2. Describe the structure of a typical eukaryotic gene. What are enhancers and how do they regulate transcription from the promoter? How do the basal transcription factors TFIID and TFIIH interact with the promoter and RNA Polymerase II to promote transcription? How do proteins that affect chromatin structure work to alter gene expression?
3. What are the typical features of any transcription factor? Select and describe a specific example of a class of transcription factors: their structural features and example(s) of how a member of the class functions in a specific developmental pathway.
4. Describe in general terms the functions of each class of maternal (anterior, posterior and terminal) and zygotic genes (gap, pair-rule, segment polarity, homeotic selector) in the development of Drosophila. Describe the phenotypes of mutants and the normal pattern of expression in each class of genes to illustrate their functions. Select a specific gene in each class and describe its function, expression pattern of mRNA and protein (if they differ), mutant phenotype, and interactions with other genes (at higher, lower, and the same functional level).
5. Explain how Sander, Kalthoff and their colleagues' classical embryological experiments with insect embryos foreshadowed NŸsslein-Volhard and Wieschaus' experiments identifying mutations that affected Drosophila early development. (For example, their ligature and other experiments suggested that anterior and posterior "organizing centers" were interacting to form the anterior-posterior axis of insects. What is the probable molecular basis for the anterior organizing center based on these experiments and then later from molecular genetic experiments with Drosophila?)
6. A conserved molecular mechanism patterns the anterior-posterior axis of all multicellular (or at least Bilaterian) animals, from nematodes to flies to vertebrates. Describe the organization and pattern of expression of the homeotic gene complex (HOM-C) in a typical animal. Describe how homeotic gene complexes evolved from an original single primordial homeobox gene (gene duplication, loss, divergence, subfunctionalization, etc.). Explain the difference between an orthologous gene and a paralogous gene. What additional changes in the homeotic gene complex occurred in vertebrate evolution? What is a homeotic mutation? What is the evidence that HOM-C genes in the vertebrates function similarly to HOM-C genes in Drosophila?
7. Describe the experiments that have lead to our current understanding of the mechanism(s) of pattern formation in the proximal-distal axis and the anterior-posterior axis of the chick forelimb. Explain how experiments suggested timing as a mechanism of proximal-distal axis specification vs. the current view of the "early allocation" model. What is the nature of the interaction between ectoderm and mesoderm in the growing limb bud? What role do Hox (HOM-C) genes play in specifying limb axes?
8. Explain what is meant by the terms "autonomous specification" versus "conditional specification" in development.
9. What is the connection between the grey crescent and the varying results Spemann got when he separated two-cell embryos? What other experiments by Spemann suggested that something important was happening during gastrulation? When Hans Spemann and Hilde Mangold performed their famous "organizer" experiment, they transplanted tissue from a darkly pigmented newt into a lightly pigmented host newt. Describe their experiment, its results, and why the use of the differently-colored tissues was critical to the interpretation of these results.
10. Cortical rotation is critical for dorsal-ventral axis formation in the amphibian embryo. Explain the current ideas about how this event creates the d-v axis and experiments that support this hypothesis. Dorsal endoderm (the "Nieuwkoop center") induces the formation of the organizer (dorsal mesoderm) -- how is this linked to cortical rotation? Explain some of the experiments that led to the development of the concept of the Nieuwkoop center. Describe parallels in the Wnt signaling pathway in amphibian axis formation with the function of Drosophila segment polarity genes.
11. What are some of the properties of the organizer, and what are the molecular bases of these properties? How is the "induction" of neural ectoderm in the frog embryo paradoxical (opposite in mechanism from what was expected)?