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Problem 1
You have discovered a new species of archaea from a hot spring in Yellowstone National Park. After growing a pure culture of this organism, what strategy might you employ to sequence its genome?Problem 1
You have discovered a new species of archaea from a hot spring in Yellowstone National Park. How would your strategy change if you were unable to grow the strain in culture?Problem 2
Repetitive DNA poses problems for genome sequencing. Why is this so?Problem 2
Repetitive DNA poses problems for genome sequencing. What types of repetitive DNA are most problematic?Problem 2
Repetitive DNA poses problems for genome sequencing. What strategies can be employed to overcome these problems?Problem 3
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs.
How can sequence gaps be closed?Problem 3
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. Why were there so many more contigs than scaffolds?Problem 3
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. What is the difference between physical and sequence gaps?Problem 3
When the whole-genome shotgun sequence of the Drosophila genome was assembled, it comprised 134 scaffolds made up of 1636 contigs. How can physical gaps be closed?Problem 3
Discuss the similarities and differences between forward and reverse genetic approaches, and when you would choose to utilize each of the approaches.Problem 4
Using the data Table B, calculate the average number of kilobase (kb) pairs per centimorgan in the six multicellular eukaryotic organisms. How would this information influence strategies to clone genes known only by a mutant phenotype in these organisms?
Problem 4
How do cDNA sequences facilitate gene annotation? Describe how the use of full-length cDNAs facilitates discovery of alternative splicing.
Problem 5
How do comparisons between genomes of related species help refine gene annotation?
Problem 5
What are the advantages and disadvantages of using insertion alleles versus alleles generated by chemicals (as in TILLING) in reverse genetic studies?Problem 6
You have cloned the mouse ortholog (see Genetic Analysis 14.2 for definition) of the gene associated with human Huntington disease (HD) and wish to examine its expression in mice. Outline the approaches you might take to examine the temporal and spatial expression pattern at the cellular level.Problem 7
Diagram the mechanism by which CRISPR–Cas functions in the immune system of bacteria and archaea.
Problem 7
You have sequenced a 100-kb region of the Bacillus anthracis genome (the bacterium that causes anthrax) and a 100-kb region from the Gorilla gorilla genome. What differences and similarities might you expect to see in the annotation of the sequences—for example, in number of genes, gene structure, regulatory sequences, repetitive DNA?
Problem 7
Diseases and conditions on the RUSP list are tested on every newborn infant, and if the baby has one of the conditions, the parents are immediately informed. What kind of information and counseling should be provided to the parents along with the diagnosis?Problem 8
Describe how CRISPR–Cas has been modified to create a genome-editing tool.
Problem 8
You have just obtained 100 kb of genomic sequence from an as-yet-unsequenced mammalian genome. What are three methods you might use to identify potential genes in the 100 kb? What are the advantages and limitations of each method?
Problem 9
Discuss the advantages (and possible disadvantages) of the different approaches to reverse genetics.Problem 11
When comparing genes from two sequenced genomes, how does one determine whether two genes are orthologous? What pitfalls arise when one or both of the genomes are not sequenced?
Problem 11
You have identified a gene encoding the protein involved in the rate-limiting step in vitamin E biosynthesis. How would you create a transgenic plant producing large quantities of vitamin E in its seeds?Problem 12
What is a reference genome? How can it be used to survey genetic variation within a species?
Problem 12
You have identified a recessive mutation that alters bristle patterning in Drosophila and have used recombinant DNA technology to identify a genomic clone that you believe harbors the gene. How would you demonstrate that your gene is on the genomic clone?Problem 13
Imagine yourself in the same position as Kristen Powers, faced with the decision of whether or not to undergo a genetic test that will discover if you have inherited Huntington disease. List five life decisions or choices that you think are likely to be affected by the results of the genetic test. Do you think you would make the same choice to test that Kristen made? Why or why not?Problem 14
Select one of the hereditary conditions from either the RUSP core conditions list or the RUSP list of secondary conditions and do some online research to find the following information:
The defect that characterizes the conditionProblem 14
Select one of the hereditary conditions from either the RUSP core conditions list or the RUSP list of secondary conditions and do some online research to find the following information:
The symptoms and consequences of the condition if it is not treatedProblem 14
Select one of the hereditary conditions from either the RUSP core conditions list or the RUSP list of secondary conditions and do some online research to find the following information:
The recommended treatment for those with the conditionProblem 14
Select one of the hereditary conditions from either the RUSP core conditions list or the RUSP list of secondary conditions and do some online research to find the following information:
The duration of treatment
