Genomics Genetic Engineering To mass-produce proteins To give species new characteristics

1. Genomics • Genetic Engineering • To mass-produce proteins • To give species new characteristics • Gene Therapy - Create a viral vector with a functional human allele – adenosine deaminase - Infect target tissue - Probably need to repeat unless you can transform stem cells

2. -first trial of gene therapy – Ashanti DeSilva. • 40 treated since then with 100% efficacy.

3. OTC - ornithine transcarbamylase deficiency syndrome. An X-linked disorder resulting in the inability to bind and convert ammonia to urea. Total loss of this protein is usually fatal shortly after birth. Jesse Gelsinger – died in 1999 at age 18, as a consequence of a gene therapy trial involving an adenovirus vector. He has an immunological reaction to the virus and died.

4. OTC - ornithine transcarbamylase deficiency syndrome. “First, although Gelsinger and his family were under the impression that the pre-clinical animal studies had affirmed the trial's safety, two monkeys had actually died. This information appeared on the consent form submitted to the National Institutes of Health review board, but did not appear on the form signed by Jesse. Moreover, the Penn researchers did not disclose to either the Gelsingers or federal regulators that human volunteers in the same study had suffered adverse reactions - side effects serious enough to have halted the trials had they been reported. Not reporting adverse events in gene therapy clinical trials is clearly wrong, but it seems to have been par for the course in the 1990s: evidence collected shortly after Gelsinger's death showed that fewer than six percent of adverse events associated with gene therapy were properly reported at this time. Lastly, the lead researcher in the Penn study - James Wilson - did not disclose to the Gelsingers that he was conducting the clinical trial with a private company in which he had a stake. Wilson had a direct financial interest - not merely an academic one - in the trial's successful outcome.” From Center for Genetics and Society - http://www.geneticsandsociety.org/article.php?id=4955

5. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Should the consumer know? • If content is < 5%, should it be labeled GMO-free? Required in Europe and Asia… why not in U.S., which produces 65% of GM food worldwide?

6. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - 2008 – Genetic Information Nondiscrimination Act • “prohibits the improper use of genetic information in health insurance and employment” ?

7. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - 2008 – Genetic Information Nondiscrimination Act • “prohibits the improper use of genetic information in health insurance and employment” Lily Ledbetter XX XY ?

8. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - 2008 – Genetic Information Nondiscrimination Act “GINA does not cover an individual's manifested disease or condition--a condition from which an individual is experiencing symptoms, being treated for, or that has been diagnosed.” Lily Ledbetter Sex discrimination in the workplace was not prohibited under GINA… so “Lily” was needed as a separate “equal pay for equal work” act. XX XY ?

9. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - GINA • - Genetic screening and embryo selection. • “Preimplantation Genetic Diagnosis” – used in in vitro fertilization, screening early embryos for genetic abnormalities… or other traits? Suppose a child needs a bone marrow transplant… should parents be allowed to select among embryos to make a sibling capable of transfer?

10. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - GINA • - PGD • - Germline engineering

11. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - GINA • - PGD • - Germline engineering • - Enhancement Gene Therapy • Why not insert “better” genes? For Youth? Strength? Health?

12. Genomics • Genetic Engineering • Bioethics • GMO’s – Genetically Modified Organisms • Genetic Testing • - GINA • - PGD • - Germline engineering • - Enhancement Gene Therapy

13. XIII. Developmental Genetics

14. XIII. Developmental Genetics • Overview: • - Multicellular organisms have different cell types, but all cells are descended from a single zygote and have the same DNA.

15. XIII. Developmental Genetics • Overview: • - Multicellular organisms have different cell types, but all cells are descended from a single zygote and have the same DNA. • - So, cell specialization is really a very special type of gene regulation; the regulation of genes that influence the developmental fate of a cell.

16. XIII. Developmental Genetics • Overview: • - Multicellular organisms have different cell types, but all cells are descended from a single zygote and have the same DNA. • - So, cell specialization is really a very special type of gene regulation; the regulation of genes that influence the developmental fate of a cell. • - This requires two more levels of genetic regulation: • - regulation of cell specialization/differentiation • - co-ordination of this specialization with other cells/tissues

17. XIII. Developmental Genetics • Overview: • - Multicellular organisms have different cell types, but all cells are descended from a single zygote and have the same DNA. • - So, cell specialization is really a very special type of gene regulation; the regulation of genes that influence the developmental fate of a cell. • - This requires two more levels of genetic regulation: • - regulation of cell specialization/differentiation • - co-ordination of this specialization with other cells/tissues • - One of the most remarkable revelations in this area of genetics is that all animals (from flies to worms to mammals, and even radially symmetrical coral) share the same genes that co-ordinate the basic body plan and its polarity (anterior-posterior axes and body regions)…. But of course, why not?

18. XIII. Developmental Genetics • Overview: • B. Genetic Control of Body Plan: • - Drosophila has been the model organism for body plan development, and resulted in Nobel Prizes in 1995…. (so flies are STILL giving up secrets).

19. XIII. Developmental Genetics • Overview: • B. Genetic Control of Body Plan: • - Drosophila has been the model organism for body plan development, and resulted in Nobel Prizes in 1995…. (so flies are STILL giving up secrets). • - 1. There are two genomes involved: • the maternal genome produces maternal proteins that form a gradient in the egg and influence the initial development of the embryo.

20. XIII. Developmental Genetics • Overview: • B. Genetic Control of Body Plan: • - Drosophila has been the model organism for body plan development, and resulted in Nobel Prizes in 1995…. (so flies are STILL giving up secrets). • - 1. There are two genomes involved: • the maternal genome produces maternal proteins that form a gradient in the egg and influence the initial development of the embryo. • The zygote’s genome produces proteins that react to these gradient in two ways:

21. XIII. Developmental Genetics • Overview: • B. Genetic Control of Body Plan: • - Drosophila has been the model organism for body plan development, and resulted in Nobel Prizes in 1995…. (so flies are STILL giving up secrets). • - 1. There are two genomes involved: • the maternal genome produces maternal proteins that form a gradient in the egg and influence the initial development of the embryo. • The zygote’s genome produces proteins that react to these gradient in two ways: • - segmentation genes (gap, pair-rule, segment polarity genes) create segments in the embryo by defining body regions (gap), then dividing the embryo into units two segments wide (pair-rule), and then an active segment polarity gene splits each segment into front and backs.

22. XIII. Developmental Genetics • Overview: • B. Genetic Control of Body Plan: • - Drosophila has been the model organism for body plan development, and resulted in Nobel Prizes in 1995…. (so flies are STILL giving up secrets). • - 1. There are two genomes involved: • the maternal genome produces maternal proteins that form a gradient in the egg and influence the initial development of the embryo. • The zygote’s genome produces proteins that react to these gradient in two ways: • - segmentation genes (gap, pair-rule, segment polarity genes) create segments in the embryo by defining body regions (gap), then dividing the embryo into units two segments wide (pair-rule), and then an active segment polarity gene splits each segment into front and backs. • - hox genes (shortened from homeoboxgenes) determine the developmental fate of cells in a particular segment.

25. XIII. Developmental Genetics • Overview: • B. Genetic Control of Body Plan: • - Drosophila has been the model organism for body plan development, and resulted in Nobel Prizes in 1995…. (so flies are STILL giving up secrets). • - 1. There are two genomes involved: • - 2. There is strong homology among animals in these genes: • Runt is a pair-rule gene involved in segmentation. In flies, it later orchestrates the development of neurons and sex determination. In mammals, it is needed for bone deposition in segments.

26. B. Genetic Control of Body Plan: - 1. There are two genomes involved: - 2. There is strong homology among animals in these genes: Runt is a pair-rule gene involved in segmentation. In flies, it later orchestrates the development of neurons and sex determination. In mammals, it is needed for bone deposition in segments. The most dramatic examples of developmental effects are in the hox genes: On chromosome 3, in order… Antennapedia cluster (Ant-C) Bithorax cluster (Bx-C)

27. B. Genetic Control of Body Plan: - 1. There are two genomes involved: - 2. There is strong homology among animals in these genes: Runt is a pair-rule gene involved in segmentation. In flies, it later orchestrates the development of neurons and sex determination. In mammals, it is needed for bone deposition in segments. The most dramatic examples of developmental effects are in the hox genes: These genes are in all cells, but each is only active in it’s respective segment - switching on a host of specific genes that lead to cell, tissue, and organ differentiation. On chromosome 3, in order… Antennapedia cluster (Ant-C) Bithorax cluster (Bx-C)

28. B. Genetic Control of Body Plan: - 1. There are two genomes involved: - 2. There is strong homology among animals in these genes: Runt is a pair-rule gene involved in segmentation. In flies, it later orchestrates the development of neurons and sex determination. In mammals, it is needed for bone deposition in segments. The most dramatic examples of developmental effects are in the hox genes: Each gene codes for a transcription factor. Each gene has a 180 bp homeobox region that encodes a 60 AA homeodomain in the protein that takes a Helix-Loop Helix configuration….

29. B. Genetic Control of Body Plan: - 1. There are two genomes involved: - 2. There is strong homology among animals in these genes: Runt is a pair-rule gene involved in segmentation. In flies, it later orchestrates the development of neurons and sex determination. In mammals, it is needed for bone deposition in segments. The most dramatic examples of developmental effects are in the hox genes: • And if you turn them on in the wrong segment, you get an incorrect pattern of body segment development! • Normal fly head, with normal antennae. • Fly with legs for antennae, cause by activating a hox gene for leg development that is normally only on in thoracic segments. (antennaepedia)

30. B. Genetic Control of Body Plan: - 1. There are two genomes involved: - 2. There is strong homology among animals in these genes: Runt is a pair-rule gene involved in segmentation. In flies, it later orchestrates the development of neurons and sex determination. In mammals, it is needed for bone deposition in segments. The most dramatic examples of developmental effects are in the hox genes: • Eye development on thoracic segments…

31. And the most dramatic examples of homology are in the hox genes, as well.

32. And the most dramatic examples of homology are in the hox genes, as well. In fact, the homology is so good that lineages of eyeless flies lacking that hox gene can have the ability to grow eyes restored by adding the homologous gene from a mouse…and flies develop compound eyes with the mouse hox gene for eye development, even though mice have camera eyes… HOW COOL IS THAT!?

33. And the most dramatic examples of homology are in the hox genes, as well. And, human diseases have been identified as hox mutants by identifying homology with fruit fly hox genes, and they have been found in the genome with ss-DNA (probe) from the fly homeobox region of that gene. Cleinocranial dysplasia (CCD), caused by a dominant mutation in the runt homeotic gene

34. And the most dramatic examples of homology are in the hox genes, as well. And, human diseases have been identified as hox mutants by identifying homology with fruit fly hox genes, and they have been found in the genome with ss-DNA (probe) from the fly homeobox region of that gene. Synpolydactyly in humans, caused by a mutation in HOXD13

35. And the most dramatic examples of homology are in the hox genes, as well. And, human diseases have been identified as hox mutants by identifying homology with fruit fly hox genes, and they have been found in the genome with ss-DNA (probe) from the fly homeobox region of that gene. And, because of evolution and common ancestry, we can use model organisms like flies to learn about how heredity and development work in all animals…including humans.

36. XIII. Developmental Genetics • Overview: • - This requires two more levels of genetic regulation: • - regulation of cell specialization/differentiation • - co-ordination of this specialization with other cells/tissues • B. Genetic control of Body Plan:

37. XIII. Developmental Genetics • Overview: • - This requires two more levels of genetic regulation: • - regulation of cell specialization/differentiation • - co-ordination of this specialization with other cells/tissues • Genetic control of Body Plan: • Co-ordination of cell differentiation with other cells

38. Co-ordination of cell differentiation with other cells • Notch genes code for a transmembrane signal receptor protein that binds another transmembrane protein called Delta…. So this binding occurs between cells:

39. Co-ordination of cell differentiation with other cells • When notch is bound, its cytoplasmic tail is cleaved and binds to the Su(H) protein – which passes into the nucleus and binds to transcription cofactors, increasing the binding of the transcription factors and activation of specific genes. So, cells can communicate and stimulate genetic activity in each other.

40. Co-ordination of cell differentiation with other cells • How such signals coordinate gene expression has been determined for the vinegar worm, Caenorhabditiselegans.

41. Co-ordination of cell differentiation with other cells • How such signals coordinate gene expression has been determined for the vinegar worm, Caenorhabditiselegans. This is a great developmental model, because the animal has a set number of somatic cells (959) and the fate of each has been mapped:

42. Organogenesis of the vulva in C. elegans There are two cells; one will become the gonadal anchor cell, and the other will become the first uterine cell. What determines their fate?

43. Organogenesis of the vulva in C. elegans There are two cells; one will become the gonadal anchor cell, and the other will become the first uterine cell. What determines their fate? Initially, they both produce delta signal protein and notch receptor protein…

44. Organogenesis of the vulva in C. elegans There are two cells; one will become the gonadal anchor cell, and the other will become the first uterine cell. What determines their fate? Initially, they both produce delta signal protein and notch receptor protein (lin-12)…by chance, these cells won’t produce exactly the same amount of signal… the one bombarded by MORE signal produces more receptor... which causes the genetic cascade that results in the cell becoming the uterine cell.

45. Organogenesis of the vulva in C. elegans The anchor cell now interacts with 6 epidermal cells. The anchor cell produces another protein, lin-3. In the closest cells where exposure to this protein are greatest, receptors trigger a signal transduction pathway that turns on 1o vulva genes.

46. Organogenesis of the vulva in C. elegans The anchor cell now interacts with 6 epidermal cells. The anchor cell produces another protein, lin-3. In the closest cells where exposure to this protein are greatest, receptors trigger a signal transduction pathway that turns on 1o vulva genes. In the closest cell, a protein is produced that activates the lin-12 gene in the neighboring cells, which arrests 1ovulvar cell development – they become 2ovulvar cells.

47. Organogenesis in flowers

48. Organogenesis in flowers

49. Organogenesis in flowers

50. Organogenesis in flowers S = sepal, p = petal, st = stamens, c = carpels Wild = s,p,st,c APETALA2 = c,st,st,c PISTILLATA = s,s,c,c AGAMOUS = s,p,s,p