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Nagy K, Ábrahám Á, Keymer JE, Galajda P. Application of Microfluidics in Experimental Ecology: The Importance of Being Spatial. Front Microbiol 2018; 9:496. [PMID: 29616009 PMCID: PMC5870036 DOI: 10.3389/fmicb.2018.00496] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/02/2018] [Indexed: 12/21/2022] Open
Abstract
Microfluidics is an emerging technology that is used more and more in biology experiments. Its capabilities of creating precisely controlled conditions in cellular dimensions make it ideal to explore cell-cell and cell-environment interactions. Thus, a wide spectrum of problems in microbial ecology can be studied using engineered microbial habitats. Moreover, artificial microfluidic ecosystems can serve as model systems to test ecology theories and principles that apply on a higher level in the hierarchy of biological organization. In this mini review we aim to demonstrate the versatility of microfluidics and the diversity of its applications that help the advance of microbiology, and in more general, experimental ecology.
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Affiliation(s)
- Krisztina Nagy
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ágnes Ábrahám
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Science, University of Szeged, Szeged, Hungary
| | - Juan E. Keymer
- School of Biological Sciences and School of Physics, Pontifical Catholic University of Chile, Santiago, Chile
| | - Péter Galajda
- Biological Research Centre, Institute of Biophysics, Hungarian Academy of Sciences, Szeged, Hungary
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2
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Kim K, Kim S, Jeon JS. Visual Estimation of Bacterial Growth Level in Microfluidic Culture Systems. SENSORS (BASEL, SWITZERLAND) 2018; 18:E447. [PMID: 29401651 PMCID: PMC5855051 DOI: 10.3390/s18020447] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/22/2022]
Abstract
Microfluidic devices are an emerging platform for a variety of experiments involving bacterial cell culture, and has advantages including cost and convenience. One inevitable step during bacterial cell culture is the measurement of cell concentration in the channel. The optical density measurement technique is generally used for bacterial growth estimation, but it is not applicable to microfluidic devices due to the small sample volumes in microfluidics. Alternately, cell counting or colony-forming unit methods may be applied, but these do not work in situ; nor do these methods show measurement results immediately. To this end, we present a new vision-based method to estimate the growth level of the bacteria in microfluidic channels. We use Fast Fourier transform (FFT) to detect the frequency level change of the microscopic image, focusing on the fact that the microscopic image becomes rough as the number of cells in the field of view increases, adding high frequencies to the spectrum of the image. Two types of microfluidic devices are used to culture bacteria in liquid and agar gel medium, and time-lapsed images are captured. The images obtained are analyzed using FFT, resulting in an increase in high-frequency noise proportional to the time passed. Furthermore, we apply the developed method in the microfluidic antibiotics susceptibility test by recognizing the regional concentration change of the bacteria that are cultured in the antibiotics gradient. Finally, a deep learning-based data regression is performed on the data obtained by the proposed vision-based method for robust reporting of data.
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Affiliation(s)
- Kyukwang Kim
- Robotics Program, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon 34141, Korea.
| | - Seunggyu Kim
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon 34141, Korea.
| | - Jessie S Jeon
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Daejeon 34141, Korea.
- KAIST Institute for Health Science and Technology, 291 Daehak-ro, Daejeon 34141, Korea.
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3
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Austin CM, Caro DM, Sankar S, Penniman WF, Perdomo JE, Hu L, Patel S, Gu X, Watve S, Hammer BK, Forest CR. Porous monolith microfluidics for bacterial cell-to-cell communication assays. BIOMICROFLUIDICS 2017; 11:044110. [PMID: 28852430 PMCID: PMC5551381 DOI: 10.1063/1.4995597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Genetically engineered bacteria can be used for a wide range of applications, from monitoring environmental toxins to studying complex communication networks in the human digestive system. Although great strides have been made in studying single strains of bacteria in well-controlled microfluidic environments, there remains a need for tools to reliably control and measure communication between multiple discrete bacterial populations. Stable long-term experiments (e.g., days) with controlled population sizes and regulated input (e.g., concentration) and output measurements can reveal fundamental limits of cell-to-cell communication. In this work, we developed a microfluidic platform that utilizes a porous monolith to reliably and stably partition adjacent strains of bacteria while allowing molecular communication between them for several days. We measured small molecule production by the bacterial populations in response to stimuli using analytical chemistry methods and measured fluorescent output. The results are compared with communication and diffusion delay models. This porous monolith microfluidic system enables bacterial cell-to-cell communication assays with dynamic control of inputs, relatively long-term experimentation with no cross contamination, and stable bacterial population size. This system can serve as a valuable tool in understanding bacterial communication and improving biosensor design capabilities.
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Affiliation(s)
- C M Austin
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - D M Caro
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - S Sankar
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - W F Penniman
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - J E Perdomo
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - L Hu
- Massachusetts Institute of Technology, Cambridge Massachusetts 02139, USA
| | - S Patel
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - X Gu
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - S Watve
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - B K Hammer
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - C R Forest
- Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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4
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Bhattacharjee A, Khan M, Kleiman M, Hochbaum AI. Effects of Growth Surface Topography on Bacterial Signaling in Coculture Biofilms. ACS APPLIED MATERIALS & INTERFACES 2017; 9:18531-18539. [PMID: 28485146 DOI: 10.1021/acsami.7b04223] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacteria form interface-associated communities called biofilms, often comprising multiple species. Biofilms can be detrimental or beneficial in medical, industrial, and technological settings, and their stability and function are determined by interspecies communication via specific chemical signaling or metabolite exchange. The deterministic control of biofilm development, behavior, and properties remains an unmet challenge, limiting our ability to inhibit the formation of detrimental biofilms in biomedical settings and promote the growth of beneficial biofilms in biotechnology applications. Here, we describe the development of growth surfaces that promote the growth of commensal Escherichia coli instead of the opportunistic pathogen Pseudomonas aeruginosa. Periodically patterned growth surfaces induced robust morphological changes in surface-associated E. coli biofilms and influenced the antibiotic susceptibilities of E. coli and P. aeruginosa biofilms. Changes in the biofilm architecture resulted in the accumulation of a metabolite, indole, which controls the competition dynamics between the two species. Our results show that the surface on which a biofilm grows has important implications for species colonization, growth, and persistence when exposed to antibiotics.
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Affiliation(s)
| | - Mughees Khan
- Wyss Institute for Biologically Inspired Engineering, Harvard University , Cambridge, Massachusetts 02138, United States
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6
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Vu TQ, de Castro RMB, Qin L. Bridging the gap: microfluidic devices for short and long distance cell-cell communication. LAB ON A CHIP 2017; 17:1009-1023. [PMID: 28205652 PMCID: PMC5473339 DOI: 10.1039/c6lc01367h] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cell-cell communication is a crucial component of many biological functions. For example, understanding how immune cells and cancer cells interact, both at the immunological synapse and through cytokine secretion, can help us understand and improve cancer immunotherapy. The study of how cells communicate and form synaptic connections is important in neuroscience, ophthalmology, and cancer research. But in order to increase our understanding of these cellular phenomena, better tools need to be developed that allow us to study cell-cell communication in a highly controlled manner. Some technical requirements for better communication studies include manipulating cells spatiotemporally, high resolution imaging, and integrating sensors. Microfluidics is a powerful platform that has the ability to address these requirements and other current limitations. In this review, we describe some new advances in microfluidic technologies that have provided researchers with novel methods to study intercellular communication. The advantages of microfluidics have allowed for new capabilities in both single cell-cell communication and population-based communication. This review highlights microfluidic communication devices categorized as "short distance", or primarily at the single cell level, and "long distance", which mostly encompasses population level studies. Future directions and translation/commercialization will also be discussed.
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Affiliation(s)
- Timothy Quang Vu
- Department of Bioengineering, Rice University, Houston, TX 77030, USA and Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Ricardo Miguel Bessa de Castro
- College of Engineering, Swansea University Singleton Park, Swansea, UK and Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA. and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
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7
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Ribbe J, Maier B. Density-Dependent Differentiation of Bacteria in Spatially Structured Open Systems. Biophys J 2016; 110:1648-1660. [PMID: 27074689 DOI: 10.1016/j.bpj.2016.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 02/09/2016] [Accepted: 03/08/2016] [Indexed: 10/21/2022] Open
Abstract
Bacterial quorum sensing is usually studied in well-mixed populations residing within closed systems. The latter do not exchange mass with their surroundings; however, in their natural environment, such as the rhizosphere, bacteria live in spatially structured open systems. Here, we tested the hypothesis that trapping of bacteria within microscopic pockets of an open system triggers density-dependent differentiation. We designed a microfluidic device that trapped swimming bacteria within microscopic compartments. The geometry of the traps controlled their diffusive coupling to fluid flow that played a dual role as nutrient source and autoinducer sink. Bacillus subtilis differentiates into a state of competence in response to quorum sensing and nutrient limitation. Using a mutant strain with a high differentiation rate and fluorescent reporters for competence, we found that the cell density required for differentiation was 100-fold higher than that required in closed systems. A direct comparison of strongly and moderately coupled reservoirs showed that strong coupling supported early differentiation but required a higher number of bacteria for its initiation. Weak coupling resulted in retardation of growth and differentiation. We conclude that spatial heterogeneity can promote density-dependent differentiation in open systems, and propose that the minimal quorum is determined by diffusive coupling to the environment through a trade-off between retaining autoinducers and accessing nutrients.
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Affiliation(s)
- Jan Ribbe
- Department of Physics, University of Cologne, Cologne, Germany
| | - Berenike Maier
- Department of Physics, University of Cologne, Cologne, Germany.
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8
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Comina G, Suska A, Filippini D. Towards autonomous lab-on-a-chip devices for cell phone biosensing. Biosens Bioelectron 2016; 77:1153-67. [DOI: 10.1016/j.bios.2015.10.092] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 01/20/2023]
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9
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Bicen AO, Austin CM, Akyildiz IF, Forest CR. Efficient Sampling of Bacterial Signal Transduction for Detection of Pulse-Amplitude Modulated Molecular Signals. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2015; 9:505-517. [PMID: 26372649 DOI: 10.1109/tbcas.2015.2465182] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The sampling of the bacterial signal transduction is investigated for molecular communication (MC). It is assumed that the finite-duration amplitude modulated, i.e., pulse-amplitude modulated (PAM), concentration of a certain type of molecule is used for information transmission. The bacterial signaling pathway is modified to transduce the input molecules to the output signal, i.e., produce green fluorescent protein (GFP). The bacterial signal transduction is composed of a set of biochemical reactions which impose randomness on the response. Therefore, the input-output relation, the timing issues, and the noise effects for the bacteria response are characterized based on both analytical and experimental observations. Sampling schemes for the raw bacteria response are proposed based on the total response duration, the peak value, the ramp-up slope, and the ramp-down slope. Each sampling scheme is shown to be providing a one-to-one and monotonic function of the input. The sampling based on the ramp-up slope is shown to be statistically favorable for the detection of PAM molecular signals. Accordingly, the time interval selection and non-coherent sampling are studied for the efficient calculation of the ramp-up slope from the raw bacteria response. This work provides a basis for the sampling of the raw bacteria response and enables accurate detection of PAM molecular signals via bacterial response for MC and sensing applications.
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10
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Nephrocyte-neurocyte interaction and cellular metabolic analysis on membrane-integrated microfluidic device. Sci China Chem 2015. [DOI: 10.1007/s11426-015-5453-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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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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12
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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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13
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Luo X, Tsao CY, Wu HC, Quan DN, Payne GF, Rubloff GW, Bentley WE. Distal modulation of bacterial cell-cell signalling in a synthetic ecosystem using partitioned microfluidics. LAB ON A CHIP 2015; 15:1842-1851. [PMID: 25690330 DOI: 10.1039/c5lc00107b] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The human gut is over a meter in length, liquid residence times span several hours. Recapitulating the human gut microbiome "on chip" holds promise to revolutionize therapeutic strategies for a variety of diseases, as well as for maintaining homeostasis in healthy individuals. A more refined understanding of bacterial-bacterial and bacterial-epithelial cell signalling is envisioned and such a device is a key enabler. Indeed, significant advances in the study of bacterial cell-cell signalling have been reported, including at length and time scales of the cells and their responses. Few reports exist, however, where signalling events that span physiologically relevant time scales are monitored and coordinated. Here, we employ principles of biofabrication to assemble, in situ, cell communities that are (i) spatially adjacent within partitioned microchannels for studying near communication and (ii) distally connected within longitudinal microfluidic networks so as to mimic long distance signalling among intestinal flora. We observed native signalling processes of the bacterial quorum sensing autoinducer-2 (AI-2) system among and between these communities. Cells in an upstream device successfully self-reported their activities and also secreted autoinducers that were carried downstream to the assembled networks of bacteria that reported on their presence. Furthermore, active signal modulation of among distal populations was demonstrated in a "programmed" manner where "enhancer" and "reducer" communities were assembled adjacent to the test population or "reporter" cells. The modulator cells either amplified or attenuated the cell-cell signalling between the distal, already communicating cell populations. Modulation was quantified with a bioassay, and the reaction rates of signal production and consumption were further characterized using a first principles mathematical model. Simulated distribution profiles of signalling molecules in the cell-gel composites agreed well with the observed cellular responses. We believe this simple platform and the ease by which it is assembled can be applied to other cell-cell interaction studies among various species or kingdoms of cells within well-regulated microenvironments.
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Affiliation(s)
- Xiaolong Luo
- Department of Mechanical Engineering, Catholic University of America, Washington, DC 20064, USA
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14
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Kim M, Lim JW, Kim HJ, Lee SK, Lee SJ, Kim T. Chemostat-like microfluidic platform for highly sensitive detection of heavy metal ions using microbial biosensors. Biosens Bioelectron 2014; 65:257-64. [PMID: 25461167 DOI: 10.1016/j.bios.2014.10.028] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/08/2014] [Accepted: 10/13/2014] [Indexed: 12/31/2022]
Abstract
Reporter-gene-based microbial biosensors have high potential for detecting small molecules, including heavy metal ions (HMIs), in a sensitive and selective manner by involving low costs. However, the sensitivity and dynamic range of the sensing mechanism are largely limited by the conventional culture environment that relies on the batch-type addition of the small molecules in nutrients and the subsequent genetic induction of sensing microbes. Here, we describe a high-throughput, chemostat-like microfluidic platform that can continuously supply both nutrients and inducers (HMIs) using microfabricated ratchet structures and a mixing microchannel network. We found that the microfluidic platform not only allowed microbial biosensors to be highly concentrated in a detection microchamber array but also enabled them to continuously grow and control synthetic genetic circuits in response to heavy metals. We also demonstrated that the combination of the platform and microbial biosensors enhanced the sensitivity for detecting divalent lead and cadmium ions by approximately three orders of magnitude relative to conventional batch-type methods. Because the platform is portable and only requires small sample volumes and fluorescent detection, the chemostat-like microfluidic platform in conjunction with microbial biosensors could be widely utilized to facilitate the specific and sensitive detection of molecular analytes on a chip.
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Affiliation(s)
- Minseok Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan 689-798, Republic of Korea
| | - Ji Won Lim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan 689-798, Republic of Korea
| | - Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Sung Kuk Lee
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan 689-798, Republic of Korea
| | - Sang Jun Lee
- Biosystems and Bioengineering Program, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea; Infection and Immunity Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea.
| | - Taesung Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Eonyang-eup, Ulsan 689-798, Republic of Korea; 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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15
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Austin CM, Stoy W, Su P, Harber MC, Bardill JP, Hammer BK, Forest CR. Modeling and validation of autoinducer-mediated bacterial gene expression in microfluidic environments. BIOMICROFLUIDICS 2014; 8:034116. [PMID: 25379076 PMCID: PMC4162443 DOI: 10.1063/1.4884519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/10/2014] [Indexed: 06/04/2023]
Abstract
Biosensors exploiting communication within genetically engineered bacteria are becoming increasingly important for monitoring environmental changes. Currently, there are a variety of mathematical models for understanding and predicting how genetically engineered bacteria respond to molecular stimuli in these environments, but as sensors have miniaturized towards microfluidics and are subjected to complex time-varying inputs, the shortcomings of these models have become apparent. The effects of microfluidic environments such as low oxygen concentration, increased biofilm encapsulation, diffusion limited molecular distribution, and higher population densities strongly affect rate constants for gene expression not accounted for in previous models. We report a mathematical model that accurately predicts the biological response of the autoinducer N-acyl homoserine lactone-mediated green fluorescent protein expression in reporter bacteria in microfluidic environments by accommodating these rate constants. This generalized mass action model considers a chain of biomolecular events from input autoinducer chemical to fluorescent protein expression through a series of six chemical species. We have validated this model against experimental data from our own apparatus as well as prior published experimental results. Results indicate accurate prediction of dynamics (e.g., 14% peak time error from a pulse input) and with reduced mean-squared error with pulse or step inputs for a range of concentrations (10 μM-30 μM). This model can help advance the design of genetically engineered bacteria sensors and molecular communication devices.
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Affiliation(s)
- Caitlin M Austin
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, USA
| | - William Stoy
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, USA
| | - Peter Su
- Department of Chemical and Biomolecular Engineering, University of California , Berkeley, California 94720, USA
| | - Marie C Harber
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, USA
| | - J Patrick Bardill
- School of Biology, Georgia Institute of Technology , Atlanta, Georgia 30332, USA
| | - Brian K Hammer
- School of Biology, Georgia Institute of Technology , Atlanta, Georgia 30332, USA
| | - Craig R Forest
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332, USA
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16
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Xie Y, Zhao C, Zhao Y, Li S, Rufo J, Yang S, Guo F, Huang TJ. Optoacoustic tweezers: a programmable, localized cell concentrator based on opto-thermally generated, acoustically activated, surface bubbles. LAB ON A CHIP 2013; 13:1772-1779. [PMID: 23511348 PMCID: PMC3988908 DOI: 10.1039/c3lc00043e] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We present a programmable, biocompatible technique for dynamically concentrating and patterning particles and cells in a microfluidic device. Since our technique utilizes opto-thermally generated, acoustically activated, surface bubbles, we name it "optoacoustic tweezers". The optoacoustic tweezers are capable of concentrating particles/cells at any prescribed locations in a microfluidic chamber without the use of permanent structures, rendering it particularly useful for the formation of flexible, complex cell patterns. Additionally, this technique has demonstrated excellent biocompatibility and can be conveniently integrated with other microfluidic units. In our experiments, micro-bubbles were generated by focusing a 405 nm diode laser onto a gold-coated glass chamber. By properly tuning the laser, we demonstrate precise control over the position and size of the generated bubbles. Acoustic waves were then applied to activate the surface bubbles, causing them to oscillate at an optimized frequency. The resulting acoustic radiation force allowed us to locally trap particles/cells, including 15 μm polystyrene beads and HeLa cells, around each bubble. Cell-adhesion tests were also conducted after cell concentrating to confirm the biocompatibility of this technique.
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Affiliation(s)
- Yuliang Xie
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chenglong Zhao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yanhui Zhao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sixing Li
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Joseph Rufo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Shikuan Yang
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Feng Guo
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tony Jun Huang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
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17
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Mao S, Zhang J, Li H, Lin JM. Strategy for Signaling Molecule Detection by Using an Integrated Microfluidic Device Coupled with Mass Spectrometry to Study Cell-to-Cell Communication. Anal Chem 2012; 85:868-76. [DOI: 10.1021/ac303164b] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sifeng Mao
- Beijing Key Laboratory of Microanalytical
Methods and
Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jie Zhang
- Beijing Key Laboratory of Microanalytical
Methods and
Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Haifang Li
- Beijing Key Laboratory of Microanalytical
Methods and
Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jin-Ming Lin
- Beijing Key Laboratory of Microanalytical
Methods and
Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
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