Homework Problem Set #8 (10 pts)

1) rRNA sequence divergence is a measure of phylogenetic relatedness (i.e., biological diversity). How is this related to what people usually think of as biological diversity?

2) Other than alignment gaps, what complexities can you think of in trying to create a reasonable evolutionary model for phylogenetic analysis of entire genome sequences?

3) Standard microbiological taxonomy relies heavily of antiquated ways to distinguish or classify organisms, such as genomic %G+C and DNA:DNA hybridization. Can you imagine this changing? What are the hurdles to such a change?

4) Why do you think RFLP methods are more likely to be used to identify individuals when used for plants & animals, but to identify strains when used for microbes?

5) Different API strips, with different array of tests, are used to identify different kinds of organisms. Why do you suppose this might be necessary? Do you think you could design a more complete method, with many more tests, to identify any kind of organism? Why or why not?

6) What do you see as the relative advantages and disadvantages of each type of motility describe in Chapter 12 of Principles of Microbial Diversity to be?

7) What do you think about the hypothesis that eukaryotic flagella might be derived from spirochetes? How would you test this hypothesis? What observations would confirm or refute this hypothesis in your mind?

8) If you were interested in obtaining some novel isolates of Deinococcus or Thermus, where would you look, and how would you set up the enrichment cultures?

9) How far do you think a bacterial intracellular parasite could minimize itself? In other words, what could it do without, and what could it not do without?

10) What is the different between a minimized, obligately intracellular bacterial parasite like Chlamydia, and a virus?

11) How would you go about determining whether the paryphoplasm was similar to the periplasm of Gram-negative bacteria?

12) Members of the Plantomycetes divide by budding, and Gemmata has a double-membrane-enclosed nucleoid. Draw a picture of how you think cell division works in this organism, given that even early buds have a “nucleus”. How is your scheme similar & different from the eukaryotic cell cycle?

13) What might be the advantages or disadvantages of labeling one primer versus the other in a t-RFLP experiment? What about labeling both primers? How would you do this experiment?

14) What might you do if the restriction enzymes you use do not identify the organisms differently? In other words, what if a set of bands could be one or more of several organisms?

15) How might you deal with the fact that many of the identifications in a t-RFLP experiment are likely to be from uncultivated organisms?

16) What limitations of molecular phylogenetic analysis does DGGE or t-RFLP not improve upon?

Homework Problem Set #8 (10 pts)

1) rRNA sequence divergence is a measure of phylogenetic relatedness (i.e., biological diversity). How is this related to what people usually think of as biological diversity?

2) Other than alignment gaps, what complexities can you think of in trying to create a reasonable evolutionary model for phylogenetic analysis of entire genome sequences?

3) Standard microbiological taxonomy relies heavily of antiquated ways to distinguish or classify organisms, such as genomic %G+C and DNA:DNA hybridization. Can you imagine this changing? What are the hurdles to such a change?

4) Why do you think RFLP methods are more likely to be used to identify individuals when used for plants & animals, but to identify strains when used for microbes?

5) Different API strips, with different array of tests, are used to identify different kinds of organisms. Why do you suppose this might be necessary? Do you think you could design a more complete method, with many more tests, to identify any kind of organism? Why or why not?

6) What do you see as the relative advantages and disadvantages of each type of motility describe in Chapter 12 of Principles of Microbial Diversity to be?

7) What do you think about the hypothesis that eukaryotic flagella might be derived from spirochetes? How would you test this hypothesis? What observations would confirm or refute this hypothesis in your mind?

8) If you were interested in obtaining some novel isolates of Deinococcus or Thermus, where would you look, and how would you set up the enrichment cultures?

9) How far do you think a bacterial intracellular parasite could minimize itself? In other words, what could it do without, and what could it not do without?

10) What is the different between a minimized, obligately intracellular bacterial parasite like Chlamydia, and a virus?

11) How would you go about determining whether the paryphoplasm was similar to the periplasm of Gram-negative bacteria?

12) Members of the Plantomycetes divide by budding, and Gemmata has a double-membrane-enclosed nucleoid. Draw a picture of how you think cell division works in this organism, given that even early buds have a “nucleus”. How is your scheme similar & different from the eukaryotic cell cycle?

13) What might be the advantages or disadvantages of labeling one primer versus the other in a t-RFLP experiment? What about labeling both primers? How would you do this experiment?

14) What might you do if the restriction enzymes you use do not identify the organisms differently? In other words, what if a set of bands could be one or more of several organisms?

15) How might you deal with the fact that many of the identifications in a t-RFLP experiment are likely to be from uncultivated organisms?

16) What limitations of molecular phylogenetic analysis does DGGE or t-RFLP not improve upon?