1. What is meant by genomic equivalence?

Explain an experiment that supportsgenomic equivalence by providing functional evidence(Hint: think about what is meant by functional evidence orproducing dolly the sheep vs. descriptive evidence like labeling achromosome and determining different cells in an organisms all havethe same chromosome structure). Describe the hypothesis, briefmethods, results and conclusion reached.

1. What is the overall message of von Baer’s Laws?

1. Why do you think Darwin was intrigued by these laws (hint:think in terms of continuity and evolution)?

1. During the earliest phases of nervous system development,morphological changes occur and result in the formation of a neuraltube.

1. What is the molecular mechanism by which the neural tubephysically separates from the epidermis? (Hint: think aboutdifferential cell-cell adhesion)

1. Define a “lose it” or loss-of-function technique that wouldallow you to support that the molecular mechanism aboveoccurs.

1. Describe what is meant by epithelial to mesenchymaltransition.

1. During early syncytial specification in Drosophila,bicoid  mRNA localizes to the anterior end ofthe embryo, where it generates a concentration gradient of theBicoid morphogen responsible for the development of the head. Youperform a chromatin IP experiment to identify new genes that areregulated by the Bicoid transcription factor. You discover Bicoidbinds very strongly to the regulatory DNA of a kinase, geneH. It is your job to design a series of experiments todetermine if gene H actually functions during headformation of Drosophila.

Briefly describe a strategy for eachof the following scientific approaches: (i) find it, (ii) lose it,and (ii) move it (that is, (i) correlation, (ii) requirement, and(iii), sufficiency).

1. It is known that specific signaling pathways promote thedevelopment of dorsal structures like the brain and spinal cord. Amutation was discovered in zebrafish that resulted in theduplication of the dorsal side of the embryo (i.e. two heads/brainsand spinal cords fused with a shared ventral belly). The loss offunction mutation was mapped to the gene Axin, that is, Axin genefunction is reduced or removed entirely from the embryo.

1. Which signaling pathway would be affected by the Axinmutation?

1. What is likely to be the effect on Axin loss-of-function on theabove signaling pathway (increased or decreased signaling)?

1. Using a reporter gene, how would you test the effect of theaxin mutation on the above signaling pathway?

1. Ectopic expression of a gene is forced expression outside ofthe genes normal domain. In Drosophila, the Gal4 system isused to ectopically express genes in specific places andtimes.

1. Describe a strategy using the Gal4 system inDrosophila to generate an additional set of eyes in placeof the antenna (Hint: think in terms of the ectopic expression aneye master regulator in the antenna domain).  

                     

1. Considering the stages of cell commitment, how mightyou characterize a cell that initially moves towards an antennacell fate but then becomes persuaded to be an eye cell? (Hint:think of the environment created by the Gal4 expression system andwhether this translates to a neutral or non-neutral developmentalcontext).

1. Dnmts are methyltransferases that function by adding a methylgroup to the cytosine of DNA.

1. Describe the importance of DNA methylation to cell identity.How does cell identity play a role in development and maintenanceof a tissue?  

1. Explain the connection between DNA methyl and histonemethylation?

1. What is an organoid and why are they useful to understandinghuman development and disease.

1. Briefly describe a strategy where you would use apatient-specific organoid to attempt to understand and cure adisease that you are most interested? (Hint: first think about thedisease, then harvesting cells, then creating a useful type oforganoid from iPS cells).

1. Describe the mechanism of syncytialspecification.  

1. How is it possible that a morphogen gradient of a proteintranscription factor can transmit a signal inside the cells of asyncytial embryo?

1. How do morphogen gradients come together to specify regions ofthe syncytial embryo? (Hint: think about levels ofmorphogens).

1. What is a stem cell niche? How does a stem cell niche regulatestem cell function?

1. Describe one example of a stem cell niche.

1. What human cell types are pluripotent?

1. Why does harvesting the above pluripotent cells create a moraldilemma?

1. What can be done in the lab to avoid the above moralcomplications?