202 research outputs found
AmelHap: Leveraging drone whole-genome sequence data to create a honey bee HapMap
Honey bee, Apis mellifera, drones are typically haploid, developing from an unfertilized egg, inheriting only their queenâs alleles and none from the many drones she mated with. Thus the ordered combination or âphaseâ of alleles is known, making drones a valuable haplotype resource. We collated whole-genome sequence data for 1,407 drones, including 45 newly sequenced Scottish drones, collectively representing 19 countries, 8 subspecies and various hybrids. Following alignment to Amel_HAv3.1, variant calling and quality filtering, we retained 17.4âM high quality variants across 1,328 samples with a genotyping rate of 98.7%. We demonstrate the utility of this haplotype resource, AmelHap, for genotype imputation, returning >95% concordance when up to 61% of data is missing in haploids and up to 12% of data is missing in diploids. AmelHap will serve as a useful resource for the community for imputation from low-depth sequencing or SNP chip data, accurate phasing of diploids for association studies, and as a comprehensive reference panel for population genetic and evolutionary analyses.For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. This work was supported by a grant from the CB Dennis British Beekeepersâ Research Trust awarded to MB and DW, and through strategic investment funding to the Roslin Institute from the Biotechnology and Biological Sciences Research Council (BBS/E/D/30002276). MP was supported by a Basque Government grant (IT1233-19)
Determination of annual periodicity in annuli formation in Atlantic bluefin tuna otoliths.
Controversies remain regarding the periodicity, or seasonality, of otolith growth band
formation which directly influences a correct age determination of Atlantic bluefin tuna using
otoliths. Thereby, the aim of this work was to apply marginal increment analysis (MIA) and
marginal edge analysis (EA) to determine the timing of band deposition. The index of
completion (MIA) was also analyzed using General Additive Models. Results indicated that the
opaque band begin to form in July and would finish forming in November. From the end of the
year and the beginning of the following year there is minimal marginal edge growth and this is
when the translucent band begins to form and reaches its maximum development in June. MIA
and EA has evidenced that the annulus has been formed in November in the Atlantic Bluefin
tuna otolith. This would mean to delay the date of the current July 1st adjustment criterion to
November 30
Evaluation of a Multiplex ELISA for Autoantibody Profiling in Patients with Autoimmune Connective Tissue Diseases
The performance of immunoassays for the detection of autoantibodies is of critical importance in the diagnosis and assessment of patients with autoimmune connective tissue diseases (ACTD). Our objective was to compare the features of two multiplexed assaysâINNO-LIA ANA and Gennova-PictArray ENA ELISAâfor measurement of multiple autoantibodies and their utility as a clinical tool in ACTD diagnosis. The antigens included SS-A/Ro (60 and 52), SSB/La, Sm, Sm/RNP, CENP-B, Jo-1, and Scl-70. Stored sera from 85 ACTD patients and 80 controls consisting of patients with vasculitis, rheumatoid arthritis and infectious diseases, as well as healthy subjects were analyzed jointly with clinical and laboratory data. Agreement between the two methods varied between 58 and 99% (Cohenâs kappa: 0.21â0.71) mostly for SSA and SSB. The frequency of specific autoantibodies measured using the two methods was more variable for SSA, SSB, and RNP/Sm. There were a higher number of ambiguous results when using INNO-LIA. The optimized cut-off values of the Gennova-PictArray resulted in over 99% specificities in samples obtained from the control group. Sensitivity patterns were more accurate in Gennova-PictArray than in INNO-LIA, as suggested in previously reported studies. A third method could be applied to determine which of the two methods is more accurate
Armed Rollers: Does Nestlingâs Vomit Function as a Defence against Predators?
Chemical defences against predators are widespread in the animal kingdom although have been seldom reported in birds. Here, we investigate the possibility that the orange liquid that nestlings of an insectivorous bird, the Eurasian roller (Coracias garrulus), expel when scared at their nests acts as a chemical defence against predators. We studied the diet of nestling rollers and vomit origin, its chemical composition and deterrent effect on a mammal generalist predator. We also hypothesized that nestling rollers, as their main prey (i.e. grasshoppers) do from plants, could sequester chemicals from their prey for their use. Grasshoppers, that also regurgitate when facing to a threat, store the harmful substances used by plants to defend themselves against herbivores. We found that nestling rollers only vomit after being grasped and moved. The production of vomit depended on food consumption and the vomit contained two deterrent chemicals (hydroxycinnamic and hydroxybenzoic acids) stored by grasshoppers and used by plants to diminish herbivory, suggesting that they originate from the rollersâ prey. Finally, we showed for the first time that the oral secretion of a vertebrate had a deterrent effect on a model predator because vomit of nestling rollers made meat distasteful to dogs. These results support the idea that the vomit of nestling rollers is a chemical defence against predators.Financial support was provided by the Junta de AndalucĂa (project P06-RNM-02177) and the Spanish Ministry of Science and Education/FEDER (projects CGL2008-00718 and CGL2011-27561)
Evaluation of Suppressed Mite Reproduction (SMR) Reveals Potential for Varroa Resistance in European Honey Bees (Apis melliferaL.)
Simple Summary The miteVarroa destructorrepresents a great threat to honey bees and the beekeeping industry. The opportunity to select and breed honey bees that are naturally able to fight the mite stands a sustainable solution. This can be achieved by evaluation of the failure of mite reproduction (SMR, suppressed mite reproduction). We conducted a large European experiment to assess the SMR trait in different populations of honey bees spread over 13 different countries, and representing different honey bee populations. The first goal was to standardize and validate the SMR evaluation method, and then to compare the SMR trait between the different populations. Our results indicate that it is necessary to examine at least 35 brood cells infested by a single mite to reliably estimate the SMR score of any given colony. Several colonies from our dataset display high SMR scores, indicating that this trait is present within the European honey bee populations. No major differences could be identified between countries for a given population, or between populations in different countries. This study shows the potential to increase selection efforts to breedV. destructorhoney bee resistant populations. In the fight against theVarroa destructormite, selective breeding of honey bee (Apis melliferaL.) populations that are resistant to the parasitic mite stands as a sustainable solution. Selection initiatives indicate that using the suppressed mite reproduction (SMR) trait as a selection criterion is a suitable tool to breed such resistant bee populations. We conducted a large European experiment to evaluate the SMR trait in different populations of honey bees spread over 13 different countries, and representing different honey bee genotypes with their local mite parasites. The first goal was to standardize and validate the SMR evaluation method, and then to compare the SMR trait between the different populations. Simulation results indicate that it is necessary to examine at least 35 single-infested cells to reliably estimate the SMR score of any given colony. Several colonies from our dataset display high SMR scores indicating that this trait is present within the European honey bee populations. The trait is highly variable between colonies and some countries, but no major differences could be identified between countries for a given genotype, or between genotypes in different countries. This study shows the potential to increase selective breeding efforts ofV. destructorresistant populations
An experimental test of hostâs life history traits modulation in response to cuckoo parasitism risk
Hosts can counteract parasites through defences based on resistance and/or tolerance.
The mechanistic basis of tolerance, which involve defensive mechanisms minimizing parasite
damage after a successful parasitic attack, remains poorly explored in the study of
cuckoo-host interactions. Here, we experimentally explore the possibility that the risk of
great spotted cuckoo Clamator glandarius parasitism may induce tolerance defences in
magpie Pica pica hosts through plasticity in life-history traits. We predict that magpies
exposed to auditory cues indicating high parasitism risk will more likely exhibit resistance
and/or modify their life-history traits to minimize parasitism costs (i.e. tolerance) compared
to magpies under low parasitism risk. We found that manipulating the perceived parasitism
risk did not affect host resistance (i.e. rejection of parasitic eggs) nor host life-history traits.
Unexpectedly, host's egg volume increased over the season in nests exposed to auditory
cues of control non-harmful hoopoes Upupa epops. Our results do not provide support for
inducible defences (either based on resistance or tolerance) in response to risk of parasitism
in magpie hosts. Even so, we encourage studying plastic expression of breeding strategies
in response to risk of cuckoo parasitism to achieve a better understanding of the mechanistic
basis of tolerance defences.This work was supported by the Spanish
Ministry of Education and Science/FEDER (Projects
CGL2011-27561/BOS and CGL2014-56769-P to D.
P. and J.M.A.). D.P. was supported by the
Government of Extremadura while writing (contract
number TA13002). M.E.G. was supported by the
Spanish Ministry of Economy and Competitiveness
(grant number BES-2012-051898).
Stereoscopic disambiguation of vector magnetograms: first applications to SO/PHI-HRT data
Spectropolarimetric reconstructions of the photospheric vector magnetic field
are intrinsically limited by the 180-ambiguity in the orientation of
the transverse component. So far, the removal of such an ambiguity has required
assumptions about the properties of the photospheric field, which makes
disambiguation methods model-dependent. The basic idea is that the unambiguous
line-of-sight component of the field measured from one vantage point will
generally have a non-zero projection on the ambiguous transverse component
measured by the second telescope, thereby determining the ``true'' orientation
of the transverse field. Such an idea was developed and implemented in the
Stereoscopic Disambiguation Method (SDM), which was recently tested using
numerical simulations. In this work we present a first application of the SDM
to data obtained by the High Resolution Telescope (HRT) onboard Solar Orbiter
during the March 2022 campaign, when the angle with Earth was 27 degrees. The
method is successfully applied to remove the ambiguity in the transverse
component of the vector magnetogram solely using observations (from HRT and
from the Helioseismic and Magnetic Imager), for the first time. The SDM is
proven to provide observation-only disambiguated vector magnetograms that are
spatially homogeneous and consistent. A discussion about the sources of error
that may limit the accuracy of the method, and of the strategies to remove them
in future applications, is also presented.Comment: 32 pages, 12 figures, accepted in A&A on 09/07/202
Formation and Photoinduced Electron Transfer in Porphyrin- and Phthalocyanine-Bearing N-Doped Graphene Hybrids Synthesized by Click Chemistry
Graphene doped with heteroatoms such as nitrogen, boron, and phosphorous by replacing some of the skeletal carbon atoms is emerging as an important class of two-dimensional materials as it offers the much-needed bandgap for optoelectronic applications and provides better access for chemical functionalization at the heteroatom sites. Covalent grafting of photosensitizers onto such doped graphenes makes them extremely useful for light-induced applications. Herein, we report the covalent functionalization of N-doped graphene (NG) with two well-known electron donor photosensitizers, namely, zinc porphyrin (ZnP) and zinc phthalocyanine (ZnPc), using the simple click chemistry approach. Covalent attachment of ZnP and ZnPc at the N-sites of NG in NGâZnP and NGâZnPc hybrids was confirmed by using a range of spectroscopic, thermogravimetric and imaging techniques. Ground- and excited-state interactions in NGâZnP and NGâZnPc were monitored by using spectral and electrochemical techniques. Efficient quenching of photosensitizer fluorescence in these hybrids was observed, and the relatively easier oxidations of ZnP and ZnPc supported excited-state charge-separation events. Photoinduced charge separation in NGâZnP and NGâZnPc hybrids was confirmed by using the ultrafast pump-probe technique. The measured rate constants were of the order of 1010â
s,â1 thus indicating ultrafast electron transfer phenomena
Inhibition of the RAGE products increases survival in experimental models of severe sepsis and systemic infection
The ratio of horizontal to vertical displacement in solar oscillations estimated from combined SO/PHI and SDO/HMI observations
In order to make accurate inferences about the solar interior using
helioseismology, it is essential to understand all the relevant physical
effects on the observations. One effect to understand is the (complex-valued)
ratio of the horizontal to vertical displacement of the p- and f-modes at the
height at which they are observed. Unfortunately, it is impossible to measure
this ratio directly from a single vantage point, and it has been difficult to
disentangle observationally from other effects. In this paper we attempt to
measure the ratio directly using 7.5 hours of simultaneous observations from
the Polarimetric and Helioseismic Imager on board Solar Orbiter and the
Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory. While
image geometry problems make it difficult to determine the exact ratio, it
appears to agree well with that expected from adiabatic oscillations in a
standard solar model. On the other hand it does not agree with a commonly used
approximation, indicating that this approximation should not be used in
helioseismic analyses. In addition, the ratio appears to be real-valued.Comment: Accepted for publication in Astronomy & Astrophysics. 8 pages, 8
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