13.A 22-kb piece of DNA has the following restriction sites:

A batch of this DNA is first fully digested by HpaI alone, then another batch is fully digested by HindIII alone, and, finally, a third batch is fully digested by both HpaI and HindIII together. The fragments resulting from each of the three digestions are placed in separate wells of an agarose gel, separated by gel electrophoresis, and stained by ethidium bromide. Draw the bands as they would appear on the gel.

*14.A linear piece of DNA that is 14 kb long is cut first by EcoRI alone, then by SmaI alone, and, finally, by both EcoRI and SmaI together. The following results are obtained:

Draw a map of the EcoRI and SmaI restriction sites on this 14-kb piece of DNA, indicating the relative positions of the restriction sites and the distances between them.

*15.A linear piece of DNA was broken into random, overlapping fragments and each fragment was sequenced. The sequence of each fragment is shown below.

On the basis of overlap in sequence, assemble the fragments into a contig.

16.In recent years, honeybee colonies throughout North America have been decimated by colony collapse disorder (CCD), which results in the rapid death of worker bees. First noticed by beekeepers in 2004, the disorder has been responsible for the loss of 50% to 90% of beekeeping operations in the United States. Evidence suggests that CCD is caused by a pathogen. Diana Cox-Foster and her colleagues (D. Cox-Foster et al. 2007. Science 318:283–287) used a metagenomic approach to try to identify the causative agent of CCD by isolating DNA from normal honeybee hives and from hives that had experienced CCD. A number of different bacteria, fungi, and viruses were identified in the metagenomic analysis. The following table gives the percentages of CCD hives and non-CCD hives that tested positive for four potential pathogens identified in the metagenomic analysis. On the basis of these data, which potential pathogen appears most likely to be responsible for CCD? Explain your reasoning. Do these data prove that this pathogen is the cause of CCD? Explain.

17.James Noonan and his colleagues (J. Noonan et al. 2005. Science 309:597–599) set out to study the genome sequence of an extinct species of cave bear. They extracted DNA from 40,000-year-old bones from a cave bear and used a metagenomic approach to isolate, identify, and sequence the cave-bear DNA. Why did they use a metagenomic approach when their objective was to sequence the genome of one species (the cave bear)?

*18.Microarrays can be used to determine relative levels of gene expression. In one type of microarray, hybridization of red (experimental) and green (control) cDNAs is proportional to the relative amounts of mRNA in the samples. Red indicates the overexpression of a gene and green indicates the underexpression of a gene in the experimental cells relative to the control cells, yellow indicates equal expression in experimental and control cells, and no color indicates no expression in either experimental or control cells.

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In one experiment, mRNA from a strain of antibiotic-resistant bacteria (experimental cells) is converted into cDNA and labeled with red fluorescent nucleotides; mRNA from a nonresistant strain of the same bacteria (control cells) is converted into cDNA and labeled with green fluorescent nucleotides. The cDNAs from the resistant and nonresistant cells are mixed and hybridized to a chip containing spots of DNA from genes 1 through 25. The results are shown in the adjoining illustration. What conclusions can you draw about which genes might be implicated in antibiotic resistance in these bacteria? How might this information be used to design new antibiotics that are less vulnerable to resistance?

19.Of the genes illustrated in the microarray shown in the lower part of Figure 15.7, are most overexpressed or underexpressed in tumors from patients that remained cancer free for at least five years? Explain your reasoning.

20.Dictyostelium discoideum is a soil-dwelling social amoeba: much of the time, the organism consists of single, solitary cells, but during times of starvation, amoebae come together to form aggregates that have many characteristics of multicellular organisms. Biologists have long debated whether D. discoideum is a unicellular or a multicellular organism. In 2005, its genome was completely sequenced. The table below lists some genomic characteristics of D. discoideum and other eukaryotes (L. Eichinger et al. 2005. Nature 435:43–57).

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*21.A group of 250 scientists sequenced and analyzed the genomes of 12 species of Drosophila (Drosophila 12 Genomes Consortium. 2007. Nature 450:203–218). Data on genome sizes and numbers of protein-encoding genes from this study are given in Table 15.4. Using the data in this table, plot the number of protein-encoding genes as a function of genome size for the 12 species of Drosophila. Is there a relation between genome size and number of genes in fruit flies? How does this result compare with the relation between genome size and number of genes across all eukaryotes?

*22.A scientist determines the complete genomes and proteomes of a liver cell and a muscle cell from the same person. Would you expect bigger differences in the genomes or in the proteomes of these two cell types? Explain your answer.