Lecture: Mon/Wed/Fri, 8:55 - 9:50, Serra 317
Lab: Thurs, 2:20 - 6:20, Serra 106 (Sept. 13 - Oct. 18)/Serra 109 (Oct. 25 - Dec. 6)
Office Hours: Mon 1:30-3:30, Tues 9:30-11:30, Thurs 11-12 or by appointment.
Email is also an excellent way to get a quick response.
Course Home Page: www.sandiego.edu/~cloer/bio176.html
This is a good place to check for announcements and handouts.
Main text (required) - Developmental Biology, 6th Edition. Author - Scott Gilbert. Sinauer Associates, 2000. 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, 2001.
(See laboratory syllabus for additional information on required/recommended 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:
| First hourly test | 20% | Second hourly test | 20% |
| Final | 20% | Lab | 25% |
| Class presentation | 10% | Discussion participation/reviewing | 3% |
| Home Page work | 2% |
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 176 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. 4 | Introduction to animal development. Course mechanics. The questions and approaches of developmental biology. Reading: pp. 3-30. |
| Sept. 6 | Development of unicellular organisms. Metazoan developmental patterns. Reading: pp. 31-47. View Vade Mecum CD-ROM, section on slime molds. Video in class: Dictyostelium development |
| Sept. 9 | Fertilization I. Gamete structure, gamete recognition, sperm activation and capacitation, acrosomal reaction. Reading: pp. 185-199. |
| Sept. 11 | Fertilization II. Gamete fusion, blocks to polyspermy, cortical reaction, egg activation, cytoplasmic rearrangements. Reading: pp 199-216. |
|
Sept. 13 8:40 AM |
Class begins 8:40.Cleavage: Patterns of metazoan cleavage, cell cycle regulation, cytoskeletal mechanisms of karyokinesis and cytokinesis. Reading: pp 223-228. |
| Sept. 16 | Gastrulation: Types of cell movement, creation of primary cell layers. Axis formation. Sea urchin and tunicate early development. Reading: pp 228-241. Video: Sea urchin, Styela early development |
| Sept. 18 | Amphibian early development: cleavage and gastrulation. Reading: pp 303-314. |
| Sept. 20 | Amniote early development: fish, birds & mammals. Reading: pp 339-350, 354-364. Video: zebrafish development, mammalian early development. |
| Sept. 23 | Vertebrate neurulation, epidermis. Reading: pp 379-388, 403-407, 411-412. Video: Xenopus, chick development |
| Sept. 25 | Mesodermal derivatives, myogenesis, heart formation. Endodermal derivatives. Extraembryonic membranes. Reading: 447-454, 471-477, 490-497. |
| Sept. 27 | Evidence for genomic equivalence, animal cloning. Reading: pp 79-89. |
| 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 91-105) and review it as needed to understand experiments using particular molecular techniques. | |
| Sept. 30 | Differential gene expression: transcriptional & post-transcriptional regulation. Dosage compensation and X-chromosome inactivation. Reading: pp 109-138. |
| Oct. 2 | First Hourly Exam |
| Oct. 4 | Drosophila development I. Early development and the maternal genes: determination of anterior-posterior polarity. Reading: pp 263-277. Also recommended reading for Drosophila lectures: Kalthoff Chapter 21, pp 493-541.Video: Drosophila embryogenesis |
| Oct. 7 | Drosophila II. Zygotic genes: gap, pair-rule and segment polarity genes in anterior-posterior patterning. Reading: pp 278-285. |
| Oct. 9 | Drosophila III. Homeotic selector genes (the homeotic complex/Hox genes). Reading: pp 285-290. |
| Oct. 11 | Hox genes: Conservation of anterior/posterior pattern formation, evolution via changes Hox gene number & expression. Reading: pp 364-369, 679-689. |
| Oct. 14 | Pattern formation in tetrapod limb. Reading: pp 503-519. |
| Oct. 16 | Mechanisms of cell specification. Experimental embryology. Reading: pp 54-66. 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. 143-176) now, and refer to it as needed for the details of specific molecular pathways discussed during class. |
| Oct. 18 | Fall Holiday |
| Oct. 21 | Morphogenesis and cell adhesion. Reading: pp 66-75. |
| Oct. 23 | Autonomous and conditional cell specification in tunicate and nematode (C. elegans) development. Reading: pp 247-257. |
| Oct. 25 | Cell-cell interactions in vertebrate development: Spemann & Mangold and the "organizer," primary embryonic induction. Reading: pp 314-319. |
| Oct. 28 | Molecular mechanisms of vertebrate axis formation and primary embryonic induction. Reading: pp 319-335. |
| Oct. 30 | Induction at the single cell level: C. elegans vulva. Reading: pp 154-158. Kalthoff (on reserve) pp 607-612. |
| Nov. 1 | Lecture catch-up, review |
| Nov. 4 | Second Hourly Exam |
| Nov. 6 | Developmental Neurobiology I. Neurogenesis and patterning of vertebrate CNS. Reading: pp 386-395. Note: Reichert, Ch.7 is recommended as an excellent overview of developmental neurobiology lecture material. |
| Nov. 8 | Developmental Neurobiology II. Neurogenesis. Neural crest cell migration and specification. Reading: pp 413-419; Hall/Anderson (on reserve) pp. 369-372. |
| Nov. 11 | Developmental Neurobiology III. Axonal outgrowth and guidance. Reading: pp 425-439. "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. 13 | Developmental Neurobiology IV. Neuron-target interactions. Neurotrophic substances. Reading: pp 434-435. Hall/Patterson pp. 438-451. |
| Nov. 15 | Programmed cell death/apoptosis I. Roles of PCD in normal development, genetics of PCD in C. elegans. Reading: pp 517-518. Kalthoff pp. 603-607. |
| Nov. 18 | Programmed cell death/apoptosis II. Molecular mechanisms. pp. 165-166. |
| Nov. 20 | Class Presentations - Genes & Development (attendance required) |
| Nov. 22 | Cancer and developmental biology I. Characteristics of transformed cells, causes of cancer. Reading: pp 592-3. Kalthoff pp. 727-737. |
| Nov. 25 | Cancer and developmental biology II. Molecular mechanisms, genetics of cancers. Reading: Gilbert website 5.6, 8.1, 9.2 |
| Nov. 27 | Class Presentations - Genes & Development (attendance required) |
| Nov. 28-29 | Thanksgiving holiday |
| Dec. 2 | Cancer and developmental biology III |
| Dec. 4 | Class Presentations - Genes & Development (attendance required) |
| Dec. 6 | Evolution and development: a new synthesis. Reading: pp 679-706. |
| Dec. 9 | Evolution and development II |
| Dec. 11 | Class Presentations - Genes & Development (attendance required) |
| Dec. 13 | Lecture catch-up, review, etc. |
| Dec. 18 | 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).
In Serra 106
| Sept. 12 |
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. 19 |
Echinoderm Gametes, Fertilization and Cleavage Vade Mecum CD-ROM, section on Sea Urchin Lab report due in class, Wed. Sept. 25, 8:55 AM |
| Sept. 26 |
Frog Embryogenesis (prepared slides and whole embryos) Vade Mecum CD-ROM, section on Amphibian early development Quiz before leaving lab |
| Oct. 3 |
Chick Embryos I (prepared slides) Vade Mecum CD-ROM, sections on chick development, histotechniques |
| Oct. 10 | Chick Embryos II (live embryos) |
| Oct. 17 | Lab Practical/Exam 1 |
Lab moves to Serra 109
| Oct. 24 | Begin Chick Teratogenesis experiments - Inject with teratogens |
| Oct. 31 | Open eggs (Teratogenesis Expt), begin evaluation and staining |
| Nov. 7 |
Complete chick embryo histology and evaluation Lab report due in class, Wed., Nov. 13, 8:55 AM |
| Nov. 14 |
Homeobox-Polymerase Chain Reaction week 1 DNA purification, set up reactions |
| Nov. 21 |
Homeobox-Polymerase Chain Reaction week 2 Agarose gel electrophoresis - analysis of PCR products Lab report due in class, Wed., Dec. 4, 8:55 AM |
| Nov. 28 | Thanksgiving Holiday - No lab |
| Dec. 5 | C. elegans and reporter genes, week 1 - project TBA |
| Dec. 12 | C. elegans and reporter genes, week 2 - project TBA |
Format: Formal 8 - 10 minute oral presentation with about 2-4 minutes for questions and discussion. Given the short format, the talk must be very well prepared and rehearsed in advance so as to fit in the allotted time (including timed rehearsals). There will be no time at the beginning of class for last minute preparations; the first talk must begin promptly at 8:55. (A 12 minute maximum per person will be strictly enforced.) Presenters are encouraged to use appropriate overheads and/or provide handouts to augment their presentations. Please remember that your presentation represents 10% of your final grade.
Students will present a summary with appropriate background of a recent paper or few closely related papers from the scientific literature (no older than 1997). The paper(s) should be primary literature, not a review article. Beside introductory material and conclusions, the talk should present some specific key experiments found in the paper(s). This part of the presentation usually is centered around presentation and explanation of one or more key figures and/or tables from the paper(s). Although some basics of the topics may be covered in lectures leading up to the presentations, the student is encouraged to read all necessary and appropriate background in preparation for the presentation. It is likely that you may need to obtain some materials by visiting the UCSD Biomedical library. Directions can be found on the Biology 176 home page.
Students should select the paper and submit a copy no later than 3 weeks prior to the date of presentation for approval by the instructor. Students are strongly encouraged to discuss paper selection with the instructor as soon as possible. It may be useful to show me several possible paper selections. The final paper selection must be completed by 2 weeks prior to the presentation. Once a topic is selected, the student should schedule at least one session with me to discuss the paper and the background/context for the paper. [As most students have limited experience reading the primary literature, you will likely need help to prepare an excellent presentation. Students without such preparation may not be able to achieve a top grade on the presentation.] It may be helpful for you to provide me a full copy of the paper several days in advance of our meeting (if you have not already given it to me).
One week prior to presentation, materials to be added to the class home page must be given to me for posting (see "Read More About It" below). Also one week prior, copies of the paper must be provided to assigned student "reviewers" and the instructor. Reviewers are required to read the paper and expected to ask questions following the presentation that reflect their knowledge of the paper, and examine the web materials provided by the presenter in the week prior to the presentation. Reviewers will also fill out a brief evaluation of the presentation in question. Following presentations, all students (not just assigned reviewers) are encouraged to ask questions or make comments; one's participation here constitutes a portion of the "Discussion participation" grade.
Presenters for a given week may coordinate their talks to cover closely related topics if they wish. This can lend a coherence to the session that benefits everyone participating. Topics are listed by week below. By prior approval, a student may deviate from the suggested topics.
Presenter responsibilities:
Select paper in consultation with instructor
Provide web materials to instructor for posting
Distribute copies of paper to reviewers and instructor on selected day
Reviewer responsibilities:
Receive paper from presenter on selected day [note: if you miss class that day, it becomes your responsibility to get the paper from the presenter].
Read paper prior to presentation
Examine web materials provided by presenter
Ask questions following presentation
Materials on reserve
(These review articles, along with your text, may serve as starting points for literature searches. More may be added during the semester.)
The evolution of the Hox cluster: insights from outgroups. Finnerty & Martindale (1998) Current Opinion in Genetics & Development 8: 681-687.
Getting your Pax straight: Pax proteins in development and disease. Chi & Epstein (2000) Trends in Genetics 18: 41-47.
Neural cell adhesion molecule L1: relating disease to function. Kenwrick& Doherty (1998) Bioessays 8:668-675.
On the shoulders of giants: p63, p73 and the rise of p53. Yang et al. (2002) Trends in Genetics 18: 90-95.
All from: Current Opinion in Genetics & Development (Genetics of Disease), June 2002
Genetics of disease Web alert, Makalowska et al.
Genetics of disease - Surprises still in store, Gitschier & Zoghbi.
Dominantly inherited, non-coding microsatellite expansion disorders, Raum & Day.
The molecular bases of spinal muscular atrophy, Frugier et al.
Heart Development: learning from mistakes, McFadden & Olson.
Genetics of Parkinson's disease and biochemical studies of implicated gene products, Lansbury & Brice.
Muscular dystrophies involving the dystrophin-glycoprotein complex: an overview of current mouse models, Durbeej & Campbell.
From: Current Opinion in Genetics & Development (Oncogenes & cell proliferation), June 2002
Oncogenes and cell proliferation Web alert, Makalowska et al.
Oncogenes and cell proliferation - Update on the big C: complexity and cross-talk between pathways, Downward & Goff.
Regulation of G1 cell-cycle progression by oncogenes and tumor suppressor genes, Ho & Dowdy.
The role of p53 and pRB in apoptosis and cancer, Hickman et al.
The BRCA1/BARD1 heterodimer, a tumor suppressor complex with ubiquitin E3 ligase activity, Baer & Ludwig.
A 'lottery' will be held to determine priority for presentation date selection (date to be announced). Be sure not to miss class or arrive late on the appointed day. (Otherwise you go to the bottom of the list.) Note that Nov. 27 is the Wednesday immediately prior to Thanksgiving holiday. Attendance is nevertheless required.
Presentation Topics and Dates
A) 1 word/phrase and 1-2 sentence definition to go into the Bio 176 Glossary from the reading or lecture, or otherwise related to Developmental Biology. Definitions will be edited and included in the glossary. You may include other words you would like to see defined (this is optional). Your word must not already be defined in the Home Page glossary, unless it requires a different or additional definition for a different context. That means you must check the glossary prior to selecting a word and submitting it. The definition should be in your own words, not simply copied verbatim from another source.
B) A URL (web address) for a Developmental Biology link that has some relationship to the principal features of development or topic currently being covered in class - these will be added to Developmental Biology Links section of the Bio 176 Home Page. Please be sure to check there to make sure you are not submitting a link we already have (for example, not to something in the textbook website). You may find my web searching utility page useful in finding an interesting link.
WWW assignment due dates (due by 5 PM of the date indicated):
| Sept. 9 | Sept. 23 | Oct. 7 | Oct. 21 | Nov. 6 |
Format: a few paragraphs, up to the equivalent of about a page of text that succinctly explains the background, significance, and main points of your paper - in your own words. This should be understandable to anyone in the class and should NOT be a copy of the paper abstract (see below).
The text will be followed by a list of at least 5 related links. The first of these links must be to the PubMed abstract of the paper being presented. Additional links may include links to review articles (especially good if you can link to an accessible full-text article) that you used to help understand the materials, laboratory websites of the paper authors, lay information about subject (there may be many of these if a human disease is involved). Not all the additional links should be to related literature. Note: in collecting web addresses ("URLs"), beware of websites that use "Frames" - it may be difficult or impossible to create a link directly to the page of interest. Be sure to test your web addresses prior to submission to make sure they work.
Use one of three different methods for submitting your mini-webpage: