International Postgraduate Course in Genomics

Universitat Autònoma de Barcelona

Bellaterra (Barcelona), June 1-15, 2004
 

INVITED PROFESSORS:

  • Pieter de Jong (Children’s Hospital Oakland research Institute, Oakland, California)

  • Manyuan Long (Department of Ecology and Evolution, University of Chicago, Chicago)

 

Sessions will take place in the Seminar of the Departament de Genètica i de Microbiologia, Facultat de Ciències (C3-329), from 9:30 to 13:30 AM.


 

 

 

PROGRAM

June 1, Tuesday

Session 1. Genomes and Genomic Cloning

Speaker: Pieter de Jong (Children’s Hospital Oakland Research Institute)

1.   Size and anatomy of eukaryotic genomes.

2.     Rationale behind genomic scale projects.

3.     Historical perspective on cloning of genomic DNA: lambda, cosmids, P1, T4 , YACs, PACs and BACs

4.     Reference library concept

5.     Screening of genomic clone libraries

 

June 2, Wednesday

Session 2. Mapping and sequencing approaches: genetic, clone contigs, radiation-hybrids, cytogenetics

Speaker: Pieter de Jong (Children’s Hospital Oakland Research Institute)

1.     Genetic mapping

2.     Cytogenetics

3.     Clone contigs

4.     Radiation hybrids

5.     Sequencing strategies: whole genome shotgun versus clone-by-clone shotgun sequencing

 

June 3, Thursday

Session 3. Whole genome Projects: How they are organized and main conclusions

Speaker: Pieter de Jong (Children’s Hospital Oakland Research Institute)

1.     E.coli

2.     C.elegans and Drosophila melanogaster

3.     Human

4.     Mouse

5.     Rat

6.     In progress: chimpanzee, chicken, cattle, dog

7.     More genomics in the post-genome era: platypus, monodelphus, pig, elephant, and?

 

June 4, Friday

Session 4. Comparative genomics: analysis of the same genes through evolution

Speaker: Pieter de Jong (Children’s Hospital Oakland Research Institute)

1.     Strategies

2.     Observations and conclusions.

3.     Gene deserts: how to tackle the perplexing questions on the functions of non-coding DNA: the ENCODE project

 

June 7, Monday

Session 5. Spin-offs from genomics: analyzing the complexity within a single organism, within a population or within a community of species

Speaker: Pieter de Jong (Children’s Hospital Oakland Research Institute)

1.     Functional genomics

2.     Population genomics

3.     Metagenomics

4.     Accessing genomic data through databases: how to find your favorite gene, map and clones.

 

June 8, Tuesday

Session 6. Functional genomics: fundamentals and applications of microarrays

Speakers: Mario Cáceres (Department of Human Genetics, Emory University School of Medicine) and Miguel Perez-Enciso (Departament de Ciencia Animal i dels Aliments, Universitat Autònoma de Barcelona)

1.     Methodology of microarrays

2.     Data analysis

3.     Applications of microarrays

4.     Functional differences between the human and chimpanzee brains

5.     Promises and pitfalls of Genetical Genomics

 

June 9, Wednesday

Session 7. Origin of new genes: case analysis and mechanisms

Speaker: Manyuan Long (Department of Ecology and Evolution, The University of Chicago)

1.     What is the matter?  Historical perspective and definition of new genes

2.     Cases analysis: jingwei, sphinx, monkey-king

Serendipity and emerging new questions

3.     General processes:

Molecular mechanisms

Evolutionary forces

4.     Gene duplication: cid and Rnase

5.     Exon shuffling: cases of Patthy and young genes

6.     TE and scrape yard of Makalowski

7.     Retroposition and seeds of evolution: prediction of Juergen Brosius

 

June 10, Thursday

Session 8. Origin of new genes: genomic analysis and the rate of origination

Speaker: Manyuan Long (Department of Ecology and Evolution, The University of Chicago)

1.     How quickly do new genes enter the genomes?

2.     Experimental genomic analysis in Drosophila:

Methods:

(1) Comparative in situ hybridization analysis

(2) Comparative microarray analysis

(3) Other complementary techniques

3.     Computational analysis of genome sequences

(1) Power and weakness of in silico analysis

-Advantages: rich data and inexpensive

-Limits: annotations, incomplete data, and molecular evolution

(2) Complementary experimental analysis

 

 

June 11, Friday

Session 9. Origin of new genes and evolution of functional systems

Speaker: Manyuan Long (Department of Ecology and Evolution, The University of Chicago)

1.     If new genes are emerging in adequately large number, are there any

patterns and underlying mechanisms?

2.     New problems raised by functional analysis of new genes: Do functional systems evolve?

3.     Evolution of sex chromosome and theories of sex-related genes.

4.     Drosophila genomes: Genes escaping from the X chromosomes.

5.     Mammalian genomes: Extensive gene traffic on the X chromosomes.

6.     Predictions and genomic tests from Drosophila and Mammalian data.

 

June 14, Monday

Session 10. Origin of genes and evolution of exon-intron structure

Speaker: Manyuan Long (Department of Ecology and Evolution, The University of Chicago)

1.     Gene evolution and exon theory of genes.

2.     Observations and evolving models of intron evolution.

3.     Early evidence and arguments

(1)Introns-early

(2)Introns-late

(3)Introns-early and late

4.     Evidence from an earl genomic analysis: distribution of intron phases

(1)Definitions and predictions

(2)Intron phase proportions

(3)Phase correlations

(4)Evidence from Molecular clock

5.     Evolving complexity of genomes: Intron loss and intron gain

(1)Definition and detecting approaches

(2)Observations and general conclusions.

6.     A new question of intron evolution: what evolutionary forces responsible and does introns have any functions?

(1)Population genetic analysis in Drosophila

(2)Intron phase correlation with conservation of splicing signals

(3)Intron size and expression levels

7.     How many eukaryotic genes were created by exon shuffling?

 

June 15, Tuesday

Session 11. Origin of new genes and related population genetic problems

Speaker: Manyuan Long (Department of Ecology and Evolution, The University of Chicago)

 

1.     A genetic question raised by new genes sphinx

2.     Bridges and Muller’s conclusion about the crossing over on the fourth chromosome of Drosophila

3.     Population genetic prediction and early experimental tests

Prediction: Genetic blackhole

Early tests: ci genes in several Drosophila species

4.     Data of sphinx and flanking regions:  long haplotype structures

5.     Data of the chromosomal variation: reflect different histories and recombination.

6.     What do we learn from this case analysis?


 

For registration and information, please contact:

  • Julia Provecho, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), SPAIN. Tel. 34-93-581-2724, FAX 34-93-581-2387, E-mail: d.genetica@uab.es.

 

  • Alfredo Ruiz, Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), SPAIN. Tel. 34-93-581-2729, FAX 34-93-581-2387, E-mail: Alfredo.Ruiz@uab.es.
     


 

 

 

 

 


 


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