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

Gendering the careers of young professionals: some early findings from a longitudinal study. in Organizing/theorizing: developments in organization theory and practice

Wonders whether companies actually have employees best interests at heart across physical, mental and spiritual spheres. Posits that most organizations ignore their workforce – not even, in many cases, describing workers as assets! Describes many studies to back up this claim in theis work based on the 2002 Employment Research Unit Annual Conference, in Cardiff, Wales

Follow-up of multi-messenger alerts with the KM3NeT ARCA and ORCA detectors

The strength of multi-messenger astronomy comes from its capability to increase the significance of a detection through the combined observation of events coincident in space and time. This is particularly valuable for transient events, since the use of a narrow time window can allow a reduction of background of the search. In KM3NeT, we are actively monitoring and analysing a variety of external triggers in real-time, including alerts like IceCube neutrinos, HAWC gamma-ray transients, LIGO-Virgo- KAGRA gravitational waves, SNEWS neutrino alerts, and others. In this contribution, we present the follow-up of various external alerts using the comple- mentary capabilities of the two KM3NeT detectors, ORCA (covering the few GeV to few TeV energy range) and ARCA (ranging from sub-TeV energies up to tens of PeV). Both detectors were collecting high-quality data with partial configurations during the period of the studied alerts, which goes from December 2021 until June 2023

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

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

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

By constantly monitoring a very large portion 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, high-energy 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. This paper summarises the results of the followup performed of the ANTARES telescope between January 2014 and February 2022, which corresponds to the end of the data-taking period

Acoustic Positioning for Deep Sea Neutrino Telescopes with a System of Piezo Sensors Integrated into Glass Spheres

Position calibration in the deep sea is typically done by means of acoustic multilateration using three or more acoustic emitters installed at known positions. Rather than using hydrophones as receivers that are exposed to the ambient pressure, the sound signals can be coupled to piezo ceramics glued to the inside of existing containers for electronics or measuring instruments of a deep sea infrastructure. The ANTARES neutrino telescope operated from 2006 until 2022 in the Mediterranean Sea at a depth exceeding 2000m. It comprised nearly 900 glass spheres with 432mm diameter and 15mm thickness, equipped with photomultiplier tubes to detect Cherenkov light from tracks of charged elementary particles. In an experimental setup within ANTARES, piezo sensors have been glued to the inside of such - otherwise empty - glass spheres. These sensors recorded signals from acoustic emitters with frequencies from 46545 to 60235Hz. Two waves propagating through the glass sphere are found as a result of the excitation by the waves in the water. These can be qualitatively associated with symmetric and asymmetric Lamb-like waves of zeroth order: a fast (early) one with $v_e \approx 5$mm/$\mu$s and a slow (late) one with $v_\ell \approx 2$mm/$\mu$s. Taking these findings into account improves the accuracy of the position calibration. The results can be transferred to the KM3NeT neutrino telescope, currently under construction at multiple sites in the Mediterranean Sea, for which the concept of piezo sensors glued to the inside of glass spheres has been adapted for monitoring the positions of the photomultiplier tubes.Comment: submitted to "Experimental Astronomy

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

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