Bio105 Exam3 Notes.txt

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Bio105 Exam3 Notes.txt
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  1. #27Oct2011
  2. Website reference
    http://biology.kenyon.edu/courses/biol114/Chap14/Chapter_14.html
  3. Endoderm
    the most internal germ layer, forms the lining of the gut and other internal organs.
  4. Ectoderm
    the most exterior germ layer, forms skin, brain, the nervous system, and other external tissues
  5. Mesoderm
    the the middle germ layer, forms muscle, the skeletal system, and the circulatory system
  6. What are the three processes of gastrulation?
    • Patterning
    • Cell fate specification
    • Morphogenetic events
  7. Describe patterning.
    • Dynamic, spatial and temporal specification of cell behaviors and tissue properties
    • e.g. formation of limbs, spinal cord, somites, etc
  8. Describe cell fate specification
    Determination (decision-making) of final fates
  9. Describe morphogenetic events
    • Cell movements that result in unique morphological and functional structures
    • e.g. neuron outside of spinal chord
    • e.g. limb outside of somite
  10. What are the different types of cell movements during gastulation?
    • Invagination
    • Ingression
    • Involution
    • Intercalation
    • Epiboly
    • Convergent extension
  11. Invagination
    Sheet of cells move inward
  12. Ingression
    Single cells migrate as mesenchymal cells from epithelium
  13. Involution
    • An epithelial group of cells rolls underneath to form a deeper level
    • e.g. formation of embryonic cavity
  14. Intercalation
    • Cells from two rows move between one other to form a single cell layer
    • Results in increase in length (cell division and flattening)
  15. Epiboly
    • Moving layer of cells on surface
    • e.g. Epithelial cells spread across the embryo
    • Most studied in zebrafish
  16. Convergent extension
    • Highly directional intercalation.
    • Cells converge by intercalating perpendicular to the axis of extension, resulting in the overall extension of the tissue in a preferred direction.
  17. Describe sea urchin gastrulation
    • Cell adhesion properties of migrating cells change (driven by cadherin expression)
    • Mesenchyme cells (multipotent embryonic connective tissue/cells) move by ingression and will form mesoderm
    • Cells in vegetal plate undergo primary invagination to form archenteron
    • Mouth forms at animal pole where archenteron meets ectoderm
    • Vegetal pole forms anus
  18. What drives cell movements?
    Cell adhesion properties of cadherins and integrins change binding to other cells and extracellular matrix
  19. Blastopore
    • Region of embryo where cells move to begin forming mesoderm
    • "Primitive streak" in mammals
  20. Describe mesenchyme
    • Migrate by ingression
    • Poorly differentiated
    • Give rise to mesoderm
  21. What cell movements occur in Xenopus gastrulation?
    • Invagination below center of gray crescent to form dorsal lip of future blastopore
    • Animal pole cells move across surface and involute into interior of embryo to form endoderm and mesoderm
    • Convergent extension when cells cover embryo and elongate
  22. What is a Bottle Cell?
    Cells forming the blastapore lip that change shape (apical constriction) in frog gastrulation allowing cells to invaginate
  23. How does the blastopore lip of the frog form?
    • Bottle cells change shape
    • Hormones released which drive invagination
    • Shape of cells allow migration between the cells (in theory)
  24. How would you show blastopore cells involved in invagination during gastrulation in frog?
    • Cell ablation should result in lack of invagination
    • Must also show hormones not produced by western or immunostaining
    • Also can use transplantation to show that it occurs
  25. How would you show hormones are involved in invagination during gastrulation in frog?
    Knockdown (not knockout since frog is not genetic organism) of hormone
  26. In frogs, the ___ cells move using ___ resulting in the ___ or ___ of the embryo.
    involuting marginal zone (IMZ), convergent extension, lengthening, stretching
  27. In frogs, ___ cells ___ and instead of ___, their movement results in a ___. These cells produce ___ and ___.
    ventral IMZ, intercalate, extending, thickening. ventral mesoderm, somites
  28. What mechanism of cell movement is involved in zebrafish gastrulation?
    Epiboly
  29. What proteins are involved in zebrafish gastrulation?
    • Wnt
    • Nodal
    • BMP
    • FGF
  30. Describe Wnt in terms of zebrafish gastrulation.
    • Both canonical (beta-catenin) and non-canonical pathways
    • Regulates organizrs in both the frog and fish
    • Regulates both cell movements and cell specification (differentiation)
  31. Describe Nodal in terms of zebrafish (all vertebrates) gastrulation.
    • Axes formation
    • mesoderm induction
    • neural patterning
    • left-right symmetry
    • tissue morphogenesis
    • Differentiation of mesodermal lineages
  32. Describe BMP in terms of zebrafish gastrulation.
    • Dorso-ventral BMP gradient formed at beginning of gastrulation
    • Mesoderm induction and dorso/ventral patterning of germ layers
    • Modulates E-cadherin expression
    • Promotes epibolic cell movements
    • Cell prolifiation
    • differentiation
    • motility
    • adhesion
    • death
  33. Describe FGF in terms of zebrafish gastrulation.
    Activates expression of Snail (transcription factor which inhibits E-cadherin transcription)
  34. What does FGF do in the chick?
    Regulates cell movement inside embryo
  35. Describe FGF8 in the chick.
    • Expressed in primitive streak
    • Chemorepellant directing cells to move away from blastopore
    • Cells move to blastopore and then release hormones to keep other cells away
  36. What does FGF8 do in the mouse?
    high levels are required for normal mesodermal migration
  37. Describe FGF4 in the chick.
    • Expressed in the extending axial mesoderm
    • Chemoattractant for the dorsal convergence of the lateral mesoderm
  38. ___ is expressed in the sphere stage of zebrafish, and is responsible for ___.
    BMP, dorsoventral patterning and convergence and extension
  39. ___ is expressed in the 50% ___ stage of zebrafish and is responsible for ___.
    Wnt/beta-catenin, epiboly, dorsoventral patterning and germ layer separation
  40. ___ is expressed in the shield stage of zebrafish and is responsible for ___.
    FGF; dorsoventral patterning, germ layer separation, convergence and extension
  41. ___ is expressed in the shield stage of zebrafish and is responsible for ___.
    Nodal/TGF-beta; germ layer separation, convergence and extension
  42. ___ is expressed in the 75% ___ stage of zebrafish and is responsible for ___.
    Wnt/PCP and Wnt/PKC; germ layer separation, convergence and extension
  43. ___ is expressed in the talibud stage of zebrafish and is responsible for ___.
    GPCR; germ layer separation, convergence and extension
  44. The zebrafish embryo develops from ___.
    the top
  45. In chick development, the ___ narrows and lengthens forming the ___ -- the chick's ___.
    primitive streak, primitive groove, blastopore
  46. In chick development, ___ cells ___ at the midline and ___ at the primitive streak.
    epiblast, converge, ingress
  47. What are epiblast cells?
    In mammals, tissue derived from the inner cell mass at the end of cleavage
  48. What are trophoblast cells?
    Form outer layer of blastocyst and develop into large part of the placenta
  49. Implantation
    The embedding of the embryo intot he wall of the uterus
  50. In the human embryo, ___ cells develop first since the ___ and ___ are needed first.
    anterior, brain, heart
  51. ___ have a distinct pattern of ___ and ___.
    Germ layer precursors, gene expression, morphogenetic movements
  52. Prospective ___ cells migrate as an ___ and go through ___.
    ectodermal, epithelial layer, intercalation
  53. Prospective ___ cells migrate as ___ cells (loosely associated).
    endodermal, mesenchymal
  54. Prospective ___ cells move as a ___ cell migration.
    mesodermal, directed
  55. Prospective ___ cells exhibit ___ behavior.
    endoderm, "random walk"
  56. What determines whether a cell becomes mesoderm or endoderm?
    Physical location
  57. ___ signalling is essential for ___ formation and ___ leading to that layer.
    Nodal, mesoderm, cell movement
  58. ___ modulation is critical for cell migration.
    E-cadherin
  59. The canonical ___ pathway is involved in regulating ___ and ___.
    Wnt, cell movements, cell specification
  60. The non-canonical ___ pathway regulates ___, but not directly to ___.
    Wnt, morphogenetic movements, specification
  61. #3Nov2011 - Part 1
  62. What are 5 common pathways used in early development and ruing patterning?
    • Canonical Wnt
    • Non-canonical Wnt
    • TGF-beta/BMP
    • Notch
    • Hedgehog
  63. The 5 common pathways in early development are ___ in ___ and ___.
    highly conserved, evolution, cancer
  64. Wnt is a ___.
    hormone
  65. For the Canonical Wnt pathway, in the absence of Wnt, ___.
    beta-catenin is hyperphosphorylated
  66. How is beta-catenin hyperphosphorylated?
    • Destroyed by "destruction" complex
    • Ubiquitin binds
    • Removed by proteosome
  67. For the Canonical Wnt pathway, when Wnt ligand binds to the receptor, ___, ___.
    Frizzled/LRP-5/6, beta-catenin is stable (i.e. non-phosphorylated)
  68. What happens after the stabilization of beta-catenin?
    • Translocated into the nucleus
    • Interacts with TCF/LEF proteins
    • Activates transcription
  69. Beta-catenin is a ___ and requires ___ to work. Its activation results in ___.
    transcription factor, a complex of proteins. activation of cell division
  70. What is ubiquitin?
    • Small molecule bound to proteins targetted for removal
    • Results in gene repression
  71. For the non-canonical Wnt pathway, Wnt binds to ___.
    • Frizzled (Fz) receptor, activating several transcription factors in the cytoplasm
    • Neither LDL receptor nor beta-catenin are used
  72. Binding of Wnt in the non-canonical pathway leads to ___.
    cell movements/migrations
  73. ___ and ___ are not used in the non-canonical Wnt pathway but are used in the canonical Wnt pathway.
    LRP receptor, beta-catenin
  74. The TGF-beta/BMP pathways lead to ___.
    Differentiation
  75. TGF stands for ___ and is a ___.
    Transforming Growth Factor, hormone
  76. TGF is a family of proteins that include ___ and is involved in ___.
    Vg1, Nodal, BMPs (bone structures); patterning
  77. TGFs are ___ that ___ receptors on the membrame and activate ___ leading to ___.
    dimers, cross-link, signal transduction pathways, differentiation
  78. SMADs activate ___.
    differentiation genes
  79. Notch receptors are ___ composed of ___, ___, and ___ domains.
    single-pass transmembrane proteins, functional extracellular (NECD), transmembrane, intracellular
  80. In mammals, members of the ___ and the ___ families, which are located in the ___ cell, function as ___ that activate ___.
    Delta-like, Jagged, signal-sending, ligands, Notch signaling receptors
  81. Upon ligand binding, the ___ is cleaved away (___ cleavage) from the ___ domain by ___.
    NECD, S2, TM-NICD, TACE (ADAM metalloprotease TNF-alpha converting enzyme)
  82. After cleavage, the ___ remains bound to the ligand and this complex undergoes ___ and ___ within the ___.
    NECD, endocytosis, recycling/degradation, signal-sending cell
  83. In the signal-receiving cell, a ___ event mediated by ___ releases the ___ from the ___ (___).
    second cleavage, gamma-secretase, NICD, TM, S3 cleavage
  84. After the third cleavage, ___ translocates to the ___ and associates with the ___ family transcription factor complex which results in ___.
    NICD, nucleus, CSL (CBF1/Su(H)/Lag-1), activation of the notch target genes
  85. Question for Dr. Soto: In notch pathway, what are the three cleavage events?
    • Intra and extra cellular domains cleave
    • TM from NICD
    • ?
  86. What occurs after NICD enters the nucleus?
    • Activation of transcription
    • Cell division
    • Differentiation
  87. ___ or ___ can bind to the notch receptor.
    Delta, Jagged
  88. Describe the Hedgehog pathway.
    • Contains a family of secreted proteins (hormones)
    • Found in vertebrates and invertebrates
    • Function in development
  89. What ligands are involved in the Hedgehog pathway?
    • Invertebrates: hedgehog
    • Vertebrates: sonic, desert, Indian hedgehob
  90. What receptors are involved in the hedgehob pathway?
    • both: Patch
    • invertebrates: smoothened
  91. What is the ultimate target of the Hedgehog pathway in the fruitfly?
    cubitus interruptus (Ci), a transcription factor
  92. What is the role in development of the Hedgehog pathway?
    Cellular proliferation, growth, axon path finding, and somite development in vertebrates
  93. Describe Patch.
    • Ptc is a membrane receptor that binds to Hh to activate Smo
    • Levels of membrane Ptc decrease after binding due to endocytosis
  94. Describe Smoothened.
    Smo is an intermembrane protein that, when activated, relays signals to HSC
  95. Describe the Intracellular Hedgehog Signalling Complex (HSC)
    • Coastal 2 (Co2): kinesin-related protein
    • Fused (Fu): Ser/Threo kinase
    • Supressor of fused (Su/Fu)
    • Ci
  96. What happens if there is no Hh?
    HSC is attached to microtubule (MT) complex which truncates Ci which becomes a repressor
  97. What happens when Hh is present?
    Differential binding of Hh to PTC leads to dissociation from MT complex and production of Ci trans-activators which activates target genes
  98. It is not understood how ___ goes from being ___ to soluble when Hh binds.
  99. Hh proteins are not released ___; they are released into ___.
    freely; cytoneme (long and thin tubes connecting cells)
  100. #3bNov to follow
  101. Describe the notochord.
    • Most dorsal region of the mesoderm
    • Ancestral structure persisting in some chordates, but only found in embryos of verterbrates
    • Function is differentiation - sends signals to somites
    • Releases hormones to ectoderm cells to form neural plate
  102. Describe somites.
    • A division of the body of an animal.
    • Ventro-lateral mesoderm (paraxial mesoderm)
    • Gives rise to bone, cartilage, skin dermis (dorsal side of body)
  103. In developing vertebrate embryo, somites are masses of ___ distributed along the two sides of the ___.
    mesoderm, neural tube
  104. Somites will eventually become ___ (___), ___ (___), and ___ (___).
    dermis (dermatome), skeletal muscle (myotome), vertebrae (sclerotome)
  105. The ___ differentiates before the ___ and ___, so the term ___ is sometimes used to describbe the combined ___ and ___.
    sclerotome, dermatome, myotome, dermomyotome, dermatome, myotome
  106. Neural tissue forms from ___ except for the ___ which develops from ___.
    ectoderm, spinal cord, mesoderm
  107. Somites bud off as cubes from ___ tissue (from ___ mesoderm).
    mesenchymal, paraxial
  108. What are the four compartments of somites?
    • sclerotome: vertebrae and rib cartilage
    • myotome: musculature of the back, ribs and limbs
    • dermatome: skin on the back
    • syndetome: tendons and some blood vessles
  109. ___ cells are transitional cells. They are ___-potent.
    Mesenchymal, multi
  110. Somites undergo MET, ___.
    Mesenchymal epithelial transitions
  111. Ventral influences on somites include ___ and ___.
    notochord, ventral portion of the neural tube
  112. The dorsal portion of the somite becomes ___, which then becomes ___ and ___.
    epithelial dermomyotome, dermatome, myotome
  113. The ventral portion of the somite becomes ___, which then becomes ___.
    the mesenchymal sclerotome, bone
  114. The gradient from the notochord yields ___ for the nearest part of the somite, and ___ for the farthest part.
    sclerotome, dermomytome
  115. Wnt and dermomyotome yields ___.
    dermatome
  116. Wnt + Shh and dermomyotome yields ___.
    myotome
  117. Describe the signals involved in early somite development.
    • Dorsally: Wnts (canonical and non-canonical)
    • Ventrally: (secreted by notochord) - Shh and Noggin
  118. What determines which eventually fate of structures?
    Location (e.g. dorsal, ventral, distance from notochord, etc.)
  119. Shh is secreted by both the the ___ and the ___.
    notochord, neural tube
  120. Bone structure differentiation is driven by ___.
    Shh and Noggin
  121. Noggin binds and inactivates ___.
    bone morphogenetic protein (BMP)
  122. #End of 3bNov2011
    #Beginning of 8Nov2011
  123. Convergent extension, migration, and thickening of cells leads to __.
    somites
  124. Describe the various models and the movements in each.
    Look this up
  125. Ventral cells are influenced by __.
    Shh and noggin
  126. Gli is activated by __ and activates what type of cell(s)?
    Shh, myogenic and dermogenic
  127. Dorsal cels are influenced by ___.
    Wnt
  128. Gli is an ortholog of ___.
  129. Noggin inhibits ___ which inhibit ___.
    BMPs, Wnt
  130. Wnts activate ___ which lead to ___.
    Epithelialization, myogenic and dermogenic cells
  131. The ___ half produces ___ from the dorsal part of the neural tube.
    medial, Wnt1 and Wnt3a
  132. The ___ half produces ___ from the ectoderm.
    Wnt4, Wnt6, and Wnt7
  133. The dorsal portion gives rise to the ___.
    dermis
  134. The midline gives rise to the ___.
    muscle
  135. Canonical wnts give rise to the ___ which, along with ___, give rise to ___.
    epithelial cells, Gli 1 and 2 (from Shh), muscle
  136. ___ and ___ are muscle-specific transcription factors activated by ___.
    MyoD, Myf5
  137. In post-mitotic myoblasts, ___ and ___ act together (or ___) to form ___.
    Dorsal Wnts, ventral Shh (along with Gli), synergize, muscle
  138. Wnts promote a ___ fate. ___ promote a ___ fate. The ___ requires both signals.
    dorsal epithelial dermomyotomal, mesenchymal sclerotomal, both
  139. In vivo experiments show that the maturing somite contain ___ for both Wnt and ___.
    antagonists, Shh and noggin
  140. Explant experiments with just ___ showed that Shh antognizes ___ by ___. Similarly, Shh is antagonized by expression of ___ in the ___.
    somites (no notochord, etc.), Wnt, upregulating Ptc1. frizzled-related protein (sfrp2), scleratome
  141. Describe the Growth-arrest specific gene 1(Gas1).
    • Its protein products work together with p53 (stops growth)
    • Prevents cells from entering S phase which stops cell division which stops Shh pathway
  142. BMP4 is expressed ___, ___ MyoD expression, and induces ___ which is required for ___.
    in the doral neural tube, represses, Wnt11 expression in the dermamyotome, dermis differentiation
  143. After the "normal" dermis is formed, ___ induces the formation of ___ dermis in ___ resulting in ___.
    BMP2, dense, the chick, feathers
  144. 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 entire early somite. scleromyotome. notochord, implantation
  145. The dermomyotome has a ___ rate of cell division, and is not ___. It is composed of a ___ pool of ___ with different ___.
    high, uniform. heterogeneous, progenitor cells, cell division patterns
  146. Some cells in the dermomyotome ___ and give rise to ___ and ___. Others undergo ___ and contribute to the ___.
    • delaminate (move away from cell line), limb muscles, blood vessels.
    • EMT (epithelial-mesenchymal transition), dermis.
  147. In the dermomyotome, cells close to the ectoderm give rise to ___.
    dermis of the back, back muscles, limbs, endothelia
  148. What are the two types of cleavage planes (or cell divisions) in the dermomyotome?
    • Planar
    • Apico-basal
  149. Describe planar cell divisions.
    Result in daughter cells adjacent to each other; both differentiate.
  150. Describe apico-dorsal cell divisions.
    One daugther cell lies ventrally into the myotome and retains multipotency. The other lies dorsally and will form the dermis.
  151. Describe myogenic precursors.
    • Express Pax3
    • Once they being differentiation, they express MyoD and Myf5
  152. Once a cell expresses ___, it has ___ to a muscle cell.
    MyoD, committed
  153. The ___ is competent to give rise to the dermis. There is no exclusive marker for the ___ in the dermamyotome.
    entire somite. dermal progenitors
  154. It is not known what ___ regulate dermis differentiation, but they appear to be released by ___.
    factors, ectodermal cells
  155. Wnt regulates ___ in ___.
    Epithelial cells, dermamyotome
  156. Myogenic cells need ___.
    Shh, Pax-3, MyoD, Myf5
  157. Describe what is required for differentiation for different cell types.
    Need to prepare this.
  158. #8Nov2011
  159. Osciallatory gene expression patterns occur during ___.
    • Somite formation
    • Neural progenitor maintenance
    • Limb development
  160. Cells migrate and "clump" every __ hours.
    2
  161. What ___ and __ these oscillations, the "___", is unknown.
    turns on, regulates, core oscillator
  162. The ___ pathway is involved in the oscillations and its expression also ___.
    Notch, oscillates
  163. What three pathways are hypothesized to control the timing of somite formation?
    Notch, Wnt, Fibroblast growth factor (FGF)
  164. What evidence is there for the three pathways to control somite formation?
    • Period of osciallation expressions matches period of somite formation.
    • 50 genes in these pathways have oscillatory patterns of expression.
  165. What two questions remain unanswered w.r.t. somite oscillations?
    • How are these oscillations generated?
    • What protein is the "master oscillator"?
  166. How do we know that the three pathways are not the master oscillator?
    Knockout in zebrafish for these three does not prevent somite formation
  167. What is one implication of these oscillations?
    Cell division for each "clump" is on a different schedule (every 2 hours)
  168. ___ is important in somitogenesis because if its knocked out, ___.
    somites are not fully differentiated
  169. The initial gene targes for Notch/NICD are ___.
    • Hairy/E (spl) family including -
    • Hes genes: mammals
    • Her genes: zebrafish
  170. Hes/Her genes are regulated by ___.
    negative feedback loops
  171. Notch is bound and activated by ___, and after 2 ___, ___ is expressed ___ the pathway.
    delta/jagged, cleavages, Hes/Her, inactivating/repressing
  172. What are two outcomes of the Notch pathway?
    Differentiation and inhibition of differentiation
  173. Describe the differentiation outcome of the Notch pathway.
    Via lateral inhibition, Notch activation leads to a downregulation of Notch signaling which results in differentiation
  174. In lateral inhibition, the cell with ___ Notch signalling activity ___ has ___ expressed and ___.
    high, Hes/her, remains undifferentiated
  175. Describe the inhibiting differentiation outcome of the Notch pathway.
    Notch activation leads to ligand expression, and contiguous cells remain similar.
  176. Different outcomes of the Notch pathway are important because ___.
    they are a way of keeping stem cells undifferentiated
  177. Somite periodicity varies by species including ___ for the chick, ___ for the zebrafish, and ___ for the mouse.
    1 hour, 30 min, 2 hours
  178. Somite periodicity is hypothesized to be regulated by a ___.
    Segmentation clock
  179. Each oscillation cycle corresponds oto the production of ___.
    an additional somite
  180. Regulators of the oscillation cycle include ___, but are ___.
    • mouse: Hes1 & Hes7
    • zebrafish: Her1 & Her7
    • chick: Hairy1 & Hairy7
    • NOT the clock
  181. Notch's defined role is ___, but is not involved in actual ___ since disruption of ___ does not prevent ___.
    keeping cell clocks synchronized, somite formation, notch signalling, somite formation
  182. Cell clocks in a clump are ___ and lead to ___.
    the same, somite
  183. Experiments in ___ embryos at different points of somite formation where treated with ___.
    zebrafish, DAPT
  184. Zebrafish were used because ___.
    They are transparent
  185. DAPT does the following: ___.
    • Directly inhibits gamma-secretase
    • Prevents Notch signalling
  186. Gamma-secretase does what?
    cuts the intracellular portion of Notch
  187. What were the results of the zebrafish experiment?
    Gradual disordering of oscillatory gene expression.
  188. Propose a cellular experiment similar to the zebrafish experiment.
    Hm...
  189. What are two proposed Notch functions w.r.t. somite development.
    • Establishment of somite boundaries
    • Establishment of anterior/posterior somite functional distinction
  190. Zebrafish DAPT experiments on somite boundaries must be done ___ because these boundaires are ___.
    early, lost after the 13th formed somite
  191. #10Nov2011
  192. Hox genes were first identified in the ___ and was called ___.
    fruit fly, the antennopedia complex
  193. The Hox genes are involved in ___.
    body plan segmentation
  194. In the fruit fly, there are ___ hox genes in ___ cluster(s).
    10, 1
  195. In mammalian species, there are ___ genes in ___ cluster(s) possibly for ___.
    39, 4, redundancy
  196. In mammalian species, there are ___ members in ___ groups based on ___ and due to ___.
    2-4, 13 paralogous, sequence similarity and position, gene duplication events
  197. The order of genes in the fruit fly is ___.
    the same as the order of features in the body plan
  198. There are ___ regions of expression for hox genes, but they are activated ___.
    overlapping, independently
  199. Expression and establishment of anterior initiated during ___.
    gastrulation
  200. Early expression of hox genes include ___.
    • 3' of cluster
    • Hoxa1, Hoxb1, Hoxa2, Hoxb2
  201. After gastrulation, expression of hox genes include ___ and in .
    5' of cluster, in the tailbud after formation of anterior somites
  202. After the notochord activates ___ and ___ activating ___, hox genes activate depending on the ___ of the somite.
    noggin, Shh, sclerotome
  203. Hox genes have ___ with position of tissue, i.e. expression correlates to ___.
    spatial colinearity, anterior/posterior axis formation
  204. AP changes of Hox expression appear ___.
    before physical boundaries are established
  205. Hox expression in somites are not due to ___, but ___ due to ___.
    cell migration, turning on/off expression, cell-cell interactions
  206. In the chick, hoxb9 expression regulates ___.
    the timing of cells ingressing thru the primitive streak
  207. Hox__ is normally expressed in ___ region. If ectopically expressed, vertebrae are ___.
    A10, lumbar. converted to lumbar
  208. If Hox__ is knocked out, ___ become ___.
    A10, lumbar, thoracic (ribs)
  209. The occiptal skull bone is derived from ___.
    the sclerotome of the first 4 somites
  210. The thoracic skeleton is ___. The ___ is derived from two bands in ___.
    not completely dervied from somitic mesoderm. sternum, lateral plate mesoderm
  211. Axial skeleton fate occurs ___.
    early in development
  212. ___ experiments in the ___ show that the skeletal axial pattern of ___.
    Transplantation, chick, transplanted donor cells is maintained in the recipient
  213. Axial fate of skeleltal somites appears to be set as ___ and ___ form from the ___ to the ___.
    Neural tube, notochord, anterior, posterior
  214. Study slide from 10Nov2011 on knockout experiments of hox genes on skeletal structure.
  215. #15Nov2011
  216. Hox genes are organized from __ to __.
    3', 5'
  217. The ___ gives rise to the vertebrate nervous system.
    neural tube
  218. The notochord induces the ___ to become the ___.
    ectoderm, neuroepithelium
  219. The neuroepithelium folds and becomes the ___.
    neural tube (future brain and spinal cord)
  220. The cells above the notochord comprise the ___.
    neural plate
  221. ___ cells migrate laterall to the neural tube and become ___.
    • Neural crest
    • Sensory neurons of the PNS
    • Autonomic nervous system
    • Melanocytes
  222. The notochord's induction of the ectoderm leads to formation of ___ and ___.
    the neural tube, neural crest
  223. Neural tube development occurs in two ways:
    • Primary neurulation - invagination
    • Secondary neurulation - cavitation
  224. Describe primary neurulation.
    • Proliferation of the neural plate cells
    • Invagination
    • Pinching off the surface to form the tube
  225. Describe secondary neurulation.
    • A cell layer sinks into the embryo.
    • Cavitation - forming of a hollow tube.
  226. ___ and ___ have a mix of primary and secondary neurulation while ___ only have secondary.
    birds, frogs. mammals
  227. Name the steps of primary neurulation in chicks.
    • 1a. Shaping (of neural plate)
    • 1b. Folding (by notochord)
    • 2. Elevation (by neural crest)
    • 3. Convergence (by neural crest)
    • 4. Closure
  228. ___ is expressed in the neural plate while ___ is expressed in the presumptive epidermis.
    N-cadherin, E-cadherin
  229. ___ is sufficient for neural tube formation. This was determined by an experiment using ___ in ___.
    N-cadherin, ectopic expression, an explant
  230. In a chick embryo at 24 hours, the anterior portion beings ___, while the posterior portion begins ___.
    neurulation, gastrulation
  231. ___ is critical in NT formation.
    Xena protein
  232. ___ cells arise from interactions and ___ from the neural tube and the ___.
    neural crest, induction, epidermis
  233. Research has show that ___ cells generte the neural plate.
    multipotent
  234. The medial ectoderm ___ and is induced by the ___ to ___.
    migrates, notochord, thicken and invaginate into the NT
  235. Surface ectoderm ___ and gives rise to ___ and ___.
    does not migrate, skin epidermis, cranial placodes
  236. Cranial placodes give rise to ___ which have special ___.
    cranial sensory ganglia, senses: auditory, vision, taste, smell
  237. Neural crest cells ___ and give rise to both ___ and ___.
    migrate, neuronal, non-neuronal
  238. ___ cells do not give rise to brain structures, but instead to ___.
    • Trunk
    • sensory neurons, melanocytes, neuroendocrine, Schwann cells
  239. ___ cells give rise to brain structures (___) as well as ___.
    • Cranial
    • cranial sensory ganglia, melanocytes, skull and facial cartilage
  240. Do neural crest cells originate from a discrete pool of cells?
    No. Lineage tracing after NT closure showed that some cells can give rise to CNS and neural crest cells.
  241. Differentiation of neural crest cells occur ___.
    after they migrate out of the influence of the neuroepithelium
  242. Before NT closure, cells in the ___ can give rise to ___.
    neural plate, neural crests, CNS, and epidermis
  243. If a cell is placed within the fold of the neural plate before closure, ___, but not after.
    it can give rise to all three fates
  244. There is evidence implicating ___ in inducing ___ NT cells to give rise to ___.
    shh, ventral, motor neurons
  245. The notochord is ___ to induce the entire NT, i.e. it ___ the ___ side of the NT.
    not sufficient, does not induce differentiation, dorsal
  246. Neural crest cells are induced by interactions with ___ cells; i.e. a ___ must be present for these cells to be formed.
    epidermal, physical interaction
  247. It has been shown that ___ prospective neural crest cells in a different location ___.
    transplanted, still gave rise to neural crest cells
  248. A neural crest inducer must be a ___ molecule. Candidates include ___.
    • diffusible.
    • Dorsalin1
    • BMP-4
    • BMP-7
  249. BMP-4/7 are ___ to induce neural crest phenotype from ___.
    sufficient, neuroepithelium
  250. What genes/proteins are expressed only in the dorsal NT?
    • Dorsalin-1
    • Wnt1
    • Wnt3a
    • Slug
  251. Neither ___ nor ___ are required for formation of all neural crest cells.
    Wnt1, Wnt3a
  252. ___ are expressed as a result of ___ interactions with the dorsal NT. They are ___ by the ___, so are only expressed on the dorsal side.
    • Slug, Pax3, Msx-1/2, dorsalin-1; epidermal
    • inhibited, notochord
  253. How do you show what genes/proteins are required for the formation of neural crest cells?
    • - Show by knockout w/ genetic organism
    • - Explant
  254. There are ___ sub-families of cadherins.
    5
  255. All cadherins bind to ___.
    calcium ions
  256. Cadherins type ___ bind to intracellular proteins alpha and beta ___ (i.e. interact with ___).
    1 and 2, catenin, cytoskeleton
  257. Some cadherins bind to ___ involved in ___ pathways.
    enzymes, signal transduction
  258. Cadherins ___ are expressed during NT development and ___.
    • E, N, 6-B, 7
    • neural crest cells formation
  259. During the formation of the NT, there are many different ___ for different ___.
    cadherins, migrations
  260. The Xena protein is expressed in the ___ and is involved in ___.
    • neural plate,
    • cellular adhesion and cytoskeleton dynamics
  261. Knockdown of Xena results in ___ and ___ cells instead of ___ ones. Earlier injections result in ___.
    • failure to close the NT, round, elongated
    • absence of the neural plate.
  262. Xena is required for ___.
    the changes in cell shape during neurulation and cell-cell adhesion.
  263. Knockdown of Xena results in more cells expressing ___.
    Sox2
  264. Xena knockdown prevents NT cells from ___.
  265. Neural tube related birth defects include ___ and ___, a failure to ___.
    Anencephaly, spina bifida, close
  266. Anencephaly is the ___.
    lack of closure of the NT
  267. Spina bifida is the ___.
    failure of closing the posterior neurospore
  268. #17Nov2011
  269. Cells in the limbs originate from ___.
    somites
  270. ___ are responsible for vertebrate limb development.
    Morphogen hormonal gradients
  271. What is the proximal signal for a new limb?
    Retinoic acid (RA)
  272. What centers coordinate PD and AP limb axis development?
    • Apical ectodermal ridge (AER)
    • Zone of polarizing activity (ZPA)
  273. What hormone(s) is(are) associated with the AER?
    Fibroblast growth factors (FGF)
  274. What hormone(s) is(are) associated with the ZPA?
    Shh
  275. What are the three compartments of the PD axis?
    • Proximal stylopod
    • zeugopod
    • distal autopod
  276. The anterior portion of the AP axis corresponds to ___.
    skeletal morphology of the zeugopod, e.g. radius/ulna or tibia/fibula
  277. The posterior portion of the AP axis corresponds to ___.
    autopod, e.g. digits
  278. What are the models of limb formation?
    • Wolpert's French flag model
    • Progress zone model
    • Early specification/expansion model
    • Differentiation Front model
    • Two signal gradient
  279. Describe Wolpert's French flag model.
    Single gradient from proximal to distal determines limb development
  280. The AER controls ___ and ___ of the PD limb-bud axis.
    outgrowth, patterning
  281. Describe the formation of the AER?
    • Initial limb bud composed of ectodermal pocket filled with mesenchymal cells
    • Outgrowth results in ectodermal thickening/elongation of epithelium at the tip
  282. If the chick AER is removed early in limb formation, ___.
    the limb will not form
  283. The PD identities of the mesenchymal cells is influenced by ___.
    the time of interaction with the ectodermal cells
  284. The most distal cells depend on the AER the ___.
    longest
  285. The limb bud is not ___.
    homogeneous
  286. If the tip on the bud is removed, ___.
    the limb does not form
  287. Grafted AER tissue or ___ induces ___.
    ectopically expressing FGFs, ectopic PD outgrowth.
  288. AER removal induces ___ which can be rescued by ___.
    cell death on the adjacent cells, FGFs
  289. Describe the progress zone model.
    • The AER determines the PROGRESS ZONE, i.e. distal mesenchyme, to acquire a PD fate
    • Determination is a result of TIME SPENT by proliferating undetermined cells in the progress zone
    • This implies cell-cell interactions as opposed to hormone interaction
  290. Transplantation of cells at tip expressing FGF shows that cells were ___ because they form ___.
    Already differentiated, extra digits
  291. What is the role of ZPA?
    It acts as an organizer of AP limb bud axis
  292. Ectopic expression of ___ OR transplantation of the posterior limb bud mesenchyme to the anterior margin recipient wing buds resulst in ___.
    Shh, mirror image duplication of digits
  293. Transplantation experiments limb bud mesenchyme cells shows that ___ depends on the ___ of cells transplanted.
    number of duplicated digits, number
  294. What two hormones are in the two-gradient model?
    Retinoic acid(RA) and FGFs
  295. RA signaling turns on ___ which are expressed in ___.
    • Meis1/2, Hox a11, Hox a13
    • the proximal portion of the limb bud
  296. RA is involved in inducing ___ and inhibiting ___.
    a proximalizing fate of the limb bud, distal fate
  297. What enzyme would you knock out to knock out RA synthesis?
    RALDH
  298. What would you expect with the knockout of RALDH?
    No RA -> short limb w/digits
  299. What happens if RA is injected into the distal region of a limb?
    No digits (but I'm not sure of this answer)
  300. What FGFs are used in limb development?
    • FGF-10
    • FGF-4, 9, 17
    • FGF-8
  301. Describe FGF-10
    • Required for AER-FGF signaling
    • Expressed in limb bud mesenchyme
    • Required for limb development
  302. Describe FGF-4, 9, 17
    • Expressed in AER
    • Offer redundancy
    • FGF-4 can rescue FGF-8
    • Not required for limb development
  303. Describe FGF-8
    • Expressed thruout AER
    • Required for formation of stylopod (e.g. humerous)
    • FGF-4 can rescue FGF-8
  304. What is the stylopod?
    most proximal skeletal element
  305. Describe FGF-9
    • Not involved in differentiation, just cell division
    • Required for most distal skeleton structures
    • Required for proliferative (cell division) expansion of early specified PD axis
  306. List the problems with the Progress Zone Model.
    • FGF-8 deficient mice have no effect on distal elements, but have no proximal elements
    • PD progenitor cells in BUD are specified early
    • Late-stage AER removal eliminates distal mesenchyme, but some stem cells remain to compensate
  307. According to the Progress Zone model, proximal structures are formed ___ than distal structures.
    earlier
  308. Good web info.
    • http://en.wikipedia.org/wiki/Limb_development#Axial_patterning_and_related_issues
    • http://www.utm.utoronto.ca/~w3bio380/lecture19.htm
    • http://www.d.umn.edu/~pschoff/documents/
  309. Describe the Differentiation Front Model.
    • AER/FGF signaling controls survival/proliferation in dose-dependent manner
    • After proliferation, proximal exposed to RA, distal exposed to AER-FGFs
  310. Shh specifies the ___ and ___ identities.
    AP limb, digit
  311. Shh is expressed in the ___.
    ZPA
  312. Hox d is involved in activation of ___.
    Shh gene expression
  313. Shh expression regulates the formation of ___.
    digits 2-5 in mouse and humans (but not thumb)
  314. Digits ___ and ___ require long-range interactions of ___.
    2, part of 3, Shh
  315. Most of digit ___ requires short term expression of ___.
    3, Shh
  316. Digits ___ and ___ require long-term expression of ___.
    4, 5, Shh
  317. In the chick, determination of progenitor cells to give rise to ___ is regulated by ___, which targets ___.
    specific digits, a BMP4 gradient, mesenchymal cells
  318. #22Nov2011
  319. Urodele ___ (___) and ___ are capable of limb regeneration.
    amphibians (salamanders), fish
  320. Salamanders can regenerate:
    limbs, tails, eye parts, spinal cord, portions of intestines and jaw
  321. Salamander regeneration requires which to germ layers to regrow?
    • mesoderm (muscles, skeletal, blood vessels)
    • ectoderm (epidermis, nerves)
  322. What is the blastema?
    A mass of rapidly-dividing mesenchymal cells that migrate to the site of the stump and replace the amputated structure
  323. What types of experiments were used to identify signal pathways of regeneration?
    transplantation, amputations, dissections, irradiations
  324. What proteins/signals were found to be involved in the regeneration pathways?
    Wnts, FGFs, BMPs, Notch, and RA
  325. Adult frogs and toads have ___ ability to regenerate lost limbs.
    limited
  326. What are three basic steps in limb regeneration?
    • 1. epidermis layer covers stump
    • 2. Mesenchymal cells interact and bind
    • 3. These cells become disorganized (less diff) and begin dividing rapidly forming the blastema
  327. Why do the cells in the blastema become disorganized?
    Mesenchymal cells are derived from the mesoderm and thus need to "go back" to be able to form neurons.
  328. Nerve enervation is required for ___.
    rapid cell division and structure formation
  329. If the nerve is amputated at the ___ of the limb, it ___.
    base, will not be regenerated
  330. Neurotrophins are a family of ___ that ___.
    proteins, induce survival/development of neurons
  331. Neurotrophic factors are required for ___.
    blastemal formation and differentiation
  332. Transplantation of nerve tissue ___.
    allows regeneration if nerve tissue is missing
  333. What are three requirements for the "inducer" of limb regeneration?
    • 1. Present in the limb nervous system tissue
    • 2. Induces blastemal formation and differentiation
    • 3. Can rescue amputated limb without nerve tissue
  334. ___ has been proposed as the inducer for limb regeneration.
    Anterior gradient (nAG)
  335. ___ is expressed by ___ of amputated limbs at day __ until day __.
    nAG, Schwann cells, 5, 12
  336. What are three steps of fin regeneration?
    • 1. Wound healing - epidermal covering
    • 2. Blastema formation - rapid cell division and mesenchymal disorganization
    • 3. Regenerative outgrowth - cell division, patterning, differentiation
  337. ___ cells don't normally divide.
    Fully differentiated
  338. During limb regeneration, differentiated adult tissue rapidly ___.
    changes to a proliferative and patterning state
  339. Proteins released due to amputation include:
    FGFs, Wnts, and Activin
  340. After amputation, FGFs trigger ___.
    the expression of microRNAs
  341. Describe miR-133.
    A microRNA which regulates skeletal and cardiac muscle cell differentiation
  342. What are three approaches used in regenerative medicine?
    • 1. Implantation of stem cells for structure regeneration
    • 2. Stem cells are provided with a scaffold to induce regeneration
    • 3. Remaining cells of affected structure are induced to regenerate
  343. Shh is ___ for digit regeneration.
    required
  344. The plasticity of differentiated cells refers to how some differentiated mammalian cells have ___, including ___.
    • some regeneration ability
    • Hepatocytes
    • Peripheral Schwann cells
    • Pancreatic beta cells
  345. It is ___ to alter mammalian gene expression patterns to induce limb regeneration.
    not possible
  346. Hox __ is expressed at high levels in the ___, but it is ___ after limb development in the mouse.
    c6, blastema, turned off

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