1. Chapters 19 - Genetic Analysis of Development:
Development refers to interaction of the genome with the cytoplasm and external environment to produce a programmed sequence of typically irreversible events.
Differentiation
Differentiation refers to the formation of cell types, tissues, and organs through specific gene regulation. A single cell with one genotype produces a variety of specialized tissues and organs.
Development and differentiation can be studied at many levels:
Morphology
Biochemistry
Genetics

2. Model systems for the study of development and differentiation and why they are studied:
Drosophila melanogaster (fruit fly)
Long tradition of study.
Lots of mutations affecting development identified.
Caenorhabditis elegans (nematode)
Genome is small (97 Mb)
# and lineage of body cells are known
Genetic crosses and selfings are easy
Body is transparent
Brachydanio rerio (zebrafish)
Embryos are transparent.
Large #s of fish can be bred.
Screening techniques are well-developed.
Arabidopsis thaliana (flowering plant)
Small, easy to cross and analyze large numbers of progeny.
Many developmental mutations identified.

3. Fruit Fly (Drosophila melanogaster)

4. Nematode
Caenorhabditis elegans
Fig. 19.2
Showing development from the two-cell stage to the adult.

5. Fig. 19.4, Zebrafish (Brachydanio rerio)

6. Fig. 19.3, Arabidopsis thaliana

7. Genetic regulation of development in Drosophila:
Fig ,
Developmental stages of Drosophila
(10-12 days)
Egg 
Larva (3 instars)
Pupa
Adult

8. Drosophila lifecycle similar to other flies like mosquitos:

9. Embryonic development in Drosophila:
Development begins with fertilization.
Prior to fertilization, molecular gradients exist within the eggs. Polar cytoplasm occurs at the posterior end---example of maternal effect.
2 nuclei fuse after fertilization to form a zygote.
9 mitotic divisions occur without cell division, and after 7 divisions, some nuclei migrate to the polar cytoplasm (posterior) creating germ-line precursors.
Other nuclei migrate to the cell surface and form blastoderm precursor.
4 more mitotic divisions occur and all nuclei are separated by cell membranes.

10. Fig. 19.19, Embryonic development in Drosophila.

11. Subsequent development depends on two processes:
Anterior-posterior and dorsal-ventral molecular gradients exist in the egg---mRNAs and proteins placed in egg by mother confer maternal effect.
Formation of (1) parasegments and (2)embryonic segments, which give rise to (3) adult segments.
Fig ,
Adult segmentation reflect
Embryo segmentation

12. Three major classes of genes control development and differentation
*Mutations identified by presence lethal or abnormal structures during development.
Maternal effect genes
Segmentation genes
Homeotic genes

13. 1. Maternal effect genes
Expressed by the mother during egg production; they control polarity of the egg and the thus embryo.
bicoid gene
Regulates formation of anterior structures (mutants possess posterior structures at each end).
Gene is transcribed during egg production, and expressed after fertilization.
nanos gene
Regulates abdomen formation (mRNAs collect in posterior of the egg).
torso gene
Transcription and translation occur during egg production.
Occurs throughout the eggs, but is only active at the poles.

14. Fig
Distribution of bicoid mRNA and protein in the egg
A = Anterior
P = Posterior

15. 2. Segmentation genes:
Determine the segments of the embryo and adult, and thus divide the embryo into regions that correspond to the adult segmentation patterns.
Gap genes
Subdivide the embryo along the anterior-posterior axis.
Mutation results in the deletion of several adjacent segments.
Pair rule genes
Divide the the embryo into regions, each containing parasegments.
Mutations cause deletions of the same part of a pattern in every other segment.
Segment polarity genes
Determine regions that become segments of larvae and adults
Mutants possess parts of segments replaced by mirror images of adjacent half segments.

16. Fig. 19.25, Functions for segmentation genes defined by mutations.

17. 3. Homeotic genes:
Homeotic genes specify the body part to develop at each segment.
Adult body parts develop from undifferentiated larval tissues called imaginal discs.
Homeotic mutants develop a different body part at a particular segment (imaginal disc) than the usual body part.
Different homeotic gene groups share similar sequences of ~180 bp called homeoboxes that code proteins.
Homeoboxes regulate development and produce proteins that bind upstream of the gene units.
Homeotic gene complexes are abbreviated Hox.
Hox genes also specify body plans in vertebrates and plants.

18. Fig. 19.21, Locations of homologous imaginal discs in larva and adult.

19. Fig
Examples of homeotic Drosophila mutant with the bithorax mutation
What is wrong with one of
these flies?

20. Fig , 2nd edition
Antennapedia and aristapedia mutants

22. Fig. 19.1, Second set of eyes in place of antennae:

23. Fig ,
Organization of bithorax homeotic genes in a 300kb region of the Drosophila genome.
T = thoracic
A = abdominal

24. Fig
Homologous Hox gene clusters occur in Drosophila and the mouse.

25. How do development biologists study differential expression of genes during development and differentiation?
Immunofluorescene assays that bind to specific mRNAs and proteins.

26. How do development biologists study differential expression of genes during development and differentiation?
Quantitative real-time RT-PCR of cDNA from mRNA transcripts.

27. RNA-Seq

28. Ribosome Profiling – sequencing of ribosome-bound mRNAs

29. How do development biologists study differential expression of genes during development and differentiation?
Gene knockout using transformation or transduction, or other gene silencing techniques like RNAi.

30.
RISC = RNA-induced silencing complex