Adenovirus E1A Activation Domain Regulates H3 Acetylation Affecting Varied Steps in Transcription at Different Viral Promoters.

How histone acetylation promotes transcription is not clearly understood. Here, we confirm an interaction between p300 and the adenovirus 2 large E1A activation domain (AD) and map the interacting regions in E1A by observing colocalization at an integrated lacO array of fusions of LacI-mCherry to E1A fragments with YFP-p300. Viruses with mutations in E1A subdomains were constructed and analyzed for kinetics of early viral RNA expression and association of acetylated H3K9, K18, K27, TBP, and RNA polymerase II (Pol II) across the viral genome. The results indicate that this E1A interaction with p300 is required for H3K18 and H3K27 acetylation at the E2early, E3, and E4 promoters and is required for TBP and Pol II association with the E2early promoter. In contrast, H3K18/27 acetylation was not required for TBP and Pol II association with the E3 and E4 promoters but was required for E4 transcription at a step subsequent to Pol II preinitiation complex assembly.IMPORTANCE Despite a wealth of data associating promoter and enhancer region histone N-terminal tail lysine acetylation with transcriptional activity, there are relatively few examples of studies that establish causation between these histone posttranslational modifications and transcription. While hypoacetylation of histone H3 lysines 18 and 27 is associated with repression, the step(s) in the overall process of transcription that is blocked at a hypoacetylated promoter is not clearly established in most instances. Studies presented here confirm that the adenovirus 2 large E1A protein activation domain interacts with p300, as reported previously (P. Pelka, J. N. G. Ablack, J. Torchia, A. S. Turnell, R. J. A. Grand, J. S. Mymryk, Nucleic Acids Res 37:1095-1106, 2009, https://doi.org/10.1093/nar/gkn1057), and that the resulting acetylation of H3K18/27 affects varied steps in transcription at different viral promoters

Online Search Tool for Graphical Patterns in Electronic Band Structures

We present an online graphical pattern search tool for electronic band structure data contained within the Organic Materials Database (OMDB) available at https://omdb.diracmaterials.org/search/pattern. The tool is capable of finding user-specified graphical patterns in the collection of thousands of band structures from high-throughput ab initio calculations in the online regime. Using this tool, it only takes a few seconds to find an arbitrary graphical pattern within the ten electronic bands near the Fermi level for 26,739 organic crystals. The tool can be used to find realizations of functional materials characterized by a specific pattern in their electronic structure, for example, Dirac materials, characterized by a linear crossing of bands; topological insulators, characterized by a "Mexican hat" pattern or an effectively free electron gas, characterized by a parabolic dispersion. The source code of the developed tool is freely available at https://github.com/OrganicMaterialsDatabase/EBS-search and can be transferred to any other electronic band structure database. The approach allows for an automatic online analysis of a large collection of band structures where the amount of data makes its manual inspection impracticable.Comment: 8 pages, 8 figure

Tracking Single Particles using Surface Plasmon Leakage Radiation Speckle

Label free tracking of small bio-particles such as proteins or viruses is of great utility in the study of biological processes, however such experiments are frequently hindered by weak signal strengths and a susceptibility to scattering impurities. To overcome these problems we here propose a novel technique leveraging the enhanced sensitivity of both interferometric detection and the strong field confinement of surface plasmons. Specifically, we show that interference between the field scattered by an analyte particle and a speckle reference field, derived from random scattering of surface plasmons propagating on a rough metal film, enables particle tracking with sub-wavelength accuracy. We present the analytic framework of our technique and verify its robustness to noise through Monte Carlo simulations.Comment: Journal of Lightwave Technolog

Sensitivity and dimensionality of atomic environment representations used for machine learning interatomic potentials

Faithfully representing chemical environments is essential for describing materials and molecules with machine learning approaches. Here, we present a systematic classification of these representations and then investigate (i) the sensitivity to perturbations and (ii) the effective dimensionality of a variety of atomic environment representations and over a range of material datasets. Representations investigated include atom centered symmetry functions, Chebyshev Polynomial Symmetry Functions (CHSF), smooth overlap of atomic positions, many-body tensor representation, and atomic cluster expansion. In area (i), we show that none of the atomic environment representations are linearly stable under tangential perturbations and that for CHSF, there are instabilities for particular choices of perturbation, which we show can be removed with a slight redefinition of the representation. In area (ii), we find that most representations can be compressed significantly without loss of precision and, further, that selecting optimal subsets of a representation method improves the accuracy of regression models built for a given dataset

Presynaptic Translation: Stepping Out of the Postsynaptic Shadow

The ability of the nervous system to convert transient experiences into long-lasting structural changes at the synapse relies upon protein synthesis. It has become increasingly clear that a critical subset of this synthesis occurs within the synaptic compartment. While this process has been extensively characterized in the postsynaptic compartment, the contribution of local translation to presynaptic function remains largely unexplored. However, recent evidence highlights the potential importance of translation within the presynaptic compartment. Work in cultured neurons has shown that presynaptic translation occurs specifically at synapses undergoing long-term plasticity and may contribute to the maintenance of nascent synapses. Studies from our laboratory have demonstrated that Fragile X proteins, which regulate mRNA localization and translation, are expressed at the presynaptic apparatus. Further, mRNAs encoding presynaptic proteins traffic into axons. Here we discuss recent advances in the study of presynaptic translation as well as the challenges confronting the field. Understanding the regulation of presynaptic function by local protein synthesis promises to shed new light on activity-dependent modification of synaptic architecture