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Genomics

Genomics. MUPGRET Weekend Workshop. Timeline Answers. http://www.jgi.doe.gov/education/timeline_2.html Another timeline at http://www.dnai.org/index.htm . Reviewing the basics. Cells are the basic working unit of an organism.

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Genomics

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  1. Genomics MUPGRET Weekend Workshop

  2. Timeline Answers • http://www.jgi.doe.gov/education/timeline_2.html • Another timeline at http://www.dnai.org/index.htm .

  3. 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.

  4. More reviewing • Chromosomes are visible with high powered microscopes.

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

  6. 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.

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

  8. Human karyotype

  9. 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

  10. 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

  11. A NOVA look into DNA. • http://www.pbs.org/wgbh/nova/photo51/jour-nf.html

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

  13. Electrophoresis • A way to separate DNA molecules. • http://gslc.genetics.utah.edu/units/biotech/gel/

  14. 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.

  15. 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

  16. 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

  17. 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.

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

  19. 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

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

  21. How Many Chromosomes Are There? • 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

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

  23. Ploidy vs. chromosome number

  24. 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.

  25. 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.

  26. The human genome project • http://www.genome.gov/Pages/EducationKit/download.html • Exploring our molecular selves video. • Ethical legal and social implications video.

  27. 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.

  28. 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.

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

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

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

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

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

  34. 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).

  35. Tools for genomics • Sequencing video from human genome project. • Downloadable from http://www.genome.gov/Pages/Hyperion/educationkit/download.html

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