chapter 8 (cell differentiation and stem cells)

Question 1

Three mechanisms for the maintaining of genetic patterns:

Answer 1

Positive feedback loops: flawed in that noise can cause a positie feedback loop to fade out
Histone Modification: can result from addition of an acetyl, or methyl group in order to change chromatin state.
DNA methylation: generally condenses DNA, binding is specific to the C-G region of DNA generally.

Question 2

Positive feedback fades:

Answer 2

A positive feedback loop could fade due to noise. This could be amplified by the cessation of DNA transcription during division, however, it is possible that the reason determination is scene is non-replicating cells, could be because the positive feedback loop is unable to maintain itself during this pause, it may also upregulate itself to prevent this.

Question 3

MyoD and Mrf will remain active once activated via auto activation.

Answer 3

true, these two genes are also functionally redundant.

Question 4

histone code:

Answer 4

refers to the fact that histones can be modified all over in order to result in changed chromatin condensation (could be methyl, acetyl, phosphate)

Question 5

Often we will see a sequential spread of an activation (relaxation) of histone proteins

Answer 5

H3 -> acetylated,
neighbors H3 -> acetylated,
etc.
This acetylation of histone three in a sequential manner will often result in the activation of a cluster of genes

Question 6

CpG

Answer 6

Cytosine phosphate Guanine

Question 7

CpG methylation is associated with

Answer 7

the condensation of the chromatin. CpG dinucleotide methylation == inactivation, condensation

Question 8

DNA methyl patterns are stable.

Answer 8

I believe this is because when a template strand is made a protein copies CpG methylation patterns to maintain this

Question 9

methylases add methyl groups to the DNA.
Acetylases remove acetyl groups from the Histones.
De-methylase will remove methyl groups from DNA (like the CpG region
De-acetylases will remove methyl groups from the Histones

Answer 9

DNA methylases will often work in a complex with DNA de-acetylases and visa versa. This reciprication is logical because methyl addition condenses chromatin, and chromatin is loosened by acetyl groups on histones, so we would wish to remove these to achieve effective transfer.
So a methylase may recruit a deacetylase or an acetylase may recruit a de-methylase

Question 10

methylases and acetylases are not sequence specific. How then are specific regulations of the genetic code performed given this?

Answer 10

The specific modifications are mediated by pioneer transcription factors. These factors are sequence specific and pioneer transcription factors will have a domain which can be recognized and bound by a methylase/de-mehtyase or any other modifying protein.

Question 11

Hiearchal differentiation :

Answer 11

differentiation can be hiearchal, this means that a cell can become differentiated down one specific path, it can only become 3 types of blood cells (bc) where ti could be 7. Soon it chooses another path, and now it can become 1 cell. each step will see different expression patterns locked into place.

Question 12

Differentiation can be controlled by extracellular signals.

Answer 12

His example of this is a granulocyte which can be Differentiated into a neutrophil or monocyte depending on which ligands it is exposed too.

Question 13

*stem cells vs embryonic stem cells

Answer 13

Note: for the purposes of this class, stem cells are not the same as embryonic stem cells. A stem cell represents a stem cell population dividing within someone’s body.

Question 14

The most simple stem cell model would be a stem cell which divides to make one stem cell, and one cell which will go on to

Answer 14

Differentiate. This does exist but is rare.

Question 15

Name the two ways to conserve a stem cell population, what are the two broad classes of mechanisms?

Answer 15

The two methods are environmental (a cell which stays in a specific environment after division will stay a stem cell, a cell which leaves will differentiate) the second method would be using divisional asymmetry, the organism could then focus determinants in one cell vs another

Question 16

Earlier I described a possible model in which cell divided, one stayed a stem cell, and one became a differentiated cell. What in actuality generally happens?

Answer 16

in reality, one cell becomes a stem cell, and once cell becomes committed, but not terminally differentiated, prior to terminal differentiation, the cell will become a progenitor cell, the progenitor cell will give rise to progeny… lots of progeny. All progeny will terminally differentiate unless… cancer… but if we don’t have cancer, all of the progenitors daughters and grand daughters will become differentiated cells.

Question 17

the stem cell niche theory:

Answer 17

Is that there are essentially niches which can support a specific population of stem cell and maintain it, his example of this is he maintenance of the basal stem cell layer by basement membrane of the skin, this is a niche which allows the cells to stay.

Question 18

Stem cell niche’s will generally correspond to an extracellular signal

Answer 18

This may not always have to be the case.

Question 19

Cells of the basal lamina stay coupled with an integrin in the ECM, this integrin along with Wnt and another ligand maintain the niche for these lamina stem cells.

Answer 19

This is an example of extracellular signaling maintaining a niche.

Question 20

Stem cells divide slowly, rapidly dividing cells divide… quickly. Cancer in progenitor cells can be targeted by drugs, while cancer in stem cells if far more difficult to target.

Answer 20

This is truth. It causes cancer to relapse.

Question 21

So gurdon took cells from a frog and from a tadpole, and using the nuclei from those cells (epithelial), would place them into uv irradiated unfertilized eggs, then he would see if tadpoles formed.

Answer 21

They did form. Genomic equivalence (cells keep their genome, was confirmed!)

Question 22

This transfer also showed that the cytoplasm of the egg was capable of reprograming the genome in order to create a reversion to embryonic state.

Answer 22

This as a significant as genomic equivalence.

Question 23

A human liver cell was placed into a mouse muscle cell. we see that the human liver cell begins to express human muscle cell genes. Why was this?

Answer 23

This shows that the cytoplasm was capable of inducing muscle cell gene expression. A human cell was used so its gene products could be told apart from the mouse products. Liver cells because it shows that a exoderm cell can be induced into a mesoderm cell type.

Question 24

Regenerative medicine, taking cells from someone, inducing a clone formation, and then inducing the clones inner cell mass to become the cells you need.

Answer 24

This allows you to use cells from you to help you, and by placing these cells in certain mediums with certain factors we can see differentiation to a specific cell type (though it is not the most reliable thing as of yet)

Question 25

To routes for regenerative medicine:

Answer 25

Take a skin cell and ovum, make a clone of your self, harvest your clones inner cell mass, grow those cells in certain media to become the tissue you need.
Alternatively, take skin cells, expose them to a retroviral infection and insertion of four genes, induction to pluripotent stem cells iPS (induced pluripotent stem cells), you can then take pluripotent stem cells and do as you wish with them.

Question 26

In a study promoting the possibility of pluripotent stem cells, it was noted that you could take mice fibroblasts, treat with retroviral therapy (used to induce both iPS transition and production of brown pigment in white mice), the cells could then be inserted within a blastocyst (a normal one), and result in the formation of a chymeric mouse.

Answer 26

This shows that these iPCs will indeed behave like an inner cell mass cell, and contribute to the organism at large, importantly, you can then breed the mouse, and it will produce perhaps 10 normal progeny mice, and one mouse that has its chimeric trait as a full trait (meaning that this stem cell came from the chimera you created with your retroviral therapy), this shows that you can place a trait into your laboratory animals and by breeding two chimeras together, or the progeny of one chimera together, you can eventually see a mouse homozygous for your desired genotype!

Question 27

iPS placed within a blastocyst become normal cells, iPS directly injected into a mouse become…

Answer 27

cancerous. Environment matters with this form of therapy. It is honestly a little naive to believe that a iPS will act just like a skin cell though without all the developmental triggers…

Question 28

Three methods of causing insulin production to return.

Answer 28

1, You can ‘transdifferentiate in vivo’, so you could treat the adult pancreas or liver with certain molecules to cause the formation of insulin producing cells.
2, Somatic cell nuclear transfer and cloning followed by inner cell mass harvest and induce to insulin producing cells
3, You could use iPS cells directly, inducing them into insulin producing cells.

All three methods seem to lack a means of inducing actual insulin production in a patients whose native host cells do not produce insulin. Maybe that is not a condition however.

Question 29

Fibroblasts ->

Answer 29

Neurons in vivo.

Shows few barriers are differentiated. This process is called transdifferentiation.