Genomic profiling of fitness in periodic salt stress

Slides:



Advertisements
Similar presentations
Xiaoshu Chen, Jianzhi Zhang  Cell Systems 
Advertisements

Fus3 is required for deletions of GIM4 and BIM1 to increase cell‐to‐cell variability Fus3 is required for deletions of GIM4 and BIM1 to increase cell‐to‐cell.
Cluster analysis of 50 genes identified as affecting variability and or pheromone response output Cluster analysis of 50 genes identified as affecting.
Microtubule perturbations cause Ste5 patches to form less reliably, delay patch formation, and cause patches to persist for less time Microtubule perturbations.
Hydration profiles of GLIC′s pore in WT and Ser6′ mutant simulations.
Microtubule perturbations affect pathway variability η2(P) and transmitted signal P at or upstream of the Ste5 recruitment step Microtubule perturbations.
A stochastic feedback loop model predicts the kinetics of DDR and growth arrest at the single cell level. A stochastic feedback loop model predicts the.
A culture‐induced TE‐like subpopulation
Statistical analysis of the influence of network regulators on topology clusters in the oleate network. Statistical analysis of the influence of network.
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)
(A) Outline of the malignant transformation process.
Sensitivity of RNA‐seq.
Dual allele labeling reveals a trans‐acting source for extrinsic noise
Validation of the CCE associations by mass spectrometry.
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.
Functional evaluation of ATR1 and PHO84 genes located at ePTL13.
HIS-24 regulates expression of infection-inducible genes.
Confirmation of pool data with isogenic culture
Dose response of pAGA1 and pFIG1 induction
Model training of generalized Lotka–Volterra (gLV) to time‐resolved measurements of monospecies and pairwise assemblages Model training of generalized.
Dual LGR5 and KI67 knock‐in PDOs enable separation of quiescent and cycling LGR5+ CRC cells Dual LGR5 and KI67 knock‐in PDOs enable separation of quiescent.
Both haematopoietic and non‐haematopoietic compartments are involved in myocarditis development.A.Kaplan‐Meier survival curves showing survival of bone.
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.
Characterization of promoters relative to pAGA1
The PRS is robust to changes in receptor abundance
PD‐L1 silencing in antigen presenting DCs results in hyperactivated pro‐inflammatory TCRhigh CD8+ T cells. PD‐L1 silencing in antigen presenting DCs results.
PM analysis of wild-type E. coli K-12 and its rpoZ-defective mutant.
RNAi causes widespread changes in cell population context leading to predictable changes in virus infection. RNAi causes widespread changes in cell population.
Mutants of the Group III have differentially impaired induction of pAGA1 and pFIG1 Mutants of the Group III have differentially impaired induction of pAGA1.
Validation of some ePTL candidates.
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.
Changes to the growth conditions break the circuit by changing host gene expression Changes to the growth conditions break the circuit by changing host.
Examples for intrachromosomal mRNA co‐regulation patches
Patient organoids respond more diverse to drugs and with lower therapeutic potential than 2D cultured patient cells Patient organoids respond more diverse.
Analysis of the phosphomimetic ProP‐PD selection results
Rational subpopulation manipulation can change TIL anti‐tumor reactivity and is accompanied by a shift in subpopulation signature. Rational subpopulation.
Calibration of a population‐average model
Direct role of HIS-24 and HPL in stress response.
Dynamics of induction of mating promoters after pheromone stimulation
Effects of ERK–GFP expression levels and cell density on ERK phosphorylation and oscillations. Effects of ERK–GFP expression levels and cell density on.
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.
Cbl protein levels in ago3, twin, and armi mutant GSCs
Proliferative advantage depends on environmental dynamics
RSLs enable internal replicate and lineage dropout analyses
Maintenance of lysogeny in bacteriophage lambda.
Construction of a genome‐scale pool of barcoded PCA strains
Volume 5, Issue 4, Pages (November 2013)
Reproducibility of DeathPro drug screens
Antisense‐mediated regulation of SUR7.
Characterising dermis expansion and gene expression changes during mouse development (related to Fig 1)‏ Characterising dermis expansion and gene expression.
Antisense expression associates with larger gene expression variability. Antisense expression associates with larger gene expression variability. (A–D)
Experimental validation of predicted endocytosis functions in human.
Shu complex condition‐dependent genetic interactions with MAG1, SLX4, PPH3, and RAD53 Shu complex condition‐dependent genetic interactions with MAG1, SLX4,
Rare and abundant codons.
Lipid presentation by CD11c+ cells controls iNKT cell subsets
Functional metabolic rearrangements in chloramphenicol‐resistant populations Functional metabolic rearrangements in chloramphenicol‐resistant populations.
Interaction of Gpr1/Gpa2 and Sch9.
Competence initiation during the progression to spore formation.
(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.
Systematic analysis of protein compensation in a heterozygous strains.
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.
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.
Oscillations in isotopic labeling of TCA cycle metabolites throughout the cell cycle from [U‐13C]‐glucose show induced glycolytic flux into TCA cycle in.
Signature A and B MEFs exhibit differential metabolic and proliferation phenotype strengths Signature A and B MEFs exhibit differential metabolic and proliferation.
BRI1 signaling at the dividing cells restores overall root growth
The Fisher information predicts the experimentally measured sensitivity. The Fisher information predicts the experimentally measured sensitivity. A, Sensitivity.
Xiaoshu Chen, Jianzhi Zhang  Cell Systems 
Presentation transcript:

Genomic profiling of fitness in periodic salt stress Genomic profiling of fitness in periodic salt stress Experimental design. Populations of yeast deletion strains are cultured in media N (no salt), S (salt) and in conditions alternating between N and S at various periods. Allele frequencies are determined by BAR‐Seq and used to compute fitness (proliferation rate relative to wild type) of each mutant.Time course of mutant abundance in the population, shown for six mutants. Relative abundance corresponds to the median of log2(y/y0) values ± SD (n = 4 replicate cultures, except for condition N at day 3: n = 3), where y is the normalized number of reads, and y0 is y at day 0. Conditions: N (blue), S (yellow), 6‐h periodic oscillations (NS6, hatching).Generalized linear models (predicted value ± SE) fitted to the data shown in (B), coloured by condition: N (blue); S (yellow); NS6 predicted by the null model (grey) or predicted by the complete model including inhomogeneity (red). ***P < 10−8. n.s., non‐significant, based on the GLM (see Materials and Methods).Fitness values (w) computed from the data of two mutants shown in (B). Bars, mean ± SEM, n = 3 (N) or 4 (S, NS6) replicate cultures, coloured according to culture condition. Grey dashed line: expected fitness in case of additivity (geometric mean of fitness in N and S weighted by the time spent in each medium).Scatterplot of all mutants showing their observed fitness under 6‐h periodic oscillations (y‐axis, NS6 regime) and their expected fitness in case of additivity (x‐axis, weighted geometric mean of fitness in N and S). Deviation from the diagonal reflects inhomogeneity. Red dots: 456 mutants with significant inhomogeneity (FDR = 0.0001, see Materials and Methods).Correlation between fitness estimates (w). Each dot corresponds to the median fitness of one mutant in one condition (N, S or NS6), measured from pooled cultures (x‐axis) or from individual assays (one mutant co‐cultured with WT cells, y‐axis). Whole data: 52 mutants. R, Pearson coefficient; grey line, y = x; red line, linear regression.Validation of inhomogeneity by cell counting. One graph shows the time course of mutant abundance when it was individually co‐cultured with GFP‐tagged wild‐type cells, measured by flow cytometry. Median values ± SD (n = 4 replicate cultures). Conditions: N (blue), S (yellow), 6‐h periodic oscillations (NS6, hatching). Jérôme Salignon et al. Mol Syst Biol 2018;14:e7823 © as stated in the article, figure or figure legend