Wednesday, July 30, 2014

July 30, yeast 2014

=> Hippo pathway, -- Eric Weiss
 ancient pathway, morphogensis, cytokinesis

Ace2 is turned on once in a life time in yeast daughter cells.  It leads to separation of mother and daughter cells.

super computing molecular dynamics simulation

=> Swe1 morphology checkpoint, Sepp Kohlwein,
triglycerides is fat for yeast cells.

cerulenin inhibit de novo synthesis of fat, triglyceride

Swe1 kinase -> lipolysis mediated cell cycle progression.
Swe1 --| Cdc28 --(P)--> Swe1

=> Cdk28 (Cdk1), Andreas Doncic, Jan Skoheim. 
Single-cell fluorescence signal detection
Yeast mating pathway, 
Yeast has 'memory" of past experiences

Far1 feed-forward regulation combined current and past signals to provide informed decisions.

Inherited Far1 total protein level give yeast cells an intergenerational memory which can make an more informed cell cycle reentry decision. 

growth    --(CDK)-->cell cycle
MAPK(t) --Far1 --> mating arrest

It seems that growth before mating must be done in haploid strains. In wild, cells can switch mating types. The argument on 'memory' must a very short memory.

=> cdk regulated expression, CDK28/CDK1 targets
Cdk --> Fkh2, Ndd1  --> G2/M genes
Hcm1 --> Fkh2, Ndd1

HCM1 targets: TUB1, SPC34, NDD1, CIN8

=> RNP granules in quiescent cells, Paul Herman's lab
ribonucleoprotein granules: Processing bodies(PBS), stress granules (translation)

Decreased P-bodies shortens CLS.

=> Linden Breeden, Quiescence
stationary phased cells have two populations: quiescent and dividing ones.

cell wall fortification improved in quiescent cells
deletion library was screened, 131 genes -> cell wall defect, and several other categories

log phase: cln3/cdk --| Whi5 --| SBF/MBF  --> Cln1/Cln2
S phase: DNA damage

In Q-cells: how G1 arrest is maintained
Xbp1 --> Cnb3/Cdk

Q: do some genes change the population fractions of dividing and quietscent cells? 

=> Cdc14 phosphatase, a hub in NaCl responsive subnetwork.

=> metabolite regulation, Sean Hackett, Joshua Rabinowitz
LC-MS, 106 metabolite
Flux balance analysis (FBA)
Flux is carried in 270 reactions
Model comparison by fitting to measured flux. a p-value is calculated.
Limiting nutrient effects

=> Calcineurin (CN) substrates in yeast, Jagoree Roy
Calcineurin has a conserved docking site.
Screen method: motif search;  hyper-phosphorylation in calcineurin-null mutant

CN signaling network evolves rapidly in the yeast species.

=> George Church, future of yeast
1. 3D/4D structure of yeast cells
2. synthesis of genomes
3. Synthesis of cells.

3D RNA fluorescence in situ sequencing, FISSEQ, Lee, Daugharthy, Science 2014

Reasons for synthetic genomes: metabolic isolation, non-canonical AA, multi-virus resistance

Cause & effect of N-terminal codon bias in bacterial genes

Mirror DNA & RNA polymerase

Synthetic biology, a lab manual.

No comments:

Post a Comment