Metodi post-genomici in biochimica cellulare

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Metodi post-genomici in biochimica cellulare
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Metodi post-genomici
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Metodi post-genomici

• Quantitative analysis of systems biology by
  taking advantage of available genomic information
  at the level of
• SNPs analysis associated to disease or drug
  response
• mRNA (transcriptomics)
• Protein (proteomics)
• Post-translational modifications (aka
  modificomics)
• Surface exposure (surfomics)
• Protein-protein interactions (interactomics)
• Small metabolites (metabolomics) and their
  relations (metabonomics)

Many other fantasy exercises (glycomics,
lipidomics, allergenomics, degradomics, excluding
perhaps comics...)
G.B Smejkal, Im an omics, youre an -omics...
Exp. Rev. Proteomics 3 (2006) 383-385
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Metodi post-genomici

• Modelli cellulari e animali
• Trascrittomica
• Proteomica
• Systems biology

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Modelli cellulari e animali(farmacologici e/o
genetici)
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Modelli cellulari(farmacologici e/o genetici)

• Facilità di mantenimento e trattamento
• Possibilità di combinare trattamento
  farmacologico e manipolazione genetica
• Utili per riprodurre un singolo meccanismo
• Cellule umane (o murine)

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Modelli animali(farmacologici)

• Intero organismo vs. cellule isolate
• Trattamento sistemico o lesione chimica locale
• Possibilità di valutare leffetto
  anterogrado/retrogrado

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Modelli animali (e vegetali?!?)(genetici)

• Organismi modello
• Genoma noto
• Non solo topo!
• Vita breve
• Invertebrati (e piante)

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Trascrittomica
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Common steps to expression analysis
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RTqPCR
microRNAs are short (around 23 nt) non coding
RNAs with roles in transcriptional regulation of
gene expression
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RTqPCR
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Quantification Analysis
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Arrays
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Arrays
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Arrays
Microarray technology has two major applications
gene expression analysis and genetic variation
analysis. All gene expression microarrays are
based on probes hybridization of labelled
cDNA. Differences arise in the labelling dye,
deployment, and probes immobilization and/or
organization. Illumina beads arrays Affymetrix
genechips Agilent microarrays
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Cluster analysis
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Cluster analysis

• Euclidean distance
• Pearson correlation

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Do it yourself
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Next generation sequencing
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1st gen. Sanger seq.
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2nd gen. Illumina
https//www.youtube.com/watch?vwomKfikWlxM
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2nd gen. IonTorrent
https//www.youtube.com/watch?vWYBzbxIfuKs
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3rd gen. Pacific Biosciences
https//www.youtube.com/watch?vv8p4ph2MAvI
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3rd gen. Oxford Nanopore
https//www.youtube.com/watch?v3UHw22hBpAk