May

• The BU Wetlab and Hardware iGEM teams participated in joint Wetlab safety and protocol training
• The team performed an initial literature review in order to learn more about the types of microfluidic devices being design
• The team was given a software overview/explanation of the three CIDAR lab microfluidic design tools: 3Duf, Fluigi, and Neptune
• The team was given an overview/explanation of the CIDAR lab microfluidic design manufacturing process: Makerfluidics

June

• From the literature review, each member chose one chip of interest to replicate and test
1. LAMP Chip^[1]
   • 3 iterations designed in Fluigi
   • 5 iterations designed in 3Duf and tested
2. Multiplex Drug Testing Chip^[2]
• 2 iterations designed in 3Duf and tested
• 1 iteration designed in Fluigi
3. Magnetic Mixer Chip^[3]
• 5 Iterations milled and tested
• Magnetic particles introduced into chip
• Experimented with different protocols
• BU Wetlab iGEM Team Collaboration began
• At the initial meeting BU Weltab provided BU Hardware with a protocol they thought could be performed in a microfluidic device
• 6 potential chips designed for Wetlab collaboration
• Submitted Microfluidics iGEM Poll to the iGEM collaborations page
• Volume Dispensing Chips
  • 3 iterations desgined in 3Duf and tested
• Alternative Tree Primitive Designs
  • Given repeat difficulties faced while using trees in designs, alternative designs were tested to determine if there was a better design
  • 3 iterations designed in 3Duf and tested
• Transformation Chip
  • 6 Iterations designed in Fluigi
  • 2 Iterations designed in 3Duf and tested
• Cell Sorting
  • 1 iteration milled and tested
  • Magnetic particles run through chip
• Attended Northeastern iGEM practice conference (NEGEM) at BU
  • Received feedback on iGEM narrative
  • Developed project ideas based off of feedback
• MARS Repository begins to form after talking with researchers from CILSE’s Biological Design Center

• Alternative Tree Primitive Designs
  • 1 iteration designed in 3Duf and tested
  • 1This design was markedly better at dispensing liquid equally, therefore it was used in later designs
• Cell Lysis Chip
  • 3 iterations designed in 3Duf and tested
  • Changes made to fix issues with fluid input and mixing
  • Initial draft of protocol written
• Wetlab Collaboration Chip
  • 4 iterations milled
  • Sealing issues improved upon
  • Testing done with shared liquid input
• DNA Digestion Chip
  • 4 iterations milled
  • Iterations made to better replicate protocol on a chip
  • Pipetting chamber designed and optimized for chip
• BU Hardware visits BosLab during monthly showcase
  • Provided insight into what small scale biohacker space is like, and what synthetic biology community is looking for in microfluidics
• Fluid Functionality begins to be developed
  • Idea of primitive level analysis developed along with some qualitative failures
• Worked with Neptune (2016 BU Hardware Team) automated syringe pumps tried to increase accuracy and improve function
• MARS Repository chips began to be placed in subsections of isolation, modification, and quantification
• Transformation Chip
  • 2 iterations designed in Fluigi
  • 8 iterations designed in 3Duf and tested
  • Changes made to overall design as well as valve sizes
• Summer Pathways
  • Participated in Summer Pathways alongside the BU Wetlab Team
  • Created an interactive microfluidics design activity for the attending high school students
  • Engaged with students to design microfluidic devices based on synbio protocols
• Harvard iGEM Team Collaboration
  • Initial meetings to discuss plans
• WPI iGEM Team Collaboration
  • During the initial Skype call we discussed the nature of their lead assay and how it might be moved onto a microfluidic
  • Their team visited our lab and performed verified their assay’s functionality on the BU spectrometer
• Tutorial Videos
  • PDMS video filmed
• Peristaltic Pump Chip^[4]
  • Design inspired by another paper with different geometries
  • 4 iterations designed in 3Duf and tested
• Metering Primitive
  • In order to allow for accurate volume dispension on a microfluidic device, a metering primitive inspired by the peristaltic pump was designed
  • 2 iterations designed in 3Duf and tested

• Transformation Chip
  • 13 iterations designed in 3Duf and tested
  • Different valve dimensions tested
• Ligation Chip
  • 2 iterations designed in 3Duf
• Tutorial Videos
  • PDMS Video finalized
  • Milling Video recording and scripting completed
• DNA Digestion
  • 2 iterations milled and tested
• Wetlab Collaboration Chip
  • 1 iteration milled and tested
• Cell Lysis Chip
  • Design finalized
  • Testing with magnetic particles in chamber
• Cell Culturing
  • Initial CAD model designed and tested
  • Spin coated PDMS
  • Second and final CAD model designed and tested
• Wiki
  • Initial pages started to be constructed
  • Wiki architecture organized
• Fluid Functionality
  • Quantitative tests begin to be developed

• Transformation Chip
  • 1 iteration designed in 3Duf and tested
  • Different valve dimension tested
• Tutorial Videos
  • Milling video finalized
  • Assembly video filmed and scripted
  • Cleaning video filmed and audio recorded
• Fluid Functionality
  • Channels quantitative tests finalized
• Antibiotic Resistance^[5]
  • Initial design developed
• Wetlab Collaboration Chip
  • 2 Iterations milled and tested
  • Protocol and design finalized
  • Chip tested by Wetlab

• Transformation Chip
  • 4 iterations designed in 3Duf and tested
  • Different metering scales tested
• PCR Chip
  • 4 iterations designed in 3Duf and tested
• Cell Sorting
  • 2 iterations milled and tested
  • Protocol finalized and documented
• Ligation Chip
  • 1 iteration designed in 3Duf
• Video tutorials
  • Assembly video finalized
  • Cleaning video finalized
• WPI iGEM Team Collaboration chip design documented finalized
• Attended Northeastern iGEM practice conference #2 (NEGEM) at MIT
  • Received feedback on iGEM presentation
  • Incorpated feedback for final presentation
• Fluid Functionality
  • Valve quantitative test finalized
  • Mixer quantitative test finalized
• Antibiotic Resistance
  • Design finalized using 3Duf
  • Milled and documented
• Harvard iGEM Collaboration
  • Validated Harvard optical density sensor

Citations

1. Tourlousse, D. M., Ahmad, F., Stedtfeld, R. D., Seyrig, G., Tiedje, J. M., & Hashsham, S. A. (2012). A polymer microfluidic chip for quantitative detection of multiple water- and foodborne pathogens using real-time fluorogenic loop-mediated isothermal amplification. Biomedical Microdevices, 14(4), 769–778. https://doi.org/10.1007/s10544-012-9658-3
2. Mohan, R., Mukherjee, A., Sevgen, S. E., Sanpitakseree, C., Lee, J., Schroeder, C. M., & Kenis, P. J. A. (2013). A multiplexed microfluidic platform for rapid antibiotic susceptibility testing. Biosensors and Bioelectronics, 49, 118–125. https://doi.org/10.1016/j.bios.2013.04.046
3. Liang-Hsuan Lu, Kee Suk Ryu, & Chang Liu. (2002). A magnetic microstirrer and array for microfluidic mixing. Journal of Microelectromechanical Systems, 11(5), 462–469. https://doi.org/10.1109/jmems.2002.802899
4. Nguyen, T. V., Duncan, P. N., Ahrar, S., & Hui, E. E. (2012). Semi-autonomous liquid handling via on-chip pneumatic digital logic. Lab on a Chip, 12(20), 3991. https://doi.org/10.1039/c2lc40466d
5. Hou, H. W., Bhagat, A. A. S., Lin Chong, A. G., Mao, P., Wei Tan, K. S., Han, J., & Lim, C. T. (2010). Deformability based cell margination—A simple microfluidic design for malaria-infected erythrocyte separation. Lab on a Chip, 10(19), 2605. https://doi.org/10.1039/c003873c
6. Lee KS, Boccazzi P, Sinskey AJ, Ram RJ. Microfluidic chemostat and turbidostat with flow rate, oxygen, and temperature control for dynamic continuous culture. Lab Chip. 2011;11(10):1730-9.https://doi.org/10.1039/c1lc20019d