2012 October 8

Matters arising

Think about your genetics project and be prepared tell us about your plans on Wednesday

OMIM Database

1. Introduce OMIM database (Online Mendelian Inheritance in Man)
2. OMIM links: | OMIM home page | OMIM advanced search | OMIM Wikipedia page |
3. Hamash, A. et al. (2005). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.Nucleic Acids Res 33: D514-517. PMCID: PMC539987
4. Sample OMIM searches: | BRCA2 | DMD |

Chapter 3 Review

1. Concepts and Jargon
2. Exercises, problems and weblems

Assignments for Wed 10 October

1. Post solutions for Chapter 3 Problems (only one is online as of noon, Oct 8)
2. Work on your planning for genetics project, especially concept and sources
3. Start work on Lesk Chapter 4 'Comparative Genomics'

Class Notes

OMIM (Online Mendialian Inheritance in Man)

Advantages:

+Narrative description of each gene

+Shows any mutations for the gene

+It has good references

+It has good links to diseases

Disadvantages:

- Not very up to date because the amount of genetic information to be added into the database keeps increasing at an exponential rate.

-Weak on complex diseases (diseases that have both a genetic and environmental component)

Mutation Vs Variation

What is the difference , if any?

Indels

Insertions or deletions that throw off the reading frame in a protein coding gene.

Classical genetics was used to identify the triplet nature of the genetic code using chemical mutagenesis studies.

Coverage

Coverage of 50 is acceptable for resequencing. 200-500 coverage of transcriptome analysis is good. De novo sequencing requires two sequencing technologies. More coverage is essential.

Lac mutations in E. Coli:

Lac operon: the Lac operon consists of 3 structural genes: LacZ (encoding beta-galaktosidase), LacY (permease), LacA (transacetylase), a repressor: LacI, a promoter and an operator. When knocking out any of the structural genes, the bacterial phenotype will be Lac-. Lac- cells cannot metabolise lactose. Knockout of the LacI repressor and operator mutations lead to constitutive expression.

Mutations:

- these mutations are involved in the utilization of lactose as a food source - Lac-mutants cannot grow on lactose as the only carbon and energy source

- these mutations affect the cell catabolism

- to isolate Lac mutations replica plating is used - on one plate media which lack lactose, on the other media which contains lactose

Trp mutations in E. Coli:

- trp mutations require tryptofan in the growth media

- these mutations are anabolic mutations

- for isolation again replica plating can be used on two different growth media: trp+ and trp-. The WT strand can grow in both conditions, whereas the mutants will grow only in the presence of tryptofan

Cis/trans test: a genetic analysis, which allows us to determine whether a mutation affects only genes with which it is linked to, r it can affect genes on a longer distance

Karyotype

Giemsa stain allows to distinguish between GC rich and AT rich regions. Chromosomes of cells in metaphase are visualized as they are most condensed and lined up for seperation. Detection of abnormal number, size variations ( large chromosomal abberations) and transcolations can be seen. Closely related organisms can be analysed for similarity in banding patterns on homologous chromosomes that may have recombined.