Biology 441, Spring 2013 Review for Third Hour Exam
"The question of how patterns originate is the Gordian Knot of Developmental Biology."
Review for Third Exam in Embryology
You will be responsible for all the photographs and drawings on the web pages for this part of the course.
That means you should be able to describe what is shown ("This is a cross section of the head of a rhinoceros, and the blue object on the left is Rathke's Pocket" That sort of thing.)
The focus will be on causation of anatomical shapes. which includes different kinds of mechanical forces, the importance of tensors, scalars, curvature, stress, elastic resistance, the use of finite element computer simulations to understand relations of forces to shapes.
Reaction-Diffusion chemical reactions, and including some about mechano-chemical cause of anatomy.
Regeneration of limb buds, especially in newts and salamanders, but also John Saunders' research on branching of chicken wing buds.
Branching of regenerating limb buds, caused by cutting off the tip and grafting it back on with the anterior posterior axis reversed (or with the dorso-ventral axis reversed). (You should know what happens in each case).
What is the distinction between morphallactic regeneration and epimorphosis ?
A joke that you don't need to think is funny or laugh at, but which I hope you will enjoy.
"What is the difference between Hans Driesch's Entelechy and Lewis Wolpert's 'Positional Information'"?
1) What is the biochemical mechanism of programmed cell death?
2) List as many specific examples as you can of apoptosis.
3) How was genetic research on the nematode C. elegans essential for the discovery of the biochemical cause of apoptosis?
4) Why was it important that C. elegans coincidentally happens to have only one gene for a caspase, rather than 2 or more?
5) What are at least two connections between cancer and apoptosis?
6) What are meristems? Where are they located? In what kinds of organisms?
7) What is a cambium? What purpose does a cambium serve?
8) What geometric shape is a cambium? (hint: cylindrical)
9) What would a plant be unable to do if it didn't have any cambia? (=plural of cambium) (Latin second declension, neuter)
10) What is a "cork cambium"? Where is it located? What does it produce?
11) In plants, mitotic divisions are located where?
12) Are these the same places that growth (in the sense of increases in volume) is concentrated? (hint: no)
13) What function does osmotic pressure serve in plant growth?
14) How is plant cell growth related to weakening of cellulose cell walls?
15) Compare the "growth" (enlargement and shaping) of plant stems and leaves with that of cartilages.
16) What is an example of a plant hormone that can cause physical weakening of cell walls?
17) What is the difference between cell walls and cell membranes?
18) By what systematic series of experimental procedures was indole acetic acid eventually discovered to be (the, until then hypothetical substance) "auxin"?
19) Besides stimulating elongation of shoots, what other effects has auxin also been discovered to stimulate?
20) Invent and describe in some detail a bioassay by which auxin could have been discovered based on its ability to cause root formation?
21) Invent and describe in some detail a bioassay for discovering the chemical that causes phototaxis?
22) Invent and describe in some detail a bioassay for discovering the hormonal cause of geotaxis?
23) What are anti-auxin herbicides, like 2,4-D?
24) How were these (multi-billion dollar per year) herbicide chemicals discovered?
25* (opinion) If you were a judge in a patent dispute between the discoverer of auxin and the inventor of 2,4-D, who deserves the royalties more?
26)* (opinion) Depending on the outcome of such a patent lawsuit, on what efforts would (will) chemical companies concentrate their funding?
27) *Based on auxin's different effects on plant cell enlargement and differentiation, would you expect Lewis Wolpert to regard auxin as a morphogen?
28) Invent a bioassay capable (in principle) of discovering a morphogen that controls the differentiation of embryonic cells to form the pattern of the French flag?
26) Contrast the bioassay method with the genetic screen method for discovering chemicals like auxin.
In other words, could the chemistry of auxin have been discovered by isolating and studying mutant plants that produced less than the usual amount of auxin, or more than the usual amount, or had effects on cells' sensitivity to auxin? (*) If auxin had been discovered by the genetic screen approach, suggest what sort of name would have been chosen for it (instead of auxin).
27) Why is ripening of apples and other fruits often stimulated by enclosing them in gas-tight containers that also contain fruits that have already ripened?
28) Explain how the chemical cause of ripening could, in principle, have been discovered either by means of a bioassay, or by genetic screens (searching for mutant apples with altered control of ripening).
The following 5 questions are not easy, but you will gain a lot from thinking carefully about them.
29**) Invent a bioassay capable of proving that some specific anatomical pattern (somite formation, or feather location, for examples) is caused by the Turing chemical instability that you learned about.
30**) Explain how the bioassay approach could be used to discover which specific chemicals serve the roles of "A" and "B".
31**) If you already had, in relatively pure form, a chemical that you thought might be what I called "A" in such a Turing mechanism for generating spatial patterns (= breaking displacement symmetry), please invent some experiments to test whether your substance really is "A".
33**) Similarly, design and explain experiments to test whether a given substance plays the role of substance "B".
34**) What would be the expected phenotype (visible effect) of mutations in genes that alter the rates of synthesis of substances A and B, that cause formation of spatial patterns by a Turing mechanism?
35**) Argue in favor or against what the textbook concludes about stripe color patterns in certain fish, as evidence that these stripes are caused by the sort of mechanism invented by Turing. i.e. that Turing mechanisms can't explain most anatomical patterns because Turing can't easily explain what Driesch discovered; but the stripes in the skins of this kind of fish stay the same size as the fish grow, and more stripes form. [This was proposed in the original Nature paper that described the color pattern in these fish.]
Some of the following are scalar variables, some are vectors, some are second order tensors, and one is a fourth order tensor. Which is which?
37) Electroosmotic pressure
38) Curvature of a surface.
39) Concentration of a chemical click for answer
40) Tension in a sheet or block of material click for answer
41) Temperature. click for answer
42) Stiffness of a material (how much force is needed to produce how much distortion) Sometimes called "elasticity", but elasticity can have another meaning. (The property that is really large in steel and small in rubber) click for answer
43) Electric field click for answer
45) By what experimental method were these facts determined in the 1920s and 1930s?
46) Describe the shape and location of the apical ectodermal ridge.
47) What happens to leg, arm or wing development if the apical ectodermal ridge is surgically removed early in embryonic development?
* Salamanders are the only kind of vertebrate that can regenerate their legs, even after total amputation, and they are also the only kind of vertebrate that does NOT have an apical ectodermal ridge during embryonic development. (not counting snakes! which don't form limb buds at all).
Try to invent a hypothesis to make sense of this fact (not AER, but much better regeneration by salamander legs), and/or suggest medical uses of this hypothesis, if it turned out to be true.
What happens in limb development if tissue is grafted from just behind the limb bud to just in front of the limb bud?
48) By what surgical operation can a leg or wing bud be caused to branch and produce the equivalent of three hands?
49) By what surgical operation did John Saunders cause chicken wing buds to graft into four wing tips, instead of three?
50) In what sense is the triple branching of a reversed limb bud analogous to ordinary wound healing and regeneration? (Hint: remember what I said about cells responding to being surgically moved to a location adjacent to other tissues that they are not normally in contact with?)
51**) Can you think of some way to make sense of the quadruple branching of chicken wing tips, that John Saunders produced? A good, creative answer to this will impress me very favorably. So please think about this for a few minutes, with your fresh, unbiased minds.
52) Explain why chemical analogs of morphogens ought to be very powerful "teratogens". (A "teratogen" is a chemical that causes birth defects)
53) For what two geometric shapes is the curvature of the surface the same in every direction?
54) If epithelial sheets of cells bend or fold themselves so as to make curvature zero in one direction or axis (e.g. the north-south diction or axis), but make it constant in the direction perpendicular to the direction in which curvature is zero, then what shape will these cells arrange themselves into?
55) In the preceding question, what geometric property of this arrangement of cells will change if their curvature becomes larger?
56) What geometric property of this arrangement of cells will change if their curvature become smaller?
57) If this arrangement of cells contains a liquid under pressure, how will the tension in the sheet of cells change, if at all, if the curvature in the cell sheet becomes larger?
58) If the tension becomes smaller, then what change will be produced in the enclosed liquid?
59) What simple equation relates the physical variables tension, curvature and pressure (in the sense of difference of pressure on one side of a surface as compared with the other
60) How can you explain the bulging lobes of the brain as being caused by changes in tension in different parts of the neural tube
61) Why can't you explain the bulges as being caused by differences in pressure in one part of the neural tube as compared with another part? (hint, it's not hard; don't be tricked by simplicity)
61) (hint) Are there any parts of the neural tube in which the tension is stronger in one direction than another. 62) How would its shape change if the tension in the stronger direction (along a tube enclosing a liquid under pressure) weakened so as to become the same as the tension in the stronger direction?
63) Would this change be the same for a blood vessel as for the neural tube? (hint, yes)
64) By what changes in directionality (meaning variations of a property with direction) of tension of the cells of the neural tube are the lobes of the brain created?
65)* Could these inflated lobes be produced (and explained) by a change in the amount of tension (if it were a scalar)? Or could lobes be explained by changes in the directionality of tension? (hint: becoming the same in all directions)
66) If tension were the same in all directions (e.g. if tension were a scalar variable) then could blood vessels, cylindrical ducts, and neural tubes exist (without bulges)?
67) What are the key differences between scalar variables as compared with tensor variables?
68) What are at least two physical variables that are second order tensors? (permeability through soil or a matrix, is also a second order tensor, by the way. Drillers of oil and water wells realize this, even if most people don't.)
69) Elastic resistance to stretching is a fourth order tensor, true or false.
70) Explain whether and how a researcher will be mislead if he/she tries to measure the elastic resistance to stretching of a cell surface, or a blastula's surface, or the surface of an artery or a capillary, using a suction pipette, or indenting it with an atomic force microscope. Discuss the confusion that will result.
71)* More generally, discuss confusions that result from biologists not realizing that some variables are tensors, and assuming that all variables are either scalars or vectors.
72) The cornea of the eyeball bulges out (in such a way as to help the lens focus light on the retina): This is equivalent to saying that it has what difference in curvature from the rest of the eyeball.
73) In order to form this outward bulge, what difference in tension is necessary (and sufficient)?
74) Why can't the bulge be produced by increasing the outward pressure at that point? (hint: because the fluid gel inflating the eyeball behaves equivalently to how liquids behave)
75)* Astigmatism of the focusing power of the cornea implies what differences in the directionality of tension and curvature in the cornea?
76) Conversely, what differences in geometry and tension produce astigmatism?
77) If curvature were a scalar variable, then would astigmatism be possible?
78) If tension were a scalar variable, then would astigmatism be possible?
79) Invent a new kind of cure for astigmatism, using a local drug treatment that weakens or strengthens cell contractility. (*Discuss the difficulties of producing directional changes in tension.)
80) If a person's cornea bulges outward with too great a curvature, what effect will that have on their vision?
81) Consider whether this problem might be cured by weakening the tension in the cornea (which is made mostly of collagen fibers, and also some cells.)
82) Most anti-microtubule drugs (colchicine, vinblastine) cause at least temporary strengthening of cell traction forces that pull on collagen. Therefore, what effect should these drugs have on the shape of the cornea?
Lasik surgery works by changing the shape of people's corneas by cutting away parts of the cornea, so as to change the curvature of the cornea. It used to be done mechanically, with the equivalent of a lathe; now it is done with a laser beam.
84)* Discuss how you would need to change the shape (curvature) of a patient's cornea in order to weaken excessively strong focusing of light.
85)* Conversely, how would you need to change the curvature in order to make the cornea focus light more strongly?
86) Although the cornea becomes much less flexible after embryonic development (so that tension no longer has as much effect on curvature) please discuss how changes in tension in the cornea could possibly be used instead of lasic surgery.
87) Weakening the tension in the wall of a capillary or an artery would have what effect on its diameter?
88) Increasing the diameter of a capillary or artery would have what effect on its tension in its wall?
89) Increasing the pressure of the blood of a capillary or artery would have what effect on its tension in its wall?
90) Severe mutations in the gene for type I collagen cause death of developing embryos by bursting of capillaries and arteries: explain whether or why this makes sense.
91) When part of an artery balloons into an abnormal bulge, how does that change the curvature and the tension of that part of the artery wall?
92)* Please consider how this produces a positive feedback (i.e. between changes in curvature and changes in tension).
93)** Figure out what shape is needed for the graph of length (on the horizontal X axis) versus tension (plotted on the vertical Y axis), in order to prevent or minimize aneurisms.
94) If the graph of stress versus strain (i.e. length versus length) were a straight line, what would happen, and why?
95) If tensions were a scalar variable, could blood vessels exist?
96) In order to cause the rudiments of salivary glands, lungs, kidney tubules etc. to evaginate outward from the wall of the archenteron (= the endodermal tube), then what changes in tension & contractility need to occur in the epithelial wall of the archenteron?
97) In order for new capillaries to bulge and branch off from the wall of an existing blood vessel, discuss what changes in the amounts and directionality of tension need to occur.
98) What changes in tension will cause an artery or capillary to decrease its diameter and eventually pinch off?
99) Budding in Hydra requires (involves; is caused by) what changes in the curvatures of its surface (both the amounts and the directionality of the curvatures of its surface)?
100) Budding of Hydra needs what changes of directionality and/or amount of contractile tension in the body wall? (assume there is some fluid pressure in the interior "gastrovascular cavity", on the average, but that at no time does this inner pressure change from one location to another).
101) Again, in Hydras, compare the curvature of the surface of the tentacles versus the curvature of the main body of the Hydra.
102)* As tentacles form and elongate by rearrangements and reorientations of body wall cells, what changes in either the amounts or directionality, or both, need to occur? (assuming, as before, that there is some fluid pressure in the enclosed cavity)
103) If you graft a salamander limb bud from one side to the other, so that either the anterior-posterior axis or the dorso-ventral axis is reversed, then what very dramatic structural reorganization can often occur?
104) Using two diffusible substances, "A" and "B", what rules could they obey that would generate a regular spatial pattern?
Substance "A" causes an increase in its own concentration, and also in the concentration of B, while the effect of B is to reduce the concentration of both A and B; and B diffuses faster than A (or in any way produces its effect at longer range than A.
You have seen the computer produce these patterns, and I hope that you will be able to sketch those patterns.
105) How can you cause the peaks in concentration to be closer together? (Increase the ratio of the diffusion constants of B and A. The faster B diffuses, relative to A, the narrower the bands and gaps.)
PLEASE DO NOT waste your time memorizing Turing's excessively complicated set of equations,
even though we put them on the web page.
Probably it is worth concluding that lots of different equations will produce patterns. It is interesting to me that Turing failed to find the more general equations (which I adapted from a book by Prof. John Maynard Smith) This is a good example of making things as simple as possible.
106) What are Liesegang rings; how are they formed; and what do the look like?
107) What are the distinctive banding patterns of copperheads?
108) What is the distinction between prepatterns versus positional information?
109) Were reaction-diffusion systems invented as a possible method for generating pre-patterns? Hint: Sure, that's the point.
110) Please notice that advocates of positional information criticize reaction-diffusion systems for the reason that they don't predict "regulation", in the sense that Driesch discovered. E.g. a half-sized animal wouldn't produce the same number of half-sized stripes or spots.
111) Please also notice the page from the research paper by me, Stopak and Warner, in which the key point is that the "Morphogen" variables "A" and "B" need not be chemical concentrations. They could be any variable that either spread or produces effects at a distance. "A" could be the population density of one cell type and "B" could be the population density of some other cell type; and cell type A could crawl slower. Alternatively "A" could be the local concentration of collagen and "B" could be mechanical tension.
In the long run, the goal should be to figure out how real patterns are actually caused; but it sure is a lot of fun to play around with computers, testing different combinations of rules and diffusion rates! A very good PhD student in the UNC Computer Science Department (Greg Turk) did his PhD thesis on this subject, and is now a professor at Georgia Tech.
This concludes the list of review questions.
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