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Qi X, Zhou Q, Li X, Hu G. Generation of Multiple Concentration Gradients Using a Two-Dimensional Pyramid Array. Anal Chem 2024; 96:856-865. [PMID: 38104274 DOI: 10.1021/acs.analchem.3c04496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Concentration heterogeneity of diffusible reactants is a prevalent phenomenon in biochemical processes, requiring the generation of concentration gradients for the relevant experiments. In this study, we present a high-density pyramid array microfluidic network for the effective and precise generation of multiple concentration gradients. The complex gradient distribution in the 2D array can be adaptively adjusted by modulating the reactant velocities and concentrations at the inlets. In addition, the unique design of each reaction chamber and mixing block in the array ensures uniform concentrations within each chamber during dynamic changes, enabling large-scale reactions with low reactant volumes. Through detailed numerical simulation of mass transport within the complex microchannel networks, the proposed method allows researchers to determine the desired number of reaction chambers within a given concentration range based on experimental requirements and to quickly obtain the operating conditions with the help of machine learning-based prediction. The effectiveness in generating a multiple concentration gradient environment was further demonstrated by concentration-dependent calcium carbonate crystallization experiments. This device provides a highly efficient mixing and adaptable concentration platform that is well suited for high-throughput and multiplexed reactions.
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Affiliation(s)
- Xinlei Qi
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Qin Zhou
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Xuejin Li
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
| | - Guoqing Hu
- Department of Engineering Mechanics, State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou 310027, China
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Lan Y, Zhou Y, Wu M, Jia C, Zhao J. Microfluidic based single cell or droplet manipulation: Methods and applications. Talanta 2023; 265:124776. [PMID: 37348357 DOI: 10.1016/j.talanta.2023.124776] [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: 02/07/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
The isolation of single cell or droplet is first and crucial step to single-cell analysis, which is important for cancer research and diagnostic methods. This review provides an overview of technologies that are currently used or in development to realize the isolation. Microfluidic based manipulation is an emerging technology with the distinct advantages of miniaturization and low cost. Therefore, recent developments in microfluidic isolated methods have attracted extensive attention. We introduced herein five strategies based on microfluid: trap, microfluidic discrete manipulation, bioprinter, capillary and inertial force. For every technology, their basic principles and features were discussed firstly. Then some modified approaches and applications were listed as the extension. Finally, we compared the advantages and drawbacks of these methods, and analyzed the trend of the manipulation based on microfluidics.
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Affiliation(s)
- Yuwei Lan
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yang Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Man Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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Richard C, Devendran C, Ashtiani D, Cadarso VJ, Neild A. Acoustofluidic cell micro-dispenser for single cell trajectory control. LAB ON A CHIP 2022; 22:3533-3544. [PMID: 35979941 DOI: 10.1039/d2lc00216g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The precise manipulation of individual cells is a key capability for the study of single cell physiological characteristics or responses to stimuli. Currently, only large cell populations can be transferred with certainty using expensive and laborious flow cytometry platforms. However, when approaching small populations of cells, this task becomes increasingly challenging. Here, we report an effective acoustofluidic micro-dispenser, utilising surface acoustic waves (SAWs), with the ability to trap and release cells on demand, which when combined with an external valve can guide the trajectory of individual cells. We demonstrate single cell trap and release with a single cell trapping effectiveness of 74%, enabling the capability of dispensing a highly controlled amount of cells without any harmful effects. This device has the potential to be easily integrated into a wide range of analytical platforms for applications such as single cell fluorescent imaging and single cell proteomic studies.
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Affiliation(s)
- Cynthia Richard
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
- Applied Micro- and Nanotechnology Laboratory, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
| | - Citsabehsan Devendran
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Dariush Ashtiani
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
| | - Victor J Cadarso
- Applied Micro- and Nanotechnology Laboratory, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- Centre to Impact Antimicrobial Resistance, Monash University, Clayton, VIC 3800, Australia
| | - Adrian Neild
- Laboratory for Micro Systems, Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia.
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Wang Y, Zhu Z, Liu K, Xiao Q, Geng Y, Xu F, Ouyang S, Zheng K, Fan Y, Jin N, Zhao X, Marchisio MA, Pan D, Huang QA. A high-throughput microfluidic diploid yeast long-term culturing (DYLC) chip capable of bud reorientation and concerted daughter dissection for replicative lifespan determination. J Nanobiotechnology 2022; 20:171. [PMID: 35361237 PMCID: PMC8973578 DOI: 10.1186/s12951-022-01379-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 03/16/2022] [Indexed: 11/30/2022] Open
Abstract
Background Budding yeast, Saccharomyces cerevisiae, has been extensively favored as a model organism in aging and age-related studies, thanks to versatile microfluidic chips for cell dynamics assay and replicative lifespan (RLS) determination at single-cell resolution. However, previous microfluidic structures aiming to immobilize haploid yeast may impose excessive spatial constraint and mechanical stress on cells, especially for larger diploid cells that sprout in a bipolar pattern. Results We developed a high-throughput microfluidic chip for diploid yeast long-term culturing (DYLC), optical inspection and cell-aging analysis. The DYLC chip features 1100 “leaky bowl”-shaped traps formatted in an array to dock single cells under laminar-perfused medium and effectively remove daughter cells by hydraulic shear forces. The delicate microstructures of cell traps enable hydrodynamic rotation of newborn buds, so as to ensure bud reorientation towards downstream and concerted daughter dissection thereafter. The traps provide sufficient space for cell-volume enlargement during aging, and thus properly alleviate structural compression and external stress on budding yeast. Trapping efficiency and long-term maintenance of single cells were optimized according to computational fluid dynamics simulations and experimental characterization in terms of critical parameters of the trap and array geometries. Owing to the self-filling of daughter cells dissected from traps upstream, an initial trapping efficiency of about 70% can rapidly reach a high value of over 92% after 4-hour cell culturing. During yeast proliferation and aging, cellular processes of growth, budding and daughter dissection were continuously tracked for over 60 h by time-lapse imaging. Yeast RLS and budding time interval (BTI) were directly calculated by the sequential two-digit codes indicating the budding status in images. With the employed diploid yeast strain, we obtained an RLS of 24.29 ± 3.65 generations, and verified the extension of BTI in the first couple of generations after birth and the last several generations approaching death, as well as cell de-synchronization along diploid yeast aging. Conclusions The DYLC chip offers a promising platform for reliable capture and culturing of diploid yeast cells and for life-long tracking of cell dynamics and replicative aging processes so that grasping comprehensive insights of aging mechanism in complex eukaryotic cells. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12951-022-01379-9.
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Affiliation(s)
- Yingying Wang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Zhen Zhu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China.
| | - Ke Liu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Qin Xiao
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Yangye Geng
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Feng Xu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Shuiping Ouyang
- College of Chemical Engineering, Nanjing Forestry University, Longpan Road 159, Nanjing, 210037, China
| | - Ke Zheng
- College of Chemical Engineering, Nanjing Forestry University, Longpan Road 159, Nanjing, 210037, China
| | - Yimin Fan
- College of Chemical Engineering, Nanjing Forestry University, Longpan Road 159, Nanjing, 210037, China
| | - Nan Jin
- ZhongDa Hospital, Southeast University, Dingjiaqiao 87, Nanjing, 210009, China
| | - Xiangwei Zhao
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Mario A Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, Weijin Road 92, Tianjin, 300072, China
| | - Dejing Pan
- Cambridge-Suda Genomic Resource Center and Jiangsu Key Laboratory of Neuropsychiatric Diseases Research, Soochow University, Ren-ai Road 199, Suzhou, 215213, China
| | - Qing-An Huang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Sipailou 2, Nanjing, 210096, China
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Tan YS, Wang L, Wang YY, He QE, Liu ZH, Zhu Z, Song K, Li BZ, Yuan YJ. Protein acetylation regulates xylose metabolism during adaptation of Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:241. [PMID: 34920742 PMCID: PMC8684234 DOI: 10.1186/s13068-021-02090-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND As the second most abundant polysaccharide in nature, hemicellulose can be degraded to xylose as the feedstock for bioconversion to fuels and chemicals. To enhance xylose conversion, the engineered Saccharomyces cerevisiae with xylose metabolic pathway is usually adapted with xylose as the carbon source in the laboratory. However, the mechanism under the adaptation phenomena of the engineered strain is still unclear. RESULTS In this study, xylose-utilizing S. cerevisiae was constructed and used for the adaptation study. It was found that xylose consumption rate increased 1.24-fold in the second incubation of the yYST12 strain in synthetic complete-xylose medium compared with the first incubation. The study figured out that it was observed at the single-cell level that the stagnation time for xylose utilization was reduced after adaptation with xylose medium in the microfluidic device. Such transient memory of xylose metabolism after adaptation with xylose medium, named "xylose consumption memory", was observed in the strains with both xylose isomerase pathway and xylose reductase and xylitol dehydrogenase pathways. In further, the proteomic acetylation of the strains before and after adaptation was investigated, and it was revealed that H4K5 was one of the most differential acetylation sites related to xylose consumption memory of engineered S. cerevisiae. We tested 8 genes encoding acetylase or deacetylase, and it was found that the knockout of the GCN5 and HPA2 encoding acetylases enhanced the xylose consumption memory. CONCLUSIONS The behavior of xylose consumption memory in engineered S. cerevisiae can be successfully induced with xylose in the adaptation. H4K5Ac and two genes of GCN5 and HPA2 are related to xylose consumption memory of engineered S. cerevisiae during adaptation. This study provides valuable insights into the xylose adaptation of engineered S. cerevisiae.
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Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Ying Wang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Qi-En He
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhen Zhu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
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