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Zhang H, Li L, Wang S, Sun X, Luo C, Hou B. Construction of dentin-on-a-chip based on microfluidic technology and tissue engineering. J Dent 2024; 146:105028. [PMID: 38719135 DOI: 10.1016/j.jdent.2024.105028] [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: 02/05/2024] [Revised: 04/23/2024] [Accepted: 04/25/2024] [Indexed: 05/19/2024] Open
Abstract
AIM Three-dimensional (3D) cell culture systems perform better in resembling tissue or organism structures compared with traditional 2D models. Organs-on-chips (OoCs) are becoming more efficient 3D models. This study aimed to create a novel simplified dentin-on-a-chip using microfluidic chip technology and tissue engineering for screening dental materials. METHODOLOGY A microfluidic device with three channels was designed for creating 3D dental tissue constructs using stem cells from the apical papilla (SCAP) and gelatin methacrylate (GelMA). The study investigated the effect of varying cell densities and GelMA concentrations on the layer features formed within the microfluidic chip. Cell viability and distribution were evaluated through live/dead staining and nuclei/F-actin staining. The osteo/odontogenic potential was assessed through ALP staining and Alizarin red staining. The impact of GelMA concentrations (5 %, 10 %) on the osteo/odontogenic differentiation trajectory of SCAP was also studied. RESULTS The 3D tissue constructs maintained high viability and favorable spreading within the microfluidic chip for 3-7 days. A cell seeding density of 2 × 104 cells/μL was found to be the most optimal choice, ensuring favorable cell proliferation and even distribution. GelMA concentrations of 5 % and 10 % proved to be most effective for promoting cell growth and uniform distribution. Within the 5 % GelMA group, SCAP demonstrated higher osteo/odontogenic differentiation than that in the 10 % GelMA group. CONCLUSION In 3D culture, GelMA concentration was found to regulate the osteo/odontogenic differentiation of SCAP. The study recommends a seeding density of 2 × 104 cells/μL of SCAP within 5 % GelMA for constructing simplified dentin-on-a-chip. CLINICAL SIGNIFICANCE This study built up the 3D culture protocol, and induced odontogenic differentiation of SCAP, thus forming the simplified dentin-on-a-chip and paving the way to be used as a well-defined biological model for regenerative endodontics. It may serve as a potential testing platform for cell differentiation.
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Affiliation(s)
- Hexuan Zhang
- Center for Microscope Enhanced Dentistry, School of Stomatology, Capital Medical University, Beijing 100162, PR China; Department of Endodontics and Operative Dentistry, School of Stomatology, Capital Medical University, Beijing 100050, PR China
| | - Lingjun Li
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou 325001, PR China.
| | - Shujing Wang
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou 325001, PR China
| | - Xiaoqiang Sun
- Department of Endodontics and Operative Dentistry, School of Stomatology, Capital Medical University, Beijing 100050, PR China
| | - Chunxiong Luo
- Wenzhou Institute University of Chinese Academy of Sciences, Wenzhou 325001, PR China; The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, PR China.
| | - Benxiang Hou
- Center for Microscope Enhanced Dentistry, School of Stomatology, Capital Medical University, Beijing 100162, PR China.
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2
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Zhao Q, Yao F, Li W, Liu S, Bi S. Identification of a dCache-type chemoreceptor in Campylobacter jejuni that specifically mediates chemotaxis towards methyl pyruvate. Front Microbiol 2024; 15:1400284. [PMID: 38784811 PMCID: PMC11111895 DOI: 10.3389/fmicb.2024.1400284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
The foodborne pathogenic bacterium Campylobacter jejuni utilizes chemotaxis to assist in the colonization of host niches. A key to revealing the relationship among chemotaxis and pathogenicity is the discovery of signaling molecules perceived by the chemoreceptors. The C. jejuni chemoreceptor Tlp11 is encoded by the highly infective C. jejuni strains. In the present study, we report that the dCache-type ligand-binding domain (LBD) of C. jejuni ATCC 33560 Tlp11 binds directly to novel ligands methyl pyruvate, toluene, and quinoline using the same pocket. Methyl pyruvate elicits a strong chemoattractant response, while toluene and quinoline function as the antagonists without triggering chemotaxis. The sensory LBD was used to control heterologous proteins by constructing chimeras, indicating that the signal induced by methyl pyruvate is transmitted across the membrane. In addition, bioinformatics and experiments revealed that the dCache domains with methyl pyruvate-binding sites and ability are widely distributed in the order Campylobacterales. This is the first report to identify the class of dCache chemoreceptors that bind to attractant methyl pyruvate and antagonists toluene and quinoline. Our research provides a foundation for understanding the chemotaxis and virulence of C. jejuni and lays a basis for the control of this foodborne pathogen.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fulian Yao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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3
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Salek MM, Carrara F, Zhou J, Stocker R, Jimenez‐Martinez J. Multiscale Porosity Microfluidics to Study Bacterial Transport in Heterogeneous Chemical Landscapes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310121. [PMID: 38445967 PMCID: PMC11132056 DOI: 10.1002/advs.202310121] [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: 12/22/2023] [Indexed: 03/07/2024]
Abstract
Microfluidic models are proving to be powerful systems to study fundamental processes in porous media, due to their ability to replicate topologically complex environments while allowing detailed, quantitative observations at the pore scale. Yet, while porous media such as living tissues, geological substrates, or industrial systems typically display a porosity that spans multiple scales, most microfluidic models to date are limited to a single porosity or a small range of pore sizes. Here, a novel microfluidic system with multiscale porosity is presented. By embedding polyacrylamide (PAAm) hydrogel structures through in-situ photopolymerization in a landscape of microfabricated polydimethylsiloxane (PDMS) pillars with varying spacing, micromodels with porosity spanning several orders of magnitude, from nanometers to millimeters are created. Experiments conducted at different porosity patterns demonstrate the potential of this approach to characterize fundamental and ubiquitous biological and geochemical transport processes in porous media. Accounting for multiscale porosity allows studies of the resulting heterogeneous fluid flow and concentration fields of transported chemicals, as well as the biological behaviors associated with this heterogeneity, such as bacterial chemotaxis. This approach brings laboratory studies of transport in porous media a step closer to their natural counterparts in the environment, industry, and medicine.
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Affiliation(s)
- M. Mehdi Salek
- Department of Biological Engineering, School of EngineeringMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Francesco Carrara
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Jiande Zhou
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Microsystems LaboratoryInstitute of MicroengineeringSchool of EngineeringEPFLLausanneSwitzerland
| | - Roman Stocker
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
| | - Joaquin Jimenez‐Martinez
- Department of CivilEnvironmental and Geomatic EngineeringInstitute of Environmental EngineeringETH ZurichZurichSwitzerland
- Department of Water Resources and Drinking WaterEawagDubendorfSwitzerland
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4
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Xu W, Cerna-Vargas JP, Tajuelo A, Lozano-Montoya A, Kivoloka M, Krink N, Monteagudo-Cascales E, Matilla MA, Krell T, Sourjik V. Systematic mapping of chemoreceptor specificities for Pseudomonas aeruginosa. mBio 2023; 14:e0209923. [PMID: 37791891 PMCID: PMC10653921 DOI: 10.1128/mbio.02099-23] [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: 08/13/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE Chemotaxis of motile bacteria has multiple physiological functions. It enables bacteria to locate optimal ecological niches, mediates collective behaviors, and can play an important role in infection. These multiple functions largely depend on ligand specificities of chemoreceptors, and the number and identities of chemoreceptors show high diversity between organisms. Similar diversity is observed for the spectra of chemoeffectors, which include not only chemicals of high metabolic value but also bacterial, plant, and animal signaling molecules. However, the systematic identification of chemoeffectors and their mapping to specific chemoreceptors remains a challenge. Here, we combined several in vivo and in vitro approaches to establish a systematic screening strategy for the identification of receptor ligands and we applied it to identify a number of new physiologically relevant chemoeffectors for the important opportunistic human pathogen P. aeruginosa. This strategy can be equally applicable to map specificities of sensory domains from a wide variety of receptor types and bacteria.
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Affiliation(s)
- Wenhao Xu
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Jean Paul Cerna-Vargas
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Centro de Biotecnología y Genómica de Plantas CBGP, Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPM, Pozuelo de Alarcón, Madrid, Spain
| | - Ana Tajuelo
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Andrea Lozano-Montoya
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Melissa Kivoloka
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Nicolas Krink
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Elizabet Monteagudo-Cascales
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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5
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Duan J, Zhao Q, Wang Y, Chi Z, Li W, Wang X, Liu S, Bi S. The dCache Domain of the Chemoreceptor Tlp1 in Campylobacter jejuni Binds and Triggers Chemotaxis toward Formate. mBio 2023:e0356422. [PMID: 37052512 DOI: 10.1128/mbio.03564-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Chemotaxis is an important virulence factor in some enteric pathogens, and it is involved in the pathogenesis and colonization of the host. However, there is limited knowledge regarding the environmental signals that promote chemotactic behavior and the sensing of these signals by chemoreceptors. To date, there is no information on the ligand molecule that directly binds to and is sensed by Campylobacter jejuni Tlp1, which is a chemoreceptor with a dCache-type ligand-binding domain (LBD). dCache (double Calcium channels and chemotaxis receptor) is the largest group of sensory domains in bacteria, but the dCache-type chemoreceptor that directly binds to formate has not yet been discovered. In this study, formate was identified as a direct-binding ligand of C. jejuni Tlp1 with high sensing specificity. We used the strategy of constructing a functional hybrid receptor of C. jejuni Tlp1 and the Escherichia coli chemoreceptor Tar to screen for the potential ligand of Tlp1, with the binding of formate to Tlp1-LBD being verified using isothermal titration calorimetry. Molecular docking and experimental analyses indicated that formate binds to the membrane-proximal pocket of the dCache subdomain. Chemotaxis assays demonstrated that formate elicits robust attractant responses of the C. jejuni strain NCTC 11168, specifically via Tlp1. The chemoattraction effect of formate via Tlp1 promoted the growth of C. jejuni, especially when competing with Tlp1- or CheY-knockout strains. Our study reveals the molecular mechanisms by which C. jejuni mediates chemotaxis toward formate, and, to our knowledge, is the first report on the high-specificity binding of the dCache-type chemoreceptor to formate as well as the physiological role of chemotaxis toward formate. IMPORTANCE Chemotaxis is important for Campylobacter jejuni to colonize favorable niches in the gastrointestinal tract of its host. However, there is still a lack of knowledge about the ligand molecules for C. jejuni chemoreceptors. The dCache-type chemoreceptor, namely, Tlp1, is the most conserved chemoreceptor in C. jejuni strains; however, the direct-binding ligand(s) triggering chemotaxis has not yet been discovered. In the present study, we found that the ligand that binds directly to Tlp1-LBD with high specificity is formate. C. jejuni exhibits robust chemoattraction toward formate, primarily via Tlp1. Tlp1 is the first reported dCache-type chemoreceptor that specifically binds formate and triggers strong chemotaxis. We further demonstrated that the formate-mediated promotion of C. jejuni growth is correlated with Tlp1-mediated chemotaxis toward formate. Our work provides important insights into the mechanism and physiological function of chemotaxis toward formate and will facilitate further investigations into the involvement of microbial chemotaxis in pathogen-host interactions.
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Affiliation(s)
- Jingjing Duan
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Yuxin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Xue Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
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6
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Chen X, Bi S, Ma X, Sourjik V, Lai L. Discovery of a New Chemoeffector for Escherichia coli Chemoreceptor Tsr and Identification of a Molecular Mechanism of Repellent Sensing. ACS BIO & MED CHEM AU 2022; 2:386-394. [PMID: 37102165 PMCID: PMC10125284 DOI: 10.1021/acsbiomedchemau.1c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Motile bacteria use chemotaxis to search for nutrients and escape from harmful chemicals. While the sensing mechanisms for chemical attractants are well established, the molecular details of chemorepellent detection are poorly understood. Here, by using combined computational and experimental approaches to screen potential chemoeffectors for the Escherichia coli chemoreceptor Tsr, we identified a specific chemorepellent, 1-aminocyclohexanecarboxylic acid (ACHC). Our study strongly suggests that ACHC directly binds to the periplasmic sensory domain of Tsr and competes with l-serine, the amino acid attractant of Tsr. We further characterized the binding features of l-serine, ACHC, and l-leucine (a natural repellent that binds Tsr) and found that Asn68 plays a key role in mediating chemotactic response. Mutating Asn68 to Ala inverted the response to l-leucine from a repellent to an attractant. Our study provides important insights into the molecular mechanisms of ligand sensing via bacterial chemoreceptors.
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Affiliation(s)
- Xi Chen
- BNLMS,
Peking-Tsinghua Center for Life Sciences at College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuangyu Bi
- Max
Planck Institute for Terrestrial Microbiology & LOEWE Center for
Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaomin Ma
- BNLMS,
Peking-Tsinghua Center for Life Sciences at College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Victor Sourjik
- Max
Planck Institute for Terrestrial Microbiology & LOEWE Center for
Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Luhua Lai
- BNLMS,
Peking-Tsinghua Center for Life Sciences at College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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7
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Abstract
Acetylcholine is a central biological signal molecule present in all kingdoms of life. In humans, acetylcholine is the primary neurotransmitter of the peripheral nervous system; it mediates signal transmission at neuromuscular junctions. Here, we show that the opportunistic human pathogen Pseudomonas aeruginosa exhibits chemoattraction toward acetylcholine over a concentration range of 1 μM to 100 mM. The maximal magnitude of the response was superior to that of many other P. aeruginosa chemoeffectors. We demonstrate that this chemoattraction is mediated by the PctD (PA4633) chemoreceptor. Using microcalorimetry, we show that the PctD ligand-binding domain (LBD) binds acetylcholine with a equilibrium dissociation constant (KD) of 23 μM. It also binds choline and with lower affinity betaine. Highly sensitive responses to acetylcholine and choline, and less sensitive responses to betaine and l-carnitine, were observed in Escherichia coli expressing a chimeric receptor comprising the PctD-LBD fused to the Tar chemoreceptor signaling domain. We also identified the PacA (ECA_RS10935) chemoreceptor of the phytopathogen Pectobacterium atrosepticum, which binds choline and betaine but fails to recognize acetylcholine. To identify the molecular determinants for acetylcholine recognition, we report high-resolution structures of PctD-LBD (with bound acetylcholine and choline) and PacA-LBD (with bound betaine). We identified an amino acid motif in PctD-LBD that interacts with the acetylcholine tail. This motif is absent in PacA-LBD. Significant acetylcholine chemotaxis was also detected in the plant pathogens Agrobacterium tumefaciens and Dickeya solani. To the best of our knowledge, this is the first report of acetylcholine chemotaxis and extends the range of host signals perceived by bacterial chemoreceptors.
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8
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Yi S, Chen JS, Wang CM, Liao WS. Manipulating Chemical Processes by Pseudosolid Spatial Limitation. JACS AU 2021; 1:1435-1444. [PMID: 34604853 PMCID: PMC8479777 DOI: 10.1021/jacsau.1c00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Indexed: 06/13/2023]
Abstract
It is always preferred to perform chemical processes in liquid or gas phases because of the merits of operation convenience, reaction efficiency, and component homogeneity. However, tremendous efforts have to be made to purify the final product and minimize procedure losses unless a well-defined chemical mechanism is found. Herein, an unconventional chemical functioning system accommodating molecule-in-pseudosolid manipulation is reported. It entails the properties of enhanced molecular effective collision and directional guidance for delicate chemical reaction spatial controls. This design achieves facilitated rates on multicomponent chemical reactions with pros of unique simultaneous final product separation through intrapseudosolid spatial limitation. Localized homogeneous component mixing, pronounced molecular collision, and pure product separation happening in this action surmount the obstacles of conventional chemical operation with a straightforward sketch. A path toward fine chemistry is therefore paved, where traditional thoughts on beneficial reaction environments may be reconsidered.
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Affiliation(s)
| | | | - Chang-Ming Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Ssu Liao
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
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9
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Ni B, Colin R, Sourjik V. Production and Characterization of Motile and Chemotactic Bacterial Minicells. ACS Synth Biol 2021; 10:1284-1291. [PMID: 34081866 PMCID: PMC8218304 DOI: 10.1021/acssynbio.1c00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
![]()
Minicells are nanosized
membrane vesicles produced by bacteria.
Minicells are chromosome-free but contain cellular biosynthetic and
metabolic machinery, and they are robust due to the protection provided
by the bacterial cell envelope, which makes them potentially highly
attractive in biomedical applications. However, the applicability
of minicells and other nanoparticle-based delivery systems is limited
by their inefficient accumulation at the target. Here we engineered
the minicell-producing Escherichia coli strain to
overexpress flagellar genes, which enables the generation of motile
minicells. We subsequently performed an experimental and theoretical
analysis of the minicell motility and their responses to gradients
of chemoeffectors. Despite important differences between the motility
of minicells and normal bacterial cells, minicells were able to bias
their movement in chemical gradients and to accumulate toward the
sources of chemoattractants. Such motile and chemotactic minicells
may thus be applicable for an active effector delivery and specific
targeting of tissues and cells according to their metabolic profiles.
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Affiliation(s)
- Bin Ni
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg D-35043, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg D-35043, Germany
| | - Remy Colin
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg D-35043, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg D-35043, Germany
| | - Victor Sourjik
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology, Marburg D-35043, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg D-35043, Germany
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10
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Yang L, Pijuan-Galito S, Rho HS, Vasilevich AS, Eren AD, Ge L, Habibović P, Alexander MR, de Boer J, Carlier A, van Rijn P, Zhou Q. High-Throughput Methods in the Discovery and Study of Biomaterials and Materiobiology. Chem Rev 2021; 121:4561-4677. [PMID: 33705116 PMCID: PMC8154331 DOI: 10.1021/acs.chemrev.0c00752] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/07/2023]
Abstract
The complex interaction of cells with biomaterials (i.e., materiobiology) plays an increasingly pivotal role in the development of novel implants, biomedical devices, and tissue engineering scaffolds to treat diseases, aid in the restoration of bodily functions, construct healthy tissues, or regenerate diseased ones. However, the conventional approaches are incapable of screening the huge amount of potential material parameter combinations to identify the optimal cell responses and involve a combination of serendipity and many series of trial-and-error experiments. For advanced tissue engineering and regenerative medicine, highly efficient and complex bioanalysis platforms are expected to explore the complex interaction of cells with biomaterials using combinatorial approaches that offer desired complex microenvironments during healing, development, and homeostasis. In this review, we first introduce materiobiology and its high-throughput screening (HTS). Then we present an in-depth of the recent progress of 2D/3D HTS platforms (i.e., gradient and microarray) in the principle, preparation, screening for materiobiology, and combination with other advanced technologies. The Compendium for Biomaterial Transcriptomics and high content imaging, computational simulations, and their translation toward commercial and clinical uses are highlighted. In the final section, current challenges and future perspectives are discussed. High-throughput experimentation within the field of materiobiology enables the elucidation of the relationships between biomaterial properties and biological behavior and thereby serves as a potential tool for accelerating the development of high-performance biomaterials.
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Affiliation(s)
- Liangliang Yang
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Sara Pijuan-Galito
- School
of Pharmacy, Biodiscovery Institute, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Hoon Suk Rho
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aliaksei S. Vasilevich
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aysegul Dede Eren
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Lu Ge
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pamela Habibović
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Morgan R. Alexander
- School
of Pharmacy, Boots Science Building, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Jan de Boer
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aurélie Carlier
- Department
of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Patrick van Rijn
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qihui Zhou
- Institute
for Translational Medicine, Department of Stomatology, The Affiliated
Hospital of Qingdao University, Qingdao
University, Qingdao 266003, China
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11
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Takahashi R, Miyazako H, Tanaka A, Ueno Y, Yamaguchi M. Tough, permeable and biocompatible microfluidic devices formed through the buckling delamination of soft hydrogel films. LAB ON A CHIP 2021; 21:1307-1317. [PMID: 33656028 DOI: 10.1039/d0lc01275k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Microchannels in soft materials play an important role in developing movable, deformable, and biocompatible fluidic systems for applications in various fields. Intensively investigated approaches to create microscale channel architectures use mechanical instability in soft materials, which can provide intricate yet ordered architectures with low cost and high throughput. Here, for microchannel fabrication, we demonstrate the use of swelling-driven buckle delamination of hydrogels, which is a mechanical instability pattern found in compressed film/substrate layer composites. By spatially controlling interfacial bonding between a thin polyacrylamide (PAAm) gel film and glass substrate, swelling-driven compressive stress induces buckle delamination at programmed positions, resulting in the formation of continuous hollow paths as microchannels. Connecting flow tubes with a 3D-printed connecter provides a deformable microfluidic device, enabling pressure-driven flows without leakage from the connecter and rupture of the channels. Furthermore, by stacking less-swellable bulk gels on the device, we obtained a tough, permeable, and biocompatible microfluidic device. Finally, we performed a cell culture on the device and chemical stimulation to cells through the diffusion of molecules from the microchannels. The results of this work shed light on designing pressure sensitive/resistant microfluidic systems based on diverse hydrogels with intricate 3D morphologies and will be useful for applications in the fields of bioanalysis, biomimetics, tissue engineering, and cell biology.
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Affiliation(s)
- Riku Takahashi
- NTT Basic Research Laboratories, Bio-Medical Informatics Research Center, NTT Corporation, 3-1 Morinosato -Wakamiya, Atsugi, Kanagawa 243-0198, Japan.
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12
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Chemotaxis-based smart drug delivery of epirubicin using a 3D printed microfluidic chip. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1162:122456. [PMID: 33296831 DOI: 10.1016/j.jchromb.2020.122456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/12/2020] [Accepted: 11/16/2020] [Indexed: 11/21/2022]
Abstract
Recent developments on self-propelled microdroplets, moving controllably in response to an external stimulus like chemical, electrical, or magnetic field, have opened a new horizon for smart drug delivery investigations. On the other hand, the new achievements in 3D printing technology has provided a promising option for the fabrication of microfluidic devices, which is an unrivalled platform for in-vitro drug delivery studies. By synergizing the features of chemotaxis, 3D printing, and microfluidic techniques a new approach was introduced to deliver the drug to targeted sites with a well-controlled method and a reasonable speed. A self-propelled ionic liquid ([P6,6,6,14][Cl]) microdroplet, as the drug carrier, was utilised for the targeted delivery of epirubicin anticancer drug within an integrated drug delivery microfluidic system. The asymmetric diffusion of [P6,6,6,14]+ ion from the microdroplet into an aqueous solution with chloride gradient concentration (created under an external electrical field) caused the microdroplet to move. The spatial and temporal position of the moving microdroplet could be controlled by changing the magnitude and polarity of the external electrical field. A piece of hollow-fiber, fixed next to the anode, was filled with phosphate buffer (as the receptor) and used to remove the drug from the carrier. The receptor solution was then taken and injected into a HPLC system for quantification of the released drug. After one-at-a-time optimization of the channel geometry and electrolyte concentration, the experimental variables affecting the drug loading including contact time, pH, and volume of carrier were optimized via a central composite design (CCD) approach.
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13
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Jeong HH. Recent Developments in Bacterial Chemotaxis Analysis Based on the Microfluidic System. SLAS Technol 2020; 26:159-164. [PMID: 33143544 DOI: 10.1177/2472630320969146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacterial motility in response to chemicals, also called bacterial chemotaxis, is a critical ability to search for the optimal environment to ensure the survival of bacterial species. Recent advances in microbiology have allowed the engineering of bacterial chemotactic properties. Conventional methods for characterizing bacterial motility are not able to fully monitor chemotactic behavior. Developments in microfluidic technology have enabled the designing of new experimental protocols in which spatiotemporal control of the cellular microenvironment can be achieved, and in which bacterial motility can be precisely and quantitatively measured and compared. This review provides an overview of recent developments of and new insights into microfluidic systems for chemotaxis assay.
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Affiliation(s)
- Heon-Ho Jeong
- Department of Chemical and Biomolecular Engineering, Chonnam National University, Yeosu, Jeonnam, Republic of Korea
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14
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Carvalho MR, Truckenmuller R, Reis RL, Oliveira JM. Biomaterials and Microfluidics for Drug Discovery and Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1230:121-135. [DOI: 10.1007/978-3-030-36588-2_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Li L, Wu T, Wang Y, Ran M, Kang Y, Ouyang Q, Luo C. Spatial coordination in a mutually beneficial bacterial community enhances its antibiotic resistance. Commun Biol 2019; 2:301. [PMID: 31428689 PMCID: PMC6687750 DOI: 10.1038/s42003-019-0533-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/04/2019] [Indexed: 02/07/2023] Open
Abstract
Microbial communities can survive in complex and variable environments by using different cooperative strategies. However, the behaviors of these mutuality formed communities remain poorly understood, particularly with regard to the characteristics of spatial cooperation. Here, we selected two Escherichia coli strains, designated as the nutrition provider and the antibiotic protector, respectively, for construction of a mutually beneficial bacterial community that could be used to study these behaviors. We found that in addition to the functional mutualism, the two strains also cooperated through their spatial distribution. Under antibiotic pressure, the bacterial distribution changed to yield different spatial distributions, which resulted in community growth advantages beyond functional cooperation. The mutualistic behavior of these two strains suggested that similar communities could also use variations in spatial distribution to improve their survival rates in a natural environment or under the action of antibiotics.
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Affiliation(s)
- Lingjun Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
| | - Tian Wu
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871 China
| | - Ying Wang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871 China
| | - Min Ran
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871 China
| | - Yu Kang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029 China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871 China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871 China
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16
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Chen D, Liu SJ, Du W. Chemotactic screening of imidazolinone-degrading bacteria by microfluidic SlipChip. JOURNAL OF HAZARDOUS MATERIALS 2019; 366:512-519. [PMID: 30562663 DOI: 10.1016/j.jhazmat.2018.12.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/19/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
The group of imidazolinone herbicides, widely used for weed control, is hazardous to some sensitive rotational crops. Thus, rapid elimination of imidazolinones from contaminated soil is significant for the environment. Biodegradation studies have demonstrated the ability of chemotaxis to enhance the biodegradation of pollutants. In this study, we used our newly developed SlipChip device for chemotactic sorting and a microfluidic streak plate device for bacterial cultivation as a new pipeline for screening imidazolinone degraders. The degradation efficiencies of an enrichment consortium and a chemotaxis consortium were determined by HPLC-MS/MS. Both consortia degraded all tested imidazolinones, with the highest efficiency (71.8%) for imazethapyr, and the chemotaxis consortium degraded these compounds approximately 10% more efficiently than the enrichment consortium. Moreover, the community diversities of the enrichment consortium and the chemotaxis consortium were analyzed by 16S rRNA gene amplicon sequencing. The results indicated that members of genus Ochrobactrum primarily contribute to the degradation of imidazolinones. This work proved that chemotaxis toward biodegradable pollutants increases their bioavailability and enhances the biodegradation rate. It also provided a new way to screen effective pollutant degraders and can be applied for the selective isolation of other chemotactic species from environmental samples.
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Affiliation(s)
- Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Zhou W, Le J, Chen Y, Cai Y, Hong Z, Chai Y. Recent advances in microfluidic devices for bacteria and fungus research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Escape band in Escherichia coli chemotaxis in opposing attractant and nutrient gradients. Proc Natl Acad Sci U S A 2019; 116:2253-2258. [PMID: 30674662 DOI: 10.1073/pnas.1808200116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
It is commonly believed that bacterial chemotaxis helps cells find food. However, not all attractants are nutrients, and not all nutrients are strong attractants. Here, by using microfluidic experiments, we studied Escherichia coli chemotaxis behavior in the presence of a strong chemoattractant (e.g., aspartate or methylaspartate) gradient and an opposing gradient of diluted tryptone broth (TB) growth medium. Our experiments showed that cells initially accumulate near the strong attractant source. However, after the peak cell density (h) reaches a critical value [Formula: see text], the cells form a "escape band" (EB) that moves toward the chemotactically weaker but metabolically richer nutrient source. By using various mutant strains and varying experimental conditions, we showed that the competition between Tap and Tar receptors is the key molecular mechanism underlying the formation of the escape band. A mathematical model combining chemotaxis signaling and cell growth was developed to explain the experiments quantitatively. The model also predicted that the width w and the peak position [Formula: see text] of EB satisfy two scaling relations: [Formula: see text] and [Formula: see text], where l is the channel length. Both scaling relations were verified by experiments. Our study shows that the combination of nutrient consumption, population growth, and chemotaxis with multiple receptors allows cells to search for optimal growth condition in complex environments with conflicting sources.
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19
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Sung YJ, Kwak HS, Hong ME, Choi HI, Sim SJ. Two-Dimensional Microfluidic System for the Simultaneous Quantitative Analysis of Phototactic/Chemotactic Responses of Microalgae. Anal Chem 2018; 90:14029-14038. [DOI: 10.1021/acs.analchem.8b04121] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young Joon Sung
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ho Seok Kwak
- Department of Food Engineering, Dongyang Mirae University, 445, Gyeongin-ro, Guro-gu, Seoul, 08221, Republic of Korea
| | - Min Eui Hong
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Hong Il Choi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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20
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Bi S, Jin F, Sourjik V. Inverted signaling by bacterial chemotaxis receptors. Nat Commun 2018; 9:2927. [PMID: 30050034 PMCID: PMC6062612 DOI: 10.1038/s41467-018-05335-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/02/2018] [Indexed: 11/09/2022] Open
Abstract
Microorganisms use transmembrane sensory receptors to perceive a wide range of environmental factors. It is unclear how rapidly the sensory properties of these receptors can be modified when microorganisms adapt to novel environments. Here, we demonstrate experimentally that the response of an Escherichia coli chemotaxis receptor to its chemical ligands can be easily inverted by mutations at several sites along receptor sequence. We also perform molecular dynamics simulations to shed light on the mechanism of the transmembrane signaling by E. coli chemoreceptors. Finally, we use receptors with inverted signaling to map determinants that enable the same receptor to sense multiple environmental factors, including metal ions, aromatic compounds, osmotic pressure, and salt ions. Our findings demonstrate high plasticity of signaling and provide further insights into the mechanisms of stimulus sensing and processing by bacterial chemoreceptors. Bacteria use chemotaxis receptors to perceive environmental factors. Here, the authors show that mutations in a chemotaxis receptor can invert the sensory response, e.g. from attractant to repellent, and use these mutants to map regions that enable the receptor to sense multiple environmental factors.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, 35043, Germany
| | - Fan Jin
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, 35043, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, 35043, Germany.
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21
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Roggo C, Picioreanu C, Richard X, Mazza C, van Lintel H, van der Meer JR. Quantitative chemical biosensing by bacterial chemotaxis in microfluidic chips. Environ Microbiol 2017; 20:241-258. [DOI: 10.1111/1462-2920.13982] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/02/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Clémence Roggo
- Department of Fundamental Microbiology; University of Lausanne; Lausanne Switzerland 1015
| | - Cristian Picioreanu
- Department of Biotechnology Faculty of Applied Sciences; Delft University of Technology; Delft 2629 HZ The Netherlands
| | - Xavier Richard
- Department of Mathematics; University of Fribourg, CH-1700; Fribourg Switzerland
| | - Christian Mazza
- Department of Mathematics; University of Fribourg, CH-1700; Fribourg Switzerland
| | - Harald van Lintel
- Microsystems Laboratory LMIS4; École Polytechnique Fédérale de Lausanne (EPFL), Station 17; Lausanne Switzerland CH-1015
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22
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ZANG XQ, LI ZY, ZHANG XY, JIANG L, REN NQ, SUN K. Advance in Bacteria Chemotaxis on Microfluidic Devices. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1016/s1872-2040(17)61050-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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23
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Bai Y, Gao M, Wen L, He C, Chen Y, Liu C, Fu X, Huang S. Applications of Microfluidics in Quantitative Biology. Biotechnol J 2017; 13:e1700170. [PMID: 28976637 DOI: 10.1002/biot.201700170] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/03/2017] [Indexed: 01/15/2023]
Abstract
Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future.
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Affiliation(s)
- Yang Bai
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Meng Gao
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Lingling Wen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Caiyun He
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Yuan Chen
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Chenli Liu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Xiongfei Fu
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
| | - Shuqiang Huang
- Center for Synthetic Biology Engineering Research, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, People's Republic of China
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24
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Kim M, Lim JW, Lee SK, Kim T. Nanoscale Hydrodynamic Film for Diffusive Mass Transport Control in Compartmentalized Microfluidic Chambers. Anal Chem 2017; 89:10286-10295. [DOI: 10.1021/acs.analchem.7b01966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Minseok Kim
- Department
of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Ji Won Lim
- Department
of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Sung Kuk Lee
- Department
of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
- Department
of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Taesung Kim
- Department
of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
- Department
of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
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25
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Arginine Is a Critical Substrate for the Pathogenesis of Pseudomonas aeruginosa in Burn Wound Infections. mBio 2017; 8:mBio.02160-16. [PMID: 28292986 PMCID: PMC5350470 DOI: 10.1128/mbio.02160-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Environmental conditions affect bacterial behavior and can greatly influence the course of an infection. However, the environmental cues that elicit bacterial responses in specific infection sites are relatively unknown. Pseudomonas aeruginosa is ubiquitous in nature and typically innocuous. However, it is also one of the most prevalent causes of fatal sepsis in burn wound patients. The aim of this study was to determine the impact of environmental factors, specifically the availability of arginine, on the pathogenesis of P. aeruginosa in burn wound infections. Comparison of burned versus noninjured tissue revealed that l-arginine (l-Arg) was significantly depleted in burn wounds as a consequence of elevated arginase produced by myeloid-derived suppressor cells. We also observed that l-Arg was a potent chemoattractant for P. aeruginosa, and while low concentrations of l-Arg increased P. aeruginosa’s swimming motility, high concentrations resulted in diminished swimming. Based on these observations, we tested whether the administration of exogenous l-Arg into the burn wound could attenuate the virulence of P. aeruginosa in thermally injured mice. Administration of l-Arg resulted in decreased P. aeruginosa spread and sepsis and increased animal survival. Taken together, these data demonstrate that the availability of environmental arginine greatly influences the virulence of P. aeruginosa in vivo and may represent a promising phenotype-modulating tool for future therapeutic avenues. Despite our growing understanding of the pathophysiology of burn wounds and the evolution of techniques and practices to manage infections, sepsis remains a significant medical concern for burn patients. P. aeruginosa continues to be a leader among all causes of bacteremic infections due to its tendency to cause complications in immunocompromised patients and its ubiquitous presence in the hospital setting. With the unforgiving emergence of multidrug-resistant strains, it is critical that alternative strategies to control or prevent septic infections in burn patients be developed in parallel with novel antimicrobial agents. In this study, we observed that administration of l-Arg significantly reduced bacterial spread and sepsis in burned mice infected with P. aeruginosa. Given the safety of l-Arg in high doses and its potential wound-healing benefits, this conditionally essential amino acid may represent a useful tool to modulate bacterial behavior in vivo and prevent sepsis in burn patients.
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26
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Li Z, Cai Q, Zhang X, Si G, Ouyang Q, Luo C, Tu Y. Barrier Crossing in Escherichia coli Chemotaxis. PHYSICAL REVIEW LETTERS 2017; 118:098101. [PMID: 28306307 PMCID: PMC5529051 DOI: 10.1103/physrevlett.118.098101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Indexed: 05/03/2023]
Abstract
We study cell navigation in spatiotemporally complex environments by developing a microfluidic racetrack device that creates a traveling wave with multiple peaks and a tunable wave speed. We find that while the population-averaged chemotaxis drift speed increases with wave speed for low wave speed, it decreases sharply for high wave speed. This reversed dependence of population-averaged chemotaxis drift speed on wave speed is caused by a "barrier-crossing" phenomenon, where a cell hops backwards from one peak attractant location to the peak behind by crossing an unfavorable (barrier) region with low attractant concentrations. By using a coarse-grained model of chemotaxis, we map bacterial motility in an attractant field to the random motion of an overdamped particle in an effective potential. The observed barrier-crossing phenomenon of living cells and its dependence on the spatiotemporal profile of attractant concentration are explained quantitatively by Kramers reaction rate theory.
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Affiliation(s)
- Zhaojun Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qiuxian Cai
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xuanqi Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Guangwei Si
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking-Tsinghua Center for Life Science, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Yuhai Tu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA
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27
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Zhang R, Yuan H, Wang S, Ouyang Q, Chen Y, Hao N, Luo C. High-throughput single-cell analysis for the proteomic dynamics study of the yeast osmotic stress response. Sci Rep 2017; 7:42200. [PMID: 28181485 PMCID: PMC5299847 DOI: 10.1038/srep42200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 01/06/2017] [Indexed: 11/22/2022] Open
Abstract
Motorized fluorescence microscopy combined with high-throughput microfluidic chips is a powerful method to obtain information about different biological processes in cell biology studies. Generally, to observe different strains under different environments, high-throughput microfluidic chips require complex preparatory work. In this study, we designed a novel and easily operated high-throughput microfluidic system to observe 96 different GFP-tagged yeast strains in one switchable culture condition or 24 different GFP-tagged yeast strains in four parallel switchable culture conditions. A multi-pipette is the only additional equipment required for high-throughput patterning of cells in the chip. Only eight connections are needed to control 96 conditions. Using these devices, the proteomic dynamics of the yeast stress response pathway were carefully studied based on single-cell data. A new method to characterize the proteomic dynamics using a single cell’s data is proposed and compared to previous methods, and the new technique should be useful for studying underlying control networks. Our method provides an easy and systematic way to study signaling pathways at the single-cell level.
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Affiliation(s)
- Rongfei Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Haiyu Yuan
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
| | - Shujing Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Yong Chen
- Ecole Normale Superieure, 24 rue Lhomond, 75231 Paris, France
| | - Nan Hao
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.,The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, China
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28
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Bi S, Pollard AM, Yang Y, Jin F, Sourjik V. Engineering Hybrid Chemotaxis Receptors in Bacteria. ACS Synth Biol 2016; 5:989-1001. [PMID: 27285081 DOI: 10.1021/acssynbio.6b00053] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Most bacteria use transmembrane sensors to detect a wide range of environmental stimuli. A large class of such sensors are the chemotaxis receptors used by motile bacteria to follow environmental chemical gradients. In Escherichia coli, chemotaxis receptors are known to mediate highly sensitive responses to ligands, making them potentially useful for biosensory applications. However, with only four ligand-binding chemotaxis receptors, the natural ligand spectrum of E. coli is limited. The design of novel chemoreceptors to extend the sensing capabilities of E. coli is therefore a critical aspect of chemotaxis-based biosensor development. One path for novel sensor design is to harvest the large natural diversity of chemosensory functions found in bacteria by creating hybrids that have the signaling domain from E. coli chemotaxis receptors and sensory domains from other species. In this work, we demonstrate that the E. coli receptor Tar can be successfully combined with most typical sensory domains found in chemotaxis receptors and in evolutionary-related two-component histidine kinases. We show that such functional hybrids can be generated using several different fusion points. Our work further illustrates how hybrid receptors could be used to quantitatively characterize ligand specificity of chemotaxis receptors and histidine kinases using standardized assays in E. coli.
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Affiliation(s)
- Shuangyu Bi
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Abiola M. Pollard
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Yiling Yang
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Fan Jin
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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Abstract
Molecular diffusive membranes or materials are important for biological applications in microfluidic systems. Hydrogels are typical materials that offer several advantages, such as free diffusion for small molecules, biocompatibility with most cells, temperature sensitivity, relatively low cost, and ease of production. With the development of microfluidic applications, hydrogels can be integrated into microfluidic systems by soft lithography, flow-solid processes or UV cure methods. Due to their special properties, hydrogels are widely used as fluid control modules, biochemical reaction modules or biological application modules in different applications. Although hydrogels have been used in microfluidic systems for more than ten years, many hydrogels' properties and integrated techniques have not been carefully elaborated. Here, we systematically review the physical properties of hydrogels, general methods for gel-microfluidics integration and applications of this field. Advanced topics and the outlook of hydrogel fabrication and applications are also discussed. We hope this review can help researchers choose suitable methods for their applications using hydrogels.
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Affiliation(s)
- Xuanqi Zhang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Dong L, Chen DW, Liu SJ, Du W. Automated Chemotactic Sorting and Single-cell Cultivation of Microbes using Droplet Microfluidics. Sci Rep 2016; 6:24192. [PMID: 27074762 PMCID: PMC4831006 DOI: 10.1038/srep24192] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 03/22/2016] [Indexed: 11/10/2022] Open
Abstract
We report a microfluidic device for automated sorting and cultivation of chemotactic microbes from pure cultures or mixtures. The device consists of two parts: in the first part, a concentration gradient of the chemoeffector was built across the channel for inducing chemotaxis of motile cells; in the second part, chemotactic cells from the sample were separated, and mixed with culture media to form nanoliter droplets for encapsulation, cultivation, enumeration, and recovery of single cells. Chemotactic responses were assessed by imaging and statistical analysis of droplets based on Poisson distribution. An automated procedure was developed for rapid enumeration of droplets with cell growth, following with scale-up cultivation on agar plates. The performance of the device was evaluated by the chemotaxis assays of Escherichia coli (E. coli) RP437 and E. coli RP1616. Moreover, enrichment and isolation of non-labelled Comamonas testosteroni CNB-1 from its 1:10 mixture with E. coli RP437 was demonstrated. The enrichment factor reached 36.7 for CNB-1, based on its distinctive chemotaxis toward 4-hydroxybenzoic acid. We believe that this device can be widely used in chemotaxis studies without necessarily relying on fluorescent labelling, and isolation of functional microbial species from various environments.
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Affiliation(s)
- Libing Dong
- Department of Chemistry, Renmin University of China, Beijing 100872, China.,State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong-Wei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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31
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Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that has long been known to chemotax. More recently, it has been established that chemotaxis is an important factor in the ability of P. aeruginosa to make biofilms. Genes that allow P. aeruginosa to chemotax are homologous with genes in the paradigmatic model organism for chemotaxis, Escherichia coli. However, P. aeruginosa is singly flagellated and E. coli has multiple flagella. Therefore, the regulation of counterclockwise/clockwise flagellar motor bias that allows E. coli to efficiently chemotax by runs and tumbles would lead to inefficient chemotaxis by P. aeruginosa, as half of a randomly oriented population would respond to a chemoattractant gradient in the wrong sense. How P. aeruginosa regulates flagellar rotation to achieve chemotaxis is not known. Here, we analyze the swimming trajectories of single cells in microfluidic channels and the rotations of cells tethered by their flagella to the surface of a variable-environment flow cell. We show that P. aeruginosa chemotaxes by symmetrically increasing the durations of both counterclockwise and clockwise flagellar rotations when swimming up the chemoattractant gradient and symmetrically decreasing rotation durations when swimming down the chemoattractant gradient. Unlike the case for E. coli, the counterclockwise/clockwise bias stays constant for P. aeruginosa. We describe P. aeruginosa’s chemotaxis using an analytical model for symmetric motor regulation. We use this model to do simulations that show that, given P. aeruginosa’s physiological constraints on motility, its distinct, symmetric regulation of motor switching optimizes chemotaxis. Chemotaxis has long been known to strongly affect biofilm formation by the opportunistic human pathogen P. aeruginosa, whose essential chemotaxis genes have homologues in E. coli, which achieves chemotaxis by biasing the relative probability of counterclockwise and clockwise flagellar rotation. However, the physiological difference between multiflagellated E. coli and singly flagellated P. aeruginosa implies that biased motor regulation should prevent P. aeruginosa populations from chemotaxing efficiently. Here, we used experiments, analytical modeling, and simulations to demonstrate that P. aeruginosa uses unbiased, symmetric regulation of the flagellar motor to maximize its chemotaxis efficiency. This mode of chemotaxis was not previously known and demonstrates a new variant of a paradigmatic signaling system in an important human pathogen.
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High-throughput screening approaches and combinatorial development of biomaterials using microfluidics. Acta Biomater 2016; 34:1-20. [PMID: 26361719 DOI: 10.1016/j.actbio.2015.09.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022]
Abstract
From the first microfluidic devices used for analysis of single metabolic by-products to highly complex multicompartmental co-culture organ-on-chip platforms, efforts of many multidisciplinary teams around the world have been invested in overcoming the limitations of conventional research methods in the biomedical field. Close spatial and temporal control over fluids and physical parameters, integration of sensors for direct read-out as well as the possibility to increase throughput of screening through parallelization, multiplexing and automation are some of the advantages of microfluidic over conventional, 2D tissue culture in vitro systems. Moreover, small volumes and relatively small cell numbers used in experimental set-ups involving microfluidics, can potentially decrease research cost. On the other hand, these small volumes and numbers of cells also mean that many of the conventional molecular biology or biochemistry assays cannot be directly applied to experiments that are performed in microfluidic platforms. Development of different types of assays and evidence that such assays are indeed a suitable alternative to conventional ones is a step that needs to be taken in order to have microfluidics-based platforms fully adopted in biomedical research. In this review, rather than providing a comprehensive overview of the literature on microfluidics, we aim to discuss developments in the field of microfluidics that can aid advancement of biomedical research, with emphasis on the field of biomaterials. Three important topics will be discussed, being: screening, in particular high-throughput and combinatorial screening; mimicking of natural microenvironment ranging from 3D hydrogel-based cellular niches to organ-on-chip devices; and production of biomaterials with closely controlled properties. While important technical aspects of various platforms will be discussed, the focus is mainly on their applications, including the state-of-the-art, future perspectives and challenges. STATEMENT OF SIGNIFICANCE Microfluidics, being a technology characterized by the engineered manipulation of fluids at the submillimeter scale, offers some interesting tools that can advance biomedical research and development. Screening platforms based on microfluidic technologies that allow high-throughput and combinatorial screening may lead to breakthrough discoveries not only in basic research but also relevant to clinical application. This is further strengthened by the fact that reliability of such screens may improve, since microfluidic systems allow close mimicking of physiological conditions. Finally, microfluidic systems are also very promising as micro factories of a new generation of natural or synthetic biomaterials and constructs, with finely controlled properties.
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Choi HI, Kim JYH, Kwak HS, Sung YJ, Sim SJ. Quantitative analysis of the chemotaxis of a green alga, Chlamydomonas reinhardtii, to bicarbonate using diffusion-based microfluidic device. BIOMICROFLUIDICS 2016; 10:014121. [PMID: 26958101 PMCID: PMC4769253 DOI: 10.1063/1.4942756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/12/2016] [Indexed: 05/24/2023]
Abstract
There is a growing interest in the photosynthetic carbon fixation by microalgae for the production of valuable products from carbon dioxide (CO2). Microalgae are capable of transporting bicarbonate (HCO3 (-)), the most abundant form of inorganic carbon species in the water, as a source of CO2 for photosynthesis. Despite the importance of HCO3 (-) as the carbon source, little is known about the chemotactic response of microalgae to HCO3 (-). Here, we showed the chemotaxis of a model alga, Chlamydomonas reinhardtii, towards HCO3 (-) using an agarose gel-based microfluidic device with a flow-free and stable chemical gradient during the entire assay period. The device was validated by analyzing the chemotactic responses of C. reinhardtii to the previously known chemoattractants (NH4Cl and CoCl2) and chemotactically neutral molecule (NaCl). We found that C. reinhardtii exhibited the strongest chemotactic response to bicarbonate at the concentration of 26 mM in a microfluidic device. The chemotactic response to bicarbonate showed a circadian rhythm with a peak during the dark period and a valley during the light period. We also observed the changes in the chemotaxis to bicarbonate by an inhibitor of bicarbonate transporters and a mutation in CIA5, a transcriptional regulator of carbon concentrating mechanism, indicating the relationship between chemotaxis to bicarbonate and inorganic carbon metabolism in C. reinhardtii. To the best of our knowledge, this is the first report of the chemotaxis of C. reinhardtii towards HCO3 (-), which contributes to the understanding of the physiological role of the chemotaxis to bicarbonate and its relevance to inorganic carbon utilization.
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Affiliation(s)
- Hong Il Choi
- Department of Chemical and Biological Engineering, Korea University , Seoul 136-713, South Korea
| | - Jaoon Young Hwan Kim
- Department of Chemical and Biological Engineering, Korea University , Seoul 136-713, South Korea
| | - Ho Seok Kwak
- Department of Chemical and Biological Engineering, Korea University , Seoul 136-713, South Korea
| | - Young Joon Sung
- Department of Chemical and Biological Engineering, Korea University , Seoul 136-713, South Korea
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Kim M, Kim T. Crack-Photolithography for Membrane-Free Diffusion-Based Micro/Nanofluidic Devices. Anal Chem 2015; 87:11215-23. [DOI: 10.1021/acs.analchem.5b02028] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Minseok Kim
- Department of Mechanical Engineering, ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan, 689-798, Republic of Korea
| | - Taesung Kim
- Department of Mechanical Engineering, ‡Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan, 689-798, Republic of Korea
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Nagy K, Sipos O, Valkai S, Gombai É, Hodula O, Kerényi Á, Ormos P, Galajda P. Microfluidic study of the chemotactic response of Escherichia coli to amino acids, signaling molecules and secondary metabolites. BIOMICROFLUIDICS 2015; 9:044105. [PMID: 26339306 PMCID: PMC4506296 DOI: 10.1063/1.4926981] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 07/02/2015] [Indexed: 05/08/2023]
Abstract
Quorum sensing and chemotaxis both affect bacterial behavior on the population level. Chemotaxis shapes the spatial distribution of cells, while quorum sensing realizes a cell-density dependent gene regulation. An interesting question is if these mechanisms interact on some level: Does quorum sensing, a density dependent process, affect cell density itself via chemotaxis? Since quorum sensing often spans across species, such a feedback mechanism may also exist between multiple species. We constructed a microfluidic platform to study these questions. A flow-free, stable linear chemical gradient is formed in our device within a few minutes that makes it suitable for sensitive testing of chemoeffectors: we showed that the amino acid lysine is a weak chemoattractant for Escherichia coli, while arginine is neutral. We studied the effect of quorum sensing signal molecules of Pseudomonas aeruginosa on E. coli chemotaxis. Our results show that N-(3-oxododecanoyl)-homoserine lactone (oxo-C12-HSL) and N-(butryl)-homoserine lactone (C4-HSL) are attractants. Furthermore, we tested the chemoeffector potential of pyocyanin and pyoverdine, secondary metabolites under a quorum sensing control. Pyocyanin is proved to be a weak attractant while pyoverdine are repellent. We demonstrated the usability of the device in co-culturing experiments, where we showed that various factors released by P. aeruginosa affect the dynamic spatial rearrangement of a neighboring E. coli population, while surface adhesion of the cells is also modulated.
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Affiliation(s)
- Krisztina Nagy
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Orsolya Sipos
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Sándor Valkai
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Éva Gombai
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Orsolya Hodula
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Ádám Kerényi
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Pál Ormos
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
| | - Péter Galajda
- Institute of Biophysics, Biological Research Centre of the Hungarian Academy of Sciences , Temesvari krt. 62, H-6726 Szeged, Hungary
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36
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Pump-free gradient-based micro-device enables quantitative and high-throughput bacterial growth inhibition analysis. Biomed Microdevices 2015; 17:67. [DOI: 10.1007/s10544-015-9971-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lim JW, Ha D, Lee J, Lee SK, Kim T. Review of micro/nanotechnologies for microbial biosensors. Front Bioeng Biotechnol 2015; 3:61. [PMID: 26029689 PMCID: PMC4426784 DOI: 10.3389/fbioe.2015.00061] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 04/20/2015] [Indexed: 01/28/2023] Open
Abstract
A microbial biosensor is an analytical device with a biologically integrated transducer that generates a measurable signal indicating the analyte concentration. This method is ideally suited for the analysis of extracellular chemicals and the environment, and for metabolic sensory regulation. Although microbial biosensors show promise for application in various detection fields, some limitations still remain such as poor selectivity, low sensitivity, and impractical portability. To overcome such limitations, microbial biosensors have been integrated with many recently developed micro/nanotechnologies and applied to a wide range of detection purposes. This review article discusses micro/nanotechnologies that have been integrated with microbial biosensors and summarizes recent advances and the applications achieved through such novel integration. Future perspectives on the combination of micro/nanotechnologies and microbial biosensors will be discussed, and the necessary developments and improvements will be strategically deliberated.
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Affiliation(s)
- Ji Won Lim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Dogyeong Ha
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Jongwan Lee
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Sung Kuk Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
- Department of Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - Taesung Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
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Shen C, Xu P, Huang Z, Cai D, Liu SJ, Du W. Bacterial chemotaxis on SlipChip. LAB ON A CHIP 2014; 14:3074-80. [PMID: 24968180 DOI: 10.1039/c4lc00213j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This paper describes a simple and reusable microfluidic SlipChip device for studying bacterial chemotaxis based on free interface diffusion. The device consists of two glass plates with reconfigurable microwells and ducts, which can set up 20 parallel chemotaxis units as duplicates. In each unit, three nanoliter microwells and connecting ducts were assembled for pipette loading of a chemoeffector solution, bacterial suspension, and 1X PBS buffer solution. By a simple slipping operation, three microwells were disconnected from other units and interconnected by the ducts, which allowed the formation of diffusion concentration gradients of the chemoeffector for inducing cell migration from the cell microwell towards the other two microwells. The migration of cells in the microwells was monitored and accurately counted to evaluate chemotaxis. Moreover, the migrated cells were easily collected by pipetting for further studies after a slip step to reconnect the chemoeffector microwells. The performance of the device was characterized by comparing chemotaxis of two Escherichia coli species, using aspartic acid as the attractant and nitrate sulfate as the repellent. It also enables the separation of bacterial species from a mixture, based on the difference of chemotactic abilities, and collection of the cells with strong chemotactic phenomena for further studies off the chip.
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Affiliation(s)
- Chaohua Shen
- Department of Chemistry, Renmin University of China, 100872 Beijing, China
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39
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Wang Z, Lee I, Jeon TJ, Kim SM. Micro-/nanofluidic device for tunable generation of a concentration gradient: application to Caenorhabditis elegans chemotaxis. Anal Bioanal Chem 2014; 406:2679-86. [DOI: 10.1007/s00216-014-7663-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/24/2022]
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40
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Discovery of novel chemoeffectors and rational design of Escherichia coli chemoreceptor specificity. Proc Natl Acad Sci U S A 2013; 110:16814-9. [PMID: 24082101 DOI: 10.1073/pnas.1306811110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial chemoreceptors mediate chemotactic responses to diverse stimuli. Here, by using an integrated in silico, in vitro, and in vivo approach, we screened a large compound library and found eight novel chemoeffectors for the Escherichia coli chemoreceptor Tar. Six of the eight new Tar binding compounds induce attractant responses, and two of them function as antagonists that can bind Tar without inducing downstream signaling. Comparison between the antagonist and attractant binding patterns suggests that the key interactions for chemotaxis signaling are mediated by the hydrogen bonds formed between a donor group in the attractant and the main-chain carbonyls (Y149 and/or Q152) on the α4 helix of Tar. This molecular insight for signaling is verified by converting an antagonist to an attractant when introducing an N-H group into the antagonist to restore the hydrogen bond. Similar signal triggering effect by an O-H group is also confirmed. Our study suggests that the Tar chemoeffector binding pocket may be separated into two functional regions: region I mainly contributes to binding and region II contributes to both binding and signaling. This scenario of binding and signaling suggests that Tar may be rationally designed to respond to a nonnative ligand by altering key residues in region I to strengthen binding with the novel ligand while maintaining the key interactions in region II for signaling. Following this strategy, we have successfully redesigned Tar to respond to l-arginine, a basic amino acid that does not have chemotactic effect for WT Tar, by two site-specific mutations (R69'E and R73'E).
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41
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Jeong HH, Lee SH, Lee CS. Pump-less static microfluidic device for analysis of chemotaxis of Pseudomonas aeruginosa using wetting and capillary action. Biosens Bioelectron 2013; 47:278-84. [DOI: 10.1016/j.bios.2013.03.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/07/2013] [Accepted: 03/14/2013] [Indexed: 12/22/2022]
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Yang W, Li Z, Zhang W, Luo C, Ouyang Q, Yang G, Wang Y. A novel density control device for the study of cancer cell autocrine effect. Biomed Microdevices 2013; 15:683-689. [PMID: 23784259 DOI: 10.1007/s10544-013-9783-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this paper, we propose a novel cell self-loading and patterning device for quantitatively study density effect on cell behaviors. Using this device, it is easy to gather different cell density colonies in different sizes of micro-chambers using one homogeneous cell solution. As a demonstration, we show that the cell number of self-patterning MCF-7 colony is in proportion to the size of liquid-absorbing cavity in the device, from single cell to tens of cells. This device can easily be used to compare the cancer cells' proliferation in different micro-environments, such as the same number of cells in micro-cavities with different sizes, or different numbers of cells in micro-cavities with the same size, or with different FBS concentrations. Our studies imply a plausible positive correlation between the local concentration of autocrine factors and tumor cell proliferation, which is also quantitative analyzed by a simple model.
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Affiliation(s)
- Wei Yang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, People's Republic of China
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China
| | - Zhaojun Li
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China
| | - Weilin Zhang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Chunxiong Luo
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, People's Republic of China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China.
| | - Qi Ouyang
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, People's Republic of China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, People's Republic of China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, People's Republic of China.
| | - Gen Yang
- State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing, 100871, People's Republic of China
| | - Yugang Wang
- State Key Laboratory of Nuclear Physics and Technology, Peking University, Beijing, 100871, People's Republic of China
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Mendelson A, Cheung Y, Paluch K, Chen M, Kong K, Tan J, Dong Z, Sia SK, Mao JJ. Competitive stem cell recruitment by multiple cytotactic cues. LAB ON A CHIP 2013; 13:1156-64. [PMID: 23364311 PMCID: PMC4093799 DOI: 10.1039/c2lc41219e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A multitude of cytotactic cues direct cell migration in development, cancer metastasis and wound healing. However, our understanding of cell motility remains fragmented partially because current migration devices only allow the study of independent factors. We developed a cell motility assay that allows competitive recruitment of a given cell population simultaneously by gradients of multiple cytotactic cues, observable under real-time imaging. Well-defined uniform gradients of cytotactic cues can be independently generated and sustained in each channel. As a case study, bone marrow mesenchymal stem/stromal cells (MSCs) were exposed to 15 cytokines that are commonly present in arthritis. Cytokines that induced robust recruitment of MSCs in multiple groups were selected to 'compete' in a final round to yield the most chemotactic factor(s) based on cell migration numbers, distances, migration indices and motility over time. The potency of a given cytokine in competition frequently differed from its individual action, substantiating the need to test multiple cytokines concurrently due to synergistic or antagonistic effects. This new device has the rare capacity to screen molecules that induce cell migration in cancer therapy, drug development and tissue regeneration.
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Affiliation(s)
- Avital Mendelson
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
- Departmental of Biomedical Engineering, Columbia University, New York, NY 10027
| | - Yukkee Cheung
- Departmental of Biomedical Engineering, Columbia University, New York, NY 10027
| | - Kamila Paluch
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
- Departmental of Biomedical Engineering, Columbia University, New York, NY 10027
| | - Mo Chen
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
| | - Kimi Kong
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
| | - Jiali Tan
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
| | - Ziming Dong
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
| | - Samuel K. Sia
- Departmental of Biomedical Engineering, Columbia University, New York, NY 10027
| | - Jeremy J. Mao
- Tissue Engineering and Regenerative Medicine Laboratory (TERML), Columbia University Medical Center, 630 W. 168 St. –PH7E, New York, NY 10032
- Departmental of Biomedical Engineering, Columbia University, New York, NY 10027
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Vereshchagina E, Mc Glade D, Glynn M, Ducrée J. A hybrid microfluidic platform for cell-based assays via diffusive and convective trans-membrane perfusion. BIOMICROFLUIDICS 2013; 7:34101. [PMID: 24404021 PMCID: PMC3663865 DOI: 10.1063/1.4804250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 04/24/2013] [Indexed: 05/07/2023]
Abstract
We present a novel 3D hybrid assembly of a polymer microfluidic chip with polycarbonate track-etched membrane (PCTEM) enabling membrane-supported cell culture. Two chip designs have been developed to establish either diffusive or convective reagent delivery using the integrated PCTEM. While it is well suited to a range of cell-based assays, we specifically employ this platform for the screening of a common antitumor chemotoxic agent (mitomycin C - MMC) on the HL60 myeloid leukemia cell line. The toxic activity of MMC is based on the generation of severe DNA damage in the cells. Using either mode of operation, the HL60 cells were cultured on-chip before, during, and after exposure to MMC at concentrations ranging from 0 to 50 μM. Cell viability was analysed off-chip by the trypan blue dye exclusion assay. The results of the on-chip viability assay were found to be consistent with those obtained off-chip and indicated ca. 40% cell survival at MMC concentration of 50 μM. The catalogue of capabilities of the here described cell assay platform comprises of (i) the culturing of cells either under shear-free conditions or under induced through-membrane flows, (ii) the tight time control of the reagent exposure, (iii) the straightforward assembly of devices, (iv) the flexibility on the choice of the membrane, and, prospectively, (v) the amenability for large-scale parallelization.
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Affiliation(s)
- Elizaveta Vereshchagina
- School of Physical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Declan Mc Glade
- School of Physical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Macdara Glynn
- Biomedical Diagnostics Institute, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
| | - Jens Ducrée
- School of Physical Sciences, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland ; Biomedical Diagnostics Institute, National Centre for Sensor Research, Dublin City University, Dublin 9, Ireland
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