Biol 358W Developmental Biology
Fall Semester 2004

URL: http://www.willamette.edu/~bstebbin/biol358w/sylfa2004.html

PROFESSOR'S CONTACT INFORMATION

Barbara Stebbins-Boaz, Ph.D., Office Olin 211, x6926, bstebbin@willamette.edu
Office Hr: TTh 12:40-1:40, or as arranged

 

CLASS MEETS

MWF AT 10:20-11:20 AM, Olin 214

LAB MEETS

M 1:50-4:50 PM OLIN 206, and as needed


Overview
This research methods course examines models, current research, and experimental approaches in animal development. It explores the basic principles that govern change through an animal's life span: growth, differentiation and morphogenesis. We will look at several vertebrate and invertebrate model systems. Though each has its idiosyncrasies, they display a remarkable degree of similarity that highlights their common evolutionary history.

As a writing centered course, writing is a key component of learning the material.

Goals
Students who take this course will gain understanding and expertise in the following areas:

1. The basic principles of developmental biology

2. Interpretation, discussion and oral and written presentation of primary literature

3. Effective use the Hatfield library resources and electronic databases for accessing specific information

4. Conceiving and writing an independent research proposal

5. Independent research using sound lab techniques and effective recording of lab experiences in a personal lab notebook

6. Presentation of research results in an oral presentation, a poster and final polished written manuscript

 

Required Materials
Textbook: Gilbert SF. 2003. Developmental Biology. 7th ed. Sunderland, MA: Sinauer Associates, Inc.

Laboratory notebook (I suggest a 3-ring binder with regular lined notebook paper so that you may add to it at will).

Expectations
Students are expected to attend all class and lab sessions prepared to learn. Should an unavoidable conflict arise such as illness or a death in the family, students should contact the professor. Students are responsible for getting class notes and must make up labs on their own time. Assigned reading should be done the day before the lecture. Always bring your lab notebook to lab and something to write with, preferably a pencil. The successful learner will ask questions when confused, in need of clarification or just plain curious.
Because this course is writing centered, students will have ample opportunity to develop and practice effective writing skills. However, plagiarism is unethical, unacceptable and will result in a costly penalty.

Disabilities
Students who need accommodation for a qualified disability must register with the Disability Office in Bishop Wellness Center.

 

EVALUATION

A 100-93%; A- 92-90%; B+ 89-87%; B 86-83%; B- 82-80%; C+ 79-77%; C 76-73%; C- 72-70%,
D+ 69-67%, D 66-63%; D- 62-60%; F <60%

Abstracts
 8 @ 10 pt 80 pt
Lab notebook
 75 pt 75 pt
Oral presentations
 2@ 25 pt 50 pt
Research proposal 75 pt 75 pt
Poster
 25 pt 25 pt
Final paper
100 pt
100 pt
Participation 25 pt 25 pt
Total
430 pt 

 

 

 

 

 

TENTATIVE SYLLABUS

Date Subject

Reading Assignment
(Gilbert or as noted)

W 9/01

Introductions
What is developmental biology?
What morphological, cellular and molecular events characterize the life cycle?

Lab 1: Set-up bark culture experiment for slime molds, fungi, cellular slime molds:Microscopy, recording of observations

 Ch 1-2

F 9/03

 Fertilization: cell-cell interactions, receptor-ligand complexes, signal transduction

 

 Ch 7

Lab 1
cont.

M 9/06

 NO CLASS: LABOR DAY  
W 9/08

Closer look at gametogenesis: spermatogenesis, oogenesis

Mitosis, meiosis,cellular differentiation, ultrastructure, gene expression

 Ch 19
F 9/10

Focus on oocyte maturation in the frog, Xenopus laevis

extra-cellular factors, hormonal induction, signaling pathways, regulation of gene expression by translation control

 Ch 19

Lab 2
Library Research (meet John Repplinger in library lobby on M 9/13 at 2 PM)

Review of translational control: gene expression during early development

M 9/13-
F 9/17

Research translational control during animal development: write mini literature review

No class meetings; Library meeting with John Repplinger (2 PM meet him in lobby of Hatfield Library)

Stebbins-Boaz presents research at 10th International Xenopus Meeting at the Marine Biological Labs in Woods Hole, Massachusetts

Lab 3
Xenopus oocytes: Isolation, microdissection, micro-injection and maturation

Make your own developmental tools

M 9/20

Beyond Fertilization: Cleavage and gastrulation in sea urchin

 Ch 8
W 9/22

Comparative analysis of cleavage and gastrulation in popular model systems:

vertebrates:frog, zebra fish, chick, mouse; invertebrates: Drosophila melanogaster(fruit fly), C. elegans (nematode)

 Ch 10, Ch 11, Ch 9, Ch 8
F 9/24

Journal Club
Vacquier VD, Moy GW. 1977. Isolation of bindin: the protein responsible for adhesion of sperm to sea urchin eggs. Proc Natl Acad Sci USA 74: 2456-2460.


Hafner et al. 1988. Wave of free calcium at fertilization in the sea urchin egg visualized with fura-2. Cell Motil Cytol 9:271-277.

Lab 4
Fertilization and embryogenesis in Xenopus:
In vitro fertilization and amplexus

Methods to identify specific proteins during development:
SDS-Polyacrylamide Gel Electrophoresis (SDS-PAGE) and Western Immunoblotting
Expression phosphorylated MAPK in immature and mature oocytes

(Observe prepared slides of chick embryogenesis independently)

M 9/27

Are embryonic cells different from each other?
Fate mapping, ablation, transplantation and recombination
Regulative vs mosaic models

Ch 1, Ch 3

 
W 9/29

Localized cytoplasmic determinants: Examples
In situ hybridization; immunohistochemistry, reporter genes

Review article

Mowry 2001.
F 10/01

Journal Club

Mowry K, Melton D. 1992. Vegetal messenger RNA localization directed by a 340-nt RNA sequence element in Xenopus oocytes. Science 255:991-994.

 

Lab 5
Western cont.

~ 72-96 hr Chick Embryos observe
Start Whole Mount protocol
M 10/04

Regulation of cell fate by differential gene expression:

transcription factors, chromatin modification, RNA processing, transport

 Ch 5
W 10/06

Drosophila Body Plan:

Differential gene expression at several levels: Example Bicoid

Ch 9

Review article on X-chromosome inactivation
F 10/08 Journal Club
Brown et al. 1992. The human XIST gene: analysis of a 17-kb inactive X-specific RNA that contains conserved repeats and is highly localized in the nucleus. Cell 71:527-42.		  

Lab 6

Whole mounts cont.: Stain

Planaria Regeneration

M 10/11

How do cells communicate to each other? Inductive mechanisms

Cell-cell interactions; secreted extracellular factors, morphogen gradients,signal transduction pathways

 Ch 3, Ch 6
W 10/13 cont. specific examples: lens development, axis formation in Xenopus; bone growth Ch 6,Ch 10
F 10/15

Journal Club
Deng C et al. 1996. Fibroblast growth factor receptor-3 is a negative regulator of bone growth. Cell 84: 911-921.

  

Lab 7
Whole Mounts cont.: dehydration, clearing and mounting

Planaria cont.

(Consider research ideas: discussions in one week)
M 10/18

Cell death as a developmental pathway: apoptosis

 

 Ch 6
W 10/20

Limb formation: example of growth, differentiation and apoptosis through secreted signaling proteins and differential gene expression

Ch 16
F 10/22 NO CLASS: MID-SEMESTER DAY

Lab 8

Individual meetings to discuss research topics

M 10/25

Metamorphosis

 Ch 18
W 10/27

Regeneration

 Ch 18
F 10/29 Journal Club
Boulet et al. 2004. The roles of Fgf4 and Fgf8 in limb bud initiation and outgrowth. Dev Biol 273: 361-72.
Lab 9
Independent Research
Due: Draft Proposals for Peer Review
M 11/01

Stem Cells: Adult, fetal, embryonic, therapeutic cloning

Atala et al. 2004. Tissue engineering and regenerative medicine concepts for clinical application. Rejuv Res 7(1): 15-31.

Ch 12, 21
W 11/03

Polished research proposal due

Journal Club
Dor et al. 2004. Adult pancreatic beta-cells are formed by self-duplication rather than by stem cell differentiation. Nature 429(6987) 41-46.

Commentary:Nature 429 (6987): 30-31 (2004)
F 11/05 Journal Club
Assady et al. 2001. Insulin production by human embryonic stem cells. Diabetes 50: 1691-1697.

Lab 10
Independent Research
M 11/08

Teratogens and Endocrine Disruptors

Reviews
Piesma A. 2004. Validation of alternative methods for developmental toxicity testing. Toxicol Lett 149:147-53.

Harvey andDarbre. 2004. Endocrine disruptor and human health: could oestrogenic chemicals in body care cosmetics adversely affect breast cancer incidnece in women? J Appl Toxicol 24(3): 167-76.

Toppari J. 2002. Environmental endocrine disruptors and disorders of sexual differnetiation. Semin Reprod Med 20(3): 305-12.

Steinhardt G. 2004. Endocrine disruption and hypospadias. Adv Exp Med Biol 545:203-215.

 Ch 22

W 11/10

Journal Club
Peng et al. 2004. A critical role of Pax6 in alcohol-induced fetal microcephaly. Neurobiol Dis. 16(2): 370-6.
F 11/12

Journal Club
Jelso et al. 2003. Gene expression patterns predict exposure to PCBs in developing Xenopus laevis tadpoles. Environ Mol Mutagen 42(1): 1-10.

Lab 11
Independent Research
M 11/15

Aging

Reviews
Kurz C. Tan M. 2004. Regulation of aging and innate immunity in C. elegans. Aging Cell 3(4):185-93

Ames B. 2004. Delaying the mitochondrial decay of aging. Ann NY Acad Sci 1019:406-11

Bower R, Atwood CS. 2004. Living and dying for sex. A theory of aging based on the metabolism of the cell cycle signaling by reproductive hormones. Gerontology 50:265-90.

Dufour E, Larsson N. 2004 Understanding aging: revealing order out of chaos. Biochem Bioohys Acta 1658:122-32.
W 11/17

Journal Club
Kenyon et al. 1993. A C elegans mutant that lives twice as long as wildtype. Nature 366:461-4

Comment: Nature 366:404-5 (1993)
F 11/19

Journal Club
Weindruch et al. 2001. Microarray profiling of gene expression in aging and its alteration by caloric restriction in mice. J Nutr 131:918S-923S.

Lab 12
Independent Research
M 11/22

Genomes, Proteomes and chip technology

W 11/24

 Format of Presentations: Talks and Posters
F 11/26 No Class: Thanksgiving Break

Lab 13
Independent Research
M 11/29

Peer review: Materials and Methods

W 12/01 Peer review: Results
F 12/03 Peer review: Introduction and Literature Cited

Lab 14
Developmental Biology Poster Session

M 12/06 Developmental Biology Research Symposium (4)

W 12/08

Developmental Biology Research Symposium (4)


F 12/10

 Developmental Biology Research Symposium (4)


F 12/17

 Due: Final research manuscript due noon Olin 211