101
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Zhuang J, Wei G, Wright Carlsen R, Edwards MR, Marculescu R, Bogdan P, Sitti M. Analytical modeling and experimental characterization of chemotaxis in Serratia marcescens. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052704. [PMID: 25353826 DOI: 10.1103/physreve.89.052704] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Indexed: 06/04/2023]
Abstract
This paper presents a modeling and experimental framework to characterize the chemotaxis of Serratia marcescens (S. marcescens) relying on two-dimensional and three-dimensional tracking of individual bacteria. Previous studies mainly characterized bacterial chemotaxis based on population density analysis. Instead, this study focuses on single-cell tracking and measuring the chemotactic drift velocity V(C) from the biased tumble rate of individual bacteria on exposure to a concentration gradient of l-aspartate. The chemotactic response of S. marcescens is quantified over a range of concentration gradients (10^{-3} to 5 mM/mm) and average concentrations (0.5 × 10(-3) to 2.5 mM). Through the analysis of a large number of bacterial swimming trajectories, the tumble rate is found to have a significant bias with respect to the swimming direction. We also verify the relative gradient sensing mechanism in the chemotaxis of S. marcescens by measuring the change of V(C) with the average concentration and the gradient. The applied full pathway model with fitted parameters matches the experimental data. Finally, we show that our measurements based on individual bacteria lead to the determination of the motility coefficient μ (7.25 × 10(-6) cm(2)/s) of a population. The experimental characterization and simulation results for the chemotaxis of this bacterial species contribute towards using S. marcescens in chemically controlled biohybrid systems.
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Affiliation(s)
- Jiang Zhuang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Guopeng Wei
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Rika Wright Carlsen
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Matthew R Edwards
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Radu Marculescu
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Paul Bogdan
- Ming Hsieh Department of Electrical Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Metin Sitti
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA and Max-Planck Institute for Intelligent Systems, 70569 Stuttgart, Germany
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102
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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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103
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Oil–water biphasic parallel flow for the precise patterning of metals and cells. Biomed Microdevices 2013; 16:245-53. [DOI: 10.1007/s10544-013-9828-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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104
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Hamon M, Hong JW. New tools and new biology: recent miniaturized systems for molecular and cellular biology. Mol Cells 2013; 36:485-506. [PMID: 24305843 PMCID: PMC3887968 DOI: 10.1007/s10059-013-0333-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 01/09/2023] Open
Abstract
Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.
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Affiliation(s)
- Morgan Hamon
- Materials Research and Education Center, Department of Mechanical Engineering, Auburn University, Auburn, AL 36849,
USA
| | - Jong Wook Hong
- Materials Research and Education Center, Department of Mechanical Engineering, Auburn University, Auburn, AL 36849,
USA
- College of Pharmacy, Seoul National University, Seoul 151-741,
Korea
- Department of Bionano Engineering, Hanyang University, Ansan 426-791,
Korea
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105
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106
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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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107
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Park D, Park SJ, Cho S, Lee Y, Lee YK, Min JJ, Park BJ, Ko SY, Park JO, Park S. Motility analysis of bacteria-based microrobot (bacteriobot) using chemical gradient microchamber. Biotechnol Bioeng 2013; 111:134-43. [DOI: 10.1002/bit.25007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/08/2013] [Accepted: 07/15/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Daechul Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Sung Jun Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Sunghoon Cho
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Yeonkyung Lee
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Yu Kyung Lee
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Jung-Joon Min
- Department of Nuclear Medicine; Chonnam National University Medical School; Gwangju Korea
| | - Bang Ju Park
- College of BioNano Technology; Gachon University; Gyeonggi-do Korea
| | - Seong Young Ko
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Jong-Oh Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
| | - Sukho Park
- School of Mechanical Systems Engineering; Chonnam National University; Gwangju 500-757 Korea
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108
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Hong JW, Song S, Shin JH. A novel microfluidic co-culture system for investigation of bacterial cancer targeting. LAB ON A CHIP 2013; 13:3033-40. [PMID: 23743709 DOI: 10.1039/c3lc50163a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Although bacterial cancer targeting in animal models has been previously demonstrated and suggested as a possible therapeutic tool, a thorough understanding of the mechanisms responsible for cancer specificity would be required prior to clinical applications. To visualize bacterial preference for cancer cells over normal cells and to elucidate the cancer-targeting mechanism, a simple microfluidic platform has been developed for in vitro studies. This platform allows simultaneous cultures of multiple cell types in independent culture environments in isolated chambers, and creates a stable chemical gradient across a collagen-filled passage between each of these cell culture chambers and the central channel. The established chemical gradient induces chemotactic preferential migration of bacteria toward a particular cell type for quantitative analysis. As a demonstration, we tested differential bacterial behavior on a two-chamber device where we quantified bacterial preference based on the difference in fluorescence intensities of green fluorescence protein (GFP)-expressing bacteria at two exits of the collagen-filled passages. Analysis of the chemotactic behavior of Salmonella typhimurium toward normal versus cancer hepatocytes using the developed platform revealed an apparent preference for cancer hepatocytes. We also demonstrate that alpha-fetoprotein (AFP) is one of the key chemo-attractants for S. typhimurium in targeting liver cancer.
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Affiliation(s)
- Jung Woo Hong
- Division of Mechanical Engineering, School of Mechanical, Aerospace and Systems Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
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109
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Wu J, Wu X, Lin F. Recent developments in microfluidics-based chemotaxis studies. LAB ON A CHIP 2013; 13:2484-99. [PMID: 23712326 DOI: 10.1039/c3lc50415h] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microfluidic devices can better control cellular microenvironments compared to conventional cell migration assays. Over the past few years, microfluidics-based chemotaxis studies showed a rapid growth. New strategies were developed to explore cell migration in manipulated chemical gradients. In addition to expanding the use of microfluidic devices for a broader range of cell types, microfluidic devices were used to study cell migration and chemotaxis in complex environments. Furthermore, high-throughput microfluidic chemotaxis devices and integrated microfluidic chemotaxis systems were developed for medical and commercial applications. In this article, we review recent developments in microfluidics-based chemotaxis studies and discuss the new trends in this field observed over the past few years.
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Affiliation(s)
- Jiandong Wu
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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110
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Abstract
Micro- and nanoscale technologies have radically transformed biological research from genomics to tissue engineering, with the relative exception of microbial cell culture, which is still largely performed in microtiter plates and petri dishes. Here, we present nanoscale culture of the opportunistic fungal pathogen Candida albicans on a microarray platform. The microarray consists of 1,200 individual cultures of 30 nl of C. albicans biofilms (“nano-biofilms”) encapsulated in an inert alginate matrix. We demonstrate that these nano-biofilms are similar to conventional macroscopic biofilms in their morphological, architectural, growth, and phenotypic characteristics. We also demonstrate that the nano-biofilm microarray is a robust and efficient tool for accelerating the drug discovery process: (i) combinatorial screening against a collection of 28 antifungal compounds in the presence of immunosuppressant FK506 (tacrolimus) identified six drugs that showed synergistic antifungal activity, and (ii) screening against the NCI challenge set small-molecule library identified three heretofore-unknown hits. This cell-based microarray platform allows for miniaturization of microbial cell culture and is fully compatible with other high-throughput screening technologies. Microorganisms are typically still grown in petri dishes, test tubes, and Erlenmeyer flasks in spite of the latest advances in miniaturization that have benefitted other allied research fields, including genomics and proteomics. Culturing microorganisms in small scale can be particularly valuable in cutting down time, cost, and reagent usage. This paper describes the development, characterization, and application of nanoscale culture of an opportunistic fungal pathogen, Candida albicans. Despite a more than 2,000-fold reduction in volume, the growth characteristics and drug response profiles obtained from the nanoscale cultures were comparable to the industry standards. The platform also enabled rapid identification of new drug candidates that were effective against C. albicans biofilms, which are a major cause of mortality in hospital-acquired infections.
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111
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Wessel AK, Hmelo L, Parsek MR, Whiteley M. Going local: technologies for exploring bacterial microenvironments. Nat Rev Microbiol 2013; 11:337-48. [PMID: 23588251 DOI: 10.1038/nrmicro3010] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms lead social lives and use coordinated chemical and physical interactions to establish complex communities. Mechanistic insights into these interactions have revealed that there are remarkably intricate systems for coordinating microbial behaviour, but little is known about how these interactions proceed in the spatially organized communities that are found in nature. This Review describes the technologies available for spatially organizing small microbial communities and the analytical methods for characterizing the chemical environment surrounding these communities. Together, these complementary technologies have provided novel insights into the impact of spatial organization on both microbial behaviour and the development of phenotypic heterogeneity within microbial communities.
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Affiliation(s)
- Aimee K Wessel
- Section of Molecular Genetics and Microbiology, Institute of Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5000, Austin, Texas 78712, USA
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112
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Baraban L, Harazim SM, Sanchez S, Schmidt OG. Chemotactic Behavior of Catalytic Motors in Microfluidic Channels. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201301460] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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113
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Baraban L, Harazim SM, Sanchez S, Schmidt OG. Chemotactic behavior of catalytic motors in microfluidic channels. Angew Chem Int Ed Engl 2013; 52:5552-6. [PMID: 23616282 DOI: 10.1002/anie.201301460] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Indexed: 01/20/2023]
Affiliation(s)
- Larysa Baraban
- Institute for Integrative Nanosciences, Leibniz Institute for Solid State and Materials Research Dresden, Helmholtzstrasse 20, 01069 Dresden, Germany
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114
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Helaine S, Holden DW. Heterogeneity of intracellular replication of bacterial pathogens. Curr Opin Microbiol 2013; 16:184-91. [DOI: 10.1016/j.mib.2012.12.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 12/20/2012] [Accepted: 12/21/2012] [Indexed: 10/27/2022]
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115
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Kashikar ND, Alvarez L, Seifert R, Gregor I, Jäckle O, Beyermann M, Krause E, Kaupp UB. Temporal sampling, resetting, and adaptation orchestrate gradient sensing in sperm. ACTA ACUST UNITED AC 2013; 198:1075-91. [PMID: 22986497 PMCID: PMC3444779 DOI: 10.1083/jcb.201204024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Sperm use temporal sampling, resetting of intracellular calcium level, and adaptation of their sensitivity to respond to a wide range of chemoattractant concentrations during their voyage toward the egg. Sperm, navigating in a chemical gradient, are exposed to a periodic stream of chemoattractant molecules. The periodic stimulation entrains Ca2+ oscillations that control looping steering responses. It is not known how sperm sample chemoattractant molecules during periodic stimulation and adjust their sensitivity. We report that sea urchin sperm sampled molecules for 0.2–0.6 s before a Ca2+ response was produced. Additional molecules delivered during a Ca2+ response reset the cell by causing a pronounced Ca2+ drop that terminated the response; this reset was followed by a new Ca2+ rise. After stimulation, sperm adapted their sensitivity following the Weber–Fechner law. Taking into account the single-molecule sensitivity, we estimate that sperm can register a minimal gradient of 0.8 fM/µm and be attracted from as far away as 4.7 mm. Many microorganisms sense stimulus gradients along periodic paths to translate a spatial distribution of the stimulus into a temporal pattern of the cell response. Orchestration of temporal sampling, resetting, and adaptation might control gradient sensing in such organisms as well.
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Affiliation(s)
- Nachiket D Kashikar
- Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, 53175 Bonn, Germany
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116
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Kojadinovic M, Armitage JP, Tindall MJ, Wadhams GH. Response kinetics in the complex chemotaxis signalling pathway of Rhodobacter sphaeroides. J R Soc Interface 2013; 10:20121001. [PMID: 23365194 DOI: 10.1098/rsif.2012.1001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chemotaxis is one of the best-characterized signalling systems in biology. It is the mechanism by which bacteria move towards optimal environments and is implicated in biofilm formation, pathogenesis and symbiosis. The properties of the bacterial chemosensory response have been described in detail for the single chemosensory pathway of Escherichia coli. We have characterized the properties of the chemosensory response of Rhodobacter sphaeroides, an α-proteobacterium with multiple chemotaxis pathways, under two growth conditions allowing the effects of protein expression levels and cell architecture to be investigated. Using tethered cell assays, we measured the responses of the system to step changes in concentration of the attractant propionate and show that, independently of the growth conditions, R. sphaeroides is chemotactic over at least five orders of magnitude and has a sensing profile following Weber's Law. Mathematical modelling also shows that, as E. coli, R. sphaeroides is capable of showing fold-change detection (FCD). Our results indicate that general features of bacterial chemotaxis such as the range and sensitivity of detection, adaptation times, adherence to Weber's Law and the presence of FCD may be integral features of chemotaxis systems in general, regardless of network complexity, protein expression levels and cellular architecture across different species.
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Affiliation(s)
- Mila Kojadinovic
- Department of Biochemistry, Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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117
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Mensack MM, Wydallis JB, Lynn NS, Dandy DS, Henry CS. Spatially resolved electrochemical sensing of chemical gradients. LAB ON A CHIP 2013; 13:208-211. [PMID: 23172274 DOI: 10.1039/c2lc41054k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Chemical gradients drive a diverse set of biological processes ranging from nerve transduction to ovulation. At present, the most common method for quantifying chemical gradients is microscopy. Here, a new concept for probing spatial and temporal chemical gradients is reported that uses a multi-layer microfluidic device to measure analyte concentration as a function of lateral position in a microfluidic channel using electrochemistry in a format that is readily adaptable to multi-analyte sensing.
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Affiliation(s)
- Meghan M Mensack
- Department of Chemistry, Colorado State University, 1872 Campus Delivery, Fort Collins, Colorado 80523, USA
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118
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Estes MD, Hurth C, Barrett M, Zenhausern F. A tuneable array of unique steady-state microfluidic gradients. Phys Chem Chem Phys 2013; 15:12805-14. [DOI: 10.1039/c3cp44640a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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119
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Adler M, Erickstad M, Gutierrez E, Groisman A. Studies of bacterial aerotaxis in a microfluidic device. LAB ON A CHIP 2012; 12:4835-47. [PMID: 23010909 PMCID: PMC3520485 DOI: 10.1039/c2lc21006a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Aerotaxis, the directional motion of bacteria in gradients of oxygen, was discovered in the late 19th century and has since been reported in a variety of bacterial species. Nevertheless, quantitative studies of aerotaxis have been complicated by the lack of tools for generation of stable gradients of oxygen concentration, [O(2)]. Here we report a series of experiments on aerotaxis of Escherichia coli in a specially built experimental setup consisting of a computer-controlled gas mixer and a two-layer microfluidic device made of polydimethylsiloxane (PDMS). The setup enables generation of a variety of stable linear profiles of [O(2)] across a long gradient channel, with characteristic [O(2)] ranging from aerobic to microaerobic conditions. A suspension of E. coli cells is perfused through the gradient channel at a low speed, allowing cells enough time to explore the [O(2)] gradient, and the distribution of cells across the gradient channel is analyzed near the channel outlet at a throughput of >10(5) cells per hour. Aerotaxis experiments are performed in [O(2)] gradients with identical logarithmic slopes and varying mean concentrations, as well as in gradients with identical mean concentrations and varying slopes. Experiments in gradients with [O(2)] ranging from 0 to ~11.5% indicate that, in contrast to some previous reports, E. coli cells do not congregate at some intermediate level of [O(2)], but rather prefer the highest accessible [O(2)]. The presented technology can be applied to studies of aerotaxis of other aerobic and microaerobic bacteria.
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Affiliation(s)
- Micha Adler
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
| | - Michael Erickstad
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
| | - Edgar Gutierrez
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
| | - Alex Groisman
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, MC 0374, La Jolla, CA, 92093, USA
- Corresponding author,
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120
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Wicher D. Functional and evolutionary aspects of chemoreceptors. Front Cell Neurosci 2012; 6:48. [PMID: 23112762 PMCID: PMC3481119 DOI: 10.3389/fncel.2012.00048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 10/08/2012] [Indexed: 02/04/2023] Open
Abstract
The perception and processing of chemical signals from the environment is essential for any living systems and is most probably the first sense developed in life. This perspective discusses the physical limits of chemoreception and gives an overview on the receptor types developed during evolution to detect chemical signals from the outside world of an organism. It discusses the interaction of chemoreceptors with downstream signaling elements, especially the interaction between electrical and chemical signaling. It is further considered how the primary chemosignal is appropriately amplified. Three examples of chemosensory systems illustrate different strategies of such amplification.
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Affiliation(s)
- Dieter Wicher
- Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology Jena, Germany
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121
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Kim J, Park HD, Chung S. Microfluidic approaches to bacterial biofilm formation. Molecules 2012; 17:9818-34. [PMID: 22895027 PMCID: PMC6268732 DOI: 10.3390/molecules17089818] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/27/2012] [Accepted: 08/09/2012] [Indexed: 12/17/2022] Open
Abstract
Bacterial biofilms-aggregations of bacterial cells and extracellular polymeric substrates (EPS)-are an important subject of research in the fields of biology and medical science. Under aquatic conditions, bacterial cells form biofilms as a mechanism for improving survival and dispersion. In this review, we discuss bacterial biofilm development as a structurally and dynamically complex biological system and propose microfluidic approaches for the study of bacterial biofilms. Biofilms develop through a series of steps as bacteria interact with their environment. Gene expression and environmental conditions, including surface properties, hydrodynamic conditions, quorum sensing signals, and the characteristics of the medium, can have positive or negative influences on bacterial biofilm formation. The influences of each factor and the combined effects of multiple factors may be addressed using microfluidic approaches, which provide a promising means for controlling the hydrodynamic conditions, establishing stable chemical gradients, performing measurement in a high-throughput manner, providing real-time monitoring, and providing in vivo-like in vitro culture devices. An increased understanding of biofilms derived from microfluidic approaches may be relevant to improving our understanding of the contributions of determinants to bacterial biofilm development.
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Affiliation(s)
- Junghyun Kim
- School of Mechanical Engineering, Korea University, Seoul 136-713, Korea
| | - Hee-Deung Park
- School of Civil, Environmental and Architectural Engineering, Korea University, Seoul 136-713, Korea
- Authors to whom correspondence should be addressed; (H.-D.P.)(S.C.); Tel.: +82-2-3290-3352 (S.C.); Fax: +82-2-926-9290 (S.C.)
| | - Seok Chung
- School of Mechanical Engineering, Korea University, Seoul 136-713, Korea
- Authors to whom correspondence should be addressed; (H.-D.P.)(S.C.); Tel.: +82-2-3290-3352 (S.C.); Fax: +82-2-926-9290 (S.C.)
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122
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Abstract
The emerging field of micro-technology has opened up new possibilities for exploring cellular chemotaxis in real space and time, and at single cell resolution. Chemotactic cells sense and move in response to chemical gradients and play important roles in a number of physiological and pathological processes, including development, immune responses, and tumor cell invasions. Due to the size proximity of the microfluidic device to cells, microfluidic chemotaxis devices advance the traditional macro-scale chemotaxis assays in two major directions: one is to build well defined and stable chemical gradients at cellular length scales, and the other is to provide a platform for quantifying cellular responses at both cellular and molecular levels using advanced optical imaging systems. Here, we present a critical review on the designing principles, recent development, and potential capabilities of the microfluidic chemotaxis assay for solving problems that are of importance in the biomedical engineering field.
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Affiliation(s)
- Beum Jun Kim
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853, USA
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123
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Si G, Yang W, Bi S, Luo C, Ouyang Q. A parallel diffusion-based microfluidic device for bacterial chemotaxis analysis. LAB ON A CHIP 2012; 12:1389-94. [PMID: 22361931 DOI: 10.1039/c2lc21219f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We developed a multiple-channel microfluidic device for bacterial chemotaxis detection. Some characteristics such as easy operation, parallel sample adding design and fast result readout make this device convenient for most biology labs. The characteristic feature of the design is the agarose gel channels, which serve as a semi-permeable membrane. They can stop the fluid flow and prevent bacteria getting across, but permit the diffusion of small molecules. In the device fabrication process a novel thermal-based method was used to control the shape of agarose gel in the microfluidic channel. The chemical gradient is established by diffusion which can be precisely controlled and measured. Combined with an 8-channel pipette, different attractants, repellent chemicals or different bacteria were analyzed by a two step operation with a readout time of one hour. This device may be useful in the high throughput detection of chemotaxis related molecules and genes.
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Affiliation(s)
- Guangwei Si
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
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124
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Zhu X, Si G, Deng N, Ouyang Q, Wu T, He Z, Jiang L, Luo C, Tu Y. Frequency-dependent Escherichia coli chemotaxis behavior. PHYSICAL REVIEW LETTERS 2012; 108:128101. [PMID: 22540625 PMCID: PMC3412125 DOI: 10.1103/physrevlett.108.128101] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Indexed: 05/03/2023]
Abstract
We study Escherichia coli chemotaxis behavior in environments with spatially and temporally varying attractant sources by developing a unique microfluidic system. Our measurements reveal a frequency-dependent chemotaxis behavior. At low frequency, the E. coli population oscillates in synchrony with the attractant. In contrast, in fast-changing environments, the population response becomes smaller and out of phase with the attractant waveform. These observations are inconsistent with the well-known Keller-Segel chemotaxis equation. A new continuum model is proposed to describe the population level behavior of E. coli chemotaxis based on the underlying pathway dynamics. With the inclusion of a finite adaptation time and an attractant consumption rate, our model successfully explains the microfluidic experiments at different stimulus frequencies.
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Affiliation(s)
- Xuejun Zhu
- Center for Microfluidic and Nanotechnology, The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
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125
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Oh KW, Lee K, Ahn B, Furlani EP. Design of pressure-driven microfluidic networks using electric circuit analogy. LAB ON A CHIP 2012; 12:515-45. [PMID: 22179505 DOI: 10.1039/c2lc20799k] [Citation(s) in RCA: 248] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This article reviews the application of electric circuit methods for the analysis of pressure-driven microfluidic networks with an emphasis on concentration- and flow-dependent systems. The application of circuit methods to microfluidics is based on the analogous behaviour of hydraulic and electric circuits with correlations of pressure to voltage, volumetric flow rate to current, and hydraulic to electric resistance. Circuit analysis enables rapid predictions of pressure-driven laminar flow in microchannels and is very useful for designing complex microfluidic networks in advance of fabrication. This article provides a comprehensive overview of the physics of pressure-driven laminar flow, the formal analogy between electric and hydraulic circuits, applications of circuit theory to microfluidic network-based devices, recent development and applications of concentration- and flow-dependent microfluidic networks, and promising future applications. The lab-on-a-chip (LOC) and microfluidics community will gain insightful ideas and practical design strategies for developing unique microfluidic network-based devices to address a broad range of biological, chemical, pharmaceutical, and other scientific and technical challenges.
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Affiliation(s)
- Kwang W Oh
- SMALL (Sensors and MicroActuators Learning Lab), Department of Electrical Engineering, University at Buffalo, The State University of New York at Buffalo (SUNY-Buffalo), New York 14260, USA.
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126
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Cai LF, Zhu Y, Du GS, Fang Q. Droplet-based microfluidic flow injection system with large-scale concentration gradient by a single nanoliter-scale injection for enzyme inhibition assay. Anal Chem 2011; 84:446-52. [PMID: 22128774 DOI: 10.1021/ac2029198] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We described a microfluidic chip-based system capable of generating droplet array with a large scale concentration gradient by coupling flow injection gradient technique with droplet-based microfluidics. Multiple modules including sample injection, sample dispersion, gradient generation, droplet formation, mixing of sample and reagents, and online reaction within the droplets were integrated into the microchip. In the system, nanoliter-scale sample solution was automatically injected into the chip under valveless flow injection analysis mode. The sample zone was first dispersed in the microchannel to form a concentration gradient along the axial direction of the microchannel and then segmented into a linear array of droplets by immiscible oil phase. With the segmentation and protection of the oil phase, the concentration gradient profile of the sample was preserved in the droplet array with high fidelity. With a single injection of 16 nL of sample solution, an array of droplets with concentration gradient spanning 3-4 orders of magnitude could be generated. The present system was applied in the enzyme inhibition assay of β-galactosidase to preliminarily demonstrate its potential in high throughput drug screening. With a single injection of 16 nL of inhibitor solution, more than 240 in-droplet enzyme inhibition reactions with different inhibitor concentrations could be performed with an analysis time of 2.5 min. Compared with multiwell plate-based screening systems, the inhibitor consumption was reduced 1000-fold.
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Affiliation(s)
- Long-Fei Cai
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou, 310058, China
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127
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Abstract
Sensory systems rescale their response sensitivity upon adaptation according to simple strategies that recur in processes as diverse as single-cell signaling, neural network responses, and whole-organism perception. Here, we study response rescaling in Escherichia coli chemotaxis, where adaptation dynamically tunes the cells' motile response during searches for nutrients. Using in vivo fluorescence resonance energy transfer (FRET) measurements on immobilized cells, we demonstrate that the design of this prokaryotic signaling network follows the fold-change detection (FCD) strategy, responding faithfully to the shape of the input profile irrespective of its absolute intensity. Using a microfluidics-based assay for free swimming cells, we confirm intensity-independent gradient responses at the behavioral level. By theoretical analysis, we identify a set of sufficient conditions for FCD in E. coli chemotaxis, which leads to the prediction that the adaptation timescale is invariant with respect to the background input level. Additional FRET experiments confirm that the adaptation timescale is invariant over an ∼10,000-fold range of background concentrations. These observations in a highly optimized bacterial system support the concept that FCD represents a robust sensing strategy for spatial searches. To our knowledge, these experiments provide a unique demonstration of FCD in any biological sensory system.
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128
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Lan G, Schulmeister S, Sourjik V, Tu Y. Adapt locally and act globally: strategy to maintain high chemoreceptor sensitivity in complex environments. Mol Syst Biol 2011; 7:475. [PMID: 21407212 PMCID: PMC3094069 DOI: 10.1038/msb.2011.8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2010] [Accepted: 02/10/2011] [Indexed: 11/09/2022] Open
Abstract
In bacterial chemotaxis, several types of ligand-specific receptors form mixed clusters, wherein receptor-receptor interactions lead to signal amplification and integration. However, it remains unclear how a mixed receptor cluster adapts to individual stimuli and whether it can differentiate between different types of ligands. Here, we combine theoretical modeling with experiments to reveal the adaptation dynamics of the mixed chemoreceptor cluster in Escherichia coli. We show that adaptation occurs locally and is ligand-specific: only the receptor that binds the external ligand changes its methylation level when the system adapts, whereas other types of receptors change methylation levels transiently. Permanent methylation crosstalk occurs when the system fails to adapt accurately. This local adaptation mechanism enables cells to differentiate individual stimuli by encoding them into the methylation levels of corresponding types of chemoreceptors. It tunes each receptor to its most responsive state to maintain high sensitivity in complex environments and prevents saturation of the cluster by one signal.
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Affiliation(s)
- Ganhui Lan
- IBM T.J. Watson Research Center, Yorktown Heights, New York, NY, USA
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129
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Vinuselvi P, Park S, Kim M, Park JM, Kim T, Lee SK. Microfluidic technologies for synthetic biology. Int J Mol Sci 2011; 12:3576-93. [PMID: 21747695 PMCID: PMC3131579 DOI: 10.3390/ijms12063576] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 05/20/2011] [Accepted: 05/26/2011] [Indexed: 12/24/2022] Open
Abstract
Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.
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Affiliation(s)
- Parisutham Vinuselvi
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (P.V.); (J.M.P.)
| | - Seongyong Park
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (S.P.); (M.K.)
| | - Minseok Kim
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (S.P.); (M.K.)
| | - Jung Min Park
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (P.V.); (J.M.P.)
| | - Taesung Kim
- School of Mechanical and Advanced Materials Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (S.P.); (M.K.)
| | - Sung Kuk Lee
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689–798, Korea; E-Mails: (P.V.); (J.M.P.)
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130
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Abstract
An optical trapping technique is implemented to investigate the chemotactic behavior of a marine bacterial strain Vibrio alginolyticus. The technique takes the advantage that the bacterium has only a single polar flagellum, which can rotate either in the counter-clock-wise or clock-wise direction. The two rotation states of the motor can be readily and instantaneously resolved in the optical trap, allowing the flagellar motor switching rate to be measured under different chemical stimulations. In this paper the focus will be on the bacterial response to an impulsive change of chemoattractant serine. Despite different propulsion apparati and motility patterns, cells of V. alginolyticus apparently use a similar response as Escherichia coli to regulate their chemotactic behavior. Specifically, we found that the switching rate of the bacterial motor exhibits a biphasic behavior, showing a fast initial response followed by a slow relaxation to the steady-state switching rate . The measured can be mimicked by a model that has been recently proposed for chemotaxis in E. coli. The similarity in the response to the brief chemical stimulation in these two different bacteria is striking, suggesting that the biphasic response may be evolutionarily conserved. This study also demonstrated that optical tweezers can be a useful tool for chemotaxis studies and should be applicable to other polarly flagellated bacteria.
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131
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Amadi OC, Steinhauser ML, Nishi Y, Chung S, Kamm RD, McMahon AP, Lee RT. A low resistance microfluidic system for the creation of stable concentration gradients in a defined 3D microenvironment. Biomed Microdevices 2011; 12:1027-41. [PMID: 20661647 DOI: 10.1007/s10544-010-9457-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The advent of microfluidic technology allows control and interrogation of cell behavior by defining the local microenvironment with an assortment of biochemical and biophysical stimuli. Many approaches have been developed to create gradients of soluble factors, but the complexity of such systems or their inability to create defined and controllable chemical gradients has limited their widespread implementation. Here we describe a new microfluidic device which employs a parallel arrangement of wells and channels to create stable, linear concentration gradients in a gel region between a source and a sink well. Pressure gradients between the source and sink wells are dissipated through low resistance channels in parallel with the gel channel, thus minimizing the convection of solute in this region. We demonstrate the ability of the new device to quantitate chemotactic responses in a variety of cell types, yielding a complete profile of the migratory response and representing the total number of migrating cells and the distance each cell has migrated. Additionally we show the effect of concentration gradients of the morphogen Sonic hedgehog on the specification of differentiating neural progenitors in a 3-dimensional matrix.
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Affiliation(s)
- Ovid C Amadi
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
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132
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Aquino G, Clausznitzer D, Tollis S, Endres RG. Optimal receptor-cluster size determined by intrinsic and extrinsic noise. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:021914. [PMID: 21405870 DOI: 10.1103/physreve.83.021914] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 10/11/2010] [Indexed: 05/30/2023]
Abstract
Biological cells sense external chemical stimuli in their environment using cell-surface receptors. To increase the sensitivity of sensing, receptors often cluster. This process occurs most noticeably in bacterial chemotaxis, a paradigm for sensing and signaling in general. While amplification of weak stimuli is useful in the absence of noise, its usefulness is less clear in the presence of extrinsic input noise and intrinsic signaling noise. Here, exemplified in a bacterial chemotaxis system, we combine the allosteric Monod-Wyman-Changeux model for signal amplification by receptor complexes with calculations of noise to study their interconnectedness. Importantly, we calculate the signal-to-noise ratio, describing the balance of beneficial and detrimental effects of clustering for the cell. Interestingly, we find that there is no advantage for the cell to build receptor complexes for noisy input stimuli in the absence of intrinsic signaling noise. However, with intrinsic noise, an optimal complex size arises in line with estimates of the size of chemoreceptor complexes in bacteria and protein aggregates in lipid rafts of eukaryotic cells.
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Affiliation(s)
- Gerardo Aquino
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
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133
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Kim M, Kim SH, Lee SK, Kim T. Microfluidic device for analyzing preferential chemotaxis and chemoreceptor sensitivity of bacterial cells toward carbon sources. Analyst 2011; 136:3238-43. [DOI: 10.1039/c1an15308k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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134
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Chung BG, Choo J. Microfluidic gradient platforms for controlling cellular behavior. Electrophoresis 2010; 31:3014-27. [PMID: 20734372 DOI: 10.1002/elps.201000137] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Concentration gradients play an important role in controlling biological and pathological processes, such as metastasis, embryogenesis, axon guidance, and wound healing. Microfluidic devices fabricated by photo- and soft lithography techniques can manipulate the fluidic flow and diffusion profile to create biomolecular gradients in a temporal and spatial manner. Furthermore, microfluidic devices enable the control of cell-extracellular microenvironment interactions, including cell-cell, cell-matrix, and cell-soluble factor interaction. In this paper, we review the development of microfluidic-based gradient devices and highlight their biological applications.
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Affiliation(s)
- Bong Geun Chung
- Department of Bionano Engineering, Hanyang University, Ansan, Korea.
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135
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Chemotaxis to the quorum-sensing signal AI-2 requires the Tsr chemoreceptor and the periplasmic LsrB AI-2-binding protein. J Bacteriol 2010; 193:768-73. [PMID: 21097621 DOI: 10.1128/jb.01196-10] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AI-2 is an autoinducer made by many bacteria. LsrB binds AI-2 in the periplasm, and Tsr is the l-serine chemoreceptor. We show that AI-2 strongly attracts Escherichia coli. Both LsrB and Tsr are necessary for sensing AI-2, but AI-2 uptake is not, suggesting that LsrB and Tsr interact directly in the periplasm.
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136
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Kim M, Kim T. Diffusion-Based and Long-Range Concentration Gradients of Multiple Chemicals for Bacterial Chemotaxis Assays. Anal Chem 2010; 82:9401-9. [DOI: 10.1021/ac102022q] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Minseok Kim
- School of Mechanical and Advanced Materials Engineering and School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689-798, Korea
| | - Taesung Kim
- School of Mechanical and Advanced Materials Engineering and School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Ulsan 689-798, Korea
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137
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Kovarik ML, Brown PJB, Kysela DT, Berne C, Kinsella AC, Brun YV, Jacobson SC. Microchannel-nanopore device for bacterial chemotaxis assays. Anal Chem 2010; 82:9357-64. [PMID: 20961116 DOI: 10.1021/ac101977f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Motile bacteria bias the random walk of their motion in response to chemical gradients by the process termed chemotaxis, which allows cells to accumulate in favorable environments and disperse from less favorable ones. In this work, we describe a simple microchannel-nanopore device that establishes a stable chemical gradient for chemotaxis assays in ≤1 min. Chemoattractant is dispensed by diffusion through 10 nm diameter pores at the intersection of two microchannels. This design requires no external pump and minimizes the effect of transmembrane pressure, resulting in a stable, reproducible gradient. The microfluidic platform facilitates microscopic observation of individual cell trajectories, and chemotaxis is quantified by monitoring changes in cell swimming behavior in the vicinity of the intersection. We validate this system by measuring the chemotactic response of an aquatic bacterium, Caulobacter crescentus, to xylose concentrations from 1.3 μM to 1.3 M. Additionally, we make an unanticipated observation of increased turn frequency in a chemotaxis-impaired mutant which provides new insight into the chemotaxis pathway in C. crescentus.
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Affiliation(s)
- Michelle L Kovarik
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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138
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Aquino G, Endres RG. Increased accuracy of ligand sensing by receptor diffusion on cell surface. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:041902. [PMID: 21230308 DOI: 10.1103/physreve.82.041902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Indexed: 05/30/2023]
Abstract
The physical limit with which a cell senses external ligand concentration corresponds to the perfect absorber, where all ligand particles are absorbed and overcounting of same ligand particles does not occur. Here, we analyze how the lateral diffusion of receptors on the cell membrane affects the accuracy of sensing ligand concentration. Specifically, we connect our modeling to neurotransmission in neural synapses where the diffusion of glutamate receptors is already known to refresh synaptic connections. We find that receptor diffusion indeed increases the accuracy of sensing for both the glutamate α-Amino-3-hydroxy-5-Methyl-4-isoxazolePropionic Acid (AMPA) and N-Methyl-D-aspartic Acid (NMDA) receptor, although the NMDA receptor is overall much noisier. We propose that the difference in accuracy of sensing of the two receptors can be linked to their different roles in neurotransmission. Specifically, the high accuracy in sensing glutamate is essential for the AMPA receptor to start membrane depolarization, while the NMDA receptor is believed to work in a second stage as a coincidence detector, involved in long-term potentiation and memory.
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Affiliation(s)
- Gerardo Aquino
- Division of Molecular Biosciences and Centre for Integrative Systems Biology at Imperial College, Imperial College London, SW7 2AZ London, United Kingdom
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139
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Spatial organization in bacterial chemotaxis. EMBO J 2010; 29:2724-33. [PMID: 20717142 DOI: 10.1038/emboj.2010.178] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/07/2010] [Indexed: 11/09/2022] Open
Abstract
Spatial organization of signalling is not an exclusive property of eukaryotic cells. Despite the fact that bacterial signalling pathways are generally simpler than those in eukaryotes, there are several well-documented examples of higher-order intracellular signalling structures in bacteria. One of the most prominent and best-characterized structures is formed by proteins that control bacterial chemotaxis. Signals in chemotaxis are processed by ordered arrays, or clusters, of receptors and associated proteins, which amplify and integrate chemotactic stimuli in a highly cooperative manner. Receptor clusters further serve to scaffold protein interactions, enhancing the efficiency and specificity of the pathway reactions and preventing the formation of signalling gradients through the cell body. Moreover, clustering can also ensure spatial separation of multiple chemotaxis systems in one bacterium. Assembly of receptor clusters appears to be a stochastic process, but bacteria evolved mechanisms to ensure optimal cluster distribution along the cell body for partitioning to daughter cells at division.
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140
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Ahmed T, Shimizu TS, Stocker R. Bacterial chemotaxis in linear and nonlinear steady microfluidic gradients. NANO LETTERS 2010; 10:3379-85. [PMID: 20669946 PMCID: PMC2935935 DOI: 10.1021/nl101204e] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Diffusion-based microfluidic devices can generate steady, arbitrarily shaped chemical gradients without requiring fluid flow and are ideal for studying chemotaxis of free-swimming cells such as bacteria. However, if microfluidic gradient generators are to be used to systematically study bacterial chemotaxis, it is critical to evaluate their performance with actual quantitative chemotaxis tests. We characterize and compare three diffusion-based gradient generators by confocal microscopy and numerical simulations, select an optimal design and apply it to chemotaxis experiments with Escherichia coli in both linear and nonlinear gradients. Comparison of the observed cell distribution along the gradients with predictions from an established mathematical model shows very good agreement, providing the first quantification of chemotaxis of free-swimming cells in steady nonlinear microfluidic gradients and opening the door to bacterial chemotaxis studies in gradients of arbitrary shape.
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Affiliation(s)
- Tanvir Ahmed
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Thomas S. Shimizu
- FOM Institute for Atomic and Molecular Physics (AMOLF), Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Roman Stocker
- Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
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141
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Chung S, Sudo R, Vickerman V, Zervantonakis IK, Kamm RD. Microfluidic platforms for studies of angiogenesis, cell migration, and cell-cell interactions. Sixth International Bio-Fluid Mechanics Symposium and Workshop March 28-30, 2008 Pasadena, California. Ann Biomed Eng 2010; 38:1164-77. [PMID: 20336839 DOI: 10.1007/s10439-010-9899-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent advances in microfluidic technologies have opened the door for creating more realistic in vitro cell culture methods that replicate many aspects of the true in vivo microenvironment. These new designs (i) provide enormous flexibility in controlling the critical biochemical and biomechanical factors that influence cell behavior, (ii) allow for the introduction of multiple cell types in a single system, (iii) provide for the establishment of biochemical gradients in two- or three-dimensional geometries, and (iv) allow for high quality, time-lapse imaging. Here, some of the recent developments are reviewed, with a focus on studies from our own laboratory in three separate areas: angiogenesis, cell migration in the context of tumor cell-endothelial interactions, and liver tissue engineering.
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Affiliation(s)
- Seok Chung
- School of Mechanical Engineering, Korea University, Seoul, Korea
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142
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Mora T, Wingreen NS. Limits of sensing temporal concentration changes by single cells. PHYSICAL REVIEW LETTERS 2010; 104:248101. [PMID: 20867338 DOI: 10.1103/physrevlett.104.248101] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Indexed: 05/29/2023]
Abstract
Berg and Purcell [Biophys. J. 20, 193 (1977)] calculated how the accuracy of concentration sensing by single-celled organisms is limited by noise from the small number of counted molecules. Here we generalize their results to the sensing of concentration ramps, which is often the biologically relevant situation (e.g., during bacterial chemotaxis). We calculate lower bounds on the uncertainty of ramp sensing by three measurement devices: a single receptor, an absorbing sphere, and a monitoring sphere. We contrast two strategies, simple linear regression of the input signal versus maximum likelihood estimation, and show that the latter can be twice as accurate as the former. Finally, we consider biological implementations of these two strategies, and identify possible signatures that maximum likelihood estimation is implemented by real biological systems.
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Affiliation(s)
- Thierry Mora
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
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143
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Miller J, Parker M, Bourret RB, Giddings MC. An agent-based model of signal transduction in bacterial chemotaxis. PLoS One 2010; 5:e9454. [PMID: 20485527 PMCID: PMC2869346 DOI: 10.1371/journal.pone.0009454] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 02/01/2010] [Indexed: 11/17/2022] Open
Abstract
We report the application of agent-based modeling to examine the signal transduction network and receptor arrays for chemotaxis in Escherichia coli, which are responsible for regulating swimming behavior in response to environmental stimuli. Agent-based modeling is a stochastic and bottom-up approach, where individual components of the modeled system are explicitly represented, and bulk properties emerge from their movement and interactions. We present the Chemoscape model: a collection of agents representing both fixed membrane-embedded and mobile cytoplasmic proteins, each governed by a set of rules representing knowledge or hypotheses about their function. When the agents were placed in a simulated cellular space and then allowed to move and interact stochastically, the model exhibited many properties similar to the biological system including adaptation, high signal gain, and wide dynamic range. We found the agent based modeling approach to be both powerful and intuitive for testing hypotheses about biological properties such as self-assembly, the non-linear dynamics that occur through cooperative protein interactions, and non-uniform distributions of proteins in the cell. We applied the model to explore the role of receptor type, geometry and cooperativity in the signal gain and dynamic range of the chemotactic response to environmental stimuli. The model provided substantial qualitative evidence that the dynamic range of chemotactic response can be traced to both the heterogeneity of receptor types present, and the modulation of their cooperativity by their methylation state.
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Affiliation(s)
- Jameson Miller
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina, United States of America
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144
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Dixit SS, Kim H, Vasilyev A, Eid A, Faris GW. Light-driven formation and rupture of droplet bilayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:6193-200. [PMID: 20361732 PMCID: PMC2896059 DOI: 10.1021/la1010067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
We demonstrate the optical manipulation of nanoliter aqueous droplets containing surfactant or lipid molecules and immersed in an organic liquid using near-infrared light. The resulting emulsion droplets are manipulated using both the thermocapillary effect and convective fluid motion. Droplet-pair interactions induced in the emulsion upon optical initiation and control provide direct observations of the coalescence steps in intricate detail. Droplet-droplet adhesion (bilayer formation) is observed under several conditions. Selective bilayer rupture is also realized using the same infrared laser. The technique provides a novel approach to studying thin film drainage and interface stability in emulsion dynamics. The formation of stable lipid bilayers at the adhesion interface between interacting water droplets can provide an optical platform on which to build droplet-based lipid bilayer assays. The technique also has relevance to understanding and improving microfluidics applications by devising Petri dish-based droplet assays requiring no substrate fabrication.
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Affiliation(s)
- Sanhita S Dixit
- Molecular Physics Laboratory, SRI International, 333 Ravenswood Avenue, Menlo Park, California 94025, USA.
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145
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Englert DL, Manson MD, Jayaraman A. A microfluidic device for quantifying bacterial chemotaxis in stable concentration gradients. J Vis Exp 2010:1779. [PMID: 20404797 DOI: 10.3791/1779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Chemotaxis allows bacteria to approach sources of attractant chemicals or to avoid sources of repellent chemicals. Bacteria constantly monitor the concentration of specific chemoeffectors by comparing the current concentration to the concentration detected a few seconds earlier. This comparison determines the net direction of movement. Although multiple, competing gradients often coexist in nature, conventional approaches for investigating bacterial chemotaxis are suboptimal for quantifying migration in response to concentration gradients of attractants and repellents. Here, we describe the development of a microfluidic chemotaxis model for presenting precise and stable concentration gradients of chemoeffectors to bacteria and quantitatively investigating their response to the applied gradient. The device is versatile in that concentration gradients of any desired absolute concentration and gradient strength can be easily generated by diffusive mixing. The device is demonstrated using the response of Escherichia coli RP437 to gradients of amino acids and nickel ions.
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Affiliation(s)
- Derek L Englert
- McFerrin Department of Chemical Engineering, Texas A&M University, TX, USA
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146
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Abstract
The plug-in-pond and capillary assays are convenient methods for measuring attractant and repellent bacterial chemotaxis. However, these assays do not provide quantitative information on the extent of migration and are not well-suited for investigating repellent taxis. Here, we describe a protocol for a flow-based microfluidic system (microFlow) to quantitatively investigate chemotaxis in response to concentration gradients of attractants and repellents. The microFlow device uses diffusive mixing to generate concentration gradients that are stable throughout the chemotaxis chamber and for the duration of the experiment. The gradients may be of any desired absolute concentration and gradient strength. GFP-expressing bacteria immediately encounter a stable concentration gradient when they enter the chemotaxis chamber, and the migration in response to the gradient is monitored by microscopy. The effects of different parameters that influence the extent of migration in the microFlow device-preparation of the motile bacterial population preparation, strength of the concentration gradient and duration of exposure to the gradient-are discussed in the context of repellent taxis of chemotactically wild-type Escherichia coli cells in a gradient of NiSO(4). Fabrication of the microfluidic device takes 1 d while preparing motile cells and carrying out the chemotaxis experiment takes 4-6 h to complete.
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147
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Repellent taxis in response to nickel ion requires neither Ni2+ transport nor the periplasmic NikA binding protein. J Bacteriol 2010; 192:2633-7. [PMID: 20233931 DOI: 10.1128/jb.00854-09] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ni(2+) and Co(2+) are sensed as repellents by the Escherichia coli Tar chemoreceptor. The periplasmic Ni(2+) binding protein, NikA, has been suggested to sense Ni(2+). We show here that neither NikA nor the membrane-bound NikB and NikC proteins of the Ni(2+) transport system are required for repellent taxis in response to Ni(2+).
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148
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Su LK, Lu CP, Wang Y, Cao DM, Sun JH, Yan YX. Lysogenic infection of a Shiga toxin 2-converting bacteriophage changes host gene expression, enhances host acid resistance and motility. Mol Biol 2010. [DOI: 10.1134/s0026893310010085] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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149
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Aquino G, Endres RG. Increased accuracy of ligand sensing by receptor internalization. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:021909. [PMID: 20365597 DOI: 10.1103/physreve.81.021909] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Revised: 12/21/2009] [Indexed: 05/29/2023]
Abstract
Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as the overcounting of the same ligand molecules is reduced. Here we show, by extending simple ligand-receptor models to out-of-equilibrium thermodynamics, that internalization increases the accuracy with which cells can measure ligand concentrations in the external environment. Comparison with experimental rates of real receptors demonstrates that our model has indeed biological significance.
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Affiliation(s)
- Gerardo Aquino
- Division of Molecular Biosciences and Centre for Integrated Systems Biology at Imperial College, Imperial College London, SW7 2AZ London, United Kingdom
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150
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Velve-Casquillas G, Le Berre M, Piel M, Tran PT. Microfluidic tools for cell biological research. NANO TODAY 2010; 5:28-47. [PMID: 21152269 PMCID: PMC2998071 DOI: 10.1016/j.nantod.2009.12.001] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Microfluidic technology is creating powerful tools for cell biologists to control the complete cellular microenvironment, leading to new questions and new discoveries. We review here the basic concepts and methodologies in designing microfluidic devices, and their diverse cell biological applications.
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Affiliation(s)
| | | | | | - Phong T. Tran
- Institut Curie, UMR 144 CNRS, Paris 75005, France
- University of Pennsylvania, Cell and Developmental Biology, Philadelphia, PA 19104, USA
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