2015 LEGO Jamboree Logistics

Dates

• December 8-10, 2015
  • Start 9am December 8
  • End at noon December 10, optionally continue through 4pm or so.

Venue

Geneva, Switzerland
Campus Biotech

Participants

Please use this link to register: https://goo.gl/1t1ybJ

Agenda

Tuesday, December 8th

BlueJeans: https://bluejeans.com/921716595

Schedule

• 10am Seminar: Using LEGO to Represent Biological Knowledge - Paul T. and Chris
  • For a more general audience
• 11:30am Workshop Begins: More specific introduction to LEGO for curators
• Lunch
• 1:30pm? Hands-on with Noctua
  • Demo: Creating simple annatons in Noctua (David)
    • A simple enzyme paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/?term=6244280
      • Main figure to annotate: Figure 1 (open circles)
    • A regulation paper Pfkl-- http://www.ncbi.nlm.nih.gov/pubmed/6446714 also see http://www.ncbi.nlm.nih.gov/books/NBK22395/
      • Main figure to annotate: Figure 4

Wednesday, December 9th

BlueJeans: https://bluejeans.com/421981965

Schedule

• Continuing on with annotation examples and suggested papers from participants:

November Annotation Consistency Exercise

• Annotating causal relationships and downstream effects
  • TAIR annotation consistency exercise: The MYB36 transcription factor orchestrates Casparian strip formation.
  • November Annotation Consistency Exercise

MGI

• Role of SWI/SNF complex during retinogenesis
  • MGI: Brg1 coordinates multiple processes during retinogenesis and is a tumor suppressor in retinoblastoma Open Access
• Autophagy and cellular differentiation
  • MGI and Swiss-Prot: PIM-2 is an independent regulator of chondrocyte survival and autophagy in the epiphyseal growth plate.

PomBase

• This paper shows that the Msd1/wdr8 complex is transported to the SPB by dynein, and then subsequently involved in microtubule attachment to the SPB
  • PomBase: The Msd1-Wdr8-Pkl1 complex anchors microtubule minus ends to fission yeast spindle pole bodies Open Access
• Localized cell polarization and GTPase cycle - to be discussed possibly at a later time
  • PomBase: The Tea4-PP1 landmark promotes local growth by dual Cdc42 GEF recruitment and GAP exclusion. Open Access

Swiss-Prot

• Regulation of cell proliferation, ubiquitin ligase activity, protein stabilization and localization
  • Swiss-Prot: A novel ARF-binding protein (LZAP) alters ARF regulation of HDM2. Open Access
• Signaling pathways and their outputs
  • Swiss-Prot:cAMP/PKA enhances interleukin-1β-induced interleukin-6 synthesis through STAT3 in glial cells
• Apoptotic cell clearance pathway
  • Swiss-Prot: Bruton's tyrosine kinase is required for apoptotic cell uptake via regulating the phosphorylation and localization of calreticulin Open Access

UCL

• miRNA-mediated regulation of transcription factor activity and transcription of enzyme responsible for H2S production and subsequent cell differentation
  • UCL: Specificity protein-1 as a critical regulator of human cystathionine gamma-lyase in smooth muscle cells. Open Access
  • UCL: MicroRNA-21 represses human cystathionine gamma-lyase expression by targeting at specificity protein-1 in smooth muscle cells.
• Mix of species in paper
  • UCL: Ubiquitin-specific protease 19 regulates the stability of the E3 ubiquitin ligase MARCH6.
• Useful example of when the substrate is a non-protein (for the ribonuclease activity).
  • UCL: Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response. Open Access
• Looks like a relatively simple annotation model
  • UCL: ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs. Open Access
• More complicated view of ER stress and UPR
  • UCL: Wolfram syndrome 1 gene negatively regulates ER stress signaling in rodent and human cells. Open Access
• Regulation of transcription factor activity via protein stabilization, localization - direct or indirect regulation?
  • UCL: DJ-1, a cancer- and Parkinson's disease-associated protein, stabilizes the antioxidant transcriptional master regulator Nrf2. Open Access

WormBase

• Annotations involving specific isoforms and feedforward circuits; also anatomical and life stage annotation context
  • WormBase: MIG-10 (Lamellipodin) stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of EGL-43 in C. elegans. Open Access

Thursday, December 10th

BlueJeans: https://bluejeans.com/161891171

Schedule

• Future plans and thoughts
  • Seeding models
  • Plans for going forward
    • Dedicated LEGO curation conference calls?

Remote Attendees

Doug Howe - ZFIN - sorry I can't be there in person! If you are able to webcast any portions, I'd be happy to drink lots of coffee on my end. Sabrina Toro - ZFIN