Patterns examples (Turing?)

Question 1

Give 5 examples of patterns observed in nature!

Answer 1

1. Uniform distribution of trichomes
2. Zebrafish stripes
3. Limb development
4. Segmentation of the Drosophila body
5. Phyllotaxis

Question 2

What are the two main groups of genes defining trichome development?

Answer 2

1. Early genes, involved in patterning of trichome distribution
2. Late genes involved in the formation of the trichome structure itself.

Question 3

If a KO of a gene results in more trichomes on a leaf what could be the role of this gene, assuming a Turing pattern mechanism?

Answer 3

Inhibitor

Question 3

What will a KO of an activator result in a trichome phenotype?

Answer 3

Less or no trichomes

Question 4

What will overexpresion of TRY(Tryptichone) and CPC(Caprice) result in the trichome leaf phenotype?

Answer 4

No trichomes

Question 5

What is the missting morphogen action needed for Turing patterning and how is the leaf still able to account for it?

Answer 5

Autocatalytic production of activator / self-activation.

Pesch and Hülskamp, 2004 were able to show that in fact restricted movement of the activator out of the cell directed by the increase in the activator concentration acounts for the Turing-like dynamics without the need for autocatalytic production.

Question 6

What is the main driving force for fish pattern variety?

Answer 6

self-organization variability rather than genetic one

Question 7

What are the 3 types of pigmenmt cells involved in zebrafish patterns?

Answer 7

Question 8

Describe the general mechanism behind zebrafish pattern formation?

Answer 8

On a cellular rather than chemical level. The cells are morphogens.

Melanophores need continuous long-range signals from xanthophores to survive while neighboring xanthophores and melanophores compete for survival. Modulation of this interactions result in various patterns.

Question 9

What is the model underlying Drosophila segmentation genes patterns?

Answer 9

not Turing, but a hierarchical cascade of signaling gradients with threshold sensitivity, “French flag model”

Question 10

How is a signaalling gradient translated in a pattern?

Answer 10

Threshold response

Question 11

What is the mathematical model dictating the sharp threshold eve patterns in Drosophila development?

Answer 11

Reinitz and Sharp (1995) model

Question 12

How is the gene network describing eve patterns determined?

Answer 12

Simulated annealing

Question 13

What are the 5 hierarchical gene categories in Drosophila body development?

Answer 13

1. Maternal genes
2. Gap genes
3. Pair-rule/Segmentation genes
4. Segmentation-polarity genes
5. Selector genes

Question 14

What does the T matrix represent in the Reinitz and Sharp model.

Answer 14

the network of gene interactions

Question 15

To achieve stripes what should be the values in the T-matrix?

Answer 15

Positive autoregulator terms and negative cross-regulation terms

-this allows for one of the molecules to completely dominate overt the other in a specific region allowing for very sharp boundaries and thus stripes.

Question 16

What is phylotaxis?

Answer 16

the regular arrangement of leaves on the stem

Question 17

What is the main morphogen in the process of phyllotaxis?

Answer 17

auxin

Question 18

What is the main process to establish optimally packed leaf primordia?

Answer 18

Auxin polar transport + PINs dynamic positioning towards auxin maxima