@article{schloop_bandodkar_reeves_2020, title={Formation, interpretation, and regulation of the Drosophila Dorsal/NF-kappa B gradient}, volume={137}, ISBN={["978-0-12-812790-2"]}, ISSN={["0070-2153"]}, DOI={10.1016/bs.ctdb.2019.11.007}, abstractNote={The morphogen gradient of the transcription factor Dorsal in the early Drosophila embryo has become one of the most widely studied tissue patterning systems. Dorsal is a Drosophila homolog of mammalian NF-κB and patterns the dorsal-ventral axis of the blastoderm embryo into several tissue types by spatially regulating upwards of 100 zygotic genes. Recent studies using fluorescence microscopy and live imaging have quantified the Dorsal gradient and its target genes, which has paved the way for mechanistic modeling of the gradient. In this review, we describe the mechanisms behind the initiation of the Dorsal gradient and its regulation of target genes. The main focus of the review is a discussion of quantitative and computational studies of the Dl gradient system, including regulation of the Dl gradient. We conclude with a discussion of potential future directions.}, journal={GRADIENTS AND TISSUE PATTERNING}, author={Schloop, Allison E. and Bandodkar, Prasad U. and Reeves, Gregory T.}, year={2020}, pages={143–191} }
 @article{al asafen_bandodkar_carrell-noel_schloop_friedman_reeves_2020, title={Robustness of the Dorsal morphogen gradient with respect to morphogen dosage}, volume={16}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.1007750}, abstractNote={In multicellular organisms, the timing and placement of gene expression in a developing tissue assigns the fate of each cell in the embryo in order for a uniform field of cells to differentiate into a reproducible pattern of organs and tissues. This positional information is often achieved through the action of spatial gradients of morphogens. Spatial patterns of gene expression are paradoxically robust to variations in morphogen dosage, given that, by definition, gene expression must be sensitive to morphogen concentration. In this work we investigate the robustness of the Dorsal/NF-κB signaling module with respect to perturbations to the dosage of maternally-expressed dorsal mRNA. The Dorsal morphogen gradient patterns the dorsal-ventral axis of the early Drosophila embryo, and we found that an empirical description of the Dorsal gradient is highly sensitive to maternal dorsal dosage. In contrast, we found experimentally that gene expression patterns are highly robust. Although the components of this signaling module have been characterized in detail, how their function is integrated to produce robust gene expression patterns to variations in the dorsal maternal dosage is still unclear. Therefore, we analyzed a mechanistic model of the Dorsal signaling module and found that Cactus, a cytoplasmic inhibitor for Dorsal, must be present in the nucleus for the system to be robust. Furthermore, active Toll, the receptor that dissociates Cactus from Dorsal, must be saturated. Finally, the vast majority of robust descriptions of the system require facilitated diffusion of Dorsal by Cactus. Each of these three recently-discovered mechanisms of the Dorsal module are critical for robustness. Our work highlights the need for quantitative understanding of biophysical mechanisms of morphogen gradients in order to understand emergent phenotypes, such as robustness. Author Summary The early stages of development of an embryo are crucial for laying the foundation of the body plan. The blueprint of this plan is encoded in long-range spatial protein gradients called morphogens. This positional information is then interpreted by nuclei that begin to differentiate by expressing different genes. In fruit fly embryos, the Dorsal morphogen forms a gradient along the dorsal-ventral axis, with a maximum at the ventral midline. This gradient, and the resulting gene expression patterns are extraordinarily robust to variations in developmental conditions, even during early stages of development. Since positional information is interpreted in terms of concentration of the morphogen, one would expect that doubling or halving dosage would result in disastrous consequences for the embryo. However, we observed that development remains robust. We quantified the effect of dosage by experimentally measuring the boundaries of 2 genes, - sna and sog, expressed along the DV axis and found that variation in the boundaries of these genes was minimal, across embryos with different dosages of Dl. We then used a mathematical model to discern components of the Dl system responsible for buffering the effects of dosage and found three specific mechanisms – deconvolution, Toll saturation and shuttling}, number={4}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Al Asafen, Hadel and Bandodkar, Prasad U. and Carrell-Noel, Sophia and Schloop, Allison E. and Friedman, Jeramey and Reeves, Gregory T.}, year={2020}, month={Apr} }
 @article{bandodkar_al asafen_reeves_2020, title={Spatiotemporal control of gene expression boundaries using a feedforward loop}, volume={249}, ISSN={["1097-0177"]}, DOI={10.1002/dvdy.150}, abstractNote={A feed forward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly been studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen-mediated tissue patterning. However, most morphogen gradients also evolve in time. We studied the spatiotemporal behavior of a coherent FFL in two contexts: (1) a generic, oscillating morphogen gradient and (2) the dorsal-ventral patterning of the early Drosophila embryo by a gradient of the NF-κB homolog Dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node – phase difference and noise filtering – that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the Dorsal gradient model, we also found that the dynamics of Dorsal require maternal pioneering factor Zelda for proper target gene expression.}, number={3}, journal={DEVELOPMENTAL DYNAMICS}, author={Bandodkar, Prasad U. and Al Asafen, Hadel and Reeves, Gregory T.}, year={2020}, month={Mar}, pages={369–382} }
 @article{reeves_bandodkar_al asafen_2020, title={Spatiotemporal control of gene expression boundaries using a feedforward loop}, volume={34}, ISSN={["1530-6860"]}, DOI={10.1096/fasebj.2020.34.s1.00347}, abstractNote={A feed forward loop (FFL) is commonly observed in several biological networks. The FFL network motif has been mostly been studied with respect to variation of the input signal in time, with only a few studies of FFL activity in a spatially distributed system such as morphogen‐mediated tissue patterning. However, most morphogen gradients also evolve in time. We studied the spatiotemporal behavior of a coherent FFL in two contexts: (1) a generic, oscillating morphogen gradient and (2) the dorsal‐ventral patterning of the early Drosophila embryo by a gradient of the NF‐κB homolog Dorsal with its early target Twist. In both models, we found features in the dynamics of the intermediate node – phase difference and noise filtering – that were largely independent of the parameterization of the models, and thus were functions of the structure of the FFL itself. In the Dorsal gradient model, we also found that the dynamics of Dorsal require maternal pioneering factor Zelda for proper target gene expression.}, journal={FASEB JOURNAL}, author={Reeves, Gregory and Bandodkar, Prasad and Al Asafen, Hadel}, year={2020}, month={Apr} }