Database services

1
Database services

2

• Contribution to
• WP5 Knowledge database
• Database development at DKFZ
• WP3 Manual curation
• Modelling of apoptosis and autophagy pathways

3
iCHIP Plattform
Concept
Collaborations and Partner projects
others....
4
Application services
Base2
Spring
Hibernate
DB
impl
Business Layer
Persistence Layer
Data Access Objects
Remote Server Interface
Spring
Xdoclet
api
Remote Client Interface
Domain Object Model
RMI
5
Administration Tool
6
secretory pathway
7
(No Transcript)
8
iCHIP projects

• 10 Mio images
• 40 Terra Bytes of data
• 2 whole genome knockout projects
• 30 studies, 10k Microarrays
• 10 research networks (incl. 5 EU partners)

9

• Contribution to
• WP3 Manual curation of programmed cell death
  ontology

10
Programmed cell death pathways

• Programmed cell death is the complex result of
  context- dependent (e.g. cancer, viral infection,
  ischemia) interactions of apoptotic and
  autophagic pathway participants.

11
Programmed cell death pathways

• Apoptosis
• Extrinsic (death receptor)
• Intrinsic (mitochondrial)
• Autophagy (dual role)
• Can protect against apoptosis during ischemic
  injury)
• Can enhance cancer cell death
• Lysosomal (linked to autophagy)
• Release of lysosomal cathepsins
• Sufficient to induce cell death
• Can activate mitochondrial apoptotic PW

12
Sub-cellular localization

• E.g., anti-apoptotic Bcl-xL and Bcl-2 function
  differently at both mitochondria (Mito) and
  endoplasmic reticulum (ER)

Mito
ER
Bcl-xL
FK506 binding protein
RTN-xS Binding protein
Bcl-2
Protects against lethal calcium signaling
Protects against pro-apoptotic Bax, Bak, oxygen
radicals.
(Tagami et al, 2000 A novel protein, RTN-xS,
interacts with both Bcl-xL and Bcl-2 on
endoplasmic reticulum and reduces their
anti-apoptotic activity) (Germain Shore, 2003
Cellular distribution of Bcl-2 family proteins.)
13
Zooming into the Apoptosis Network

• Superposition of apoptotic pathways

• CD95 (Fas/APO-1) Receptor
• FADD
• Caspases 8,3
• IAPs
• c-FLIPlong,short
• IKK, I?B?, NF-?B