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Team 20 : A dvanced Gel Electrophoresis

Team 20 : A dvanced Gel Electrophoresis. Han Zhang, Yuxiao Ji, Xiangfei Zhou ECE 445 Senior Design M ay 6 th, 2014. What we do. Advanced gel electrophoresis with 96 vertical wells running simultaneously Operation for each well is systematically controlled and monitored through LabVIEW.

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Team 20 : A dvanced Gel Electrophoresis

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  1. Team 20:Advanced Gel Electrophoresis Han Zhang, Yuxiao Ji, Xiangfei Zhou ECE 445 Senior Design May6th, 2014

  2. What we do • Advanced gel electrophoresis with 96 vertical wells running simultaneously • Operation for each well is systematically controlled and monitored through LabVIEW

  3. Why we do it • Horizontal gel electrophoresis are slow- can contain at most 8 samples at a time • DNA samples are required to be injected and gathered manually, which is not efficient when the amount is large

  4. Typical horizontal gel electrophoresis

  5. Our design

  6. What we can achieve • Compatible to most existing robot systems • Software-wise visualization and voltage monitoring • Wireless communication* • DNA molecule recycling ability

  7. Explosive view PCB lays abovethis layer Top layer for electrodes Replaceable, vertical tubes for DNA, Gel and agarose Sample Protection Sample gathering layer Optic filter

  8. How it works Ladder wells (contains DNA of known size)

  9. DNA Sample Dyed with EB Samplelayer Gel Gel Gathering layer TAE Buffer

  10. Voltage Reading from LabVIEW Time Photodiode

  11. Voltage Reading from LabVIEW Time Photodiode

  12. Voltage Reading from LabVIEW Time Photodiode

  13. Voltage Reading from LabVIEW Time Photodiode

  14. System Overview • Hardware: - Power Supply - Microcontroller (ArduinoNano) - Wireless Transceiver (XBee) - Light Sensor (600nm) - Well Control Board with DNA Samples • Software: - LabView - Arduino Interface

  15. Block Diagram

  16. Hardware • Power Supply - 5V and 3.3V from ArduinoNano chip - 100V, 20W Power Supply • Microcontroller - ArduinoNano • DNA Control Board - J-K Flip-Flop, Decoder, Relay

  17. Hardware Wireless Transceiver - Xbee between Arduino and Computer with Xstick Light Sensor - Good performance for 600nm - Voltage Amp - Intensity indicates the location of DNA

  18. Schematic 1 for DNA Control Board

  19. Schematic 2 for DNA ControlBoard

  20. PCB (DNA Control Board)

  21. PCB (Sensor System)

  22. PCB (Connector Part)

  23. Microcontroller (Requirements) • Each digital output can generate at least 4V for logic 1, and lease than 1V for logic 0. • Receive analog input correctly from Light Sensor • Generate all digital pins correctly to DNA Control Board

  24. Microcontroller (Verifications) • Measure the digital outputs when it generates logic 1 or 0, and the outputs are 4.3V and 0.5V. • We can use the LabView to see the analog values, and check with the measure from the outputs of Light Sensor, which are consistent. • Measure all digital pins to check the logic value for each, and they are all correct.

  25. Light Sensor (Requirements) • Able to detect the light with wavelength of 600nm • Generate Voltage output for 2.8V when it is light, and 0.7V when it is dark. http://www.vishay.com/docs/81520/bpw24r.pdf

  26. Light Sensor (Verifications) • Using dyed DNA sample under the UV light, the sensor can detect the emitted orange light and generate a waveform in LabVIEW.

  27. Well Control Board with DNA Samples (Requirements) • Able to control the modes for each single channel for 48 DNA samples • The bubbles generated during the process of electrophoresis won’t result the open circuit, and they will be popped out.

  28. Well Control Board with DNA Samples (Verifications) • By using 48 LEDs instead of DNA samples, which is easier to check the modes for each channel, it can perfectly control the switching for each LEDs. • The Bubbles are too small to see, but they don’t result the open circuit.

  29. Modification • Communication removed from the original design - Avoid signal delay and communication error

  30. Failed Requirement • Relays we used worked properly under 40V but cannot handle 100V high voltage and burned • 3-D Printing has rough surface, which causes leakage of buffer and cause open circuit.

  31. Software • Arduino Nano w/ ATmega328 ArduinoNano functions as an interface between LabVIEW and PCB • LabVIEW 2013 Most algorithm was programmed using LabVIEW

  32. Users interface

  33. Macro-control panel • Turn on 48 wells all at once • Turn off all 48 wells at the same time • Disable macro-control functions • Shut down the LabVIEW control completely

  34. Manually control panel • Manually turn off each well individually • Indicators showing the state of each digital output pin

  35. Voltage pulse detector • Detect analog voltage input pulse according to the pre-set threshold voltage

  36. Clock • Clock output for J-K Flip-flop

  37. Future Work • More efficient PCB design with small board area • Use Wall Power for each component • Use precision instrument to produce and avoid leakage of electrolyte • Increasing the intensity of emitted light from dyed DNA (such as convex lens) or use CCD camera.

  38. Appendices • DNA Control Board PCB Drawing

  39. Thank You

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