Chapter 3 & 5 Mouse and Chick Development Part 2

Question 1

area pelucida

Answer 1

The region in the middle of the chick embryo (pelucida : it will be paler then the other regions)

Question 2

Area opaca

Answer 2

This is the region surrounding the area pelucida. It is a clustering of cells.

Question 3

posterior marginal zone.

Answer 3

The posterior marginal zone is the future posterior of the animal. It will be located on region of the epiblast which is gravitationally highest. The first visible sign will likely be the formation of Koller’s sickle. The posterior marginal zone is important not just as an arbitrary designation. Transplantation of the cells of the posterior marginal zone to a new region will result in a new posterior marginal zone. Furthermore ectopic transfer of the posterior marginal zone from one embryo to another will result in two marginal zones, each of which being its own ‘posterior’ for the animal. This shows us that the posterior marginal zone is likely some type of organizer.

Question 4

Blastocoel :

Answer 4

Blastocoel : The region within the epiblast.

Question 5

What becomes the posterior marginal zone?

Answer 5

The uppermost region of the of the epiblast. The egg has a gentle rotation, this keeps the epiblast from being centered over the top of the egg. The uppermost region, closest to the top will be the size of the posterior marginal zone. The mechanism is not well known for why this occurs. But its the truth.

Question 6

Epiblast :
Hypoblast :
Endoblast :

Answer 6

Epiblast : is the top layer of cells in our future embryo
Hypoblast : is the bottom layer of cells in our early embryo
Endoblast is the bottom layer of cells after cells from something (sorry future me) migrate into the hypoblast

Question 7

Describe the initiation of the primitive streak from a signaling perspective.

Answer 7

Epiblast cells in the posterior margina region begin the game : they signal with WnT and Vg1.
Signalling with Wnt and Vg1 from the posterior marginal zone promote a region of the epiblast which begins to produce nodal. Nodal however is inhibited by the production of Cerberus and other inhibitors by the hypoblast. But behold, all nope is not lost! For even the hypoblast whall change its way and become replaced/cells will transfer into it and induce it to become endoblast. Endoblast does not produce cerberus. Meanwhile, Koller’s sickle, a growth of cells between the epiblast and hypo/endoblast on the border of the area opeca begins a little signalling of its own… a signal of… FGF (fibroblast growth factor B words!!! ) Dang straight! With FGF, WnT and Vg1 cheering it on, and no cerberus beneath to get in the way, the primitive streak marches on boldly, crossing the cell.

Question 8

Suppose we are a mass embryo, is there a bias towards the position in the eight the cell embryo, and future fate?

Answer 8

Yes. The bias is as follows.
If you are outside 97 % chance you will be trophectoderm, and 3 % chance you will be inner cell mass.
If you are inside of the cell 60% chance you will be inner cell mass, and a 40% chance you just trophoctoderm. So the position does bias, but it does not determine true fate of the inner cell mass. Note this information was gathered using… wait for it… science. To be mores specific it was gathered using labelling of cells inside and outside in the early embryo to determine their eventual fate.

Question 9

Trophoectoderm -> extraembryonic materials.

Answer 9

True…

Question 10

Divisions

8 cell stage goes to ->

Answer 10

16 cell stage morula -> 32 cell stage morula

Question 11

Cdx2 does what?

Answer 11

In the 8 cell cdx2 is transcription factor

Question 12

Oct4 is what?

Answer 12

A transcription factor.

Question 13

Cell stage eight describe the embryo

Answer 13

cdx2 and oct 4 are both being expressed in low levels in the eight cell stage.

Question 14

What happens as the cells transition from the 8 cell -> 16 cell early morula?

Answer 14

cdx2 begins to be expressed more strongly in the outer cells. The inner cells begin to express more oct4. Mutual inhibition of the transcription factors solidifies the difference made between external and internal environmental expression (cells on the outside which begin to express more cdx2 start to inhibit more and more oct4, in the center oct4 expression inhibits cdx2.)
Cells with oct4 are also expressing low levels of nanog and gata6.

Question 15

What is seen in the 32 stage morula stage?

Answer 15

The same thing which is seen in the 16 morula stage. A solidification of the differential gene expression between cdx2 in outside cells and oct4 in inside cells. Cells expressing oct4 will also be producing gata6 and nanog

Question 16

What is the fate of cells expressing cdx2?

Answer 16

They will become the trophoctoderm! dang straight!

Question 17

What is the fate of cell cells expressing oct4?

Answer 17

They will become part of the inner cell mass.

Question 18

Cells in the inner cell mass will either end up expressing one of which two transcription factors? Implications?

Answer 18

Nanog -> stronger adhesins -> forms the inner cell mass
Gata6 -> weaker adhesins -> form the outer layer of the inner cell mass
Facing into the blastocoel

Question 19

Why does either nanog or gata6 end up being expressed in the inner cell mass?

Answer 19

Nanog and Gata6 are mutual inhibition against each other and promote their own expression. Stochastic differences then reinforcement allow them to differentiate according to their adhesins afterwards. There are not positional clues for the placement of gata 6 and nanog.

Question 20

Embryonic axis

Abembryonic axis

Answer 20

Embryonic axis: the side the embryo is on, thus embryonic…

Abembryonic axis: side that doesn’t have the embryo (has the blastocoel instead)

Question 21

What corresponds to the dorsal ventral axis?

Answer 21

These axis correspond to the embryonic and abembryonic axis.
Dorsal is inward initially. embryonic?
Ventral is outwards initially, Abembryonic

Question 22

Distal Visceral endoderm

Answer 22

Distal -> far
Visceral -> within the body
Endoderm -> endoderm (right now for the mouse the yellow cells surrounding the epiblast. I believe these yellow cells are those who expressed gata6

Question 23

A signaling center forms in the endoderm… what happens next?

Answer 23

Signalling center forms, this initial signalling center is the distal visceral endoderm. It is speculated, and probably likely, that the trophoctoderm is producing inhibitors, the distal visceral endoderm sets up shop as far away as possible from the trophectoderm.
The signaling center expands upwards, the mechanism of this is not completely known, but could be due to a difference in the proximity of the trophoctoderm, which appears inhibitory, the epiblast appears to be promoting the expansion of the anterior visceral endoderm. The AVE and DVE are the source of nodal, Wnt and BMP inhibitors.

Question 24

Expansion of the DVE to AVE

Answer 24

As the DVE expands into the AVE it produces inhibitors for Wnts, BMP, and Nodal. Inhibition of nodal, wnts and bmps helps to set the Anterior posterior axis. Just like what is seen in xenopus the Anterior axis will correspond to low levels of Wnt, Nodal, and BMP. This gradient of Wnt Nodal and BMP expression created via inhibition from the AVE, after expansion up one side of the visceral endoderm will set the anterior axis. The high levels of Wnt, BMP, and nodal will be found in the posterior axis. The primitive streak forms at the site of the posterior axis, on the opposite lip of the cup from the anterior visceral endoderm AVE, where BMP, Nodal, and Wnt will be at their highest concentration. Note though the AVE is endoderm it is influencing the epiblast through its production of Wnt, Nodal and BMP inhibitors (which likely bind to Wnt, Nodal, and BMP as all three are ligands and this is a form of inhibition seen in previous organisms development (xenopus and drosophilia).
Mice also have a primitive streak, A mouse primitive streak begins on the opposite side of the cup from the anterior visceral endoderm.

Question 25

If the node is equivalent to the spemann organizer then the posterior marginal zone is mostly equivalent to…

Answer 25

the nieuwkoop center. But the morale here is that the node is equivelant to the spemann organizer.

Question 26

After cells ingress into the primitive streak, what goes down?

Answer 26

The cells which ingress into the primitive streak will migrate laterally (note : lateral movement is analogous to moving ventral as lateral will become ventral…) and anterior. The primitive streak is also in the business of moving anterior at this point. Following henson’s node, our portable spemann organizer.

Question 27

Note the information I am about to disclose is true for both mammals and birds. It is even true for you…

Answer 27

Henson’s node begins its migration, the primitive streak is advancing across the surface of the epiblast, and cells are ingressing. As cells ingress into the blastocoel they migrate lateral (ventrally) and anterior, which is anterior… Therefor the further posterior a somite is, the more it will have a chance to migrate into the lateral realm of structures. Let’s look at some stuff.

Question 28

How do we know that henson’s node is the spemann organizer equivalent?

Answer 28

It is the site of tissue induction. If we perform an ectopic transfer of Henson’s node to the area opacea (and possibly if we transfer to the area pelucida as well) then we will see induction of the surrounding tissue and the beginning of a little primitive streak of its own. This induction of tissue is due to the fact that henson’s node acts like a the spemann organizer, it also is a site of BMP inhibitor production, simply a traveling one. Furthermore if we take a henson’s node which is further anterior and perform an ectopic transfer of this node we will see that the tissue it induces is further anterior as well (meaning that it is a tissue type which would be seen further anterior, so a head fold may be induced by very anterior material, but a stomach… may be… induced from a henson node taken earlier (more posterior).

Question 29

Explanation of previous materials aided by Dr. Podgorski

Answer 29

Initially Wnt is localized dorsal due to cortical rotation, this is truth, however this b-catenin gradient which results from wnt gradients and the vg1 will produce a nieuwkoop center. The neiuwkoop center will produce nodal. Nodal will be produced in any region with vg1 and vgt but will be produced more in regions with vg1, vgt and beta catenin. Nodal will induce the formation of the spemann organizer. Now things are getting serious. The spemann organizer does not mess, it produces the serious inhibitors, things like cerberus, which goes about inhibiting nodal, wnt, and BMP. This results in a change in the previous gradient. The embryo then turns itself about, aka gastrulation getting real. The spemann organizer travells up the butt of the embryo, and to the site of the head. Here the organizer says uh uh ah (no) to wnts, BMP, and Nodal, just like it did before it traveled up a bottom. Only now its doing something far more important, it is setting the anterior posterior axis baby! That’s right, the organizer gets it done. No messing. To axis set. Boom, roasted, just one organizer. Kind of sexy? ya just a bit.

Question 30

Henson’s node like unto spemann organizer produces BMP inhibitors.

Answer 30

Truth!

Question 31

An experiment was performed to show the conservation of signals and function between the spemann organizer and Henson’s node. Describe this experiment. Do it. Describe…

Answer 31

Spemann organizer induces neural ectoderm. In this experiments regions of the chick epiblast where transfered to the xenopus ectoderm to see if neural ectoderm could be induced.
four tissues were tested.
- Tissue from the epiblast, not from prim streak or henson’s node
- Tissue from primitive streak
- Tissue from henson’s node
- Tissue from traditionally neurally induced ectoderm found in xenopus, aka a control.
Three genes where looked at, two expressed only in neural ectoderm and a house keeping gene. A house keeping gene is a gene which is expressed in all tissue types (a control, to see if your gel is running correctly at all).
mRNA from these cells was ran on a gel. It was found that the house keeping gene was present in all tissues (aka mRNA extraction was done properly, the gel did not run backwards, etc.)
It was also found that neither normal epiblast or cells from the primitive streak induced activation of neural ectoderm genes, henson’s node however, when put together in a sweet sweet ectoderm henson’s node sandwich induced the activation of neural ectoderm in a manner similar to what the spemann organizer does. Showing a conservation of signalling mechanisms between the spemann organizer and henson’s node.

Question 32

What is the node a source of? what previous evidence of this did we have that should have allowed me to already know this?

Answer 32

In the early chick embryo FBF (fibroblast growth factor) is produced by cells which appear to be part of koller’s sickle. These cells, or at least production of FGF stay with henson’s node. That is correct henson’s node is a source of FGF. I repeat, Henson’s node is a source of FGF. Since henson’s node and the spemann organizer enjoy being essentially the same thing, we can also ascertain that spemann organizer is a source of FGF. They are therefor both sources of FGF (source) and inhibitors of BMP (inhibitor).
- This is necessarily true because the node is capable of inducing neural ectoderm, and this requires high levels of FGF and low levels of BMP. Therefor henson’s node and the spemann organizer must do both.

Question 33

Somites: they be mattering cause why? They are what tissue type.

Answer 33

The somites matter because they give rise to skeleton, skeletal muscle and the dermis. Somite formation travels A -> P the opposite direction as posterior streak formation. This is because henson’s node gets to the top and then… travels back posterior.

Question 34

How do we know that somite specification occurs prior to formation.

Answer 34

If we take the region which would normally form somites 6 - 10 prior to the formation of any of these, invert the sequence, and place the somites back into the embryo, inverted. We will see formation of the somites backwards 1 - 5, 10 - 6, 11 - 14 etc.
This means that they must be pre specified, as they formed what they would have formed anyways. They also still formed in normal order, six forming after five, even though they are now spatially seperated. This implies that in somitogenesis, whichever form of specification which occurs also includes some form of timer mechanism which is at least at the point of this inversion not spatially dependent within the embryo (though likely is spatially dependent at some point, as this is basically required in the physical world)

Question 35

So what is going down in somitogenesis.

Answer 35

Oh. Let me tell you about somatogenesis. Let me tell you all the dirty, dark secrets of molecular timers which are not dirty, but are dark in the fact that they are obscured from are ability to discern information about them except when we do… Ok… ignore that. There are two aspects to the molecular timer, the wavefront and the oscillator. Continue to next slide!

Question 36

So we have the clock and wavefront model. The clock is waves of gene expression and is an oscilator.

Answer 36

Let’s go to this side. The oscilitar is controlled by Notch. Let’s talk notch. Notch is complicated… But I know understand it. I got some learning… Notch works in the following manner. Notch receptors are placed on the cell they have a cytoplasmic and an extracellular domain. Ligands still attached to cells bind to notch receptors. This causes a the extracellular domain to be cut off, it is endocytosed along with the ligand which bound it, back into the cell which sent the signal, where it can be recycled. Meanwhile the cytoplasmic domain of the notch receptor is excited, it is finally free of the plasma membrane, and it goes on to activate genes, which causes are cyclic gene expression. These genes are involved in negative feedback loop (not to mention that the nature of notch signaling is somewhat of a negative feedback loop as it destroys its own receptors.) In addition to being sexy, this form of cyclic gene expression sets the timer for somite formation. When this cyclic gene expression controlled by notch signalling reaches the wavefront, the old somite is closed off and a new somite is formed. Therefore this oscilator controls the rate at which somites are developed. If a notch signaling mediated gene wave reaches the wavefront every 15 minutes, a new somite is formed every fifteen minutes.

Question 37

Let’s talk FGF (Wnt is also there :( ) and retinoic acid gradients and the wavefront.

Answer 37

FGF mRNA is made in Henson’s node. This mRNA translated to produce FGF, it is also degraded at a steady rate. This results in a gradient of FGF, which exists independent of diffusion (since it is internal to the cells as an mRNA gradient) and fades the farther we are away from Henson’s node.

Question 38

Let’s talk retinoic acid.

Answer 38

Retinoic acid is synthesized in newly formed somites (where does the first retinoic acid source come from for the beginning of the wavefront… ;P), regardless, Retinoic acid is broken down by molecules produced in the primitive streak and stem zone (the region right in front of henson’s node), this is the sink of retinoic acid. This means that when we run out of primitive streak/stem zone we will lose are sink for retinoic acid, this may be how the embryo determines that it is done making somites. That would be cool. Regardless we have a gradient of retinoic acid high in somites and getting progressively lower in the direction of the primitive streak which is also the direction of henson’s node. Therefor we see awesomeness. No not really. We see somite formation where FGF is low enough, and retinoic acid is high enough, we see somitogenesis. This region, this goldilocks zone where we have high enough retinoic acid formation and low enough FGF formation is where we make sweet, sweet somites. This decides the size of the somites. If the wavefront is progressing quickly and the oscilitor is moving at the same speed, we will see a larger segment, while this is true I would say it is combinatorial, if the oscilator can change speed (notch regulated cyclical gene expression could possibly occur faster?) then we would see a change in the size of somites, additionally if we increase the speed of the wavefront, by lowering the amount of FGF mRNA for example and increasing node speed, we would see larger segments, but they would hit the cyclical expression sooner, except they wouldn’t, because the cyclical expression (notch regulated) would have farther to travel… spooky…

Question 39

How does retinoic acid work… How does it…

Answer 39

Retinoic acid functions essentially the same way as a steriod. Let’s break it down. A steriod crosses the plasma membrane, binds to an internal receptor, generally exposes a nuclear localization signal and then the steroid causes the receptor factor (often a transcription factor) to be localized in the nucleus. This localization causes new genes to be expressed and the steroid has done its work.
We see the same thing for retinoic acid. Retinoic acid crosses the plasma membrane. After retinoic acid crosses the plasma membrane, it binds to a receptor, it causes a conformational shift, that exposes a nuclear localization signal, the receptor is sent to the nucleus, and it turns out it is also a transcription factor! (ok it was one all along), after nuclear localization it changes expression. Morale of the story, well two morales, retinoic acid is cool, and it crosses the plasma membrane and acts similar to a steroid, exposing a nuclear localization signal, and changing gene expression that way. It’s sexy as crap… which… isn’t sexy. But it’s a really cool mechanism.

Question 40

Science: explain it. But specifically explain the science behind the derivates of somites:

Answer 40

So we have a somite, how do we form a somite you may ask? Strange, because you know the answer. A somite is formed because cells enter the blastocoel during an epithelial to mesenchymal shift, these cells then go back to epithelial when the form somites. These somites will transition back to mesenchymal but not before environmental factors further determine them. Let’s dive in. So at this point of development, not much exists within the embryo proper, which is good, because it simplifies what could be signaling. Three sources of signals exist. We have the neural tube, the roof of the neural tube, which is our dorsal most structure (it is also perfectly medial) will produce a signal, the notochord will produce another signal and induce some of the lower neural tube to produce the same signal (note: The notochord is ventral, and medial), and the lateral mesoderm, will produce a signal of its own. This lateral mesoderm is eventually going to be ventral tissue, as the embryo will fold around on itself, but for now it is simply lateral.

Question 41

tome tome tome, why so much tome?

Answer 41

The age old poem of John’s written just a few seconds prior to this about the frequency of the word tome in somite differientation is a classic work. It also highlights that tome is used a lot. the initial division that will happen to the somite is that some of it will differentiate to become scleratome (tissue near the notochord), scleratome, as it starts with an S is fated to become the axial skeleton. You may not know what the axial skeleton is, but the sclerotome does, it will become it. The axial skeleton is the ribs, spine and head, though some of the head will not be from the somites. Sclerotomes sacred duty, is to become the axial skeleton. Now we turn our attention to what the roof of the neural tube is up to… It looks suspicously like it is trying to induce myotome, muscle it can control… However the lateral mesoderm is also trying to induce dermatome! what happens? We get dermamyotome and sclerotome initally. Then dermamyotome becomes either myotome or dermatome. Let’s get deep.

Question 42

Let’s get deep. What makes a sclerotome, really, in the grand scheme of things?

Answer 42

We know that the induction of sclerotome form they somites is due to signaling from the notochord. This much is obvious, if you are reading that statement or have a textbook in hand. However, how does the notochord accomplish this differentiation? Sonic Hedge Hog. Damn straight. Sonic Hedgehog (SHH) does not mess when it comes to making sclerotome which is future axial skeleton. How do we remember this? Child’s play. Literally, go play like a child and then you’ll remember (false)! Sclerotome, Skeleton and Sonic hedhehog all begin with S, so ya! top that sucka!

Question 43

So new situation. We graft an additional notochord near the neural tube roof on one side. What happens sunny D?

Answer 43

Well, we know have an additional source of sonic hedhehog, and we know that the notochord is capable of inducing neural tube to produce sonic hedgehog. Therefore in this situation we will see only sclerotome formation on one side. That’s right puppy, the amount of sonic hedgehog being produced will result in only sclerotome induction from the somite. This makes sense.

Question 44

Floor plate. It’s real, it’s induced by the notochord, and it makes sonic hedgehog, why you may ask?

Answer 44

Cause sclerotome son. Always sclerotome and the sonic hedgehog and the axial muscle formation when it comes to the notochord. You get me?

Question 45

You know what every child should be told about though? Damn straight, Wnts signalling by the roof plate of the neural tube.

Answer 45

The neural tube is a sneaky little blighter. Wnts are also sneaky… The Wnt signalling form the neural tube roof promotes the formation of myotome/dermamyotome. Meanwhile let’s talk about induction. The neural roof does not stop there, oh heck no. It also involves the actual dorsal layers of cells above it (future epithelial, at least in my world, which is earth, thanks for asking), these dorsal cells will also produce wnts, which will further aid the formation of dermamyotome (possibly myotome, fieldtrip). Ok so what is the lateral mesoderm producing… New page!

Question 46

Lateral mesoderm

Answer 46

Lateral mesoderm produces a BMP-4 signal. These signals may produce the Dermatome directly, or they may just contribute to the induction of the dermamyotome, either way they are important and you should keep them in your body. I’m going to repeat this because its important. And you should not forget it. The lateral mesoderm is busy making a batch of BMP-4 and its inducing all sorts of dermomyotome formation, because that is what it does. BOOM!!!!

Question 47

Summation: after a short break brought to you by the need to use the toilet, which will double a time period to absorb info and then reinforce recall. GO…

Answer 47

We have three signaling centers for the specification of somites they are.
Notochord: ventral most (currently, prior to folding of the embryo). Produces sonic hedge hog. Induces sclerotomes, which become axial muscle. SHH/notochord also helps to induce signalling from the floor of the neural tube, which also helps in sclerotome differientation.
Lets talk about the…
Neural tube roof. The roof of the neural tube, in conjunction with the dorsal roof of the ectoderm, produce wnt signalling. It is possible that the neural tube roof is inducing the ectoderm, it is also possible that the ectoderm (dorsal medialish) is inducing the neural tube roof to produce wnt. Either way, both produce wnt, and wnt cause dermamyotome formation and possible progression towards the mytome cell type from the somite. But maybe just formation of the dermamyotome.
The …
Lateral mesoderm is the source of BMP-4, which is poorly named. Either way lateral mesoderm via BMP - 4 induces the formation of dermamyotome in the somite. Oh what was that sound? Oh ya winning. Next thing.

Question 48

Man let’s talk specification of the somite formation in terms of positional identity (alignment on the anterior to posterior axis)
Here is the experiment. An ectopic transfer of presomatic mesoderm from one chick embryo to another occurs. presomatic mesoderm which was taken from a position which would normally form thoracic vertebre (and therefor ribs) was transferred into another epiblast, into the location of the primitive streak which would normally form cervical vertebre. The result was as follows. The ectopically transfered presomatic mesoderm still became thoracic vertebre, but in the location of the cervical vertebre in the other chick embryo. Explain this result.

Answer 48

We see that even presomatic mesoderm has been determined. The determination of this tissue occurs before somite formation. We know the tissue is determined because even when it was transfered to a new site, which would become cervical vertebre, it still became thoracic vertebre, complete with rib formation. Which is sweet, and kind of awesome.
What could prespecify somite identity within the embryo? Well, let’s be honest, its a combinatorial control of Hox genes. Hox genes gradients are creating somite identity.

Question 49

Hox clusters is a term. Explain it.

Answer 49

This refers to the multiple duplications of hox genes which have occured throughout the years within vertebrates. Let’s read some of my notes.

Question 50

Homologs

• Paralogs
• Orthologs

Answer 50

Homologs : genes which are very similar in appearance because they come from the same ancestral gene, there is two types of homologs, namely, paralogs and orthologs.
Paralogs come from very recently related genes., they did not diverge long ago. You could say the a1, and b1 are paralogs in the vertebre lineage. they both occurred relatively recently. The said could be said about a7 and b7.
Orthologs : are homologs from a distant gene. The fly drosophilia and myself both have hox genes, but we would be considered orthologs of each other. There has been enough time between are lineages for are genes to be a tad different but there is still very conserved resemblances.

Question 51

Let’s talk about implications of this. Well, more of trends. Our hox genes and drosophilias are orthologs, Are hox genes also come in duplicate, which in theory provides functional redundancy. The majority of vertebre have paralogs of hox genes. These paralogs are very similar, and provide room for adjustment of our body models. Fish have 7 hox genes sets. a1, b1, and d1 would all be part of the same set.

Answer 51

So a1, b1, and d1 would all be paralogs of each other in development.
Additional info you know :
- The order of hox genes corresponds to the physical order they are expressed in. This is due to chromotin condensation.

Question 52

Combinatorial control. Talk to me, we see both quantitive and qualitative control, what does that mean?

Answer 52

So this is fairly simple. Qualitative control means that certain genes, certain gene names, correspond to certain expression phenotypes (in the somites in this case). If a system was under qualitative control alone, the only thing dictating which somite you would be would be the ‘name’ of the gene being expressed there. If we expand this to make it combinatorial qualitative, I would expect that gene 1 specified one somite type, gene 1 and 2 another, and gene 2 another. You can see how this would increase the effectiveness of the amount of somite phenotypes you could encode. But this is a combinitorial control that is quantitative and qualitative in nature. Which means that we take into account whether gene 1 is there, and whether gene 2 is there, and how much of gene 2 and 1 is there, and gene 3 and 4 and 5. This is a very rich code, and technically could encode infinite combinations. However since a biological system cannot have somite one be triggered by something too similar to somite two for fear they both become somite 1 or somite 2, there is a finite amount of realistic combinations. I don’t have to know them.

Question 53

What I mentioned above explains…

Answer 53

Concept of combinatorial patterning of the code, specifically in terms of somite specification. It is of note that the patterns of the hox genes are there prior to somite formation as we know from the presomatic ectopic transfer of thoracic vertebre study in chicks.

Question 54

Explain to yourself the concept of posterior dominance as it applies to hox gene expression.

Answer 54

Posterior dominance : this is a description of a phenomena, not a law of nature though the phenomena may predominate throughout nature. The posterior gene, aka the hox gene with an expression domain farther posterior tends to inhibit the expression of the anterior expression domain. Let’s walk through a few examples
A1, and B1, are both as far anterior as you can get in the realm of hox genes. Therefore their expression will likely be inhibited by A2, and B2, and D2, whose domains of expression will likely be inhibited by A3, B3, C3, which will be inhibited by the fours, then the fives and so on. The clear pattern is… new slide

Question 55

The clear pattern is…

Answer 55

In posterior dominance, we see that the more posterior gene, the one further posterior in expression/higher in number is going to inhibit the expression of the gene anterior to it. Or in other words, the expression of a1 begin to end where expression of a2 begins, and a2 in turn will end where a3 begins, continuing further and further down. Note: a1 and b1 are in the same location.

Question 56

You can see a homeotic mutation in mice, tell the world about how they go down.

Answer 56

The example we see in class is a gene which causes the first lumbar vertebre to become thoracic aka grow ribs. This is significant as mutations like this explain the difference in vertebre number and distribution in different animal species. Homeotic mutations however are harder to create in vertebrates, this is in large part due to functional redundancy and the presence of paralogs in vertebrates. If I want to knock out the actions of hox gene 1, I have to knock out 1a, 1b and 1d. Note: this is not definitively the case. Perhaps the paralogs are different enough that loss of one makes a change as was seen in the mutation of one vertebre to another. This is the norm for hox genes.

Question 57

I repeat sir and sirs :

Answer 57

The hox genes in vertebrates are often functionally redundant. Knock out all the puppies to get a result. Puppies in the case have the same number in front of them, like a1, a2, a4. Who’s expression ends at the beginning of B2, what! Winning. This also explains why a thoracic vertebrae takes the place of a lumbar vertebrae in their homeotic mutation. If the domain of the region specifying this thoracic vertebrae was ended by hox gene 8c which was knocked out, then you would likely see a continuation of what 7 did because 8 isn’t there to inhibit the posterior expression of seven. Interesting huh? Kind of really cool!

Question 58

Let us say we are making the transition from thoracic to lumbar, how will functional redundancy protect this line?

Answer 58

Most expression domains for functionally redundant genes which guard an important boundary will occur at the exact same point. So if A9, B9, and c9 are guarding the to lumbar boundary, then expression will likely form a solid line of kind of important.
Additionally we see very similar expression between different vertebrates of hox genes. With the same hox genes setting the same boundaries, even if they do so at different somites.

Question 59

How do you form the neural tube and neural crest.

Answer 59

First we have formation of the notochord. The notochord likely induces formation of neural tissue in the ectoderm above it. The neural ectoderm will invaginate towards the notochord, meeting itself at the top and pinching off to form a tube. The neural crest is a bit of tissue which is sneaky. This sneaky tissue does not just pinch together to form like the rest of the neural tube. Instead the neural crest does what it must necessarily due to free itself from epithelial cells, make an epithelial to mesenchymal transition. It is possible that the neural crests epithelial to mesenchymal transition is performed to allow the neural tube to develop, at least initially. Either way the neural crest will becomes mesenchymal and will aggregate above the neural tube prior to migration. This migration is awesome. It also allows the neuro-crest to give rise to a large variety of tissues.

Question 60

Name some tissue types the neural crest contributes too!

Answer 60

Nerve cells support and sensory are formed, cartilaginous cells (structural), kidney cells are formed, some of the bones of the head surprisingly result from the neural crest.

Question 61

Schwann, glial, sensory, kidney secretory, cartilaginous, and head bone cell can all arise from a surprising background… what is it?

Answer 61

The neural crest. These tissues can be secretory, nervous, or structural, and it all comes from induced ectoderm, performing tasks ectoderm normally could not do, this is likely why some people consider the neural crest a germ tissue in its own right.

Question 62

What ends up determining what the neural crest cells will ultimately end up becoming?

Answer 62

The migration of the neural crest cells and there differientation is set along the anterior to posterior axis by hox gene expression. No surprise. Hox genes determine differentiation of the neural crest. This means that these cells have entered a different gene expression state, that interacts differently with their hox genes then endoderm, mesoderm, and traditional ectoderm, which in a way is not surprising, but is also shocking. Go neural crest cells!!! :D

Question 63

Note : combinatorial patterning by hox genes is also causing differentiation in the neural crest.

Answer 63

Preach brother! Preach about the neural crest and Hox genes.

Question 64

Not all cilia are motile, you forgot that once.

Answer 64

You really did, not all cilia are motile.

Question 65

What is not motor protein which grants ciliary motility?

Answer 65

Dynien, cilia will have the classic 9 - 2 arrangement of microtubules. They will slide past each other using motor proteins.

Question 66

So John, Pretend you are trying to differentiate left and right, how do you do it?

Answer 66

Well let me tell you about a totally original idea I just got! This could totally work!
What if we used cilia to determine our left and right axis at the node (henson’s node in a chick). No, hear me out. You have motor cilia, ones with dynein, and these push fluid a specific direction. The direction they push the fluid is left, by genetic definition. These cilia push fluid across non-motile cilia (from hereon out called non-motile cilia). The non-motile cilia will be pushed, a specific direction by the fluid, this direction is defined as left.

Question 67

Describe mutations and the left and right axis determination.

Answer 67

So, i’m a motile cilia, oh wait, i’m not, you see there was a loss of function mutation in my motor dynien. Crap. Well there is now a 50-50 chance that the fluid will flow towards what would normally be my left (in which case i’ll be left alone) or that it will would flow towards the right side, in which case right is the new left, right?
Another posibility is that I have a mutation which reverses the direction of motile cilia, instead they push fluid the opposite direction in the node. You may think this wouldn’t change anything. If so you have not read the previous 2 paragraphs I wrote about how the fluid flows in the direction of what is now, by definition left. So if we reverse positioning of these motor dyniens we will see a 100% chance of reversing the left right axis. Remember there’s fluid left (fluid flows left). You want there to be fluids left, not there to be fluids right? Leftover, left is the direction of fluid flow.

Question 68

Nodal and the left and right axis.

Answer 68

You will see more nodal left, the left axis will have a higher level of nodal then the right side. You can say more nodal is leftover. This high expression of nodal results in the actual gene expression dictating the left axis. So nodal is left.