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Developmental Biology Questions

DEVELOPMENTAL BIOLOGY
Assigned Questions, Fall 2012
Aug 29: No assignment Aug 31: (chapter 1) 1. 2. 3. 4. 5. 6. 7. 8. Outline the basic steps in development. Compare epigenesis with preformation. How does this relate to current thinking? What are the primary germ layers and what types of structures do they develop into? Describe von Baer's principles. What might these principles say about the progress of evolutionary development? What basic cellular processes result in morphogenesis in epithelial and mesenchymal cells? What is a fate map? Describe at least one method for determining a fate map. Define homology and analogy. Give an example of each. What is a teratogen? Why does a teratogen have a different effect depending on when it is present?

Sept 03: No Class: Labor Day Sept 05 (chapter 2: pp 31-52) 1. How was Dolly cloned? What mammals have been cloned? How perfect of a copy is a cloned mammal? 2. Why was Dolly cloned? What developmental principle was demonstrated by this cloning? Discuss some benefits and some potential problems of animal cloning. See textbook website section 2.6. 3. What are histones, what is their role and how can they be modified? 4. Discuss the different parts of the structure of a typical eukaryotic gene. How is the initial transcription product modified to produce a mature mRNA? 5. What are promoters, enhancers and silencers? What are transcription factors? What is the difference between basal, TAF and specific transcription factors? 6. Review table 2.1, recalling the basic families of transcription factors. 7. What is DNA methylation and how does this affect gene expression? How does this affect histones and differentiation? 8. What is X-chromosome inactivation and genomic imprinting? Sept 07 (chapter 2: pp 53-66) 1. What is nRNA selection? Why is this important? 2. Discuss how different families of proteins can be produced in general and tropomyosin isoforms in particular. 3. What are the three major categories of ways that translation can be controlled? Discuss the mechanisms by which this is accomplished. Discuss developmental examples in each category. 4. Discuss the role that miRNA plays in controlling translation and transcription. 5. What is postranslational modification? Sept 10 (Part II introduction: pp 109-119; chapter 3: pp 69-73)
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Developmental Biology Questions

1. Differentiate between specification and determination. 2. Describe autonomous specification and discuss one example. 3. Describe conditional specification. Why did Roux's experiments suggest autonomous specification while Driesch's suggested conditional? 4. Define prospective fate, prospective potency. 5. What are morphogens? What effect does a gradient of these have? 6. What is syncitial specification? 7. Think about (do not write down) the basic questions to be asked in regards to morphogenesis. 8. Describe the reconstitution experiments that support the differential affinity hypothesis. 9. How does the thermodynamic model explain the reconstitution experiments? Sept 12 (chapter 3: pp 73-84) 1. Discuss the structure of cadherins and how they function, in general. Choose two types of cadherins and describe their use. 2. Give a developmental example of how cadherins are used in morphogenesis. 3. Define induction and competence. Discuss how lens induction by the optic vesicle illustrates these ideas. 4. What is meant by reciprocal and sequential inductions. How is this illustrated by eye development? 5. Differentiate between instructive and permissive interactions. 6. What are epithelial-mesenchymal interactions. What is meant by regional and genetic specificity of these interactions. Provide an example of each. Sept 14 (Part II introduction: pp 323-331; chapter 3: pp 84-87) 1. 2. 3. 4. 5. 6. 7. Define stem cells. What are embryonic vs. adult stem cells? Differentiate between totipotent, pluripotent, committed and progenitor cells. What is a stem cell niche? What are MSCs, where can you find them and what do they do? Define paracrine, endocrine, autocrine and juxtacrine interactions. Outline the typical RTK pathway. What type of molecule is Ras? How does FGF-8 use the RTK pathway during eye development? The stem cell factor during melanoblast differentiation?

Sept 17 (chapter 3: pp 88-97) 1. 2. 3. 4. 5. 6. Outline the JAK-STAT pathway. What developmental process uses this pathway? Describe the Hedgehog pathway. Describe both the "canonical" and "non-canonical" Wnt pathways. Study the TGF- b superfamily. How do these paracrine factors utilize the Smad pathway? Define apoptosis. Give some examples of when apoptosis is used in developmental systems. Outline the apoptotic pathway for mammals.

Sept 19 (chapter 3: pp 98-105) 1. Outline the Notch pathway. 2. Give one example showing how chance and juxtacrine signaling are involved in induction events in C. elegans. 3. How are cells able to maintain their differentiated state after signaling? 4. Describe the structure of the integrins.
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Developmental Biology Questions

5. How are the integrins able to participate in movements? In the control of gene expression? 6. Describe the process involved in epithelial-mesenchymal transitions. Sept 21 (chapter 4 pp 121-124 and chapter 16 pp 607-610) 1. What was Hartsoeker's view of the importance of spermatozoa? What did others think? 2. Name the stages during spermatogenesis. Describe the formation of syncitial clones. What is the ramification of this syncitium? 3. Discuss the function of Sertoli cells and their relationship to the developing sperm. 4. Describe the factors that control spermatogenesis at each stage. What would be the stem cell niche in this case, and how would cells get out of that niche? 5. Be prepared to review the structure of the mammalian testis. 6. Describe, in detail, the structure of a mature spermatozoan. 7. Describe the process of spermiogenesis. 8. What happens to the nuclear material during spermiogenesis? 9. Describe gene expression during spermatogenesis Sept 24 (chapter 4 pp 124-127 and chapter 16 pp 602-613 ) 1. Why is it that mammals are only able to produce a limited number of oocytes during their lifetime while fish and amphibians can produce many oocytes each year? Describe the situation in humans. 2. Outline the differences between oogenesis and spermatogenesis. 3. At what stage of maturation can eggs be in at the time of fertilization? Give an example for each case. 4. Discuss how meiosis completion is controlled in amphibians. Include the role of progesterone, MPF, cyclin, p34, c-mos, cdk-2 and CSF. 5. Discuss gene transcription oocytes. Include the rate of production and the types of molecules that may be produced. 6. What are lampbrush chromosomes? 7. What is meant by gene amplification? How is this used during oogenesis? Sept 26: No Questions, Exam I Sept 28 (chapter 4 pp 124-127 and chapter 16 pp 602-613 ) 1. Describe the deposition of yolk in frog eggs - go to http://9e.devbio.com/article.php?id=195 for additional information. 2. What material is finally stored in the egg after oogenesis is complete? Think broadly and give some specific examples. 3. Discuss how the material in the egg is distributed assymetrically. 4. Describe the egg envelopes present surrounding eggs. What envelopes surround the mammalian egg? 5. How do the follicle cells affect the growth of the mammalian oocyte and vice/versa? 6. Describe the human menstrual cycle. Include the stages, what goes on in the ovary and uterus and the hormonal changes that occur including the way that ovulation is triggered in mammals (see textbook website 16.7). 7. What causes the resumption of meiosis in mammals prior to ovulation (see textbook website 16.8)? Oct 01 (Chapter 4: pp 127-138) 1. What is resact and what are its functions? Describe the intracellular signaling involved. 2. Describe the two parts of the acrosome reaction in sea urchins. Discuss the stimulus and mechanism of
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Developmental Biology Questions

3. 4. 5. 6. 7.

this reaction. How is this species specific? Discuss sperm-egg recognition in sea urchins. How is this species specific? Describe the process leading to the fusion of the sperm-egg membranes in sea urchins. What events occur within one minute of sperm-egg binding? (see table 4.1) What is the fast block to polyspermy? What initiates the cortical reaction? Describe the cortical granule reaction and all that results from it in sea urchins.

Oct 03 (Chapter 4: pp 139-149) 1. Describe the mechanism of egg activation in sea urchins. Start from sperm-egg binding through the release of calcium ions. 2. Describe the late responses of the egg to sperm entry. Include the mechanisms by which these responses are controlled. 3. Describe what happens to the cytoplasm after sperm entry. What causes these changes? (see figure 7.1, p 242 and figure 5.35, p 188) 4. Discuss the process leading to the fusion of the genetic material (amphimixus) in sea urchins. 5. What is the role of the mammalian female reproductive tract in gamete transport? 6. What is capacitation of sperm in mammals? What types of changes occur on the sperm during this process? 7. How does the mammalian sperm find the egg? Oct 05 (Chapter 4: pp 149-155) 1. 2. 3. 4. 5. 6. 7. 8. Discuss the early and late stages of gamete adhesion. Describe the induction of the acrosome reaction in mammals. What is the result of this reaction? Describe secondary binding of the sperm to the zona. Why is this necessary? Discuss sperm-egg fusion and the prevention of polyspermy in mammals. Compare egg activation in the mammal to that discussed earlier for the sea urchin. Describe how the second meiosis block is removed after fertilization (see page 604). Discuss the fusion of genetic material in mammals. Discuss the idea that male and female pronuclei are non-equivalent. (see Sidelights and Speculations)

Oct 08 (Chapter 5: pp 159-172) 1. Describe what happens during cleavage. What is significant about the mid-blastula transition? 2. How is the cell cycle different during early cleavage compared to later in development? How is this change reflected in the mechanism of controlling the cell cycle (MPF)? 3. What is the cytoskeletal mechanism of cleavage? 4. Describe the different cleavage patterns possible, providing an example for each. How does this relate to the amount of yolk present in the egg? 5. How is gastrulation different from cleavage? 6. Describe the different ways that cells can migrate. 7. Describe cleavage as it occurs in sea urchins through the formation of the blastula. 8. Cell fate appears to be specified already in sea urchin cleavage. Describe the layering of the 60-cell embryo and the fates of the layers. What appears to be the mechanism of cell specification for micromeres and vegetal cells? Oct 10 (Chapter 5: pp 172-185)
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Developmental Biology Questions

1. Describe the basic changes that occur during sea urchin gastrulation. 2. Explain how the primary mesenchyme ingresses. Include in your answer any changes in cellular affinities. 3. Discuss the three steps of archenteron invagination. 4. Describe the cleavage pattern present in snails. How is coiling of the shell genetically inherited? 5. What is the polar lobe in molluscs? What cells retain this lobe? 6. What is the developmental importance of the polar lobe? Provide one piece of experimental evidence that supports this role. Oct 12: No Questions, Reading Day Oct 15: (Chapter 5: pp 187-199) 1. Describe the reorganization of the cytoplasmic pigments in tunicates that occurs after fertilization. What is the fate of each pigmented area? 2. Discuss the specification of the muscle tissue in tunicates. 3. How is the endoderm specified in tunicates? 4. Discuss the specification of the mesenchyme and notochord in tunicates. 5. Describe the fate and role of the PAR proteins and P-granules in C. elegans development. 6. Briefly discuss how the fate of the P1 cells is determined in C. elegans. 7. Discuss one example of how the P2 cell in C. elegans controls the fate of neighboring cells. Oct 17: (Chapter 7: pp 242-251) 1. Describe the cytoplasmic changes immediately after fertilization in frogs. 2. Briefly describe cleavage in the amphibian including the structure of the blastula. What is the function of the blastocoel? What adhesion molecule is important? 3. What triggers the mid-blastula transistion? 4. In studying the fate map of Xenopus, where are the prospective ectodermal, mesodermal and vegetal cells located? 5. Discuss roles that vegetal rotation, bottle cells, convergent extension and epiboly play during gastrulation. Include which types of cells are moving during the various phases and any mechanisms involved. How is the position of the blastopore determined? 6. What role does fibronectin play in mesodermal migration? Give one piece of experimental evidence. Oct 19: No Questions, Exam II - Don't forget the Blue Book! Oct 22: (Chapter 7: pp 252-258) 1. What is the importance of the gray crescent during amphibian development? What experiments demonstrated this? 2. Describe experiments that demonstrate a progressive determination of prospective fate as development proceeds. 3. Describe the Speeman and Mangold experiment. What was concluded from this experiment? What questions were raised? 4. How is mesodermal tissue induced? What is the function of the Nieuwkoop center? 5. Describe the blastula recombination experiments supporting this mesodermal induction model. 6. Describe the 32 cell embryo recombination experiments demonstrating the location of the Nieuwkoop center.
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Developmental Biology Questions

Oct 24: (Chapter 7: pp 258-271) 1. How does b -catenin, TGF- b factors, GSK-3 and Disheveled interact in order to specify those cells that will become the Nieuwkoop center? How does this affect siamois and goosecoid? 2. What role do the Nodal-related proteins (Xnr) play in the specification by the endoderm of the mesoderm in general and the organizer in particular? 3. What are the specific functions of the organizer? What gene must be activated in the organizer region? 4. How does BMP4 and the BMP inhibitors (noggin, chordin and follistatin) interact to specify the fate of the ectoderm? 5. What signals from the organizer are involved in the specification of the neural ectoderm to become head structures? In general, how do these work? 6. Describe the transplantation experiments demonstrating the regional specificity of induction by the organizer. 7. What signals are involved in head and trunk induction? Oct 26: (Chapter 7: pp 273-283; Chapter 8: 287-300) 1. Briefly describe cleavage in fish including the structure of the blastula. 2. Describe the early changes that occur during fish gastrulation ending with the formation of the hypoblast. 3. What is the embryonic shield in fish? Describe its formation and its function. Where is the Nieuwkoop center? Note (do not write down) how the induction events in fish are similar to that in the amphibian. 4. Briefly describe cleavage in birds including the structure of the blastula. 5. Describe the early changes that occur during bird gastrulation ending with the formation of the secondary hypoblast. 6. Describe the formation of Hensen's node and the primitive streak in birds and the types of cells that pass through it. What happens to the ectoderm? What is homologous to Hensen's node in fish and amphibians? Where is the Nieuwkoop center? 7. How are activin and sonic hedgehog able to dictate the left and right sides of the bird embryo? Oct 29: (Chapter 8: pp 300-320) 1. How is cleavage different in mammals? Include a discussion of compaction including the molecules involved. Describe the structure of the blastocyst and the fate of the different regions. How does the blastocyst escape from the zona pellucida? 2. Describe gastrulation in mammals. 3. Describe how the embryo implants into the uterus (use fig 8.22 as your guide). 4. What is the difference between the syncitiotrophoblast and the cytotrophoblast? 5. Discus the Hox-code hypothesis for patterning of the ant/post axis. What role do different signaling molecules play in this? Oct 31: (Chapter 9: pp 333-345) 1. What are the three basic types of ectoderm? Name 3 derivatives of each type. 2. Describe the basic process of primary neurulation from the ectoderm. Include the tissues and cells that result from it. 3. What mechanism allows for the shaping and bending of the neural plate? 4. What is the anterior and posterior neuropore? What happens if these don't close? 5. Describe the changes in cell adhesion molecules that occur during neurulation. 6. What is secondary neurulation and when does it occur?
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Developmental Biology Questions

7. Name the primary brain vesicles and the secondary vesicles that arise from them. Name one adult brain structure that arises from each of the secondary vesicles. 8. Describe the signals that are needed for the ventral and dorsal patterning of the neural tube. Nov 02: (Chapter 9: pp 345-358) 1. 2. 3. 4. What types of cells develop from the neuroepithelium? Describe the structure of a neuron. How do axons grow out to their destinations? How do Schwann cells myelinate axons? Describe the transition from a single layered neuroepithelium to a 3-layered tissue as found in the spinal cord and medulla. 5. The 3-layered CNS is modified in higher regions of the brain. How do neurons move about in the developing brain in order to position themselves? 6. Read the section "Unique Development of the Human Brain" (sidelights and speculations). Respond to the following. How fast is the human neuron growth rate at birth? How does the human brain at birth compare to apes? What implications does this have on the concept of childhood and brain development? Why do you think we have such an extended period of brain development outside of the uterus? Outline the other four phenomena that have been identified. 7. Discuss adult neural stem cells (sidelights and speculations). Nov 05: (Chapter 9: pp 359-370) 1. Review the basic development of the eye as discussed in chapter 3 (do not write any of it down). What layer becomes the retina? 2. What is the role of Pax6 and sonic hedgehog in eye development? 3. Describe the formation of the lens. 4. Why don't babies see well (must go to textbook website)? 5. Discuss the development of the epidermis and the factors that control it. 6. What are placodes in the skin and what do they develop into? 7. Briefly describe the development of hair follicles. How do induction events regulate this? Nov 07: (Chapter 10: 372-390) 1. Discuss BMP and Wnt interact to specify the ectoderm, including the neural crest. 2. Describe a model for how multipotent neural crest cells become increasingly specified. 3. What are the four basic categories of neural crest cells? Name at least one neural crest derivative from each of the categories. 4. Describe the two migratory pathways of the trunk neural crest and the types of cells that are derived from each of these pathways. 5. What role do BMP, Wnt, Snail, RhoB, cadherins, fibronectin, laminin, tenascin, collagen, integrins, thrombospondin, ephrin, semaphorin play in trunk neural crest migration? 6. Discuss the specification of melanocytes and how they migrate along the correct path. 7. Outline the skeletal derivatives for each of the pharyngeal arches. What group of genes play a role in specifying fate in these cells? 8. NOTE: We are skipping the intramembranous ossification section until chapter 11. 9. What are cranial placodes? Nov 09: (Chapter 10: 392-409) 1. What are the hierarchical decisions that must be made during neuron specification? Briefly describe
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Developmental Biology Questions

these decisions as made by motor neurons. 2. What is meant by pathway selection for axons. Name and briefly describe using examples of the various ways this can occur in the developing nervous system. 3. Define and briefly describe target selection and address selection. Include a discussion of activity dependent selection and neurotrophic factors. 4. The outgrowth of retinal axons into the brain provides a good example of various methods of axon migration. Answer the following for this system (pages 404-409): How are the retinal axons targeted to the optic disc and into the optic nerve? How do the axons grow along the optic nerve? How do the axons decide whether or not to cross the optic chiasm? How do the axons migrate along the optic tract towards the tectum? How do the axons find the appropriate area of the optic tectum? How do the axons finally obtain their point-point specificity in the brain? Nov 12: No questions Nov 14: (Chapter 11: 413-426) 1. 2. 3. 4. 5. 6. 7. Name the different regions of mesoderm and summarize what develops from each region. Describe the basic process of somite formation. Describe how Notch, hairy, ephrin-B2 and EphA4 are involved in somite formation. How are the factors above coordinated (see sidelights and speculations)? What role do the Hox genes play in somite specification? Describe how the somite differentiates into different regions and what each of these regions becomes. Discuss the signals that controls the differentiation of the various somite regions (figure 11.13)

Nov 16: No Questions, Exam III - Don't forget the Blue Book! Nov 19: (Chapter 11: 426-432) 1. What is the importance of the MyoD and Myf5? What type molecule are they? 2. Describe the process of muscle development from myoblasts to full maturation including the factors that are required. 3. Describe the process of intramembranous ossification (not the genes or factors). See pages 385-386 4. Describe the five phases of endochondral ossification (not the genes or factors). How is this process reflected in what happens in the epiphyseal plate? 5. Describe how sclerotomes become vertebrae. Nov 21: (Chapter 11: 434-442) 1. 2. 3. 4. Describe the progression of 3 kidney types during kidney development. List the nine reciprocal signaling steps that lead to the formation of the metanephros. Describe the reciprocal signaling interactions that occur steps 1-6. What is the cloaca? Discuss how the cloaca changes in mammals.

Nov 23: No Class - Thanksgiving Holiday Nov 26: (Chapter 12: 445-458) 1. Discuss the formation of the coelom. 2. What is the cardiogenic mesoderm? Where does it come from? Where is it located?
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Developmental Biology Questions

3. Discuss the specification, migration and establishment of the anterior/posterior domains of the heart. 4. Discuss the early differentiation, fusion and beating of the heart. 5. Describe the looping of the primitive heart and the formation of heart chambers. Do not worry about the signals involved. 6. Discuss the various constraints on blood vessel formation. 7. Study figure 12.13. What is the simple arterial aortic arch plan in the early embryo? Be prepared to discuss how this changes to form the final configuration of blood vessels. Nov 28: (Chapter 12: 456-471) 1. Study figure 12.12. Describe 3 things that are different between fetal circulation and adult circulation. 2. What is the functional difference between fetal hemoglobin and adult hemoglobin? Why is this important? 3. What is a hemangioblast? What is its function? 4. Describe the process of vasculogenesis. Briefly, what roles do FGF2, VEGF and angiopoietins play in this process. 5. What is the basic difference between angiogenesis and vasculogenesis? Describe angiogenesis and how VEGF, TGF- b , PDGF and ephrin are involved. 6. What is the stem cell for blood cell formation? What is the origin of this cell? Where does this process occur? How does this change over the course of embryogenesis? 7. Describe the "niche" that the blood cell stem cell is in (figure 12.23). Nov 30: (Chapter 12: 471-480) 1. 2. 3. 4. Study figure 12.26. Note how the folding of the embryo produces the digestive tract. Define stomodeum, proctodeum and Rathke's pouch. What do the different pharyngeal pouches develop into (see figure 12.27)? How does the endoderm and mesoderm interact to regionally specify gut tissue? Include the roles of shh, Hox genes, retinoic acid, FGF, Wnt and Wnt inhibitors. 5. Describe the development of the liver, gall bladder and pancreas from the foregut. 6. Describe the formation of the lung. What role does the mesenchyme play in this development? Dec 03: (Chapter 13) 1. What is the limb field and how are the Hox genes involved? What mesoderm contributes to the limb bud? 2. What factors induce the limb bud, and how is the forelimb vs. the hindlimb specified? 3. What is the apical ectodermal ridge and progress zone? What role do these regions play in proximal/distal axis formation and the type of limb that develops? How are the factors FGF10 and FGF8 involved? 4. Briefly outline the three models for proximal/distal axis formation. How are the Hox genes involved in this? 5. What is the zone of polarizing activity, what is its function, and how is sonic hedgehog involved? 6. How are the Hox genes involved in specifying the limb skeleton? 7. Study figure 13.20 and think about how the AER and ZPA interact in limb formation. 8. What factors specify dorsal/ventral polarity. 9. How is cell death involved in limb formation? Dec 05: (Chapter 14: 513-543)
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Developmental Biology Questions

1. Describe the general structure of the indifferent gonad and explain how this common structure differentiates into either an ovary or a testis (fig 14.2). 2. Describe the indifferent stage in terms of the ducts that are present and explain how these are altered to produce the ducts typical of males and females (fig 14.3). 3. Outline the roles that Sry, Sox9, FGF9, Sf1, DAX1, Wnt4 and RSPO1 play in specifying ovary vs. testis. 4. Discuss how testosterone, DHT, AMF and estrogen lead to differentiation of male and female secondary sex characteristics. Dec 07: No additional questions - finish up loose ends.

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