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The presence of nuclear cactus in the early Drosophila embryo may extend the dynamic range of the dorsal gradient.

O'Connell MD, Reeves GT - PLoS Comput. Biol. (2015)

Bottom Line: We found that two assumptions are required for the model to match experimental data in both Dorsal distribution and gene expression patterns.And second, we assume that fluorescence measurements of Dorsal reflect both free Dorsal and Cactus-bound Dorsal.Our results have a general implication for interpreting fluorescence-based measurements of signaling molecules.

View Article: PubMed Central - PubMed

Affiliation: North Carolina State University Department of Chemical and Biomolecular Engineering, Raleigh, North Carolina, United States of America.

ABSTRACT
In a developing embryo, the spatial distribution of a signaling molecule, or a morphogen gradient, has been hypothesized to carry positional information to pattern tissues. Recent measurements of morphogen distribution have allowed us to subject this hypothesis to rigorous physical testing. In the early Drosophila embryo, measurements of the morphogen Dorsal, which is a transcription factor responsible for initiating the earliest zygotic patterns along the dorsal-ventral axis, have revealed a gradient that is too narrow to pattern the entire axis. In this study, we use a mathematical model of Dorsal dynamics, fit to experimental data, to determine the ability of the Dorsal gradient to regulate gene expression across the entire dorsal-ventral axis. We found that two assumptions are required for the model to match experimental data in both Dorsal distribution and gene expression patterns. First, we assume that Cactus, an inhibitor that binds to Dorsal and prevents it from entering the nuclei, must itself be present in the nuclei. And second, we assume that fluorescence measurements of Dorsal reflect both free Dorsal and Cactus-bound Dorsal. Our model explains the dynamic behavior of the Dorsal gradient at lateral and dorsal positions of the embryo, the ability of Dorsal to regulate gene expression across the entire dorsal-ventral axis, and the robustness of gene expression to stochastic effects. Our results have a general implication for interpreting fluorescence-based measurements of signaling molecules.

No MeSH data available.


Related in: MedlinePlus

Effect of Cact background subtraction.(a) From raw fluorescence measurements (red), lateral and dorsal nuclei should have trouble interpreting their position in the DV axis because of signal noise (dotted curves). If only the active pool of dl is taken into account (blue), noise is not prohibitive to accurate boundary placement, meaning that dl can indeed pattern the whole of the DV axis. (b) If we consider a simple example of background subtraction, the shape of the dl gradient remains the same (solid lines, from red to blue) while the relative error due to noise (dotted lines, in no. of nuclei) at each point in the DV axis significantly decreases (especially beyond 40% DV) as a greater percentage of the basal concentration is subtracted.
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pcbi.1004159.g007: Effect of Cact background subtraction.(a) From raw fluorescence measurements (red), lateral and dorsal nuclei should have trouble interpreting their position in the DV axis because of signal noise (dotted curves). If only the active pool of dl is taken into account (blue), noise is not prohibitive to accurate boundary placement, meaning that dl can indeed pattern the whole of the DV axis. (b) If we consider a simple example of background subtraction, the shape of the dl gradient remains the same (solid lines, from red to blue) while the relative error due to noise (dotted lines, in no. of nuclei) at each point in the DV axis significantly decreases (especially beyond 40% DV) as a greater percentage of the basal concentration is subtracted.

Mentions: As seen from our dl gradient and gene expression simulations (Fig. 5), subtracting the inactive component of the dl gradient from that measured by fluorescence reveals an active dl gradient that is able to convey spatial information over a greater proportion of the DV axis due to its expanded dynamic range. One may ask how this “background subtraction” mechanism achieves this. As illustrated in Fig. 7a, background subtraction via Cact increases the relative difference in active dl concentration between the ventral and dorsal midlines. This effect is achieved even if the dl/Cact profile is flat, in which case the shape and slope of the dl activity gradient is the same as that of the total dl gradient, but the dynamic range is greatly improved. According to our analysis, this becomes most important in the issue of overcoming noise. To quantify this effect, we calculate the potential for nuclei to misinterpret their position in the x-direction due to noise (Fig. 7b).


The presence of nuclear cactus in the early Drosophila embryo may extend the dynamic range of the dorsal gradient.

O'Connell MD, Reeves GT - PLoS Comput. Biol. (2015)

Effect of Cact background subtraction.(a) From raw fluorescence measurements (red), lateral and dorsal nuclei should have trouble interpreting their position in the DV axis because of signal noise (dotted curves). If only the active pool of dl is taken into account (blue), noise is not prohibitive to accurate boundary placement, meaning that dl can indeed pattern the whole of the DV axis. (b) If we consider a simple example of background subtraction, the shape of the dl gradient remains the same (solid lines, from red to blue) while the relative error due to noise (dotted lines, in no. of nuclei) at each point in the DV axis significantly decreases (especially beyond 40% DV) as a greater percentage of the basal concentration is subtracted.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4400154&req=5

pcbi.1004159.g007: Effect of Cact background subtraction.(a) From raw fluorescence measurements (red), lateral and dorsal nuclei should have trouble interpreting their position in the DV axis because of signal noise (dotted curves). If only the active pool of dl is taken into account (blue), noise is not prohibitive to accurate boundary placement, meaning that dl can indeed pattern the whole of the DV axis. (b) If we consider a simple example of background subtraction, the shape of the dl gradient remains the same (solid lines, from red to blue) while the relative error due to noise (dotted lines, in no. of nuclei) at each point in the DV axis significantly decreases (especially beyond 40% DV) as a greater percentage of the basal concentration is subtracted.
Mentions: As seen from our dl gradient and gene expression simulations (Fig. 5), subtracting the inactive component of the dl gradient from that measured by fluorescence reveals an active dl gradient that is able to convey spatial information over a greater proportion of the DV axis due to its expanded dynamic range. One may ask how this “background subtraction” mechanism achieves this. As illustrated in Fig. 7a, background subtraction via Cact increases the relative difference in active dl concentration between the ventral and dorsal midlines. This effect is achieved even if the dl/Cact profile is flat, in which case the shape and slope of the dl activity gradient is the same as that of the total dl gradient, but the dynamic range is greatly improved. According to our analysis, this becomes most important in the issue of overcoming noise. To quantify this effect, we calculate the potential for nuclei to misinterpret their position in the x-direction due to noise (Fig. 7b).

Bottom Line: We found that two assumptions are required for the model to match experimental data in both Dorsal distribution and gene expression patterns.And second, we assume that fluorescence measurements of Dorsal reflect both free Dorsal and Cactus-bound Dorsal.Our results have a general implication for interpreting fluorescence-based measurements of signaling molecules.

View Article: PubMed Central - PubMed

Affiliation: North Carolina State University Department of Chemical and Biomolecular Engineering, Raleigh, North Carolina, United States of America.

ABSTRACT
In a developing embryo, the spatial distribution of a signaling molecule, or a morphogen gradient, has been hypothesized to carry positional information to pattern tissues. Recent measurements of morphogen distribution have allowed us to subject this hypothesis to rigorous physical testing. In the early Drosophila embryo, measurements of the morphogen Dorsal, which is a transcription factor responsible for initiating the earliest zygotic patterns along the dorsal-ventral axis, have revealed a gradient that is too narrow to pattern the entire axis. In this study, we use a mathematical model of Dorsal dynamics, fit to experimental data, to determine the ability of the Dorsal gradient to regulate gene expression across the entire dorsal-ventral axis. We found that two assumptions are required for the model to match experimental data in both Dorsal distribution and gene expression patterns. First, we assume that Cactus, an inhibitor that binds to Dorsal and prevents it from entering the nuclei, must itself be present in the nuclei. And second, we assume that fluorescence measurements of Dorsal reflect both free Dorsal and Cactus-bound Dorsal. Our model explains the dynamic behavior of the Dorsal gradient at lateral and dorsal positions of the embryo, the ability of Dorsal to regulate gene expression across the entire dorsal-ventral axis, and the robustness of gene expression to stochastic effects. Our results have a general implication for interpreting fluorescence-based measurements of signaling molecules.

No MeSH data available.


Related in: MedlinePlus