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  1. 1. Classification Taxon TIger Lion Gray Wolf Domestic Cat Mountain Lion Kingdom Animalia Animalia Animalia Animalia Animalia Phylum Chordata Chordata Chordata Chordata Chordata Class Mammalia Mammalia Mammalia Mammalia Mammalia Order Carnivora Carnivora Carnivora Carnivora Carnivora Family Felidae X Canidae Felidae Felidae Genus Panthera Panthera Canis Felis Puma Species Panthera tigris Panthera leo Canis lupus Felis catus Puma Concolor
  2. 2. <ul><li>What is the scientific name of a gray wolf? </li></ul><ul><li>Which taxon includes the broadest characteristics? </li></ul><ul><li>Which taxon includes the most specific characteristics? </li></ul><ul><li>Which taxa do they all have in common? </li></ul><ul><li>Which taxon can interbreed and produce fertile offspring? </li></ul><ul><li>In the lion column, what name would you put instead of the X? </li></ul><ul><li>Which organisms in the chart is most closely related to Panthera Onca ? </li></ul><ul><li>The red fox classification is Animalia, Chordata, mammalia, Carnivora, Canidae, Vulpus, Vulpus vulpus. Is more related to a dog or big cat? </li></ul>
  3. 3. Chapter 26 Biotechnology and Genomics
  4. 4. 1. DNA Cloning <ul><li>First of all, what is the difference between gene cloning and cloning? </li></ul><ul><li>Cloning </li></ul><ul><ul><li>Production of identical copies of an organism through asexual means </li></ul></ul><ul><li>Gene cloning </li></ul><ul><ul><li>Production of many identical copies of a single gene </li></ul></ul>
  5. 5. A. Uses of gene cloning <ul><ul><li>Might want to produce large quantities of the gene ’s protein product </li></ul></ul><ul><ul><li>Learn how a cloned gene codes for a particular protein </li></ul></ul><ul><ul><li>Use the genes to alter the phenotypes of other organisms in a beneficial way </li></ul></ul><ul><ul><ul><li>Produces transgenic organism </li></ul></ul></ul><ul><ul><ul><li>Gene therapy - cloned genes are used to modify a human </li></ul></ul></ul>
  6. 6. Figure 12.2
  7. 7. Example: Making Humulin <ul><ul><li>In 1982, the world ’s first genetically engineered pharmaceutical product was produced. </li></ul></ul><ul><ul><ul><li>Humulin, human insulin, was produced by genetically modified bacteria. </li></ul></ul></ul>
  8. 8. B. Polymerase chain reaction (PCR) <ul><ul><li>Create billions of copies of a segment of DNA in a test tube in a matter of hours </li></ul></ul><ul><ul><li>Amplifies targeted DNA sequence </li></ul></ul><ul><ul><li>Needs: </li></ul></ul><ul><ul><ul><li>Your DNA sample </li></ul></ul></ul><ul><ul><ul><li>DNA polymerase (the enzyme involved in DNA replication) </li></ul></ul></ul><ul><ul><ul><li>a supply of DNA nucleotides </li></ul></ul></ul>
  9. 9. Figure 12.14 So a lot of DNA can be made from a tiny bit of DNA sample , such as a tiny blood sample taken from a crime scene
  10. 10. 2. DNA analysis <ul><li>DNA fingerprint </li></ul><ul><ul><li>The DNA is cut into fragments </li></ul></ul><ul><ul><ul><li>Specific enzymes called restriction enzymes recognizes specific small DNA sequences and cut the DNA. </li></ul></ul></ul><ul><ul><li>Fragments separated by gel electrophoresis </li></ul></ul><ul><ul><ul><li>Smaller fragments move faster than larger fragments </li></ul></ul></ul><ul><ul><li>Results in distinctive pattern of bands </li></ul></ul>
  11. 12. How does gel electrophoresis work? DNA has negative charges, so it will migrate towards the positive charge Long fragments (move slower) Shorter fragments (Move Faster) - +
  12. 13. Use of DNA fingerprinting Murder, Paternity, and Ancient DNA <ul><li>DNA fingerprinting </li></ul><ul><ul><li>Has become a standard criminology tool . </li></ul></ul><ul><ul><li>Has been used to identify victims of the September 11, 2001, World Trade Center attack. </li></ul></ul><ul><ul><li>Can be used in paternity cases . </li></ul></ul><ul><ul><li>To study ancient pieces of DNA , such as that of Cheddar Man. </li></ul></ul><ul><ul><li>And the list goes on… </li></ul></ul>
  13. 14. Figure 12.12
  14. 15. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Mother Child Male 1 Male 2 few many DNA Band patterns
  15. 16. Figure 12.13 Cheddar Man <ul><li>Oldest complete skeleton found in Britain. </li></ul><ul><li>9 000 year old </li></ul><ul><li>Compared his DNA with a number of living resident from Cheddar village and found some matching, suggesting that they share a common ancestor with the Cheddar man. </li></ul>
  16. 17. 3. Biotechnology Products <ul><li>Transgenic organisms are called GMOs </li></ul><ul><ul><li>G enetically M odified O rganisms </li></ul></ul><ul><ul><li>Products they produce are biotechnology products </li></ul></ul><ul><li>Transgenic bacteria </li></ul><ul><ul><li>Grown in bioreactors </li></ul></ul><ul><ul><li>Bacteria express cloned gene </li></ul></ul><ul><ul><li>Gene product collected from the media </li></ul></ul><ul><ul><li>Products include insulin, human growth hormone, tPA, and hepatitis B vaccine </li></ul></ul>
  17. 18. <ul><ul><li>Can be selected for their ability to degrade a particular substance </li></ul></ul><ul><ul><li>Ability can be enhanced by bioengineering </li></ul></ul><ul><ul><li>Eat oil, remove sulfur from coal </li></ul></ul>A. Transgenic bacteria
  18. 19. B. Transgenic plants <ul><ul><li>Foreign genes introduced into: </li></ul></ul><ul><ul><ul><ul><li>Immature plant embryos </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Protoplasts – plant cells with cell wall removed </li></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>Go on to develop into mature plants </li></ul></ul></ul></ul></ul>
  19. 20. <ul><ul><li>Pomato: </li></ul></ul><ul><ul><li>Not obtained from transfer of gene but from </li></ul></ul><ul><ul><li>the fusion of 2 cells (one from a tomato plant </li></ul></ul><ul><ul><li>and one from a potato plant.) </li></ul></ul><ul><ul><li>Pest resistance in cotton, corn, and potato strains </li></ul></ul><ul><ul><li>Introduced a gene for insect </li></ul></ul><ul><ul><li>resistance from a bacteria into </li></ul></ul><ul><ul><li>a plant </li></ul></ul><ul><ul><li>Soybeans resistant to herbicide </li></ul></ul><ul><ul><li>Can also be engineered to produce human proteins </li></ul></ul>EXAMPLES GM PLANTS
  20. 21. C. Transgenic animals <ul><ul><li>Insert genes into eggs </li></ul></ul><ul><ul><li>Example: </li></ul></ul><ul><ul><li>Insert gene for bovine growth hormone (bGH) to produce larger fishes, cows, pigs, rabbits, and sheep </li></ul></ul><ul><ul><li>Gene pharming </li></ul></ul><ul><ul><ul><li>Use of transgenic farm animals to produce pharmaceuticals </li></ul></ul></ul><ul><ul><ul><li>Proteins harvested from animals milk </li></ul></ul></ul>
  21. 22. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. milk human gene for growth hormone human growth hormone microinjection of human gene donor of egg development within a host goat Transgenic goat produces human growth hormone.
  22. 24. 3. Gene Therapy <ul><li>Testing DNA for genetic disorders </li></ul><ul><ul><li>What is a Genetic markers? </li></ul></ul><ul><ul><ul><li>Disease caused by an abnormality in the sequence of their bases at a particular location on a chromosome </li></ul></ul></ul><ul><ul><ul><li>Abnormality in sequence is called a genetic marker </li></ul></ul></ul>
  23. 25. A. Testing DNA for genetic disorders DNA microarray or “gene chip <ul><li>Spot hundreds to thousands of known disease-associated mutant gene alleles onto chip </li></ul><ul><ul><li>Genomic DNA from person labeled with fluorescent dye added to chip </li></ul></ul><ul><ul><li>Any spots that fluoresce correspond to mutant alleles in the person </li></ul></ul><ul><ul><li>Genetic profiling </li></ul></ul>
  24. 26. What is a microarray?
  25. 27. B. Preventing or curing disease through Gene Therapy What is Gene Therapy? <ul><ul><li>It involves the Insertion of genetic material into human cells to fight or prevent diseases. </li></ul></ul><ul><ul><li>The mutant version of a gene is replaced or supplemented with a properly functioning one </li></ul></ul><ul><ul><li>Viruses genetically modified to be safe can be used to ferry a normal gene into the body. </li></ul></ul><ul><ul><li>2 ways of administrating virus: </li></ul></ul><ul><ul><ul><li>Ex vivo (cells taken out of the body and injected with virus than put back into body) </li></ul></ul></ul><ul><ul><ul><li>In vivo ( directly injected into body) </li></ul></ul></ul>
  26. 28. defectivegene 1. Remove bone marrow stem cells. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. EX VIVO GENE THERAPY
  27. 29. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. retrovirus viral recombinant RNA normal gene defectivegene 2. Use retroviruses to bring the normal gene into the bone marrow stem cells. 1. Remove bone marrow stem cells. EX VIVO GENE THERAPY
  28. 30. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. retrovirus viral recombinant RNA normal gene viral recombinant RNA normal gene defectivegene viral recombinant DNA reverse transcription 2. Use retroviruses to bring the normal gene into the bone marrow stem cells. 3. Viral recombinant DNA carries normal gene into genome. 4. Return genetically engineered cells to patient. 1. Remove bone marrow stem cells. EX VIVO GENE THERAPY
  29. 31. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Brain (gene transfer by injection)* • Huntington disease – Parkinson disease • Alzheimer disease – Brain tumors Skin (gene transfer by modified blood cells)** - skin cancer Lungs (gene transfer by aerosol spray)* • cystic fibrosis - hereditary emphysema Liver (gene transfer by modified implants)** • familial hypercholesterolemia Blood (gene transfer by bone marrow transplant)* • sickle-cell disease Endothelium (blood vessel lining) (gene transfer by implantation of modified implants)** • hemophilia - diabetes mellitus Muscle (gene transfer by injection)* • Duchenne muscular dystrophy <ul><li>Bone marrow (gene transfer by implantation of modified stem cells)** </li></ul><ul><li>SCID (Severe Combined ImmunoDeficiciency) </li></ul><ul><li>sickle-cell disease </li></ul>* invivo ** ex vivo
  30. 32. Example: GENE THERAPY AND CANCER <ul><li>Different approaches to treat cancer through gene therapy: </li></ul><ul><li>Replace missing or altered gene that can cause cancer </li></ul><ul><li>Improve patient’s immune response to cancer (enhance the natural ability of body to fight cancer cells) </li></ul><ul><li>Insert genes into cancer cells to make them more susceptible to chemotherapy/radiotherapy… or make normal cells more resistants </li></ul>
  31. 33. 4 Genomics and Bioinformatics <ul><li>Genomics: Study of the complete genetic sequences of humans and other organisms </li></ul>
  32. 34. <ul><li>Sequencing the human genome </li></ul><ul><ul><li>Accomplished by 13-year effort of the Human Genome Project (HGP) </li></ul></ul><ul><ul><li>Humans have 20,000  25,000 genes </li></ul></ul><ul><ul><li>Most of the genes are expected to code for proteins </li></ul></ul><ul><ul><li>Found large area of Noncoding DNA , first called “junk DNA”, may have important functions </li></ul></ul><ul><ul><li>New genomes being sequenced all the time and at a much faster rate now </li></ul></ul>
  33. 35. Comparative genomics <ul><ul><li>Compare genomes of organisms </li></ul></ul><ul><ul><ul><li>Identify similarities between the sequence of human bases and those of other organisms </li></ul></ul></ul><ul><ul><li>Offers a way to study changes in the genome through time </li></ul></ul><ul><ul><ul><ul><li>Track evolution of HIV </li></ul></ul></ul></ul><ul><ul><li>Understand the evolutionary relationships among organisms </li></ul></ul><ul><ul><ul><ul><li>Human and chimpanzee 98% alike </li></ul></ul></ul></ul><ul><ul><ul><ul><li>Human and mouse 85% alike </li></ul></ul></ul></ul>
  34. 36. Comparative genomics Genome size does not correlate with evolutionary status, nor is the number of genes proportionate with genome size. Organism Homo sapiens (human) Mus musculus (mouse) Drosophila melanogaster (fruit fly) Arabidopsis thalania (flowering plant) C. Elegans (round worm) S. Cerevisia (yeast) Number of bases 3,000 millions 2,500 millions 180 millions 125 millions 97 millions 12 millions Number of genes 20,500 30,000 13,600 25,500 19,100 6,300 Number of chromosomes 46 40 8 10 12 32
  35. 37. <ul><ul><li>Structural genomics </li></ul></ul><ul><ul><ul><li>knowing the sequence of the bases and how many genes we have </li></ul></ul></ul><ul><ul><li>Functional genomics </li></ul></ul><ul><ul><ul><li>what does it code for (proteins) </li></ul></ul></ul>
  36. 38. <ul><ul><li>Understand the function of the various genes discovered within each genomic sequence and how these genes interact </li></ul></ul><ul><ul><li>Help deduce the function of human genes by comparison to other genomes </li></ul></ul><ul><ul><li>Use of a microarray can tell what genes are turned on in a specific cell or tissue type in a particular organism at a particular point in time and under certain environmental circumstances </li></ul></ul>Functional genomics