Annotation Conf. Call 2016-06-28: Difference between revisions

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==Annotation Consistency Exercise==
==Annotation Consistency Exercise==
*[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.]
*[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.]
  The mechanisms that constrain memory formation are of special interest because they provide insights into the brain's memory management systems and potential avenues for correcting cognitive disorders. RNAi knockdown in the Drosophila mushroom body neurons (MBn) of a newly discovered memory suppressor gene, Solute Carrier DmSLC22A, a member of the organic cation transporter family, enhances olfactory memory expression, while overexpression inhibits it. The protein localizes to the dendrites of the MBn, surrounding the presynaptic terminals of cholinergic afferent fibers from projection neurons (Pn). Cell-based expression assays show that this plasma membrane protein transports cholinergic compounds with the highest affinity among several in vitro substrates. Feeding flies choline or inhibiting acetylcholinesterase in Pn enhances memory, an effect blocked by overexpression of the transporter in the MBn. The data argue that DmSLC22A is a memory suppressor protein that limits memory formation by helping to terminate cholinergic neurotransmission at the Pn:MBn synapse.
*'''How to capture biological process aspects of memory?'''
*'''How to capture biological process aspects of memory?'''
**The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?
**The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?

Revision as of 05:37, 27 June 2016

Bluejeans URL

https://bluejeans.com/993661940

Agenda

Annotation Consistency Exercise

  • Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.
  • How to capture biological process aspects of memory?
    • The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?
    • Leave the expression/mechanistic sections and have a look at these four sections of this paper:
      • Drosophila CG7442 Is a Memory Suppressor Gene Functioning in MBn and DAn
      • Drosophila CG7442 Overexpression Impairs Memory
      • DmSLC22A Regulates Both Memory Acquisition and Retention
      • DmSLC22A Modulates Memory Strength by Regulating Cholinergic Neurotransmission in the MB Calyx

Protein Binding Annotations

  • Review Protein Binding Annotation Guidelines
  • Use of With/From vs Annotation Extensions
  • Annotation of Direct vs Indirect Binding
    • Types of Experiments Used to Inform Physical Interactions
      • Yeast two hybrid
      • CoIP followed by Western blot
      • CoIP followed by mass spec
      • GST pull down using recombinant proteins
      • GST pull down using lysate
  • Use Cases
    • GO:0030674 protein binding, bridging - The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way. Source: GOC:mah, GOC:vw, GOC:bf
      • Evidence codes: IDA, IPI
      • IPI has With/From, AE, or both With/From and AE
      • AE uses has_input or has_direct_input for relation
    • GO:0043495 protein anchor - Interacting selectively and non-covalently with both a protein or protein complex and a membrane, in order to maintain the localization of the protein at a specific location on the membrane. Source: GOC:go_curators
      • Evidence codes: IDA, IGI, IMP, IPI
      • IPI only uses With/From