The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications

Background: Rice is an important staple food and, with the smallest cereal genome, serves as a reference species for studies on the evolution of cereals and other grasses. Therefore, decoding its entire genome will be a prerequisite for applied and basic research on this species and all other cereals. Results: We have determined and analyzed the complete sequences of two of its chromosomes, 11 and 12, which total 55.9 Mb (14.3% of the entire genome length), based on a set of overlapping clones. A total of 5,993 non-transposable element related genes are present on these chromosomes. Among them are 289 disease resistance-like and 28 defense-response genes, a higher proportion of these categories than on any other rice chromosome. A three-Mb segment on both chromosomes resulted from a duplication 7.7 million years ago (mya), the most recent large-scale duplication in the rice genome. Paralogous gene copies within this segmental duplication can be aligned with genomic assemblies from sorghum and maize. Although these gene copies are preserved on both chromosomes, their expression patterns have diverged. When the gene order of rice chromosomes 11 and 12 was compared to wheat gene loci, significant synteny between these orthologous regions was detected, illustrating the presence of conserved genes alternating with recently evolved genes. Conclusion: Because the resistance and defense response genes, enriched on these chromosomes relative to the whole genome, also occur in clusters, they provide a preferred target for breeding durable disease resistance in rice and the isolation of their allelic variants. The recent duplication of a large chromosomal segment coupled with the high density of disease resistance gene clusters makes this the most recently evolved part of the rice genome. Based on syntenic alignments of these chromosomes, rice chromosome 11 and 12 do not appear to have resulted from a single whole-genome duplication event as previously suggested

Charcot-Marie-Tooth–Linked Mutant GARS Is Toxic to Peripheral Neurons Independent of Wild-Type GARS Levels

Charcot-Marie-Tooth disease type 2D (CMT2D) is a dominantly inherited peripheral neuropathy caused by missense mutations in the glycyl-tRNA synthetase gene (GARS). In addition to GARS, mutations in three other tRNA synthetase genes cause similar neuropathies, although the underlying mechanisms are not fully understood. To address this, we generated transgenic mice that ubiquitously over-express wild-type GARS and crossed them to two dominant mouse models of CMT2D to distinguish loss-of-function and gain-of-function mechanisms. Over-expression of wild-type GARS does not improve the neuropathy phenotype in heterozygous Gars mutant mice, as determined by histological, functional, and behavioral tests. Transgenic GARS is able to rescue a pathological point mutation as a homozygote or in complementation tests with a Gars null allele, demonstrating the functionality of the transgene and revealing a recessive loss-of-function component of the point mutation. Missense mutations as transgene-rescued homozygotes or compound heterozygotes have a more severe neuropathy than heterozygotes, indicating that increased dosage of the disease-causing alleles results in a more severe neurological phenotype, even in the presence of a wild-type transgene. We conclude that, although missense mutations of Gars may cause some loss of function, the dominant neuropathy phenotype observed in mice is caused by a dose-dependent gain of function that is not mitigated by over-expression of functional wild-type protein

Constraints on the intergalactic magnetic field using Fermi-LAT and H.E.S.S. blazar observations

Magnetic fields in galaxies and galaxy clusters are believed to be the result of the amplification of intergalactic seed fields during the formation of large-scale structures in the universe. However, the origin, strength, and morphology of this intergalactic magnetic field (IGMF) remain unknown. Lower limits on (or indirect detection of) the IGMF can be obtained from observations of high-energy gamma rays from distant blazars. Gamma rays interact with the extragalactic background light to produce electron-positron pairs, which can subsequently initiate electromagnetic cascades. The $\gamma$-ray signature of the cascade depends on the IGMF since it deflects the pairs. Here we report on a new search for this cascade emission using a combined data set from the Fermi Large Area Telescope and the High Energy Stereoscopic System. Using state-of-the-art Monte Carlo predictions for the cascade signal, our results place a lower limit on the IGMF of $B > 7.1\times10^{-16}$ G for a coherence length of 1 Mpc even when blazar duty cycles as short as 10 yr are assumed. This improves on previous lower limits by a factor of 2. For longer duty cycles of $10^4$ ($10^7$) yr, IGMF strengths below $1.8\times10^{-14}$ G ($3.9\times10^{-14}$ G) are excluded, which rules out specific models for IGMF generation in the early universe.Comment: 20 pages, 7 figures, 4 tables. Accepted for publication in ApJ Letters. Auxiliary data is provided in electronic format at https://zenodo.org/record/801431

Limits on the nuclearite flux using the ANTARES neutrino telescope

In this work, a search for nuclearites of strange quark matter by using nine years of ANTARES data taken in the period 2009-2017 is presented. The passage through matter of these particles is simulated %according to the model of de R\'{u}jula and Glashow taking into account a detailed description of the detector response to nuclearites and of the data acquisition conditions. A down-going flux of cosmic nuclearites with Galactic velocities ($\beta = 10^{-3}$) was considered for this study. The mass threshold for detecting these particles at the detector level is \mbox{ $4 \times 10^{13}$ GeV/c$^{2}$}. Upper limits on the nuclearite flux for masses up to $10^{17}$ GeV/c$^{2}$ at the level of $\sim 5 \times 10^{-17}$ cm$^{-2}$ s$^{-1}$ sr$^{-1}$ are obtained. These are the first upper limits on nuclearites established with a neutrino telescope and the most stringent ever set for Galactic velocities.Comment: 17 pages, 7 figure

Review of the online analyses of multi-messenger alerts and electromagnetic transient events with the ANTARES neutrino telescope

By constantly monitoring at least one complete hemisphere of the sky, neutrino telescopes are well designed to detect neutrinos emitted by transient astrophysical events. Real-time searches with the ANTARES telescope have been performed to look for neutrino candidates coincident with gamma-ray bursts detected by the Swift and Fermi satellites, highenergy neutrino events registered by IceCube, transient events from blazars monitored by HAWC, photon-neutrino coincidences by AMON notices and gravitational wave candidates observed by LIGO/Virgo. By requiring temporal coincidence, this approach increases the sensitivity and the significance of a potential discovery. Thanks to the good angular accuracy of neutrino candidates reconstructed with the ANTARES telescope, a coincident detection can also improve the positioning area of non-well localised triggers such as those detected by gravitational wave interferometers. This paper summarises the results of the follow-up performed by the ANTARES telescope between 01/2014 and 02/2022, which corresponds to the end of the data taking period.Comment: 21 pages, 10 figures, JCAP08 (2023) 072 (19 p

TeV flaring activity of the AGN PKS 0625-354 in November 2018

Most $\gamma$-ray detected active galactic nuclei are blazars with one of their relativistic jets pointing towards the Earth. Only a few objects belong to the class of radio galaxies or misaligned blazars. Here, we investigate the nature of the object PKS 0625-354, its $\gamma$-ray flux and spectral variability and its broad-band spectral emission with observations from H.E.S.S., Fermi-LAT, Swift-XRT, and UVOT taken in November 2018. The H.E.S.S. light curve above 200 GeV shows an outburst in the first night of observations followed by a declining flux with a halving time scale of 5.9h. The $\gamma\gamma$-opacity constrains the upper limit of the angle between the jet and the line of sight to $\sim10^\circ$. The broad-band spectral energy distribution shows two humps and can be well fitted with a single-zone synchrotron self Compton emission model. We conclude that PKS 0625-354, as an object showing clear features of both blazars and radio galaxies, can be classified as an intermediate active galactic nuclei. Multi-wavelength studies of such intermediate objects exhibiting features of both blazars and radio galaxies are sparse but crucial for the understanding of the broad-band emission of $\gamma$-ray detected active galactic nuclei in general.Comment: 9 pages, 6 figures, accepted for publication in Astronomy & Astrophysic

HESS J1809−-193: a halo of escaped electrons around a pulsar wind nebula?

Context. HESS J1809$-$193 is an unassociated very-high-energy $\gamma$-ray source located on the Galactic plane. While it has been connected to the nebula of the energetic pulsar PSR J1809$-$1917, supernova remnants and molecular clouds present in the vicinity also constitute possible associations. Recently, the detection of $\gamma$-ray emission up to energies of $\sim$100 TeV with the HAWC observatory has led to renewed interest in HESS J1809$-$193. Aims. We aim to understand the origin of the $\gamma$-ray emission of HESS J1809$-$193. Methods. We analysed 93.2 h of data taken on HESS J1809$-$193 above 0.27 TeV with the High Energy Stereoscopic System (H.E.S.S.), using a multi-component, three-dimensional likelihood analysis. In addition, we provide a new analysis of 12.5 yr of Fermi-LAT data above 1 GeV within the region of HESS J1809$-$193. The obtained results are interpreted in a time-dependent modelling framework. Results. For the first time, we were able to resolve the emission detected with H.E.S.S. into two components: an extended component that exhibits a spectral cut-off at $\sim$13 TeV, and a compact component that is located close to PSR J1809$-$1917 and shows no clear spectral cut-off. The Fermi-LAT analysis also revealed extended $\gamma$-ray emission, on scales similar to that of the extended H.E.S.S. component. Conclusions. Our modelling indicates that based on its spectrum and spatial extent, the extended H.E.S.S. component is likely caused by inverse Compton emission from old electrons that form a halo around the pulsar wind nebula. The compact component could be connected to either the pulsar wind nebula or the supernova remnant and molecular clouds. Due to its comparatively steep spectrum, modelling the Fermi-LAT emission together with the H.E.S.S. components is not straightforward. (abridged)Comment: 14 pages, 10 figures. Accepted for publication in A&A. Corresponding authors: Vikas Joshi, Lars Mohrman

Search for neutrino counterparts to the gravitational wave sources from O3 catalogues with the ANTARES detector

Since 2015 the LIGO and Virgo interferometers have detected gravitational waves from almost one hundred coalescences of compact objects (black holes and neutron stars). This article presents the results of a search performed with data from the ANTARES telescope to identify neutrino counterparts to the gravitational wave sources detected during the third LIGO/Virgo observing run and reported in the catalogues GWTC-2, GWTC-2.1, and GWTC-3. This search is sensitive to all-sky neutrinos of all flavours and of energies $>100\,$GeV, thanks to the inclusion of both track-like events (mainly induced by $\nu_\mu$ charged-current interactions) and shower-like events (induced by other interaction types). Neutrinos are selected if they are detected within $\pm 500\,$s from the GW merger and with a reconstructed direction compatible with its sky localisation. No significant excess is found for any of the 80 analysed GW events, and upper limits on the neutrino emission are derived. Using the information from the GW catalogues and assuming isotropic emission, upper limits on the total energy $E_{\rm tot, \nu}$ and on the fraction of the total energy budget $f_\nu = E_{\rm tot, \nu}/E_{\rm rad}$ emitted as neutrinos of all flavours are also computed. Finally, a stacked analysis of all the 72 binary black hole mergers (respectively the 7 neutron star - black hole merger candidates) has been performed to constrain the typical neutrino emission within this population, leading to the limits: $E_{\rm tot, \nu} < 4.0 \times 10^{53}\,$erg and $f_\nu < 0.15$ (respectively, $E_{\rm tot, \nu} < 3.2 \times 10^{53}\,$erg and $f_\nu < 0.88$) for $E^{-2}$ spectrum and isotropic emission. Other assumptions including softer spectra and non-isotropic scenarios have also been tested.Comment: 13 pages, 4 figure

Searches for neutrinos in the direction of radio-bright blazars with the ANTARES telescope

Active galaxies, especially blazars, are among the most promising neutrino source candidates. To date, ANTARES searches for these objects considered GeV-TeV $\gamma$-ray bright blazars. Here, a statistically complete radio-bright blazar sample is used as the target for searches of origins of neutrinos collected by the ANTARES neutrino telescope over 13 years of operation. The hypothesis of a neutrino-blazar directional correlation is tested by pair counting and by a complementary likelihood-based approach. The resulting post-trial $p$-value is $3.0\%$ ($2.2\sigma$ in the two-sided convention), possibly indicating a correlation. Additionally, a time-dependent analysis is performed to search for temporal clustering of neutrino candidates as a mean of detecting neutrino flares in blazars. None of the investigated sources alone reaches a significant flare detection level. However, the presence of 18 sources with a pre-trial significance above $3\sigma$ indicates a $p=1.4\%$ ($2.5\sigma$ in the two-sided convention) detection of a time-variable neutrino flux. An \textit{a posteriori} investigation reveals an intriguing temporal coincidence of neutrino, radio, and $\gamma$-ray flares of the J0242+1101 blazar at a $p=0.5\%$ ($2.9\sigma$ in the two-sided convention) level. Altogether, the results presented here suggest a possible connection of neutrino candidates detected by the ANTARES telescope with radio-bright blazars

H.E.S.S. follow-up observations of GRB221009A

GRB221009A is the brightest gamma-ray burst ever detected. To probe the very-high-energy (VHE, $>$\!100 GeV) emission, the High Energy Stereoscopic System (H.E.S.S.) began observations 53 hours after the triggering event, when the brightness of the moonlight no longer precluded observations. We derive differential and integral upper limits using H.E.S.S. data from the third, fourth, and ninth nights after the initial GRB detection, after applying atmospheric corrections. The combined observations yield an integral energy flux upper limit of $\Phi_\mathrm{UL}^{95\%} = 9.7 \times 10^{-12}~\mathrm{erg\,cm^{-2}\,s^{-1}}$ above $E_\mathrm{thr} = 650$ GeV. The constraints derived from the H.E.S.S. observations complement the available multiwavelength data. The radio to X-ray data are consistent with synchrotron emission from a single electron population, with the peak in the SED occurring above the X-ray band. Compared to the VHE-bright GRB190829A, the upper limits for GRB221009A imply a smaller gamma-ray to X-ray flux ratio in the afterglow. Even in the absence of a detection, the H.E.S.S. upper limits thus contribute to the multiwavelength picture of GRB221009A, effectively ruling out an IC dominated scenario.Comment: 10 pages, 4 figures. Accepted for publication in APJL. Corresponding authors: J. Damascene Mbarubucyeye, H. Ashkar, S. J. Zhu, B. Reville, F. Sch\"ussle