Exact results for one dimensional stochastic cellular automata for different types of updates

We study two common types of time-noncontinuous updates for one dimensional stochastic cellular automata with arbitrary nearest neighbor interactions and arbitrary open boundary conditions. We first construct the stationary states using the matrix product formalism. This construction then allows to prove a general connection between the stationary states which are produced by the two different types of updates. Using this connection, we derive explicit relations between the densities and correlation functions for these different stationary states.Comment: 7 pages, Late

A deterministic sandpile automaton revisited

The Bak-Tang-Wiesenfeld (BTW) sandpile model is a cellular automaton which has been intensively studied during the last years as a paradigm for self-organized criticality. In this paper, we reconsider a deterministic version of the BTW model introduced by Wiesenfeld, Theiler and McNamara, where sand grains are added always to one fixed site on the square lattice. Using the Abelian sandpile formalism we discuss the static properties of the system. We present numerical evidence that the deterministic model is only in the BTW universality class if the initial conditions and the geometric form of the boundaries do not respect the full symmetry of the square lattice.Comment: 7 pages, 8 figures, EPJ style, accepted for publication in European Physical Journal

The asymmetric exclusion model with sequential update

We present a solution for the stationary state of an asymmetric exclusion model with sequential update and open boundary conditions. We solve the model exactly for random hopping in both directions by applying a matrix-product formalism which was recently used to solve the model with sublattice-parallel update[1]. It is shown that the matrix-algebra describing the sequential update and sublattice-parallel update are identical and can be mapped onto the random sequential case treated by Derrida et al[2].Comment: 7 pages, Late

The asymmetric exclusion process: Comparison of update procedures

The asymmetric exclusion process (ASEP) has attracted a lot of interest not only because its many applications, e.g. in the context of the kinetics of biopolymerization and traffic flow theory, but also because it is a paradigmatic model for nonequilibrium systems. Here we study the ASEP for different types of updates, namely random-sequential, sequential, sublattice-parallel and parallel. In order to compare the effects of the different update procedures on the properties of the stationary state, we use large-scale Monte Carlo simulations and analytical methods, especially the so-called matrix-product Ansatz (MPA). We present in detail the exact solution for the model with sublattice-parallel and sequential updates using the MPA. For the case of parallel update, which is important for applications like traffic flow theory, we determine the phase diagram, the current, and density profiles based on Monte Carlo simulations. We furthermore suggest a MPA for that case and derive the corresponding matrix algebra.Comment: 47 pages (11 PostScript figures included), LATEX, Two misprints in equations correcte

Exact density profiles for fully asymmetric exclusion process with discrete-time dynamics

Exact density profiles in the steady state of the one-dimensional fully asymmetric simple exclusion process on semi-infinite chains are obtained in the case of forward-ordered sequential dynamics by taking the thermodynamic limit in our recent exact results for a finite chain with open boundaries. The corresponding results for sublattice parallel dynamics follow from the relationship obtained by Rajewsky and Schreckenberg [Physica A 245, 139 (1997)] and for parallel dynamics from the mapping found by Evans, Rajewsky and Speer [J. Stat. Phys. 95, 45 (1999)]. By comparing the asymptotic results appropriate for parallel update with those published in the latter paper, we correct some technical errors in the final results given there.Comment: About 10 pages and 3 figures, new references are added and a comparison is made with the results by de Gier and Nienhuis [Phys. Rev. E 59, 4899(1999)

Mixed messages: re-initiation factors regulate translation of animal mRNAs

When ribosomes encounter upstream open reading frames (uORFs) during scanning of the 5' untranslated region (5' UTR), translation of the downstream ORF requires re-initiation. In a recent paper in Nature, Schleich et al. describe metazoan factors which specifically promote re-initiation

Charting a tissue from single-cell transcriptomes

Massively multiplexed sequencing of RNA in individual cells is transforming basic and clinical life sciences. However, in standard experiments, tissues must first be dissociated. Thus, after sequencing, information about the spatial relationships between cells is lost although this knowledge is crucial for understanding cellular and tissue-level function. Recent attempts to overcome this fundamental challenge rely on employing additional in situ gene expression imaging data which can guide spatial mapping of sequenced cells. Here we present a conceptually different approach that allows to reconstruct spatial positions of cells in a variety of tissues without using reference imaging data. We first show for several complex biological systems that distances of single cells in expression space monotonically increase with their physical distances across tissues. We therefore seek to map cells to tissue space such that this principle is optimally preserved, while matching existing imaging data when available. We show that this optimization problem can be cast as a generalized optimal transport problem and solved efficiently. We apply our approach successfully to reconstruct the mammalian liver and intestinal epithelium as well as fly and zebrafish embryos. Our results demonstrate a simple spatial expression organization principle and that this principle (or future refined principles) can be used to infer, for individual cells, meaningful spatial position probabilities from the sequencing data alone

Identification of proteins and miRNAs that specifically bind an mRNA in vivo

Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were thus far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to selected mRNAs in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR will provide a platform for investigating RNA in vivo regulation in diverse biological systems

circBase: a database for circular RNAs

Recently, several laboratories have reported thousands of circular RNAs (circRNAs) in animals. Numerous circRNAs are highly stable and have specific spatiotemporal expression patterns. Even though a function for circRNAs is unknown, these features make circRNAs an interesting class of RNAs as possible biomarkers and for further research. We developed a database and website, "circBase," where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic context. circBase also provides scripts to identify known and novel circRNAs in sequencing data. The database is freely accessible through the web server at http://www.circbase.org/

Post-transcriptional regulation by 3' UTRs can be masked by regulatory elements in 5' UTRs

In mRNA sequences, 3' UTRs are thought to contain most elements that specifically regulate localization, turnover, and translation. Although high-throughput experiments indicate that many RNA-binding proteins (RBPs) also bind 5' UTRs, much less is known about specific post-transcriptional control exerted by 5' UTRs. GLD-1 is a conserved RBP and a translational repressor with essential roles in Caenorhabditis elegans germ cell development. Previously, we showed that GLD-1 binds highly conserved sites in both 3' and 5' UTRs. Here, by targeted single-copy insertion of transgenes, we systematically tested in vivo functionality of 5' and 3' UTR binding sites individually and in combination. Our data show that sites in 5' UTRs mediate specific and strong translational repression, independent of exact position. Intriguingly, we found that the functionality of 3' UTR sites can be masked by 5' UTR sites and vice versa. We conclude that it is important to study both UTRs simultaneously