607 research outputs found
The Ry-f(sto) gene from Solanum stoloniferum for extreme resistant to Potato virus Y maps to potato chromosome XII and is diagnosed by PCR marker GP122(718) in PVY resistant potato cultivars
Two allelic or tightly linked genetic factors at the PLRV.4 locus on potato chromosome XI control resistance to potato leafroll virus accumulation
The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation
Predicting a multicellular organismâs phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. The three candidate mechanisms tested did not explain this organic acid accumulation. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits
Genomic landscape of drug response reveals novel mediators of anthelmintic resistance
Like other pathogens, parasitic helminths can rapidly evolve resistance to drug treatment. Understanding the genetic basis of anthelmintic drug resistance in parasitic nematodes is key to tracking its spread and improving the efficacy and sustainability of parasite control. Here, we use an in vivo genetic cross between drug-susceptible and multi-drug-resistant strains of Haemonchus contortus in a natural host-parasite system to simultaneously map resistance loci for the three major classes of anthelmintics. This approach identifies new alleles for resistance to benzimidazoles and levamisole and implicates the transcription factor cky-1 in ivermectin resistance. This gene is within a locus under selection in ivermectin-resistant populations worldwide; expression analyses and functional validation using knockdown experiments support that cky-1 is associated with ivermectin survival. Our work demonstrates the feasibility of high-resolution forward genetics in a parasitic nematode and identifies variants for the development of molecular diagnostics to combat drug resistance in the field
A combined maximum-likelihood analysis of the high-energy astrophysical neutrino flux measured with IceCube
Evidence for an extraterrestrial flux of high-energy neutrinos has now been
found in multiple searches with the IceCube detector. The first solid evidence
was provided by a search for neutrino events with deposited energies
TeV and interaction vertices inside the instrumented volume. Recent
analyses suggest that the extraterrestrial flux extends to lower energies and
is also visible with throughgoing, -induced tracks from the Northern
hemisphere. Here, we combine the results from six different IceCube searches
for astrophysical neutrinos in a maximum-likelihood analysis. The combined
event sample features high-statistics samples of shower-like and track-like
events. The data are fit in up to three observables: energy, zenith angle and
event topology. Assuming the astrophysical neutrino flux to be isotropic and to
consist of equal flavors at Earth, the all-flavor spectrum with neutrino
energies between 25 TeV and 2.8 PeV is well described by an unbroken power law
with best-fit spectral index and a flux at 100 TeV of
.
Under the same assumptions, an unbroken power law with index is disfavored
with a significance of 3.8 () with respect to the best
fit. This significance is reduced to 2.1 () if instead we
compare the best fit to a spectrum with index that has an exponential
cut-off at high energies. Allowing the electron neutrino flux to deviate from
the other two flavors, we find a fraction of at Earth.
The sole production of electron neutrinos, which would be characteristic of
neutron-decay dominated sources, is rejected with a significance of 3.6
().Comment: 16 pages, 10 figures; accepted for publication in The Astrophysical
Journal; updated one referenc
Measurement of the Atmospheric Spectrum with IceCube
We present a measurement of the atmospheric spectrum at energies
between 0.1 TeV and 100 TeV using data from the first year of the complete
IceCube detector. Atmospheric originate mainly from the decays of kaons
produced in cosmic-ray air showers. This analysis selects 1078 fully contained
events in 332 days of livetime, then identifies those consistent with particle
showers. A likelihood analysis with improved event selection extends our
previous measurement of the conventional fluxes to higher energies. The
data constrain the conventional flux to be times a
baseline prediction from a Honda's calculation, including the knee of the
cosmic-ray spectrum. A fit to the kaon contribution () to the neutrino
flux finds a kaon component that is times the baseline
value. The fitted/measured prompt neutrino flux from charmed hadron decays
strongly depends on the assumed astrophysical flux and shape. If the
astrophysical component follows a power law, the result for the prompt flux is
times a calculated flux based on the work by Enberg, Reno
and Sarcevic.Comment: PRD accepted versio
Search for astrophysical sources of neutrinos using cascade events in IceCube
The IceCube neutrino observatory has established the existence of a flux of
high-energy astrophysical neutrinos inconsistent with the expectation from
atmospheric backgrounds at a significance greater than . This flux has
been observed in analyses of both track events from muon neutrino interactions
and cascade events from interactions of all neutrino flavors. Searches for
astrophysical neutrino sources have focused on track events due to the
significantly better angular resolution of track reconstructions. To date, no
such sources have been confirmed. Here we present the first search for
astrophysical neutrino sources using cascades interacting in IceCube with
deposited energies as small as 1 TeV. No significant clustering was observed in
a selection of 263 cascades collected from May 2010 to May 2012. We show that
compared to the classic approach using tracks, this statistically-independent
search offers improved sensitivity to sources in the southern sky, especially
if the emission is spatially extended or follows a soft energy spectrum. This
enhancement is due to the low background from atmospheric neutrinos forming
cascade events and the additional veto of atmospheric neutrinos at declinations
.Comment: 14 pages, 9 figures, 1 tabl
Search for non-relativistic Magnetic Monopoles with IceCube
The IceCube Neutrino Observatory is a large Cherenkov detector instrumenting
of Antarctic ice. The detector can be used to search for
signatures of particle physics beyond the Standard Model. Here, we describe the
search for non-relativistic, magnetic monopoles as remnants of the GUT (Grand
Unified Theory) era shortly after the Big Bang. These monopoles may catalyze
the decay of nucleons via the Rubakov-Callan effect with a cross section
suggested to be in the range of to
. In IceCube, the Cherenkov light from nucleon decays
along the monopole trajectory would produce a characteristic hit pattern. This
paper presents the results of an analysis of first data taken from May 2011
until May 2012 with a dedicated slow-particle trigger for DeepCore, a
subdetector of IceCube. A second analysis provides better sensitivity for the
brightest non-relativistic monopoles using data taken from May 2009 until May
2010. In both analyses no monopole signal was observed. For catalysis cross
sections of the flux of non-relativistic
GUT monopoles is constrained up to a level of at a 90% confidence level,
which is three orders of magnitude below the Parker bound. The limits assume a
dominant decay of the proton into a positron and a neutral pion. These results
improve the current best experimental limits by one to two orders of magnitude,
for a wide range of assumed speeds and catalysis cross sections.Comment: 20 pages, 20 figure
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