Invert dev - new Flashcards
1
Q
Describe complementation analysis and when it might be used.
A
- When used: To see if two seperate mutant organisms with same phenotype have mutation on same gene.
Process:
- cross mutant A with mutant B
- If offspring are wild-type:
- mutations of different genes –> complementary
- If offspring are mutant phenotype:
- mutations on same gene –> not complementary
2
Q
Explain the difference between regulative and mosaic development
A
- Regulative development:
- Cell will develop according to signals from cells surrounding it, is not fated to become a specific type of cell.
- Mosaic development:
- Cell is fated to become a specific cell type. C. elegans is like this
3
Q
How does sperm promote posterior cell fate in C. elegans?
A
The sperm provides the polarity cue, causing the polarization of PAR-2 and PAR-3.
4
Q
- What are SynMuv genes?
- Where are they located?
- How many classes of them exist and why is this important?
- What is their function in terms of VPCs?
- How do they mostly regulate?
A
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What are SynMuv genes?
- Synthetic Multivulval genes
-
Where are they located?
- located in Hyp7 epidermis rather than VPCs
-
How many classes of them exist and why is this important?
- Class A and B
- Are functionally redundent, so both have to be mutated to have an effect
-
What is their function in terms of VPCs?
- prevent inappropriate lin-3 expression in the hyp7
-
How do they mostly regulate?
- are epigenetic regulators controlling transcription
5
Q
What role does lateral inhibition play in VPC patterning?
A
- Inductive signal tells P5.p, P6.p and P7.p to become 1 and 2 cells.
- Is strongest with P6.p, so it becomes 1 cell first
- 1 cells send out signal telling cells next to them not to become 2 cells
6
Q
What is lin-12 and what happens in case of a lin-12(lf) mutation?
A
- Encodes a notch-like receptor important in lateral inhibition
- In case of lin-12(lf), all 1 and 2 VPCs will become 1 VPCs
7
Q
List the 5 vulval development steps
A
- generation of VPCs
- Vulval precursor patterning
- generation of adult cells
- Anchor cell invasion
- Morphogenesis of vulva
8
Q
Describe the basic role of PAR proteins
A
- Ensure taht first embryonic division is asymmetric
- Can regulate localization patterns of each other
- Activities of Par proteins ensure asymmetric partitioning of P-granules and cell fate determinants like SKN-1
9
Q
Role of PIE-1
A
- essential regulator of germ cell fates
- can inhibit mRNA transcription to block somatic development
- prevents P2 from becoming EMS
- encodes CCCH zinc finger protein that is partitioned into P1, P2, P3, P4
- Is required for expression of NOS-2 which promotes primordial germ development
- PIE-1 remaining in anterior blastomere is degraded, requiring ZIF-1
10
Q
Role of ZIF-1
A
- Is SOCS-box protein
- interacts with different proteins that are required for CCCH finger protein degredation
- Segregation of germ plasm involves both stabilization of germline proteins in germ line and cullin-dependent degredation in the soma
11
Q
Describe function of Mex5/6
A
- Function to establish Soma/Germline asymmetry in early C. elegans embryos
- Regulate cell fate by regulating mRNA translation, incluidng zif-1 mRNA
- localiztion regultated by PAR-1
- diffuses faster in posterior (doesn’t stay as long)
- likely that Mex-5 function is to inhibit anterior expression of germline proteins
12
Q
Describe the role of Wnt signaling in C. elegans embryonic development
A
- Wnt ligand binds LRP and Frizzled to start signaling pathway
- Lit-1(ts) permits wide scale blockage of Wnt signaling
- Wnt signaling polarizes an early C. elegans blastomere to distinguish endoderm from mesoderm
- Regulates orientation of cell division
- a posterior center establishes and maintains polarity of C. elegans embryo by Wnt-dependent signaling
- posterior cells assumer anterior fates when Wnt signaling is blocked
13
Q
Give a brief description of heterochronics and heterochrony
what are Alae?
A
- Heterochrony: developmental change in timing or rate of events, leading to changes in size and shape
- Alae: adult specific ridges in cuticle on worm (is a way to say that it is an adult)
- A hierarchy of genes control larva to adult development in C. elegans
14
Q
Describe role of Lin-14 and 2 types of mutations
A
- Role: works in early stages of development to inhibit lin-29 and stop if from flipping switch to go from larval to adult form
mutations:
- Retarded: semidominant mutant, is seen in T-lineage
- in L2 stage, T.ap generates a cell division pattern and ascendent cell types similar to those normally generated during L1 by T cell.
- Precocious: in recessive lin-14 mutant
- T cell precociously generates cell division pattern normally generated during L2 by T.ap
15
Q
Function of lin-4 and how it works
A
- Encodes small RNAs with antisense complimentarity to 3’ UTR of lin-14
- inhibits lin-14 translation
- Mediates temporal pattern formation in C. elegans by creating temporal gradient in lin-14
16
Q
Describe role and method of let-7
A
- regulates temporal timing in C. elegans
- transition from late larva to adult requires let-7 RNA
- binds to 3’UTRs of target mRNAs
17
Q
Describe role of daf-12
A
- Encodes a nuclear receptor that regulates the dauer diapause and development age in C. elegans
- when daf-12 is active, it inhibits activity of let-7, allowing larva to go to adult form
18
Q
Describe transposable elements and how they are evolutionarily useful.
A
- are mobile genetic elements that are moved from one position in the genome to another
- each carries unique set of genes
- catalyzed by transposases
- useful because induce genetic variance
- diagram depicts “cut and paste” transposition
19
Q
How can GFP be useful in fly genetics
A
Can be inserted into genome to trace cells in space and time
20
Q
Name some ways in which flies may be messed with
A
- Can possibly kill specific cells and see what happens
- Can interfere with gene function in specific cells (RNAi, over expression)
- Can induce recombination during mitosis in specific cells (generation of a clone)
- Can block or force electrical activity (neurons)
- Induced by shining light at right wavelength at different neurons and can induce electrical activity
21
Q
Describe an enhancer trap and what it may be used for
A
- Timing of gene expression is controlled via small pieces of DNA called enhancers which help control gene expression patterns
- can insert DNA into fly genome with weak promotor and reporter gene
- DNA will only be activated if enhancer activates, telling you when and where that enhancer becomes activated.
22
Q
Describe Uas/Gal4 system
A
- A tissue specific enhancer triggers the expression of the Gal4 transcriptional activator
- Gal4 can be regulated by any chosen promotor
- Gal4 binds to UAS enhancer sequences
- DNA downstream of the UAS sequence will then only be expressed when Gal4 is expressed.
- Can thus use this system to turn genes on and off
- Can mate a fly line with the Gal4 with a fly line containing UAS connected to a different gene, rather than creating a new fly each time
23
Q
Descripe Gap genes
A
-
Gap: Blocks of segments are missing
- Mutation results in loss of contiguous body segment, resulting in fly missing that part
24
Q
Describe pair rule genes
A
-
Pair rule: even or odd segments are missing
- Result of differing concentration of Gap gene proteins
- Defined by effect of mutation that causes loss of normal development patter in alternating segments
25
Q
Describe segment polarity genes
A
-
Segment polarity: denticle are duplicated in a mirror image
- Hedgehog, Wnt signaling
- Mutation leads to segments not being properly separated
26
Q
What are Cis-regulatory elements?
A
-
Cis-regulatory elements:
- Regions of non-coding DNA that regulate the transcription of neighboring genes
- Contain multiple binding sites for various factors (transcription factors)
27
Q
How is patterning information coded in cis-regulatory elements?
A
- A morphogen activates expression of target genes
- Target gene activation and therefore the patterning output depends on:
- Morphogen concentration
- Binding site affinity in target genes
28
Q
Describe Bicoid mutants
A
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Bicoid mutants: form posterior structures instead of a head, and lose anterior segments
- Phenotype found in embryos where mother is homozygous for bicoid. Bicoid gene must be provided maternally
29
Q
What are the different types of genes needed for embryonic development and a good analogy for them?
A
- “realisator” genes (“workers”)
- “selector or architect” genes (“architects”) that coordinate and regulate the realisator
30
Q
Define an imaginal disc
A
- Proginator tissue in larvae from which adult tissues develop
- Example: wing imaginal disc corresponds to a developing hemi-thorax and a wing
31
Q
Give a brief summary of the stepwise process in terms of gene progression (imaginal disc to adult structure)
A
-
Prepattern
- Regional expression of patterning genes
- Establishment of a pre-pattern of cell territories
-
Acquisition of neuronal competence
- Expression of proneural genes in small groups of cells
-
Singling out a neural precursor
- Mutual inhibition among proneural cells
- Emergence of a precursor
-
Lateral inhibition
- Neuronal precursor inhibit remaining cells of the proneural group
- Proneural cells return to epidermal fate
-
Fixed neuronal lineage
- Fixed number of divisions
- Asymmetrical segregation of fate determinants
-
Differentiation
- Sister cells assume their final shape and acquire their properties
- Neurons grow neurites and establish their final connectivity
32
Q
describe step 1 of the notum development
A
-
Step 1: defining a large region where sense organs will develop
- Prepatterning genes
- e.g. - Iroquois
More info:
- iroquois complex defines top domain
- Other genes define the central domains: pannier, u-shaped
- These genes are called pre-patterning genes; they are transcription factors and are expressed very early during thorax development
33
Q
describe step 2 of the notum development
A
-
Step 2: defining smaller regions of neural competence
- Proneural genes
- e.g. achaete, scute
More info:
- Small groups of epidermal cells (~30-40) acquire the transient competence to become a sensory organ precursor
- This competence is give to the so-called proneural genes, and it later restricted to a single precursor per group, the sensory organ precursor (SOP)
- For the bristles, the proneural genes are the transcription factors achaete and scute
- Other proneural genes determine the formation of other sense organs (e.g. atonal, amos)
- Proneural genes and their function are generall conserved in vertibrates
- From prepattern to proneural genes
- The patchy expression of achaete and scute is determined by an array of regulatory elements responding to iroquois
34
Q
describe step 3 of the notum development process
A
-
Step 3: singling out a sensory precursor cell
- Mutual inhibition - Notch/Delta cell-cell interactions
- SOP (sensory organ precursor) defined here
More info:
- The emergence of a single precursor among the proneural group results from competition among the cells in this group.
- This competition, called mutual inhibition happens through cell-cell interactions mediated by the receptor Notch (N) and the ligand Delta (DI)
- When the competition does not happen (mutants), all proneural cells become sensory precursors
- Notch, Delta and the entire signaling pathway they trigger constitute the neurogenic genes, which restrict the development of proneural cells into SOPs
- The Notch/Delta system
- Notch (N) and Delta (DI) are transmembrane receptors expressed at the cell surface.
- Upon binding by DI, Notch undergoes cleavage of its intracellular domain (ICE) which triggers a signaling pathway
- The output of the signaling pathway downstream of N is the repression of the neural fate.
- DI expression is promoted by Scute
- A cell that expressed more Delta may win the competition
- The proneural group may transition from a situation where all the cells maintain each other in a repressed state, to a situation where one cell expressing more DI represses its neighbors and becomes the SOP
35
Q
describe step 4 of the notum development process
A
-
Step 4: Lineage control and asymmetric divisions
- SOP (sensory organ precursor) divides
- Has a fixed lineage
More info:
- A freshly selected SOP starts to divide. The pattern and number of divisions is constant for a given type of sensory organ. This is a Fixed lineage
- The lineage generates a bristle, a socket, a glial cell and one or more neurons
- At each step of the lineage, cellular decisions are made
- Any mistake leads to an aberrant sensory organ
- Decision-making in the sensory lineages
- Asymmetric segregation of specific proteins result in distinct daughter cells
- Recycling Notch and Delta to choose cell fate during the lineage
- The daughter cells of the second division of the SOP lineage “fight” to choose their fates
The fight is biased by the asymmetric segregation of a cytoplasmic determinant
36
Q
describe step 5 of the notum development process
A
-
Step 5: an aspect of differentiation, establishing the correct neuronal connections
- sensory neurons extend an axon to VNC
- Neurons start connecting to each other
- this step is an aspect of differentiation
More info:
- Sensory neurons of the thorax extend an axon to the ventral chord VNC, the posterior part of the central nervous system
- In the VNC, each neuron extends 2 branches along the antero-posterior axis
- The shape and position of these projections vary with the organ.
- The ultimate aspect of sense organ differentiation is controlled by the earliest gene in the cascade
- Although the proneural genes achaete and scute give an information on the type of sense organ, interfering with their function does not affect the projection
- In contrast, the function of Iroquois is necessary and sufficient to determine where and how the neuron projects to the brain.
37
Q
Which genes are important in development of wing primordium?
A
- This wing identity results in wing cells expressing the genes vestigial and scalloped
- The wing primordium is determined by the intersection of dpp and wg expression
38
Q
To which segments is the wing primordium restricted, and how?
A
T2 and T3 by HOX genes
39
Q
Purpose of clonal analysis
A
- Mark cells at defined developmental times and see where they end up in the adult wing
- Cells can be marked genetically by making them homozygous for a recessive mutation as they grow.
40
Q
How can cells be modified to grow faster in clonal analysis and why does this help?
A
- A growth advantage can be conferred to the cells of the clone by exploiting the mutation Minute
- Minute: a mutation modifying a genetic factor involved in rate of development
- This gives big clones, but also reveals rules of cell growth.
41
Q
how is compartmental identity defined?
A
- The compartmental identity is defined by expression of the selector genes
- Engrailed: Posterior
- Apterous: dorsal
42
Q
What does Dpp do?
A
-
Dpp is a morphogen that signals at short and long distance
- Once the AP boundary exists, dpp is produced there and diffuses, creating a symmetrical gradient
- The dpp gradient is read by target genes responding to different concentrations, thereby creating different domains in the wing.
43
Q
How can a cell undergo mitosis and at the same time retain a stem cell state?
A
- A microenvironment facilitating self-renewal or asymmetrical distribution of cell fate determinants (or both)
- Microenvironment: stem cell niche created by support cells
- Allows to maintain proliferative potential of stem cells and allows differentiation.
44
Q
4 steps in the life cycle of a germ cell and the processes that affect germ cell formation and maintenance
A
- Germ cells first have to be specified = Primordial Germ Cells (PGCs)
- PGCs Migrate to find the SOMATIC GONAD
- In the niche PGCs adopt sexual identity and form a stem cell population = Germline Stem Cells (GSC)
- Germ cells initiate meiosis and form gametes
45
Q
What is the function of germ plasm?
A
- Primordial germ cells are specified by the GERM PLASM
- The function of the Germ Plasm is to prevent differentiation of progenitors of germ cells into somatic tissues
- Nuclei which end up in the Germ plasm will become PGCs
46
Q
- Name 5 maternal mRNAs localized to the germ plasm and necessary for germ cell formation (8 total, 5 important ones to remember)
A
- Oskar
- Nanos
- Vasa (conserved germ cell marker)
- Pole granule component (pgc)
- Trapped in endoderm-1 (tre-1)
- Tudor
- Pumilo
- Germ cell less (gcl)
47
Q
What is the role of Oskar in germ plasm formation?
A
- Localizing oskar at the anterior pole is sufficient to induce germ plasm and ectopic PGC formation:
- Oskar is the only sufficient factor
- Role of oskar in germ plasm formation: has a central, duel role.
- As an RNA-binding protein it crosslinking to nanos, pgc, and gcl mRNAs; RNA-binding maps in vitro to the C-terminal domain of Oskar
- The highly conserved N-terminal domain forms dimers and mediates Oskar interaction with the germline-specific RNA helicase Vasa.
- Oskar localizes nanos mRNA at the extreme posterior pole of the unfertilized egg
48
Q
role of nanos
A
- mRNA and protein binding protein
- translational repressor of maternal mRNAs
- role in AP patterning and germ plasm assembly
49
Q
What is the role of pgc?
A
- pgc = polar granule component
- Required for maintanance of Primordial Germ Cells (PGCs)
- so what is the role of the pgc protein in PGC formation?
- PGCs are transcriptionally silenced by the pgc gene product
