Papers Flashcards
What is epigenetic regulation?
Changing how much a gene is expressed, but not the gene itself; Rather than inserting genes/virus (along with promoter) which will then be transcribed
Here everything is from the original genome, nothing is added
Summarize Zhang’s paper
This study demonstrates the chemical reprogramming of human astrocytes → functional neurons with a cocktail of 9 small molecules
Mediated through epigenetic and transcriptional regulation
✘ Epigenetic silencing of glial genes
✔ Transcriptional activation of neural TFs
Summarize Doyle’s paper
Studying structure of K+ channel to discovery molecular basis for selectivity and conduction
How was Zhang’s conversion mediated
Astrocyte –> neuron
9-mol cocktail
Mediated through epigentic and transcriptional regulation
✘ Epigenetic silencing of glial genes
✔ Transcriptional activation of neural TFs
Zhang steps
- Determine candidate pool (based on the 3 criteria)
- Test whether identity changed (via GFP)
- Test whether functional (via ion currents)
- Figure out type (markers - glutamatergic, hippocampal)
- Investigated whether epigenetic reg involved
Zhang steps
- Determine candidate pool (based on the 3 criteria)
- Test whether identity changed (via GFP)
- Test whether functional (via ion currents)
- Figure out type (via immunostaining - glutamatergic, hippocampal)
- Epigenetic tests
- Tested role of each mol
- In vivo testing (via GFP)
GABA
Inhib
Methylation
Decreases T
Makes DNA less accessible
DOWNREGULATION
Acetylation
increases T
loosens DNA
UPREGULATION
Acetylation
increases T
loosens DNA
UPREGULATION
Negative control v. positive control
Negative control - no response expected
Positive control - response expected
D: Trp and Tyr relationship
Trp residues from pore helix
Tyr residues from s.f
Together form a massive aromatic AA sheet. The hydrogen bonding and the van der Waals force within this sheet help the pore to be open at its proper diameter and achieves high potassium selectivity
D: Kcsa signature sequence
Thr-Val-Gly-Try-Gly
D: What was the reason for using Rb+ and Cs+, and what was the finding from this experiment?
Rb+ and Cs+ have similar size and charge with potassium ion but have more electron-dense than potassium. This allowed visualization of the locations of permeant ions in the pore
How does the potassium channel achieve high selectivity for potassium ions over sodium ions despite the smaller size of sodium ion
The carbonyl groups of the backbone structure of the selectivity filter allow access of only dehydrated molecules. These carbonyl groups of the selectivity filter act like surrogate water and compensate for the energetic cost of dehydration. While a potassium ion fits in the filter precisely, the accommodating of a sodium ion is prevented by adhered open state of selectivity filter
