The limiting, degrading entity hypothesis

Slides:

Advertisements

Similar presentations

GFP‐Sed5p localization defect in sgt2Δ.

Advertisements

Statistical colorings of 1H NMR estimates of biochemical variables.

Abundance of proteins matching selected subcellular locations and functions in CaCo‐2 cells. Abundance of proteins matching selected subcellular locations.

Simulation of oxygen and substrate demands for ammonia detoxification.

Schematic diagram of the three circuits analysed in this work.

Bifurcation diagrams showing quasi‐steady‐state solutions and simulation of models. Bifurcation diagrams showing quasi‐steady‐state solutions and simulation.

Experimental confirmation of in vitro GPCR activity of compounds and their scaffolds screened from a chemical library. Experimental confirmation of in.

Glucose withdrawal induces supra‐physiological levels of tyrosine phosphorylation in cells sensitive to glucose withdrawal. Glucose withdrawal induces.

Most promoters preserve their relative activity levels across conditions. Most promoters preserve their relative activity levels across conditions. (A)

Analysis of in silico flux changes along the exponential growth phase: (A) In silico flux changes from 24 to 36 h, from 36 to 48 h, and from 48 to 60 h.

Illustration of the reactions and metabolites obtained from random sampling. Illustration of the reactions and metabolites obtained from random sampling.

Tight regulation of gene expression variation is coupled to promoter architecture. Tight regulation of gene expression variation is coupled to promoter.

Exo‐metabolomics profiling of major metabolites elucidated the metabolic capabilities of monospecies Exo‐metabolomics profiling of major metabolites elucidated.

Two competing models for Rab domain identity generation and endosome conversion. Two competing models for Rab domain identity generation and endosome conversion.

Functional analysis of duplicate pair CIK1–VIK1 (A) Genetic interaction profile similarity. Functional analysis of duplicate pair CIK1–VIK1 (A) Genetic.

Proteins with hotspot mutations are often in the interaction networks with known cancer driver proteins Proteins with hotspot mutations are often in the.

(C–F) Complete interaction networks (representing both baits and preys) for selected groups of baits. (C–F) Complete interaction networks (representing.

Comparative analysis of RNA and protein profiles.

Buffering of non‐functional mRNA co‐regulation likely is a passive process Buffering of non‐functional mRNA co‐regulation likely is a passive process Percentage.

Luminex phosphorylation measurements are reproducible and have broad dynamic range Individual difference in insulin‐induced phosphorylation of ERK measured.

Correlating protein to mRNA and proteins per mRNA ratios

Coupling immunophenotypes to Drop‐seq data

Network derived from large‐scale fractionation predicts 48 protein complexes and communities Network derived from large‐scale fractionation predicts 48.

Heat maps showing global relative growth phenotype and comparison between measured and predicted values. Heat maps showing global relative growth phenotype.

Mutants of the Group III have differentially impaired induction of pAGA1 and pFIG1 Mutants of the Group III have differentially impaired induction of pAGA1.

Glucose pulses induce brief, heightened protein and nucleic synthesis in non‐dividing Escherichia coli Glucose pulses induce brief, heightened protein.

Western blots validate ClpXP‐mediated degradation of FtsZ in vivo during starvation and synthesis of FtsZ with glucose pulsing Western blots validate ClpXP‐mediated.

Lag time to division depends on the frequency of pulsed glucose for a subpopulation Lag time to division depends on the frequency of pulsed glucose for.

Collective shifts of abundance for nuclear and extracellular proteins in colorectal cancer Collective shifts of abundance for nuclear and extracellular.

Phenotypic profiling by between‐well comparison of feature profiles

Titrations of other division proteins support FtsZ as the division limitation Titrations of other division proteins support FtsZ as the division limitation.

Effect of the loss of Kar4 on the induction of various promoters

The cell cycle influences circadian phase progression Circadian intervals with divisions (p1,d1,p2) last 21.95 ± 3.8 h (n = 1,926) and are significantly.

Computational wound healing gradients and in vivo imaging of the wound bed at PW2 (related to Fig 6)‏ Computational wound healing gradients and in vivo.

A dynamic model of FtsZ abundance predicts division timing

Francis Crick's central dogma of biology revolves around the transcription of mRNA from DNA, the translation of proteins from mRNA, and the degradation.

ClpX facilitates FtsZ depletion during carbon starvation

QRT–PCR analysis of tissue‐specific candidate gene expression in response to reduced IIS qRT–PCR analysis of tissue‐specific candidate gene expression.

Evaluation of assay performance with positive and negative binary reference sets Evaluation of assay performance with positive and negative binary reference.

Allele‐specific expression at single‐cell resolution

Two‐way unsupervised uncentered unnormalized hierarchical clustering using a Pearson's correlation of the phenotypic profiles of 4281 nonessential genes.

Transcriptomic and epigenetic changes associated with Factor 1 in the scMT data Transcriptomic and epigenetic changes associated with Factor 1 in the scMT.

Comparison of proteomics and RNA‐Seq data.

Simulation showing that the cell length variability of the entire population can mask abnormal cell length variability at a specific cell cycle period.

An integrated NHR network.

Stage‐dependent diurnal transcript changes.

Example transcript and protein patterns.

Reproducibility of DeathPro drug screens

Maintenance metabolism alone cannot explain non‐division

Melting behavior of protein complexes

In vivo imaging of the wound bed at later time points (related to Fig 7)‏ In vivo imaging of the wound bed at later time points (related to Fig 7) A–CRepresentative.

TIPI mediates rapid degradation of proteins in yeast.

Nedd4 proteins. Nedd4 proteins. (A) Schematic representation of rNedd4‐1, hNedd4‐1 and hNedd4‐2 (not to scale), with % amino‐acid identity between them.

Experimental validation of predicted endocytosis functions in human.

Global and focused views of human interaction map.

PDE1 predominantly regulates the threshold for RP induction.

Schematics for nutrient pulse systems

Rare and abundant codons.

FtsZ‐limited division applies for various nutrient limitations

Interaction of Gpr1/Gpa2 and Sch9.

Time‐course analysis of NICD degradation.

Integration of proteomic data into the model

Glucose pulses incorporate directly into the de novo biomass in non‐dividing cells Glucose pulses incorporate directly into the de novo biomass in non‐dividing.

(A) Observed significant protein fold‐changes during the fed–fasting transition in C57BL/6J (B6) and 129Sv (S9) mice fed with a normal diet (T0). (A) Observed.

Sequence dependence of Met4 recruitment.

PhoB also translocates to plant nuclei in leaf and crown cells in response to HK activation with exogenous cytokinin. PhoB also translocates to plant nuclei.

Metabolic differences in the small intestine AMetabolic genes as well as the associated reactions involved in the formation of glutathione (GSH) are presented.B,

DuMPLING oligonucleotide plasmid library design and production

Topologies, synthetic implementations and expression profiles of the networks studied Topologies, synthetic implementations and expression profiles of.

Changes in fibroblast activation and proliferation outside the wound and CHP staining in the wound bed (related to Fig 5)‏ Changes in fibroblast activation.

Presentation transcript:

The limiting, degrading entity hypothesis The limiting, degrading entity hypothesis The dependence of lag time on glucose pulse frequency can be explained with constitutive degradation of the limiting entity. In the model shown, the entity abundance is synthesized with each glucose pulse and depletes constitutively. Three example frequencies (f1 > f2 > f3) are shown where slight changes in period time dramatically change the time for the entity to reach the threshold needed to engender division. When synthesis and degradation of the entity are equal, the TI feedrate is at the critical rate (f3). Arrows indicate the glucose pulse frequency. Karthik Sekar et al. Mol Syst Biol 2018;14:e8623 © as stated in the article, figure or figure legend