Zool 303

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Zool 303
2014-10-09 00:05:46

Up to MT 1
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  1. What do all embryos start out as?
    A single celled organism called a zygote
  2. What are the three arising layers from a zygote?
    • Ectoderm (outer layer)
    • Mesoderm (middle layer)
    • Endoderm (Internal layer)
  3. What type of cells does the ectoderm, mesoderm and endoderm give rise to?
    • Ectoderm: Outer surface, Central nervous system, neural crest
    • Mesoderm: Notochord, Bone tissue, Red blood cell
    • Endoderm: Digestive tube, stomach cell
  4. What is a teratogen? Provide examples
    • Chemicals that alter embryonic development
    • Ethanol - growth and mental retardation
    • Thalidomide
    • Estrogen receptor binding chemicals
    • DDT
    • Polychlorinated biphenyls (PCB)
    • TCDD (Tetrachloro dibenzodioxin)
    • BPA
  5. What is Thaliodomide?
    • A teratogen
    • Developed as sedative and anti-emetic. Not toxic in mice or healthy humans
    • Causes malformations in babies
  6. What are three main genetic causes of birth defects?
    • Trisomies and Monosomies
    • Copy number variations
    • Point Mutations
  7. What is the frequency of clinically significant chromosomal abnormalities at birth?
    1 in 100
  8. What is one thing that is very poor in humans and is a result of trisomies and monosomies?
    • Fertility.
    • Humans have a fertility of around 20%, where as close ape species have a fertility of around 70%
  9. How are trisomies created?
    Usually during anaphase two pairs of homologous chromosomes are paired. In trisomies they are not paired equally and the division in metaphase 2 is unequal.
  10. Describe Down's Syndrome
    • Discovered in 1862
    • Extra copy of chromosome 21
    • Impaired cognitive ability ,distinctive craniofacial features and decreased stature
  11. What is the first chromosome where trisomies can yield live births? Why is this?
    • Chromosome 13
    • This is because the chromosomes are organized by size, and amount of genetic information.
  12. Describe Patau's Syndrome
    • 1 in 12 000 live births
    • Rarely survive 1 year
    • Trisomy 13
  13. Describe Edwards Syndrome
    • 1 in 6000 live birthds
    • Median lifespan 10 days
    • Trisomy 18
  14. What are two Sex chromosome abnormalities
    • Klinefelters Syndrome: 47 XXY
    • Turner Syndrome 45 XO
  15. What are Five types of copy number variation mutations?
    • Deletion: Removal of one section of genetic information
    • Duplication: Copy of one area of genetic information. Twice that amount
    • Inversion: The order of genetic information for an area of the chromosome is flipped
    • Insertion: Insertion of extra information into a chromosome
    • Translocation: Trading of information from one chromosome into another and vice-versa
  16. What are ways we can detect copy number variation mutations?
    • Array Comparative genome hybridization
    • DNA from a control individual and patients are individually labeled with fluorescent dye then compared.
  17. What was originally thought to be the sole cause of mutations
    Point blank mutations
  18. What is the definition of a Mutation
    Changes to the nucleotide sequence of the genetic material of an organism
  19. What are two types of germ line mutations?
    • Germ line mutation: Hereditable
    • Somatic: Somatic cell changes
  20. What are the two general effects of a mutation?
    • Gain-of-function = increase in protein activity
    • Loss-of-function = Decrease in protein activity
  21. Describe the different categories of mutations regarding inheritance
    • Dominant or Semi-dominant = only one copy matters
    • Recessive = both must be mutant to see phenotype
  22. What are different causes of point shift mutations?
    • missense: change of one amino acid into another
    • Nonsense: Change of one amino acid into the codon for stop
    • Frameshift by addition: addition of one 'A, C, T or G'
    • Frameshift by deletion: removal of one
  23. Who was the first embryologist
  24. What is embryology?
    The study of animal development
  25. What is fertilization
    The fusion of the mature sex cells, sperm and egg which are collectively called the gametes
  26. Describe the two parts of an egg
    • Vegetal hemisphere: Bottom part where the yolk is. Provides food for the animal
    • Animal hemisphere: Upper half of the egg
  27. Is frog fertilization internal or external?
  28. Describe fertilization in frog
    • External
    • Haploid nucleus of egg (Female pronucleus) to merge with the haploid nucleus of the sperm (male pronucleus) to form diploid zygote nuceus.
  29. What forms in the animal hemisphere after fertilization?
    A fluid filled cavity - the blastocoel
  30. Describe gastrulation in the frog embryo
    • Begins at a point opposite the point of sperm entry with a formation of a dimple called the blastopore
    • Blastopore expands to a ring and cells migrating through blastopore become the mesoderm.
    • Cells outside become ectoderm
    • Cells in vegetal pole become endoderm
  31. What is a notochord?
    A rod of mesodermal cells in the most dorsal portion of the embryo
  32. What are the steps in Meiosis
    • Meiosis 1: Interphase, Prophase 1, Metaphase 1, Anaphase 1, Telophase
    • Meiosis 2: Metaphase 2, Anaphase 2, Telophase 1
  33. What phase in development to embryos usually look the same?
    Beginning of neurulation
  34. Describe fate mapping
    • Traces cell lineages: following individual cells to see what those cells become
    • Use of molecular dyes and computer imaging to determine what cells develop into
  35. What is an example of a dye that can be used to fate map?
    Fluorescein-Conjugated dextran
  36. What is a chimeric embryo?
    Embryos made from tissues of more than one genetic source
  37. What is GFP
    • Green fluorescent protein
    • Altered gene called a transgene
    • Give cells a virus so that they fluoresce
  38. Describe homologous structures
    • Organs whose underlying similarity arises from their being derived from a common ancestral structure
    • Example wing of bird and human arm
  39. Describe analogous structures
    • Those whose similarity comes from their performing a similar function rather than their arising from a common ancestor.
    • Example wing of butterfly and wing of a bird. Did not arise from common ancestral structure
  40. What are the two major periods in development?
    • Embryonic period (up to 8 weeks in humans)
    • Fetal period (remaining time in utero)
  41. Where is BPA commonly found
    Plastic bottles
  42. What is a fundamental difference between eukaryotic genes from prokaryotic genes?
    • Eukaryotic genes are contained within a complex of DNA and protien called Chromatin.
    • Protein component is around have the weight of chromatin and is composed mostly of histones.
  43. What is the on/off switch for gene expression?
  44. Describe exons and introns
    • Exons are the regions of DNA that code for protein.
    • In between exons are intervening sequences called introns that have nothing to do with the AA sequence of the protein.
  45. In the drosophila oocyte what does Bicoid protein initiate?
    Head and thorax formation
  46. What are the two things that Bicoid does in Drosophila. Explain
    • Bicoid can act as a transcription factor
    • -This activates genes such as hunchback that are necessary for forming the fly anterior
    • Also acts as a translational inhibitor of those genes such as caudal that are critical for making the fly posterior.
  47. Describe Model Organisms
    • Can be both animals and plants
    • An experimental tool to investiage a particular biological process. Model organisms are typically easy to grow in a lab setting and have been an effective means of investigating the cause of human disease without conducting unethical research directly on humans.
  48. Describe how cloning was done in sheep
    • Take the oocyte from a sheep and remove the meiotic spindle (where the genetic information is)
    • Transfer cells grown in G1 stage into the enucleated egg
    • Fuse with electric current, and transfer to a uterus.
  49. What controls cell fate?
    The nucleus
  50. If each cell has the same genetic content in embryogenesis, how do different regions evolve into different parts?
    While the nucleus controls cell fate, differential gene expression underlies cell fate specification .
  51. Describe the basic steps in protein formation
    • Transcription of genetic information
    • RNA processing,
    • Translation
    • Protein folding
  52. Describe how transcription factors form bridges? What is the point of this?
    • They loop the chromatin such that the transcription factors on enhancers are brought into proximity with the promoter.
    • The point of this is to link the genetic information together.
  53. Describe the mediator complex
    • Usually bridges the enhancer and promoter regions.
    • The mediator initiates a chromatin loop connecting the enhancer and promoter
  54. Describe the Fgf Family
    • fibroblast growth factor
    • Often work by activating a set of receptor tyrosine kinases called fibroblast growth factor receptors (FGFRs)
  55. What is essential in enabling the Hedgehog protein to anchor to its receptor cell's cell membrane?
  56. Describe the hedgehog family
    Often created by the embryo to induce particular cell types and to create boundaries between tissues
  57. Vertebrates have at least __ homologues of the Drosophila hedge hog gene
  58. ___ of the Hedgehog family function by binding to a receptor called ___
    • Proteins
    • Patched
  59. Patched protein prevents ___ protein from functioning
  60. When Hedgehog binds to ___ the protein's shape is altered so that it no longer inhibits ___. this releases proteins from microtubles and prevents it from being cleaved. The protein enters the nucleous where it acts as a ___ ___ of the same genes it used to repress.
    • Patched
    • Smoothened
    • Transcriptional activator
  61. What is the hedgehog pathway extremely important in? What happens when animals are homozygous with a mutant allele?
    • Hedgehog pathway is extremely important in vertebrate limb development, neural differentiation and faction morphogenesis.
    • When mice were made homozygous for a mutant allele of Sonic  hedgehog, they had major limb and facial abnormalities. The midline of the face  was reduced and a single eye formed in the center of the forehead
  62. Members of the Wnt family usually interact with a pair of transmembrane receptors called ___.
  63. What is a frizzled?
    A transmembrane receptor that Wnt binds to
  64. In the absence of Wnt, the transcriptional co factor ___  is constantly being ___
    • B-Catenin
    • Degraded
  65. Describe Wnt Signalling (Briefly)
    • Wnt binds to frizzled
    • Frizzled interacts with a protein called Disheveled which stablizes the axin and prevent phosphorylation of B-catenin.
    • B-catenin binds within the nucleus and activates Wnt responsive genes
  66. What is a natural inhibitor of the Wnt pathway
  67. What is Wnt essential in?
    • Critical in establishing polarity of insect and vertebrate limbs, promoting the proliferation of cells, and in some steps within the mammal urogenital system.
    • Related to Wingless gene in Drosophilia
  68. What is BMP a member of?
    The TGF-B family
  69. What are important families within the TGF-B super family
    • Nodal and activin
    • BMP
    • GDNF
  70. What is distinguishable from the BMP family
    They have 7 rather than 9 conserved cysteines
  71. What does BMP stand for
    Bone morphogenetic proteins
  72. What is the function of BMP
    • Bone formation
    • Regulate cell division and apoptosis
    • Regulate cell migration and differentiation
  73. What are Nodal and activin proteins important in?
    Specifying the different regions of the mesoderm and distinguishing the left and right sides of the vertebrate body axis
  74. The TGF super family activates the ___ Pathway. The TGF __ binds to the TGF ___ which allows for two ___ to bind. The activated ___ can now phosphorylate the ___ Proteins. Eventually the phosphorylated protein forms a ___ which enters the ___
    • Smad
    • Ligand
    • Receptor
    • Receptors
    • TGF receptor
    • Smad
    • Transcription factor complex
    • Nucleus
  75. Why is notch unique?
    It extends through the cell membrane and it's external factor contacts with Delta of another cell.
  76. How does Notch work?
    Its external part of the cell binds to Delta (a ligand from another cell) which causes a Notch to change shape activating a protease. The activation of the protease cleaves notch, which enters the nucleus and binds the transcription factor, which transcribes target genes
  77. What are classical embryological methods of Developmental Biology? (4)
    • Observation of cells
    • Fate mapping
    • Cutting up embryos
    • Transplantation
  78. What are Molecular Biology methods of Developmental biology? (7)
    • Gene cloning
    • Gene expression analysis
    • Gene loss of function
    • Gene gain of function
    • Protein localization
    • Protein-protein interact
    • Protein activity
  79. Describe In situ hybridization
    • A RNA is made complementary to a specif mRNA and inserted through a hole in the cell membrane.
    • The RNA is labelled (radiolabelled)
    • One example of a label is Digoxigenin
    • The label is then bound using an antibody
    • After phosphorylation the colorless compound becomes dyed.
  80. What is another name for 'loss of function'
  81. What is a method to analyze gain of function?
    Creating a knockout organism
  82. How are knockout organisms created?
    • Essential create a mutant gene and inject it into the embryo.
    • Inject heterozygous cells into blastocyst
    • Inject blastocysts into the uterus
    • Formation of a chimeric animal.
    • Then breeder the Chimeric animals to the wild type to get more wild types
    • Breed wildtypes together to get a homozygous mutant lacking the gene.
  83. What are cadherins
    • Calcium Dependent adhesion molecules
    • Critical for establishing and maintaining intercellular connections
  84. Cadherins are anchored inside the cell by a complex of proteins called ___
  85. What are the four stages of cell migration?
    • Polarization, where a cell defines its front and back
    • The protrusion of the cell's leading edge. Mechanical force for this is the polymerization of the actin micro filaments at the cell membrane.
    • The adhesion of the cell to its extracellular substrate. Integrins span the cell membrane and connect the extracellular matrix outside the cell to the actin cytoskeleton on the inside of the cell.
    • Release of adhesions in the rear, allowing the cell to migrate in the forward direction.
  86. What is DDT
    • A teratogen
    • Affects animals at the top of the food chain
    • In embryos can cause preterm birth and low birth weight
    • some links with cancer
    • it is an estrogen receptor binding chemical
  87. How are chromosomes numbered?
    By size
  88. Which organism can be used to study gametogenesis?
    Strongylocentrotus pupartus
  89. Why are nemotodes studied?
    • Transparant
    • Can watch cell division for the entire organism (very few cells)
    • convenient and easy to raise in the lab
  90. Why are chickens losing favor in developmental biology?
    • Currently unable to make mutations of genes
    • Much more limited scope of techniques can be done
  91. What is an advantage of zebra fish?
    • Hardy
    • Inexpensive
    • Transparent embryos
  92. What was the key study that was done to show that the key repository for information was the nucleous?
    • Take a nucleous from an albino frog and inject that in an unfertilized embryo.
    • New embryo is albino
  93. How do ligands work?
    • Bind to a ligand-binding domain that can activate an enzymatic activity
    • Activates an active protein
  94. How do two cells that are touching each other signal?
    Notch-Delta signalling
  95. What is ISH?
    In Situ hybridization
  96. What does the degree of colour in In Situ Hybridization mean?
    • The proportion of the gene expression
    • Does not give an exact numerical value
  97. Why are Drosophila used?
    • Short generation time
    • Four pairs of chromosomes
    • High fecundity
    • Easy anesthesia
    • Salivary polytene chromosomes are highly duplicated and lined up
    • first behavioural screens
  98. Describe the early divisions in drosophila and how it is different
    • Nuclear division - not cell division
    • It is a syncytium - multiple nuclei
    • Any kind of timing that occurs in early division is going to be synchronous
  99. What is a key step in alternating the cell cycle?
    • Activation of the zygotic genome in one of the following transition:
    • MBT (Mid blastula transition)
    • MZT (Maternal zygote transition)
  100. Describe the genetic screen
    • Mutagenize generation ZO (randomly mutates some genes in the organism)
    • Cross to Wild type organism to generate F1 (One of the chromosomes will be a mutant, One will be normal)
    • Intercross F1 generation to generate F2 (some chromosomes will be homozygous - both mutant)
    • Screen progeny (F3) for defects in segmentation
  101. What are GAP genes?
    • Regional identifiers
    • Large portions of embryo are deleted
    • Gene hypothesized to function in defining segment identity.
  102. What are the different segments in Drosophila?
    • Head region
    • 3 Thoracic
    • 8 Abdominal
  103. The first ___ cell cycles in Drosophila are in a syncytium
  104. The creation of the __ phase is dependent on activation of zygotic __
    • G1 Phase
    • Transcription
  105. The activation of what drives cells into mitosis?
    Activation of Cyclin E
  106. Why does the embryo have different compartments?
  107. What are pair rule genes
    • Function to specify parasegmenta identity
    • Affect embryo two-segment periodicity
  108. Describe segment polarity genes
    • Regulate a subdomain of every segment
    • Also function to define anterior vs posterior polarity within segments
    • Specify cell identity within segments
  109. What functions to define anterior vs posterior polarity within segments?
    Segment polarity genes!
  110. What is the French Flag Model?
    • A model to show that different gradients can cause different outputs.
    • There is a blue, white and a red colour indicating an output and a correlating threshold for each of the colours
  111. What transports bicoid mRNA?
    Polarized microtubules
  112. What does bicoid control?
    Anterior fate
  113. Describe the normal development of an embryo compared with the development of a bicoid deficient mutant
    • Normal development has bicoid at the anterior end of the embryo.
    • An embryo will have two tail regions in a bicoid deficient mutant
  114. What was an experiment that was done to determine that bicoid controlled anterior fate?
    • Bicoid was added to the anterior end of a mutant => lead to normal development
    • Bicoid was added to the middle of the mutant => Formation of a head in the middle of the ebmryo, with two tail regions either side
    • Bicoid was added to the posterior region of the embryo => two heads with a tail in the middle.
  115. What does nanos do?
    • Nanos is on the posterior side of the embryo
    • Inhibits Bicoid
  116. When in Drosophila development do cell membranes form?
    Not until after the 13th nuclear division
  117. In Drosophila, what forms the dorsal-ventral polarity in the embryo?
    Gurken protein enters the nucleus and ventralizes the cell
  118. What is the function of Dorsal? Where is it located?
    In Drosophila
    • Dorsal is located all throughout the embryo.
    • It is only transcribed into the nuclei on the ventral region of the embryo.
    • This represses the dorsal cell types, causing for the ventralization of the region.
    • Yes, Dorsal leads to Ventralization. Cray.
  119. How many segments are affected in a pair rule gene mutant in drosophila? Segment polarity?
    • 7/14
    • 14/14
  120. Does protein always show the same distribution of mRNA? What does this mean?
    • No, because the step from RNA to protein is regulated
    • Can create a gradient
  121. What does DNA make?
    RNA, which makes proteins
  122. Where is hunchback mRNA made? What does it do?
    Hunchback protein is made in the anterior region of the embryo in drosophila. This allows for the the creation of Hunchback protein and promotes anterior structures.
  123. How does nanos interact with Hunchback?
    Nanos in the posterior region of the embryo inhibits hunchback protein and allows for abdominal formation.
  124. Why are transgenic flies made?
    To examine regulation of pair rule genes
  125. Where is the caudal protein in drosophila made?
    The Posterior region
  126. Bicoid is made in the ___ region and Nanos is made in the ___ region (Posterior or Anterior_
    • Anterior
    • Posterior
  127. What is found in between segment polarity genes?
    Individual cells
  128. Describe the wingless molecule
    • Wg gene
    • A small polypeptide is made by the cells in the embryo
    • Diffuses out of the cell
    • Diffuses in a gradient
    • There are lots of cells along the embryo that releases the cell, so there are many small gradients of Wg expression
    • The polypeptide binds to a receptor in adjacent cells
  129. How do wingless and engrailed work together?
    • The cell that creates wingless is adjacent to the cell that creates engrailed
    • Engrailed has a receptor that can detect the wingless gene
    • Releases a hedgehog signal that goes to the initial cell and binds to patched. This causes for more wingless expression - signal amplification.
    • Essentially the two are required for normal development. Absence of one causes the mutation
  130. __ and __ are inhibited by __ inhibiting dorsal structures of the embryo. This means that this section of the embryo will develop in to the __ region
    • Tolloid
    • Decapentaplegic
    • Dorsal
    • Ventra
  131. How do we make the termini of the embryo in drosophila
    • Interact with support cells containing a ligand and a receptor. Eventually transcription factors are activated. Torsolike activates torso at the poles of the embryo, causing for the formation of the poles.
    • Bicoid determines head vs. tail
  132. What is homeosis? Provide an example
    • The transformation of one body part/segment into another via the activation, mis expression or inactivation of a critically important developmental regulator
    • An example would be Ultrabithorax: fly with two sets of wings
  133. What is ultrabithorax? how is it formed
    • Fly with extra set of wings
    • Example of homeosis
    • Loss of Ubx gene function
  134. What is Antennapedia? How is it formed?
    • When a fly has legs growing on its head where antenna should be growin
    • An example of homeosis
    • Caused by gain of Antp gene function
  135. What is the function of Hox transcription factors?
    DNA binding domain
  136. Where are genes causing homeotic mutations located in drosophila?
    All on the same chromosome next to each other
  137. What is meant by Hox genes are highly conserved?
    • Genes are expressed in different animals, just in varying clusters. Less in flies, more in mouse etc.
    • Some sections are elongated within the Hox, and other Hox sections are removed.
  138. What is a Hox gene?
    A homeotic selector Gene
  139. Describe fertilization in sea urchin
    • Sperm contacts jelly layer
    • Acrosome reaction
    • Digestion of jelly layer
    • Binding to vitelline envellope
    • Fusion of acrosomal process membrane and egg membrane
  140. What is the final stage in sperm development? Where does it occur?
    • Capacitation
    • Occurs in female reproductive tract
  141. How are sperm usually attracted to the egg?
  142. In echinoderms, how are sperm provided with direction to the egg? Why is this needed
    • This is needed because of the external fertilization process
    • Sperm-activated peptides are released along with the eggs.
  143. What is important in the acrosomal reaction (in sea urchins) in mediating recognition
    • A protein called bindin.
    • Species specific
  144. Describe the acrosomal reaction in sea urchins
    • Bindin binds to the surface of the egg
    • Actin microfilaments extends by actin polymerization.
  145. What facilitates species specificity in acrosomal reaction?
  146. How is polyspermy prevented (sea urchins)
    • Two blocks
    • Fast block to polyspermy: Na Channel-dependent depolarization of membranes
    • Cortical granule reaction (Slow block to polyspermy): Cortical granules fuse with the egg cell membrane => form a fertilization membrane.
  147. Describe early cleavage divisions in the frog
    • Mesolesical egg - more yolk at ventral pole
    • Displaced radial cleavage
    • Cells at the bottom larger
  148. Where are the animal pole and vegetal poles located?
    Vegetal pole is at the bottom => all of the yolk to support the embryo at the animal pole (top)
  149. Describe cell movements of the frog embryo
    • Blastocoel originally at the top of the embryo
    • The yolk at the bottom moves up, displacing the blastocoel and creating the archenteron (another area of space)
    • Then the cells being to fold along the inside of the sphere giving rise to the mesoderm
  150. What does gastrulation give rise to?
    • Three tissue layers
    • Endoderm
    • Ectoderm
    • Mesoderm
  151. In frogs, how is the archentron formed?
    • Bottle cells change shape dramatically
    • Main body of each cell is displaced toward the inside of the embryo while maintaining contact with the outside surface.
  152. What is another name for archentron
    Primitive gut
  153. Describe early zebra fish development
    • telolecithal - lots of yolk throughout (incomplete meroblastic cleavage)
    • Formation of a blastodisc - a kind of bubble that forms out of the embryo
    • Bottom part does not divide (mostly yolk)
    • Formation of Yolk syncytial layer: yolk all in one area
    • Continued separation. As yolk continues to push up, cells continue to be pushed along the side (like headphones).
  154. What is the shield?
    • The shield is near the animal pole in zebra fish, and is on the side of the egg that becomes the dorsal region of the egg.
    • Mesoderm and dorsal inducing signals are released
    • *Note* In frogs dorsal creates the dorsal region. In flies everything is fucked the hell up.
  155. During gastrulation in zebra fish, describe the movement of cells
    • Cells involute and ingress (fold inwards)
    • Move toward the midline of the embryo/egg
  156. What is significant about the embryonic shield?
    • Cells of the epiblast and hypoblast intercalate to form a thickening.
    • The cells converge and extend anteriorly. (move up)
    • Dorsal side
  157. What parts of the blastula give rise to the ectoderm, mesoderm and endoderm?
    • Animal cap cells => ectoderm
    • Marginal cells => Mesoderm
    • Vegetal cells => endoderm
  158. The animal is usually converted into the __ but can be converted into the __. How?
    • Ectoderm
    • Mesoderm
    • This is done by factors released from vegetal cells - usually when the marginal cells have been removed experimentally
  159. What are key modulators of development?
    Growth factors
  160. What do cell lines use for continued proliferation?
    Growth factors
  161. What is the Nieuwkoop center?
    The dorsalmost vegetal cells in frogs that are capable of inducing the organizer.
  162. What is the 'organizer' in xenapus?
    • dorsal lip cells and their derivatives (notochord and head endomesoderm)
    • They induce hosts ventral tisues to change fates to form a neural tube and dorsal mesodermal tissue
    • Organized host and donor tissues into a secondary embryo with clear anterior-posterior and dorsal-ventral axis
  163. Describe a transplantation experiment
    • The experiment showed that only one of the tissues in the early gastrula has its fate predetermined
    • This tissue was dorsal lip of the blastopore (Later named the organizer)
    • When the tissue was transplanted into the presumptive belly skin region of another gastrula it continued to be dorsal blastopore lip but also initiated gastrulation and embryogenesis in the surrounding tissue.
  164. What are XTC cells?
    • Cells that are grown in a dish
    • They grow without adding a growth factor
    • This suggests that they secrete their own mesoderm inducing signal
  165. What is the importance of XTC cells?
    XTC cells create growth factor - this was important in diagnosing what the specific mesoderm inducing signal is.
  166. How was actin determined to be the mesoderm inducing factor?
    • through cell culture work. Both XTC and Actin A have mesoderm inducing factor
    • However Actin is not the mesoderm inducing factor.
  167. Molecular screening was tried to find out what __ was. How was this done?
    • Mesoderm inducing factor
    • Separated the eight cell embryo into four vegetal poll cells and four animal blastomeres
    • They isolate the mRNA's from the two types of cells and compare
    • Convert mRNA's into a label probe using a radioactive tracer and then hybridize and compare.
  168. What is VegT?
    • A transcription factor that is important in activating the mesoderm inducing factor
    • Regulated nodal related
    • Nodal related is the mesoderm inducing factor
  169. What is the mesoderm inducing factor
    • Nodal related
    • Xnr in frogs (Xenapus nodal related)
  170. What did the study of the frog embryo give us?
    • Large embryo
    • Allowed us to find the mesoderm inducing factor (nodal related)
    • Also large number of embryos - a very large amount of source material.
  171. What does VegT regulate?
    • Derriere and Nodal related genes
    • Induces them so that they can form mesoderm
  172. What is the source of mesoderm induction in zebra fish?
    Yolk syncytial layer
  173. What is the most common human forebrain birth defect?
  174. What does Cyclopamine cause?
    Cyclopia in sheep
  175. What induces the ventral forebrain?
    Prechordal plate
  176. What is the prechordal plate?
    • The embryonic shield forms the prechordal plate
    • The prechordal plate cells are the first to involute and migrate toward the animal pole
    • Responsible for inducing ectoderm to become neural ectoderm.
  177. What are some downfalls in using the frog embryo
    • Tetraploid
    • Takes a long time to reach maturity
  178. What is a genetic screen
    Very powerful methods in an unbiased method to ask the embryo what genes are important for specific functions/characteristics
  179. What are a couple forebrain zebra fish mutants? What is the gene of importance
    • Cyclops
    • One eye pin head

    • They lack mesoderm
    • Gene of importance is squint
  180. Where is the squint gene found? In what Organism? What happens if it is removed? Added?
    • Found in the group of nuclei between the yolk syncytial layer and the embryo
    • In zebra fish
    • Remove mesodermal induction
    • Increased mesoderm induction
  181. What is a morphogen? How can we help conceptualize this?
    • A molecule that:
    • Acts directly on cells at a distance
    • Usually present in a gradient
    • causes fate changes in dose-dependant manner

    The French flag model can hep conceptualize this.
  182. What is the definition of an organizer?
    • A group of cells that can alter the fates of surrounding cells.
    • Importantly, once formed, an organizer independent of outside signals. This means that you can transplant an organizer to another place and it will retain its activity.
  183. When does Dorsal-Ventral specification start in Xenapus?
    Starts as early as the 2-4 cell stage.
  184. What is required for dorsal specification in Xenapus?
    Cortical rotation
  185. How was the source of dorsal identity found?
    • Through transplantation experiments
    • Identifying the Nieuwkoop center and dorsal organizer
    • Look for localized proteins and mRNA that move during cortical rotation
  186. What is the gene in Xenapus that ventralizes the embryo?
  187. Where on the Xenapus embryo is B-catenin stabilized?
    The dorsal side of the embryo
  188. After fertilization in a xenapus, what happens? In terms of genes
    • There is cortical rotation
    • The Dishevelled protein (Dsh) and Wnt 11 mRNA relocalize to the presumptive Dorsal side of the embryo
    • This leads to the dorsal enrichment of B-catenin
  189. What does B-catenin regulate (in xenapus)
  190. What drives Nodal? What drives it in Xenapus? What happens when Nodal drives?
    • Nodal is the mesoderm inducing factor
    • B-Catenin + vg1 + Veg T drives Nodal
    • Low Nodal related leads to ventral mesoderm, Nodal related high leads to the organizer
    • Organizer specifies the dorsal region
  191. What are the organizer molecules? What do they do
    • Chordin, Noggin, Follistatin and Xnr 3
    • Specifies the dorsal region of the embryo
  192. What is the dorsal organizer in zebrafish?
    The zebrafish shield
  193. What does the removal of ndr1 containing cells result in, in zebrafish?
    The loss of dorsal structures
  194. Localization of Nodal apparent in the zebrafish?
    The 4-cell stage
  195. What is swirl? What does the overexpression of swirl cause?
    • It is a BMP mutant phenotype
    • over expression of swirl causes ventralization
  196. Describe the overall D/V patterning in zebrafish
    • Dorsal region: Wnt binds to Dsh which leads to beta-catenin allowing for organizer to be expressed. This causes for dorsalization. The organizer releases three molecules that prevent the ventral region from developing (chordin, noggin and follistatin)
    • Ventral region: Gdf6 and BMP2/7 are expressed and lead to the ventralization of the section.
  197. What are the three primary vesicles of the brain?
    • Forebrain: Telencephalon and Diencephalon
    • Midbrain
    • Hindbrain: Metencephalon and Myelencephalon
  198. What is Frzb?
    • Wnt binds to it instead of the receptor (Frizzle)
    • When there is a lot of Frzb, there is no Wnt binding
  199. What are Row 1 cells?
    The cells that make the anterior neural border
  200. What does the injection of a synthetic Wnt in an embryo do?
    No development of anterior markers in neural tube development
  201. What happens when synthetic Frzb is injected into an embryo?
    • No development of posterior markers
    • Lots of anterior neural tube development
  202. What does Frzb and Wnt tell us?
    • Frzb is expressed in the anterior region of the neural tube
    • Wnt is expressed in the posterior region of the neural tube
  203. What sort of pattern are Hox genomes expressed in?
  204. What is a Rhombomere?
    • A hindbrain segment of an embryo
    • Hox genes show exquisite segmental expression pattern in the hindbrain
  205. What is a morpholino
    • A molecule that contains a multiple nucleotide analogue
    • Derivative of oligonucleotide
  206. What is the transgenic approach in how Hox genes are regulated?
    • Find candidate regulatory sequences
    • Create a DNA construct with candidate regulatory sequences linked to a reporter
    • Integrate into organism
    • Does reporter recapitulate expression pattern?
    • Analyze your newly discovered regulatory sequence
    • Test putative regulators
  207. What is retinoic acid a derivative of?
    Vitamin A
  208. Why would one want to make a transgene?
    • To label a portion of the embryo
    • To study gene regulation
    • To overexpress/ectopically express gene (ectopically = different region)
  209. What does conservation in genes mean?
    • If genes mutate and they are kept it is likely that they serve a purpose. There is some genetic noise, but it can be used to find candidate regulatory sequences
    • Regulatory sequences being conserved area between species
  210. What is unique about the dorsal ventral axis in flies?
    It is flipped in comparison with other animals
  211. Describe the retinoic acid signaling pathway
    • Aldh1a leads to retinoic acid signalling
    • leads to retinoic acid receptors (RAR) and Retinoid receptors (RXR)
    • These receptors lead the expression of the Hox gene
    • cyp26 inhibits retinoic acid (creates an enzyme that degrades RA)
  212. What are the expression patterns of cyp26 and aldh1a?
    • important in the retinoic acid pathway
    • cyp26 is located in the anterior region.
    • aldh1a2 is located in the posterior region