BCH 512: DEVELOPMENTAL GENOMICS - Week 4 - Sept. 22 & 24, 2015

Instructor:  Marc Halfon

E-mail: mshalfon@buffalo.edu

Topic: Segmentation and patterning in Drosophila


In the next few weeks, we'll use Drosophila to explore the general mechanisms of pattern formation during embryonic development. We'll look at early axis formation, segmentation, and establishment of segmental identity. At the end of these four weeks, you'll understand the basics of how an animal is built from a single cell into a multi-cellular organism with the right organs in the right places!


This week we'll discuss pattern formation in the anterior-posterior axis, using mainly a lecture format. In the successive weeks, we'll learn about dorsal-ventral patterning by reading in depth a series of the key papers that elucidated the process. It's important to make sure the reading is done thoroughly and on time.


The "recommended reading" chapters below can provide details and clarifications if the papers get confusing. Most of the lecture figures are drawn from these two sources, as well.


Note that unlike most of the other sections in this course, there is a paper or exercise assigned for ALMOST EVERY class. So make sure to look ahead at the assignments for each following week.


Assigned reading:


This paper should be read BEFORE the first class on Sept. 22.


Nusslein-Vohlhard and Wieschaus. (1980). Mutations affecting segment number and polarity in Drosophila. Nature  287:795.


A seminal paper in the history of developmental genetics describing work for which the authors were awarded the 1995 Nobel prize. We will go over the major findings both in their historical context and in light of what is known today.


This tutorial should be read by next Tuesday's class:


Roote, J., & Prokop, A. (2013). How to Design a Genetic Mating Scheme: A Basic Training Package for Drosophila Genetics. G3 (Bethesda, Md.), 3(2), 353–358. doi:10.1534/g3.112.004820 


A guide to Drosophila genetics: this will aid in understanding the papers we will be reading starting next week. You will need to read it to do the homework assignment (below)! Make sure to note your questions and any parts you don't understand to go over in class next Tuesday.



Homework for Tuesday 9/29:

Do "Task 3" from the "Crossing Tasks" problem set. This should be handed in by the beginning of class. It might be helpful to first work through this example first. Note that unlike the example, the assigned Task 3 is NOT a recombination task as the genes you are dealing with are on different chromosomes. This is actually simpler to carry out, but don't get confused by just blindly following the example in the ppt file!



Recommended reading:


Wolpert, Tickle, and Martinez Arias "Principles of Development," Chapter 2 (5th edition).

A very clear and up-to-date treatment of pattern formation in Drosophila.


Gilbert, "Developmental Biology (10th ed.)," Chapter 6.

A more in-depth treatment than that found in Wolpert; more detail than we'll cover in class, but worth the read.


Eric Wieschaus' Nobel lecture gives a more personal spin on the segmentation screens.



Slides and lecture notes will be posted here following class :


Web resources:


If the gene names and fly-speak in the paper are getting you confused, the Interactive Fly gives a nice synopsis of what many of these genes do and where they act in development.



The internet source for all things Drosophila is Flybase: http://flybase.bio.indiana.edu


Ever wonder how fly genes ended up with their often whimsical names? Try Flynome for etymologies of many genes, such as ken and barbie and seven up.    http://www.flynome.org/