BME103 s2013:T900 Group9 L3: Difference between revisions
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| [[Image:BME103 Group9ColeyWhite Assembly.jpg|100px|thumb|Name: Coley White<br>Role(s): Protocol Planner]] | | [[Image:BME103 Group9ColeyWhite Assembly.jpg|100px|thumb|Name: Coley White<br>Role(s): Protocol Planner]] | ||
| [[Image:Nordy.gif|100px|thumb|Name: Brady Falk, Commander <br> Role: Machine Operator]] | | [[Image:Nordy.gif|100px|thumb|Name: Brady Falk, Not Commander <br> Role: Machine Operator]] | ||
| [[Image:clown.jpg|100px|thumb|Name: Aimen Vanood <br>Role: ]] | | [[Image:clown.jpg|100px|thumb|Name: Aimen Vanood <br>Role: Research and Development Scientist]] | ||
| [[Image:BME 103 Group 9 Vignesh.jpg|100px|thumb|Name: Vignesh Senthil<br>Role(s)]] | | [[Image:BME 103 Group 9 Vignesh.jpg|100px|thumb|Name: Vignesh Senthil<br>Role(s): Research and Development Scientist]] | ||
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| Sample Name || Ave. INTDEN* || Calculated μg/mL || Conclusion (pos/neg) | | Sample Name || Ave. INTDEN* || Calculated μg/mL || Conclusion (pos/neg) | ||
|- | |- | ||
| Positive Control (+) || 4438005 || | | Positive Control (+) || 4438005 || 13.50 || N/A | ||
|- | |- | ||
| Negative Control(-) || 2361911 || - | | Negative Control(-) || 2361911 || -8.43 || N/A | ||
|- | |- | ||
| Tube Label: <u>A1</u> Patient ID: <u>10840</u> rep 1 || 818350 || | | Tube Label: <u>A1</u> Patient ID: <u>10840</u> rep 1 || 818350 || -24.74 || Neg | ||
|- | |- | ||
| Tube Label:<u>A2</u> Patient ID: <u>10840</u> rep 2 || 829045 || | | Tube Label:<u>A2</u> Patient ID: <u>10840</u> rep 2 || 829045 || -24.63 || Neg | ||
|- | |- | ||
| Tube Label:<u>A3</u> Patient ID: <u>10840</u> rep 3 || 331978 || | | Tube Label:<u>A3</u> Patient ID: <u>10840</u> rep 3 || 331978 || -29.878 || Neg | ||
|- | |- | ||
| Tube Label:<u>B1</u> Patient ID: <u>12675</u> rep 1 || 905925 || | | Tube Label:<u>B1</u> Patient ID: <u>12675</u> rep 1 || 905925 || -23.814 || Neg | ||
|- | |- | ||
| Tube Label:<u>B2</u> Patient ID: <u>12675</u> rep 2 || 540926 || | | Tube Label:<u>B2</u> Patient ID: <u>12675</u> rep 2 || 540926 || -27.670 || Neg | ||
|- | |- | ||
| Tube Label:<u>B3</u> Patient ID: <u>12675</u> rep 3 || 2729798 || | | Tube Label:<u>B3</u> Patient ID: <u>12675</u> rep 3 || 2729798 || -4.546 || Pos | ||
|} | |} | ||
<nowiki>* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images</nowiki> | <nowiki>* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images</nowiki> | ||
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Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.<br> | Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal. <br> | ||
* A = | * A = frequency of cancer positive conclusions = 9/20= .45 = 45% | ||
* B = | * B = frequency of positive PCR reaction = 26/60 = 0.43 = 43% | ||
* P (B|A) = | * P (B|A) = frequency of positive PCR given cancer-positive conclusion = 25/26 = 0.96 = 96% | ||
* '''P(A|B) = | * '''P(A|B) = 100= 100%''' | ||
<br> | <br> | ||
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Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.<br> | Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.<br> | ||
* A = | * A = Frequency of mismatch for positive = .35= 35% | ||
* B = | * B = Frequency of all mismatches = 9/20 = .45 = 45% | ||
* P (B|A) = | * P (B|A) = Given the patient will develop cancer, what is the probability of a cancer DNA sequence= 6/7 = 0.86 = 86% | ||
* '''P(A|B) = | * '''P(A|B) = 67%''' | ||
<br> | <br> <br> | ||
<!-- Bonus points for Calculation 4! | <!-- Bonus points for Calculation 4! | ||
Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence.<br> | Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence.<br> | ||
* A = | * A = | ||
* B = | * B = | ||
* P (B|A) = | * P (B|A) = | ||
* '''P(A|B) = [answer]''' --> | * '''P(A|B) = [answer]''' --> | ||
<br> | <br> | ||
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'''We concluded that a good system ''Should Avoid'':''' | '''We concluded that a good system ''Should Avoid'':''' | ||
* | * High Energy Consumption | ||
* | As with any scientific process, using a PCR must take into mind the resources expended for samples to be analyzed. In order to have an efficient, affordable collection of data, the power consumption should be limited to avoid unnecessary consumption of resources. This could prove to be a problem when analyzing large quantities of samples with multiple trials, which could greatly tax energy resources. While this is a major problem that cannot be allowed, it would't greatly affect the actual experimental process of the PCR, thus making it something we should avoid. | ||
* Analyzing Individual Samples | |||
In most PCR experimentation there needs to be large quantities of sample analyzed, and this form of data collection would be tedious and take absurd amounts of time. This is highly inefficient when compared with analyzing multiple samples simultaneously, wasting precious time in collecting the necessary data for an experiment. It would be harder to identify an accurate data among a set when each sample is analyzed individually rather than as a whole. While this would greatly slow down the pace of the data, it doesn't disrupt the actual experimentation process or harm the user in any way. | |||
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''' We chose to include these new features''' | ''' We chose to include these new features''' | ||
* Feature 1 - '''Heat Resistant Exterior''' - The heat resistant exterior is a main concern that our group had with the original product. As soon as we realized that the machine would be heating up to temperatures that would easily start the thin plywood on fire, it was obvious that the materials needed to be changed. The new material that we will use will be a thin sheet of metal that is light and has an extremely high melting point. The metal needs to be light so that it can be portable, and the melting point needs to be high so that the temperatures in the system do not melt the machine. The meltal also needs to have low conductivity because the outside of the machine can't be hot while the operator is working with the device. | * Feature 1 - '''Heat Resistant Exterior''' - The heat resistant exterior is a main concern that our group had with the original product. As soon as we realized that the machine would be heating up to temperatures that would easily start the thin plywood on fire, it was obvious that the materials needed to be changed. The new material that we will use will be a thin sheet of metal that is light and has an extremely high melting point. The metal needs to be light so that it can be portable, and the melting point needs to be high so that the temperatures in the system do not melt the machine. The meltal also needs to have low conductivity because the outside of the machine can't be hot while the operator is working with the device. | ||
* Feature 2 - | * Feature 2 - '''Fast Imaging Results''' - One of the problems that was found during testing was that the time it took to find the actual values took much longer than it should have. A solution to this problem would be to develop a software that automatically does the calculations that ''Image J'' currently does. The reason why this is important s because it would be much faster and much more accurate with a computer making the precise decisions that a human would have to do. The computer would be able to be quick and accurate, making the lab go much smoother and with less error in the results. <br> <br> | ||
'''STEP-BY-STEP INSTRUCTIONS''' <br> | '''STEP-BY-STEP INSTRUCTIONS''' <br> | ||
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'''Our primers address the following design needs''' | '''Our primers address the following design needs''' | ||
* These primers bind to the cancer gene, amplifying a mutated sequence. Due to this, the presence of cancer is easy to detect, increasing the efficiency of the PCR process. What is more, this results in more precise results, because annealing will only occur if cancer is present. | * These primers bind to the cancer gene, amplifying a mutated sequence. Due to this, the presence of cancer is easy to detect, increasing the efficiency of the PCR process. What is more, this results in more precise results, because annealing will only occur if cancer is present. The fact that the material used to make this new PCR is more durable in the face of high temperatures, the primes will also have a more stable environment to function in, lowering the risk of burning and improper binding. | ||
Latest revision as of 21:14, 16 April 2013
BME 103 Spring 2013 | Home People Lab Write-Up 1 Lab Write-Up 2 Lab Write-Up 3 Course Logistics For Instructors Photos Wiki Editing Help | ||||||||||||||||||||||||||||||||||||||||||||||||
OUR TEAMLAB 3 WRITE-UPOriginal System: PCR ResultsPCR Test Results
* Ave. INTDEN = Average of ImageJ integrated density values from three Fluorimeter images
Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B)
Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.
New System: Design StrategyWe concluded that a good system Must Have:
In order for the PCR to be efficient when analyzing samples, it needs to have fast imaging results. In practical uses, the PCR will be testing large numbers of samples, where fast imaging would be needed to determine information in limited time. Using this component, it is possible to even run multiple trials to determine the accuracy of the data received. The time saved using this key necessity could then be directed towards utilizing the data to understand relationships between patients. This feature is imperative to allow us to understand the correlation between the samples and the patients on a larger scale.
The sample volume used by the PCR needs to be small, as there is a limited amount of a given sample, with many tests needed to be taken to attain accurate data. This directly correlates to the size of the PCR, where a larger sample size would require a larger machine, which is inefficient. When the initial sample size is minimal, there is still a possibility to run multiple trials without risk of depleting the sample source. This feature is required to suit any given circumstance of initial sample volume, and will allow multiple PCR measurements, regardless of the size.
If the PCR is portable, this will eliminate the need for samples to be sent to centers that house the device. This will allow scientists to reduce the time wasted for the sample to be sent to these facilities, and data can be collected much earlier. With the device being compact, it will allow for multiple PCR's to be housed in a given area, which will allow a greater quantity of samples to be analyzed simultaneously. While these components would greatly improve the process, they are not the main priority when attempted to analyze samples through the PCR.
With the price of the PCR being relatively low (Open PCR: $600, Fluorimeter: $300), this allows for more widespread use of the machine. This would allow private use of the PCR to the public, making it affordable to accumulate important data. This component would also allow for the purchase of additional PCR machines or other supplemental equipment. This greatly supports the spread of scientific thinking, making it a possibility to use this resource by those lacking numerous funds. While this would be ideal to have for the machine, it is not necessary to have such a low price, as research can still be headed by large institutions or companies.
It is necessary for the PCR to have strong USB connectivity, as it is through this that the images are created and analyzed for data. Problems associated with this connectivity would greatly impair the overall process as well as by effecting the data received from the device. This is one of the most important parts of the PCR, as it allows for the entire image analysis to take place. PCR machines would only be approved for use if this problem did not exist, as it would defeat the purpose of using the machine.
The most important part of any experiment is the safety of the scientist(s) who are involved. Without the temperature of the casing optimized, the machine cannot be safely used to investigate a set of samples. Not only could this lead to possible harm to the scientist and the laboratory, but it could also release chemicals that can release toxins into the surrounding area. Health is a primary concern, and the PCR cannot have this issue for the safety of those utilizing it for scientific purposes.
As with any scientific process, using a PCR must take into mind the resources expended for samples to be analyzed. In order to have an efficient, affordable collection of data, the power consumption should be limited to avoid unnecessary consumption of resources. This could prove to be a problem when analyzing large quantities of samples with multiple trials, which could greatly tax energy resources. While this is a major problem that cannot be allowed, it would't greatly affect the actual experimental process of the PCR, thus making it something we should avoid.
In most PCR experimentation there needs to be large quantities of sample analyzed, and this form of data collection would be tedious and take absurd amounts of time. This is highly inefficient when compared with analyzing multiple samples simultaneously, wasting precious time in collecting the necessary data for an experiment. It would be harder to identify an accurate data among a set when each sample is analyzed individually rather than as a whole. While this would greatly slow down the pace of the data, it doesn't disrupt the actual experimentation process or harm the user in any way.
New System: Machine/ Device EngineeringSYSTEM DESIGN The only thing changed in our design is the type of material used. Our materials will be changed to be cheaper, and to provide for a safer machine. Photo of the Single-Drop Fluorimeter Device.
KEY FEATURES We chose to include these new features
STEP-BY-STEP INSTRUCTIONS
New System: ProtocolsDESIGN We chose to include these new features
Heated Lid: 110°C Initial Step: temp: 95°C time: 180 sec Number of Cycles: 35 Denaturing: temp: 95°C time: 30 sec Annealing: temp: 57°C time: 30 sec Extending: temp: 72°C time: 30 sec Final Hold: temp: 4°C
New System: Research and DevelopmentBACKGROUND
CHEK2 gene stands for Checkpoint Kinase 2 and is plays a role in cancer. This gene is a protein kinase. A protein kinase is involved in the phosphorylation of proteins. In other words, they add phosphate groups to proteins in order to regulate cellular pathways. The CHEK2 gene specifically is associated with DNA repair. When DNA is damaged, the CHEK2 gene is triggered. The protein that this gene encodes is involved in tumor suppression. Thus, when a damaged, the protein begins to phosphorylate in a way that prevents the occurrence of mitosis. Thus, the damaged DNA is not replicated. However, a mutation or polymorphism of the CHEK2 gene results in the improper prevention of DNA replication. This is because, without this gene, the damaged DNA-containing cells do not undergo apoptosis, or programmed cell death. Thus, the mutated DNA is replicated, causing an increase in susceptibility of cancer. An SNP, or single nucleotide polymorphism, occurs when a single nucleotide in a gene is changed, resulting in a change in sequence of the replicated DNA. An example of this can be seen in CHEK2. Take for instance the normal allele ATT. An polymorphism of this allele is ACT. This SNP causes a change in the complementary DNA strand. Instead of having an allele of TAA, the complementary strand would have TGA instead. This small mutation in DNA if, amplified repeatedly in the body, can result in cancer. DESIGN
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