TY - THES AB - Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. The recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. Finally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. AU - Cepeda Humerez, Sarah A ID - 6473 KW - Information estimation KW - Time-series KW - data analysis SN - 2663-337X TI - Estimating information flow in single cells ER - TY - THES AB - Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. AU - Prizak, Roshan ID - 6071 SN - 2663-337X TI - Coevolution of transcription factors and their binding sites in sequence space ER - TY - JOUR AB - For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. AU - Srivastava, Tanya K ID - 7436 JF - Documenta Mathematica SN - 1431-0635 TI - On derived equivalences of k3 surfaces in positive characteristic VL - 24 ER - TY - JOUR AB - We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t. AU - Ferrari, Patrick AU - Ghosal, Promit AU - Nejjar, Peter ID - 72 IS - 3 JF - Annales de l'institut Henri Poincare (B) Probability and Statistics SN - 0246-0203 TI - Limit law of a second class particle in TASEP with non-random initial condition VL - 55 ER - TY - JOUR AB - In this article a model is described how Open Access definitions can be formed on the basis of objective criteria. The common Open Access definitions such as "gold" and "green" are not exactly defined. This becomes a problem as soon as one begins to measure Open Access, for example if the development of the Open Access share should be monitored. This was discussed in the working group on Open Access Monitoring of the AT2OA project and the present model was developed, which is based on 5 critics with 4 characteristics: location, licence, version, embargo and conditions of the Open Access publication are taken into account. In the meantime, the model has also been tested in practice using R scripts, and the initial results are quite promising. AU - Danowski, Patrick ID - 6657 IS - 1 JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare TI - An Austrian proposal for the classification of Open Access Tuples (COAT) - distinguish different open access types beyond colors VL - 72 ER - TY - CONF AB - We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature. AU - Khatoniar, Mandeep AU - Yama, Nicholas AU - Ghazaryan, Areg AU - Guddala, Sriram AU - Ghaemi, Pouyan AU - Menon, Vinod ID - 6646 SN - 9781943580576 T2 - CLEO: Applications and Technology TI - Room temperature control of valley coherence in bilayer WS2 exciton polaritons ER - TY - CONF AB - We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm. AU - Rueda Sanchez, Alfredo R AU - Sedlmeir, Florian AU - Leuchs, Gerd AU - Kumari, Madhuri AU - Schwefel, Harald G.L. ID - 7233 SN - 9781557528209 T2 - Nonlinear Optics, OSA Technical Digest TI - Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity ER - TY - JOUR AB - For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles. AU - Alt, Johannes AU - Erdös, László AU - Krüger, Torben H AU - Nemish, Yuriy ID - 6240 IS - 2 JF - Annales de l'institut Henri Poincare SN - 0246-0203 TI - Location of the spectrum of Kronecker random matrices VL - 55 ER - TY - JOUR AB - Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use of model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing factors to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs for silencing distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model, we found interactions enriched on the maternal allele across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a2, Pde10a and Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Furthermore, we found that silent imprinted genes were covered with large blocks of H3K27me3 on the repressed paternal allele. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established. AU - Andergassen, Daniel AU - Muckenhuber, Markus AU - Bammer, Philipp C. AU - Kulinski, Tomasz M. AU - Theussl, Hans-Christian AU - Shimizu, Takahiko AU - Penninger, Josef M. AU - Pauler, Florian AU - Hudson, Quanah J. ID - 7399 IS - 7 JF - PLoS Genetics SN - 1553-7404 TI - The Airn lncRNA does not require any DNA elements within its locus to silence distant imprinted genes VL - 15 ER - TY - JOUR AB - Origin and functions of intermittent transitions among sleep stages, including short awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing the sleep-wake cycle results from an underlying non-equilibrium critical dynamics, bridging collective behaviors across spatio-temporal scales. We investigate θ and δ wave dynamics in control rats and in rats with lesions of sleep-promoting neurons in the parafacial zone. We demonstrate that intermittent bursts in θ and δ rhythms exhibit a complex temporal organization, with long-range power-law correlations and a robust duality of power law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, typical features of non-equilibrium systems self-organizing at criticality. Crucially, such temporal organization relates to anti-correlated coupling between θ- and δ-bursts, and is independent of the dominant physiologic state and lesions, a solid indication of a basic principle in sleep dynamics. AU - Wang, Jilin W. J. L. AU - Lombardi, Fabrizio AU - Zhang, Xiyun AU - Anaclet, Christelle AU - Ivanov, Plamen Ch. ID - 7103 IS - 11 JF - PLoS Computational Biology SN - 1553-7358 TI - Non-equilibrium critical dynamics of bursts in θ and δ rhythms as fundamental characteristic of sleep and wake micro-architecture VL - 15 ER -