The overall goal of our research effort is to produce a quantitative description, and ultimately a mathematical theory, of how spatial patterns of gene expression are established in a developing embryo. Our experimental system is the Bicoid (Bed)morphogen gradient in the Drosophila embryo, the primary maternal determinant of the anterior-posterior axis. Our project brings together modern methods of experimental and theoretical biophysics with those of molecular biology and genetics to provide an integrated attack on (1) how the Bed gradient is established and maintained, (2) how is it scaled proportionately across embryos of different size, and (3) how is it read out to produce precise patterns of downstream gene expression. The dynamics of the formation and stabilization of the Bed gradient will be measured in living embryos expressing eGFP-Bcd. Image sequences from time-lapse two photon microscopy will be used, together with photobleaching methods and computational analysis, to assess passive and active contributions to gradient dynamics, to determine the protein half life of Bed, and to determine absolute concentrations of Bed in nuclei and cytoplasm at various stages of development. The scaling of Bed and gap gene expression patterns across closely related dipteran species that have bodies of different size but almost identical proportions will be analyzed using classical staining methods, extended by more sophisticated image processing methods. In addition, transformants expressing eGFP labeled-bicoid genes from different sized fly species will be expressed in Drosophla melanogaster to probe the biophysical mechanisms behind this scaling. Although genes appear to be activated by Bed at specific concentration thresholds along the length of the embryo, noise in transcriptional regulation places limits on the accuracy with which such thresholds can be marked. Theoretical work will define the nature of these limits in progressively more realistic models of each regulatory step. To test these models, the mean and variance of target genes (hunchback, orthodenticle) will be measured as functions of local concentration of Bed,both in wild type embryos, and in mutants and genetic mosaics where levels and activities can be artificially manipulated. Spatial correlations in the variance will also be measured, testing the hypothesis that communication among nuclei plays a role in suppressing noise and enhancing the precision of developmental boundaries. Our project addresses the fundamental question of how small changes in the concentration of signaling molecules produce robust control of cell fate. Precise read-out of such signaling pathways is required for normal development. Perturbations in signaling are associated with birth defects and cancer in adults.
| Dubuis, Julien O; Tkacik, Gasper; Wieschaus, Eric F et al. (2013) Positional information, in bits. Proc Natl Acad Sci U S A 110:16301-8 |
| Grimm, Oliver; Sanchez Zini, Victoria; Kim, Yoosik et al. (2012) Torso RTK controls Capicua degradation by changing its subcellular localization. Development 139:3962-8 |
| Drocco, J A; Wieschaus, E F; Tank, D W (2012) The synthesis-diffusion-degradation model explains Bicoid gradient formation in unfertilized eggs. Phys Biol 9:055004 |
| Tkacik, Gasper; Walczak, Aleksandra M; Bialek, William (2012) Optimizing information flow in small genetic networks. III. A self-interacting gene. Phys Rev E Stat Nonlin Soft Matter Phys 85:041903 |
| Morrison, Alexander H; Scheeler, Martin; Dubuis, Julien et al. (2012) Quantifying the Bicoid morphogen gradient in living fly embryos. Cold Spring Harb Protoc 2012:398-406 |
| Drocco, Jeffrey A; Grimm, Oliver; Tank, David W et al. (2011) Measurement and perturbation of morphogen lifetime: effects on gradient shape. Biophys J 101:1807-15 |
| Grimm, Oliver; Wieschaus, Eric (2010) The Bicoid gradient is shaped independently of nuclei. Development 137:2857-62 |
| Walczak, Aleksandra M; Tkacik, Gasper; Bialek, William (2010) Optimizing information flow in small genetic networks. II. Feed-forward interactions. Phys Rev E Stat Nonlin Soft Matter Phys 81:041905 |
| Tkacik, Gasper; Bialek, William (2009) Diffusion, dimensionality, and noise in transcriptional regulation. Phys Rev E Stat Nonlin Soft Matter Phys 79:051901 |
| Tkacik, Gasper; Walczak, Aleksandra M; Bialek, William (2009) Optimizing information flow in small genetic networks. Phys Rev E Stat Nonlin Soft Matter Phys 80:031920 |
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