A quantitative understanding of how transcription factors interact with genomic target sites is crucial for reconstructing transcriptional networks in vivo. Here, we use Hac1, a well-characterized basic leucine zipper (bZIP) transcription factor involved in the unfolded protein response (UPR) as a model to investigate interactions between bZIP transcription factors and their target sites. Durin...

The endoplasmic reticulum (ER) is essential to many cellular processes including protein processing, lipid metabolism and calcium storage. The ability to longitudinally monitor ER homeostasis in the same organism would offer insight into progressive molecular and cellular adaptations to physiologic or pathologic states, but has been challenging. We recently described the creation of a Gaussia l...

Total Variation (TV) regularization is a popular method for solving a wide variety of inverse problems in image processing. In order to optimize the reconstructed image, it is important to choose a good regularization parameter. The Unbiased Predictive Risk Estimator (UPRE) has been shown to give a good estimate of this parameter for Tikhonov regularization. In this paper we propose an extensio...

The unfolded protein response (UPR) is a signalling pathway leading to transcriptional activation of genes that protect cells from accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER). In yeast, the only known ER stress signalling pathway originates at the type I transmembrane protein kinase/endoribonuclease Ire1p. Ire1p regulates synthesis of the basic leucine-zippe...

The unfolded protein response (UPR), a conserved eukaryotic signaling pathway to ensure protein homeostasis in the endoplasmic reticulum (ER), coordinates biotrophic development in the corn smut fungus Ustilago maydis. Exact timing of UPR activation is required for virulence and presumably connected to the elevated expression of secreted effector proteins during infection of the host plant Zea ...

operators To verify Aμ-formulas, we need to abstract the operators. For each p in Π, let π(p) be an element of P ] such that π(p) ⊆ γ(π(p)), and π(p) an element of P ] such that Σ\π(p) ⊆ γ(π(p)). For each subset I of P, we define the abstract controllable predecessor relation CPre]I ∈ P ] → P ] and the abstract uncontrollable predecessor relation UPre ] I ∈ P ] → P . These relations must satisf...