BME103: Difference between revisions
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* '''Experimental protocol planners''' set up and ran the PCR reactions. These were set aside to run for ~2 hours. | * '''Experimental protocol planners''' set up and ran the PCR reactions. These were set aside to run for ~2 hours. | ||
* Each team practiced operating the Single Drop Fluorimeter with plain water samples. | * Each team practiced operating the Single Drop Fluorimeter with plain water samples. | ||
Students were introduced to a '''Single Drop Fluorimeter''' fluorescence-based DNA detection device that was designed by Dr. Garcia. When a natural or PCR-amplified double-stranded DNA sample is stained with SYBR green and exposed to a blue LED light, the drop fluoresces green. The signal is captured as an image with the user's '''camera phone'''. | Students were introduced to a '''Single Drop Fluorimeter''' fluorescence-based DNA detection device that was designed by Dr. Garcia. When a natural or PCR-amplified double-stranded DNA sample is stained with SYBR green and exposed to a blue LED light, the drop fluoresces green. The signal is captured as an image with the user's '''camera phone'''. | ||
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<div style="background-color: #F0F0FF; padding: 10px;"> | <div style="background-color: #F0F0FF; padding: 10px;"> | ||
The students | |||
Activities: | |||
* '''Open PCR machine engineers''' used Solid Works to explore the computer-aided design file of the Open PCR system (provided by Josh Perfetto, Open PCR). | |||
* '''Experimental protocol planners''' planned a Polymerase Chain Reaction (PCR) protocol for the Open PCR system and programmed the machine for thermal cycling with the guidance of a worksheet. | |||
* '''Research and development scientists''' learned how the Polymerase Chain Reaction works so that they could explain the process to their teammates. This was done with the guidance of the instructor and the [http://openpcr.org/use-it/ OpenPCR Virtual Lab] tutorial. | |||
<center> | |||
<gallery style="background-color: #F0F0FF; border: 0;" widths=200px heights=200px> | |||
Image:Waterdrop-BME103-Group2.png|Negative control water droplet.<br>Photo credit: [http://openwetware.org/wiki/BME103:W930_Group7 Thurs 9:30am Group 9] | |||
Image:Bme_103_group7_setup_diagram2.png|Digital rendition of the fluorimeter.<br>Photo credit: [http://openwetware.org/wiki/BME103:W930_Group7 Wed 9:30am Group 7] | |||
</gallery> | |||
</center> | |||
[[Image:Waterdrop-BME103-Group2.png|200px|thumb|Negative control water droplet.<br>Photo credit: Wed. 9:30am Group 2]] | [[Image:Waterdrop-BME103-Group2.png|200px|thumb|Negative control water droplet.<br>Photo credit: Wed. 9:30am Group 2]] | ||
'''Lab Report 1''': Each team created a Wiki page write-up of their learning experiences | |||
</div> | </div> |
Revision as of 17:13, 17 December 2012
BME 103 Fall 2012 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help |
Introduction to Biomedical Engineering - Lab Part 2
GETTING STARTED
THE COURSE IN REVIEWSet-up: OpenPCR BuildingBefore this unit began, a group of ~10 upper level undergrads and graduate students assembled the OpenPCR machines. This was a great experience for the graduate students, and saved our Freshmen engineers the time and trouble of assembling the delicate pieces from scratch in a very limited amount of time. Thanks to our assembly team and Dr. Pizziconi's Design Studio team for your help! Week 1: Introduction - DNA as a Biomarker, 10/17/12Students were introduced to basic DNA science and its relationship to diagnostics and health. Sequence-specific DNA hybridization uses primers designed to base-pair with a target disease-associated marker. This leads to exponential amplification of an invisible DNA target. A mismatch (non-disease DNA sequence) does not produce amplification. Team members chose roles as Open PCR machine tester, Experimental protocol planner, and Research and development scientist.
In concurrent work sessions...
Week 2: DNA Amplification Reactions, 10/24/12Students used their experience from the previous week to set up and run a PCR experiment. The students were provided with personal protective equipment, 8 tubes of 50 μL PCR reaction mix, 8 tubes of 50 μL diluted template + primers. The instructors provided positive and negative "patient" samples so that some samples would test positive for a DNA marker (produce amplification), and others would test negative.
Activities:
Students were introduced to a Single Drop Fluorimeter fluorescence-based DNA detection device that was designed by Dr. Garcia. When a natural or PCR-amplified double-stranded DNA sample is stained with SYBR green and exposed to a blue LED light, the drop fluoresces green. The signal is captured as an image with the user's camera phone.
Week 3: Measuring DNA Using Fluorescence, 10/31/12The students Activities:
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