Weekly outline

• 

  General

  
  "Ce qui est simple est faux,
  ce qui est compliqué est inutile"
  Paul Valéry

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  • podcast of the lectures (mp3) Folder
  • Student's talk CALENDAR Wiki
  • Subjects for Student's talks, important Page
  • INFO: student's talk - AVVISO importante per presentazioni Page

  
  

  Weeks index:
  

  • signalling - protein scaffolding - molecular sorting
  • intracellular transport - interphasic nucleus and genome organization
  • cytoplasmic-nuclear shuttling - ubiquitination - unfolded protein response
  • Autophagy - Stem Cells - Biosafety and biosecurity
  • neuronal migration and axon pathfinding: Ephrin/Eph, Slit/Robo and Netrin/DCC, ADAM proteins and ectodomain shedding
  • Neuronal migration and axon pathfinding: ADAM proteins, ErbB4-NRG1, animali transgenici e animali knockout (ripasso)
  • ERBB4 ubiquitination. Intracellular domains go nuclear and control transcription. Semaphorins- Plexins-Neuropilins
  • Genomes, genome-wide RNA analysis by microarrays and deep-sequencing methods.
  • Pervasive transcription in geneomes. Noncoding RNA classes. Promoter definition. One gene more products.
  • Chromatin. Epigenetic modifications to DNA and histones. Genomic imprinting. Transcriptome vs proteome.
  • Back to chromatin: heterochromatin determinants and boundaries
  • Methylation, transcription and gene activation
  • Post-trancriptional regulation. Alternative splicing, mRNA export, cis- and trans-factors to localize mRNAs.
  • Special Lectures: Silver papers by students & Seminar by Dr Venesio on Alternative Splicing in Disease
  • Week name or summary not defined.

  
  
• 

  28 September - 4 October

  signalling - protein scaffolding - molecular sorting

  • Signal transduction - scaffold protein
    

  • read this article: Whitmarsh_jip_98 File
  • podcast of the lecture: Sept. 30, 2009 URL
  • pdf lezioni Folder
  • venerdì 2 ottobre: lezione sospesa

• 

  5 October - 11 October

  intracellular transport - interphasic nucleus and genome organization
  

  • Signal transduction and protein transport
    

  • Task N.7: site-directed mutagenesis Wiki
  • Read the article: Verhey et al. 2001 File
  • Read the article: Blasius et al. File
  • supplementary material: movies of Blasius et al Folder
  • podcast of the lecture: october 05: part 1 URL
  • podcast of the lecture: october 05: part 2 URL
  • podcast of the lecture: october 07, part 1 URL
  • podcast of the lecture: october 07, part 2 URL
  • pdf_lezioni Folder
  • Interphasic nucleus
    

  • Find and read the article: Parada et al. 2004 Assignment
  • podcast of the lecture: october 09, part 1 URL
  • podcast of the lecture: october 09, part 2 URL
  • pdf_lezioni Folder
• 

  12 October - 18 October

  cytoplasmic-nuclear shuttling - ubiquitination - unfolded protein response

  • cytoplasmic-nuclear shuttling

  • Read the articles Folder
  • podcast of the lecture: october 12: part 1 URL
  • podcast of the lecture: october 12, part 2 URL
  • podcast of the lecture: october 14, part 1 URL
  • podcast of the lecture: october 14, part 2 URL
  • pdf_lezioni Folder
  • Ubiquitination - Unfolded protein response
    

  • podcast of the lecture: october 16, part 1 URL
  • podcast of the lecture: october 16, part 2 URL
  • Read the article: Dikic et al 09, ubiquitin structure & function File
  • pdf_lezioni Folder
• 

  19 October - 25 October

  Autophagy - Stem Cells - Biosafety and biosecurity

  • Autophagocytosis

  • Read this article: Lum et al. Autophagy Cell 2005 File
  • Read the article (optional): Mol_Cell_2009_Kirkin.pdf File
  • pdf delle lezioni Folder
  • Stem Cells

  • pdf of the lecture N.09 File
  • podcast 091021_01: stem cells
  • podcast 091021_02: stem cells
  • read this article: Takahashi et al, stem cells cell 2006 File
  • Read the article (optional): Pei et al. 2009, dedifferentiation review.pdf File
  • Task 8: Where is the mistake.... Assignment
  • Biosafety and Biosecurity

  • Seminario "biosafety/biosecurity tools and policies", Malcom Dando and Giulio Mancini. Venerdì 23 ottobre 2009, 11-13 Page
  • ppt_seminar File
• 

  26 October - 1 November

  neuronal migration and axon pathfinding: Ephrin/Eph, Slit/Robo and Netrin/DCC, ADAM proteins and ectodomain shedding
  
  

  • Ephrin/Eph

  • 261009 lezione I parte File
  • 261009 lezione II parte File
  • 261009-articolo Zimmer File
  • 261009-movie1 File
  • 261009-movie2 File
  • 261009-movie3 File
  • 261009-movie4 File
  • 261009-MP3-1 parte File
  • 261009-MP3-2 parte File
  • Slit/Robo - Netrin/DCC
    

  • 281009_read this article: Stein-Lavigne File
  • 281009 MP3 1 parte File
  • 281009 MP3 2 parte File
  • lezione 281009 File
  • 301009 - MP3- I parte File
  • ADAM proteins and ectodomain shedding
    

  • 301009 - MP3- II parte File
  • lezione 301009 File
• 

  2 November - 8 November

  Neuronal migration and axon pathfinding: ADAM proteins, ErbB4-NRG1, animali transgenici e animali knockout (ripasso)
  

  • 021109 MP3 1 parte File
  • 021109 MP3 2 parte File
  • Topi transgenici e topi knockout (ripasso)

  • lezione 021109 transgenici-knockout File
  • 041109 MP3 1 parte File
  • NRG1/ErbB4
    

  • lezione 021109 NRG1/ErbB4 alternative splicing File
  • 041109 MP3 2 parte File
  • lezione 041109 NRG1/ErbB4 migrazione I parte File
  • read this paper: Anton_NatNeuro_2004 File
  • paper Flames 2004 per "Stripe Choice Assay" File
  • protocollo stripe choice assay Assignment
  • task "stripe choice assay" File
  • 061109 MP3 1 parte File
  • 061109 MP3 2 parte File
  • lezione 061109 NRG1/ErbB4 migrazione II parte File
• 

  9 November - 15 November

  ERBB4 ubiquitination. Intracellular domains go nuclear and control transcription. Semaphorins- Plexins-Neuropilins

  • lezione 06-091109 NRG1/ErbB4 ubiquitinazione File
  • paper Sundvall 2008 File
  • 091109 MP3 1 parte File
  • 091109 MP3 2 parte File
  • paper Sardi 2006 File
  • lezione 091109 ErbB4 nucleare 1 parte File
  • 111109 MP3 1 parte File
  • 111109 MP3 2 parte File
  • lezione 111109 ErbB4 nucleare 2 parte File
  • Semaphorins/Plexin/Neuropilin
    

  • materiale su Semaphorins-Plexin-Neuropilin File
  • read this paper about RNA interference false positives and negatives File
• 

  16 November - 22 November

  Genomes, genome-wide RNA analysis by microarrays and deep-sequencing methods.

  • lecture: 13 Nov - The Organization of Genomes (slides) File
  • Assignment BMG1: nucleotide sequence in database
  • Assignment BMG2 - Identificazione delle parti di una sequenza genica
  • lezione 16 novembre - Analysis of gene expression File
  • Audio-Analysis of gene expression_MP3_stream Page
  • Article: Microarray of sporulating yeast (Chu et al, 1998) File
  • Assignement BMG3 Choose a microarray for your experiment Assignment
  • Assignment BMG4 - Choose a beadarray for your experiment
  • lezione 18 novembre - Genome level transcriptome analysis File
  • Review: Tiling arrays (Jonhson et al., 2005) File
  • Review: What is a gene post-ENCODE? (Gernstein 2007) File
  • Audio lezione 18-11-09 Page
  • Lezione 20 novembre Pervasive genomic transcription (with happenings...) File
  • Review: On RNA-Seq methods and outcome (Wang et al 2009) File
  • Article: RNA-Seq on human poly(A)+ (Sultan et al. 2008) File
  • Audio-lesson 4-Part 1 URL
  • Audio-lesson 4-Part 2 URL
  • Audio lesson 4 - Part 3 URL
• 

  23 November - 29 November

  Pervasive transcription in geneomes. Noncoding RNA classes. Promoter definition. One gene more products.

  • Lezione 23 novembre - Transcripts and promoters File
  • Review: Mammalian promoters (Sandelin 2007) File
  • Assignment BMG5: how to verify bioinformatic results
  • Lezione 25 novembre - Genome annotations File
  • Audio lezione 25-11-09 Page
  • Review: A very good review on small RNAs (Ghildiyal, 2009) File
  • Article: Identification of human promoters (Kim et al 2005) File
  • Assignment BMG6 - what can we conclude ?
  • Assignment BMG7: micro RNA specificity
  • Lezione 27 novembre - One gene more products File
  • Audio lezione 27-11-09 Page
  • Review: A review on Alternative Splicing in the pre-deep-sequencing era. (Matlin 2005). File
  • Article: Alternative Splicing by RNA-Seq (Wang et al 2008) File
  • Assignment BGM8: find the right protocol
• 

  30 November - 6 December

  Chromatin. Epigenetic modifications to DNA and histones. Genomic imprinting. Transcriptome vs proteome.

  • Lezione 30 novembre - Chromatin File
  • Review: Histone modifications and interacting proteins (Kouzarides 2007) File
  • Audio lezione 30-11-09 Page
  • Lezione 2 dicembre - Silencing & epigenetics File
  • Review: Microarrays for chromatin status (Hoheisel 2006) File
  • Review: Epigenetics and developent (Reik 2007) File
  • Lezione 4 dicembre - Post-transcription & proteomics File
  • Audio lezione 4-12-2009 Page
  • Review: Proteome analysis using Mass Spectrometry (Gstaiger 2009) File
  • Article: Comparative miRNA effect on mRNA and proteome (Selbach et al., 2008) File
  • Programma svolto dal 13/1 al 4/12 (modulo per NU e BI) File
• 

  7 December - 13 December

  Back to chromatin: heterochromatin determinants and boundaries

  • Lezione 9 dicembre - Heterochromatin File
  • Audio lezione 09-12-2009 Page
  • Lezione 11 dicembre - Boundaries and territories File
  • Audio lezione 11-12-2009 Page
  • Review: Boundaries (Lunyak 2008) File
  • Review: Active loops (Fraser 2007) File
• 

  14 December - 20 December

  Methylation, transcription and gene activation

  • Lezione 14 dicembre - Methylomes File
  • Audio lezione 14-12-2009 1° parte Page
  • Audio lezione 14-12-2009 2° parte Page
  • Article: genome-wide promoter CpG-methylation analysis (Weber 2007) File
  • Assignment BMG8: problems with bisulfite conversion and deep-sequencing
  • Lezione 16 dicembre - Transcriptional activation File
  • Audio lezione 16-12-2009 Page
  • Article: interchromosomal interactions mediate Olfactory Receptor choice (Lomvardas 2006) File
  • Lezione del 18 dicembre - transcription factor mapping File
  • Article: ER mapping genome-wide (Carroll 2006) (Not mandatory) File
  • Review: Transcription factor mapping genome-wide File
  • Audio lezione 18-12-2009 Page
  • Lezione 21 dicembre - coregulator dynamics File
  • Article: Coactivator dynamics at a single gene after activation (Metivier 2003) File
  • Review on coregulator cycling on nuclear receptors (Perissi 2006) File
  • Audio lezione 21-12-2009 Page
  • Lezione 8 gennaio 2010 - Signals and combinatorial transcriptional control File
  • Audio lezione 08-01-2010 Page
  • Résumé (Zhu et al., 2006) File
  • Assignment BMG 9 - Differences between signal transduction pathways
  • Assignment BMG 10 - How to resolve an interaction dilemma?
• 

  21 December - 27 December

  Not available
• 

  28 December - 3 January

  Not available
• 

  4 January - 10 January

  Not available
• 

  11 January - 17 January

  Post-trancriptional regulation. Alternative splicing, mRNA export, cis- and trans-factors to localize mRNAs.

  • This part must be complemented with subjects of lectures November 27 and October 9. Matlin review included in 27/11 is also strongly recommended.
  • Lezione 11 gennaio - Regulated Alternative Splicing File
  • Audio lezione 11-01-2010 Page
  • Review on the mechanisms of Alternative Splicing regulation - Chen & Manley, 2009. File
  • Review on RNA processing regulation, with genome-wide methods. Licatalosi & Darnell, 2010. File
  • Lezione del 13 gennaio - Processing to export File
  • Audio lezione 13-01-2010 Page
  • Review on "Cotranscriptionality" - Perales & Bentley, 2009. File
  • Review on the biogenesis of RNA and export (Luna 2008) File
  • Assignment BMG 11 - A method to study RNA-binding protein targets
  • Assignment BMG 12 - Hypothesis on Dscam mechanism.
  • Lezione del 15 gennaio - RNA localization File
  • Audio lezione 15-01-2010 Page
  • Review on RNA localization - Holt 2009 File
  • Article: RNA localization in yeast (Jambhekar 2005) File
• 

  18 January - 24 January

  Special Lectures: Silver papers by students & Seminar by Dr Venesio on Alternative Splicing in Disease

  • Lezione 18 gennaio - Control of RNA decay and translation File
  • Article: miRNA targets (Grimsom et al., 2007) File
  • Audio lezione 18-01-2010 1°parte Page
  • Audio lezione 18-01-2010 2°parte Page
  • Lezione supplementare 1 - 20/1/2010 - Clock genes (by Iachia-i- Blaca / Fava) File
  • Lezione supplementare 2 - 20/1/2010 - Imprinted genes (by Bethaz-Ferrero) File
  • Lezione supplementare 3 - 20/1/2010 "Methylome" by Macrì, Macrì, Raimo. File
  • Audio lezione 20-01-2010 Page
  • Article: Clock gene analysis (Zhang 2009) File
  • Article: Imprinted gene by microarray (Steinhoff 2009) File
  • Article: Methylome by deep-sequencing (Lister 2009) File
  • Lezione del 22 gennaio - Alternative splicing in disease File
  • Audio lezione 22-01-2010 Page
• 

  25 January - 31 January