Bio105 Exam3 Notes.txt

#27Oct2011

Website reference

Endoderm

Ectoderm

Mesoderm

What are the three processes of gastrulation?

Describe patterning.

Describe cell fate specification

Describe morphogenetic events

What are the different types of cell movements during gastulation?

Invagination

Ingression

Involution

Intercalation

Epiboly

Convergent extension

Describe sea urchin gastrulation

What drives cell movements?

Blastopore

Describe mesenchyme

What cell movements occur in Xenopus gastrulation?

What is a Bottle Cell?

How does the blastopore lip of the frog form?

How would you show blastopore cells involved in invagination during gastrulation in frog?

How would you show hormones are involved in invagination during gastrulation in frog?

In frogs, the ___ cells move using ___ resulting in the ___ or ___ of the embryo.

In frogs, ___ cells ___ and instead of ___, their movement results in a ___. These cells produce ___ and ___.

What mechanism of cell movement is involved in zebrafish gastrulation?

What proteins are involved in zebrafish gastrulation?

Describe Wnt in terms of zebrafish gastrulation.

Describe Nodal in terms of zebrafish (all vertebrates) gastrulation.

Describe BMP in terms of zebrafish gastrulation.

Describe FGF in terms of zebrafish gastrulation.

What does FGF do in the chick?

Describe FGF8 in the chick.

What does FGF8 do in the mouse?

Describe FGF4 in the chick.

___ is expressed in the sphere stage of zebrafish, and is responsible for ___.

___ is expressed in the 50% ___ stage of zebrafish and is responsible for ___.

___ is expressed in the shield stage of zebrafish and is responsible for ___.

___ is expressed in the shield stage of zebrafish and is responsible for ___.

___ is expressed in the 75% ___ stage of zebrafish and is responsible for ___.

___ is expressed in the talibud stage of zebrafish and is responsible for ___.

The zebrafish embryo develops from ___.

In chick development, the ___ narrows and lengthens forming the ___ -- the chick's ___.

In chick development, ___ cells ___ at the midline and ___ at the primitive streak.

What are epiblast cells?

What are trophoblast cells?

Implantation

In the human embryo, ___ cells develop first since the ___ and ___ are needed first.

___ have a distinct pattern of ___ and ___.

Prospective ___ cells migrate as an ___ and go through ___.

Prospective ___ cells migrate as ___ cells (loosely associated).

Prospective ___ cells move as a ___ cell migration.

Prospective ___ cells exhibit ___ behavior.

What determines whether a cell becomes mesoderm or endoderm?

___ signalling is essential for ___ formation and ___ leading to that layer.

___ modulation is critical for cell migration.

The canonical ___ pathway is involved in regulating ___ and ___.

The non-canonical ___ pathway regulates ___, but not directly to ___.

#3Nov2011 - Part 1

What are 5 common pathways used in early development and ruing patterning?

The 5 common pathways in early development are ___ in ___ and ___.

Wnt is a ___.

For the Canonical Wnt pathway, in the absence of Wnt, ___.

How is beta-catenin hyperphosphorylated?

For the Canonical Wnt pathway, when Wnt ligand binds to the receptor, ___, ___.

What happens after the stabilization of beta-catenin?

Beta-catenin is a ___ and requires ___ to work. Its activation results in ___.

What is ubiquitin?

For the non-canonical Wnt pathway, Wnt binds to ___.

Binding of Wnt in the non-canonical pathway leads to ___.

___ and ___ are not used in the non-canonical Wnt pathway but are used in the canonical Wnt pathway.

The TGF-beta/BMP pathways lead to ___.

TGF stands for ___ and is a ___.

TGF is a family of proteins that include ___ and is involved in ___.

TGFs are ___ that ___ receptors on the membrame and activate ___ leading to ___.

SMADs activate ___.

Notch receptors are ___ composed of ___, ___, and ___ domains.

In mammals, members of the ___ and the ___ families, which are located in the ___ cell, function as ___ that activate ___.

Upon ligand binding, the ___ is cleaved away (___ cleavage) from the ___ domain by ___.

After cleavage, the ___ remains bound to the ligand and this complex undergoes ___ and ___ within the ___.

In the signal-receiving cell, a ___ event mediated by ___ releases the ___ from the ___ (___).

After the third cleavage, ___ translocates to the ___ and associates with the ___ family transcription factor complex which results in ___.

Question for Dr. Soto: In notch pathway, what are the three cleavage events?

What occurs after NICD enters the nucleus?

___ or ___ can bind to the notch receptor.

Describe the Hedgehog pathway.

What ligands are involved in the Hedgehog pathway?

What receptors are involved in the hedgehob pathway?

What is the ultimate target of the Hedgehog pathway in the fruitfly?

What is the role in development of the Hedgehog pathway?

Describe Patch.

Describe Smoothened.

Describe the Intracellular Hedgehog Signalling Complex (HSC)

What happens if there is no Hh?

What happens when Hh is present?

It is not understood how ___ goes from being ___ to soluble when Hh binds.

Hh proteins are not released ___; they are released into ___.

#3bNov to follow

Describe the notochord.

Describe somites.

In developing vertebrate embryo, somites are masses of ___ distributed along the two sides of the ___.

Somites will eventually become ___ (___), ___ (___), and ___ (___).

The ___ differentiates before the ___ and ___, so the term ___ is sometimes used to describbe the combined ___ and ___.

Neural tissue forms from ___ except for the ___ which develops from ___.

Somites bud off as cubes from ___ tissue (from ___ mesoderm).

What are the four compartments of somites?

___ cells are transitional cells. They are ___-potent.

Somites undergo MET, ___.

Ventral influences on somites include ___ and ___.

The dorsal portion of the somite becomes ___, which then becomes ___ and ___.

The ventral portion of the somite becomes ___, which then becomes ___.

The gradient from the notochord yields ___ for the nearest part of the somite, and ___ for the farthest part.

Wnt and dermomyotome yields ___.

Wnt + Shh and dermomyotome yields ___.

Describe the signals involved in early somite development.

What determines which eventually fate of structures?

Shh is secreted by both the the ___ and the ___.

Bone structure differentiation is driven by ___.

Noggin binds and inactivates ___.

#End of 3bNov2011

Convergent extension, migration, and thickening of cells leads to __.

Describe the various models and the movements in each.

Ventral cells are influenced by __.

Gli is activated by __ and activates what type of cell(s)?

Dorsal cels are influenced by ___.

Gli is an ortholog of ___.

Noggin inhibits ___ which inhibit ___.

Wnts activate ___ which lead to ___.

The ___ half produces ___ from the dorsal part of the neural tube.

The ___ half produces ___ from the ectoderm.

The dorsal portion gives rise to the ___.

The midline gives rise to the ___.

Canonical wnts give rise to the ___ which, along with ___, give rise to ___.

___ and ___ are muscle-specific transcription factors activated by ___.

In post-mitotic myoblasts, ___ and ___ act together (or ___) to form ___.

Wnts promote a ___ fate. ___ promote a ___ fate. The ___ requires both signals.

In vivo experiments show that the maturing somite contain ___ for both Wnt and ___.

Explant experiments with just ___ showed that Shh antognizes ___ by ___. Similarly, Shh is antagonized by expression of ___ in the ___.

Describe the Growth-arrest specific gene 1(Gas1).

BMP4 is expressed ___, ___ MyoD expression, and induces ___ which is required for ___.

After the "normal" dermis is formed, ___ induces the formation of ___ dermis in ___ resulting in ___.

N-cadherin is expressed in ___. But as it differentiates, the ___ loses expression. The ___ is responsible for this downregulation which was demonstrated by a ___ experiment.

The dermomyotome has a ___ rate of cell division, and is not ___. It is composed of a ___ pool of ___ with different ___.

Some cells in the dermomyotome ___ and give rise to ___ and ___. Others undergo ___ and contribute to the ___.

In the dermomyotome, cells close to the ectoderm give rise to ___.

What are the two types of cleavage planes (or cell divisions) in the dermomyotome?

Describe planar cell divisions.

Describe apico-dorsal cell divisions.

Describe myogenic precursors.

Once a cell expresses ___, it has ___ to a muscle cell.

The ___ is competent to give rise to the dermis. There is no exclusive marker for the ___ in the dermamyotome.

It is not known what ___ regulate dermis differentiation, but they appear to be released by ___.

Wnt regulates ___ in ___.

Myogenic cells need ___.

Describe what is required for differentiation for different cell types.

#8Nov2011

Osciallatory gene expression patterns occur during ___.

Cells migrate and "clump" every __ hours.

What ___ and __ these oscillations, the "___", is unknown.

The ___ pathway is involved in the oscillations and its expression also ___.

What three pathways are hypothesized to control the timing of somite formation?

What evidence is there for the three pathways to control somite formation?

What two questions remain unanswered w.r.t. somite oscillations?

How do we know that the three pathways are not the master oscillator?

What is one implication of these oscillations?

___ is important in somitogenesis because if its knocked out, ___.

The initial gene targes for Notch/NICD are ___.

Hes/Her genes are regulated by ___.

Notch is bound and activated by ___, and after 2 ___, ___ is expressed ___ the pathway.

What are two outcomes of the Notch pathway?

Describe the differentiation outcome of the Notch pathway.

In lateral inhibition, the cell with ___ Notch signalling activity ___ has ___ expressed and ___.

Describe the inhibiting differentiation outcome of the Notch pathway.

Different outcomes of the Notch pathway are important because ___.

Somite periodicity varies by species including ___ for the chick, ___ for the zebrafish, and ___ for the mouse.

Somite periodicity is hypothesized to be regulated by a ___.

Each oscillation cycle corresponds oto the production of ___.

Regulators of the oscillation cycle include ___, but are ___.

Notch's defined role is ___, but is not involved in actual ___ since disruption of ___ does not prevent ___.

Cell clocks in a clump are ___ and lead to ___.

Experiments in ___ embryos at different points of somite formation where treated with ___.

Zebrafish were used because ___.

DAPT does the following: ___.

Gamma-secretase does what?

What were the results of the zebrafish experiment?

Propose a cellular experiment similar to the zebrafish experiment.

What are two proposed Notch functions w.r.t. somite development.

Zebrafish DAPT experiments on somite boundaries must be done ___ because these boundaires are ___.

#10Nov2011

Hox genes were first identified in the ___ and was called ___.

The Hox genes are involved in ___.

In the fruit fly, there are ___ hox genes in ___ cluster(s).

In mammalian species, there are ___ genes in ___ cluster(s) possibly for ___.

In mammalian species, there are ___ members in ___ groups based on ___ and due to ___.

The order of genes in the fruit fly is ___.

There are ___ regions of expression for hox genes, but they are activated ___.

Expression and establishment of anterior initiated during ___.

Early expression of hox genes include ___.

After gastrulation, expression of hox genes include ___ and in .

After the notochord activates ___ and ___ activating ___, hox genes activate depending on the ___ of the somite.

Hox genes have ___ with position of tissue, i.e. expression correlates to ___.

AP changes of Hox expression appear ___.

Hox expression in somites are not due to ___, but ___ due to ___.

In the chick, hoxb9 expression regulates ___.

Hox__ is normally expressed in ___ region. If ectopically expressed, vertebrae are ___.

If Hox__ is knocked out, ___ become ___.

The occiptal skull bone is derived from ___.

The thoracic skeleton is ___. The ___ is derived from two bands in ___.

Axial skeleton fate occurs ___.

___ experiments in the ___ show that the skeletal axial pattern of ___.

Axial fate of skeleltal somites appears to be set as ___ and ___ form from the ___ to the ___.

Study slide from 10Nov2011 on knockout experiments of hox genes on skeletal structure.

#15Nov2011

Hox genes are organized from __ to __.

The ___ gives rise to the vertebrate nervous system.

The notochord induces the ___ to become the ___.

The neuroepithelium folds and becomes the ___.

The cells above the notochord comprise the ___.

___ cells migrate laterall to the neural tube and become ___.

The notochord's induction of the ectoderm leads to formation of ___ and ___.

Neural tube development occurs in two ways:

Describe primary neurulation.

Describe secondary neurulation.

___ and ___ have a mix of primary and secondary neurulation while ___ only have secondary.

Name the steps of primary neurulation in chicks.

___ is expressed in the neural plate while ___ is expressed in the presumptive epidermis.

___ is sufficient for neural tube formation. This was determined by an experiment using ___ in ___.

In a chick embryo at 24 hours, the anterior portion beings ___, while the posterior portion begins ___.

___ is critical in NT formation.

___ cells arise from interactions and ___ from the neural tube and the ___.

Research has show that ___ cells generte the neural plate.

The medial ectoderm ___ and is induced by the ___ to ___.

Surface ectoderm ___ and gives rise to ___ and ___.

Cranial placodes give rise to ___ which have special ___.

Neural crest cells ___ and give rise to both ___ and ___.

___ cells do not give rise to brain structures, but instead to ___.

___ cells give rise to brain structures (___) as well as ___.

Do neural crest cells originate from a discrete pool of cells?

Differentiation of neural crest cells occur ___.

Before NT closure, cells in the ___ can give rise to ___.

If a cell is placed within the fold of the neural plate before closure, ___, but not after.

There is evidence implicating ___ in inducing ___ NT cells to give rise to ___.

The notochord is ___ to induce the entire NT, i.e. it ___ the ___ side of the NT.

Neural crest cells are induced by interactions with ___ cells; i.e. a ___ must be present for these cells to be formed.

It has been shown that ___ prospective neural crest cells in a different location ___.

A neural crest inducer must be a ___ molecule. Candidates include ___.

BMP-4/7 are ___ to induce neural crest phenotype from ___.

What genes/proteins are expressed only in the dorsal NT?

Neither ___ nor ___ are required for formation of all neural crest cells.

___ are expressed as a result of ___ interactions with the dorsal NT. They are ___ by the ___, so are only expressed on the dorsal side.

How do you show what genes/proteins are required for the formation of neural crest cells?

There are ___ sub-families of cadherins.

All cadherins bind to ___.

Cadherins type ___ bind to intracellular proteins alpha and beta ___ (i.e. interact with ___).

Some cadherins bind to ___ involved in ___ pathways.

Cadherins ___ are expressed during NT development and ___.

During the formation of the NT, there are many different ___ for different ___.

The Xena protein is expressed in the ___ and is involved in ___.

Knockdown of Xena results in ___ and ___ cells instead of ___ ones. Earlier injections result in ___.

Xena is required for ___.

Knockdown of Xena results in more cells expressing ___.

Xena knockdown prevents NT cells from ___.

Neural tube related birth defects include ___ and ___, a failure to ___.

Anencephaly is the ___.

Spina bifida is the ___.

#17Nov2011

Cells in the limbs originate from ___.

___ are responsible for vertebrate limb development.

What is the proximal signal for a new limb?

What centers coordinate PD and AP limb axis development?

What hormone(s) is(are) associated with the AER?

What hormone(s) is(are) associated with the ZPA?

What are the three compartments of the PD axis?

The anterior portion of the AP axis corresponds to ___.

The posterior portion of the AP axis corresponds to ___.

What are the models of limb formation?

Describe Wolpert's French flag model.

The AER controls ___ and ___ of the PD limb-bud axis.

Describe the formation of the AER?

If the chick AER is removed early in limb formation, ___.

The PD identities of the mesenchymal cells is influenced by ___.

The most distal cells depend on the AER the ___.

The limb bud is not ___.

If the tip on the bud is removed, ___.

Grafted AER tissue or ___ induces ___.

AER removal induces ___ which can be rescued by ___.

Describe the progress zone model.

Transplantation of cells at tip expressing FGF shows that cells were ___ because they form ___.

What is the role of ZPA?

Ectopic expression of ___ OR transplantation of the posterior limb bud mesenchyme to the anterior margin recipient wing buds resulst in ___.

Transplantation experiments limb bud mesenchyme cells shows that ___ depends on the ___ of cells transplanted.

What two hormones are in the two-gradient model?

RA signaling turns on ___ which are expressed in ___.

RA is involved in inducing ___ and inhibiting ___.

What enzyme would you knock out to knock out RA synthesis?

What would you expect with the knockout of RALDH?

What happens if RA is injected into the distal region of a limb?

What FGFs are used in limb development?

Describe FGF-10

Describe FGF-4, 9, 17

Describe FGF-8

What is the stylopod?

Describe FGF-9

List the problems with the Progress Zone Model.

According to the Progress Zone model, proximal structures are formed ___ than distal structures.

Good web info.

Describe the Differentiation Front Model.

Shh specifies the ___ and ___ identities.

Shh is expressed in the ___.

Hox d is involved in activation of ___.

Shh expression regulates the formation of ___.

Digits ___ and ___ require long-range interactions of ___.

Most of digit ___ requires short term expression of ___.

Digits ___ and ___ require long-term expression of ___.

In the chick, determination of progenitor cells to give rise to ___ is regulated by ___, which targets ___.

#22Nov2011

Urodele ___ (___) and ___ are capable of limb regeneration.

Salamanders can regenerate:

Salamander regeneration requires which to germ layers to regrow?

What is the blastema?

What types of experiments were used to identify signal pathways of regeneration?

What proteins/signals were found to be involved in the regeneration pathways?

Adult frogs and toads have ___ ability to regenerate lost limbs.

What are three basic steps in limb regeneration?

Why do the cells in the blastema become disorganized?

Nerve enervation is required for ___.

If the nerve is amputated at the ___ of the limb, it ___.

Neurotrophins are a family of ___ that ___.

Neurotrophic factors are required for ___.

Transplantation of nerve tissue ___.

What are three requirements for the "inducer" of limb regeneration?

___ has been proposed as the inducer for limb regeneration.

___ is expressed by ___ of amputated limbs at day __ until day __.

What are three steps of fin regeneration?

___ cells don't normally divide.

During limb regeneration, differentiated adult tissue rapidly ___.

Proteins released due to amputation include:

After amputation, FGFs trigger ___.

Describe miR-133.

What are three approaches used in regenerative medicine?

Shh is ___ for digit regeneration.

The plasticity of differentiated cells refers to how some differentiated mammalian cells have ___, including ___.

It is ___ to alter mammalian gene expression patterns to induce limb regeneration.

Hox __ is expressed at high levels in the ___, but it is ___ after limb development in the mouse.