zhong
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Annette Lu
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Tony Jun Huang
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Matthew L Becker
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Orthopedic Surgery, Duke University, Durham, North Carolina 27708, United States
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36
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Nakamura M, Matsumoto M, Ito T, Hidaka I, Tatsuta H, Katsumoto Y. Microfluidic device for the high-throughput and selective encapsulation of single target cells. LAB ON A CHIP 2024; 24:2958-2967. [PMID: 38722067 DOI: 10.1039/d4lc00037d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Droplet-based microfluidic technologies for encapsulating single cells have rapidly evolved into powerful tools for single-cell analysis. In conventional passive single-cell encapsulation techniques, because cells arrive randomly at the droplet generation section, to encapsulate only a single cell with high precision, the average number of cells per droplet has to be decreased by reducing the average frequency at which cells arrive relative to the droplet generation rate. Therefore, the encapsulation efficiency for a given droplet generation rate is very low. Additionally, cell sorting operations are required prior to the encapsulation of target cells for specific cell type analysis. To address these challenges, we developed a cell encapsulation technology with a cell sorting function using a microfluidic chip. The microfluidic chip is equipped with an optical detection section to detect the optical information of cells and a sorting section to encapsulate cells into droplets by controlling a piezo element, enabling active encapsulation of only the single target cells. For a particle population including both targeted and non-targeted particles arriving at an average frequency of up to 6000 particles per s, with an average number of particles per droplet of 0.45, our device maintained a high purity above 97.9% for the single-target-particle droplets and achieved an outstanding throughput, encapsulating up to 2900 single target particles per s. The proposed encapsulation technology surpasses the encapsulation efficiency of conventional techniques, provides high efficiency and flexibility for single-cell research, and shows excellent potential for various applications in single-cell analysis.
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Affiliation(s)
- Masahiko Nakamura
- Life Science Technology Research & Development Dept., Application Technology Research & Development Div., Technology Development Laboratories, Sony Corporation, Tokyo, Japan.
| | - Masahiro Matsumoto
- Life Science Technology Research & Development Dept., Application Technology Research & Development Div., Technology Development Laboratories, Sony Corporation, Tokyo, Japan.
| | - Tatsumi Ito
- Life Science Technology Research & Development Dept., Application Technology Research & Development Div., Technology Development Laboratories, Sony Corporation, Tokyo, Japan.
| | - Isao Hidaka
- Life Science Technology Research & Development Dept., Application Technology Research & Development Div., Technology Development Laboratories, Sony Corporation, Tokyo, Japan.
| | - Hirokazu Tatsuta
- Life Science Technology Research & Development Dept., Application Technology Research & Development Div., Technology Development Laboratories, Sony Corporation, Tokyo, Japan.
| | - Yoichi Katsumoto
- Life Science Technology Research & Development Dept., Application Technology Research & Development Div., Technology Development Laboratories, Sony Corporation, Tokyo, Japan.
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Guo Z, Zhao Y, Jin Z, Chang Y, Wang X, Guo G, Zhao Y. Monolithic 3D nanoelectrospray emitters based on a continuous fluid-assisted etching strategy for glass droplet microfluidic chip-mass spectrometry. Chem Sci 2024; 15:7781-7788. [PMID: 38784731 PMCID: PMC11110156 DOI: 10.1039/d4sc01700e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Glass microfluidic chips are suitable for coupling with mass spectrometry (MS) due to their flexible design, optical transparency and resistance to organic reagents. However, due to the high hardness and brittleness of glass, there is a lack of simple and feasible technology to manufacture a monolithic nanospray ionization (nESI) emitter on a glass microchip, which hinders its coupling with mass spectrometry. Here, a continuous fluid-assisted etching strategy is proposed to fabricate monolithic three-dimensional (3D) nESI emitters integrated into glass microchips. A continuous fluid of methanol is adopted to protect the inner wall of the channels and the bonding interface of the glass microfluidic chip from being wet-etched, forming sharp 3D nESI emitters. The fabricated 3D nESI emitter can form a stable electrospray plume, resulting in consistent nESI detection of acetylcholine with an RSD of 4.5% within 10 min. The fabricated 3D emitter is integrated on a glass microfluidic chip designed with a T-junction droplet generator, which can realize efficient analysis of acetylcholine in picoliter-volume droplets by nESI-MS. Stability testing of over 20 000 droplets detected by the established system resulted in an RSD of 9.1% over approximately 180 min. The detection of ten neurochemicals in rat cerebrospinal fluid droplets is achieved. The established glass droplet microfluidic chip-MS system exhibits potential for broad applications such as in vivo neurochemical monitoring and single-cell analysis in the future.
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Affiliation(s)
- Ziyang Guo
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Yingqi Zhao
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Zhao Jin
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Yaran Chang
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Xiayan Wang
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Guangsheng Guo
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
- Minzu University of China Beijing 100081 China
| | - Yaoyao Zhao
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
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38
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Deng E, Shen Q, Zhang J, Fang Y, Chang L, Luo G, Fan X. Systematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms. J Adv Res 2024:S2090-1232(24)00210-8. [PMID: 38782298 DOI: 10.1016/j.jare.2024.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/23/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION The rapid development of next-generation sequencing (NGS)-based single-cell RNA sequencing (scRNA-seq) allows for detecting and quantifying gene expression in a high-throughput manner, providing a powerful tool for comprehensively understanding cellular function in various biological processes. However, the NGS-based scRNA-seq only quantifies gene expression and cannot reveal the exact transcript structures (isoforms) of each gene due to the limited read length. On the other hand, the long read length of third-generation sequencing (TGS) technologies, including Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), enable direct reading of intact cDNA molecules. OBJECTIVES Both ONT and PacBio have been used in conjunction with scRNA-seq, but their performance in single-cell analyses has not been systematically evaluated. METHODS To address this, we generated ONT and PacBio data from the same single-cell cDNA libraries containing different amount of cells. RESULTS Using NGS as a control, we assessed the performance of each platform in cell type identification. Additionally, the reliability in identifying novel isoforms and allele-specific gene/isoform expression by both platforms was verified, providing a systematic evaluation to design the sequencing strategies in single-cell transcriptome studies. CONCLUSION Beyond gene expression analysis, which the NGS-based scRNA-seq only affords, TGS-based scRNA-seq achieved gene splicing analyses, identifying novel isoforms. Attribute to higher sequencing quality of PacBio, it outperforms ONT in accuracy of novel transcripts identification and allele-specific gene/isoform expression.
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Affiliation(s)
- Enze Deng
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Qingmei Shen
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China; GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
| | - Jingna Zhang
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Yaowei Fang
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
| | - Lei Chang
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
| | - Guanzheng Luo
- MOE Key Laboratory of Gene Function and Regulation, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China; GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China.
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39
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Ghosh R, Arnheim A, van Zee M, Shang L, Soemardy C, Tang RC, Mellody M, Baghdasarian S, Sanchez Ochoa E, Ye S, Chen S, Williamson C, Karunaratne A, Di Carlo D. Lab on a Particle Technologies. Anal Chem 2024; 96:7817-7839. [PMID: 38650433 PMCID: PMC11112544 DOI: 10.1021/acs.analchem.4c01510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 04/25/2024]
Affiliation(s)
- Rajesh Ghosh
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Alyssa Arnheim
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Mark van Zee
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Lily Shang
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Citradewi Soemardy
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Rui-Chian Tang
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Michael Mellody
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Sevana Baghdasarian
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Edwin Sanchez Ochoa
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Shun Ye
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Siyu Chen
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Cayden Williamson
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Amrith Karunaratne
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Dino Di Carlo
- Department
of Bioengineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
- Jonsson
Comprehensive Cancer Center, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Mechanical and Aerospace Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States
- California
NanoSystems Institute, Los Angeles, California 90095, United States
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40
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Zhao Z, Zhai H, Zuo P, Wang T, Xie R, Tian M, Song R, Xu X, Li Z. Image-activated pico-injection for single-cell analysis. Talanta 2024; 272:125765. [PMID: 38346358 DOI: 10.1016/j.talanta.2024.125765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/29/2024] [Accepted: 02/06/2024] [Indexed: 03/17/2024]
Abstract
The addition of reagents into preformed droplets is a crucial yet intricate task in droplet-based applications where sequential reactions is required. Pico-injection offers high throughput and robustness in accomplishing this task, but the existing pico-injection techniques work in an indiscriminate manner, making it difficult to target particular groups of droplets. Here we report image-activated pico-injection (imgPico) for label-free, on-demand reagent supplementation into droplets. The imgPico detects the droplets of interest by real-time image analysis and makes decisions for the downstream pico-injection operation. We studied the performance of different algorithms for the image analysis and optimized the experimental settings of the imgPico. In the validation experiment, the imgPico successfully injected fluorescent dyes into droplets encapsulating one, two, and three cells, respectively, as expected. We further demonstrated the utility of imgPico by targeting droplets encapsulating single cells in droplet-based single-cell RNA sequencing (scRNA-seq) using exceedingly high cell density, and the results showed that the imgPico effectively reduced the presence of doublets in the scRNA-seq data. With the merits of being label-free and versatile, the imgPico represents a technical advance with potential applications in single-cell analysis.
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Affiliation(s)
- Zhantao Zhao
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Heng Zhai
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Peng Zuo
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Tao Wang
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Run Xie
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Mu Tian
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China
| | - Ruyuan Song
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Xiaonan Xu
- ThunderBio Innovation, Shenzhen, 518108, China
| | - Zida Li
- Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China; Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, Department of Biomedical Engineering, Medical School, Shenzhen University, Shenzhen, 518060, China.
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Moses E, Atlan T, Sun X, Franek R, Siddiqui A, Marinov GK, Shifman S, Zucker DM, Oron-Gottesman A, Greenleaf WJ, Cohen E, Ram O, Harel I. The killifish germline regulates longevity and somatic repair in a sex-specific manner. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.18.572041. [PMID: 38187630 PMCID: PMC10769255 DOI: 10.1101/2023.12.18.572041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Classical evolutionary theories propose tradeoffs between reproduction, damage repair, and lifespan. However, the specific role of the germline in shaping vertebrate aging remains largely unknown. Here, we use the turquoise killifish ( N. furzeri ) to genetically arrest germline development at discrete stages, and examine how different modes of infertility impact life-history. We first construct a comprehensive single-cell gonadal atlas, providing cell-type-specific markers for downstream phenotypic analysis. Next, we show that germline depletion - but not arresting germline differentiation - enhances damage repair in female killifish. Conversely, germline-depleted males instead showed an extension in lifespan and rejuvenated metabolic functions. Through further transcriptomic analysis, we highlight enrichment of pro-longevity pathways and genes in germline-depleted male killifish and demonstrate functional conservation of how these factors may regulate longevity in germline-depleted C. elegans . Our results therefore demonstrate that different germline manipulation paradigms can yield pronounced sexually dimorphic phenotypes, implying alternative responses to classical evolutionary tradeoffs.
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42
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Pranauskaite E, Milkus V, Ritmejeris J, Zilionis R, Mazutis L. Increasing Fluid Viscosity Ensures Consistent Single-Cell Encapsulation. Anal Chem 2024; 96:6898-6905. [PMID: 38649796 PMCID: PMC11079858 DOI: 10.1021/acs.analchem.3c05243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/09/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
High-throughput single-cell analysis typically relies on the isolation of cells of interest in separate compartments for subsequent phenotypic or genotypic characterization. Using microfluidics, this is achieved by isolating individual cells in microdroplets or microwells. However, due to cell-to-cell variability in size, shape, and density, the cell capture efficiencies may vary significantly. This variability can negatively impact the measurements and introduce undesirable artifacts when trying to isolate and characterize heterogeneous cell populations. In this study, we show that single-cell isolation biases in microfluidics can be circumvented by increasing the viscosity of fluids in which cells are dispersed. At a viscosity of 40-50 cP (cP), the cell sedimentation is effectively reduced, resulting in a steady cell flow inside the microfluidics chip and consistent encapsulation in water-in-oil droplets over extended periods of time. This approach allows nearly all cells in a sample to be isolated with the same efficiency, irrespective of their type. Our results show that increased fluid viscosity, rather than cell-adjusted density, provides a more reliable approach to mitigate single-cell isolation biases.
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Affiliation(s)
- Emile Pranauskaite
- Institute of Biotechnology,
Life Sciences Center, Vilnius University, Vilnius LT 10257, Lithuania
| | - Valdemaras Milkus
- Institute of Biotechnology,
Life Sciences Center, Vilnius University, Vilnius LT 10257, Lithuania
| | | | - Rapolas Zilionis
- Institute of Biotechnology,
Life Sciences Center, Vilnius University, Vilnius LT 10257, Lithuania
| | - Linas Mazutis
- Institute of Biotechnology,
Life Sciences Center, Vilnius University, Vilnius LT 10257, Lithuania
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43
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Horne RI, Andrzejewska EA, Alam P, Brotzakis ZF, Srivastava A, Aubert A, Nowinska M, Gregory RC, Staats R, Possenti A, Chia S, Sormanni P, Ghetti B, Caughey B, Knowles TPJ, Vendruscolo M. Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning. Nat Chem Biol 2024; 20:634-645. [PMID: 38632492 PMCID: PMC11062903 DOI: 10.1038/s41589-024-01580-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/12/2024] [Indexed: 04/19/2024]
Abstract
Machine learning methods hold the promise to reduce the costs and the failure rates of conventional drug discovery pipelines. This issue is especially pressing for neurodegenerative diseases, where the development of disease-modifying drugs has been particularly challenging. To address this problem, we describe here a machine learning approach to identify small molecule inhibitors of α-synuclein aggregation, a process implicated in Parkinson's disease and other synucleinopathies. Because the proliferation of α-synuclein aggregates takes place through autocatalytic secondary nucleation, we aim to identify compounds that bind the catalytic sites on the surface of the aggregates. To achieve this goal, we use structure-based machine learning in an iterative manner to first identify and then progressively optimize secondary nucleation inhibitors. Our results demonstrate that this approach leads to the facile identification of compounds two orders of magnitude more potent than previously reported ones.
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Affiliation(s)
- Robert I Horne
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ewa A Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Parvez Alam
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Z Faidon Brotzakis
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ankit Srivastava
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Alice Aubert
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Magdalena Nowinska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Rebecca C Gregory
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Roxine Staats
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andrea Possenti
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sean Chia
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byron Caughey
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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Tan L, Zeng Q, Xu F, Zhao Q, Chen A, Wang T, Tao X, Yang Y, Wang X. Controllable Manipulation of Large-Volume Droplet on Non-Slippery Surfaces Based on Triboelectric Contactless Charge Injection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2313878. [PMID: 38364828 DOI: 10.1002/adma.202313878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Controllable droplet manipulation is crucial in diverse scientific and engineering fields. Traditional electric-based methods usually rely on commercial high-voltage (HV) power sources, which are typically bulky, expensive, and potentially hazardous. The triboelectric nanogenerator (TENG) is a highly studied device that can generate HV output with limited current, showing great potential in droplet manipulation applications. However, current TENG-based approaches usually utilize traditional free-standing TENGs that produce short-pulsed alternating-current signals. This limitation hinders continuous electrostatic forces necessary for precise droplet control, leading to complex circuitry and suboptimal droplet motion control in terms of volume, distance, direction, and momentum. Here, a triboelectric contactless charge injection (TCCI) method employing a novel dual-functional triboelectric nanogenerator (DF-TENG), is proposed. The DF-TENG can produce both high voltage and constant current during unidirectional motion, enabling continuous corona discharges for contactless charge injection into the droplets. Using this method, a large-volume droplet (3000 µL) can be controlled with momentum up to 115.2 g mm s-1, quintupling the highest value recorded by the traditional methods. Moreover, the TCCI method is adaptable for a variety of non-slippery substrates and droplets of different compositions and viscosities, which makes it an ideal manipulation strategy for droplet transport, chemical reactions, and even driving solids.
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Affiliation(s)
- Liming Tan
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Qixuan Zeng
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Fan Xu
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Qing Zhao
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Ai Chen
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Tingyu Wang
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Xingming Tao
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Yuchen Yang
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
| | - Xue Wang
- Department of Applied Physics, Chongqing University, Chongqing, 400044, P. R. China
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45
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Yin K, Zhao M, Xu Y, Zheng Z, Huang S, Liang D, Dong H, Guo Y, Lin L, Song J, Zhang H, Zheng J, Zhu Z, Yang C. Well-Paired-Seq2: High-Throughput and High-Sensitivity Strategy for Characterizing Low RNA-Content Cell/Nucleus Transcriptomes. Anal Chem 2024; 96:6301-6310. [PMID: 38597061 DOI: 10.1021/acs.analchem.3c05785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) is a transformative technology that unravels the intricate cellular state heterogeneity. However, the Poisson-dependent cell capture and low sensitivity in scRNA-seq methods pose challenges for throughput and samples with a low RNA-content. Herein, to address these challenges, we present Well-Paired-Seq2 (WPS2), harnessing size-exclusion and quasi-static hydrodynamics for efficient cell capture. WPS2 exploits molecular crowding effect, tailing activity enhancement in reverse transcription, and homogeneous enzymatic reaction in the initial bead-based amplification to achieve 3116 genes and 8447 transcripts with an average of ∼20000 reads per cell. WPS2 detected 1420 more genes and 4864 more transcripts than our previous Well-Paired-Seq. It sensitively characterizes transcriptomes of low RNA-content single cells and nuclei, overcoming the Poisson limit for cell and barcoded bead capture. WPS2 also profiles transcriptomes from frozen clinical samples, revealing heterogeneous tumor copy number variations and intercellular crosstalk in clear cell renal cell carcinomas. Additionally, we provide the first single-cell-level characterization of rare metanephric adenoma (MA) and uncover potential specific markers. With the advantages of high sensitivity and high throughput, WPS2 holds promise for diverse basic and clinical research.
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Affiliation(s)
- Kun Yin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Meijuan Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Yiling Xu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhong Zheng
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Shanqing Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Dianyi Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - He Dong
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Ye Guo
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Li Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Jia Song
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Huimin Zhang
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Junhua Zheng
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200120, China
| | - Zhi Zhu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Chaoyong Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
- Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200120, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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46
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Yang B, Hu S, Jiang Y, Xu L, Shu S, Zhang H. Advancements in Single-Cell RNA Sequencing Research for Neurological Diseases. Mol Neurobiol 2024:10.1007/s12035-024-04126-3. [PMID: 38564138 DOI: 10.1007/s12035-024-04126-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024]
Abstract
Neurological diseases are a major cause of the global burden of disease. Although the mechanisms of the occurrence and development of neurological diseases are not fully clear, most of them are associated with cells mediating neuroinflammation. Yet medications and other therapeutic options to improve treatment are still very limited. Single-cell RNA sequencing (scRNA-seq), as a delightfully potent breakthrough technology, not only identifies various cell types and response states but also uncovers cell-specific gene expression changes, gene regulatory networks, intercellular communication, and cellular movement trajectories, among others, in different cell types. In this review, we describe the technology of scRNA-seq in detail and discuss and summarize the application of scRNA-seq in exploring neurological diseases, elaborating the corresponding specific mechanisms of the diseases as well as providing a reliable basis for new therapeutic approaches. Finally, we affirm that scRNA-seq promotes the development of the neuroscience field and enables us to have a deeper cellular understanding of neurological diseases in the future, which provides strong support for the treatment of neurological diseases and the improvement of patients' prognosis.
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Affiliation(s)
- Bingjie Yang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Shuqi Hu
- Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Yiru Jiang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Lei Xu
- Department of Neurology, Zhejiang Rongjun Hospital, Jiaxing, Zhejiang, China
| | - Song Shu
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China
| | - Hao Zhang
- Department of Neurology, The Fourth Clinical School of Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China.
- Department of Neurology, Affiliated Hangzhou First People's Hospital, Westlake University School of Medicine, Hangzhou, Zhejiang, China.
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Verbist W, Breukers J, Sharma S, Rutten I, Gerstmans H, Coelmont L, Dal Dosso F, Dallmeier K, Lammertyn J. SeParate: multiway fluorescence-activated droplet sorting based on integration of serial and parallel triaging concepts. LAB ON A CHIP 2024; 24:2107-2121. [PMID: 38450543 DOI: 10.1039/d3lc01075a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a versatile high-throughput sorting tool that is, unlike most fluorescence-activated cell sorting (FACS) platforms, capable of sorting droplet-compartmentalized cells, cell secretions, entire enzymatic reactions and more. Recently, multiplex FADS platforms have been developed for the sorting of multi-fluorophore populations towards different outlets in addition to the standard, more commonly used, 2-way FADS platform. These multiplex FADS platforms consist of either multiple 2-way junctions one after the other (i.e. serial sorters) or of one junction sorting droplets in more than 2 outlets (i.e. parallel sorters). In this work, we present SeParate, a novel platform based on integrating s̲e̲rial and p̲a̲r̲allel sorting principles for accura̲t̲e̲ multiplex droplet sorting that is able to mitigate limitations of current multiplex sorters. We show the SeParate platform and its capability in highly accurate 4-way sorting of a multi-fluorophore population into four subpopulations with the potential to expand to more. More specifically, the SeParate platform was thoroughly validated using mixed populations of fluorescent beads and picoinjected droplets, yielding sorting accuracies up to 100% and 99.9%, respectively. Finally, transfected HEK-293T cells were sorted employing two different optical setups, resulting in an accuracy up to 99.5%. SeParate's high accuracy for a diverse set of samples, including highly variable biological specimens, together with its scalability beyond the demonstrated 4-way sorting, warrants a broad applicability for multi-fluorophore studies in life sciences, environmental sciences and others.
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Affiliation(s)
- Wannes Verbist
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Jolien Breukers
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Sapna Sharma
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Iene Rutten
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Lotte Coelmont
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Francesco Dal Dosso
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
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Rashidi N, Slater A, Peregrino G, Santin M. A novel, microfluidic high-throughput single-cell encapsulation of human bone marrow mesenchymal stromal cells. JOURNAL OF MATERIALS SCIENCE. MATERIALS IN MEDICINE 2024; 35:19. [PMID: 38526655 DOI: 10.1007/s10856-024-06785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 02/17/2024] [Indexed: 03/27/2024]
Abstract
The efficacy of stem-cell therapy depends on the ability of the transplanted cells to escape early immunological reactions and to be retained at the site of transplantation. The use of tissue engineering scaffolds or injectable biomaterials as carriers has been proposed, but they still present limitations linked to a reliable manufacturing process, surgical practice and clinical outcomes. Alginate microbeads are potential candidates for the encapsulation of mesenchymal stromal cells with the aim of providing a delivery carrier suitable for minimally-invasive and scaffold-free transplantation, tissue-adhesive properties and protection from the immune response. However, the formation of stable microbeads relies on the cross-linking of alginate with divalent calcium ions at concentrations that are toxic for the cells, making control over the beads' size and a single-cell encapsulation unreliable. The present work demonstrates the efficiency of an innovative, high throughput, and reproducible microfluidic system to produce single-cell, calcium-free alginate coatings of human mesenchymal stromal cells. Among the various conditions tested, visible light and confocal microscopy following staining of the cell nuclei by DAPI showed that the microfluidic system yielded an optimal single-cell encapsulation of 2000 cells/min in 2% w/v alginate microcapsules of reproducible morphology and an average size of 28.2 ± 3.7 µm. The adhesive properties of the alginate microcapsules, the viability of the encapsulated cells and their ability to escape the alginate microcapsule were demonstrated by the relatively rapid adherence of the beads onto tissue culture plastic and the cells' ability to gradually disrupt the microcapsule shell after 24 h and proliferate. To mimic the early inflammatory response upon transplantation, the encapsulated cells were exposed to proliferating macrophages at different cell seeding densities for up to 2 days and the protection effect of the microcapsule on the cells assessed by time-lapse microscopy showing a shielding effect for up to 48 h. This work underscores the potential of microfluidic systems to precisely encapsulate cells by good manufacturing practice standards while favouring cell retention on substrates, viability and proliferation upon transplantation.
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Affiliation(s)
- Narjes Rashidi
- Centre for Regenerative Medicine and Devices, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK
- School of Applied Sciences, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK
| | - Alex Slater
- Centre for Regenerative Medicine and Devices, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK
- School of Applied Sciences, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK
| | - Giordana Peregrino
- Centre for Regenerative Medicine and Devices, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK
- School of Applied Sciences, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK
| | - Matteo Santin
- Centre for Regenerative Medicine and Devices, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK.
- School of Applied Sciences, University of Brighton, Huxley Building Lewes Road, Brighton, BN2 4GJ, UK.
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Liu R, Li X, Liu Y, Du L, Zhu Y, Wu L, Hu B. A high-speed microscopy system based on deep learning to detect yeast-like fungi cells in blood. Bioanalysis 2024; 16:289-303. [PMID: 38334080 DOI: 10.4155/bio-2023-0193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Background: Blood-invasive fungal infections can cause the death of patients, while diagnosis of fungal infections is challenging. Methods: A high-speed microscopy detection system was constructed that included a microfluidic system, a microscope connected to a high-speed camera and a deep learning analysis section. Results: For training data, the sensitivity and specificity of the convolutional neural network model were 93.5% (92.7-94.2%) and 99.5% (99.1-99.5%), respectively. For validating data, the sensitivity and specificity were 81.3% (80.0-82.5%) and 99.4% (99.2-99.6%), respectively. Cryptococcal cells were found in 22.07% of blood samples. Conclusion: This high-speed microscopy system can analyze fungal pathogens in blood samples rapidly with high sensitivity and specificity and can help dramatically accelerate the diagnosis of fungal infectious diseases.
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Affiliation(s)
- Ruiqi Liu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, Guangxi, P.R. China
| | - Xiaojie Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Yingyi Liu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, Guangxi, P.R. China
| | - Lijun Du
- Department of Clinical Laboratory, Huadu District People's Hospital of Guangzhou, Guangdong, China
| | - Yingzhu Zhu
- Guangzhou Waterrock Gene Technology, Guangdong, China
| | - Lichuan Wu
- Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning, Guangxi, P.R. China
| | - Bo Hu
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
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Wang W, Vahabi H, Taassob A, Pillai S, Kota AK. On-Demand, Contact-Less and Loss-Less Droplet Manipulation via Contact Electrification. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308101. [PMID: 38233209 PMCID: PMC10933654 DOI: 10.1002/advs.202308101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/25/2023] [Indexed: 01/19/2024]
Abstract
While there are many droplet manipulation techniques, all of them suffer from at least one of the following drawbacks - complex fabrication or complex equipment or liquid loss. In this work, a simple and portable technique is demonstrated that enables on-demand, contact-less and loss-less manipulation of liquid droplets through a combination of contact electrification and slipperiness. In conjunction with numerical simulations, a quantitative analysis is presented to explain the onset of droplet motion. Utilizing the contact electrification technique, contact-less and loss-less manipulation of polar and non-polar liquid droplets on different surface chemistries and geometries is demonstrated. It is envisioned that the technique can pave the way to simple, inexpensive, and portable lab on a chip and point of care devices.
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Affiliation(s)
- Wei Wang
- Department of Mechanical and Aerospace EngineeringNorth Carolina State UniversityRaleighNC27695USA
- Department of MechanicalAerospace and Biomedical EngineeringUniversity of Tennessee KnoxvilleKnoxvilleTN37996USA
| | - Hamed Vahabi
- Department of Mechanical EngineeringColorado State UniversityFort CollinsCO80525USA
| | - Arsalan Taassob
- Department of Mechanical and Aerospace EngineeringNorth Carolina State UniversityRaleighNC27695USA
| | - Sreekiran Pillai
- Department of Mechanical and Aerospace EngineeringNorth Carolina State UniversityRaleighNC27695USA
| | - Arun Kumar Kota
- Department of Mechanical and Aerospace EngineeringNorth Carolina State UniversityRaleighNC27695USA
- Department of Mechanical EngineeringColorado State UniversityFort CollinsCO80525USA
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