295 research outputs found
Family Size Evolution in Drosophila Chemosensory Gene Families: A Comparative Analysis with a Critical Appraisal of Methods
Gene turnover rates and the evolution of gene family sizes are important aspects of genome evolution. Here, we use curated sequence data of the major chemosensory gene families from Drosophila-the gustatory receptor, odorant receptor, ionotropic receptor, and odorant-binding protein families-to conduct a comparative analysis among families, exploring different methods to estimate gene birth and death rates, including an ad hoc simulation study. Remarkably, we found that the state-of-the-art methods may produce very different rate estimates, which may lead to disparate conclusions regarding the evolution of chemosensory gene family sizes in Drosophila. Among biological factors, we found that a peculiarity of D. sechellia's gene turnover rates was a major source of bias in global estimates, whereas gene conversion had negligible effects for the families analyzed herein. Turnover rates vary considerably among families, subfamilies, and ortholog groups although all analyzed families were quite dynamic in terms of gene turnover. Computer simulations showed that the methods that use ortholog group information appear to be the most accurate for the Drosophila chemosensory families. Most importantly, these results reveal the potential of rate heterogeneity among lineages to severely bias some turnover rate estimation methods and the need of further evaluating the performance of these methods in a more diverse sampling of gene families and phylogenetic contexts. Using branch-specific codon substitution models, we find further evidence of positive selection in recently duplicated genes, which attests to a nonneutral aspect of the gene birth-and-death process
Female Behaviour Drives Expression and Evolution of Gustatory Receptors in Butterflies
Secondary plant compounds are strong deterrents of insect oviposition and feeding, but may also be attractants for specialist herbivores. These insect-plant interactions are mediated by insect gustatory receptors (Grs) and olfactory receptors (Ors). An analysis of the reference genome of the butterfly Heliconius melpomene, which feeds on passion-flower vines (Passiflora spp.), together with whole-genome sequencing within the species and across the Heliconius phylogeny has permitted an unprecedented opportunity to study the patterns of gene duplication and copy-number variation (CNV) among these key sensory genes. We report in silico gene predictions of 73 Gr genes in the H. melpomene reference genome, including putative CO2, sugar, sugar alcohol, fructose, and bitter receptors. The majority of these Grs are the result of gene duplications since Heliconius shared a common ancestor with the monarch butterfly or the silkmoth. Among Grs but not Ors, CNVs are more common within species in those gene lineages that have also duplicated over this evolutionary time-scale, suggesting ongoing rapid gene family evolution. Deep sequencing (∼1 billion reads) of transcriptomes from proboscis and labial palps, antennae, and legs of adult H. melpomene males and females indicates that 67 of the predicted 73 Gr genes and 67 of the 70 predicted Or genes are expressed in these three tissues. Intriguingly, we find that one-third of all Grs show female-biased gene expression (n = 26) and nearly all of these (n = 21) are Heliconius-specific Grs. In fact, a significant excess of Grs that are expressed in female legs but not male legs are the result of recent gene duplication. This difference in Gr gene expression diversity between the sexes is accompanied by a striking sexual dimorphism in the abundance of gustatory sensilla on the forelegs of H. melpomene, suggesting that female oviposition behaviour drives the evolution of new gustatory receptors in butterfly genomes
Deep sea tests of a prototype of the KM3NeT digital optical module
The first prototype of a photo-detection unit of the future KM3NeT neutrino telescope has been deployed in the deepwaters of the Mediterranean Sea. This digital optical module has a novel design with a very large photocathode area segmented by the use of 31 three inch photomultiplier tubes. It has been integrated in the ANTARES detector for in-situ testing and validation. This paper reports on the first months of data taking and rate measurements. The analysis results highlight the capabilities of the new module design in terms of background suppression and signal recognition. The directionality of the optical module enables the recognition of multiple Cherenkov photons from the same (40)Kdecay and the localisation of bioluminescent activity in the neighbourhood. The single unit can cleanly identify atmospheric muons and provide sensitivity to the muon arrival directions
Letter of intent for KM3NeT 2.0
The main objectives of the KM3NeT Collaboration are
(
i
)
the discovery and
subsequent observation of high-energy neutrino sources in the Universe and
(
ii
)
the determination of the mass hierarchy of neutrinos. These objectives are
strongly motivated by two recent important discoveries, namely:
(
1
)
the high-
energy astrophysical neutrino signal reported by IceCube and
(
2
)
the sizable
contribution of electron neutrinos to the third neutrino mass eigenstate as
reported by Daya Bay, Reno and others. To meet these objectives, the
KM3NeT Collaboration plans to build a new Research Infrastructure con-
sisting of a network of deep-sea neutrino telescopes in the Mediterranean Sea.
A phased and distributed implementation is pursued which maximises the
access to regional funds, the availability of human resources and the syner-
gistic opportunities for the Earth and sea sciences community. Three suitable
deep-sea sites are selected, namely off-shore Toulon
(
France
)
, Capo Passero
(
Sicily, Italy
)
and Pylos
(
Peloponnese, Greece
)
. The infrastructure will consist
of three so-called building blocks. A building block comprises 115 strings,
each string comprises 18 optical modules and each optical module comprises
31 photo-multiplier tubes. Each building block thus constitutes a three-
dimensional array of photo sensors that can be used to detect the Cherenkov
light produced by relativistic particles emerging from neutrino interactions.
Two building blocks will be sparsely con
fi
gured to fully explore the IceCube
signal with similar instrumented volume, different methodology, improved
resolution and complementary
fi
eld of view, including the galactic plane. One
building block will be densely con
fi
gured to precisely measure atmospheric
neutrino oscillations.
Original content from this work may be used under the ter
The Control Unit of the KM3NeT Data Acquisition System
The KM3NeT Collaboration runs a multi-site neutrino observatory in the Mediterranean Sea. Water Cherenkov particle detectors, deep in the sea and far off the coasts of France and Italy, are already taking data while incremental construction progresses. Data Acquisition Control software is operating off-shore detectors as well as testing and qualification stations for their components. The software, named Control Unit, is highly modular. It can undergo upgrades and reconfiguration with the acquisition running. Interplay with the central database of the Collaboration is obtained in a way that allows for data taking even if Internet links fail. In order to simplify the management of computing resources in the long term, and to cope with possible hardware failures of one or more computers, the KM3NeT Control Unit software features a custom dynamic resource provisioning and failover technology, which is especially important for ensuring continuity in case of rare transient events in multi-messenger astronomy. The software architecture relies on ubiquitous tools and broadly adopted technologies and has been successfully tested on several operating systems
Probing invisible neutrino decay with KM3NeT-ORCA
In the era of precision measurements of the neutrino oscillation parameters,
upcoming neutrino experiments will also be sensitive to physics beyond the
Standard Model. KM3NeT/ORCA is a neutrino detector optimised for measuring
atmospheric neutrinos from a few GeV to around 100 GeV. In this paper, the
sensitivity of the KM3NeT/ORCA detector to neutrino decay has been explored. A
three-flavour neutrino oscillation scenario, where the third neutrino mass
state decays into an invisible state, e.g. a sterile neutrino, is
considered. We find that KM3NeT/ORCA would be sensitive to invisible neutrino
decays with ~ at confidence
level, assuming true normal ordering. Finally, the impact of neutrino decay on
the precision of KM3NeT/ORCA measurements for ,
and mass ordering have been studied. No significant effect of neutrino decay on
the sensitivity to these measurements has been found.Comment: 27 pages, 14 figures, bibliography updated, typos correcte
Embedded Software of the KM3NeT Central Logic Board
The KM3NeT Collaboration is building and operating two deep sea neutrino
telescopes at the bottom of the Mediterranean Sea. The telescopes consist of
latices of photomultiplier tubes housed in pressure-resistant glass spheres,
called digital optical modules and arranged in vertical detection units. The
two main scientific goals are the determination of the neutrino mass ordering
and the discovery and observation of high-energy neutrino sources in the
Universe. Neutrinos are detected via the Cherenkov light, which is induced by
charged particles originated in neutrino interactions. The photomultiplier
tubes convert the Cherenkov light into electrical signals that are acquired and
timestamped by the acquisition electronics. Each optical module houses the
acquisition electronics for collecting and timestamping the photomultiplier
signals with one nanosecond accuracy. Once finished, the two telescopes will
have installed more than six thousand optical acquisition nodes, completing one
of the more complex networks in the world in terms of operation and
synchronization. The embedded software running in the acquisition nodes has
been designed to provide a framework that will operate with different hardware
versions and functionalities. The hardware will not be accessible once in
operation, which complicates the embedded software architecture. The embedded
software provides a set of tools to facilitate remote manageability of the
deployed hardware, including safe reconfiguration of the firmware. This paper
presents the architecture and the techniques, methods and implementation of the
embedded software running in the acquisition nodes of the KM3NeT neutrino
telescopes
Implementation and first results of the KM3NeT real-time core-collapse supernova neutrino search
The authors acknowledge the financial support of the funding agencies: Agence Nationale de la Recherche (contract ANR-15-CE31-0020), Centre National de la Recherche Scientifique (CNRS), Commission Europeenne (FEDER fund and Marie Curie Program), Institut Universitaire de France (IUF), LabEx UnivEarthS (ANR-10-LABX-0023 and ANR-18-IDEX-0001), Paris ile-de-France Region, France; Shota Rustaveli National Science Foundation of Georgia (SRNSFG, FR-18-1268), Georgia; Deutsche Forschungsgemeinschaft (DFG), Germany; The General Secretariat of Research and Technology (GSRT), Greece; Istituto Nazionale di Fisica Nucleare (INFN), Ministero dell'Universita e della Ricerca (MIUR), PRIN 2017 program (Grant NAT-NET 2017W4HA7S) Italy; Ministry of Higher Education Scientific Research and Professional Training, ICTP through Grant AF-13, Morocco; Nederlandse organisatie voor Wetenschappelijk Onderzoek (NWO), the Netherlands; The National Science Centre, Poland (2015/18/E/ST2/00758); National Authority for Scientific Research (ANCS), Romania; Ministerio de Ciencia, Innovacion, Investigacion y Universidades (MCIU): Programa Estatal de Generacion de Conocimiento (refs. PGC2018-096663-B-C41, -A-C42, -B-C43, -B-C44) (MCIU/FEDER), Generalitat Valenciana: Prometeo (PROMETEO/2020/019), Grisolia (ref. GRISOLIA/2018/119) and GenT (refs. CIDEGENT/2018/034, /2019/043, /2020/049) programs, Junta de Andalucia (ref. A-FQM-053-UGR18), La Caixa Foundation (ref. LCF/BQ/IN17/11620019), EU: MSC program (ref. 101025085), Spain.The KM3NeT research infrastructure is unconstruction
in the Mediterranean Sea. KM3NeT will study
atmospheric and astrophysical neutrinos with two multipurpose
neutrino detectors, ARCA and ORCA, primarily
aimed at GeV–PeV neutrinos. Thanks to the multiphotomultiplier
tube design of the digital optical modules,
KM3NeT is capable of detecting the neutrino burst from
a Galactic or near-Galactic core-collapse supernova. This potential is already exploitable with the first detection units
deployed in the sea. This paper describes the real-time implementation
of the supernova neutrino search, operating on the
two KM3NeT detectors since the first months of 2019. A
quasi-online astronomy analysis is introduced to study the
time profile of the detected neutrinos for especially significant
events. Themechanism of generation and distribution of
alerts, aswell as the integration into theSNEWSandSNEWS
2.0 global alert systems, are described. The approach for the
follow-up of external alerts with a search for a neutrino excess
in the archival data is defined. Finally, an overviewof the current
detector capabilities and a report after the first two years
of operation are given.French National Research Agency (ANR)European Commission ANR-15-CE31-0020Centre National de la Recherche Scientifique (CNRS)Commission EuropeenneInstitut Universitaire de France (IUF)LabEx UnivEarthS ANR-10-LABX-0023
ANR-18-IDEX-0001Shota Rustaveli National Science Foundation of Georgia (SRNSFG), Georgia FR-18-1268German Research Foundation (DFG)Greek Ministry of Development-GSRTIstituto Nazionale di Fisica Nucleare (INFN)Ministry of Education, Universities and Research (MIUR)PRIN 2017 program, Italy NAT-NET 2017W4HA7SMinistry of Higher Education Scientific Research and Professional Training, ICTP, Morocco AF-13Netherlands Organization for Scientific Research (NWO)
Netherlands GovernmentNational Science Centre, Poland 2015/18/E/ST2/00758National Authority for Scientific Research (ANCS), RomaniaMinisterio de Ciencia, Innovacion, Investigacion y Universidades (MCIU): Programa Estatal de Generacion de Conocimiento PGC2018-096663-B-C41
PGC2018-096663-A-C42
PGC2018-096663-B-C43
PGC2018-096663-B-C44Generalitat Valenciana PROMETEO/2020/019Grisolia program GRISOLIA/2018/119
CIDEGENT/2018/034Junta de Andalucia A-FQM-053-UGR18La Caixa Foundation LCF/BQ/IN17/11620019EU: MSC program 101025085Paris Ile-de-France Region, FranceGenT program CIDEGENT/2018/034
CIDEGENT/2019/043
CIDEGENT/2020/04
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