Getting to the Root of Microfluidics

Academic Research
Lab on a Chip
Stephen Quake
Stanford University



March 7, 2012

It’s not hard to see that a lot here at Microfluidic Future focuses on the medical applications of microfluidics, but that doesn’t mean that I’m not interested in other ways the technology can be used. I love to see novel applications of microfluidics because progress for anyone is progress for everyone. That brings me to today’s post on the RootChip. If the name isn’t a total give away, I recently came across an article that uses a microfluidic chip to study the roots of plants. In the article, “The RootChip: An Integrated Microfluidic Chip for Plant Science” by Stephen Quake and other researchers from Stanford University, a device is developed to study the roots of Arabidopsis thaliana.

Studying Arabidopsis Thaliana Roots

Arabidopsis thaliana has been extensively studied and is akin to the drosophila or zebrafish. It’s not easy to study the roots of a plant because they are sensitive to dehydration and physical damage, which could occur with mounting. Ideally they would be observed as close to in vivo as possible. The authors set out to study the Arabidopsis roots in parallel perfusion chambers, allowing many seedlings to be studied at once. To prove their concept, they used roots “expressing a genetically encoded fluorescence sensor for Glc and Gal.” This would allow them to non-invasively detect the Glc and Gal metabolite levels in real time.

Before introduction to the RootChip, Arabidopsis seeds are germinated in agar medium filled micropipette tips. This germination prior to attachment to the RootChip allows the roots to be screened for adequate growth and desired properties. After 5 days of germination, the tips are mounted on the RootChip. The roots continue to grow into the RootChip’s observation chambers which are filled with liquid medium. The microfluidic channel that leads from the inserted tip transitions from vertical to horizontal and the root typically aligns with the direction of flow. The entire RootChip is encased in a chip carrier that includes water reservoirs to ensure that proper humidity is maintained throughout the study.

The current RootChip handles 8 seedlings with independent control. After previous germination, tips containing the seedlings are inserted. The roots can readily be analyzed and observed in the flow chamber.

The roots were subjected to pulses of medium spiked with either Glc or Gal. Geneticaly encoded fluorescence sensors allowed for cytosolic Glc and Gal measurements, and the authors recorded reproducible elevations in the roots’ corresponding sugar concentrations. Gal is a well-known root growth inhibitor and the authors examined its effect while perfusing the roots with Gal for a long period of time. They observed darkening of the tissue and a loss of normal cytosolic signal distribution, indicating cell death and tissue alterations due to the long Gal exposure. The authors also noticed swelling epidermal cells, which would indicate a defect in the integrity of the cell wall.

Each seedling in the RootChip feeds into its own flow chamber. The entire RootChip can be mounted on a microscope and is enclosed to maintain humidity.

The authors demonstrated the RootChip’s use to observe developing roots in parallel. Their method allows for different properties of the roots to be studied at once with live imaging. Further, the chip’s total control over the perfusion environment allows for complicated experiments. The authors also claim:

“The RootChip will greatly facilitate the ability to investigate nutrient uptake in different root zones, cell type-dependent metabolite flux, and the response of individual cells (such as root hair cells) to different environmental stimuli.”

Value of RootChip Design

I don’t have any experience in plant study, but this device seems very promising, and I’m excited to see what it leads to in both plant and biomedical microfluidic research. While the use of Gal and Glc may be exciting to some, it is really irrelevant and could be replaced by any other fluorescent markers. Let’s look instead at the capabilities that the RootChip demonstrated. First, the chip allowed the researchers to process 8 seedlings in parallel, which is always a timesaver! The authors noted that in its current configuration, 8 seedlings could be used, but modifications to the design could enable them to use more than 30 seedlings. The design also saves time since the seeds can begin germination externally before introduction to the chip. This allows researchers to select ‘high-achieving’ seedlings, and they won’t have wasted space on a dud.

Moving onto the experiment-enabling design of the chip, we can see that each perfusion chamber is independent and gives the user total control over several simultaneous experiments. This by itself is fine: You could use the RootChip to control your experiments and then use some other means to analyze the results. But with bright-field microscopy, the roots can be observed during and after the experiment in their ‘natural’ environment. I said before that I’m not an expert on plants, so I really don’t know the extent to which roots can be at least partially transparent. The transparency of the root and the bright-field microscopy allowed them to track the fluorescently-labeled metabolite activity, the swelling of the cells and the darkening of the root from death. What else could you observe about a root in the RootChip? And what else besides a root could you observe in the perfusion chamber? I guess you could look at some parasites like a tapeworm and watch them grow and respond to environmental changes. But would you really want to? I have a 100 yard rule about how close I let tapeworms get to my insides.


Grossmann, G., Guo, W., Ehrhardt, D., Frommer, W., Sit, R., Quake, S., & Meier, M. (2011). The RootChip: An Integrated Microfluidic Chip for Plant Science THE PLANT CELL ONLINE, 23 (12), 4234-4240 DOI: 10.1105/tpc.111.092577