1. Engineering magnetosomes to express novel proteins Which ones? Tweaking p18 Linker Deleting or replacing GFP Something else? TRZN Oxalate decarboxylases or oxidases

2. Genome projects 1) Prepare map of genome

3. Genome projects 1)Prepare map of genome To find genes must know their location

4. Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library FISH to find their chromosome

5. Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library FISH to find their chromosome identify overlapping AC using ends as probes assemble contigs until chromosome is covered

6. Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs

7. Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into plasmids 6) sequence the plasmids

8. Sequencing Genomes 1) Map the genome 2) Prepare an AC library 3) Order the library 4) Subdivide each AC into lambda contigs 5) Subdivide each lambda into plasmids 6) sequence the plasmids 7) Nowadays sometimes “shotgun sequence”: Sequence libraries directly, then assemble genome by computer

9. Sequencing Genomes Nowadays sometimes “shotgun sequence”: Sequence libraries directly, then assemble genome by computer OK for non-redundant genomes No good for genomes with repeated sequences

10. Using the genome Studying expression of all genes simultaneously Microarrays (reverse Northerns) Attach probes that detect genes to solid support cDNA or oligonucleotides

11. Using the genome Studying expression of all genes simultaneously Microarrays (reverse Northerns) Attach probes that detect genes to solid support cDNA or oligonucleotides Tiling path = probes for entire genome

12. Microarrays (reverse Northerns) Attach probes that detect genes to solid support cDNA or oligonucleotides Tiling path = probes for entire genome Hybridize with labeled targets

13. Microarrays Attach cloned genes to solid support Hybridize with labeled targets Measure amount of target bound to each probe

14. Microarrays Measure amount of probe bound to each clone Use fluorescent dye : can quantitate light emitted

15. Microarrays Compare amounts of mRNA in different tissues or treatments by labeling each “target” with a different dye

16. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” Fix probes to slide at known locations, hyb with labeled targets, then analyze data

17. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” Ephraim L. Tsalik et al. Host gene expression classifiers diagnose acute respiratory illness etiology. Science Translational Medicine 20 Jan 2016:Vol. 8, Issue 322, pp. 322ra11 Used microarrays to compare gene expression from blood of healthy & patients with respiratory ailments Found gene expression signatures that corresponded to bacterial, viral, or non-infectious causes of disease with 87% accuracy

18. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” 2.High-throughput sequencing

19. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” 2.High-throughput sequencing “Re-sequencing” to detect variation

20. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” 2.High-throughput sequencing “Re-sequencing” to detect variation Sequencing all mRNA to quantitate gene expression

21. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” 2.High-throughput sequencing “Re-sequencing” to detect variation Sequencing all mRNA to quantitate gene expression Sequencing all mRNA to identify and quantitate splicing variants

22. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” 2.High-throughput sequencing “Re-sequencing” to detect variation Sequencing all mRNA to quantitate gene expression Sequencing all mRNA to identify and quantitate splicing variants Sequencing all RNA to identify and quantitate ncRNA

23. Using the genome Studying expression of all genes simultaneously 1.Microarrays: “reverse Northerns” 2.High-throughput sequencing 3. Bisulfite sequencing to detect C methylation

24. Using the genome Bisulfite sequencing to detect C methylation