BIOL 69 Developmental Biology

Laboratory Schedule and Syllabus, Spring 2003
Thursdays 1:00-4:15
Instructor:
Professor Mary K. Montgomery

More Info @ Lecture Schedule and Syllabus, Spring 2003

 Week

  Date

 Lab

 Reading

 1

 Jan 29

Nematode Development: Meiosis
Concepts: meiosis, oogenesis, spermatogenesis, hermaphroditism
Techniques:
" Find It": DAPI staining and epifluorescence microscopy
Organism(s):
C. elegans

 Ch. 1, 2, 3 Tyler

hand-outs

 2

 Feb 5

Echinoid Fertilization and Development
Concepts:
fertilization, radial holoblastic cleavage
Techniques:
" Find It": dark-field and polarizing techniques in microscopy to view cilia and spicule skeleton; epifluorescence microscopy using DAPI and anti-tubulin antibody staining to view chromosomes and mitotic spindles
Organism(s):
sea urchin Arbacia punctulata

(continue observations over next few days)

 Ch. 6 Tyler

 hand-outs

 3

 Feb 12

 Echinoid Development Continued
Concepts:
axis formation, gastrulation, differentiation
Techniques: " Find It": histochemistry to view gut; formation of dauerblastula and exogastrulae
Organism(s): sea urchin Arbacia punctulata

(continue observations over next few days)

 hand-outs

 4

 Feb 19

Echinoid Development Continued
Concepts:
totipotency, regulative ability, environmental perturbation
Techniques: experiments with UV radiation and temperature
Organism(s): sea urchin Arbacia punctulata

 Ch. 7 Tyler

hand-outs

 5

 Feb 26

Zebrafish
Concepts: meroblastic cleavage, vertebrate development, transgenes
Techniques: " Find It": GFP transgene reporters
"Block It": morpholinos
Organism(s): teleost fish Danio rerio

(continue observations over next few days)

PAPER #1 DUE

  hand-outs

Nasevicius& Ekker paper

 6

 Mar 4

The Early Chick
Concepts: meroblastic cleavage, vertebrate development
Techniques: microdissection
Organism(s): chicken Gallus gallus

 

Ch. 9,10,11 Tyler

 7

  Mar 11

More Chick Development/ Cardia bifida
Concepts: organogenesis, developmental "windows", mosaic vs regulative development, in vitro
culture
Techniques: " Block It": microsurgery
Organism(s): chicken Gallus gallus


(view results of cardia bifida experiment over next 24-48 hrs)

 hand-outs

  8

 Mar 18

  Spring Break

 

  9

 Mar 25

Drosophila Development
Concepts:
axis specification; analysis of gene function (loss-of-function vs gain-of-function)
Techniques: " Find It": lacZ and gfp transgenic lines
"Block It": loss-of-function genetic mutants
"Move It": misexpression using heat shock-driven transgenes
Organism(s): fruitfly Drosophila melanogaster

PAPER #2 DUE

Ch. 8 Tyler

hand-outs

 10

 Apr 1

Regeneration

Concepts: stem cells, regeneration

Techniques: microdissection

Organism(s):   hydra and planaria

 Ch. 13 Tyler

Newmark paper

 11

 Apr 8

Developmental Symbiosis

Concepts: influence of microbiotic environment

Techniques: " Find It": measuring luminescence

Organism(s): sepiolid squid Euprymna scolopes and the luminescent bacterium Vibrio fischeri

 McFall-Ngai paper

 12

 Apr 15

Nematode Development
Concepts:
inheritance of maternal factors, asymmetric cleavage, autonomous specification
Techniques: " Block It": RNAi, laser ablation, blocking transcription
Organism(s): worms from the wild

(experiments and observations continued through following week)

PAPER #3 DUE

 hand-outs

 13

 Apr 22

Nematode Development Continued

 hand-outs

 14

 Apr 29

Wrap Up & Clean Up

PAPER #4 DUE ON 5/6

 

 


These labs have been designed to introduce you to many of the concepts of developmental biology and the various techniques and model organisms used to address questions in this currently exploding field. Each week we will cover methods that fall under one of three broad experimental approaches (referred to here as "Find It (Show It), Block It, Move It" experiments-- coined by Professor Dany Adams when she worked at Smith College). Find It experiments typically involve labeling of specific gene products, cell types or tissues. Development is a process by which the totipotent fertilized egg undergoes rounds of cell division followed by differentiation (i.e., cells become specicialized to perform specific functions). This process involves differential gene expression (i.e., muscle cells are different from neurons because the former express muscle-specific proteins that mediate contraction whereas neurons express neuron-specific proteins, e.g. neurotransmitters) as well as localized and global signaling events. Labeling or “find it” experiments allow the investigator to localize in the embryo where and when certain genes or cell types are expressed. This type of observational study is often used to establish a correlation between the presence of a gene product or cell type and a developmental event under study. To establish cause and effect more experimental approaches are needed. Blocking expression or activity of specific genes, cells, or tissues can show that they are necessary for a specific developmental process; these types of experiments are considered loss-of-function (i.e. "Block It ") experiments. An even more powerful approach is to show that a gene or cell's activity is sufficient to cause a developmental process to occur; the results of such experiments are referred to as gain-of-function evidence and are obtained by moving expression or activity to a time or place in the embryo when/where it would not normally be present ("Move It "). All three experimental approaches are necessary for an investigator to establish that a particular molecule, cell, or tissue is both necessary and sufficient to cause a downstream event: e.g., (1) Find It experiments might establish that a particular protein is present at the right place and time to affect the event; (2) Block It experiments might show that the event does not take place in the absence of the protein; and (3) Move It experiments might demonstrate that the protein will cause the event to occur at a time or place in which neither would normally be present/occur. Often labeling methods will be used to determine whether gene expression, cell fates, etc. have been altered by blocking or moving activity. If this hypothetical protein behaves as predicted in all three experiments, we can say that it is both necessary and sufficient to cause the event. It is not uncommon, however, to find that a product is necessary but not sufficient to cause a process to occur; more rarely, some products are sufficient but not necessary. Finally, a well-designed experiment includes all proper controls, and we will discuss and include during the course of the semester appropriate controls for all of our experiments.

I have designed the laboratory section of this course so that it correlates with the lecture material, presenting you with a cohesive approach to the study of developmental biology such that concepts are mutually reinforced by the lectures and labs. Although I have done my best to design labs that can be covered within a 3 hour time period, the reality is that organisms develop on their own timetables and real science is hard to do under such time constraints. Some of the most interesting and fun labs will require that you come back to make additional observations or finish an experiment at times later that day or week. As we are in Minnesota, this means there will be times when you will have to trudge back through the snow to peer down your microscope. In most cases, you will find your efforts well rewarded!

 

LAB PAPERS : You will be asked to write a total of four papers to be written in scientific format. Mary Tyler has a very good section on how to write a scientific paper in the 1st chapter of her Developmental Biology: A Guide for Experimental Study. I will also have some additional handouts on writing scientific papers. The format of your papers should strictly follow that of the journal Development . For each lab I will hand out one paper from the primary literature that is related to the work we are doing for that particular lab; each paper can serve as a starting point from which you can delve deeper into the subject at hand either for your own paper or simply your pleasure. Writing these papers should give you ideas about what you might want to do for an Independent Project. Equally important, you will get critical feedback from me that should allow you to improve your writing skills. Papers that miss the deadlines listed in the syllabus will be assessed a 10 point penalty for each day they are late (just like most libraries and credit card companies- unlike most granting and hiring agencies, which simply toss the proposal or job application in the trash if the deadline is missed)- so you can turn your papers in late but you will pay a price.

LAB NOTEBOOK : I will also ask that you keep a laboratory notebook. Keeping a lab notebook is an absolutely essential part of doing science. The better notes that you take, the easier it will be for you to write your papers, and the more you will get out of the laboratory section of this course. I will periodically review your notebooks throughout the semester and will then assess them near the end for a final grade. You should feel free to include illustrations, photographs, timelapse files, etc. in your notebook. I will also provide some data sheets that you should fill out and keep in your notebook; these sheets will help you to organize your notes and make writing your papers easier.

LAB PORTION OF GRADE (50% OF FINAL GRADE):

 ITEM

 DUE

 POSSIBLE POINTS

 Paper #1 (sea urchin development)

 2/26

 100

 Paper #2 (fish or chick development)

 3/25

 100

 Paper #3 (fly, squid, or regeneration)

 4/15

 100

 Paper #4 (nematode development) 

 5/6

 100

 Lab Notebook

 5/6

 100

  (See Lecture Syllabus for more details.)

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