Sample review questions for second exam:

You should be sure to know what subdivision of which germ layer each of the following develops from:

For example: Lens: develops from somatic ectoderm, more specifically from a placode.

    Pigmented retina: Develops from neural tube ectoderm.

    Sensory retina

    Olfactory nerves

    Semi-circular canals




    Spinal cord

    Skeletal muscles: Develop from myotomes of somites, paraxial mesoderm




    (Reptile) Scales

    Heart: Lateral plate mesoderm

    Adult kidney: Metanephros; posterior part of intermediate mesoderm

    Motor nerves: Neural tube ectoderm

    Sensory nerves: Neural crest ectoderm

    Schwann cells

    Postganglionic autonomic nerves: Neural crest ectoderm

    Facial Skeleton: Neural crest ectoderm

    Skeleton in the rest of the body: Sclerotome off somites, and also lateral plate mesoderm

    Pituitary gland: Partly from stomodeal, somatic ectoderm.

    Salivary glands: Most are endoderm; one pair may be stomodeal ectoderm.

    Thyroid gland: Endoderm

    Lungs: Endoderm (plus some mesodermal mesenchyme)

    Liver: Endoderm (plus some mesodermal mesenchyme)

    Pancreas: Endoderm (plus some mesodermal mesenchyme)

    Intestine: Endoderm (plus some mesodermal mesenchyme)

    Stomach: Endoderm (plus some mesodermal mesenchyme)

    Capillaries, veins, arteries: Mesoderm (mostly or all from lateral plate mesoderm)


What simple set of three rules that govern changes in the concentrations of two substances will cause spontaneous formation of wave-like spatial variations in the concentrations of the two substances?
Hint: which substance diffuses faster than the other substance?

The clock and wave-front hypothesis is another way of producing what?

If it is really true that cutting off the rear third of a chicken embryo during somite formation will cause the further somites (i.e. those formed after the cutting) to be smaller, how is this analogous to the phenomenon discovered by Driesch, and what theories can you propose to explain the mechanism that causes these later somites to be smaller?
(In terms of the Clock and Wave-front hypothesis? In terms of Turing's mechanism?)
(As analogous to Liesegang Rings?) In some other way?


More Review Questions for third 2012 exam (posted March 6th):

What are meristems? Where are they located? In what kinds of organisms?

What is a cambium? What purpose does a cambium serve?

What geometric shape is a cambium? (hint: cylindrical)

What would a plant be unable to do if it didn't have any cambia? (=plural of cambium) (Latin second declension, neuter)

What is a "cork cambium"? Where is it located? What does it produced?

In plants, mitotic divisions are located where?

Are these the same places that growth (in the sense of increases in volume) is concentrated? (hint: no)

What function does osmotic pressure serve in plant growth?

How is plant cell growth related to weakening of cellulose cell walls?

What is an example of a plant hormone that can cause physical weakening of cell walls?

What is the difference between cell walls and cell membranes?

What are sepals and petals? How are they related to the leaves of plants?

Are they similar to leaves?

What are stamens and carpels?

Historically, how did early German embryologists get the idea of germ layers in animal embryos, from studying flowers of plants?

Do homeotic mutations ever occur in plants?

What are some (reasonably specific) examples of phenotypic changes that are sometimes produced by homeotic mutants in plants?

What does a plant's flowers look like as the result of a homeotic mutation in which each petal, sepal etc. develops into an entire flower, all of whose sepals, petals, etc. ALSO try to develop into an entire flower?
Hint: It looks like the edible part of a certain vegetable?

In what sense does this edible part have dilation symmetry?

Imagine a mutation in starfish that would cause each of its five arms to try to develop into a whole starfish, and caused each of the 5 arms of these additional bodies themselves to develop 5 arms?

Imagine a mutation that caused the arms of pluteus larvae to bud off entire blastula-stage embryos? Compare the result with cauliflower!

(*) Imagine that Hans Driesch had been a geneticist, and had discovered such a homeotic mutation in sea urchin larvae (instead of what he really did discover), when would he have concluded that development is controlled by entelechies?

How many planes of reflection symmetry occur in the flowers of the plant Arabidopsis?
(based on the photographs and diagrams of these flowers in the textbook)

Do all flowers have more than one plane of reflection symmetry?
(Hints: no; look at the illustrations in the textbook)

What is "phyllotaxis"? What are two or three different patterns of phyllotaxis that occur in actual plants?

Between now and the time of the next exam, please notice as many examples of phyllotaxis as you can (in budding leaves and flowers), and be prepared to sketch 3 different examples on the next exam. (including either the name of the kind of plant, or a sketch of the plant, and its location)

By what systematic series of experimental procedures was indole acetic acid eventually discovered to be (the, until then hypothetical substance "auxin"?

Besides stimulating elongation of shoots, what other effects has auxin also been discovered to stimulate?

(Hint: phototaxis, geotaxis, root formation, including redifferentiation of stem cells into root cells)

Invent and describe in some detail a bioassay by which auxin could have been discovered based on its ability to cause root formation?

Ditto: a bioassay for discovering the chemical that causes phototaxis?

Ditto: a bioassay for discovering the hormonal cause of geotaxis?

What are anti-auxin herbicides, like 2,4 D?

How were these (multi-billion dollar per year) herbicide chemicals discovered?
(Or would you argue, either pro or con, that they were invented?)

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?

Depending on the outcome of such a patent lawsuit, on what efforts would (will) chemical companies concentrate their funding?

Based on auxin's different effects on plant cell enlargement and differentiation, would you expect Lewis Wolpert to regard auxin as a morphogen?

Invent a bioassay capable (in principle) of discovering a morphogen that controls the differentiation of embyonic cells to form the pattern of the French flag?

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).

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?

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.

*) 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.

*) Explain how the bioassay approach could be used to discover which specific chemicals serve the roles of "A" and "B".

*) 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".

*) Similarly, design and explain experiments to test whether a given substance plays the role of substance "B".

*) 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?

Consider what the textbook suggests about stripe color patterns in certain fish, as evidence that these stripes are caused by the sort of mechanism invented by Turing.

Hint: He thinks 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.
[To be fair, this was proposed in the original Nature paper that described the color pattern in these fish.]


More questions, added Thursday March 8th

Compare the embryologist's and the neurologist's meanings of the word "dermatome". (The word is used by embryologists to refer to one of the subdivisions of a somite, as compared with the neurologist's region of the surface of the body that is innervated by a particular sensory nerve ganglion.)

Describe what you saw in the Youtube videos of somites forming in fluorescently labeled fish embryos (the address is on the course web site).

What is the clock and wave-front hypothesis? What process is it designed to explain? Approximately how does it work? What kind of symmetry does it "break"?

*) Invent a bioassay for identifying which specific chemicals serve as the wave-front, and which serves to form the clock (out of a set of 20, let's say, that you have available in pure form, to test with)

*) Can you invent one or more specific experimental results or observations that could conclusively disprove that the locations of boundaries between somites are caused to form by a clock and wave-front mechanism?

Early bird embryos, at the time of somite formation, are paper-thin and can be cut away from the yolk and floated in a saline solution. Supposing that it is possible to put one chicken embryo directly on top of another embryo, how could you directly test the truth of the clock and wave-front hypothesis?

Compare the function of the foramen ovale and the ductus arteriosus.

What mechanical forces cause them to close? Is it the same force for both?

When do they normally close, during development?

What would happen if one or the other of them closed prematurely, before birth? (If in doubt, explain your reasoning).

Sketch the path of blood flow before birth (in mammals) as compared with the pattern of blood flow after birth.

Visualize a heart developing abnormally, with no wall of cells and collagen that normally separates the right and left ventricles ("interventricular septum").
Would that harm the developing embryo before birth? Why not?
Why would this have bad consequences after birth? Would the tissues of the body receive the normal amount of oxygen? Why not?

Which direction does blood flow through the foramen ovale, prior to the moment of birth?

Which direction does blood flow through the ductus arteriosus before birth?

Why doesn't the blood flow in the other direction in the foramen ovale?

Why doesn't it flow in the other direction in the ductus arteriosus?

When the lungs expand and fill with air, that reduces the mechanical resistance to blood flowing through the capillaries: How should that change the relative pressures in left versus right atria?

What about the relative amounts of pressure in the aorta versus the pulmonary artery, before and after the lungs expand at birth.

The thickness and strength of the cardiac muscle walls of the right and left ventricles are the same before birth! But after birth, the muscles of the left wall gradually become about four-times thicker and stronger on the left side than the right side. What does that tell you?

How can an embryologist (easily) cause a chicken embryo to form two complete hearts? Compare this result with Driesch's famous experiment

*) It is not unusual for humans to develop with only one kidney (metanephros), but with two ureters (urine ducts). What might cause this to happen?

What do the pronephric ducts develop into in male vertebrates? And why do they undergo programmed cell death in females?

Imagine that a (medical) genetic syndrome is discovered in which two of the symptoms are male infertility and defective excretion during embryonic development (in both sexes). Suggest a single cause, that could explain both effects.

Why do our embryos first develop two pronephric kidneys, then two mesonephric kidneys, and then finally two metanephric kidneys? Contrast this with the development of a single heart, which begins as a simple tube, and becomes more and more complicated, while beating all the time during this development.

*) Imagine a science fiction animal in which a series of different blood-pumping organs develop, one after the other, each replacing the function of the previous one. Sketch the geometry of blood flow.

*) It has been hypothesized by some mathematicians that the real reason the heart begins development very early is not really because tissues need oxygen, but because proper development of arteries and veins cannot occur without mechanical effects of blood flow. Can you invent some embryological experiments capable of either conclusively disproving or convincingly proving the truth of this hypothesis.
(You could start with the effects of removing the heart rudiment; but please also suggest some better and more clever experiments.)

*) Formation of mesonephric kidneys seems to me very much contrary to this mathematical theory; can you figure out my reasoning? I will be even more impressed if you propose a counter-argument to mine.

Two separate oviducts normally develop, each from an invagination in lateral plate mesoderm. In many mammals, including humans, the posterior ends of these two cylinders fuse into a single uterus. Compare this to the formation of a single heart from parts of the left and right lateral plate mesoderm.

A certain human birth defect consists of the development of two uteruses? Do you suppose the uterus splits into two, or what?

Hint: Compare the causes of spina bifida, cleft palate, and cleft lip. (Are these split apart, or what?)

Describe the formation of capillary networks in tadpole tails (or other tissues).

Compare the formation of salivary glands, thyroid glands, lungs, livers and pancreases (and with the development of kidney tubules)

Compare embryonic development of the ear canal, tonsils, parathyroid glands, and thymus organs. Compare them all to development of gills in fish?

Why do mutations that cause defective development of T-lymphocytes also tend to cause abnormal metabolism of calcium and phosphate? Hint: guess the function of hormones secreted by parathyroid glands.

Compare the structure of mammal lungs and cauliflowers.

Contrast the structure of bird lungs with mammal lungs.

What does it mean to say that a certain tissue is not vascularized? (As: "Cartilage, the cornea, and the lens are not vascularized.") (What does that mean in a simple anatomical sense, rather than in the sense of function or causation.)

What is fetal hemoglobin?

What happens to a person if their red blood cells continue to make fetal hemoglobin, throughout their life?

*) Why might the consequences be worse in women than men. (Hint: if they got pregnant.)

How could fetal hemoglobin be used to cure sickle cell anemia?

Is the amino acid sequence of fetal hemoglobin coded for by the same genes as those that code for "adult" alpha and beta chains of hemoglobin. (hint: no. Even though processing of RNA transcripts would seem like a good way to produce the differences between embryonic, fetal, and adult hemoglobins, that isn't how it works.)

What is the geometric relation between the DNA that codes for embryonic, fetal and adult hemoglobins?

How is this similar to the linkage between hox genes?

*) Could either "Clock and wave-front" or Turing mechanisms cause the spatial patterns of expression of hox genes?

What is meant by "colinearity", in relation to hox genes?

What causal relationship is to be expected between hox gene colinearity versus "regulation" (as first discovered by Driesch), and also versus embryonic regulation (Spemann's phenomenon)

If you cut off the posterior third of an early chicken embryo, would you expect a shift in the anterior borders of the parts of the body where each hox gene is transcribed, and where the hox gene messenger RNAs are located?

*) Can you invent experiments to distinguish whether the locations of hox gene expression are responses to a long-range gradient of something like retinoic acid, as opposed to being caused by some interaction between each hox gene and the genes near it on the chromosomes (including other hox genes).

Do any of the hox gene proteins bind selectively to certain DNA sequences, and control transcription of other genes. (Hint, yes, absolutely! Based on their amino acid sequence, they are all transciption factors)

*) Would you expect the boundaries between areas where a given hox gene is expressed to correspond to the edges of specific organs, or boundaries between areas where specific differentiated cell types form? Why or why not?


More questions yet, posted March 16:

Does electro-osmosis result from water tending to flow so as to dilute the concentration of dissolved ions? Hint: Yes

How many atmospheres of pressure are exerted by a cartilage containing one gram molecular weight of sodium ion?

What change in this pressure would occur if calcium ions replaced most of the sodium, potassium and hydrogen ions?

In electo-osmosis, what force prevents the dissolved ions from diffusing away, and being diluted by inflow of water?

How can osmosis occur without a semi-permeable membrane?

If you push down on a sheet of cartilage (every time you stand up, you push down on dozens of sheets of cartilage), what force pushes back and resists compression?

Imagine if there were some kind of germ that could penetrate through your tissues and secreted an enzyme that cleaves sulfate groups from sugar chains, make a list of the medical consequences. For adults? For growing children? For developing embryos and fetuses?

Invent some possible new treatments for the pain of herniated intervertebral disks. (hint: based on substituting divalent or trivalent cations; based on selective local digestion or detachment of either sulfates or of sulfated sugars; maybe based on the mechanism that removed cartilage when bones elongate!

If you steadily pushed water at high pressure through a sheet of cartilage, where would you create a positive electrical voltage and where would you create a negative electrical voltage. (Hint: toward where would you be pushing positively charged ions? Away from where would you be pulling negatively charged ions?

What are at least two major errors of the following Wikipedia definition of electroosmosis?

"Electroosmotic flow (or electro-osmotic flow, often abbreviated EOF; synonymous with electroosmosis) is the motion of liquid induced by an applied potential across a porous material, capillary tube, membrane, microchannel, or any other fluid conduit."

? Hint: will this occur for ANY material? (not unless it has charged groups, as glass does, and cartilage does)

(Does it only involve flow? And can you produce flow of a liquid except by a pressure difference?

(Will such flow also occur parallel to, and very close to, the surface of a piece of glass or a sheet of cartilage? Yes?)

Note: Wikipedia's article on osmosis, ironically, is much more accurate, yet is besieged by pedants whose only valid point is that osmosis can occur with any solvent, not just water. Of course, they also wrongly assume that semi-permeable membranes are the only way to restrict diffusion of dissolved molecules and ions. In fact, you could have a U tube with oil filling the lower part, and get osmotic effects with solutions having some components that can dissolve in oil and others that cannot. Furthermore, you could have an upside down U tube with air in the top, and two liquid solutions, containing some components that can evaporate and others that cannot. Osmosis doesn't require membranes; many sorts of barrier can produce the same effect. Elementary Biology textbooks create some damaging misunderstandings, mostly because they all copy each other, and seldom are written by actual scientists.

Can you draw a sketch of an elongating bone, indicating locations of cartilage and of bone, and the zone in which cartilage is being destroyed and bone being formed where cartilage had been since embryonic development?

Could you recognize a drawing or sketch of an elongating bone, correctly labeling the cartilage, the bone and the zone where cartilage is destroyed?

Not only long bones, but also vertebral bones, are originally made entirely out of cartilage, and remain partly cartilage until fully grown. Does that mean that the boundaries between intervertebral disks and the vertebral centra above and below them were all previously like the zones in long bones where cartilage is destroyed and bone created. I thing the answer is yes; but I confess not having previously realized this! Don't worry about exam questions on such a difficult issue; at most you could be asked to discuss the issue, pro and/or con.

Some other interesting implications are the following: The cartilage that gets replaced during ossification is said to be hyaline cartilage, in contrast to the elastic cartilage that supports our ears and the fibrous cartilage that intervertebral discs are made of!

Does this mean vertebrae were made of fibrous cartilage before they ossify? Or does it mean the vertebral column starts as a long column of alternating bands of fibrous and hyaline cartilage, and that ossification is somehow stopped at the boundary from hyaline to fibrous collagen?

Some other interesting implications are the following: The cartilage that gets replaced during ossification is said to be hyaline cartilage, in contrast to the elastic cartilage that supports our ears and the fibrous cartilage that intervertebral discs are made of!

Does this mean vertebrae were made of fibrous cartilage before they ossify? Or does it mean the vertebral column starts as a long column of alternating bands of fibrous and hyaline cartilage, and that ossification is somehow stopped at the boundary from hyaline to fibrous collagen?

Compare the mechanical forces that cause elongation of cartilages with the mechanical forces that cause elongation of plant stems and roots.

Both in plant stems and (animal) cartilages, what causes elongation to be directed along a certain axis, instead of producing an expanding blob?

Hint: why can't the weakening of collagen fibers and cellulose fibers be spherically symmetrical? Must there now be selective weakening of those fibers that run in certain directions, with less weakening of those fibers that run in other directions?

Alternatively, can the same elongations and shape changes also be achieved by selectively weakening those fibers that are located at certain locations, and not weakening (or not as much) those collagen or cellulose fibers that are at other locations?

Would you think that the concentrations of dissolved ions and sugars etc. must be substantially higher inside chondrocytes as compared with other cell types (i.e. in order not to have all the water sucked out of them by electroosmosis, such as occurs when you put ordinary cells in a very concentrated solution of salt or sugar)? I would expect that! Can you suggest how this expectation could be proved true or false?

What if I took a thin piece of living cartilage, and soaked it in a very hypertonic solution of sugar? Would it shrink? Would the chondrocytes shrink within it? Would only the larger chondrocytes shrink within it? Would the piece of cartilage shrink?

Would the piece of cartilage become more flexible? Would the same shrinkage or increased flexibility occur whether or not the chondrocytes inside the cartilage were still alive?

What if I squeezed some other kinds of cells between two sheets of cartilage: should these shrink? What do you expect? Why?


New questions related to tensors (posted March 16, 5:30 pm):

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?

    Osmotic pressure.
    answer: scalar (zeroeth order tensor)

    Curvature of a surface.
    answer: second order tensor

    Concentration of a chemical
    click for answer

    Tension in a sheet or block of material
    click for answer

    click for answer

    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

    Electric field
    click for answer


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