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Module 1 Flashcards

1
Q

What are cytoplasmic determinants?

A
  • Maternal substances that influence early development through cell determination (syncytial blastoderm), gradient formation, and gene activation
  • Typically proteins, RNAs, and other molecules
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2
Q

Define cell specification, differentiation, and determination.

A

Specification: Initial process in which a cell becomes committed to a specific developmental fate

Differentiation: When a less specialized cell undergoes changes in gene expression and morphology to become specialized

Determination: Cells have undergone molecular changes which make them resist changes in fate

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3
Q

What is the difference between cell determination and differentiation?

A

Determination is when the cell’s commitment is irreversible after specification. Differentiation is the process of a specified cell undergoing changes in gene expression and morphology.

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4
Q

Is cell specification reversible? Why? How would you experimentally show?

A

Yes it is, If a cell is specified but is transplanted to a different tissue it will adapt to the tissue. if it has already been determined even if it is transplanted it will go as it would have where it was taken from.

(IMAGE)

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5
Q

What is the difference between instructive and permissive induction?

A

Instructive induction is when a group of cells sends a signal for another group of cells directing their differentiation. Permissive induction is when a group of cells provide a permissive environment in which responsive cells have more autonomy over what their fate is.

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6
Q

Define what morphogen gradient is and how it is generated. What so important about gradients generated by morphogens important?

A
  • A morphogen is a signaling molecule
  • Morphogen gradients can be generated by diffusion across tissue, degredation as a molecule travels far from its source, or specific tissue producing morphogens
  • These can lead to patterns such as the french flag model which can signal for tissue differentiation
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7
Q

(T/F) Epigenesis is the theory that explains how development of a plant or animal from an egg or spore differentiate into an organism.

A

True

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8
Q

(T/F) During development, if a cell has committed to a particular fate, it is said to be
Differentiated.

A

False

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9
Q

(T/F) The determination state of a cell is defined by culturing a cell in an artificial medium (saline solution) and observing what tissues form from it.

A

False

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10
Q

(T/F) In instructive interaction, a signal from the inducing cell is necessary for initiating new gene expression in the responding cell.

A

True

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11
Q

List key developmental processes required for the formation of multicellular organisms from gametes.

A

Generation of reproductive cells, Fusion of sperm and egg, Cell Division (mitosis), Generation of diverse cell type, Tissue organization, Postembryonic development

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12
Q

How is a morphogen gradient formed and interpreted by responding cells? Use the following terms: morphogen, threshold, positional information

A

Morphogens are long-range signaling molecules that pattern developing tissues in a concentration-dependent manner. The graded activity of morphogens within tissues exposes cells to different signal levels (thresholds) and leads to region-specific cell fates (positional information) along the plane of tissue.

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13
Q

What are the differences between maternal vs, zygotic genes? What is zygotic transcription?

A
  • Maternal genes, as well as maternal mRNA and proteins, are present before the egg is fertilized. They control axis formation and formation of germ layer but degrade over time
  • Zygotic genes come from DNA in the zygote and transcription of the genes occurs after fertilization. Responsible for tissue differentiation, patterns, and organs. These genes will be translated through adulthood
  • Zygotic transcription marks the transition from maternal genes to zygotic genes
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14
Q

When does the basic body plan of a fly embryo established?

A
  • The fertilized egg will transcribe zygotic proteins and mRNA
  • The egg will then enter a syncytial phase in which the egg is a single multinucleated cell undergoing rapid cellular divisions (bicoid and dorsal gradients set up in this phase)
  • During Gastrulation the blastoderm will undergo cellularization. Invagination of the ventral side, Gut formation, sementation, andgerm band expression, then Hox gene expression marks the end of the gastrulation phase.
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15
Q

What are the advantages of using Drosophila as an experimental model organism?

A
  • 9 Day life cycle
  • Similar stages: Cleavage,blastoderm formation, gastrulation, differentiation
  • Small genome
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16
Q

What are maternal determinants? What do they do?

A
  • Specific molecules that are present before fertilization and help establish initial polarity, axis formation, cell fate specification, cell migration, and differentiation
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17
Q

What is syncytium and how does it influence the early Drosophila development?

A
  • When the proteins are able to diffuse through embryo and enter nuclei to form concentration gradients before cellularization occurs
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18
Q

What happens during cellularization in Drosophila embryos? At the cellular blastoderm stage, can transcription factors function as morphogens? Why and why not?

A
  • Membranes begin to form around the nuclei forming a monolayer of cells
  • During syncytial blastoderm phase, transcription factors such as bicoid and dorsal may indirectly act as morphogens by establishing gradients which creates a response in cell’s gene activation
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19
Q

Know how cells move around to form different germ layer cells during gastrulation.

A

~15 Poll cells set aside to become germline cells
- cells that become mesoderm invaginate ventrally
- Gut cells invaginate from anterior to posterior
- Cells that remain outside are ectodermal cells

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20
Q

(T/F) Drosophila gastrulation is completed 10 hours after fertilization.

A

False

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21
Q

(T/F) The Drosophila embryo contains a large number of nuclei in a single cell surrounding a central mass of yolky cytoplasm. This embryo is at cellular blastoderm
stage.

A

False

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22
Q

What is the result of the first 12 nuclear divisions of a Drosophila embryo where roughly 6,000 nuclei share a single cytoplasm?

A

Proteins can diffuse throughout the blastoderm and enter nuclei.

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23
Q

(T/F) During Drosophila gastrulation, anterior and posterior mesodermal cells migrate inside from the two anterior and posterior ends and connect in the middle of the embryo to form body muscles.

A

False

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24
Q

During Drosophila gastrulation ~15 cells at posterior are set aside to eventually become
____________ cells.

A

Pole

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25
How many abdominal segments are there in the Drosophila embryo?
8
26
When does germ band extension occurs?
Shortly after Gastrulation
27
(T/F) Zygotic genome activation in Drosophila begins during cellular blastoderm.
False
28
What are three types of maternal mutants and phenotypes of bicoid, nanos and torso mutants?
Bicoid: - Responsible for specifying anterior-posterior axis - Mutation may result in missing or underdeveloped head region while the posterior structure is enlarged or duplicated Nanos: - Responsible for posterior patterning - Mutation results in anterior structures are expanded while posterior structures are missing or underdeveloped Torso: - Responsible for determining terminal regions of embryo (head and tail) - Mutations result in defects at the terminal ends of embryo resulting in missing or absent structures
29
Identify evidence showing that there exists an anterior morphogen.
- Bicoid larva show no head or defects in thoracic region
30
Identify evidence showing that Bicoid is the anterior morphogen?
- Bicoid mRNA is concentrated in the anterior of the egg
31
Understand how Bicoid forms a morphogen gradient.
- mRNA is translated after fertilization, Bicoid protein diffuses and forms gradient along A/P axis
32
Understand how Nanos and Caudal work.
Nanos: - mRNA localized at posterior pole of egg and when fertilization occurs it remains in high concentration at the posterior end Caudal: - Responsible for establishing A/P axis - Evenly distributed mRNA - Bicoid supresses Caudal
33
Understand how a Hunchback gradient is formed.
- Nanos binds hunchback mRNA and prevents translation which makes hunchback gradient
34
Describe how torso functions to specify terminal regions.
- Torso encodes a tkr that is evenly distributed and only activated at terminal ends. Ligands activate torso (vitelline membrane) and is released after fertilization - Torso signals to nuclei to direct zygotic gene expression to termini
35
Understand the order of hierarchy, who works upstream and who works downstream.
Maternal -> Zygotic -> Gap -> Pair-rule -> Segment polarity
36
Comprehend the logic behind gap gene activation. Try to understand the rationale behind each experiment.
- Gap genes are zygotic genes that help divide the embryo into large regions and activation is influenced by maternal and zygotic interactions - Bicoid and hunchback are two maternal factors that regulate gap gene expression along the A/P axis - Giant and Kruppel also play an important role by responding to bicoid and hunchback
37
Know the general phenotypes of gap gene mutations.
Bicoid - Mutations can result in loss of anterior region structures - Severe cases may result in headless phenotypes - Posteriorization of embryo may result in anterior structures replacing posterior ones Giant - Mutations affect central region resulting in gap or malformations of segmentation pattern Hunchback - Mutations result in defects in the anterior segments of embryo. Severe cases may result in loss of head structures Kruppel - Mutations affect central regions leading to gap in segmentation patterns
38
Describe the maternal and zygotic activity of hunchback.
- Maternal mRNA is localized in the anterior region of the developing egg. Works with bicoid to specify anterior head structures in the embryo - Zygotic hunchback further refines and maintains the anterior expression of target genes
39
Describe how the changes in Bicoid will affect the overall expression of hunchback.
- Bicoid acts as a maternal morphogen which forms a gradient which influences the expression of various target genes - Increased bicoid concentration can result in expansion of anterior head structures - Low levels of bicoid will result in activation of hunchback which may result in a loss of anterior head structures
40
Understand how krupple is expressed as a narrow band.
- Bicoid regulates Kruppel expression since bicoid is concentrated anteriorly which means krupple is expressed posteriorly - Kruppel is only expressed in a narrow window of Hunchback concentration
41
(T/F) The gradient of maternal hunchback protein is formed as a result of translational repression by the Nanos protein.
True
42
T/F) If a female Drosophila carries a homozygous recessive mutation in a maternal effect gene, 100% of her progeny will show developmental defects.
True
43
(T/F) Caudal mRNA is distributed in a gradient in the embryo with the highest concentration at the posterior.
False
44
If torso is expressed uniformly in an embryo, why does the loss of function mutation of torso only affect terminal regions?
The active ligand that binds Torso is only available in the terminal regions.
45
(T/F) In a gap gene mutation, the resulting phenotypes will result in missing every other segment.
False
46
Identify four major groups of zygotic genes that regulate Drosophila anterior posterior specification.
gap genes, pair rule genes, segment polarity genes, homeotic selector genes
47
(T/F) Expression of zygotic hunchback is regulated by Bicoid protein.
True
48
(T/F) In the absence of zygotic hunchback, the anterior boarder of Kruppel expression shifts anteriorly.
True
49
Know the difference between parasegments and segments.
- A parasegment is a basic unit of segmental body plan of which there are 14 in flies. The parasegments consist of an anterior and posterior portion early in development - Segments are distinct regions in the late embryo
50
Understand how specific stripe patterns can be generated by enhancers.
- Enhancers on the DNA sequence that control spatial expression of genes are responsible for making specific stripe patterns
51
Know the expression patterns of even-skipped and fushitarazu.
- Even skipped patterns are shown as blue stripes which define the odd parasegments - Fushi-tarazu patterns are shown as brown stripes which define the even parasegments
52
What are differences between primary and secondary pair-rule genes?
- Primary (eve, hairy) pair-rule genes are directly regulated by gap genes and control secondary pair-rule genes - Secondary pair-rule genes are expressed later and are regulated by interactions among primary pair-rule genes
53
Describe how it was shown that multiple enhancers could produce the 7-stripe even skipped (eve) expression pattern.
- The eve gene contained multiple independently regulated modules for individual stripes
54
How is the stripe 2 pattern generated by Bicoid, Giant, Hunchback and Knurps.
Eve stripe 2 is activated by bicoid and Hb while Giant represses anterior and Kruppel represses posterior
55
What are segment polarity genes? What are the expected phenotypes of segmentation polarity mutations?
- Genes that act after cellularization. They’re expressed as 14 stripes and are regulated by pair-rule genes - Some SP genes code for wingless/winged or dendricles (would only normally be present in anterior segment)
56
(T or F) All segment polarity genes are transcription factors
True
57
(T or F) evenskipped defines the odd parasegments in Drosophila.
True
58
(T or F) Reporter gene analysis of even-skipped enhancers supports the notion that these enhancers are modular.
True
59
(T or F) Loss-of-function mutations in segment polarity genes cause a series of deletions affecting alternate segment.
False
60
What will happen to the expression of eve stripe 2 if you eliminate Giant protein throughout the embryo?
Anterior expression boundary shifts more anteriorly.
61
What class of patterning genes encodes members of intercellular signaling pathways?
Pair-rule genes
62
What is the common feature of all homeotic proteins?
All homeotic proteins function as transcription factors which switch on other genes
63
What is the function of Hox genes?
- They regulate body segmentation and are essential to specifying the identity of each body segment. Misregulation can lead to significant developmental abnormalities. Flies have 2 Hox gene complexes Antennapedia and Bithorax - Mutations in the antennapedia gene cause the antenna to become legs. Bithorax mutation causes transformation of halteres to wings
64
What is meant by colinearity of Hox genes?
- The organization of Hox genes in the chromosome and the order of expression along theA/P axis is related which is known as colinearity
65
What is the major difference between homeotic mutations and others AP mutations?
- The mutation of a homeotic gene results in the transformation of one body part to the identity of another along the AP axis. Other AP mutations disrupt normal patterning but do not involve a complete switch in segment identites
66
Why do loss-of-function mutations of homeotic genes result in anterior transformation?
- When a homeotic gene loses its identity due to a mutation, the segment that is normally active loses its specification. The segment with lost identity will take on the identity of a more posterior segment transforming it to a different segment type
67
Understand various phenotypes caused by mutations of individual genes in the Bithorax complex.
- Bithorax complex is composed of three genes: Ubx, Abd-A, and Abd-B - Wt will have parasegments 3-14 expressed normally - Mutations of all of the parasegments will result in parasegments 5-13 being replaced as parasegment 4 - Mutation of Abd-A and Abd-B results in parasegments 7-13 being replaced by parasegment 6 - Mutation of Ubx results in parasegment 5 and 6 being replaced by parasegment 4 - Mutation in Abd-B results in parasegments 10-13 being replaced by parasegment 9
68
Discuss the similarities and differences between Drosophila and mammalian HOX clusters.
- Drosophila contain 2 HOX clusters, the Antennapedia and Bithorax Complex, Mammalian contains 4 HOX clusters that are on 4 different chromosomes - Drosophila and Mammals have spatial colinearity, meaning the order of the genes and the ways they are expressed are the same. - Drosophila and Mammals are orthologs: two different species containing similar/same genes.
69
Understand the roles of the Polycomb and Trithorax group proteins.
- Polycomb blocks Ubx expression in the anterior region - Trithorax maintains Ubx expression in the thoracic region
70
(T/F) All homeotic genes are transcription factors.
True
71
(T/F) Homeotic genes are expressed along anteroposterior axis of the fly embryo.
True
72
In Drosophila, there are two Hox gene complexes. They are the __________ and _______ complexes.
Antennapedia and Ultrabithorax
73
(T/F) In general, loss-of-function mutations of homeotic genes in Drosophila result in a transformation of anterior to posterior identity.
False
74
What is posterior dominance?
Hox genes specifying more posterior structures repress the expression of more anterior Hox genes. This rule explains the apparent spatial complementarity of Hox gene expression patterns in Drosophila.
75
Each homeotic gene contains a conserved 180-nucleotide sequence that encodes for 60 amino acids. What is this DNA sequence called? _______________
homeodomain
76
Ubx is expressed PS5 & posteriorly. Abd-A is expressed PS7 & posteriorly, and Abd-B is expressed PS10 & posteriorly. An embryo lacking both Abd-A and Abd-B will result in transforming all parasegment posterior to PS ____ to develop as PS _____. Fill in segment numbers.
PS7, PS6
77
How does Toll signaling activation lead to the accumulation of nuclear Dorsal protein in the ventral region?
- Spätzel activates Toll signaling which occurs on the ventral side. Cactus is holding the Dorsal protein, and the Toll signaling causes the Cactus Kinase to degrade Cactus and allow the Dorsal protein to enter the nucleus. - The high concentration of the Dorsal protein is highest in the ventral nuclei while having little to no concentration on the dorsal side.
78
Predict the DV phenotypes associated with mutations of spaetzle, toll, dorsal, and cactus.
Spaetzle: Unable to activate toll -> unable to degrade Cactus -> Dorsal cannot enter nucleus -> Dorsalized Toll: Unable to degrade cactus -> Dorsal cannot enter nucleus -> Dorsalized Dorsal: Dorsal is unable to enter nucleus causing each cell to be dorsalized Cactus: Cactus is unable to prevent Dorsal from entering each cell -> every cell is ventralized
79
How is the gradient of Dpp generated? When is Dpp morphogen gradient formed?
- Dpp gradient is established by sog, acting as an inhibitor to dpp by binding to it and preventing interactions with the dpp receptors. - The Dpp gradient is formed in the dorsal ectoderm stage
80
How does Sog function and where is it expressed?
- Sog is neuroectodermal gene that is activated by low levels of Dorsal - Sog functions as a secreted factor
81
(T/F) Twist positive cells invaginate and become mesodermal cells.
True
82
(T/F) A spaetzle mutation abolishes the development of ventral structures in Drosophila.
True
83
(T/F) A homolog of IL receptor(toll) in Drosophila is dorsal.
False
84
(T/F) The Dorsal protein concentration is highest in ventral nuclei, and little or none in nuclei on the dorsal side.
True
85
(T/F) A loss-of-function mutation of sog results in embryos lacking neurogenic ectoderm.
True
86
(T/F) Dorsal protein is found only in the future aminoserosa of the embryo
False
87
(T/F) A gain-of-function mutation of dorsal results in dorsalization of Drosophila embryos.
False

Developmental Biology (6 decks)

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