Interpretation of electrophoresis results

• What is the date of the lichen DNA barcoding extraction method testing?

  07/01/2023 BD
• What charge do DNA fragments have during electrophoresis?

  Negatively charged
• What does the PC (positive control) confirm in electrophoresis?

  Assay success
• What are the key takeaways from the results of the different extraction methods?

  • The 1Dr, 1HS, 2HS, 3HS, 4HS, 5HS, and 6HS methods all failed
  • The 1Dp, 2Dp, 3Dp, 4Dp, 5Dp, and 6Dp methods all produced amplicons, some with possible contamination
  • The 3Dr, 4Dr, and 5Dr methods produced amplicons
  • The 6Dr and 6Dp methods produced double amplicons
  • The NC method showed faint contamination
• What do the L lanes in the electrophoresis result show?

  DNA ladder (size standards)
• What do the Dr, Dp, and HS columns represent in the electrophoresis result?

  Different extraction methods
• What is the gel matrix commonly used in gel electrophoresis?

  Agarose
• What does each band in electrophoresis represent?

  • A collection of DNA fragments
  • Fragments of similar size
• What are the three extraction methods used in this testing?

  ITS1F/ITS4, standard protocol with direct PCR (Dr), dipstick extraction (Dp), and HotSHOT extraction (HS)
• What happens to negatively charged DNA fragments when the electric current is switched on?

  They move toward the positive electrode
• What is the purpose of the buffer solution in a gel electrophoresis apparatus?

  To allow the flow of electric current through the gel
• How do smaller DNA fragments behave compared to larger ones during electrophoresis?

  Smaller fragments move faster
• What is the main component of a gel electrophoresis apparatus?

  Buffer solution
• What were the results of the different extraction methods?

  • 1Dr - failed
  • 1Dp - amplicon (plus NC contam?)
  • 1HS - failed
  • 2Dr - amplicon
  • 2Dp - double amplicon (plus NC contam?)
  • 2HS - failed
  • 3Dr - amplicon
  • 3Dp - amplicon
  • 3HS - failed
  • NC - faint contamination
  • 4Dr - amplicon
  • 4Dp - amplicon
  • 4HS - failed
  • 5Dr - amplicon
  • 5Dp - amplicon
  • 5HS - failed
  • 6Dr - double amplicon
  • 6Dp - double amplicon
  • 6HS - failed
  • PC - amplicon
• What direction do DNA fragments move in electrophoresis?

  Toward the positive electrode
• Where are DNA samples loaded in the gel electrophoresis apparatus?

  Sample wells
• How do DNA fragments separate during gel electrophoresis?

  By size through the gel matrix
• Which extraction method appears to be the most successful based on the results?

  The 3Dr, 4Dr, and 5Dr methods which produced amplicons
• What factors affect the distance DNA fragments travel during electrophoresis?

  Fragment size and gel density
• What are the main components of the heterostructure shown in the image?

  • Graphene
  • h-BN
  • WSe2
• What are the main components of the gel electrophoresis apparatus?

  • Buffer solution (conducts electricity)
  • Gel matrix (usually agarose)
  • Sample wells (for DNA loading)
  • Electrodes (generate electric current)
• How do you estimate the size of DNA fragments using a size marker?

  • Compare sample bands to the DNA ladder
  • Use the position of bands to estimate sizes
• What can differences in band number indicate?

  Variations in DNA between samples
• What is the purpose of the buffer solution in gel electrophoresis?

  To conduct electricity
• What information can be determined from the different restriction enzyme digests of plasmid DNA shown in the image?

  • The size and number of DNA fragments produced by each restriction enzyme digest can provide information about the structure and sequence of the plasmid DNA.
  • Comparing the fragment patterns can help identify the specific restriction enzymes used.
  • This analysis can be used to map the location of restriction enzyme recognition sites on the plasmid.
• What are the main components of a gel electrophoresis apparatus and their functions?

  • Buffer solution: Allows flow of electric current through the gel
  • Gel: Medium for sample separation (e.g. agarose for DNA)
  • Electrodes: Apply electric field to drive sample migration
  • Sample wells: Load samples into the gel
  • Direction of movement: Samples migrate towards the positive electrode
• If the radius of the circle in the image is 5 cm, what is the area of the circle?

  $25\pi \text{ cm}^2$
• What does it mean if observed band sizes align with predicted sizes?

  It confirms accurate electrophoresis execution
• What is the material shown in the image?

  Graphene
• What is the purpose of using a size marker in this gel electrophoresis experiment?

  To determine the size of the DNA fragments in the other lanes
• If you wanted to separate DNA fragments of different sizes, which type of gel would you use in the electrophoresis apparatus?

  Agarose gel
• What does the table of expected sizes and observed bands indicate?

  • Expected sizes (bp) and corresponding observed bands
  • Lane 1 & 2: 1000 bp
  • Lane 3: 2000 bp
  • No bands for 3000 bp
• What might inconsistencies in observed band sizes indicate?

  Procedural errors or sample contamination
• In the WSe2 study, what does panel d indicate about DNA quality?

  It shows high-quality DNA fragment separation
• What are the potential issues with the extraction methods that failed?

  • The 1Dr, 1HS, 2HS, 3HS, 4HS, 5HS, and 6HS methods all failed, suggesting potential problems with the extraction process or sample quality
  • The NC method showed faint contamination, indicating the need for more stringent contamination controls
• What should bands appear like when analyzing electrophoresis results?

  Sharp and distinct
• What role do electrodes play in gel electrophoresis?

  They generate an electric current
• What is the purpose of the WSe2 layer in the image?

  It is used to form a heterostructure with graphene
• What is the purpose of a size marker in determining DNA fragment size?

  It provides a reference for estimating sizes
• If you wanted to determine the size of a plasmid DNA fragment, which lane in the image would you use as a size marker?

  The rightmost lane, labeled "size marker"