PHPY 403 - Final Exam Questions

29. Discuss in detail (and give the reasons for) the epigenetic reprogramming that occurs in both the germ line and the early embryo.

- At each stage of development there is a change in expression of genes as they require different functions. Same goes with the genome at each stage, but with different expressions. - Epigenetics reprogramming refers to the erasing and re-adding of modifications to the genome. - Marked and often tissue specific changes in overall methylation accompany gametogenesis and embryonic development. 1. Epigenetic reprogramming in the Germ Line: - The primordial germ line cells (PGC) have all their parental epigenetic marks removed, however, as gonadal differentiation and germ cell development takes place, de novo methylation and establishment of imprinting marks takes place. - In sperm cells, certain regions are differentially activated to allow for genes that are only involved in spermatogenesis to be active while the pluripotent and somatic function genes to be silent, sperm cells also need to compact their chromosomes as tightly as they can for transferring. This can also occur in oocytes. 2. Early Embryo Reprogramming: - After fertilization, there is a removal of all epigenetic marks where all the methylations are removed until the blastocyst is formed. Afterwards, there is a de novo methylation that occurs in all somatic cells which then persists until adulthood. Only the gametes reset their epigenetic marks. -The resetting of epigenetic marks means that chromosomes mostly lose their parental epigenetic identities and are re-established based on the sex of the individual producing variation.

39. Describe two skeletal muscle channelopathies, including the channel involved, the type of mutation in that channel, and the change in channel physiology that results in the genetic disorder.

1. Congenital Myogenic Syndrome: - Autosomal recessive mutation of CHRNE gene (affects epsilon su in nAChR in skeletal muscles) - Physiological symptoms are same as myogenia gravis (facial and proximal limb weakness) a) Most common cause: deletion causes a frameshift mutation b) Low levels of fetal gamma partially compensate for epsilon absence - results in presence of some functional nAChRs c) However - reduced amount of skeletal nAChR results in decreased ability to create large end-late potentials required for APs, tf results in weakness of the skeletal muscles in proximal limbs and eye lids 2. Central Core Disease: - Autosomal dominant mutation of the RYR1 Gene (affects Ryanodine Receptors making them leaky) - Symptoms: muscle atrophy and weakness - Formation of light coloured cores due to absence of mitochondria and oxidative enzymes - Mutation Causes: a) leaky Ryanodine Receptors: ↑ Ca2+ intracellular levels that cause mitochondrial damage that were trying to buffer Ca2+, and depletion of Ca2+ stores b) Also may be due to altered excitation contraction coupling (uncoupling) - another proposed mechanism where the mutation leads to a linkage of 2 proteins (uncoupling) which inhibits their function

31. Briefly describe each of the three main categories of gene therapy: somatic stem cell therapy, gene transfer therapy and RNA modification therapy.

1. Somatic Stem Cells: - replaces entire genome - organ transplantation for a monogenic hereditary disorder for genetic medicine - Involves replacing relevant somatic stem cells, differentiated cells, and the organ that's malfunctioning 2o to the abnormal phenotype - Ex: Hematopoeitic stem cell transplantation (allogenic, from diff person), Autologous stem cell transplantation (same person), Non-hematopoietic stem cells 2. Gene Transfer: - Transfers normal copies of gene to PT - Mostly used when mutation is caused by a single gene - Ex Vivo Methods: remove cells from body, expose to gene therapy vector to repair mutation, grow in dish, insert back into individual - In Vivo Methods: introducting gene therapy vector into the body near the tissue with the problem, with the hopes that the gene therapy vector gets into the cells to repair the DNA or to produce the proper version of the protein --> All gene transfer requires expression cassette (parts of cassette: promoter, transgene (healthy version of gene), and polyadenylation site, consists of cDNA (or genomic DNA if there is no room) 3. RNA Modification: - Targets mRNA, either to suppress mRNA levels or by correcting, or adding function to the mRNA - RNA modifications are changes to the chemical composition of RNA molecules post-synthesis that have the potential to alter function or stability - In general, the mRNA of the diseased host is targeted to be suppressed or corrected. This helps in diseases which suppressing the expression of proteins (via inhibition of RNA's) would lead to favourable phenotypic outcomes - Diff. techniques to introduce new genes include RNAi and the use of trans-splicer pre-mRNA - The methods of RNA modification therapy include: antisense oligonucleotides, RNAi, trans-splicing, segmental trans-splicing, and ribozymes.

27. Describe in detail the process of maintenance methylation.

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26. Why does behavioural epigenetics have deep implications for the historical debate of the role of genetics versus environment in controlling behaviour?

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32. Compare and contrast the different delivery methods of gene transfer therapy.

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33. Compare and contrast the different methods of RNA modification therapy.

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34. Create a feasible genetic treatment for an actual genetic disorder, complete with a brief description of the mutation causing the disorder, a proposed gene therapy including specifics on vector and delivery and finally explain how the proposed treatment will reduce/ameliorate the negative phenotype.

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35. A new genome editing technique known as CRISPR Cas9 has been recently utilized. Briefly describe how CRISPR Cas9 works and its implication in treating genetic disorders or creating animal models of disease.

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36. The CRISPR Cas9 system has been modified to perform functions besides genome editing. Describe the adapted functions of the CRISPR Cas9 system.

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37. It has recently become apparent that a particular Nav channel is important in pain processing. What is this Nav channel, what is its role in pain processing, and what is different about the function of this channel that allows it to achieve this role? Different mutations in the gene that encodes this Nav channel can lead to completely opposite pain-related conditions. Describe each condition, the type of non-synonymous mutation that occurs, and how it causes the genetic pain-related disorder.

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38. A genetically inherited form of migraine headache (Familial Hemiplegic Migraine; FHM) supports the cortical spreading depression theory of migraine. Briefly describe what cortical spreading depression is, how it may initiate migraine and the channelopathy discussed in class that underlies FHM.

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40. Briefly summarize one or two presentation(s) that you found particularly interesting (other than your own).

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41. Several student presentations focused on longevity and/or resistance to cancer Describe the major points of two of these presentations.

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42. Several student presentations used animal models of a human disease or human phenotype. Describe the major points of two of these presentations.

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43. Several student presentations highlighted the use of gene editing techniques or modifications to gene editing techniques. Describe the major points of two of these presentations.

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44. Several student presentations focused on or included aspects of evolution. Describe the major points of two of these presentations.

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30. Discuss in detail what the "conflict hypothesis" argues for the reason why genomic imprinting has evolved.

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28. Describe each of the 5 models for how noncoding RNA are thought to work to influence the epigenetic state.

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