BME100 f2013: Difference between revisions
(18 intermediate revisions by the same user not shown) | |||
Line 42: | Line 42: | ||
{| style="background-color: #F0F0FF;" | {| style="background-color: #F0F0FF;" | ||
|- | |- | ||
| valign="top" | [[Image:PCRmachineG7.jpg|thumb| | | valign="top" rowspan="4" | [[Image:PCRmachineG7.jpg|thumb|150px|Snapshot of an OpenPCR plugged into a computer. Photo from [http://openwetware.org/wiki/BME100_f2013:W900_Group7_L4 AM Group 7]]]<br> | ||
[[Image: | [[Image:PCR_STORY_BOARD.png|thumb|150px|Snapshots of a PCR video. Photo from [http://openwetware.org/wiki/BME100_f2013:W900_Group8_L4 AM Group 8]]]<br> | ||
| valign="top" | Students 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 a DNA target. A mismatch (non-disease DNA sequence) does not produce amplification. <br><br> | | valign="top" colspan="2" | Students 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 a DNA target. A mismatch (non-disease DNA sequence) does not produce amplification. <br><br> | ||
PRE-LAB READING & QUIZ: | |- | ||
* '''[http://openpcr.org/what-is-pcr OpenPCR Polymerase Chain Reaction | | valign="top" width="180px" | PRE-LAB READING & QUIZ: | ||
* '''[http://learn.genetics.utah.edu/content/labs/pcr/ PCR Virtual Lab]''' - | | valign="top" | | ||
* | * '''[http://openpcr.org/what-is-pcr OpenPCR Polymerase Chain Reaction Information Page]''' | ||
LAB ACTIVITIES: | * '''[http://learn.genetics.utah.edu/content/labs/pcr/ PCR Virtual Lab]''' - ''University of Utah'' | ||
* Quiz: students answered 5-10 questions at the beginning of the class and received assistance from the TA's to assess and reinforce comprehension of the pre-lab material. | |||
|- | |||
| valign="top" | LAB ACTIVITIES: | |||
| valign="top" | | |||
* '''Open PCR Machine Testing''' - Students partially disassembled and identified parts in a thermal cycling machine with the guidance of a worksheet and the OpenPCR machine manual. Students tested the machine for proper function. | * '''Open PCR Machine Testing''' - Students partially disassembled and identified parts in a thermal cycling machine with the guidance of a worksheet and the OpenPCR machine manual. Students tested the machine for proper function. | ||
* '''Protocol Planning''' - Students 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. | * '''Protocol Planning''' - Students [http://openwetware.org/wiki/Image:BME103_f2012_PCRreactions.png 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''' - Students learned how the Polymerase Chain Reaction can be used to detect cancer-associated mutations with the guidance of a step-by-step worksheet. | * '''Research and Development''' - Students learned how the Polymerase Chain Reaction can be used to detect cancer-associated mutations with the guidance of a step-by-step worksheet. | ||
OPTIONAL | |- | ||
* '''[http://learn.genetics.utah.edu/content/begin/dna/builddna/ Build a DNA Molecule]''' - | | valign="top" | OPTIONAL MATERIAL: | ||
| valign="top" | | |||
* '''[http://learn.genetics.utah.edu/content/begin/dna/builddna/ Build a DNA Molecule]''' - ''University of Utah'' | |||
|} | |} | ||
</div> | </div> | ||
===Week 2: DNA Amplification Reactions, 10/ | ===Week 2: DNA Amplification Reactions, 10/30/13=== | ||
<div style="background-color: #F0F0FF; padding: 10px;"> | <div style="background-color: #F0F0FF; padding: 10px;"> | ||
Students 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, and disposable | {| style="background-color: #F0F0FF;" | ||
|- | |||
| valign="top" | Students 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, a 200 μL micropipettor, and disposable pipette tips. The instructors provided positive and negative "patient" samples so that some samples would test positive (produce amplification) for a specific single nucleotide polymorphism (SNP), and others would test negative (no amplification). | |||
<br> | |||
PRE-LAB READING & QUIZ: | |||
* '''[http://www.youtube.com/watch?v=NgosWmRjjAo Pipetting Technique Video]''' | |||
* '''[http://lsteam.org/iet/pipetting/index.html Interactive Micropipetting Tutorial]''' - Choose Helene as the employee you want to observe. | |||
* '''[http://www.youtube.com/watch?v=tJjXpiWKMyA What are SNPs?]''' - ''23andMe and Kahn Academy'' | |||
* '''Finding a Cancer-Associated Mutation Online''' - Follow the steps shown in the slides in CancerSNP.pptx (from Blackboard) to explore the NCBI SNP database. | |||
* Quiz: students answered 5-10 questions at the beginning of the class and received assistance from the TA's to assess and reinforce comprehension of the pre-lab material. Students also completed a colored dye pipetting exercise to practice good technique.<br> | |||
LAB ACTIVITIES: | |||
* '''Pipetting Practice''' - Students practiced good micropipetting technique, using food coloring. | |||
* '''PCR Reaction''' - Students ran PCR reactions on real DNA samples. | |||
* '''Cancer-specific Primer Design''' - Students learned how PCR can be applied to detect a cancer-associated DNA sequence (SNP) with a hands-on exercise (guided by a worksheet) in designing a SNP-specific primer pair.<br> | |||
<br><br> | <br><br> | ||
|} | |||
</div> | </div> | ||
===Week 3: Computer-Aided Design with TinkerCAD, | ===Week 3: Computer-Aided Design with TinkerCAD, 11/06/13=== | ||
<div style="background-color: #F0F0FF; padding: 10px;"> | <div style="background-color: #F0F0FF; padding: 10px;"> | ||
Activities: | Activities: |
Latest revision as of 12:33, 6 January 2014
BME 100 Fall 2013 | Home People Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3 Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6 Course Logistics For Instructors Photos Wiki Editing Help | ||||||||||
Introduction to Biomedical Engineering DNA Lab Learning Objectives: Students should leave this unit equipped with a theoretical understanding of how to detect DNA biomarkers and the relevance of this technology to human healthcare. Emphasis will be on good lab/experimental controls and the collection of statistically valid measurements. Students will also understand how commonly used lab devices function, and explore the recent efforts to simplify experiments and to lower costs. At the end of the section, students will explore creative new biosensor designs based on PCR and fluorescent imaging.
GETTING STARTED
THE DNA LABS 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, 10/23/13
Week 2: DNA Amplification Reactions, 10/30/13
Week 3: Computer-Aided Design with TinkerCAD, 11/06/13Activities:
Week 4: Measuring DNA Using Fluorescence, 11/7/12Samples were mixed with SYBR green dye and analyzed on Single Drop Fluorimeters. Students used 2 μg/mL purified calf thymus DNA to calibrate the DNA measurement process. Using this value, they were able to convert the PCR results from brightness into DNA concentration. Summaries of their results are available on the Lab Report 1 page.
Lab Report 1: Each team created a Wiki page write-up of their learning experiences. Week 5: Designing a New System, 11/14/12The class discussed some of the strengths and areas for possible improvement of the DNA amplification and detection system. Each team then conceptualized a new DNA detection system based on OpenPCR and the Single Drop Fluorimeter. Concurrent work sessions:
Week 6 & 7: Advertisement Videos, 11/28/12 & 12/6/12The instructors presented PCR and DNA detection systems that are currently on the market. The systems included super-compact personal PCR machines to very large systems that were capable of both amplifying and measuring the levels of DNA in real time. Lab Report 3: Each team created an advertisement video for their new system. These videos were showcased in class. How Well Did OpenPCR + Single Drop Imaging Perform?The instructors compared traditional gel electrophoresis with the results from the new single drop Fluorimeter approach. Each Sample either has template DNA or is blank. Only DNA Samples should produce amplification (visible band as a Gel result, or high Fluorimeter value). The OpenPCR system successfully amplified products of the expected size, and the Single Drop Fluorimeter measurements agreed with gel electrophoresis data. Overall, the system is a success.
|