Actinomyces Identification and Phylogeny

• What is the purpose of the antibody in the image?

  To bind to the proteins cross-linked to DNA fragments
• How do $Actinomyces$ bacteria grow?


  In branched growth patterns
• What can you infer about the sample or specimen based on the visual characteristics of the image?

  • The image shows a complex, intricate pattern of structures, suggesting a biological sample
  • The purple/pink coloration indicates some type of staining or dye was used to highlight certain features
  • The irregular, branching shapes and textures suggest this could be a sample of cells, tissues, or other biological material
• What type of microscopic image is shown in the image?

  This appears to be a microscopic image of some biological cells or structures.
• What color do $Actinomyces$ appear when stained?


  Purple
• What can $Actinomyces$ form under a microscope?


  Dense clumps or branching patterns
• What is the purpose of the annealing step in the PCR process?

  • Annealing (55°C) allows the DNA primers to bind to the complementary sequences on the template DNA.
• How do $Actinomyces$ appear under a microscope?


  As purple-stained threads
• What enzyme is used during the elongation phase of PCR?

  DNA polymerase (Taq)
• What role do $Actinomyces$ play in mammals?


  Part of the normal flora
• How many cycles are typically needed to achieve millions of DNA copies in PCR?

  20-40 cycles
• What temperature is used during the elongation phase of PCR?

  72°C
• What is the result of each PCR cycle?

  Each cycle doubles DNA copies
• How does the PCR process shown in the image differ from a typical PCR setup with individual primer pairs?

  The PCR in the image uses all four primer pairs in a single tube, while a typical PCR setup would use each primer pair in a separate tube
• What occurs during the elongation phase of PCR?

  DNA polymerase builds new strands
• What are the key steps in the process shown in the image?

  1. Proteins cross-linked to DNA fragments
  2. Antibody binds to the proteins
  3. DNA-protein complex is formed
  4. Proteins are removed
  5. DNA is amplified by PCR
• What are the four strains of the organism shown in the image?

  Strain A, Strain B, Strain C, Strain D
• What are the four primer pairs used in the PCR process?

  • Primer pair for Strain A
  • Primer pair for Strain B
  • Primer pair for Strain C
  • Primer pair for Strain D
• What is the main purpose of Multiplex PCR?

  To amplify multiple DNA regions simultaneously
• If you wanted to determine the genetic relationship between the four strains, which microscopy technique would be most appropriate?

  Scanning electron microscopy (SEM)
• What is the unit of measurement shown in the image?

  Centimeters
• What is the significance of band patterns in gel electrophoresis after Multiplex PCR?

  • Unique band patterns identify different strains
  • Each band represents a specific DNA region
  • Bands correspond to their respective primer pairs
• What occurs first in nested PCR?

  Standard PCR occurs first
• What is the purpose of the PCR (Polymerase Chain Reaction) process shown in the image?

  To amplify all four primer pairs in a single tube
• What is a characteristic morphology of $Actinomyces$?


  Filamentous morphology
• What is the allele number for gene2 in ST2?

  2
• Why is nested PCR less likely to amplify unwanted DNA fragments?

  Because of its highly specific amplification
• What is the purpose of DNA denaturation in the PCR process?

  • DNA denaturation (95°C) separates the double-stranded DNA into single strands to allow primers to bind.
• How does the DNA replication process work to determine the DNA sequence?

  • The DNA strand to be sequenced is primed
  • Four separate reactions are prepared, each with a different replication-stopping nucleotide (A, T, C, G)
  • The replication products from the 'C' reaction are separated by electrophoresis
  • The sequence is read as complementary bands containing the labeled strands
• What type of microscope technique was likely used to generate this image?

  Based on the level of detail and the staining/coloration, this was likely produced using a transmission electron microscope (TEM) or a scanning electron microscope (SEM), which can provide high-resolution images of microscopic biological structures.
• How does the PCR process ensure the amplification of a specific DNA sequence?

  By using DNA primers that bind to the complementary sequences flanking the target DNA region
• What type of bacteria are $Actinomyces$?


  Gram-positive
• What is the allele number for gene1 in ST2?

  1
• How could you use this ruler to measure the length of an object?

  • Place the object against the ruler
  • Align the start of the object with the 0 cm mark
  • Read off the measurement at the end of the object
• What is the allele number for gene4 in ST1?

  1
• What are nested primers in nested PCR?

  Primers that bind inside the first PCR product
• Why is understanding gene regulation important?

  It helps in understanding protein-DNA interactions
• What is the total length of the ruler shown in the image?

  30 cm
• What do specific antibodies target in this process?

  DNA-protein complexes
• Where are $Actinomyces$ commonly found?


  In soil, water, and mammals