Limits...
Light and circadian regulation of clock components aids flexible responses to environmental signals.

Dixon LE, Hodge SK, van Ooijen G, Troein C, Akman OE, Millar AJ - New Phytol. (2014)

Bottom Line: However, these and earlier data showed that the O. tauri network retains surprising flexibility, despite its simple circuit.We found that models constructed from experimental data can show flexibility either from multiple loops and/or from multiple light inputs.Our results suggest that O. tauri has adopted the latter strategy, possibly as a consequence of genomic reduction.

View Article: PubMed Central - PubMed

Affiliation: SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

Show MeSH
Variations in clock flexibility with feedback loops and light inputs. Circles denote the flexibility dimension d of a model in 12 : 12 h, light : dark cycles, while triangles denote the flexibility under constant light conditions (continuous light for Arabidopsis and Ostreococcus; continuous dark for Neurospora). (a) Flexibility increases with loop number under constant conditions. In each case, the computed value of d is higher in light : dark cycles than in constant light conditions, showing that incorporating light entrainment yields a more flexible circuit. In particular, the single-loop O. tauri circuit (T2011) exhibits a significant increase in flexibility compared with the single-loop A. thaliana circuit (L2005A). (b) Plotting flexibility against the sum total of loops and light inputs for each model reveals a positive trend, implying that light inputs augment clock flexibility in a similar manner to feedback loops. (Note that in both plots, points with the same x-axis value have been slightly offset for clarity.) For all models, d is defined as the number of significant singular values of the matrix M* that maps parameter perturbations to perturbations of the corresponding free-running or entrained limit cycle (the singular value spectra {σk} of the entrained models are shown in Fig. S7).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4286021&req=5

fig04: Variations in clock flexibility with feedback loops and light inputs. Circles denote the flexibility dimension d of a model in 12 : 12 h, light : dark cycles, while triangles denote the flexibility under constant light conditions (continuous light for Arabidopsis and Ostreococcus; continuous dark for Neurospora). (a) Flexibility increases with loop number under constant conditions. In each case, the computed value of d is higher in light : dark cycles than in constant light conditions, showing that incorporating light entrainment yields a more flexible circuit. In particular, the single-loop O. tauri circuit (T2011) exhibits a significant increase in flexibility compared with the single-loop A. thaliana circuit (L2005A). (b) Plotting flexibility against the sum total of loops and light inputs for each model reveals a positive trend, implying that light inputs augment clock flexibility in a similar manner to feedback loops. (Note that in both plots, points with the same x-axis value have been slightly offset for clarity.) For all models, d is defined as the number of significant singular values of the matrix M* that maps parameter perturbations to perturbations of the corresponding free-running or entrained limit cycle (the singular value spectra {σk} of the entrained models are shown in Fig. S7).

Mentions: The comparison of the calculated flexibility dimensions of the A. thaliana and O. tauri models in constant conditions showed that flexibility increases with the total number of feedback loops in the circuit (Fig. 4). To increase the generality of this analysis, a two-loop model of the N. crassa clock (A2010; Fig. S1c) was also included (Akman et al., 2010). When entrainment was incorporated, the flexibility of each model network also increased. Fig. 4 shows that in LL, the flexibility of the single loop O. tauri (T2011) network (Troein et al., 2011) is close to that of the single loop A. thaliana (L2005A) network (Locke et al., 2005a). However, the addition of light : dark cycles to O. tauri results in a flexibility that is intermediate between the multiloop A. thaliana L2005B (Locke et al., 2005b) and L2006 (Locke et al., 2006) circuits.


Light and circadian regulation of clock components aids flexible responses to environmental signals.

Dixon LE, Hodge SK, van Ooijen G, Troein C, Akman OE, Millar AJ - New Phytol. (2014)

Variations in clock flexibility with feedback loops and light inputs. Circles denote the flexibility dimension d of a model in 12 : 12 h, light : dark cycles, while triangles denote the flexibility under constant light conditions (continuous light for Arabidopsis and Ostreococcus; continuous dark for Neurospora). (a) Flexibility increases with loop number under constant conditions. In each case, the computed value of d is higher in light : dark cycles than in constant light conditions, showing that incorporating light entrainment yields a more flexible circuit. In particular, the single-loop O. tauri circuit (T2011) exhibits a significant increase in flexibility compared with the single-loop A. thaliana circuit (L2005A). (b) Plotting flexibility against the sum total of loops and light inputs for each model reveals a positive trend, implying that light inputs augment clock flexibility in a similar manner to feedback loops. (Note that in both plots, points with the same x-axis value have been slightly offset for clarity.) For all models, d is defined as the number of significant singular values of the matrix M* that maps parameter perturbations to perturbations of the corresponding free-running or entrained limit cycle (the singular value spectra {σk} of the entrained models are shown in Fig. S7).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4286021&req=5

fig04: Variations in clock flexibility with feedback loops and light inputs. Circles denote the flexibility dimension d of a model in 12 : 12 h, light : dark cycles, while triangles denote the flexibility under constant light conditions (continuous light for Arabidopsis and Ostreococcus; continuous dark for Neurospora). (a) Flexibility increases with loop number under constant conditions. In each case, the computed value of d is higher in light : dark cycles than in constant light conditions, showing that incorporating light entrainment yields a more flexible circuit. In particular, the single-loop O. tauri circuit (T2011) exhibits a significant increase in flexibility compared with the single-loop A. thaliana circuit (L2005A). (b) Plotting flexibility against the sum total of loops and light inputs for each model reveals a positive trend, implying that light inputs augment clock flexibility in a similar manner to feedback loops. (Note that in both plots, points with the same x-axis value have been slightly offset for clarity.) For all models, d is defined as the number of significant singular values of the matrix M* that maps parameter perturbations to perturbations of the corresponding free-running or entrained limit cycle (the singular value spectra {σk} of the entrained models are shown in Fig. S7).
Mentions: The comparison of the calculated flexibility dimensions of the A. thaliana and O. tauri models in constant conditions showed that flexibility increases with the total number of feedback loops in the circuit (Fig. 4). To increase the generality of this analysis, a two-loop model of the N. crassa clock (A2010; Fig. S1c) was also included (Akman et al., 2010). When entrainment was incorporated, the flexibility of each model network also increased. Fig. 4 shows that in LL, the flexibility of the single loop O. tauri (T2011) network (Troein et al., 2011) is close to that of the single loop A. thaliana (L2005A) network (Locke et al., 2005a). However, the addition of light : dark cycles to O. tauri results in a flexibility that is intermediate between the multiloop A. thaliana L2005B (Locke et al., 2005b) and L2006 (Locke et al., 2006) circuits.

Bottom Line: However, these and earlier data showed that the O. tauri network retains surprising flexibility, despite its simple circuit.We found that models constructed from experimental data can show flexibility either from multiple loops and/or from multiple light inputs.Our results suggest that O. tauri has adopted the latter strategy, possibly as a consequence of genomic reduction.

View Article: PubMed Central - PubMed

Affiliation: SynthSys, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3JD, UK; Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.

Show MeSH