Schematics for nutrient pulse systems

Slides:



Advertisements
Similar presentations
Statistical colorings of 1H NMR estimates of biochemical variables.
Advertisements

Growth rate‐dependent gene expression under glucose limitation.
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.
A kinetic model reconciles observed ERK phosphorylation, localization, and activity responses A Schematic of a simple kinetic model including cytosolic.
Melting behavior of proteins identified in the Escherichia coli meltome and their properties Melting behavior of proteins identified in the Escherichia.
Overview of the experimental setting.
Single‐molecule tracking in living cells.
Thermal proteome profiling in Escherichia coli
Melting behavior of protein complexes
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.
Activity flow of the mTOR signaling network.
Epistatic interactions and gene expression variation.
(A) Protein biosynthesis on a chip and in solution.
Validation of the CCE associations by mass spectrometry.
(C–F) Complete interaction networks (representing both baits and preys) for selected groups of baits. (C–F) Complete interaction networks (representing.
Structure of in‐frame deletions.
Correlating protein to mRNA and proteins per mRNA ratios
Expression of FUT9 supports tumor development
Intracellular noise in the cAMP circuit drives observed population behaviors Firing rate phase diagrams for single cells in a population (top) and the.
Heat maps showing global relative growth phenotype and comparison between measured and predicted values. Heat maps showing global relative growth phenotype.
Schematic of the integration and results of the alveolar macrophage (iAB‐AMØ‐1410) and Mycobacterium tuberculosis (iNJ661) reconstructions. Schematic of.
Alignment time for Clustal Omega (red), MAFFT (blue), MUSCLE (green) and Kalign (purple) against the number of sequences of HomFam test sets. Alignment.
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.
The limiting, degrading entity hypothesis
Feature‐based COG enrichment analysis
Sensor optimization for thiosulfate and tetrathionate detection in the gut Sensor optimization for thiosulfate and tetrathionate detection in the gut A–F(A.
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.
Experimental approach and reproducibility
Multi‐Omics Factor Analysis: model overview and downstream analyses
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
Characterization of Factor 5 (oxidative stress response factor) in the CLL data Characterization of Factor 5 (oxidative stress response factor) in the.
Patient organoids respond more diverse to drugs and with lower therapeutic potential than 2D cultured patient cells Patient organoids respond more diverse.
Chemical inhibitors of microtubule function attenuate signal but do not affect pathway variability Chemical inhibitors of microtubule function attenuate.
Schematic summary of experimental findings.
A dynamic model of FtsZ abundance predicts division timing
Drug‐induced cell death and proliferation inhibition can be quantified from serial confocal images Drug‐induced cell death and proliferation inhibition.
Antisense transcription, measurement, and correction
Building and using sequence‐expression‐activity maps (SEAMAPs) AThe RBS Library Calculator designs a synthetic RBS library to efficiently search a multi‐dimensional.
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.
Live‐cell imaging uncovers a slowly cycling drug‐resistant state involved in adaptation to RAF inhibition Live‐cell imaging uncovers a slowly cycling drug‐resistant.
Impact of growth phase on the Escherichia coli meltome and proteome
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.
The metabolic network of arachidonic acid in human PMN, EC and PLT
Stage‐dependent diurnal transcript changes.
Reproducibility of DeathPro drug screens
When grown with biofuel, strains with beneficial pumps dominate the culture. When grown with biofuel, strains with beneficial pumps dominate the culture.
Maintenance metabolism alone cannot explain non‐division
Melting behavior of protein complexes
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.
Drug sensitivity described by LD50 is similar in cells cultured in 2D or as organoids Drug sensitivity described by LD50 is similar in cells cultured in.
Global and focused views of human interaction map.
Rare and abundant codons.
BT_0370 galactokinase and BT_371 glucose/galactose transporter
FtsZ‐limited division applies for various nutrient limitations
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.
Many of the diseases associated with high coevolution scores share genetic components. Many of the diseases associated with high coevolution scores share.
DuMPLING oligonucleotide plasmid library design and production
Fraction of flux entering the PEP‐glyoxylate cycle as a function of hexose uptake rate in batch (A) and chemostat (B) cultures. Fraction of flux entering.
Network recovery for isoenzymes and protein complexes
Validation of select PDN drug candidates in an in vivo endotoxemia model Validation of select PDN drug candidates in an in vivo endotoxemia model Therapeutic.
Presentation transcript:

Schematics for nutrient pulse systems Schematics for nutrient pulse systems Three separate systems were used to pulse glucose to starved Escherichia coli. The spin flask system (I) and plate reader system (II) provided glucose pulses at defined frequencies. In the real‐time metabolomics configuration (Link et al, 2015), another pump circulated culture and injected 2 μl of culture directly into a time‐of‐flight (QTOF) mass spectrometer every 10–15 s from the spin flask system. A microfluidic platform (III) reproduced the pulse feeding and tracked division events. A pulsing period is defined as the time between the start of successive glucose medium exposures. During each pulse, glucose medium was flowed for 10 s, and the no glucose buffer was flowed in the intervening period. Karthik Sekar et al. Mol Syst Biol 2018;14:e8623 © as stated in the article, figure or figure legend