Developmental Biology 3022 Spring 2006

Instructor: Alice Heicklen
Time: TR 1:10pm-2:25pm
Place: 253 Engineering Terrace
Dept.: Biological Sciences
Office: 744B Mudd Bldg.
Office Hours: Monday 10-11am
Phone: 212-854-5952
TA: Will Parks
Prerequisite: c2005/2006 or a comparable year of intro biology

A. Grades :

There will be 3 exams. The final is cumulative. You will also receive a grade for your in-class presentations and participation. The final grade will be distributed as follows:

Exam I = 200
Exam II = 200
Presentation = 200
Lead Discussion = 50
Participation = 50
Final = 300
1000 points total

B. Student Presentations :
Aim : Isolate the main points of an article. Methods for breaking down an article will be discussed.
Presentation : Each student will present an article to the class. The talks should be 10 minutes long with 5 minutes of discussion. Each student will turn in a 1-2 page summary (5 of the 20 points for the presentation) of the article they are presenting a week before they present and set up an appointment to discuss the main findings with the instructor.

C. Class Schedule/Readings
Topic Gilbert

1/17 Development Overview

Fate mapping Ch1: 3-14

Stem Cells/Cloning Ch4:81-91; Ch21:708-711


1/19 X-Chromosome Inactivation Ch5: 107-8; 123-7



1/24 Spermatogenesis Ch19: 628-646


Mammalian Menstrual Cycle

The Pill

IVF Ch21: 683-7; 693-4


1/26 Sex Determination in mammals Ch 17


1/31 Cytoplasmic Determinants Ch 19: 613-628

PGC Migration


2/2 Fertilization Ch7


2/7 Differentiation Ch3: 56-79





2/9 Presentation of Okamote et al. 2005


2/14 Exam I


2/16 Induction (Wnt, Vulva & lens) Ch6


Early Development/Cell Movements Ch8: 221-227


2/21 Sea Urchin Development Ch8:227-239

Deuterostomes/Protosomes Ch2: 44-47

2/23 Presentations I


2/28 Amphibian Development Ch2: 25-30; Ch10


3/2 Presentations II


3/7 Early Mammalian Development Ch11: 363-380


3/9 Presentations III


3/13-17 Spring Break


3/21 Fly Development Ch19: 637-8; Ch9


3/23 Presentation IV


3/28 Exam II


3/30 Evo Devo Ch23



4/4 Presentation V


4/6 Germ Layers

Heart Development Ch15: 491-500


4/11 Presentation VI


4/13 No Class


4/18 Presentation VII


4/20 Presentation VIII


4/25 Presentation IX


4/27 Presentation X


Cumulative Final Exam (including Research Articles)

Tuesday, May 9 th from 1:10-4:00pm

D. Article Summaries

Steps to Breaking down an article:

Novice : read introduction to get the background you need to get started. Go to results section.

Some experience : skip to the results section. Read this along with the accompanying figures. Determine what are the main findings in this article – this is obtained directly from the figures. If they want to claim to have determined something the proof must be in the figures or they have not really found it. Stating findings in the abstract aren’t enough they have to back it up with research. It is your job to figure out what they really proved by examing the figures. If you are lost go back and read the introduction or look up a specific method that is not clear on the internet.

Abstract : Read after you decide what the main points are and see if they obtained the same results. If they claim something that you didn’t, go back to the figures and see if this result is supported by data.

Methods : In general you can skip this section unless you are missing a specific detail about how they set up the experiment – you would realize this while you are reading the results section and would go to the methods section to look up the information you are missing.

Discussion : tells how the author integrated their findings with the known literature. Read this before write your 2 questions/article for class. It will help you think of questions and analyze the data.

The summary of the article you are presenting should include:

  • Background in bullet format to explain article to the class
  • 3 main findings (bullets: 1-2 sentences/finding)
  • Summary of 3 figures that support the main findings listed in 2 (avoid describing each subfigure – describe in words the point the figure conveys)

-The summary should not be a repeat of the abstract

-Student presentations should include all information in the summary but also include enough background to explain the article to the class. Discussion of the article will follow each lecture or each group of lectures and will be lead by a different student in the class.


E. Student Participation

All articles presented in class are required reading for the entire class. The more articles you read and analyze the easier it will get.

Each student will submit two questions regarding each article on the class before the article is presented. An additional copy with only the questions will be given to the students that will present during the next class period. These questions will be reviewed by the presenter(s) and used to organize their presentation.

Participation (50 points): Students will receive a grade on their participation during the article discussions.

Lead Discussion (50 points): Students will receive a grade on leading the discussion of an article discussion.


F. Required Books/Articles

  • Gilbert, Scott F. Developmental Biology, 7th Edition, 2003. Sinauer.
  • Wilmut, Schnieke, McWhir, Kind, and Campbell (1997) Viable offspring derived from fetal and adult mammalian cells. Nature 385: 810-813.


Recommended Books

  • Jonathan M.W. Slack, 2006, Essential Developmental Biology, second edition, Blackwell Publishing
  • S. Carroll, J. Grenier and S. Weatherbee, 2005, From DNA to Diversity second edition, Blackwell Publishing
  • Shirley J. Wright, 2005 A photographic Atlas of Developmental Biology, Morton Publishing Company


Helpful Books

  • Kalthoff, 1996 Analysis of Biological Development, McGraw-Hill
  • Wolpert, 1998 Principles of Development, Oxford University Press
  • Wilt & Hake, 2004 Principles of Developmental Biology, Norton
  • Alberts et al, 1994 Molecular Biology of the Cell, Third Edition, Garland


G. Readings Assignments: Papers for Lectures

The first article, Okamoto et al, will be presented in class, 2/9/06 , by the instructor. All students are required to read the paper prior to class and participate in class discussion.

Okamoto, Arnaud, Le Baccon, Otte, Disteche, Avner and Heard (2005) Evidence for de novo imprinted X-chromosome inactivation independent of meiotic inactivation in mice. Nature 438: 369-373 News & Reviews: Flintoft (2005) X inactivation: Imprinted inactivation: narrowing down the options. Nature Reviews Genetics 6: 875-877


H. Student Presentations

Presentations I: Chromatin Regulation

  • Nguyen & Disteche (2006) Dosage Compensation of the Active X Chromosome in Mammals. Nature Genetics 38: 47-53
  • Hao et al. (2005) Short Telomeres, Even in the Presence of Telomerase, Limit Tissue Renewal Capacity. Cell 123: 1121-1131

Review : Bekaert et al. (2004) Telomere Biology in Mammalian Germ Cells and During Development. Developmental Biology 274: 15-30

Presentation II:Determination of PGCs/Sex

  • Geijsen et al. (2004) Derivation of Embryonic Germ Cells and Male Gametes From Embryonic Stem Cells. Nature 427: 148-154
  • Dumstrei, Mennecke, and Raz (2004) Signaling pathways controlling primordial germ cell migration in zebrafish. Journal of Cell Science 117: 4787-4795

Review : Raz (2004) Guidance of primordial germ cell migration. Current Opinion in Cell Biology 16: 169-173

  • Sediko et al. (2004) SOX9 is Up-regulated by Transient Expression of SRY Specifically in Sertoli Precursor Cells. Developmental Biology 274: 271-279

Presentation III:Centrosomes

  • Shirato et al. (2005) Centrosome destined to decay in starfish oocyte. Development 133: 343-350
  • Januschke, Gervais, Gillet, Keryer, Bornens and Guichet (2005) The Centrosome-nucleus Complex and Microtubule Organization in the Drosophila oocyte. Development 133: 129-139

Presentation IV:Early Development 1

  • Angerer et al. (2005) SoxB1 Downregulation in Vegetal Lineages of Sea Urchin Embryos is Achieved by Both Transcriptional Repression and Selective Protein Turnover. Development 132(5): 999-1008
  • Croce et al. (2006) Frizzled5/8 is required in secondary mesenchyme cells to initiate archenteron invagination during sea urchin development. Development 133: 547-557
  • Kloc, Wilk, Vargas, Shirato, Bilinskia and Etkin (2005) Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus. Development 132: 3445-3457

Presentation V:Early Development 2

  • Birsoy, Kofron, Schaible, Wylie and Heasman (2005) Vg1 is an essential signaling molecule in Xenopus development. Development 133: 15-20
  • Gore et al. (2005) The zebrafish dorsal axis is apparent at the four-cell stage. Nature 438: 1030-1035 News & Views: Driever (2005) A Message to the Backside. Nature 438: 926-7

Presentation VI:Fly Axis Polarity

  • Steinhauser and Kalderon (2005) The RNA-binding protein Squid is required for the establishment of anteroposterior polarity in the Drosophila oocyte. Development 132: 5515-5525
  • Crank & Dostatni (2005) Bicoid Determines Sharp & Precise Target Gene Expression in the Drosophila Embryo. Curr. Biol. 15: 1888-1898

Presentation VII:Homeotic Gene Regulation/EvoDevo A

  • Galant, R. and Carroll S. B. 2002 Evolution of transcriptional repression domain in insect Hox protein. Nature 415: 910-914
  • Hittinger, Stern and Carroll (2005) Pleiotropic functions of a conserved insect-specific Hox peptide motif. Development 132: 5261-5270
  • Foronda, Estrada, Navas and Sanches-Herrero, et al. (2005) Requirement of abdominal-A and Abdominal-B in the development genitalia of Drosophila breaks the posterior downregulation rule. Development 133, 117-127 News & Reviews: Breaking the Hox posterior prevalence rule, Bradbury, Development 133

Presentation VIII: Cellular Memory Modules

  • Rank G., Prestel M. and Paro R. 2002 Transcription through intergenic chromosomal memory elements of the drosophila bithorax complex correlates with an epigenetic switch. Mol. Cell. Biol. 22(22): 8026-8034.
  • Bantignies F., Grimaud C., Lavrov S., Gabut M. and Cavalli G. 2003 Inheritance of polycomb-dependent chromosomal interactions in drosophila. Genes & Dev. 17: 2406-2420.

Presentation IX: Heart Regeneration

  • Poss, K. D., Wilson , L.G. and Keating et al. 2002 Heart Regeneration in zebrafish. Science 298: 2188-2190
  • Lanza R. et al. 2004 Regeneration of the infracted heart with stem cells derived by nuclear transplantation Circ. Res. 94: 820-827
  • Raya, Koth, Buscher, Kawakami, Itoh, Raya, Sternik, Tsai, Rodriguez-Esteban, Izpisua-Belmonte (2003) Activation of Notch signaling pathway precedes heart regeneration in zebrafish. PNAS (2003) 100 suppl 1: 11889-11895

Review : Solloway, M. J. and Harvey, R. P. 2003 Molecular pathways in myocardial development: a stem cell perspective. Cardiovascular Research 58: 264-277

Review : Cohen S. and Leor J. Rebuilding Broken Hearts Scientific American Nov. 2004 p45-51.

Presentation X: TGF b & Stem Cells

  • James, Levine, Besser and Hemmati-Brivanlou (2005) TGFβ/activin/nodal signaling is necessary for the maintenance of pluripotency in human embryonic stem cells, Development 132: 1273-1282
  • Levine and Brivanlou (2005) GDF3, a BMP inhibitor, regulates cell fate in stem cells and early embryos. Development 133: 209-216