Oscillations in isotopic labeling of TCA cycle metabolites throughout the cell cycle from [U‐13C]‐glucose show induced glycolytic flux into TCA cycle in.

Slides:

Advertisements

Similar presentations

Statistical colorings of 1H NMR estimates of biochemical variables.

Advertisements

Predicted growth, yield, and secretion.

Tuning the response of the DPI

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

Central carbon metabolic flux patterns under glucose‐limited and glucose‐excess conditions. Central carbon metabolic flux patterns under glucose‐limited.

A kinetic model reconciles observed ERK phosphorylation, localization, and activity responses A Schematic of a simple kinetic model including cytosolic.

Overview of the experimental setting.

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.

Motif detectability corresponds to the phylogenetic profile of the cognate transcription factor. Motif detectability corresponds to the phylogenetic profile.

Predicted and measured double‐ring formation.

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

Evaluating other shRNA data and methods.

The TBON model. The TBON model. (A) Representative confocal images of E14Tg2A cells stained for Tcf3 (green), Nanog (red), Oct4 (magenta), and total β‐catenin.

Skin proliferation kinetics and in vivo fibroblast lineage tracing during dermal maturation (related to Fig 4)‏ Skin proliferation kinetics and in vivo.

Confirmation of pool data with isogenic culture

Model training of generalized Lotka–Volterra (gLV) to time‐resolved measurements of monospecies and pairwise assemblages Model training of generalized.

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

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.

Intracellular noise in the cAMP circuit drives observed population behaviors Firing rate phase diagrams for single cells in a population (top) and the.

Evaluating CRISPR negative selection screens.

Genomic profiling of fitness in periodic salt stress

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

Dermal architecture is defined by an inverse correlation between fibroblast proliferation and ECM deposition Dermal architecture is defined by an inverse.

Networks of ERK substrates.

RNAi causes widespread changes in cell population context leading to predictable changes in virus infection. RNAi causes widespread changes in cell population.

Alignment time for Clustal Omega (red), MAFFT (blue), MUSCLE (green) and Kalign (purple) against the number of sequences of HomFam test sets. Alignment.

Dynamic map of the Nap1p/Kcc4p interaction.

Sensor optimization for thiosulfate and tetrathionate detection in the gut Sensor optimization for thiosulfate and tetrathionate detection in the gut A–F(A.

Lysozyme expression in isolated Paneth cells and linage tracing of Notch1+ cells Lysozyme expression in isolated Paneth cells and linage tracing of Notch1+

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

Patient organoids respond more diverse to drugs and with lower therapeutic potential than 2D cultured patient cells Patient organoids respond more diverse.

Dynamics and expression level of mating‐dependent 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.

Chemical inhibitors of microtubule function attenuate signal but do not affect pathway variability Chemical inhibitors of microtubule function attenuate.

Neurogenins induce a network of transcription factors that mediate iNGN neurogenesisA network of transcription factors involved in iNGN neurogenesis was.

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

Notch activation in Notch1 positive feedback knock‐out intestine organoids Notch activation in Notch1 positive feedback knock‐out intestine organoids Intestine.

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

Calibration of a population‐average model

Comparison of proteomics and RNA‐Seq data.

Development of a 3D tissue model and in vivo live imaging during dermal maturation Development of a 3D tissue model and in vivo live imaging during dermal.

Glutamine has pleiotropic role of positively regulating respiration and maintaining redox balance selectively in high‐invasive ovarian cancer (OVCA) cells.

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.

Proliferative advantage depends on environmental dynamics

RSLs enable internal replicate and lineage dropout analyses

Example transcript and protein patterns.

Distinct collagen structures in the upper and lower neonatal dermis (related to Fig 1)‏ Distinct collagen structures in the upper and lower neonatal dermis.

Reproducibility of DeathPro drug screens

Cluster analysis of all identified models.

Protein interactions at the nuclear pore.

Noise in hoxb1a/krox20 expression leads to boundary sharpening.

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

Dynamic transcriptome analysis in yeast.

Experimental validation of predicted endocytosis functions in human.

Effects of CDK4/6 knockdown on growth and glucose and glutamine metabolism of HCT116 cells Effects of CDK4/6 knockdown on growth and glucose and glutamine.

Competence initiation during the progression to spore formation.

Integration of proteomic data into the model

Model of differentiation from pluripotent stem cells to terminal dopaminergic neurons Model of differentiation from pluripotent stem cells to terminal.

The transcriptional behavior of GREB1 changes with estrogen dose and exhibits considerable cell‐to‐cell variation (see also Fig EV2 and Movie EV2)‏ The.

Perturbation of ligand depletion affects the ultrasensitivity of long‐term P‐Smad2 responses to different doses of TGF‐β stimulation. Perturbation of ligand.

Inhibitory effect of perhexiline on the proliferation of the HepG2 cell line A, BPerhexiline was used to mimic the effect of the l‐carnitine analog on.

Kinetics of GREB1 induction by estrogen in single cells (see also Fig EV4 and Movie EV3)‏ Kinetics of GREB1 induction by estrogen in single cells (see.

Sch9 plays a minor role in glucose signaling.

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.

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

TT‐seq analysis of immediate response to T‐cell stimulation

Presentation transcript:

Oscillations in isotopic labeling of TCA cycle metabolites throughout the cell cycle from [U‐13C]‐glucose show induced glycolytic flux into TCA cycle in G1/S Oscillations in isotopic labeling of TCA cycle metabolites throughout the cell cycle from [U‐13C]‐glucose show induced glycolytic flux into TCA cycle in G1/S AExperimental scheme for a series of pulse‐chase isotope tracing experiments in synchronized cells.BAtom tracing of TCA cycle metabolites from [U‐13C]‐glucose (blue) and [U‐13C]‐glutamine (red).C–EMeasured relative fraction of the m + 2 labeling of TCA cycle intermediates after feeding [U‐13C]‐glucose (red, mean and s.d. of n = 3), the deconvoluted signal (green), and the expected labeling dynamics considering the loss in synchronization (black, representing TCA cycle oxidation of glucose‐derived acetyl‐CoA).FOscillations in citrate m + 4 labeling after feeding [U‐13C]‐glutamine (mean and s.d. of n = 3; experimentally measured labeling dynamics shown in red, the deconvoluted signal in green, and the expected labeling dynamics considering the synchronization loss in black).GOscillations in the total citrate concentration throughout the cell cycle (mean and s.d. of n = 5; experimentally measured concentration dynamics shown in red, the deconvoluted signal in green, the expected concentration dynamics considering the synchronization loss in black, and the measured concentration in non‐synchronized cells in blue).HThe measured lactate secretion flux in synchronized cells shown in red (mean and s.d. of n = 5, fi(t) in equation 9), the deconvoluted secretion flux dynamics, in case of no synchronization loss (green, in equation 10), and the expected secretion flux based on the deconvoluted fluxes and considering the loss in synchronization, matching the measured fluxes (black, equation 10). Eunyong Ahn et al. Mol Syst Biol 2017;13:953 © as stated in the article, figure or figure legend