Hydrogen properties and charges in a sub-1.2 Å resolution cryo-EM structure revealed by a cold field emission beam

The cold field emission (CFE) beam produces the less-attenuated contrast transfer function of electron microscopy, thereby enhancing high-resolution signals and this particularly benefits higher-resolution single particle cryogenic electron microscopy. Here, we present a sub-1.2 Å resolution structure of a standard protein sample, apoferritin. Image data were collected with the CFE beam in a high-throughput scheme while minimizing beam tilt deviations from the coma-free axis. A difference map reveals positive densities for most hydrogen atoms in the core region of the protein complex including those in water molecules, while negative densities around acidic amino-acid side chains likely represent negative charges. The position of the hydrogen densities depends on parent bonded-atom type, which is validated by an estimated level of coordinate errors.

High-cadence observations and variable spin behaviour of magnetar Swift J1818.0−1607 after its outburst

ABSTRACT We report on multifrequency radio observations of the new magnetar Swift J1818.0−1607, following it for more than one month with high cadence. The observations commenced less than 35 h after its registered first outburst. We obtained timing, polarization, and spectral information. Swift J1818.0−1607 has an unusually steep spectrum for a radio emitting magnetar and also has a relatively narrow and simple pulse profile. The position angle swing of the polarization is flat over the pulse profile, possibly suggesting that our line of sight grazes the edge of the emission beam. This may also explain the steep spectrum. The spin evolution shows large variation in the spin-down rate, associated with four distinct timing events over the course of our observations. Those events may be related to the appearance and disappearance of a second pulse component. The first timing event coincides with our actual observations, while we did not detect significant changes in the emission properties that could reveal further magnetospheric changes. Characteristic ages inferred from the timing measurements over the course of months vary by nearly an order of magnitude. A longer-term spin-down measurement over approximately 100 d suggests a characteristic age of about 500 yr, larger than previously reported. Though Swift J1818.0−1607 could still be one of the youngest neutron stars (and magnetars) detected so far, we caution using the characteristic age as a true-age indicator given the caveats behind its calculation.

Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release

Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle cryo-electron microscopy (cryo-EM) with a cold-field emission beam. The cryo-EM map reveals a unique structure composed of three capsid proteins Vp25, Vp20, and Vp24. Strikingly Vp25 has a long N-terminal extension, which substantially stabilises the capsid frame of Vp25 and Vp20 subunits. Cryo-EM images also resolve RNA genome leaking from a pentameric protrusion of Vp24 subunits. The structures and observations suggest that genome release occurs through occasional opening of the Vp24 subunits, possibly suppressed to a low frequency by the rigid frame of the other subunits.

On the beam properties of radio pulsars with interpulse emission

ABSTRACT In the canonical picture of pulsars, radio emission arises from a narrow cone centred on the star’s magnetic axis but many basic details remain unclear. We use high-quality polarization data taken with the Parkes radio telescope to constrain the geometry and emission heights of pulsars showing interpulse emission, and include the possibility that emission heights in the main and interpulse may be different. We show that emission heights are low in the centre of the beam, typically less than 3 per cent of the light cylinder radius. The emission beams are underfilled in longitude, with an average profile width only 60 per cent of the maximal beamwidth and there is a strong preference for the visible emission to be located on the trailing part of the beam. We show substantial evidence that the emission heights are larger at the beam edges than in the beam centre. There is some indication that a fan-like emission beam explains the data better than conal structures. Finally, there is a strong correlation between handedness of circular polarization in the main and interpulse profiles, which implies that the hand of circular polarization is determined by the hemisphere of the visible emission.

Arecibo 4.5/1.4/0.33-GHz polarimetric single-pulse emission survey

ABSTRACT We report on an Arecibo 4.5-GHz polarimetric single-pulse survey of the brightest pulsars at high frequency within its sky. The high-frequency profiles are accompanied by a collection of both previously published and unpublished high quality 1.4- and 0.33-GHz observations. Here our analyses and discussion primarily involve the average and statistical properties of the 46 pulsars polarimetric pulse sequences, profile classification and frequency evolution, and polarimetric profiles and peak-occurrence histograms. In most cases both the fractional linear polarization and profile widths decrease with frequency as expected, but there are some exceptions. Similarly, we were able to review and/or extend the profile classifications for this population of pulsars and work out their beaming characteristics quantitatively showing that almost all show properties compatible with the core/double-cone emission beam model. The entirety of these observations’ average profiles are accessible for download.

Numerical study of dynamic noseleaf models in greater horseshoe bats, Rhinolophus ferrumequinum

Echolocating greater horseshoe bats (Rhinolophus ferrumequinum) emit biosonar pulses through nostril. The nostrilis surrounded by sophisticated and delicate appendages, i.e. noseleaf. It is known that the static part of noseleaf can cause different effects on bat biosonar pulse. In addition, the dynmaic noseleaf was found to be able to shape their emission beam. For detailed investigation of the effects of dynamic lancet on the ultrasonic beam, a 3D noseleaf model was constructed using the micro CT scanning of the noseleaf samples, and a simple model was constructed digitally for comparison. The model consists of two parts, for which one is the triangle on the top and the other one is the rectangle at the bottom. Quantitative numerical investigation on the lancet dynamic effect on the ultrasonic beam was performed using finite element analysis for both models.

Long-term observations of pulsars in the globular clusters 47 Tucanae and M15

Multi-decade observing campaigns of the globular clusters 47 Tucanae and M15 have led to an outstanding number of discoveries. Here, we report on the latest results of the long-term observations of the pulsars in these two clusters. For most of the pulsars in 47 Tucanae we have measured, among other things, their higher-order spin period derivatives, which have in turn provided stringent constraints on the physical parameters of the cluster, such as its distance and gravitational potential. For M15, we have studied the relativistic spin precession effect in PSR B2127+11C. We have used full-Stokes observations to model the precession effect, and to constrain the system geometry. We find that the visible beam of the pulsar is swiftly moving away from our line of sight and may very soon become undetectable. On the other hand, we expect to see the opposite emission beam sometime between 2041 and 2053.

Core/Double-Cone Emission-Beam Structure in a Millisecond Pulsar

Slow pulsars show a great deal of qualitative and quantitative regularity in the structure of their radio emission beams as described by the core/double-cone model; however, millisecond pulsars (MSPs) have shown little. It is thus arresting to encounter a 2.7-s MSP with what appears to be a double-cone/core profile—and even more so to find that the arrangement of the cones around the core suggest aberration/retardation emission heights that are very reasonable. This and several other pulsars then represent rare opportunities for analysis and raise questions about why a few MSPs show such orderly beam structure while so many do not.