(A)–(D) shows the SIF cores of the mutations studied in the MAPK model.

<p>(A) The reduced model; (B) the reduced model with initial conditions from Fujioka et al; (C) the reduced model with initial conditions from Fujioka et al and parameters optimized by fitting to the time course data in Fujioka et al; (D) the original non-reduced model. (E) A scheme shows the relationship between the key proteins and their clinical syndromes.</p

The mutations studied in the MAPK model.

<p>(A) A scheme of the MAPK pathway. (B) Mapping the mutations onto the three dimensional structures; mutations located at or close to the active site are colored in blue, otherwise colored in red.</p

<i>In vivo</i> length of the yeast trains in the G2-M model.

<p><i>In vivo</i> length of the yeast trains in the G2-M model.</p

Correlation between SIF and <i>in vivo</i> cell length of missense mutations in the G2-M model.

<p>The experimentally measured cell lengths and the calculated SIF scores at 25°C and 30°C are shown in grey and black, respectively. The x-axis error bars show the standard error of cell lengths; the y-axis error bars show the standard error of SIF scores, resulting from the evaluation of ΔΔG.</p

The sensitivity of the key proteins in the MAPK pathway in terms of regulating the Erk expression.

<p>(A) The reduced G2-M model. (B) The original non-reduced (Brightman and Fell) model.</p

<i>In silico</i> measurements of the mutant cells in the G2-M model.

a<p>Each mutation is considered to have mainly functional (F) or structural (F) impact according to their locations in its target protein.</p>b<p>ΔΔG of the mutations in individual Cdk1 or CycB; each of them is an average value considering structures sampled from molecular dynamic simulations.</p>c<p>ΔΔG of the mutations in Cdk1-CycB complex (MPF); each of them is an average value considering structures sampled from molecular dynamic simulations.</p>d<p>Maximum of ΔΔG considering both complexed and uncomplexed states of the target protein.</p>e<p>Perturbation on CycB degradation was weighted 0.3 for the degradation of monomeric CycB and weighted 0.7 for the degradation of complexed CycB (MPF).</p>f<p>Perturbation on Cdk1 degradation was estimated through the degradation of MPF only since the amount of total Cdk1 is constant.</p>g<p>Perturbation on the interaction between CycB and Cdk1 was estimated through J_wee and J₂₅ with a weighting 0.9*J_wee+0.1*J₂₅.</p>h<p>The high ΔΔG is a result of van der Waals clashes when the target residue is mutated to a larger side chain.</p

The procedure of calculating SIF scores.

<p>(A) Identifying the target system for study. In this case we show the scheme of the G2-M model that regulates the G2 to mitosis transition in the cell cycle. (B) Mapping mutations onto their 3D structures (Cdk1 and CycB in this example) and associating them with the ODE parameters. Mutations located at or close to the active site (colored in blue) are considered to perturb the ODE rate constants that describe interactions between MPF and their regulating kinases wee1 and cdc25 (shown with blue circles). Mutations that are not in the functional sites (colored in red) are considered to perturb the ODE rate constants describing the rate of protein degradation (shown with red circles). Also, for each mutation we evaluate its ΔΔG that is considered as the perturbation of ODE parameters. (C) Calculating the C^S_pi that reflects the sensitivity of perturbing ODE parameters in terms of regulating the downstream reporter protein (MPF in the G2-M model). Here we show the perturbation on the degradation rate of MPF as an example: The green arrows mark the effect of perturbation on CycB concentration when cells enter mitosis, which is a result of MPF curve shifts (the red line represents wild type whereas orange and purple lines are mutant types). (D) Inferring the systemic consequences of mutations based on ΔΔG and C^S_pi. Mutations that have smaller or larger SIF scores are likely to have smaller or larger sizes at septation, respectively. The scale bars shown in the microscopic photos represent the average length of wild-type yeasts.</p

Colony formation from spores produced in triploid fission yeast.

<p>(A) Heterogeneously sized colonies. Colonies were incubated on YE medium at 30°C for 5 d. (B) Representative morphologies of C1- (left) and C2- (right) type microcolonies. Colonies were incubated on YE medium at 30°C for 48 h.</p

Synergistic effects of DNA repair-related mutants on the <i>gtb1 mad2</i> double mutant.

<p>See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002776#pgen-1002776-g002" target="_blank">Figure 2</a> legend for details. *Enlarged black and white image of this portion is shown on the right side.</p

Segregation analysis of chromosome 3 disome.

(a)<p>P219 (<i>h</i>⁻<i>leu1 ade6-M210/ade6-M216</i>) was crossed with a haploid strain that was <i>h</i>⁺ with <i>ade6-M216</i> (or <i>ade6-M210</i>) and one of the indicated alleles (except <i>not2</i>, which is mapped on chromosome 3). Strain 56-1 (<i>h</i>⁻<i>leu1 ade6-M210 not2::kan/ade6-M216 not2</i>⁺) was crossed with <i>h</i>⁺<i>ade6-M216 not2::kan</i>. Ade⁺ segregants were selected on an EMM2 plate at 30°C.</p>(b)<p>Ade⁺ colonies were randomly selected and tested for drug resistance. For the <i>not2</i> mutant, see (d).</p>(c)<p>All tested 12 Ade⁺ segregants had the “unstable Ade⁺” phenotype, indicating a chromosome 3 disome. Note, wild-type did not produce drug-resistant segregants.</p>(d)<p>For this cross, 24 of 26 Ade⁺ (disomic for chromosome 3) were G-418 resistant. Of these 24 segregants, 15 were homozygous for the <i>not2::kan</i> mutant, while 9 were heterozygous (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002776#s4" target="_blank">Materials and methods</a>).</p>(e)<p>G-418 resistant Ade⁺ segregants in this mutant were generally small, and upon restreaking on YE plates only stable Ade⁺ colonies (probably diploids) and Ade⁻ haploid colonies were produced. Chromosome 3 disome was hardly recovered thereafter.</p