506 research outputs found
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
Escalation of error catastrophe for enzymatic self-replicators
It is a long-standing question in origin-of-life research whether the
information content of replicating molecules can be maintained in the presence
of replication errors. Extending standard quasispecies models of non-enzymatic
replication, we analyze highly specific enzymatic self-replication mediated
through an otherwise neutral recognition region, which leads to
frequency-dependent replication rates. We find a significant reduction of the
maximally tolerable error rate, because the replication rate of the fittest
molecules decreases with the fraction of functional enzymes. Our analysis is
extended to hypercyclic couplings as an example for catalytic networks.Comment: 6 pages, 4 figures; accepted at Europhys. Let
Viral infection identifies micropeptides differentially regulated in smORF-containing lncRNAs
Viral infection leads to a robust cellular response whereby the infected cell produces hundreds of molecular regulators to combat infection. Currently, non-canonical components, e.g., long noncoding RNAs (lncRNAs) have been added to the repertoire of immune regulators involved in the antiviral program. Interestingly, studies utilizing next-generation sequencing technologies show that a subset of the >10,000 lncRNAs in the mammalian genome contain small open reading frames (smORFs) associated with active translation, i.e., many lncRNAs are not noncoding. Here, we use genome-wide high-throughput methods to identify potential micropeptides in smORF-containing lncRNAs involved in the immune response. Using influenza as a viral infection model, we performed RNA-seq and ribosome profiling to track expression and translation of putative lncRNAs that may encode for peptides and identify tens of potential candidates. Interestingly, many of these peptides are highly conserved at the protein level, strongly suggesting biological relevance and activity. By perusing publicly available data sets, four potential peptides of interest seem common to stress induction and/or are highly conserved; potential peptides from the MMP24-AS1, ZFAS1, RP11-622K12.1, and MIR22HG genes. Interestingly, using an antibody against the potential peptide encoded by MIR22HG RNA, we show that the peptide is stably expressed in the absence of infection, and upregulated in response to infection, corroborating the prediction of the ribosome profiling results. These data show the utility of perturbation approaches in identifying potentially relevant novel molecules encoded in the genome
Stress-Energy Tensor for the Massless Spin 1/2 Field in Static Black Hole Spacetimes
The stress-energy tensor for the massless spin 1/2 field is numerically
computed outside and on the event horizons of both charged and uncharged static
non-rotating black holes, corresponding to the Schwarzschild,
Reissner-Nordstrom and extreme Reissner-Nordstr\"om solutions of Einstein's
equations. The field is assumed to be in a thermal state at the black hole
temperature. Comparison is made between the numerical results and previous
analytic approximations for the stress-energy tensor in these spacetimes. For
the Schwarzschild (charge zero) solution, it is shown that the stress-energy
differs even in sign from the analytic approximation. For the
Reissner-Nordstrom and extreme Reissner-Nordstrom solutions, divergences
predicted by the analytic approximations are shown not to exist.Comment: 5 pages, 4 figures, additional discussio
SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud
Background: Single cell omics technologies present unique opportunities for biomedical and life sciences from lab to clinic, but the high dimensional nature of such data poses challenges for computational analysis and interpretation. Furthermore, FAIR data management as well as data privacy and security become crucial when working with clinical data, especially in cross-institutional and translational settings. Existing solutions are either bound to the desktop of one researcher or come with dependencies on vendor-specific technology for cloud storage or user authentication. Results: To facilitate analysis and interpretation of single-cell data by users without bioinformatics expertise, we present SCelVis, a flexible, interactive and user-friendly app for web-based visualization of pre-processed single-cell data. Users can survey multiple interactive visualizations of their single cell expression data and cell annotation, and download raw or processed data for further offline analysis. SCelVis can be run both on the desktop and cloud systems, accepts input from local and various remote sources using standard and open protocols, and allows for hosting data in the cloud and locally. Methods: SCelVis is implemented in Python using Dash by Plotly. It is available as a standalone application as a Python package, via Conda/Bioconda and as a Docker image. All components are available as open source under the permissive MIT license and are based on open standards and interfaces, enabling further development and integration with third party pipelines and analysis components. The GitHub repository is https://github.com/bihealth/scelvis
SCelVis: exploratory single cell data analysis on the desktop and in the cloud
BACKGROUND: Single cell omics technologies present unique opportunities for biomedical and life sciences from lab to clinic, but the high dimensional nature of such data poses challenges for computational analysis and interpretation. Furthermore, FAIR data management as well as data privacy and security become crucial when working with clinical data, especially in cross-institutional and translational settings. Existing solutions are either bound to the desktop of one researcher or come with dependencies on vendor-specific technology for cloud storage or user authentication. RESULTS: To facilitate analysis and interpretation of single-cell data by users without bioinformatics expertise, we present SCelVis, a flexible, interactive and user-friendly app for web-based visualization of pre-processed single-cell data. Users can survey multiple interactive visualizations of their single cell expression data and cell annotation, define cell groups by filtering or manual selection and perform differential gene expression, and download raw or processed data for further offline analysis. SCelVis can be run both on the desktop and cloud systems, accepts input from local and various remote sources using standard and open protocols, and allows for hosting data in the cloud and locally. We test and validate our visualization using publicly available scRNA-seq data. METHODS: SCelVis is implemented in Python using Dash by Plotly. It is available as a standalone application as a Python package, via Conda/Bioconda and as a Docker image. All components are available as open source under the permissive MIT license and are based on open standards and interfaces, enabling further development and integration with third party pipelines and analysis components. The GitHub repository is https://github.com/bihealth/scelvis
Emergence of robust nucleosome patterns from an interplay of positioning mechanisms
Proper positioning of nucleosomes in eukaryotic cells is determined by a complex interplay of factors, including nucleosome-nucleosome interactions, DNA sequence, and active chromatin remodeling. Yet, characteristic features of nucleosome positioning, such as geneaveraged nucleosome patterns, are surprisingly robust across perturbations, conditions, and species. Here, we explore how this robustness arises despite the underlying complexity. We leverage mathematical models to show that a large class of positioning mechanisms merely affects the quantitative characteristics of qualitatively robust positioning patterns. We demonstrate how statistical positioning emerges as an effective description from the complex interplay of different positioning mechanisms, which ultimately only renormalize the model parameter quantifying the effective softness of nucleosomes. This renormalization can be species-specific, rationalizing a puzzling discrepancy between the effective nucleosome softness of S. pombe and S. cerevisiae. More generally, we establish a quantitative framework for dissecting the interplay of different nucleosome positioning determinants
A freely relaxing polymer remembers how it was straightened
The relaxation of initially straight semiflexible polymers has been discussed
mainly with respect to the longest relaxation time. The biologically relevant
non-equilibrium dynamics on shorter times is comparatively poorly understood,
partly because "initially straight" can be realized in manifold ways. Combining
Brownian dynamics simulations and systematic theory, we demonstrate how
different experimental preparations give rise to specific short-time and
universal long-time dynamics. We also discuss boundary effects and the onset of
the stretch--coil transition.Comment: 14 pages, 5 figures, 3 table
Pinwheel stabilization by ocular dominance segregation
We present an analytical approach for studying the coupled development of
ocular dominance and orientation preference columns. Using this approach we
demonstrate that ocular dominance segregation can induce the stabilization and
even the production of pinwheels by their crystallization in two types of
periodic lattices. Pinwheel crystallization depends on the overall dominance of
one eye over the other, a condition that is fulfilled during early cortical
development. Increasing the strength of inter-map coupling induces a transition
from pinwheel-free stripe solutions to intermediate and high pinwheel density
states.Comment: 10 pages, 4 figure
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