BME100 f2013:W1200 Group7 L6

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
OUR COMPANY Name: Ambar Khare Name: student Name: student Name: student Name: student Name: student [SilverWare] LAB 6 WRITE-UP Computer-Aided Design TinkerCAD What is TinkerCad and How we Used it: In this lab, we used Tinkercad which is basically a browser-based 3D modeling program that lets people design whatever is on their mind. It is intuitive with several tutorials and easy to use for all ages. People can tweak an existing product or create a completely new model. The design can be saved and the file can be used to 3D print it. In this lab, we used Tinkercad to create a better design for the tubes that holds solution in the PCR. We changed it by connecting all the tubes for stability sort of like an accordion style and users can expand tubes for use or collapse it for storage. Also, the tubes are pre-labeled for efficiency and recognition. An image of your TinkerCAD PCR tube design: Implications/Benefits of Using TinkerCAD for Design Benefits Open PCR can be use to create or redesign a product. A practical sense for Tinkercad in relation to our lab would be redesigning the fluorometer camera setup. In our previous two labs, the camera setup was inefficient because the fluorometer didn’t have a place to hold the camera in place and so each time it was difficult to position the camera at the set distance. There could have been different camera angles that could have flawed our results. Additionally, the fluorometer device couldn’t be adjusted to a certain amount of height which could be a problem since people have cameras that are different sizes. We could use Tinkercad program to redesign this product by having an attachment to the device that has a place for people to put a camera. Or better yet, we can make a built in camera that is always facing the fluorometer at the slide level. Implication An implication for using the Tinkercad program is that one, it only is used to tweak physical features. If we wanted to change something internally of a PCR machine, it wouldn’t show in the 3D model at all. Feature 1: Cancer SNP-Specific Primers [Instructions: This information will come from the Week 9 exercises you did in lab. Your notes should be in a pdf file that is saved on Blackboard under your group.] Background on the cancer-associated mutation What is rs17879961? rs17879961 is a type of SNP which stands for single nucleotide polymorphism. A nucleotide is a subunit of nucleic acids like DNA or RNA. It is composed of a nucleotide base (A-T, G-C), five-carbon sugar, and a phosphate group. Polymorphism is when there are two or more differences existing in a population of species. From this, we can conclude that rs17879961 is a type of mutation which is found in homosapiens and extremely pathogenic. Humans have 46 chromosomes in their body and on chromosome number 22 is where this SNP is located. This type of SNP is significant over time in increasing the risk of breast cancer. The gene that rs17879961 affects is called the CHEK2 gene which stands for checkpoint kinase 2. Because SNP causes a mutation in this gene, it can lead to breast cancer. Basically the mutation this causes is the deletion of a single nucleotide at position 1100 at the CHEK2 gene. Deletion in this position causes production of a nonfunctional version of CHK2 protein. Without any healthy version of this protein, cells can’t regulate cell division leading to DNA damage. After a while, cells start to uncontrollably divide leading to cancerous tumors. Primer design Forward Primer: 5’ – T G T A A G G A C A G G A C A A A T T T Cancer-specific Reverse Primer: 5’ – G G T C C T A A A A A C T C T T A C A C How the Primers Work: [Instructions: explain what makes the primers cancer-sequence specific. In other words, explain why the primers will amplify DNA that contains the cancer-associated SNP rs17879961, and will not exponentially amplify DNA that has the non-cancer allele.] Feature 2: Consumables Kit [Instructions: Summarize how the consumables will be packaged in your kit. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look awesome and easy to score.] [Instructions: IF your consumables packaging plan addresses any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.] Feature 3: PCR Machine Hardware [Instructions: Summarize how you will include the PCR machine in your system. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look really awesome and easy to score.] [Instructions: IF your group has decided to redesign the PCR machine to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.] Feature 4: Fluorimeter Hardware [Instructions: Summarize how you will include the fluorimeter in your system. You may add a schematic image. An image is OPTIONAL and will not get bonus points, but it will make your report look really REALLY awesome and easy to score.] [Instructions: IF your group has decided to redesign the fluorimeter to address any major weakness discussed by your group or mentioned by others (see the Virtual Comment Board Powerpoint files on Blackboard, Lab Week 12) explain how in an additional paragraph.] Bonus Opportunity: What Bayesian Stats Imply About The BME100 Diagnostic Approach [Instructions: This section is OPTIONAL, and will get bonus points if answered thoroughly and correctly. Here is a chance to flex some intellectual muscle. In your own words, discuss what the results for calculations 3 and 4 imply about the reliability of CHEK2 PCR for predicting cancer. Please do NOT type the actual numerical values here. Just refer to them as being "less than one" or "very small." The instructors will ask you to submit your actual calculations via e-mail. We are doing so for the sake of academic integrity and to curb any temptation to cheat.]