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central european institute of technology
CEITEC
Genomics and proteomics at MUJiří Fajkus
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Genomics interested in GENOME – complete genetic info
(DNA/RNA sequence) of an organism (3Gb-human) ca. 25 000 human genes 2% genome
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Potential of genomics : fast analysis of gene mutations and changes in gene expression (at the mRNA level) detection of inherited disorders, pathogens,
genetic manipulations, molecular oncology...
Novel DNA sequencing platformscDNA microarrays
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Why PROTEOMICS?Only limited repertoire of events directly
depends on DNA sequence (25 000 genes several millions proteins )
1 organism 1 genome many proteomes
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transcription translation
DNA RNA Protein
mRNACatalysis
& regulationrRNAtRNA
ncRNA
replication
PhenotypeGenotype
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Core facility “Genomics and Proteomics”
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The Desperate Man, Gustave Courbet, 1844-45
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proteome analysis bacteria, plants, animals, human, stem cells, etc.
protein characterization
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Core facility “Genomics and Proteomics”: integration of sophisticated technologies
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isolation, separation of proteins identification of proteins, posttranslational modifications
analysis of protein complexes
mass spectrometry – major proteomic tool
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Core facility “Genomics and Proteomics”
CEITECBRNO | CZECH REPUBLIC
CF Genomics &proteomics
CEITEC
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Examples of present scientific projectsBacterial genetics and genomicsPlant cytogenomicsMolecular analysis of plant developmentBiology of telomeres Molecular diagnostics and therapy (collab.
UH Brno, UH S.A.)
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Bacterial genetics and genomics Human, emerging and re-emerging
pathogens Whole genome sequencing strategies
Whole genome fingerprinting (physical mapping)
Comparative genome sequencing (microarray)
Pyrosequencing, Solexa sequencing, SOLiD sequencing, Sanger sequencing
Analyses of bacterial transcriptome Gene annotations Analyses of gene regulatory networks
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Goals of whole-genome sequencing Identification of virulence factors (better
treatment of infectious diseases)
Identification of prominent bacterial antigens (development of new vaccines)
Identification of unique genomic sequences (better diagnostics)
Metagenomic sequencing (definition of human microbiome)
Epidemiological studies (better preventive measures)
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Restriction digestInterval B
BamH I EcoR I
Hind II I
Interval B
BamH I EcoR I
Hind II I
XL PCRXL PCR
Nic
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Cunic
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Sam
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SS14/ 4
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DNA fingerprinting:
Analysis of restriction fragments
Se Sequencing of heterologous regionsSe
• 97 TPI inetrvals• Average size of TPI interval: 12.7 kb
•
•
P4
Interval B
P3 P4
Interval B
P3
Genomic DNA
Interval A
P1P2
Interval A
P1P2
P6Interval B
Interval CP5
•
•
•
•
•
•
•
•
Primer control
P4
Interval B
P3 P4
Interval B
P3
Interval A
P1P2
Interval A
P1P2
P6Interval B
Interval CInterval CP5
Restriction digestInterval B
BamH I EcoR I
Hind II I
Interval B
BamH I EcoR I
Hind II I
Interval B
BamH I EcoR I
Hind II I
Interval B
BamH I EcoR I
Hind II I
XL PCRXL PCR
Nic
hols
Cunic
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Sam
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SS14/ 4
934
SS14/ 4
933
Nic
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Cunic
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Sam
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Nic
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Cunic
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Sam
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SS14/ 4
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SS14/ 4
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DNA fingerprinting:
Analysis of restriction fragments
Se Sequencing of heterologous regionsSe
• 97 TPI inetrvals• Average size of TPI interval: 12.7 kb
•
•
P4
Interval B
P3 P4
Interval B
P3
Genomic DNA
Interval A
P1P2
Interval A
P1P2
P6Interval B
Interval CP5
•
•
•
•
•
•
•
•
Primer control
P4
Interval B
P3 P4
Interval B
P3
Interval A
P1P2
Interval A
P1P2
P6Interval B
Interval CInterval CP5
CGS sequencing
DNA microarray
Transriptome prediction
Physical mapping of the genome
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Plant Sciences at MU - Why plants?Scientific reasons: unique
developmental model
Political and economical reasons: Plants as the only sustainable and self-renewable tool of energy conservation on Earth; Plants as a multipurpose and low-cost production system
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Laboratory of Plant CytogenomicsMethodology construction of large insert DNA libraries high-throughput DNA sequencing genome comparisons on a sequence
and chromosomal level
- bioinformatics
- molecular cytogenetics
- comparative phylogenomics
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Genetix Qpix system
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Laboratory of Plant Cytogenomics
analysis of inter-species chromosome and genome collinearity
karyotype and genome evolution within phylogenetic frameworks (phylogenomics)
evolution of repetitive DNA elements and structure of plant genomes
karyotype evolution and speciation
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Molecular analysis of plant growth and development Functional genomics and proteomics of model plants
(Arabidopsis) and crop plants (oil-seed rape) as a low-cost production systems for e.g. pharmaceutically active proteins (antibodies) and biomass production
Analysis of the protein structure and protein engineering
Identification of Proteins Regulating Plant Biomass Production - cytokinins and their receptors regulate biomass production in plants (in frame of collaboration with Korean colleagues) - application for patent cooperation treaty (PCT) submitted by MU and Korean partner.
CEITECBRNO | CZECH REPUBLIC
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Biology of telomeresStructure, evolution
and maintenance of plant telomeres (DNA, proteins, chromatin structure, epigenetics
Telomeres and telomerase in oncology diagnostics and therapy
CEITECBRNO | CZECH REPUBLIC
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Key processes in telomere biology (and in living cell, in general): interaction networks of proteins, DNA and RNA
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Laboratory of separation and analysis
of proteins and their complexes
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description of important protein complexes and their compositions
kinetics and thermodynamics of protein-protein and protein-DNA interactions
study of mechanisms of function and action of biomolecular complexes
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SUMMARY – Genomics and proteomics
Concentration of “universal” and sophisticated genomic and proteomic equipment and expertise in core facility – optimum cost-efficiency
Potential for synergistic interactions among research groups, capability to solve complex projects
Higher competitive strength and attractiveness to international R&D community raising of funds for science
Emphasis on current internationally competitive research groups, yet flexibility in routing of future development
Connection to major medical institutions (university hospitals, res. institutes), biotechnology incubators and institutes of Czech Academy of Sciences
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