Review for "A defined platform of human peri-gastrulation-like biological fate patterning reveals coordination between Reaction-Diffusion and Positional-Information"

Completed on 24 Jun 2017 by Hosein Fooladi. Sourced from http://biorxiv.org/content/early/2017/01/23/102376.

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I found this paper very amazing and interesting. Thanks for your great work; But I became puzzled a little and want to ask you some question to clear my mind.

1- You have mentioned in the paper “We noted that an hour after BMP4 induction, the pSMAD1 activity appeared evenly at all colony radii (Fig 2a). This implies that signaling capabilities of the cells immediately after the BMP4 presentation are position-independent.”

Can I ask you what is the dosage/concentration of BMP4 in this experiment? Etoc et al. have done the same experiment and in supplementary figure1-F they have shown the radial pattern can emerge after 1 hr treatment of BMP4 (I think because receptor localization) and emergence of pattern depends on dosage of BMP4 treatment.
Have you seen similar dosage dependent pattern emergence in your work?

2- In Etoc et al. paper we can see clearly that behavior of pSMAD1 completely depends on cell density. For example we can see this fact in figure1 of their paper. I am seeing cell density as a bifurcation parameter in their paper. But you have not mentioned anything about cell density. Can I ask you in which cell density you have done your experiment and have you ever seen cell density dependent behavior?

3- Can you say a little about value of parameters in your proposed Reaction-Diffusion Model? For example what is diffusion rate of BMP4 and NOGGIN in your model? And which Reaction-Diffusion Model you have used (for example activator-substrate depletion model)

Again congratulation for your amazing work. I have mentioned some problems that made me a little bit confused.



Hi Hosein,

Thanks a lot for your interest in the preprint of our study. Our study is currently under review, and many of these questions should be answered in some detail when the complete version of our study is published. Please see brief responses to your questions below. I hope they are helpful.

1- You have mentioned in the paper “We noted that an hour after BMP4 induction, the pSMAD1 activity appeared evenly at all colony radii (Fig 2a). This implies that signaling capabilities of the cells immediately after the BMP4 presentation are position-independent.”

Can I ask you what is the dosage/concentration of BMP4 in this experiment? Etoc et al. have done the same experiment and in supplementary figure1-F they have shown the radial pattern can emerge after 1 hr treatment of BMP4 (I think because receptor localization) and emergence of pattern depends on dosage of BMP4 treatment.
Have you seen similar dosage dependent pattern emergence in your work?

Our figure panels 3A-E in the preprint version of the paper detail a dose response study.

2- In Etoc et al. paper we can see clearly that behavior of pSMAD1 completely depends on cell density. For example we can see this fact in figure1 of their paper. I am seeing cell density as a bifurcation parameter in their paper. But you have not mentioned anything about cell density. Can I ask you in which cell density you have done your experiment and have you ever seen cell density dependent behavior?

We do not interpret the data presented by Etoc et al as a pSMAD1 gradient formation as a 'complete dependence on cell density', and will try to address our interpretation of these data in the discussion of our study. To answer your question about the densities used in our experiments - our studies were done at approximately 5000 cells/sq mm for all our colonies.

3- Can you say a little about value of parameters in your proposed Reaction-Diffusion Model? For example what is diffusion rate of BMP4 and NOGGIN in your model? And which Reaction-Diffusion Model you have used (for example activator-substrate depletion model)

We used the RD model that was described by Kondo et al (Science 2010). It was an activator/inhibitor model, not the substrate depletion one. The diffusivities used were 11, and 55 squm/sec for BMP4, and Noggin respectively.