Dr. Curtis Loer, SCST 437, 260-4129
Eddress: cloer at sandiego dot edu [spam-blocked address]
Lecture: Mon/Wed/Fri, 8:55 - 9:50, SCST 261
Lab: Wednesday, 2:20 - 6:20, SCST 330
Office Hours: Mon 1:30-3:30, Tues 8:30-10:30, Thurs 11-12 or by appointment.
Email is also an excellent way to get a quick response.
Course Home Page: www.sandiego.edu/~cloer/bio376.html
This is a good place to check for announcements and handouts.
Main text (required) - Developmental Biology, 7th Edition. Author - Scott Gilbert. Sinauer Associates, 2003. Note the text includes the CD-ROM Vade Mecum. (Textbook Home Page: www.devbio.com)
Items on reserve -
Analysis of Biological Development. Klaus Kalthoff. McGraw-Hill, 1996.
Excerpts from An Introduction to Molecular Neurobiology. Zach Hall, editor. Sinauer Associates, 1992.
Excerpt from Introduction to Neurobiology. Heinrich Reichert. Oxford University Press, 1992. (Ch. 7 - Development)
Required for laboratory -
Atlas of Descriptive Embryology, 5th Ed. Mathews & Schoenwolf. Macmillan/Collier, 1999.
Animal Development Laboratory Manual. C. Loer, 2004 (this will be sold by the department).
(See below or in the laboratory syllabus for additional lab supplies.)
Goals of the Course
Students will become familiar with patterns and mechanisms of animal development, with an emphasis on model organisms such as C. elegans, Drosophila, Xenopus, chick and mouse. A central theme will be the examination of development as a phenomenon of differential gene regulation. Stages of embryogenesis, morphogenesis, pattern formation and differentiation of developing organisms will be examined. Developmental mechanisms, especially at a molecular level, will be examined for differences and commonality among organisms. The relationships between developmental mechanisms and the molecular genetic basis of human disease will also be examined and discussed.
Course Mechanics
Attendance at all lectures is strongly recommended, but not required, except in cases noted below. In order to keep a record of attendance, however, I ask that students initial an attendance sheet at the beginning of each class. Students who miss more than a few lectures often do poorly in class; such students will find little sympathy for their plight. For any missed lecture, a student should consult a fellow student for notes. The instructor will gladly provide any printed material handed out, but not a repeat of material presented in lecture. Please note that attendance at class presentations/discussions is required. Four weekly sessions are scheduled during the Wednesday lecture time beginning November 17. Attendance at any guest lectures is also required.
Missed quizzes or tests may be made up only for excused absences (e.g., sickness). Students should inform the instructor of the reason for their absence as soon as possible. Note also that grades on problem sets, papers or lab reports turned in late will be severely reduced except for excused absences.
Attendance at all laboratory sessions is required. If you miss a lab for a legitimate reason (e.g., sickness) you may have an opportunity to make it up later; however, if that lab session uses living material, this may be impossible. Some other form of makeup may be arranged.
Tests and Grading
There will be two hourly tests during the semester covering the material in lectures preceding them. Each will count for 20% of your grade. The final exam will cover mainly previously untested material and also counts for 20% of your grade. The lab portion of the class will be 25% of your final grade (see the lab syllabus for more specifics). Your class presentation and participation will count for a total of 13%. Work done for the class home page will count for 2% of your grade. More details will follow on class presentations and home page work. For breakdown on lab grade, see lab syllabus in the lab manual.
Tests will strongly emphasize lecture material. Assigned readings contain more material than will be covered in lecture. The quality of your writing on exams is important. Your answer to a question must be clear (and legible) to be correct. Spelling must also be correct, especially of new words you are adding to your biological vocabulary.
Grading Summary:
| 1st hourly test | 20% | Class presentation | 10% |
| 2nd hourly test | 20% | Discussion participation/reviewing | 3% |
| Final (3rd hourly) | 20% | Home Page work | 2% |
| Lab | 25% |
Academic Integrity
Please note that the text of all lab reports and papers must also be submitted electronically
via the appropriate web submission form to become a part of a searchable electronic database.
(Be sure to submit a regular paper copy for grading purposes.) Copying of any material from former Biology 376
students is plagiarism and will not be tolerated. Do your own work and demand that others do theirs. Take similar
care in your use of material from the class lab manual and the textbook. All portions of lab reports and papers
are expected to reflect ONLY your own work and your own writing. When working in groups, each member of the group
is expected to synthesize the information, analyze data and prepare an individual report. If you use literature in
your report, cite it appropriately. [For example, copying sentences from the book, followed by a parenthetical
citation (Gilbert, 2000), is plagiarism.] Be sure you understand what constitutes plagiarism. If you have
any questions about this, or any other item related to academic integrity, please ask. USD Academic Integrity
policy will be strictly enforced. [Report/Paper database submission form]
Provisional Lecture Schedule
Unless stated otherwise, readings are from Gilbert, Developmental Biology, 6th Edition.
| Sept. 3 | Introduction to animal development. Course mechanics. The questions and approaches of developmental biology. Reading: pp. 3-30. |
| Sept. 6 | Labor Day Holiday |
| Sept. 8 | Development of unicellular organisms. Metazoan developmental patterns. Reading: pp. 31-47. View Vade Mecum CD-ROM, section on slime molds. Video: Dictyostelium development |
|
Sept. 10 8:40 AM |
Class begins 8:40. Fertilization I. Gamete structure, gamete recognition, sperm activation and capacitation, acrosomal reaction. Reading: pp. 183-197. |
| Sept. 13 | Fertilization II. Gamete fusion, blocks to polyspermy, cortical reaction, egg activation, cytoplasmic rearrangements. Reading: pp 197-213. Add/Drop Deadline |
| Sept. 15 | Cleavage: Patterns of metazoan cleavage, cell cycle regulation, cytoskeletal mechanisms of karyokinesis and cytokinesis. Reading: pp 221-225. |
| Sept. 17 | Gastrulation: Types of cell movement, creation of primary cell layers. Axis formation. Sea urchin and tunicate early development. Reading: pp 226-239. Video: Sea urchin early development |
| Sept. 20 | Amphibian early development: cleavage and gastrulation. Reading: pp 305-317. |
| Sept. 22 | Amniote early development: fish, birds & mammals. Reading: pp 345-360, 363-374. Video: zebrafish development, mammalian early development. |
| Sept. 24 | Vertebrate neurulation, neural crest. Reading: pp 391-400, 427-429. Video: Xenopus (frog), chick development |
| Sept. 27 | Mesodermal derivatives, myogenesis, heart formation. Endodermal derivatives. Extraembryonic membranes. Reading: 465-474, 491-497, 510-517. |
| Sept. 29 | Evidence for genomic equivalence, animal cloning, embryonic stem cells. Reading: pp 81-89, 708-711. |
| Note: Molecular biological techniques used to study developmental biology will be discussed as needed throughout the course. Students should read this section of the book (pp 92-105) and review it as needed to understand experiments using particular molecular techniques. | |
| Oct. 1 | Differential gene expression: transcriptional & post-transcriptional regulation. Dosage compensation and X-chromosome inactivation. Reading: pp 107-137. |
| Oct. 4 | First Hourly Exam |
| Oct. 6 | Drosophila development I. Early development and the maternal genes: determination of anterior-posterior polarity. Reading: pp 263-278. Video: Drosophila embryogenesis |
| Oct. 8 | Drosophila II. Zygotic genes: gap, pair-rule and segment polarity genes in anterior-posterior patterning. Homeotic selector genes (the homeotic complex/Hox genes). Reading: pp 278-290. |
| Oct. 11 | Drosophila III. Dorsal-ventral patterning. Reading: pp 290-298. |
| Oct. 13 | The Homeotic Complex/Hox genes: Conservation of anterior/posterior pattern formation, evolution via changes Hox gene number & expression. Reading: pp 377-380, 751-761. |
| Oct. 15 | Pattern formation in tetrapod limb. Reading: pp 523-538. |
| Oct. 18 | Mechanisms of cell specification. Experimental embryology. Reading: pp 56-76. Note: Molecules and signaling pathways involved in cell-cell communication will be discuss throughout the course (especially beginning here). Students should read Chapter 6 (pp. 143-175) now, and refer to it as needed for the details of specific molecular pathways discussed during class. |
| Oct. 20 | Autonomous and conditional cell specification in tunicate and nematode development. Reading: pp 246-257. VIDEO: Styela development, C. elegans development |
| Oct. 22 | Cell-cell interactions in vertebrate development: Spemann & Mangold and the "organizer," primary embryonic induction. Reading: pp 317-325. |
| Oct. 25 | Molecular mechanisms of vertebrate axis formation and primary embryonic induction. Reading: pp 325-338. |
| Oct. 27 | Induction at the single cell level: C. elegans vulva. Reading: pp 154-158. Kalthoff (on reserve) pp 607-612. |
| Oct. 29 | Lecture catch-up, review, etc. |
| Nov. 1 | Second Hourly Exam |
| Nov. 3 | Developmental Neurobiology I. Neurogenesis and patterning of vertebrate CNS. Reading: pp 401-407. Note: Reichert, Ch.7 is recommended as an excellent overview of developmental neurobiology lecture material. |
| Nov. 5 | Developmental Neurobiology II. Neurogenesis. Neural crest cell migration and specification. Reading: pp 429-442; Hall/Anderson (on reserve) pp. 369-372. |
| Nov. 8 | Developmental Neurobiology III. Axonal outgrowth and guidance. Reading: pp 410-412, 444-451. "Molecular Biology of Axon Guidance," Tessier-Lavigne & Goodman, 1996 (on reserve), especially pp 1123-4 (Introductory section) and pp 1130-31 (Conclusions). Also recommended: Hall/Patterson pp. 388-410. Video: Retinal growth cone migration and repulsion. |
| Nov. 10 | Developmental Neurobiology IV. Neuron-target interactions. Neurotrophic substances. Reading: pp 451-457. Hall/Patterson pp. 438-451. |
| Nov. 12 | Programmed cell death/apoptosis I. Roles of PCD in normal development, genetics of PCD in C. elegans. Reading: pp 538-540. Kalthoff pp. 603-607. |
| Nov. 15 | Programmed cell death/apoptosis II. Molecular mechanisms. pp. 164-166. |
| Nov. 17 | Class Presentations - Genes & Development (attendance required) |
| Nov. 19 | Lecture catch-up, etc. |
| Nov. 22 | Cancer and developmental biology I. Characteristics of transformed cells, causes of cancer. Reading: pp 621-622, 703-705. Kalthoff pp. 727-737. |
| Nov. 24 | Class Presentations - Genes & Development (attendance required) |
| Nov. 25-26 | Thanksgiving holiday |
| Nov. 29 | Cancer and developmental biology II. Molecular mechanisms, genetics of cancers. Reading: Gilbert website 5.6, 8.1, 9.2 |
| Dec. 1 | Class Presentations - Genes & Development (attendance required) |
| Dec. 3 | Cancer and developmental biology III |
| Dec. 6 | Evolution and development: a new synthesis. Reading: pp 751-780. |
| Dec. 8 | Class Presentations - Genes & Development (attendance required) |
| Dec. 10 | Evolution and development II |
| Dec. 13 | Lecture catch-up, review, etc. |
| Dec. 15 | Final Exam - 8:00 - 10:00 AM |
Preparation for lab always includes reading the appropriate sections of the class lab manual, and may include (as indicated below) viewing sections of the CD-ROM Vade Mecum (packaged with the main text).
| Sept. 8 |
Introduction to lab, safety, microscopy and measurements Reading: "How cells are studied: Microscopy," Alberts et al., Molecular Biology of the Cell, pp 143-148, on reserve. Vade Mecum CD-ROM, sections on microscopy and lab safety. Quiz before leaving lab |
| Sept. 15 |
Echinoderm Gametes, Fertilization and Cleavage Vade Mecum CD-ROM, section on Sea Urchin Lab report due in lab, Mon. Sept. 29 |
| Sept. 22 |
Frog Embryogenesis (prepared slides and whole embryos) Vade Mecum CD-ROM, section on Amphibian early development Quiz before leaving lab |
| Sept. 29 |
Chick Embryos I (prepared slides), begin serial section reconstruction project Vade Mecum CD-ROM, sections on chick development, histotechniques |
| Oct. 6 | Chick Embryos II (live embryos), continue reconstruction project |
| Oct. 13 | Lab Practical/Exam, 3D Reconstruction project due |
| Oct. 24 |
Begin Chick Teratogenesis experiments - Inject with teratogens ANOVA practice report due Oct. 27 in lab |
| Oct. 27 | Open eggs (Teratogenesis Expt), begin evaluation and staining |
| Nov. 3 |
Complete chick embryo histology and evaluation Lab report due in lab Wed., Nov. 10 |
| Nov. 10 |
Homeobox-Polymerase Chain Reaction week 1 DNA purification, set up reactions |
| Nov. 17 |
Homeobox-Polymerase Chain Reaction week 2 Agarose gel electrophoresis - analysis of PCR products. Quiz at beginning of class. Lab report due in lab, Wed., Dec. 1, 8:55 AM |
| Nov. 24 |
C. elegans developmental genetics and RNAi project Quiz likely (on supplemental reading for project lab) |
| Dec. 1 | C. elegans developmental genetics and RNAi project, continued |
| Dec. 8 |
Project lab wrap-up, etc. TBA (presentations?) Lab report due by 5 PM, Mon. Dec 13 |
Additional Lab Supplies needed