- 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
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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