DEVELOPMENTAL BIOLOGY
Assigned Questions, Fall 2008

Aug 29 (chapters 1 and 2: pp 3-23, 25-26)

  1. Outline the basic steps in development (chapter 2, pages 25-26).
  2. Compare epigenesis with preformation.  How does this relate to current thinking?
  3. What are the primary germ layers and what types of structures do they develop into?
  4. What is a fate map?  Describe one method for determining a fate map.
  5. Describe von Baer's principles.  What might these principles say about the progress of evolutionary development?
  6. What basic cellular processes result in morphogenesis in epithelial and mesenchymal cells?
  7. Define homology and analogy.  Give an example of each.
  8. What is a teratogen?  Why does a teratogen have a different effect depending on when it is present?
  9. How can Turing's reaction-diffusion model result in pattern formation?

Sept 03 (chapter 3: pages 49-66)

  1. Discuss one example of how the environment affects development.
  2. Describe autonomous specification and discuss one example.
  3. What is syncitial specification?
  4. Describe conditional specification.  Why did Roux's experiments suggest autonomous specification while Driesch's suggested conditional?
  5. Define prospective fate, prospective potency.
  6. What are morphogens?  What effect does a gradient of these have?  Discuss the experiments demonstrating Nodal's action in zebrafish.
  7. What is a morphogenetic field? 

Sept 05 (chapter 3: pages 66-74; Chapter 4: pp 81-83)

  1. Define stem cells.  Differentiate between pluripotent stem cells, committed stem cells and progenitor cells.
  2. What are the basic questions to be asked in regards to morphogenesis?
  3. Describe the reconstitution experiments that support the differential affinity hypothesis.
  4. How does the thermodynamic model explain the reconstitution experiments?
  5. Discuss the structure of cadherins and how they function, in general. Choose two types of cadherins and describe their use.
  6. Give a developmental example of how cadherins are used in morphogenesis.
  7. What is nuclear totipotency? 
  8. Describe the process of amphibian cloning.  How successful is it? 

Sept 08 (chapter 4: pp 83-98)

  1. How was Dolly cloned?  What mammals have been cloned? How perfect of a copy is a cloned mammal?
  2. Discuss some benefits and some potential problems of animal cloning.
  3. What is differential gene expression?  What are the 3 postulates regarding differential gene expression?
  4. Read about polytene chromosomes and how they support the idea of differential gene expression.
  5. Read website section 4.5 (don't write and answer) about how the immunoglobulin genes provide an exception to the rule of nuclear totipotency.
  6. What is a Northern blot, RT-PCR, microarray, and in situ hybridization?  How can these be used to demonstrate differential gene expression?
  7. How are embryonic stem cells are derived?
  8. What are chimeric, transgenic and knockout animals and how can they be used to study the function of a gene during development?
  9. How can RNA expression be blocked?  Why would you do this?

Sept 10 (chapter 5)

  1. What are histones, what is their role and how can they be modified?
  2. Discuss the different parts of the structure of a typical eukaryotic gene.  How is the initial transcription product modified to produce a mature mRNA?
  3. What are promoters, enhancers and silencers?  What are transcription factors?  What is the difference between basal, TAF and specific transcription factors?
  4. Review table 5.1, recalling the basic families of transcription factors.
  5. What is DNA methylation and how does this affect gene expression?  How does this affect histones and differentiation?
  6. What is dosage compensation and why is it important?
  7. What is nRNA selection?  Why is this important?
  8. Discuss how different families of proteins can be produced in general and tropomyosin isoforms in particular.
  9. What are the three ways that translation can be controlled?  How is this accomplished?  Provide one developmental example of each category.
  10. What is postranslational modification?

Sept 12 (chapter 6: pages 139-145)

  1. Define induction and competence.  Discuss how lens induction by the optic vesicle illustrates these ideas.
  2. What is meant by reciprocal and sequential inductions.  How is this illustrated by eye development?
  3. Differentiate between instructive and permissive interactions.
  4. What are epithelial-mesenchymal interactions.  What is meant by regional and genetic specificity of these interactions.  Provide an example of each.
  5. Define paracrine, endocrine, autocrine and juxtacrine interactions.

Sept 15 (chapter 6: pages 145-160)

  1. What is the basic mechanism of many signal transduction pathways?
  2. Outline the details of 3 of the following: RTK, JAK-STAT, Wnt, Hedgehog and TGFb/Smad pathways.  Provide a developmental example of the pathways chosen.
  3. Define apoptosis.  Give some examples of when apoptosis is used in developmental systems.
  4. Outline the apoptotic pathway for mammals.

Sept 17 (chapter 6: pages 160-171)

  1. Outline the Notch pathway.
  2. Give one example showing how chance and juxtacrine signaling are involved in induction events in C. elegans (pp 162-164).
  3. Describe the components of the extracellular matrix and discuss how they affect development.
  4. Describe the structure of the integrins.
  5. How are the integrins able to participate in movements?  In the control of gene expression?
  6. Discuss the developmental importance of gap junctions.
  7. What is meant by cross-talk between signaling pathways?  Discuss how this happens during lymphocyte differentiation.
  8. How are cells able to maintain their differentiated state after signaling?

Sept 19 (chapter 7 pp 175-178 and chapter 19 pp 612-614)

  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. What factors control spermatogenesis?
  4. Be prepared to review the structure of the mammalian testis.
  5. Describe, in detail, the structure of a mature spermatozoan.
  6. Describe the process of spermiogenesis.
  7. What happens to the nuclear material during spermiogenesis?
  8. Discuss gene expression during spermatogenesis (must go to the textbook website).  Focus on gene activity during male meiosis and haploid gene expression.

Sept 22 (chapter 7 pp 178-180 and chapter 19 pp 615-622)

  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 24: No Questions; Exam I

Sept 26 (chapter 7 pp 178-180 and chapter 19 pp 615-622)

  1. Describe the deposition of yolk in frog eggs.  How is this hormonally controlled (must go to textbook website).
  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 the sea urchin egg.  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 (must go to textbook website).
  7. What causes the resumption of meiosis in mammals prior to ovulation (must go to textbook website)?

Sept 29 (Chapter 7: pp 181-193)

  1. What is the mechanism of sperm attraction to the egg in sea urchins?
  2. Describe the two parts of the acrosome reaction in sea urchins.  Discuss the stimulus and mechanism of this reaction.
  3. Discuss sperm-egg recognition in sea urchins.  How is this species specific?
  4. Describe the process leading to the fusion of the sperm-egg membranes in sea urchins.
  5. What events occur within one minute of sperm-egg binding?
  6. What is the fast block to polyspermy?
  7. What initiates the cortical reaction?  Describe the cortical granule reaction and all that results from it in sea urchins.

Oct 01 (Chapter 7: pp 193-202)  - NOTE: You don't have to prepare written answers to the questions for lecture, but come to class prepared to discuss them.  Be sure to prepare written answers to the discussion questions on the ethical reading for lab found on the Developmental Links page.

  1. Describe the late responses of the egg to sperm entry.  Include the mechanisms by which these responses are controlled.
  2. Describe the mechanism of egg activation due to sperm binding/fusion to the egg in the sea urchin. (see Sidelights and Speculations)
  3. Describe what happens to the cytoplasm after sperm entry.  What causes these changes?  (see Chapter 10, pp 290-291 and figure 8.35, p 238)
  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 03 (Chapter 7: pp 202-207)

  1. Discuss the early and late stages of gamete adhesion.
  2. Describe the induction of the acrosome reaction in mammals.  What is the result of this reaction?
  3. Describe secondary binding of the sperm to the zona.  Why is this necessary?
  4. Discuss sperm-egg fusion and the prevention of polyspermy in mammals.
  5. Describe how the second meiosis block is removed after fertilization (see page 617).
  6. Discuss the fusion of genetic material in mammals.
  7. Discuss the idea that male and female pronuclei are non-equivalent. (see Sidelights and Speculations)

Oct 06  (Chapter 8: pp 211-223)

  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 endoderm?

Oct 08 (Chapter 8: pp 223-236)

  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 10 (Chapter 8: pp 237-257)

  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 13 (Chapter 10: pp 291-302)

  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 15: No Questions; Exam II; Be sure to prepare written answers to the discussion questions on the ethical reading for lab found on the Developmental Links page.

Oct 17: No Class; Reading Day

Oct 20 (Chapter 10: pp 302-307)

  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.

Oct 22 (Chapter 10: pp 307-323)

  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, Xnr3 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 24: Class Cancelled - CEA Convention

Oct 27 (Chapter 11: pp 325-348)

  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.
  4. How are the induction events in fish similar to that discussed in amphibians?  Include a discussion of dorsal/ventral patterning, the Nieuwkoop center and anterior/posterior patterning.
  5. Briefly describe cleavage in birds including the structure of the blastula.
  6. Describe the early changes that occur during bird gastrulation ending with the formation of the secondary hypoblast.
  7. 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?
  8. How does the signaling that occurs during axis formation in birds compare to that seen in amphibians?  Where is the Nieuwkoop center?
  9. How are activin and sonic hedgehog able to dictate the left and right sides of the bird embryo?

Oct 29 (Chapter 11: pp 348-368)

  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 11.33 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 12: pp 373-385)

  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?
  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 03 (Chapter 12: pp 385-396)

  1. Describe the transition from a single layered neuroepithelium to a 3-layered tissue as found in the spinal cord and medulla.
  2. 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?
  3. What evidence is there that the CNS continues to develop after birth and into adulthood?
  4. 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.
  5. Discuss adult neural stem cells.
  6. Describe how axons grow out to their destinations.
  7. How do Scwann cells myelinate axons?

Nov 05 (Chapter 12: pp 497-405)

  1. Review the basic development of the eye as discussed in chapter 6 (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.  What roles do TGF-a and KGF play in epidermal differentiation?
  6. Briefly describe the development of hair follicles.  How do induction events regulate this?

Nov 07 (Chapter 13: 407-423)

  1. Discuss the signals involved in neural crest specification.
  2. What are the four basic categories of neural crest cells?  Name at least one neural crest derivative from each of the categories.
  3. Describe the two migratory pathways of the trunk neural crest and the types of cells that are derived from each of these pathways.
  4. What role do the BMP's play in trunk neural crest cell migration?  Slug?  RhoB?  Cadherins?  Fibronectin? Integrins? Thrombospondin?  Epherin?  Semaphorin?
  5. Discuss the pluripotency of the trunk neural crest cells.  Are they or aren't they?  If so, how much?
  6. Describe the signals that control trunk neural crest cell fate.
  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 14.
  9. What are cranial placodes?

Nov 10 (Chapter 13: 424-440)

  1. What are the hierarchical decisions that must be made during neuron specification?  Briefly describe 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 436-440):

Nov 12 (Chapter 14: 443-453)

  1. Name the different regions of mesoderm and summarize what develops from each region.
  2. Describe the basic process of somite formation. 
  3. Describe how Notch, hairy, ephrin-B2 and EphA4 are involved in somite formation.
  4. How are the factors above coordinated (see sidelights and speculations)?
  5. What role do the Hox genes play in somite specification?
  6. Describe how the somite differentiates into different regions and what each of these regions becomes.
  7. Discuss the signals that controls the differentiation of the various somite regions (figure 14.12)

Nov 14: No Questions; Exam III

Nov 17 (Chapter 14: 453-460)

  1. What is the importance of the MyoD family of genes?  What kind of molecule is it?
  2. Describe the process of muscle cell fusion including the factors that are required.
  3. Discuss muscle stem cells.
  4. Describe the process of intramembranous ossification (not the genes or factors). See pages 420-421
  5. Describe the five phases of endochondral ossification (not the genes or factors).
  6. What is the epiphyseal plate?  What roles do FGF, IGF-I, growth hormone (GH), estrogen and testosterone play at the epiphyseal plate.  See pages 525-526.
  7. What is an osteoclast?  Where does it come from?

Nov 19 (Chapter 14: 460-468)

  1. Describe the progression of 3 kidney types during kidney development.
  2. What are the nine signaling steps that lead to the formation of the metanephros?
  3. Describe the reciprocal interactions that occur steps 1-6.
  4. What is the cloaca?  Discuss how the cloaca changes in mammals.

Nov 21 (Chapter 15: 471-482)

  1. Describe what initially happens to the lateral plate mesoderm.
  2. What is the cardiogenic mesoderm?  Where does it come from?  Where is it located?
  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 15.12.  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 24 (Chapter 15: 480-493)

  1. Study figure 15.11.  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 and VEGF 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. Distinguish between embryonic and definitive hematopoiesis  in terms of when and where it occurs.
  7. Study figure 15.21 (don't worry, you won't have to learn it).  What is the key stem cell?  What does this figure tell you about the process of differentiation of blood cells?
  8. Describe the "niche" that the stem cell above is in.

Nov 26 (Chapter 15: 493-517)

  1. Study figure 15.24.  Note how the folding of the embryo produces the digestive tract.
  2. Discuss the formation of the mouth.
  3. Describe the development of the pituitary gland in the pharynx region.
  4. What do the different pharyngeal pouches develop into (see figure 15.25)?
  5. How does the endoderm and mesoderm interact to specify gut tissue?
  6. Describe the development of the liver, gall bladder and pancreas from the first portion of the small intestine.
  7. Describe the formation of the lung.  What role does the mesenchyme play in this development?

Nov 28: No Class; Thanksgiving Break

Dec 01 (Chapter 16)

  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. Describe the two 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. Study figure 16.19 and think about how the AER and ZPA interact in limb formation.

  7. What factors specify dorsal/ventral polarity.

  8. How are the 3 axes in limb development coordinated?

  9. How is cell death involved in limb formation?

Dec 03 (Chapter 17: 531-543)

  1. Describe the general structure of the indifferent gonad and explain how this common structure differentiates into either an ovary or a testis (fig 17.2).

  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 17.3).

  3. Outline the roles that Sry, Sox9, FGF9, Sf1, Dax1 and Wnt4 play in sexual specification.

  4. How is male and female secondary sex determination regulated?  Include important hormonal regulators.

Dec 05: Project Presentations