Metodi post-genomici in biochimica cellulare
Metodi post-genomici
Quantitative analysis of systems biology by taking advantage of available genomic information at the level of 1.SNPs analysis associated to disease or drug response 2.mRNA (transcriptomics) 3.Protein (proteomics) 4.Post-translational modifications (aka “modificomics”) 5.Surface exposure (surfomics) 6.Protein-protein interactions (interactomics) n 7.Small metabolites (metabolomics) and their relations (metabonomics) Many other fantasy exercises (glycomics, lipidomics, allergenomics, degradomics, excluding – perhaps – comics...) G.B Smejkal, “I’m an –omics, you’re an -omics... ” Exp. Rev. Proteomics 3 (2006) Metodi post-genomici
Modelli cellulari e animali Trascrittomica Proteomica Systems biology
Modelli cellulari e animali (farmacologici e/o genetici)
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)
Modelli animali (farmacologici) Intero organismo vs. cellule isolate Trattamento sistemico o lesione chimica locale Possibilità di valutare l’effetto anterogrado/retrogrado
Modelli animali (e vegetali?!?) (genetici) Organismi modello Genoma noto Non solo topo! Vita breve Invertebrati (e piante…)
Trascrittomica
Common steps to expression analysis
RTqPCR microRNAs are short (around 23 nt) non coding RNAs with roles in transcriptional regulation of gene expression
RTqPCR
Quantification & Analysis
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
Cluster analysis
Euclidean distance Pearson correlation
Do it yourself:
Next generation sequencing
1 st gen. Sanger seq.
2 nd gen. Illumina
2 nd gen. IonTorrent
3 rd gen. Pacific Biosciences
3 rd gen. Oxford Nanopore