Name: window on a microworld: simple microfluidic systems for studying microbial transport in porous media
Uploaded: 2010-05-03T16:11:00
Description: Watch this Scientific Journal Video about Window on a Microworld: Simple Microfluidic Systems for Studying Microbial Transport in Porous Media at JoVE.com

<p class="jove_content">This study was supported by grant # 0649883 from the National Science Foundation, by the Vanderbilt Institute for Integrative Biosystems Research and Education (VIIBRE), and by the Searle Systems Biology and Bioengineering Undergraduate Research Experience (Searle SyBBURE).</p>

<p class="jove_title">I. Microfluidic Device Fabrication</p>
  <ol>
    <li>The first step in creating a microfluidic device is to draw a two dimensional layout of the device in a computer assisted drawing (CAD) program.  We have used AutoCAD, but other drawing programs are also available, such as CleWin, or CorelDraw.</li>
    <li>The next step is to fabricate a photolithographic mask.  Depending on the device dimensions, required resolution and budget, these masks could be fabricated in chrome (highest resolution, high cost), created on ph...

<ol>
	<li>Whitesides, G., Ostuni, E., Takayama, S., Jiang, X., Ingber, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soft+lithography+in+biology+and+biochemistry.">Soft lithography in biology and biochemistry.</a> <em style='font-style: italic'>Annual Review of Biomedical Engineering</em>. <b>3</b>, 335-373 (2001).</li><li>Wang, W., Shor, L. M., LeBoeuf, E. J., Wikswo, J. P., Kosson, D. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mobility+of+protozoa+through+narrow+channels.">Mobility of protozoa through narrow channels.</a> <em style='font-style: italic'>Applied and Environmental Microbiology</em>. <b>71</b>, 4628-4637 (2005).</li></ol>

<p class="jove_content">The EcoChip system is adaptable to the needs of an individual experiment. New masters can be created relatively easily, and once a master is fabricated, additional exactly replicated devices can be cast as needed. The flow module is simple to use, requires no special equipment or complex connections, and can be modeled as a simple falling head pressure-driven flow system. Additional extensions to this work are ongoing, and include creating humic acid coated channels, and systematically varying the aqueous chemistry of th...

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>PDMS</td>
<td>&nbsp;</td>
<td>Dow Corning</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>SU8-2025</td>
<td>&nbsp;</td>
<td>MicroChem Corp.</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Fluorescent Beads</td>
<td>&nbsp;</td>
<td>Polysciences, Inc.</td>
<td>&nbsp;</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>
	

window on a microworld: simple microfluidic systems for studying microbial transport in porous media

Microbial growth and transport in porous media have important implications for the quality of groundwater and surface water, the recycling of nutrients in the environment, as well as directly for the transmission of pathogens to drinking water supplies. Natural porous media is composed of an intricate physical topology, varied surface chemistries, dynamic gradients of nutrients and electron acceptors, and a patchy distribution of microbes. These features vary substantially over a length scale of microns, making the results of macro-scale investigations of microbial transport difficult to interpret, and the validation of mechanistic models challenging. Here we demonstrate how simple microfluidic devices can be used to visualize microbial interactions with micro-structured habitats, to identify key processes influencing the observed phenomena, and to systematically validate predictive models. Simple, easy-to-use flow cells were constructed out of the transparent, biocompatible and oxygen-permeable material poly(dimethyl siloxane). Standard methods of photolithography were used to make micro-structured masters, and replica molding was used to cast micro-structured flow cells from the masters. The physical design of the flow cell chamber is adaptable to the experimental requirements: microchannels can vary from simple linear connections to complex topologies with feature sizes as small as 2 &mu;m. Our modular EcoChip flow cell array features dozens of identical chambers and flow control by a gravity-driven flow module. We demonstrate that through use of EcoChip devices, physical structures and pressure heads can be held constant or varied systematically while the influence of surface chemistry, fluid properties, or the characteristics of the microbial population is investigated. Through transport experiments using a non-pathogenic, green fluorescent protein-expressing <em>Vibrio</em> bacterial strain, we illustrate the importance of habitat structure, flow conditions, and inoculums size on fundamental transport phenomena, and with real-time particle-scale observations, demonstrate that microfluidics offer a compelling view of a hidden world.

Watch this Scientific Journal Video about Window on a Microworld: Simple Microfluidic Systems for Studying Microbial Transport in Porous Media at JoVE.com

Window on a Microworld: Simple Microfluidic Systems for Studying Microbial Transport in Porous Media

<p class="jove_content">Microfluidic devices can be used to visualize complex natural processes in real time and at the appropriate physical scales.  We have developed a simple microfluidic device that mimics key features of natural porous media for studying growth and transport of bacteria in the subsurface. </p>

Microbial growth and transport in porous media have important implications for the quality of groundwater and surface water, the recycling of nutrients in ...

Research

JoVE Journal

Biology

A Microfluidic Device with Groove Patterns for Studying Cellular Behavior

We describe a microfluidic device with microgrooved patterns for studying cellular behavior.  This microfluidic platform consists of a top fluidic channel ...

Using Micro-Electro-Mechanical Systems (MEMS) to Develop Diagnostic Tools

Using Micro-Electro-Mechanical Systems MEMS to Develop Diagnostic Tools

CD4+ T-Lymphocyte Capture Using a Disposable Microfluidic Chip for HIV

Pyrosequencing: A Simple Method for Accurate Genotyping

Pharmacogenetic research benefits first-hand from the abundance of information provided by the completion of the Human Genome Project. With such a ...

Measuring <em>Caenorhabditis elegans</em> Life Span on Solid Media

Measuring Caenorhabditis elegans Life Span on Solid Media

Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The nematode ...

Quantitative Phosphoproteomics in Fatty Acid Stimulated <em>Saccharomyces cerevisiae</em>

Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae

This protocol describes the growth and stimulation, with the fatty acid oleate, of isotopically heavy and light S. cerevisiae cells. Cells are ground ...

A Microfluidic Device for Quantifying Bacterial Chemotaxis in Stable Concentration Gradients

Chemotaxis allows bacteria to approach sources of attractant chemicals or to avoid sources of repellent chemicals. Bacteria constantly monitor the ...

Performing Vaginal Lavage, Crystal Violet Staining, and Vaginal Cytological Evaluation for Mouse Estrous Cycle Staging Identification

A rapid means of assessing reproductive status in rodents is useful not only in the study of reproductive dysfunction but is also required for the ...

The Use of Chemostats in Microbial Systems Biology

Cells regulate their rate of growth in response to signals from the external world. As the cell grows, diverse cellular processes must be coordinated ...