Deck 1

Question 1

What is a morphogen?

Answer 1

When inducing factors are present as gradients with multiple responses, they are called morphogens.

Question 2

What is haploinsufficiency ?

Answer 2

A genetically dominant mutation because loss of 50% of the WT protein is sufficient to cause an abnormal phenotype.

Question 3

What does the term constitutive mean?

Answer 3

Gene products that are active all of the time.

Question 4

What is a dominant negative mutation?

Answer 4

This mutation is genetically dominant but it is not constitutive. The mutant form of the gene product has no function itself but interferes with the WT protein.

Question 5

What is a maternal-effect gene?

Answer 5

Causes a phenotype in the individual that is not dependent on its own genotype but that of the mothers.

Question 6

What is a fate map?

Answer 6

Is a diagram that shows what will become of each region of an embryo in the course of normal development: where it will move, how it will change shape, and what structures it will turn into. (The C.elegans fate map is very precise - resolution down to the cellular level)

Question 7

How are fate maps constructed?

Answer 7

They are constructed by labelling single cells or regions of embryo and locating the position and shape of the labelled patch at a later stage in development. The labelling methods used are…

Question 8

What is clonal analysis?

Answer 8

Is a form of fate mapping in which a single cell is labelled in and the position and cell types of its progeny identified at a later date. A clonal analysis can prove lack of commitment but not the presence of commitment. The labelling may be carried out by:

• injection of one cell with a lineage label. This is simple method suitable for large cells and embryos that do not grow significantly, e.g. early stage xenopus or zebrafish.
• injection of one cell with a genetic label. This is will persist without dilution. Useful for chick and mouse embryos.

Question 9

What is specification?

Answer 9

A cell or tissue explant is said to be specified to become a particulary structure if it will develop autonomously into that structure after isolation from an embryo.

Question 10

What is a specification map?

Answer 10

This shows what the cells have been progammed to be by a particular stage in development

Question 11

Orthotopic graft

Answer 11

A graft to the same position of another embryo. A technique used for fate mapping.

Question 12

Heterotopic graft

Answer 12

A graft to a differernt position in a host. It is used to test determination. If the pathway is unaltered by the graft then it is said to be determined. If the graft develops according to its new postition then it follows that it was not determined, although it may have been specified at the time of grafting. A series of such grafts can find out when the cell or tissue becomes determined.

Question 13

What is determination?

Answer 13

A determined region will also develop autonomously in isolation (like specification) but differs in that its commitment is irreversible with respect to a range of environments present in the embryo. In a molecular sence, determination means that the cells have lost their reponsiveness, or compentance, to the signals that originally turned on the relevant combination of transcription factors.

Question 14

What three methods are required for proof that a particular molecule performs a particlar function?

Answer 14

• Expression. The molecule in question must be present in the right place, int the right stage and in a biologically active form. Studied by ISH or immunostaining.
• Activity. The molecule must have the appropiate biological activity.
• Inhibition. If the molecule is inhibited in vivo then the process for which it is thought responsible should fail.

Question 15

Why is Xenopus not a good model organism for genetics?

Answer 15

Because of its long life cycle. It takes at least 9 months to rear an animal to sexual maturity.

Question 16

Testing for Determinates by embryological techniques.

Answer 16

If cytoplasm containing a determimant is transplanted to a different part of the egg, then it will cause formation of the appropiate structure from the new cells that now contain it.

Question 17

Well defined examples of morphogens?

Answer 17

• SHH in the neural tube and limb bud - Zone of polariosing activity
• BMP in the early xenopus embryo - coming from the ventral centre
• Decapentaplegic protein (DPP) in drosophila imaginal discs

Question 18

Cross-species phenotype pheotype comparisons?

Answer 18

• Our understanding of gene function can be informed by the comparison of mutant and ‘wild-type’ phenotypes in a single organism as well as by the comparison of the phenotype consequences of mutation of a particular gene in species A with those of a mutation of the evolutionarily homologous gene in species B.
• Conservation of gene function across species is strongly supported by similar phenotype consequences of loss-of-function mutations in orthologous genes in both species [1] and functional replacement of mouse genes by their human counterparts [2, 3] as well as the remarkable phylogenetic conservation of patterns of gene expression [4].
• There are profound challenges in relating disease processes in humans and other animals, partly as a consequence of intrinsic variation in normal and pathobiology between species, and partly through historical, conceptual and pragmatic differences between clinical and lab approaches to describing diseases and phenotypes. Many such challenges are being faced head-on by those working with animal models of human disease, specifically with regard to inbred strains of laboratory mice. Robert Koch’s exhortation, ‘Gentlemen, never forget that mice are not human beings’ [5], reminds us that although use animal models of human disease can be extremely valuable, knowledge of comparative anatomy, pathology and pharmacology are needed to bridge the species gap. While genetic models often faithfully reflect the major features of human diseases, differences in phenotypes between mice and humans with mutations in orthologous genes can be as informative on the biological processes as those where there is a good match. Several diseases were first defined in mice and later in humans [6, 7] and more recently we have seen examples where apparent differences between mouse and human phenotypes were resolved with the realization that the clinical phenotype description in humans is incomplete and the mouse phenotypes are actually seen in the human disease [8]. Here, the mouse phenotype informs and expands the human clinical picture and provides new insights into the pathogenetic mechanism.
• We have been remarkably unsuccessful at being able to predict gene function at a physiological or whole organism level from gene sequence alone, and our understanding of gene function must ultimately depend on experimental manipulation of the genome and assessment of its consequences.
• Phenotype-similarity searches

Question 19

Studying gene expression

Answer 19

• Biochemical - accurate quantiitive discriptionn but no anatomical information
  
  • RT-PCR
  • Microarrays - often used for comparison between cells tat have or have not been treated to an inducer
  • RNA-seq - quantitive profile of whole transcriptome
    
    • Chip-seq - genome wide view of binding of specific proteins of interest
• In situ - anatomical but limited quantitative
  
  • ISH
  • Immunostaining
  • Reporter genes

Question 20

Studying protein expression

Answer 20

• Immunochemical staining
• Chip-seq

Question 21

Working out gene function

Answer 21

1. Classically approach begin with random mutagenesis
2. Genetic screens identifying mutants deficient in particular cellular process
   
   1. Phenotypes that are more complex will require more elaborate screens e.g learning and memory