Programmed trapping of individual bacteria using micrometre-size sieves† Min-Cheol Kim, a Brett C. Isenberg, a Jason Sutin, b Amit Meller, ab Joyce Y. Wong a and Catherine M. Klapperich * a Received 31st August 2010, Accepted 6th January 2011 DOI: 10.1039/c0lc00362j Monitoring the real-time behavior of spatial arrays of single living bacteria cells is only achieved with much experimental difficulty due to the small size and mobility of the cells. To address this problem, we have designed and constructed a simple microfluidic device capable of trapping single bacteria cells in spatially well-defined locations without the use of chemical surface treatments. The device exploits hydrodynamics to slow down and trap cells flowing near a narrow aperture. We have modeled this system numerically by approximating the motion of Escherichia coli cells as rigid 3-D ellipsoids. The numerical predictions for the speed and efficiency of trapping were tested by fabricating the devices and imaging GFP expressing E. coli at a high spatio-temporal resolution. We find that our numerical simulations agree well with the actual cell flow for varying trap geometries. The trapped cells are optically accessible, and combined with our ability to predict their spatial location we demonstrate the ease of this method for monitoring multiple single cells over a time course. The simplicity of the design, inexpensive materials and straightforward fabrication make it an accessible tool for any systems biology laboratory. Introduction The ability to monitor the molecular machinery of individual live cells over extended periods of time will open up new horizons in cell biology, as well as in emerging fields, including systems biology. When cells are individually monitored, their dynamical behavior does not need to be synchronized, and their individual responses are not masked by averaging over a bulk population of cells. These are powerful properties that drive the development of methods for live, individual cell probing. From an engineering perspective, an efficient, high-throughput, method for probing live cells depends on our ability to rationally design and fabricate devices in which cells are individually trapped, enabling prolonged high-resolution imaging. Since the trapping process itself can impact cell behavior, it is important that the trapping mechanism minimally affects the cells’ phenotypic behavior, through either chemical or mechanical interactions. Here, we present a microfluidic platform suitable for high-resolution imaging of individually trapped bacteria that can be fabricated and operated in a simple manner and does not require special surface treatments to tether the trapped cells. Much of the previous research requiring the isolation of single bacterial cells has been carried out in microtiter plates or un-patterned microfluidic channels under very low flow speeds (10 mms 1 ), or in stationary conditions. Many labs use these techniques, but they can be very tedious, as it is extremely difficult to locate and/or track several different single cells when they are randomly located on a surface. As a result, it is easier to monitor one cell over a long period of time, an experimental practice that requires significant amounts of time to generate statistics. Several groups have begun to develop microtechnologies to confine, address and monitor single cells. Most of these tech- nologies were developed for mammalian cells. 1–4 Confinement of single bacteria cells in wet etched silicon microwells has been recently reported. 5 This method is limited, requires input of a very dilute bacteria solution and depends on sedimentation of the cells into the microwells in the absence of external flow controls. In other laboratories, analyses of individual bacteria have generally been performed by spreading cells on a glass cover slide coated with agarose gel. 6 These methods are also hampered by the fact that very dilute solutions must be used to assure single cell resolution, and that finding a cell requires panning over an entire slide, making returning to a cell after looking at another on the same slide very difficult. It has been somewhat more common to ‘‘trap’’ adherent cells using soft lithography surface patterning, but most of these studies have been focused on changes in the attached cells as a function of the trapping geometry. 7–9 For systems biology experiments, minimal impact of the trapping technology on the cell behavior is desired. Single cells have been trapped by several groups using droplet methods. 10 Droplet based methods have great promise, but at this time they still require significant expertise to achieve. a Department of Biomedical Engineering, Boston University, 44 Cummington St., Boston, MA, 02215, USA. E-mail: catherin@bu.edu b Department of Physics, Boston University, Boston, MA, 02215, USA † Electronic supplementary information (ESI) available: Details of ellipsoidal E. coli modeling and device fabrication. See DOI: 10.1039/c0lc00362j This journal is ª The Royal Society of Chemistry 2011 Lab Chip, 2011, 11, 1089–1095 | 1089 Dynamic Article Links C < Lab on a Chip Cite this: Lab Chip, 2011, 11, 1089 www.rsc.org/loc PAPER Downloaded by Massachusetts Institute of Technology on 02 March 2011 Published on 04 February 2011 on http://pubs.rsc.org | doi:10.1039/C0LC00362J View Online