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1

What the main model organisms?

Yeast, plant (arabidopsis), c.elegans, drosphila melanogaster, zenopus, zebrafish and mice (musculus musculus)

2

List of the order of genetic similarity to humans of the main model organisms.

Mice, xenopus, fish, fly, c.elegan, yeast, e.coli

3

what percentage of coding DNA is different in mice compared to humans?

10%

4

what percentage of coding DNA is different in fish compared to humans?

25%

5

what should be kept in mind when studying the role of regulatory non-coding DNA in your model organism in relation to human application?

differences in non-coding DNA greatly, a lot more than protein DNA, for example there is an average change of 50% of non-coding DNA when compared to primates. It is better to use mice for such experiments as closely related.

6

what makes a good model organism?

- short-breeding cycle - large brood size- high relating freqeuncy - robustness- simple feeding and other maintenance requirements- ability to store special strains in an inactive state- history (linkage maps, mutant collections, genome sequence) - molecular techqniues (transgenesis, targetted mutations) - you can do gene targeting and targeted mutagenesis

7

what type of study is normally done in zebrafish?

development, disease, behaviour

8

what type of study is normally done in mice?

behaviour, optogenetics, brain imaging, genetics, obesity

9

what type of study is normally done in mice?

- cell signalling, nervous system study

10

give two examples of model organisms not mirroring the behaviour of genuinely wild type animals?

- wild mice are more aggressive and less maternal instincts- c.elegans in the wild form clumps in response to high oxygen concentrations

11

Why are c.elegans good for Knock out experiments?

there are libraries containing a strain expressing a KO for every c.elegan gene (save this)

12

why list 9 reasons why c.elegans are a good model organism

- easy to maintain - short life cycle (around 3 days)- small number of cells- around 1000 somatic cells - transparent - fully cell-lineaged- detailed anatomy and full connective - genome fully sequenced (first animal)- ease of transgenesis - forward and reverse RNAi genetics

13

why are c.elegans good to study development in?

- there re conserved genes in worms and in other organisms (transcription factors, homeodomains, bHLH, miRNAs, signalling pathways such as Notch, Wnt and TGF-beta)-There are conserved mechanisms: cell autonomous dell fate specification (cascades of TFs and miRNAs), cell non-autonomous signalling (tissue patterning, lateral inhibition)- cell lineage is invariable in the worm so you can ablate cells and look at inductive vs autonomous development .- because worms are transparent so can track lineage the entire time translational and transcriptional reporters can be used.

14

how can c.elegns be stored for a long time?

in the dater state- dont need to be fed

15

how many neurons do c.elegans have?

302

16

how many glial cells to c..elegans have?

56

17

how many morphological classes of neurons are there?

118

18

what is considered the brain of the worm?

the nerve ring

19

why is having a connectome not hugely important?

you want to know the precise interactions between the components, are the signals positive or negative long range or short range?

20

why is the c.elegan being transparent a good thing?

- because worms are transparent so can track lineage the entire time translational and transcriptional reporters can be used.

21

when are transcriptional reporters used? what are their down falls?

- to monitor gene expression or for cis-regulatory analysis (identify enhancer regions) - not all mRNA is translated- can't be used to look at protein localisation

22

when are translational reporters used?

- monitor gene expression - monitor protein localisation - cis regulatory analysis - over-expression or mutant rescue

23

how do you make translational reporters in the c.elegans and how are they put into c.elegans in particular?

you produce a DNA construct containing the gene of interest and its regulatory regions upstream of it. Then you produce an overhanging sticky end which is complimentary to another construct's end that contains the a gene for a reporter such as GFP with a 3' unc- 54 UTR on the end of it. SO that they can anneal to each other and act as primers to each other during PCR. These can then be injected into the gonad for form an array (mini chromosomes) that is inherited in a mosaic fashion (can be generated in a week). They can be integrated into the genome for mendelian segregation using gamma/ uv-irradiation (how?)- cam also bombard using gold particles into the genome (how?)

24

when can a mini chromosome be used in c.elegans and for what?

They can be used to study cell lineages- if you have a construct that has a fluorescence reporter downstream of a universal promoter and inject, it will be inherited mosaically so one cell will inherit fluorescence and the other won't after division.

25

what is a fosmid construct and why is it used?

- In order to ensure that the gene of interest that is being inserted into the worm genome is being authentically regulated, a fosmid construct. This fosmid can contain a bicistronic region. A GFP can be inserted after a gene within a fomid but due to the intercistronic region, the primary transcript will undergo trans-splicing. This will result in the protein localising to the normal site while the GFP can undergo nuclear localisation (if has an NLS) and allows for cell identification.

26

what can be carried out in c.elegans?

forward genetic screens ,genetic dissection of developmental pathways (epistasis), mapping and cloning, reverse genetics (RNAi)

27

how many chromosomes does the fly have?

4

28

what percentage of human disease genes have genes in the fly?

60%

29

how many of the fly genes have homologues in mammals?

more than half

30

why are flies good for tracking recessive genes?

there is no recombination in male flies so you can associate a recessive gene to a visible marker (such as curly wings or white eyes) and you know there will not be recombination between this (but does it not matter about the females?- maybe if passed on from father to and only males used then it doesn't|)