Acknowledgment: This assignment is based in part on Boedicker JQ, Vincent ME, Ismagilov RF. Microfluidic confinement of single cells of bacteria in small volumes initiates high-density behavior of quorum sensing and growth and reveals its variability. Angew Chem Int Ed Engl. 2009;48(32):5908-11. doi: 10.1002/anie.200901550. Feel free to read/skim this paper, but note that I have changed many of the details for the purposes of this assignment, and the details I provide for the assignment are fictitious/hypothetical (assuming…then…).
Background: Conventional dogma is that microbes use “quorum sensing” to determine if a certain threshold of other microbes of the same species are present; once this threshold is met, the microbes change their behavior. For example, some species of bacteria form biofilms when enough other bacteria of the same species are present. Microbes release chemical signals that let other microbes know that they are nearby. (The terminology “quorum sensing” is reminiscent of the concept of a “quorum” in some political institutions whereby enough people must be present for a vote or other official business to continue.) For more background, please see: https://en.wikipedia.org/wiki/Quorum_sensing#Mechanism and https://en.wikipedia.org/wiki/Autoinducer (or other literature).
Overview of the Design Project problem: Although quorum sensing has typically been thought of as a “group” behavior, your research group is interested in testing the hypothesis that it is merely dependent on the concentration of autoinducers (small molecules that initiate quorum sensing) around a bacterium. The overarching objective of this design project is to design an experiment to test the hypothesis that quorum sensing behavior can be observed in small populations (~1-20 bacterial cells) when they are confined in small volumes (paraphrased from Boedicker, 2009).
Fictitious/hypothetical details for this assignment: Assume that you will use model organism Bacteria xxx that produces Enzyme A only when quorum sensing behavior is initiated. You can purchase a fluorogenic substrate, Reagent Y, which is not fluorescent itself but becomes fluorescent when Enzyme A cleaves it (recall that we’ve talked about fluorogenic substrates in class, and they are also used in many papers cited in the droplet-based microfluidics review articles posted on Canvas). Your research group has preliminary data suggesting that when ~1-20 cells of Bacteria xxx are encapsulated into volumes of ~750 pL, quorum sensing behavior begins after ~12 h. Your group would like to gather more data (tens of thousands of droplets) to further test the overarching hypothesis; to achieve this you will use a droplet-based microfluidics approach. The aqueous phase (dispersed phase) will contain Bacteria xxx, and Reagent Y (aq) will be added. A fluorinated oil will be used for the continuous phase.One quick reason “why we care”: One of the many reasons this problem is interesting is that some bacteria form biofilms as a result of quorum sensing. Biofilms cause significant problems across numerous areas including medical devices and food production
Assignment: 1) Delay time [10 points total] *be based on file “very similar to this project”-figure1*
(a) Method [5 points]: How will you incubate your droplets to achieve the necessary incubation time (12 hours)? What factors are important to consider for your approach to work? Summarize your approach in a short paragraph (include citations). Either provide a sketch of your approach here or include this as a clearly labelled region of your overall device design sketch in question 2.
(b) Rationale [5 points]: What factors are important? What other approaches did you consider? Why did you choose this approach instead of the other approaches? (Include citations and/or reference class notes to support your case.)
2) Reynolds number calculation using a channel you find in the literature [20 points]
Find a microfluidic channel in the literature and calculate the Reynolds number for the channel with the specific fluid that is used within that channel (if you choose a droplet-based microfluidics application, you can use the viscosity and density of the carrier fluid to estimate the Reynolds number). Please show your work, use units, and indicate where you found the relevant numbers (please give citations or website urls) to plug into the Reynolds number calculation. Please structure your answer as follows:
a) Provide a citation for the publication you chose. Please choose a publication that has not yet been provided in this course and is not cited in the group part of this design project.
b) Provide a schematic (either hand drawn or copy/paste from the article) of the microfluidic device. Indicate the channel dimensions for the region of the channel that you focus on in part c.
c) Calculate the Reynolds number for the device (if the device contains different dimension channels, you may pick one region of the channel to focus on for your calculation; indicate the region you chose in your schematic in part b). Please show your work and include units in the calculation. Please provide citations (or urls) for the parameters (density, viscosity) that you needed to look up to do the calculation.
d) What is the device used for (2 sentence summary)? Based on the Reynolds number you calculated, will this device be in a laminar flow or turbulent regime? What implications does this have (or might this have) for the application of the microfluidic device (1 sentence)? [I realize that this last question may be difficult to answer for some applications. If you are having trouble answering it, please state that you are uncertain and instead give 1 sentence describing an area for future work.]