BME100 f2014:Group24 L5

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Lab Write-Up 1 | Lab Write-Up 2 | Lab Write-Up 3
Lab Write-Up 4 | Lab Write-Up 5 | Lab Write-Up 6
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Our Team

Name: Erik Parkhurst
Name: Connor McCausland
Name: Safiya Shaikh
Name: Ainsley Pfeiffer
Name: Felix Madrid
Name: Martin Pelagio


Procedures

Camera Settings:

  • Type of Smartphone: iPhone 5s
  • Flash: No Flash
  • ISO Setting:
  • White Balance:
  • Exposure:
  • Saturation:
  • Contrast:

Calibration

  • 1) Using the switch for the Blue LED, turn on the excitation light.
  • 2) Turn on camera of smartphone and ensure the following settings. Make sure that the flash is inactive, set ISO to 180 or higher, set white balance to auto, set exposure and saturation to the highest setting, and set contrast to the lowest setting.
  • 3)Place the smart phone on the cradle at a right angle from the slide.
  • 4) Adjust the height of the fluorimeter using the plastic trays so that the camera takes a picture of the drop sideways.
  • 5) Ensure that the distance between the smartphone on the cradle and the first two rows of the slide are as close as possible without making the image blurry (at least 4 cm away from the drop).
  • 5) Record the distance between the smart phone cradle and drop.

Distance between camera and drop: 6.5 cm


Set Up For Smartphone Fluorimeter

Fluorimeter Set Up


Solutions Used for Calibration:

Solutions Used.png

Procedure for Placing Samples onto the Fluorimeter:

  • 1)Put on fresh pair of gloves
  • 2)Obtain a slide and place the smooth side down in the fluorimeter
  • 3)Place 80 uL drop of SYBR Green I solution on first 2 clear circles in middle of slide
  • 4)On top of the 80 uL drop of SYBR Green I, place 80 uL drop of sample/calibration solution
  • 5)Adjust slide so that the light illuminates the center of the drop and the drop focuses the light on the other side

Data Analysis

SNP Info & Primer Design

Background:

An SNP is a single nucleotide polymorphism. SNPs are common DNA sequence variations in which a single nucleotide is different between two members of a biological species. These genetic variations between individuals can result in changes in the phenotypes of individuals. In addition, SNPs also affect how people develop diseases and how they react to medicine. Studying SNPs is important for comparing certain parts of dna with diseases and without diseases.


Primer Design and Testing:

Non-disease Primer Non-disease Primer

Disease Primer Disease Primer

Lab D

PCR LAB D

What is a nucleotide? It is the basic building block of DNA

What is a polymorphism? a common variation of DNA among individuals.

What species is this variation found in? Homo Sapiens

What chromosome is this variation found on? 21:34370656

What is listed as the Clinical Significance of this SNP? pathogenic

What gene is this SNP associated with? KCNW2

What diesease is linked to this SNP? Congentital Long QT syndrome

What does KCNE2 stand for? potassium voltage-gated channel

Describe the molecular function of this gene: This gene encodes a member of the potassium channel. This member is a small integral membrane subunit that assembles with the KCNH2 gene product, a pore-forming protein, to alter its function. This gene is expressed in heart and muscle.

What is an allele? An allele is an alternative form of a gene that is located at a specific position on a specific chromosome.

The disease-associated allele contains what sequence? CTC

The numerical position of the SNP is: 34370656

Non-disease forward primer (20nt): CAT GGT GAT GAT TGG AAT GT

The numerical position exactly 200 bases to the right of the disease SNP is 34370856

Non disease reverse primer: CCC TTA TCA GGG GGA CAT TTT

Disease forward primer: CAT GGT GAT GAT TGG AAT GC

Disease reverse primer (20nt): CCC TTA TCA GGG GGA CAT TT