1
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Lv Q, Zhou T, Zheng R, Li X, Xiao K, Dong Z, Li J, Wei F. CO2 Mobility Control in Porous Media by Using Armored Bubbles with Silica Nanoparticles. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c05648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qichao Lv
- Unconventional Petroleum Research Institute, China University of Petroleum (Beijing), Beijing 102249, China
| | - Tongke Zhou
- Unconventional Petroleum Research Institute, China University of Petroleum (Beijing), Beijing 102249, China
| | - Rong Zheng
- Unconventional Petroleum Research Institute, China University of Petroleum (Beijing), Beijing 102249, China
| | - Xiangling Li
- Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing 100083, China
| | - Kang Xiao
- Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing 100083, China
| | - Zhaoxia Dong
- Unconventional Petroleum Research Institute, China University of Petroleum (Beijing), Beijing 102249, China
| | - Junjian Li
- College of Petroleum Engineering, China University of Petroleum (Beijing), Beijing 102249, China
| | - Falin Wei
- Research Institute of Petroleum Exploration and Development, China National Petroleum Corporation, Beijing 100083, China
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2
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Li X, Feng H, Li Z, Shi Y, Tian J, Zhao C, Yu M, Liu Z, Li H, Shi B, Wang Q, Li L, Wang D, Zhu L, Liu R, Li Z. High-Throughput Identification and Screening of Single Microbial Cells by Nanobowl Array. ACS APPLIED MATERIALS & INTERFACES 2019; 11:44933-44940. [PMID: 31675212 DOI: 10.1021/acsami.9b08662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput screening and fast identification of single bacterial cells are crucial for clinical diagnosis, bioengineering, and fermentation engineering. Although single-cell technologies have been developed extensively in recent years, the single-cell technologies for bacteria still need further exploration. In this study, we demonstrate an identification and screening technology for single bacterial cells based on a large-scale nanobowl array, which is well-ordered and size-adjustable for use with different kinds of bacteria. When the culture medium with monodispersed bacteria was placed on the nanobowl array, it successfully enabled loading of single bacterium into a single nanobowl. Because of the limitative size and depth of the nanobowls, mixture of different bacteria species could be screened according to their sizes. In addition, with the help of a low electrical current, the bacteria can be further screened according to their intrinsic surface charges. If combined with micromanipulation technology, high-throughput single bacterial selection can be achieved in future.
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Affiliation(s)
- Xiuyan Li
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Hongqing Feng
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Zhe Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Yue Shi
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Jingjing Tian
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Chaochao Zhao
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
| | - Min Yu
- School of Stomatology and Medicine , Foshan University , Foshan 528000 , P. R. China
| | - Zhuo Liu
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
| | - Hu Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
| | - Bojing Shi
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
| | - Qian Wang
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Luhai Li
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Dongshu Wang
- State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Biotechnology , Beijing 100071 , P. R. China
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity , Beijing Institute of Biotechnology , Beijing 100071 , P. R. China
| | - Ruping Liu
- Beijing Institute of Graphic Communication , Beijing 102600 , P. R. China
| | - Zhou Li
- CAS Center for Excellence in Nanoscience, Beijing Key Laboratory of Micro-nano Energy and Sensor , Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences , Beijing 100083 , P. R. China
- School of Nanoscience and Technology , University of Chinese Academy of Sciences , Beijing 100049 , P. R. China
- Center on Nanoenergy Research, School of Physical Science and Technology , Guangxi University , Nanning 530004 , P. R. China
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3
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TERAMURA Y. Design and Application of Cell Glue. KOBUNSHI RONBUNSHU 2018. [DOI: 10.1295/koron.2017-0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuji TERAMURA
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo
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4
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Catón L, Yurkov A, Giesbers M, Dijksterhuis J, Ingham CJ. Physically Triggered Morphology Changes in a Novel Acremonium Isolate Cultivated in Precisely Engineered Microfabricated Environments. Front Microbiol 2017; 8:1269. [PMID: 28769882 PMCID: PMC5509762 DOI: 10.3389/fmicb.2017.01269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 06/23/2017] [Indexed: 01/06/2023] Open
Abstract
Fungi are strongly affected by their physical environment. Microfabrication offers the possibility of creating new culture environments and ecosystems with defined characteristics. Here, we report the isolation of a novel member of the fungal genus Acremonium using a microengineered cultivation chip. This isolate was unusual in that it organizes into macroscopic structures when initially cultivated within microwells with a porous aluminum oxide (PAO) base. These “templated mycelial bundles” (TMB) were formed from masses of parallel hyphae with side branching suppressed. TMB were highly hydrated, facilitating the passive movement of solutes along the bundle. By using a range of culture chips, it was deduced that the critical factors in triggering the TMB were growth in microwells from 50 to 300 μm in diameter with a PAO base. Cultivation experiments, using spores and pigments as tracking agents, indicate that bulk growth of the TMB occurs at the base. TMB morphology is highly coherent and is maintained after growing out of the microwells. TMB can explore their environment by developing unbundled lateral hyphae; TMB only followed if nutrients were available. Because of the ease of fabricating numerous microstructures, we suggest this is a productive approach for exploring morphology and growth in multicellular microorganisms and microbial communities.
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Affiliation(s)
| | - Andrey Yurkov
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweig, Germany
| | - Marcel Giesbers
- Wageningen Electron Microscopy Centre, Wageningen University Plant SciencesWageningen, Netherlands
| | - Jan Dijksterhuis
- Westerdijk Fungal Biodiversity Centre-KNAW Fungal Biodiversity CentreUtrecht, Netherlands
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5
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Publisher's note. Regen Ther 2016. [DOI: 10.1016/j.reth.2016.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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6
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A hybrid of cells and pancreatic islets toward a new bioartificial pancreas. Regen Ther 2016; 3:68-74. [PMID: 31245475 PMCID: PMC6581840 DOI: 10.1016/j.reth.2016.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 01/31/2016] [Accepted: 02/12/2016] [Indexed: 01/30/2023] Open
Abstract
Cell surface engineering using single-stranded DNA-poly(ethylene glycol)-conjugated phospholipid (ssDNA-PEG-lipid) is useful for inducing cell-cell attachment two and three dimensionally. In this review, we summarize our recent techniques for cell surface engineering and their applications to islet transplantation. Because any DNA sequence can be immobilized onto the cell surface by hydrophobic interactions between ssDNA-PEG-lipid and the cellular membrane without impairing cell function, a cell-cell hybrid can be formed through the DNA hybridization. With this technique, it would be possible to create three-dimensional hybrid structures of pancreatic islets coated with various accessory cells, such as patients' own cells, mesenchymal and adipose-derived stem cells, endothelial progenitor cells, neural crest stem cells or regulatory T cells, which might significantly improve the outcome of islet transplantation in diabetic patients.
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7
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Recent Advances in Genetic Technique of Microbial Report Cells and Their Applications in Cell Arrays. BIOMED RESEARCH INTERNATIONAL 2015; 2015:182107. [PMID: 26436087 PMCID: PMC4576000 DOI: 10.1155/2015/182107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/26/2015] [Indexed: 11/21/2022]
Abstract
Microbial cell arrays have attracted consistent attention for their ability to provide unique global data on target analytes at low cost, their capacity for readily detectable and robust cell growth in diverse environments, their high degree of convenience, and their capacity for multiplexing via incorporation of molecularly tailored reporter cells. To highlight recent progress in the field of microbial cell arrays, this review discusses research on genetic engineering of reporter cells, technologies for patterning live cells on solid surfaces, cellular immobilization in different polymers, and studies on their application in environmental monitoring, disease diagnostics, and other related fields. On the basis of these results, we discuss current challenges and future prospects for novel microbial cell arrays, which show promise for use as potent tools for unraveling complex biological processes.
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8
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Bragazzi NL, Gasparini R, Amicizia D, Panatto D, Larosa C. Porous Alumina as a Promising Biomaterial for Public Health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 101:213-29. [PMID: 26572980 DOI: 10.1016/bs.apcsb.2015.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Porous aluminum is a nanostructured material characterized by unique properties, such as chemical stability, regular uniformity, dense hexagonal porous lattice with high aspect ratio nanopores, excellent mechanical strength, and biocompatibility. This overview examines how the structure and properties of porous alumina can be exploited in the field of public health. Porous alumina can be employed for fabricating membranes and filters for bioremediation, water ultrafiltration, and microfiltration/nanofiltration, being a promising technique for having clean and fresh water, which is essential for human health. Porous alumina-based nanobiosensor coated with specific antibodies or peptides seem to be a useful tool to detect and remove pathogens both in food and in water, as well as for environmental monitoring. Further, these applications, being low-energy demanding and cost-effective, are particularly valuable in resource-limited settings and contexts, and can be employed as point of use devices in developing countries, where there is an urgent need of hygiene and safety assurance.
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Affiliation(s)
- Nicola Luigi Bragazzi
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Roberto Gasparini
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy.
| | - Daniela Amicizia
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Donatella Panatto
- Department of Health Sciences (DISSAL), Via Antonio Pastore 1, University of Genoa, Genoa, Italy
| | - Claudio Larosa
- Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy
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9
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Yagur-Kroll S, Schreuder E, Ingham CJ, Heideman R, Rosen R, Belkin S. A miniature porous aluminum oxide-based flow-cell for online water quality monitoring using bacterial sensor cells. Biosens Bioelectron 2015; 64:625-32. [DOI: 10.1016/j.bios.2014.09.076] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 10/24/2022]
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10
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Ma L, Datta SS, Karymov MA, Pan Q, Begolo S, Ismagilov RF. Individually addressable arrays of replica microbial cultures enabled by splitting SlipChips. Integr Biol (Camb) 2014; 6:796-805. [PMID: 24953827 PMCID: PMC4131746 DOI: 10.1039/c4ib00109e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Isolating microbes carrying genes of interest from environmental samples is important for applications in biology and medicine. However, this involves the use of genetic assays that often require lysis of microbial cells, which is not compatible with the goal of obtaining live cells for isolation and culture. This paper describes the design, fabrication, biological validation, and underlying physics of a microfluidic SlipChip device that addresses this challenge. The device is composed of two conjoined plates containing 1000 microcompartments, each comprising two juxtaposed wells, one on each opposing plate. Single microbial cells are stochastically confined and subsequently cultured within the microcompartments. Then, we split each microcompartment into two replica droplets, both containing microbial culture, and then controllably separate the two plates while retaining each droplet within each well. We experimentally describe the droplet retention as a function of capillary pressure, viscous pressure, and viscosity of the aqueous phase. Within each pair of replicas, one can be used for genetic analysis, and the other preserves live cells for growth. This microfluidic approach provides a facile way to cultivate anaerobes from complex communities. We validate this method by targeting, isolating, and culturing Bacteroides vulgatus, a core gut anaerobe, from a clinical sample. To date, this methodology has enabled isolation of a novel microbial taxon, representing a new genus. This approach could also be extended to the study of other microorganisms and even mammalian systems, and may enable targeted retrieval of solutions in applications including digital PCR, sequencing, single cell analysis, and protein crystallization.
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Affiliation(s)
- Liang Ma
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, California 91125, USA.
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11
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Park S, Hong X, Choi WS, Kim T. Microfabricated ratchet structure integrated concentrator arrays for synthetic bacterial cell-to-cell communication assays. LAB ON A CHIP 2012; 12:3914-3922. [PMID: 22729033 DOI: 10.1039/c2lc40294g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We describe a microfluidic concentrator array device that is integrated with microfabricated ratchet structures to concentrate motile bacterial cells in desired destinations with required cell densities. The device consists of many pairs of concentrators with a wide range of spacing distances on a chip, and allows cells in one concentrator to be physically separated from but chemically connected to cells in the other concentrator. Therefore, the device facilitates quantification of the effect of spacing distance on the cell-to-cell communication of synthetically engineered bacterial cells. In addition, the device enables us to control the cell number density in each concentrator unit by adjusting the concentration time and the density of cell suspensions, and the basic concentrator unit of the device can be repeatedly duplicated on a chip. Hence, the device not only facilitates an investigation of the effect of cell densities on cell-to-cell communication, but it can also be further applied to an investigation of cellular communication among multiple types of cells. Lastly, the device can be easily fabricated using a single-layered soft-lithography technology so that we believe it would provide a simple but robust means for many synthetic and systems biologists to simplify and speed up their investigations of the synthetic genetic circuits in bacterial cells.
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Affiliation(s)
- Seongyong Park
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, UNIST-gil 50, Eonyang-eup, Ulsan 689-798, Republic of Korea
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12
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Costello CM, Yeung CL, Rawson FJ, Mendes PM. Application of nanotechnology to control bacterial adhesion and patterning on material surfaces. JOURNAL OF EXPERIMENTAL NANOSCIENCE 2012; 7:634-651. [PMID: 24273593 PMCID: PMC3836354 DOI: 10.1080/17458080.2012.740640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Revised: 10/13/2012] [Indexed: 06/02/2023]
Abstract
Bacterial adhesion and biofilm formation on surfaces raises health hazard issues in the medical environment. Previous studies of bacteria adhesion have focused on observations in their natural/native environments. Recently, surface science has contributed in advancing the understanding of bacterial adhesion by providing ideal platforms that attempt to mimic the bacteria's natural environments, whilst also enabling concurrent control, selectivity and spatial control of bacterial adhesion. In this review, we will look at techniques of how nanotechnology is used to control cell adhesion on a planar scale, in addition to describing the use of nanotools for cell micropatterning. Additionally, it will provide a general background of common methods for nanoscale modification enabling biologist unfamiliar with nanotechnology to enter the field.
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Affiliation(s)
- Cait M. Costello
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Chun L. Yeung
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Frankie J. Rawson
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Paula M. Mendes
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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13
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Jang MJ, Nam Y. Aqueous micro-contact printing of cell-adhesive biomolecules for patterning neuronal cell cultures. BIOCHIP JOURNAL 2012. [DOI: 10.1007/s13206-012-6201-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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14
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Hesselman MC, Odoni DI, Ryback BM, de Groot S, van Heck RGA, Keijsers J, Kolkman P, Nieuwenhuijse D, van Nuland YM, Sebus E, Spee R, de Vries H, Wapenaar MT, Ingham CJ, Schroën K, Martins dos Santos VAP, Spaans SK, Hugenholtz F, van Passel MWJ. A multi-platform flow device for microbial (co-) cultivation and microscopic analysis. PLoS One 2012; 7:e36982. [PMID: 22606321 PMCID: PMC3351485 DOI: 10.1371/journal.pone.0036982] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 04/11/2012] [Indexed: 01/06/2023] Open
Abstract
Novel microbial cultivation platforms are of increasing interest to researchers in academia and industry. The development of materials with specialized chemical and geometric properties has opened up new possibilities in the study of previously unculturable microorganisms and has facilitated the design of elegant, high-throughput experimental set-ups. Within the context of the international Genetically Engineered Machine (iGEM) competition, we set out to design, manufacture, and implement a flow device that can accommodate multiple growth platforms, that is, a silicon nitride based microsieve and a porous aluminium oxide based microdish. It provides control over (co-)culturing conditions similar to a chemostat, while allowing organisms to be observed microscopically. The device was designed to be affordable, reusable, and above all, versatile. To test its functionality and general utility, we performed multiple experiments with Escherichia coli cells harboring synthetic gene circuits and were able to quantitatively study emerging expression dynamics in real-time via fluorescence microscopy. Furthermore, we demonstrated that the device provides a unique environment for the cultivation of nematodes, suggesting that the device could also prove useful in microscopy studies of multicellular microorganisms.
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Affiliation(s)
| | - Dorett I. Odoni
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Brendan M. Ryback
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Suzette de Groot
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Ruben G. A. van Heck
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Jaap Keijsers
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Pim Kolkman
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - David Nieuwenhuijse
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Youri M. van Nuland
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Erik Sebus
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Rob Spee
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Hugo de Vries
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | - Marten T. Wapenaar
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
| | | | - Karin Schroën
- Food Process Engineering, Wageningen University, Wageningen, The Netherlands
| | | | - Sebastiaan K. Spaans
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Floor Hugenholtz
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands
| | - Mark W. J. van Passel
- Wageningen UR iGEM 2011 Team, Wageningen University, Wageningen, The Netherlands
- Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
- * E-mail:
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15
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Melamed S, Elad T, Belkin S. Microbial sensor cell arrays. Curr Opin Biotechnol 2012; 23:2-8. [DOI: 10.1016/j.copbio.2011.11.024] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 11/16/2011] [Accepted: 11/23/2011] [Indexed: 11/29/2022]
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16
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Choi WS, Kim M, Park S, Lee SK, Kim T. Patterning and transferring hydrogel-encapsulated bacterial cells for quantitative analysis of synthetically engineered genetic circuits. Biomaterials 2012; 33:624-33. [DOI: 10.1016/j.biomaterials.2011.09.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Accepted: 09/26/2011] [Indexed: 01/24/2023]
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17
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Tuson HH, Renner LD, Weibel DB. Polyacrylamide hydrogels as substrates for studying bacteria. Chem Commun (Camb) 2011; 48:1595-7. [PMID: 22039586 DOI: 10.1039/c1cc14705f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyacrylamide hydrogels can be used as chemically and physically defined substrates for bacterial cell culture, and enable studies of the influence of surfaces on cell growth and behaviour.
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Affiliation(s)
- Hannah H Tuson
- Department of Biochemistry, University of Wisconsin - Madison, 433 Babcock Drive, Madison, WI 53706, USA
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18
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Ingham CJ, ter Maat J, de Vos WM. Where bio meets nano: the many uses for nanoporous aluminum oxide in biotechnology. Biotechnol Adv 2011; 30:1089-99. [PMID: 21856400 DOI: 10.1016/j.biotechadv.2011.08.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 07/28/2011] [Accepted: 08/03/2011] [Indexed: 01/17/2023]
Abstract
Porous aluminum oxide (PAO) is a ceramic formed by an anodization process of pure aluminum that enables the controllable assembly of exceptionally dense and regular nanopores in a planar membrane. As a consequence, PAO has a high porosity, nanopores with high aspect ratio, biocompatibility and the potential for high sensitivity imaging and diverse surface modifications. These properties have made this unusual material attractive to a disparate set of applications. This review examines how the structure and properties of PAO connect with its present and potential uses within research and biotechnology. The role of PAO is covered in areas including microbiology, mammalian cell culture, sensitive detection methods, microarrays and other molecular assays, and in creating new nanostructures with further uses within biology.
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19
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Mitchell RJ, Lee SK, Kim T, Ghim CM. Microbial linguistics: perspectives and applications of microbial cell-to-cell communication. BMB Rep 2011; 44:1-10. [PMID: 21266100 DOI: 10.5483/bmbrep.2011.44.1.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.
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Affiliation(s)
- Robert J Mitchell
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
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Sakurai K, Teramura Y, Iwata H. Cells immobilized on patterns printed in DNA by an inkjet printer. Biomaterials 2011; 32:3596-602. [PMID: 21353304 DOI: 10.1016/j.biomaterials.2011.01.066] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 01/27/2011] [Indexed: 11/16/2022]
Abstract
The ability to two-dimensionally align various kinds of cells freely onto substrate would be a useful tool for analysis of cell-cell interactions. In this study, we aimed to establish a method for attaching cells to the substrate, in which the pattern is drawn by an inkjet printer. Poly-deoxyribonucleic acid (DNA) was immobilized onto the cell surface by use of DNA-conjugated poly(ethylene) glycol-phospholipid (DNA-PEG-lipid), which is the amphiphilic conjugate of PEG-lipid and single-stranded DNA. The surface of the substrate was then modified with the complementary DNA using an inkjet printer. Finally, DNA-immobilized cells were attached onto the substrate through DNA hybridization. The use of the inkjet printer enabled us to draw the DNA pattern accurately on the substrate with a resolution of a few hundred micrometers. DNA-immobilized cells could be attached precisely along the DNA pattern on the substrate. In addition, various kinds of cells could be attached simultaneously by using various sequences of DNA. Our technique is promising for analysis of cell-cell interactions and differentiation induction in stem cell research.
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Affiliation(s)
- Kengo Sakurai
- Department of Reparative Materials, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawara-Cho, Shogoin, Sakyo-Ku, Kyoto 606-8507, Japan
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Kim LN, Choi SE, Kim J, Kim H, Kwon S. Single exposure fabrication and manipulation of 3D hydrogel cell microcarriers. LAB ON A CHIP 2011; 11:48-51. [PMID: 20981360 DOI: 10.1039/c0lc00369g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present a simple and high-throughput method for fabricating free-floating hydrogel cell microcarriers using single exposure UV patterning. We also demonstrate magnetic manipulation of the free-floating cell microcarriers using a magnetic nanoparticle-embedded structure for an active agitation and a solution exchange.
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Affiliation(s)
- Lily Nari Kim
- School of Electrical Engineering and Computer Science, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-744, Korea
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A method of printing uniform protein lines by using flat PDMS stamps. J Colloid Interface Sci 2011; 353:143-8. [DOI: 10.1016/j.jcis.2010.09.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 09/05/2010] [Accepted: 09/08/2010] [Indexed: 11/21/2022]
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Cheng CM, Mazzeo AD, Gong J, Martinez AW, Phillips ST, Jain N, Whitesides GM. Millimeter-scale contact printing of aqueous solutions using a stamp made out of paper and tape. LAB ON A CHIP 2010; 10:3201-5. [PMID: 20949218 DOI: 10.1039/c004903d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
This communication describes a simple method for printing aqueous solutions with millimeter-scale patterns on a variety of substrates using an easily fabricated, paper-based microfluidic device (a paper-based "stamp") as a contact printing device. The device is made from inexpensive materials, and it is easily assembled by hand; this method is thus accessible to a wide range of laboratories and budgets. A single device was used to print over 2500 spots in less than three minutes at a density of 16 spots per square centimetre. This method provides a new tool to pattern biochemicals-reagents, antigens, proteins, and DNA-on planar substrates. The accuracy of the volume of fluid delivered in simple paper-to-paper printing is low, and although the pattern transfer is rapid, it is better suited for qualitative than accurate, quantitative work. By patterning the paper to which the transfer occurs using wax printing or an equivalent technique, accuracy increases substantially.
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Affiliation(s)
- Chao-Min Cheng
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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Ghim CM, Lee SK, Takayama S, Mitchell RJ. The art of reporter proteins in science: past, present and future applications. BMB Rep 2010; 43:451-60. [PMID: 20663405 DOI: 10.5483/bmbrep.2010.43.7.451] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Starting with the first publication of lacZ gene fusion in 1980, reporter genes have just entered their fourth decade. Initial studies relied on the simple fusion of a promoter or gene with a particular reporter gene of interest. Such constructs were then used to determine the promoter activity under specific conditions or within a given cell or organ. Although this protocol was, and still is, very effective, current research shows a paradigm shift has occurred in the use of reporter systems. With the advent of innovative cloning and synthetic biology techniques and microfluidic/nanodroplet systems, reporter genes and their proteins are now finding themselves used in increasingly intricate and novel applications. For example, researchers have used fluorescent proteins to study biofilm formation and discovered that microchannels develop within the biofilm. Furthermore, there has recently been a "fusion" of art and science; through the construction of genetic circuits and regulatory systems, researchers are using bacteria to "paint" pictures based upon external stimuli. As such, this review will discuss the past and current trends in reporter gene applications as well as some exciting potential applications and models that are being developed based upon these remarkable proteins.
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Affiliation(s)
- Cheol-Min Ghim
- Ulsan National Institute of Science and Technology, Korea
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Yaguchi T, Lee S, Choi WS, Kim D, Kim T, Mitchell RJ, Takayama S. Micropatterning bacterial suspensions using aqueous two phase systems. Analyst 2010; 135:2848-52. [DOI: 10.1039/c0an00464b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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