Difference between revisions of "Assignment 8 Overview: flow channel & two-color microscope"

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==Overview==
 
==Overview==
  
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In Assignments 6 and 7, you familiarized yourselves with the basic tools and measurement techniques used in electronics. In the remaining assignments this semester, we'll work towards measuring the frequency-dependent osmotic shock response of yeast cells. We'll build a few circuits, but more importantly, we'll apply the framework that we've learned - using transfer functions, feedback, and Fourier transforms - to understanding a biological system.  
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In Assignment 7, you familiarized yourselves with the basic tools and measurement techniques used in electronics. In the remaining assignments this semester, we'll work towards measuring the frequency-dependent osmotic shock response of yeast cells. We'll build a few circuits, but more importantly, we'll apply the framework that we've learned - using transfer functions, feedback, and Fourier transforms - to understanding a biological system.  
  
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Our experiments are based on work published in ''Science'' by MIT researchers in 2008 <ref>[http://science.sciencemag.org/content/319/5862/482 | J. T. Mettetal, D. Muzzey, C. Gomez-Uribe, and A. van Oudenaarden, "The Frequency Dependence of Osmo-Adaptation in Saccharomyces cerevisiae," Science, vol. 319, no. 5862, pp. 482–484, 2008]</ref>. The basic idea is that we will use a fluidic device to stimulate the yeast cells with high- or low-salt media, and measure the nuclear localization of the protein Hog1 using our fluorescence microscopes. We'll oscillate the flow of media from low to high salt at varying frequencies, and measure the amplitude and phase of Hog1's response.  
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You'll start off this week's assignment 8 by examining the effects of gain on an electronic feedback system (Part 1). Then you'll build a microfluidic device and interface your microscope with computer controls for the LEDs and fluidic device (Part 2). Finally in Part 3, you'll validate that everything is working together by flowing fluorescent dyes through the device and recording how the fluorescence changes over time.  
  
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You'll start off this week's assignment with a few practice convolution questions (Part 0). Then head to the lab, where you'll implement a few upgrades to your microscope (Part 2), and incorporate the fluidic device and control components (Parts 1 and 3).  
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# [[Electronics bootcamp II: feedback systems|Part 1: electronics bootcamp II]];
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# [[Assignment 8, Part 2: fabricate a microfluidic device| Part 2: fabricate a microfluidic device]];
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# [[Assignment 8, Part 3: add flow control and test your device| Part 3: test your device with fluorescent dyes]].
  
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# [[Assignment 8, Part 0: convolution practice| Part 0: practice convolution]];
 
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# [[Assignment 8, Part 1: fabricate a microfluidic device| Part 1: fabricate a microfluidic device]];
 
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# [[Assignment 8, Part 2: build a two-color microscope| Part 2: implement 2-color imaging]];
 
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# [[Assignment 8, Part 3: add flow control and test your device| Part 3: test your device with fluorescein]].
 
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WARNING: this assignment is heavy on the in-lab component. Start early to make sure you have enough time to get everything built!
 
  
 
Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment8.pdf.
 
Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment8.pdf.

Latest revision as of 15:51, 26 March 2020

20.309: Biological Instrumentation and Measurement

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Overview

In Assignment 7, you familiarized yourselves with the basic tools and measurement techniques used in electronics. In the remaining assignments this semester, we'll work towards measuring the frequency-dependent osmotic shock response of yeast cells. We'll build a few circuits, but more importantly, we'll apply the framework that we've learned - using transfer functions, feedback, and Fourier transforms - to understanding a biological system.

You'll start off this week's assignment 8 by examining the effects of gain on an electronic feedback system (Part 1). Then you'll build a microfluidic device and interface your microscope with computer controls for the LEDs and fluidic device (Part 2). Finally in Part 3, you'll validate that everything is working together by flowing fluorescent dyes through the device and recording how the fluorescence changes over time.

  1. Part 1: electronics bootcamp II;
  2. Part 2: fabricate a microfluidic device;
  3. Part 3: test your device with fluorescent dyes.


Submit your work on Stellar in a single PDF file with the naming convention <Lastname><Firstname>Assignment8.pdf.

References


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