2. Genomics MUPGRET Weekend Workshop

3. Timeline Answers http://www.jgi.doe.gov/education/timeli ne_2.html http://www.jgi.doe.gov/education/timeli ne_2.html Another timeline at http://www.dnai.org/index.htm. http://www.dnai.org/index.htm

4. Reviewing the basics Cells are the basic working unit of an organism. DNA (deoxyribonucleic acid) contains all of the instruction needed to direct the activities in the cell. DNA is arranged into chromosomes.

5. More reviewing Chromosomes are visible with high powered microscopes.

6. Human Chromosomes Metaphase Chromosome Chromosomes are Dynamic Structures Fruit Fly CONDENSED EXTENDED

7. More review Chromosomes contain hundreds of genes encoded within their DNA. Genes compromise a very small percentage of the DNA that makes up the chromosome, <5% generally. DNA containing genes is called euchromatin.

8. Heterochromatin Non-genic DNA is called heterochromatin. Heterochromatin and euchromatin stain differently. This difference causes the bands we see in a karyotype.

9. Human karyotype

10. Genome composition Euchromatin (genes) usually contains a higher proportion of GC. Euchromatin has more unique DNA sequences. Heterochromatin (non-coding) usually contains a higher proportion of AT. Heterochromatin contains more repetitive sequence.s

11. DNA Content The amount of heterochromatin varies dramatically between organisms. Much of the difference in DNA content among closely related organisms is often due to changes in heterochromatin amount. Maize 2500 Mb Wheat 16,000 Mb Rice 430 Mb Mb=Mega base pairs

12. A NOVA look into DNA. http://www.pbs.org/wgbh/nova/photo5 1/jour-nf.html http://www.pbs.org/wgbh/nova/photo5 1/jour-nf.html

13. PCR Polymerase Chain Reaction A way to “xerox” a DNA fragment.

14. Electrophoresis A way to separate DNA molecules. http://gslc.genetics.utah.edu/units/biot ech/gel/ http://gslc.genetics.utah.edu/units/biot ech/gel/

15. What is genomics? The study of the entire DNA complement of an individual. The term genome refers to all of the DNA contained in one copy of the chromosomes of an organism. It contains both coding (genes) and non-coding DNA sequences.

16. The Genome Nearly every cell in an organims contains a full copy of the genome. Most mammal cells contain two complete copies of the genome. Skin Lung Heart

17. The Genome II Gametic cells like sperm, ovules, or pollen contain one copy of the genome. Some special cell types contain more than two copies of the genome. Human bone marrow Regenerating liver cells

18. Plant Genome Corn plants contain two copies of the genome in their cells except for pollen, ovules, and endosperm (the fleshy part of the corn kernel). Pollen and ovules have one copy of the genome. Endosperm has three copies.

19. Plant Genome Other plants like corn include: Arabidopsis Barley Beans Tomato Pepper Rice

20. Multicopy Plant Genomes Some plants normally have more than two copies of the genome in their cells. Wheat – six copies Potato – four copies Sugarcane – >twelve copies Strawberry – >eight copies Banana – three copies Watermelon – three copies

21. Chromosome number The term haploid refers to the base number of chromosomes in an organism. Diploid cells have two copies of all the chromosomes.

22. Bacteria usually have one circular chromosome and no nucleus Organisms with nuclei have variable numbers of chromosomes depending on the species: Mosquito 6 Chimpanzees 48 Goldfish 94 How Many Chromosomes Are There?

23. Some plants have few chromosomes like Arabidopsis. Others, like sugarcane, have many. How Many Chromosomes Are There? Wheat Rice Arabidopsis Sugarcane Maize Potato Tomato Cabbage Carrot 10 20 +100 48 24 42 20 18

24. Ploidy vs. chromosome number OrganismPloidyChromosome number CornDiploid (2X)20 TomatoDiploid (2X)24 ArabidopsisDiploid (2X)10 PotatoTetraploid (4X)48 WheatHexaploid (6X)42

25. How many genes? The number of genes varies between organisms. Humans – 30,000 to 40,000 Maize – 55,000 Most genes between closely related species are conserved. Many genes between less closely related species are conserved.

26. The human genome project Complete DNA sequence Understand the sequence variation between individuals. Understand the function of genes. Compare the sequences to other related organisms. Study the ethical, legal and social implications.

27. The human genome project http://www.genome.gov/Pages/Educati onKit/download.html http://www.genome.gov/Pages/Educati onKit/download.html Exploring our molecular selves video. Ethical legal and social implications video.

28. Insight from the human genome draft sequence Protein coding region <2%. Repetitive DNA minimum of 50%. Genes are randomly distributed. 3X as many proteins as Drosophila or C. elegans because of post-transcriptional modifications.

29. Insight from the human genome draft sequence II Humans, C. elegans, Drosophila, and plants have most of the same proteins. There are 2X as many germline mutations in males vs. females. DNA sequence between two individuals is almost identical. Only 0.1% of sequence is different.

30. Where do we go from here? Gene Expression Proteomics Structural genomics Mutagenesis Comparative genomics

31. Medicine and the New Genomics Gene Testing Gene Therapy Pharmacogenomics Human Genome Program, U.S. Department of Energy, Genomics and Its Impact on Medicine and Society: A 2001 Primer, 2001 improved diagnosis of disease earlier detection of genetic predispositions to disease rational drug design gene therapy and control systems for drugs personalized, custom drugs Anticipated Benefits

32. Ethical Considerations Privacy/confidentiality Reproductive issues Accuracy of genetic testing Access to technology Genetically modified foods and microbes Commercialization/Patents

33. Benefits of Genomics Improved diagnostic tools. Rational drug design. Rapid identification of pathogens. Better understanding of mutagenesis. DNA forensics Improved agricultural products

34. Plant Genome Projects Initiative began in 1998. Arabidopsis was the first model plant. Small genome size. Little repetitive DNA. Short life cycle.

35. Arabidopsis 2010 Project Complete sequence of Arabidopsis in 2000. 2010 Project started in 2001. Goal was to determine the function of the 25,000 genes in Arabidopsis by the year 2010 (ie. functional genomics of Arabidopsis).

36. Tools for genomics Sequencing video from human genome project. Downloadable from http://www.genome.gov/Pages/Hyperio n/educationkit/download.html http://www.genome.gov/Pages/Hyperio n/educationkit/download.html