Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure

Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated chromatin emanated from chromosomes is planar and forms multilayered plates. The layer thickness was measured accounting for the contrast transfer function fringes at the plate edges, yielding a width of similar to 7.5 nm, which is compatible with the dimensions of a monolayer of nucleosomes slightly tilted with respect to the layer surface. Individual nucleosomes are visible decorating distorted plates, but typical plates are very dense and nucleosomes are not identifiable as individual units, indicating that they are tightly packed. Two layers in contact are similar to 13 nm thick, which is thinner than the sum of two independent layers, suggesting that nucleosomes in the layers interdigitate. X-ray scattering of whole chromosomes shows a main scattering peak at similar to 6 nm, which can be correlated with the distance between layers and between interdigitating nucleosomes interacting through their faces. These observations support a model where compact chromosomes are composed of many chromatin layers stacked along the chromosome axis

Mira's wind explored in scattering infrared CO lines

We have observed the intermediate regions of the circumstellar envelope of Mira (o Ceti) in photospheric light scattered by three vibration-rotation transitions of the fundamental band of CO, from low-excited rotational levels of the ground vibrational state, at an angular distance of beta = 2"-7" away from the star. The data were obtained with the Phoenix spectrometer mounted on the 4 m Mayall telescope at Kitt Peak. The spatial resolution is approximately 0.5" and seeing limited. Our observations provide absolute fluxes, leading to an independent new estimate of the mass-loss rate of approximately 3e-7 Msun/yr, as derived from a simple analytic wind model. We find that the scattered intensity from the wind of Mira for 2" < beta < 7" decreases as beta^-3, which suggests a time constant mass-loss rate, when averaged over 100 years, over the past 1200 years.Comment: accepted for publication in the Astrophysical Journa

Modelling CO emission from Mira's wind

We have modelled the circumstellar envelope of {\it o} Ceti (Mira) using new observational constraints. These are obtained from photospheric light scattered in near-IR vibrational-rotational lines of circumstellar CO molecules at 4.6 micron: absolute fluxes, the radial dependence of the scattered intensity, and two line ratios. Further observational constraints are provided by ISO observations of far-IR emission lines from highly excited rotational states of the ground vibrational state of CO, and radio observations of lines from rotational levels of low excitation of CO. A code based on the Monte-Carlo technique is used to model the circumstellar line emission. We find that it is possible to model the radio and ISO fluxes, as well as the highly asymmetric radio-line profiles, reasonably well with a spherically symmetric and smooth stellar wind model. However, it is not possible to reproduce the observed NIR line fluxes consistently with a `standard model' of the stellar wind. This is probably due to incorrectly specified conditions of the inner regions of the wind model, since the stellar flux needs to be larger than what is obtained from the standard model at the point of scattering, i.e., the intermediate regions at approximately 100-400 stellar radii (2"-7") away from the star. Thus, the optical depth in the vibrational-rotational lines from the star to the point of scattering has to be decreased. This can be accomplished in several ways. For instance, the gas close to the star (within approximately 2") could be in such a form that light is able to pass through, either due to the medium being clumpy or by the matter being in radial structures (which, further out, developes into more smooth or shell-like structures).Comment: 18 pages, 3 figures, accepted for publication in Ap

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Bispectrum speckle interferometry of IRC+10216: the dynamic evolution of the innermost circumstellar environment from 1995 to 2001

We present new near-infrared (JHK) bispectrum speckle-interferometry monitoring of the carbon star IRC+10216 obtained between 1999 and 2001 with the SAO 6m telescope. The J-, H-, and K-band resolutions are 50mas, 56mas, and 73mas, resp. The total sequence of K-band observations covers now 8 epochs from 1995 to 2001 and shows the dynamic evolution of the inner dust shell. The present observations show that the appearance of the dust shell has considerably changed compared to the epochs of 1995 to 1998. Four main components within a 0.2" radius can be identified in the K-band images. The apparent separation of the two initially brightest components A and B increased from ~191mas in 1995 to ~351mas in 2001. Simultaneously, component B has been fading and almost disappeared in 2000 whereas the initially faint components C and D became brighter (relative to peak intensity). These changes can be related to changes of the optical depth caused, e.g., by mass-loss variations or new dust condensation in the wind. Our 2D radiative transfer model suggests that the observed relative motion of A and B is not consistent with the known terminal wind velocity of 15 km/s. The apparent motion with a deprojected velocity of 19 km/s on average and of recently 27 km/s appears to be caused by adisplacement of the dust density peak due to dust evaporation in the optically thicker and hotter environment. Our monitoring, covering more than 3 pulsation periods, shows that the structural variations are not related to the stellar pulsation cycle in a simple way. This is consistent with the predictions of hydrodynamical models that enhanced dust formation takes place on a timescale of several pulsation periods. The timescale of the fading of component B can well be explained by the formation of new dust in the circumstellar envelope.Comment: 11 pages including 6 PostScript figures; also available from http://www.mpifr-bonn.mpg.de/div/ir-interferometry/publications.html; Astronomy & Astrophysics, in pres

Software Citation Checklist for Developers

This document provides a minimal, generic checklist that developers of software (either open or closed source) used in research can use to ensure they are following good practice around software citation. This will help developers get credit for the software they create, and improve transparency, reproducibility, and reuse

Enzymatic Blockade of the Ubiquitin-Proteasome Pathway

Ubiquitin-dependent processes control much of cellular physiology. We show that expression of a highly active, Epstein-Barr virus-derived deubiquitylating enzyme (EBV-DUB) blocks proteasomal degradation of cytosolic and ER-derived proteins by preemptive removal of ubiquitin from proteasome substrates, a treatment less toxic than the use of proteasome inhibitors. Recognition of misfolded proteins in the ER lumen, their dislocation to the cytosol, and degradation are usually tightly coupled but can be uncoupled by the EBV-DUB: a misfolded glycoprotein that originates in the ER accumulates in association with cytosolic chaperones as a deglycosylated intermediate. Our data underscore the necessity of a DUB activity for completion of the dislocation reaction and provide a new means of inhibition of proteasomal proteolysis with reduced cytotoxicity.National Institutes of Health (U.S.)EMBO (long term Fellowship 2008-379)Boehringer Ingelheim Fond

An HDAC9-MALAT1-BRG1 complex mediates smooth muscle dysfunction in thoracic aortic aneurysm

Thoracic aortic aneurysm (TAA) has been associated with mutations affecting members of the TGF-β signaling pathway, or components and regulators of the vascular smooth muscle cell (VSMC) actomyosin cytoskeleton. Although both clinical groups present similar phenotypes, the existence of potential common mechanisms of pathogenesis remain obscure. Here we show that mutations affecting TGF-β signaling and VSMC cytoskeleton both lead to the formation of a ternary complex comprising the histone deacetylase HDAC9, the chromatin-remodeling enzyme BRG1, and the long noncoding RNA MALAT1. The HDAC9–MALAT1–BRG1 complex binds chromatin and represses contractile protein gene expression in association with gain of histone H3-lysine 27 trimethylation modifications. Disruption of Malat1 or Hdac9 restores contractile protein expression, improves aortic mural architecture, and inhibits experimental aneurysm growth. Thus, we highlight a shared epigenetic pathway responsible for VSMC dysfunction in both forms of TAA, with potential therapeutic implication for other known HDAC9-associated vascular diseases

C-terminal UBA domains protect ubiquitin receptors by preventing initiation of protein degradation

The ubiquitin receptors Rad23 and Dsk2 deliver polyubiquitylated substrates to the proteasome for destruction. The C-terminal ubiquitin-associated (UBA) domain of Rad23 functions as a cis-acting stabilization signal that protects this protein from proteasomal degradation. Here, we provide evidence that the C-terminal UBA domains guard ubiquitin receptors from destruction by preventing initiation of degradation at the proteasome. We show that introduction of unstructured polypeptides that are sufficiently long to function as initiation sites for degradation abrogates the protective effect of UBA domains. Vice versa, degradation of substrates that contain an unstructured extension can be attenuated by the introduction of C-terminal UBA domains. Our study gains insight into the molecular mechanism responsible for the protective effect of UBA domains and explains how ubiquitin receptors can shuttle substrates to the proteasome without themselves becoming subject to proteasomal degradation